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	diff --git a/Applications/AppList.cmake b/Applications/AppList.cmake
	index 96d4a8abb8..87fc225656 100644
	--- a/Applications/AppList.cmake
	+++ b/Applications/AppList.cmake
	@@ -1,23 +1,21 @@

	# This file is included in the top-level MITK CMakeLists.txt file to
	# allow early dependency checking

	option(MITK_BUILD_APP_CoreApp "Build the MITK CoreApp" OFF)
	option(MITK_BUILD_APP_Workbench "Build the MITK Workbench executable" ON)
	-option(MITK_BUILD_APP_Diffusion "Build the MITK Diffusion executable" OFF)

	# This variable is fed to ctkFunctionSetupPlugins() macro in the
	# top-level MITK CMakeLists.txt file. This allows to automatically
	# enable required plug-in runtime dependencies for applications using
	# the CTK DGraph executable and the ctkMacroValidateBuildOptions macro.
	# For this to work, directories containing executables must contain
	# a CMakeLists.txt file containing a "project(...)" command and a
	# target_libraries.cmake file setting a list named "target_libraries"
	# with required plug-in target names.

	# Format is "Directory Name^^CMake Option Name^^Executable Name (without file suffix)"
	set(MITK_APPS
	CoreApp^^MITK_BUILD_APP_CoreApp^^MitkCoreApp
	Workbench^^MITK_BUILD_APP_Workbench^^MitkWorkbench
	- Diffusion^^MITK_BUILD_APP_Diffusion^^MitkDiffusion
	)
	diff --git a/Applications/Diffusion/CMakeLists.txt b/Applications/Diffusion/CMakeLists.txt
	deleted file mode 100644
	index feeb951778..0000000000
	--- a/Applications/Diffusion/CMakeLists.txt
	+++ /dev/null
	@@ -1,109 +0,0 @@
	-project(MitkDiffusion)
	-
	-set(DIFFUSIONAPP_NAME MitkDiffusion)
	-
	-set(_app_options)
	-if(MITK_SHOW_CONSOLE_WINDOW)
	- list(APPEND _app_options SHOW_CONSOLE)
	-endif()
	-
	-# Create a cache entry for the provisioning file which is used to export
	-# the file name in the MITKConfig.cmake file. This will keep external projects
	-# which rely on this file happy.
	-set(DIFFUSIONIMAGINGAPP_PROVISIONING_FILE "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${DIFFUSIONAPP_NAME}.provisioning" CACHE INTERNAL "${DIFFUSIONAPP_NAME} provisioning file" FORCE)
	-
	-# should be identical to the list in /CMake/mitkBuildConfigurationmitkDiffusion.cmake
	-# remember to set plugins which should be automatically toggled in target_libraries.cmake
	-set(_plugins
	- org.commontk.configadmin
	- org.commontk.eventadmin
	- org.blueberry.core.runtime
	- org.blueberry.core.expressions
	- org.blueberry.core.commands
	- org.blueberry.ui.qt
	- org.blueberry.ui.qt.log
	- org.blueberry.ui.qt.help
	- org.mitk.core.services
	- org.mitk.gui.common
	- org.mitk.planarfigure
	- org.mitk.core.ext
	- org.mitk.gui.qt.application
	- org.mitk.gui.qt.ext
	- org.mitk.gui.qt.diffusionimagingapp
	- org.mitk.gui.qt.common
	- org.mitk.gui.qt.stdmultiwidgeteditor
	- org.mitk.gui.qt.datamanager
	- org.mitk.gui.qt.measurementtoolbox
	- org.mitk.gui.qt.segmentation
	- org.mitk.gui_qt.multilabelsegmentation
	- org.mitk.gui.qt.python
	- org.mitk.gui.qt.volumevisualization
	- org.mitk.gui.qt.diffusionimaging
	- org.mitk.gui.qt.diffusionimaging.connectomics
	- org.mitk.gui.qt.diffusionimaging.fiberfox
	- org.mitk.gui.qt.diffusionimaging.fiberprocessing
	- org.mitk.gui.qt.diffusionimaging.ivim
	- org.mitk.gui.qt.diffusionimaging.odfpeaks
	- org.mitk.gui.qt.diffusionimaging.preprocessing
	- org.mitk.gui.qt.diffusionimaging.reconstruction
	- org.mitk.gui.qt.diffusionimaging.tractography
	- org.mitk.gui.qt.diffusionimaging.registration
	- org.mitk.gui.qt.diffusionimaging.python
	- org.mitk.gui.qt.diffusionimaging.denoising
	- org.mitk.gui.qt.diffusionimaging.partialvolume
	- org.mitk.gui.qt.matchpoint.algorithm.browser
	- org.mitk.gui.qt.matchpoint.algorithm.control
	- org.mitk.gui.qt.matchpoint.mapper
	- org.mitk.gui.qt.imagenavigator
	- org.mitk.gui.qt.moviemaker
	- org.mitk.gui.qt.basicimageprocessing
	- org.mitk.gui.qt.properties
	- org.mitk.gui.qt.viewnavigator
	-)
	-
	-if(NOT MITK_USE_Python)
	- list(REMOVE_ITEM _plugins org.mitk.gui.qt.diffusionimaging.python)
	- list(REMOVE_ITEM _plugins org.mitk.gui.qt.python)
	-endif()
	-
	-
	-
	-# Plug-ins listed below will not be
	-# - added as a build-time dependency to the executable
	-# - listed in the provisioning file for the executable
	-# - installed if they are external plug-ins
	-
	-set(_exclude_plugins
	- org.blueberry.test
	- org.blueberry.uitest
	- org.mitk.gui.qt.coreapplication
	- org.mitk.gui.qt.extapplication
	-)
	-
	-set(_src_files
	- MitkDiffusion.cpp
	-)
	-
	-qt5_add_resources(_src_files splashscreen.qrc)
	-
	-mitkFunctionCreateBlueBerryApplication(
	- NAME ${DIFFUSIONAPP_NAME}
	- DESCRIPTION "MITK Diffusion"
	- PLUGINS ${_plugins}
	- EXCLUDE_PLUGINS ${_exclude_plugins}
	- SOURCES ${_src_files}
	- ${_app_options}
	-)
	-
	-mitk_use_modules(TARGET ${DIFFUSIONAPP_NAME} MODULES MitkAppUtil)
	-
	-# Add meta dependencies (e.g. on auto-load modules from depending modules)
	-if(TARGET ${CMAKE_PROJECT_NAME}-autoload)
	- add_dependencies(${DIFFUSIONAPP_NAME} ${CMAKE_PROJECT_NAME}-autoload)
	-endif()
	-
	-# Add a build time dependency to legacy BlueBerry bundles.
	-if(MITK_MODULES_ENABLED_PLUGINS)
	- add_dependencies(${DIFFUSIONAPP_NAME} ${MITK_MODULES_ENABLED_PLUGINS})
	-endif()
	-
	diff --git a/Applications/Diffusion/CPackConfig.cmake b/Applications/Diffusion/CPackConfig.cmake
	deleted file mode 100644
	index a5ccbb3139..0000000000
	--- a/Applications/Diffusion/CPackConfig.cmake
	+++ /dev/null
	@@ -1,28 +0,0 @@
	-if(CPACK_GENERATOR MATCHES "NSIS")
	-
	- # set the package header icon for MUI
	- SET(CPACK_PACKAGE_ICON "/home/neher/coding/mitk/mitk\\mitk.bmp")
	- # set the install/unistall icon used for the installer itself
	- # There is a bug in NSIS that does not handle full unix paths properly.
	- SET(CPACK_NSIS_MUI_ICON "/home/neher/coding/mitk/mitk\\mitk.ico")
	- SET(CPACK_NSIS_MUI_UNIICON "/home/neher/coding/mitk/mitk\\mitk.ico")
	-
	- set(CPACK_NSIS_DISPLAY_NAME "MITK Diffusion")
	-
	- # tell cpack to create links to the doc files
	- SET(CPACK_NSIS_MENU_LINKS
	- "http://www.mitk.org" "MITK Web Site"
	- )
	-
	- # tell cpack the executables you want in the start menu as links
	- SET(CPACK_PACKAGE_EXECUTABLES "MitkDiffusion;Start MITK Diffusion" CACHE INTERNAL "Collecting windows shortcuts to executables")
	-
	- # tell cpack to create a desktop link to mitkDiffusion
	- SET(CPACK_CREATE_DESKTOP_LINKS "mitkDiffusion")
	- SET(CPACK_NSIS_INSTALLED_ICON_NAME "bin\\\\mitk.ico")
	- SET(CPACK_NSIS_HELP_LINK "http:\\\\www.mitk.org")
	- SET(CPACK_NSIS_URL_INFO_ABOUT "http:\\\\www.mitk.org")
	- SET(CPACK_NSIS_CONTACT mitk@mitk.org)
	- SET(CPACK_NSIS_MODIFY_PATH ON)
	-
	-endif(CPACK_GENERATOR MATCHES "NSIS")
	diff --git a/Applications/Diffusion/CPackConfig.cmake.in b/Applications/Diffusion/CPackConfig.cmake.in
	deleted file mode 100644
	index b9214faa3b..0000000000
	--- a/Applications/Diffusion/CPackConfig.cmake.in
	+++ /dev/null
	@@ -1,28 +0,0 @@
	-if(CPACK_GENERATOR MATCHES "NSIS")
	-
	- # set the package header icon for MUI
	- SET(CPACK_PACKAGE_ICON "@MITK_SOURCE_DIR@\\mitk.bmp")
	- # set the install/unistall icon used for the installer itself
	- # There is a bug in NSIS that does not handle full unix paths properly.
	- SET(CPACK_NSIS_MUI_ICON "@MITK_SOURCE_DIR@\\mitk.ico")
	- SET(CPACK_NSIS_MUI_UNIICON "@MITK_SOURCE_DIR@\\mitk.ico")
	-
	- set(CPACK_NSIS_DISPLAY_NAME "MITK Diffusion")
	-
	- # tell cpack to create links to the doc files
	- SET(CPACK_NSIS_MENU_LINKS
	- "http://www.mitk.org" "MITK Web Site"
	- )
	-
	- # tell cpack the executables you want in the start menu as links
	- SET(CPACK_PACKAGE_EXECUTABLES "MitkDiffusion;Start MITK Diffusion" CACHE INTERNAL "Collecting windows shortcuts to executables")
	-
	- # tell cpack to create a desktop link to mitkDiffusion
	- SET(CPACK_CREATE_DESKTOP_LINKS "mitkDiffusion")
	- SET(CPACK_NSIS_INSTALLED_ICON_NAME "bin\\\\mitk.ico")
	- SET(CPACK_NSIS_HELP_LINK "http:\\\\www.mitk.org")
	- SET(CPACK_NSIS_URL_INFO_ABOUT "http:\\\\www.mitk.org")
	- SET(CPACK_NSIS_CONTACT mitk@mitk.org)
	- SET(CPACK_NSIS_MODIFY_PATH ON)
	-
	-endif(CPACK_GENERATOR MATCHES "NSIS")
	diff --git a/Applications/Diffusion/CPackOptions.cmake b/Applications/Diffusion/CPackOptions.cmake
	deleted file mode 100644
	index 5c33b2ae11..0000000000
	--- a/Applications/Diffusion/CPackOptions.cmake
	+++ /dev/null
	@@ -1,19 +0,0 @@
	-# Set Diffusion specific CPack options
	-
	-set(CPACK_PACKAGE_EXECUTABLES "MitkDiffusion;MITK Diffusion")
	-set(CPACK_PACKAGE_NAME "MITK-Diffusion")
	-set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "MITK application for processing of MR diffusion imaging data.")
	-# Major version is the year of release
	-set(CPACK_PACKAGE_VERSION_MAJOR "2018")
	-# Minor version is the month of release
	-set(CPACK_PACKAGE_VERSION_MINOR "09")
	-# Patch versioning is not intended to be done
	-set(CPACK_PACKAGE_VERSION_PATCH "99")
	-
	-# this should result in names like 2011.09, 2012.06, ...
	-# version has to be set explicitly to avoid such things as CMake creating the install directory "MITK Diffusion 2011.."
	-set(CPACK_PACKAGE_VERSION "${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}")
	-#set(CPACK_PACKAGE_VERSION "${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}")#.${CPACK_PACKAGE_VERSION_PATCH}")
	-
	-set(CPACK_PACKAGE_FILE_NAME "MITK-Diffusion-${CPACK_PACKAGE_VERSION}-${CPACK_PACKAGE_ARCH}")
	-
	diff --git a/Applications/Diffusion/MitkDiffusion.cpp b/Applications/Diffusion/MitkDiffusion.cpp
	deleted file mode 100644
	index 51ab1e6dc9..0000000000
	--- a/Applications/Diffusion/MitkDiffusion.cpp
	+++ /dev/null
	@@ -1,65 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkBaseApplication.h>
	-
	-#include <QPixmap>
	-#include <QSplashScreen>
	-#include <QTimer>
	-#include <QVariant>
	-
	-int main(int argc, char **argv)
	-{
	- mitk::BaseApplication app(argc, argv);
	-
	- app.setSingleMode(true);
	- app.setApplicationName("MitkDiffusion");
	- app.setOrganizationName("DKFZ");
	-
	- /*
	- bool showSplashScreen(true);
	-
	- QPixmap pixmap(":/splash/splashscreen.png");
	- QSplashScreen splash(pixmap);
	- splash.setMask(pixmap.mask());
	- splash.setWindowFlags(Qt::SplashScreen \| Qt::WindowStaysOnTopHint \| Qt::FramelessWindowHint);
	-
	- if (showSplashScreen)
	- {
	- splash.show();
	-
	- app.sendPostedEvents();
	- app.processEvents();
	- qSafeApp.flush();
	-
	- QTimer::singleShot(4000, &splash, SLOT(close()));
	- }
	- */
	- // Preload the org.mitk.gui.qt.ext plug-in (and hence also QmitkExt) to speed
	- // up a clean-cache start. This also works around bugs in older gcc and glibc implementations,
	- // which have difficulties with multiple dynamic opening and closing of shared libraries with
	- // many global static initializers. It also helps if dependent libraries have weird static
	- // initialization methods and/or missing de-initialization code.
	- QStringList preloadLibs;
	- preloadLibs << "liborg_mitk_gui_qt_ext";
	- app.setPreloadLibraries(preloadLibs);
	-
	- // app.setProperty(mitk::BaseApplication::PROP_APPLICATION, "org.mitk.qt.diffusionimagingapp");
	- app.setProperty(mitk::BaseApplication::PROP_PRODUCT, "org.mitk.gui.qt.diffusionimagingapp.diffusion");
	-
	- // Run the workbench.
	- return app.run();
	-}
	\ No newline at end of file
	diff --git a/Applications/Diffusion/MitkDiffusion.ini b/Applications/Diffusion/MitkDiffusion.ini
	deleted file mode 100644
	index 5b1f9b5200..0000000000
	--- a/Applications/Diffusion/MitkDiffusion.ini
	+++ /dev/null
	@@ -1,3 +0,0 @@
	-BlueBerry.home=@BLUEBERRY_BINARY_DIR@
	-BlueBerry.provisioning=@DIFFUSIONIMAGINGAPP_PROVISIONING_FILE@
	-BlueBerry.qtplugin_path=@BLUEBERRY_QTPLUGIN_PATH@
	diff --git a/Applications/Diffusion/QDiffusionImagingSplashScreen.cpp b/Applications/Diffusion/QDiffusionImagingSplashScreen.cpp
	deleted file mode 100644
	index d1ecd8381a..0000000000
	--- a/Applications/Diffusion/QDiffusionImagingSplashScreen.cpp
	+++ /dev/null
	@@ -1,105 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QDiffusionImagingSplashScreen.h"
	-#include <QtGui>
	-#include <iostream>
	-
	-QDiffusionImagingSplashScreen::QDiffusionImagingSplashScreen(const QImage &image, QWidget *parent)
	- : QWidget(parent, Qt::FramelessWindowHint \| Qt::WindowStaysOnTopHint \| Qt::SplashScreen), backgroundImage(image)
	-{
	- setAttribute(Qt::WA_TranslucentBackground);
	- resize(image.size());
	- resizeEvent(nullptr);
	-}
	-
	-QDiffusionImagingSplashScreen::~QDiffusionImagingSplashScreen()
	-{
	-}
	-
	-QSize QDiffusionImagingSplashScreen::sizeHint() const
	-{
	- return backgroundImage.size();
	-}
	-
	-void QDiffusionImagingSplashScreen::paintEvent(QPaintEvent *)
	-{
	- QPainter painter(this);
	- painter.drawImage(rect(), backgroundImage);
	-}
	-
	-void QDiffusionImagingSplashScreen::resizeEvent(QResizeEvent *)
	-{
	- setMask(createMaskRegion(backgroundImage));
	-}
	-
	-QRegion QDiffusionImagingSplashScreen::createMaskRegion(const QImage &image, bool posMask)
	-{
	- if (image.isNull())
	- return QRegion();
	-
	- if (image.depth() != 32)
	- {
	- QImage img32 = image.convertToFormat(QImage::Format_RGB32);
	- return createMaskRegion(img32, posMask);
	- }
	-
	- int width = image.width();
	- int height = image.height();
	- QRegion retVal;
	-
	- for (int y = 0; y < height; ++y)
	- {
	- // guarented to be 32 bit by the check above
	- QRgb currLine = (QRgb )image.scanLine(y);
	- int xstart = -1;
	- int xcurr = -1;
	- QRgb *currVal = currLine;
	- for (int x = 0; x < width; ++x, ++currVal)
	- {
	- int alpha = qAlpha(*currVal);
	- if ((posMask && alpha != 0) \|\| (!posMask && alpha == 0))
	- {
	- // on non-alpha pixel
	- if (xstart == -1)
	- {
	- // remember start of non-alpha line-segment (if necessary)
	- xstart = x;
	- }
	- xcurr = x;
	- }
	- else // alpha-pixel
	- if (xcurr != -1) // if this alpha pixel is following a non-alpha line-segment
	- {
	- retVal += QRegion(xstart, y, xcurr - xstart + 1, 1);
	- xstart = -1;
	- xcurr = -1;
	- }
	- }
	- if (xcurr != -1)
	- {
	- retVal += QRegion(xstart, y, xcurr - xstart + 1, 1);
	- }
	- }
	-
	- return retVal;
	-}
	-
	-void QDiffusionImagingSplashScreen::mouseReleaseEvent(QMouseEvent *mouseEvent)
	-{
	- QWidget::mouseReleaseEvent(mouseEvent);
	- hide();
	-}
	diff --git a/Applications/Diffusion/QDiffusionImagingSplashScreen.h b/Applications/Diffusion/QDiffusionImagingSplashScreen.h
	deleted file mode 100644
	index 6f95b05405..0000000000
	--- a/Applications/Diffusion/QDiffusionImagingSplashScreen.h
	+++ /dev/null
	@@ -1,42 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef QDiffusionImagingSplashScreen_h_included
	-#define QDiffusionImagingSplashScreen_h_included
	-
	-#include <QImage>
	-#include <QWidget>
	-
	-class QDiffusionImagingSplashScreen : public QWidget
	-{
	- Q_OBJECT
	-
	-public:
	- QDiffusionImagingSplashScreen(const QImage &image, QWidget *parent = 0);
	- ~QDiffusionImagingSplashScreen();
	- virtual QSize sizeHint() const;
	-
	-protected:
	- virtual void paintEvent(QPaintEvent *paintEvent);
	- virtual void resizeEvent(QResizeEvent *resizeEvent);
	- virtual void mouseReleaseEvent(QMouseEvent *mouseEvent);
	-
	- QRegion createMaskRegion(const QImage &image, bool posMask = true);
	-
	- QImage backgroundImage;
	-};
	-
	-#endif
	diff --git a/Applications/Diffusion/icons/icon.icns b/Applications/Diffusion/icons/icon.icns
	deleted file mode 100644
	index a113602951..0000000000
	Binary files a/Applications/Diffusion/icons/icon.icns and /dev/null differ
	diff --git a/Applications/Diffusion/icons/icon.ico b/Applications/Diffusion/icons/icon.ico
	deleted file mode 100644
	index 77a2f03ee8..0000000000
	Binary files a/Applications/Diffusion/icons/icon.ico and /dev/null differ
	diff --git a/Applications/Diffusion/icons/icon.png b/Applications/Diffusion/icons/icon.png
	deleted file mode 100644
	index a517c0ee25..0000000000
	Binary files a/Applications/Diffusion/icons/icon.png and /dev/null differ
	diff --git a/Applications/Diffusion/icons/mitkDiffusion.rc b/Applications/Diffusion/icons/mitkDiffusion.rc
	deleted file mode 100644
	index bb10963fb3..0000000000
	--- a/Applications/Diffusion/icons/mitkDiffusion.rc
	+++ /dev/null
	@@ -1 +0,0 @@
	-IDI_ICON1 ICON DISCARDABLE "icon.ico"
	\ No newline at end of file
	diff --git a/Applications/Diffusion/splashscreen.png b/Applications/Diffusion/splashscreen.png
	deleted file mode 100644
	index 283fb8bbd2..0000000000
	Binary files a/Applications/Diffusion/splashscreen.png and /dev/null differ
	diff --git a/Applications/Diffusion/splashscreen.qrc b/Applications/Diffusion/splashscreen.qrc
	deleted file mode 100644
	index 2ec5e013ea..0000000000
	--- a/Applications/Diffusion/splashscreen.qrc
	+++ /dev/null
	@@ -1,6 +0,0 @@
	-<!DOCTYPE RCC>
	-<RCC version="1.0">
	- <qresource prefix="/splash">
	- <file>splashscreen.png</file>
	- </qresource>
	-</RCC>
	diff --git a/Applications/Diffusion/splashscreen.xcf b/Applications/Diffusion/splashscreen.xcf
	deleted file mode 100644
	index 61edc29dcd..0000000000
	Binary files a/Applications/Diffusion/splashscreen.xcf and /dev/null differ
	diff --git a/Applications/Diffusion/startMitkDiffusion.bat.in b/Applications/Diffusion/startMitkDiffusion.bat.in
	deleted file mode 100644
	index 26c42ff33d..0000000000
	--- a/Applications/Diffusion/startMitkDiffusion.bat.in
	+++ /dev/null
	@@ -1,2 +0,0 @@
	-PATH=@MITK_RUNTIME_PATH@;%PATH%
	-@VS_BUILD_TYPE@\MitkDiffusion.exe
	diff --git a/Applications/Diffusion/target_libraries.cmake b/Applications/Diffusion/target_libraries.cmake
	deleted file mode 100644
	index 0b880357cb..0000000000
	--- a/Applications/Diffusion/target_libraries.cmake
	+++ /dev/null
	@@ -1,42 +0,0 @@
	-
	-# A list of plug-in targets which should be automatically enabled
	-# (or be available in external projects) for this application
	-
	-set(target_libraries
	- org_blueberry_ui_qt
	- org_blueberry_ui_qt_help
	- org_mitk_planarfigure
	- org_mitk_gui_qt_diffusionimagingapp
	- org_mitk_gui_qt_ext
	- org_mitk_gui_qt_datamanager
	- org_mitk_gui_qt_segmentation
	- org_mitk_gui_qt_multilabelsegmentation
	- org_mitk_gui_qt_python
	- org_mitk_gui_qt_volumevisualization
	- org_mitk_gui_qt_diffusionimaging
	- org_mitk_gui_qt_diffusionimaging_connectomics
	- org_mitk_gui_qt_diffusionimaging_fiberfox
	- org_mitk_gui_qt_diffusionimaging_fiberprocessing
	- org_mitk_gui_qt_diffusionimaging_ivim
	- org_mitk_gui_qt_diffusionimaging_odfpeaks
	- org_mitk_gui_qt_diffusionimaging_preprocessing
	- org_mitk_gui_qt_diffusionimaging_reconstruction
	- org_mitk_gui_qt_diffusionimaging_tractography
	- org_mitk_gui_qt_diffusionimaging_registration
	- org_mitk_gui_qt_diffusionimaging_python
	- org_mitk_gui_qt_diffusionimaging_denoising
	- org_mitk_gui_qt_diffusionimaging_partialvolume
	- org_mitk_gui_qt_matchpoint_algorithm_browser
	- org_mitk_gui_qt_matchpoint_algorithm_control
	- org_mitk_gui_qt_matchpoint_mapper
	- org_mitk_gui_qt_imagenavigator
	- org_mitk_gui_qt_moviemaker
	- org_mitk_gui_qt_measurementtoolbox
	- org_mitk_gui_qt_basicimageprocessing
	- org_mitk_gui_qt_viewnavigator
	-)
	-
	-if(NOT MITK_USE_Python)
	- list(REMOVE_ITEM target_libraries org_mitk_gui_qt_diffusionimaging_python)
	- list(REMOVE_ITEM target_libraries org_mitk_gui_qt_python)
	-endif()
	diff --git a/CMake/BuildConfigurations/All.cmake b/CMake/BuildConfigurations/All.cmake
	index 6a8d90677e..4e6438d150 100644
	--- a/CMake/BuildConfigurations/All.cmake
	+++ b/CMake/BuildConfigurations/All.cmake
	@@ -1,59 +1,50 @@
	set(MITK_CONFIG_PACKAGES )

	set(_apple_package_excludes)

	set(_package_excludes
	${_apple_package_excludes}
	OpenCL
	SYSTEM_Boost
	Boost_LIBRARIES
	SYSTEM_PYTHON
	SUPERBUILD
	BiophotonicsHardware_SpectroCam
	POLHEMUS_TRACKER

	US_DiPhAS_SDK
	GALIL_HARDWARE
	OPHIR_PYRO_HARDWARE

	MICROBIRD_TRACKER
	MICROBIRD_TRACKER_INCLUDE_DIR
	MICROBIRD_TRACKER_LIB
	MICRON_TRACKER
	OPTITRACK_TRACKER
	SPACENAVIGATOR
	TOF_KINECT
	TOF_KINECTV2
	TOF_MESASR4000
	TOF_PMDCAMBOARD
	TOF_PMDCAMCUBE
	TOF_PMDO3
	US_TELEMED_SDK
	videoInput
	WIIMOTE
	)

	get_cmake_property(_cache_vars CACHE_VARIABLES)
	foreach(_cache_var ${_cache_vars})
	string(REGEX REPLACE "MITK_USE_(.+)" "\\1" _package "${_cache_var}")
	if(_package AND NOT _package STREQUAL _cache_var)
	list(FIND _package_excludes ${_package} _index)
	if(_index EQUAL -1)
	list(APPEND MITK_CONFIG_PACKAGES ${_package})
	endif()
	endif()
	endforeach()

	set(MITK_BUILD_ALL_APPS ON CACHE BOOL "Build all MITK applications" FORCE)
	set(MITK_BUILD_ALL_PLUGINS ON CACHE BOOL "Build all MITK plugins" FORCE)
	set(MITK_BUILD_EXAMPLES ON CACHE BOOL "Build the MITK examples" FORCE)
	set(BLUEBERRY_BUILD_ALL_PLUGINS ON CACHE BOOL "Build all BlueBerry plugins" FORCE)
	-
	-set(BUILD_DiffusionCoreCmdApps ON CACHE BOOL "Build commandline tools for diffusion" FORCE)
	-set(BUILD_DiffusionFiberProcessingCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber processing" FORCE)
	-set(BUILD_DiffusionFiberfoxCmdApps ON CACHE BOOL "Build commandline tools for diffusion data simulation (Fiberfox)" FORCE)
	-set(BUILD_DiffusionMiscCmdApps ON CACHE BOOL "Build miscellaneous commandline tools for diffusion" FORCE)
	-set(BUILD_DiffusionQuantificationCmdApps ON CACHE BOOL "Build commandline tools for diffusion quantification (IVIM, ADC, ...)" FORCE)
	-set(BUILD_DiffusionTractographyCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber tractography" FORCE)
	-set(BUILD_DiffusionTractographyEvaluationCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber tractography evaluation" FORCE)
	-set(BUILD_DiffusionConnectomicsCmdApps ON CACHE BOOL "Build commandline tools for diffusion connectomics" FORCE)
	diff --git a/CMake/BuildConfigurations/DiffusionAll.cmake b/CMake/BuildConfigurations/DiffusionAll.cmake
	deleted file mode 100644
	index 75e57fa11e..0000000000
	--- a/CMake/BuildConfigurations/DiffusionAll.cmake
	+++ /dev/null
	@@ -1,32 +0,0 @@
	-message(STATUS "Configuring MITK Diffusion with all Plugins")
	-
	-# Enable non-optional external dependencies
	-set(MITK_USE_Vigra ON CACHE BOOL "MITK Use Vigra Library" FORCE)
	-set(MITK_USE_HDF5 ON CACHE BOOL "MITK Use HDF5 Library" FORCE)
	-set(MITK_USE_MatchPoint ON CACHE BOOL "" FORCE)
	-set(MITK_USE_DCMTK ON CACHE BOOL "" FORCE)
	-set(MITK_USE_DCMQI ON CACHE BOOL "" FORCE)
	-set(MITK_USE_OpenMP ON CACHE BOOL "" FORCE)
	-set(MITK_USE_Python ON CACHE BOOL "" FORCE)
	-set(MITK_USE_BetData ON CACHE BOOL "" FORCE)
	-
	-set(MITK_BUILD_APP_Diffusion ON CACHE BOOL "Build MITK Diffusion" FORCE)
	-
	-set(BUILD_DiffusionFiberProcessingCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber processing" FORCE)
	-set(BUILD_DiffusionFiberfoxCmdApps ON CACHE BOOL "Build commandline tools for diffusion data simulation (Fiberfox)" FORCE)
	-set(BUILD_DiffusionMiscCmdApps ON CACHE BOOL "Build miscellaneous commandline tools for diffusion" FORCE)
	-set(BUILD_DiffusionQuantificationCmdApps ON CACHE BOOL "Build commandline tools for diffusion quantification (IVIM, ADC, ...)" FORCE)
	-set(BUILD_DiffusionTractographyCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber tractography" FORCE)
	-set(BUILD_DiffusionTractographyEvaluationCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber tractography evaluation" FORCE)
	-set(BUILD_DiffusionConnectomicsCmdApps ON CACHE BOOL "Build commandline tools for diffusion connectomics" FORCE)
	-set(BUILD_DiffusionPythonCmdApps ON CACHE BOOL "Build commandline tools for diffusion with python" FORCE)
	-
	-# Build neither all plugins nor examples
	-set(BUILD_TESTING ON CACHE BOOL "Build the MITK tests" FORCE)
	-
	-# Activate in-application help generation
	-set(MITK_DOXYGEN_GENERATE_QCH_FILES ON CACHE BOOL "Use doxygen to generate Qt compressed help files for MITK docs" FORCE)
	-set(BLUEBERRY_USE_QT_HELP ON CACHE BOOL "Enable support for integrating bundle documentation into Qt Help" FORCE)
	-
	-# Disable console window
	-set(MITK_SHOW_CONSOLE_WINDOW ON CACHE BOOL "Use this to enable or disable the console window when starting MITK GUI Applications" FORCE)
	diff --git a/CMake/BuildConfigurations/DiffusionRelease.cmake b/CMake/BuildConfigurations/DiffusionRelease.cmake
	deleted file mode 100644
	index c98f87ba1f..0000000000
	--- a/CMake/BuildConfigurations/DiffusionRelease.cmake
	+++ /dev/null
	@@ -1,48 +0,0 @@
	-message(STATUS "Configuring MITK Diffusion Release Build")
	-
	-# Enable non-optional external dependencies
	-set(MITK_USE_Vigra ON CACHE BOOL "MITK Use Vigra Library" FORCE)
	-set(MITK_USE_HDF5 ON CACHE BOOL "MITK Use HDF5 Library" FORCE)
	-set(MITK_USE_MatchPoint ON CACHE BOOL "" FORCE)
	-set(MITK_USE_DCMTK ON CACHE BOOL "" FORCE)
	-set(MITK_USE_DCMQI ON CACHE BOOL "" FORCE)
	-set(MITK_USE_OpenMP ON CACHE BOOL "" FORCE)
	-if(UNIX AND NOT APPLE)
	- set(MITK_USE_Python ON CACHE BOOL "" FORCE)
	- set(MITK_USE_BetData ON CACHE BOOL "" FORCE)
	- set(BUILD_DiffusionPythonCmdApps ON CACHE BOOL "Build commandline tools for diffusion with python" FORCE)
	-else()
	- set(MITK_USE_Python OFF CACHE BOOL "" FORCE)
	- set(MITK_USE_BetData OFF CACHE BOOL "" FORCE)
	- set(BUILD_DiffusionPythonCmdApps OFF CACHE BOOL "Build commandline tools for diffusion with python" FORCE)
	-endif()
	-
	-# Disable all apps but MITK Diffusion
	-set(MITK_BUILD_ALL_APPS OFF CACHE BOOL "Build all MITK applications" FORCE)
	-set(MITK_BUILD_APP_CoreApp OFF CACHE BOOL "Build the MITK CoreApp" FORCE)
	-set(MITK_BUILD_APP_Workbench OFF CACHE BOOL "Build the MITK Workbench" FORCE)
	-set(MITK_BUILD_APP_Diffusion ON CACHE BOOL "Build MITK Diffusion" FORCE)
	-
	-# Activate Diffusion Mini Apps
	-set(BUILD_DiffusionFiberProcessingCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber processing" FORCE)
	-set(BUILD_DiffusionFiberfoxCmdApps ON CACHE BOOL "Build commandline tools for diffusion data simulation (Fiberfox)" FORCE)
	-set(BUILD_DiffusionMiscCmdApps ON CACHE BOOL "Build miscellaneous commandline tools for diffusion" FORCE)
	-set(BUILD_DiffusionQuantificationCmdApps ON CACHE BOOL "Build commandline tools for diffusion quantification (IVIM, ADC, ...)" FORCE)
	-set(BUILD_DiffusionTractographyCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber tractography" FORCE)
	-set(BUILD_DiffusionTractographyEvaluationCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber tractography evaluation" FORCE)
	-set(BUILD_DiffusionConnectomicsCmdApps OFF CACHE BOOL "Build commandline tools for diffusion connectomics" FORCE)
	-
	-# Build neither all plugins nor examples
	-set(MITK_BUILD_ALL_PLUGINS OFF CACHE BOOL "Build all MITK plugins" FORCE)
	-set(MITK_BUILD_EXAMPLES OFF CACHE BOOL "Build the MITK examples" FORCE)
	-set(BUILD_TESTING OFF CACHE BOOL "Build the MITK tests" FORCE)
	-
	-# Activate in-application help generation
	-set(MITK_DOXYGEN_GENERATE_QCH_FILES ON CACHE BOOL "Use doxygen to generate Qt compressed help files for MITK docs" FORCE)
	-set(BLUEBERRY_USE_QT_HELP ON CACHE BOOL "Enable support for integrating bundle documentation into Qt Help" FORCE)
	-
	-# Enable console window
	-set(MITK_SHOW_CONSOLE_WINDOW ON CACHE BOOL "Use this to enable or disable the console window when starting MITK GUI Applications" FORCE)
	-
	-set(MITK_VTK_DEBUG_LEAKS OFF CACHE BOOL "" FORCE)
	-set(CMAKE_BUILD_TYPE Release CACHE STRING "" FORCE)
	diff --git a/CMake/BuildConfigurations/DiffusionRelease_NoPython.cmake b/CMake/BuildConfigurations/DiffusionRelease_NoPython.cmake
	deleted file mode 100644
	index 0fb51dbc67..0000000000
	--- a/CMake/BuildConfigurations/DiffusionRelease_NoPython.cmake
	+++ /dev/null
	@@ -1,41 +0,0 @@
	-message(STATUS "Configuring MITK Diffusion Release Build")
	-
	-# Enable non-optional external dependencies
	-set(MITK_USE_Vigra ON CACHE BOOL "MITK Use Vigra Library" FORCE)
	-set(MITK_USE_HDF5 ON CACHE BOOL "MITK Use HDF5 Library" FORCE)
	-set(MITK_USE_MatchPoint ON CACHE BOOL "" FORCE)
	-set(MITK_USE_DCMTK ON CACHE BOOL "" FORCE)
	-set(MITK_USE_DCMQI ON CACHE BOOL "" FORCE)
	-set(MITK_USE_OpenMP ON CACHE BOOL "" FORCE)
	-set(MITK_USE_Python OFF CACHE BOOL "" FORCE)
	-
	-# Disable all apps but MITK Diffusion
	-set(MITK_BUILD_ALL_APPS OFF CACHE BOOL "Build all MITK applications" FORCE)
	-set(MITK_BUILD_APP_CoreApp OFF CACHE BOOL "Build the MITK CoreApp" FORCE)
	-set(MITK_BUILD_APP_Workbench OFF CACHE BOOL "Build the MITK Workbench" FORCE)
	-set(MITK_BUILD_APP_Diffusion ON CACHE BOOL "Build MITK Diffusion" FORCE)
	-
	-# Activate Diffusion Mini Apps
	-set(BUILD_DiffusionFiberProcessingCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber processing" FORCE)
	-set(BUILD_DiffusionFiberfoxCmdApps ON CACHE BOOL "Build commandline tools for diffusion data simulation (Fiberfox)" FORCE)
	-set(BUILD_DiffusionMiscCmdApps ON CACHE BOOL "Build miscellaneous commandline tools for diffusion" FORCE)
	-set(BUILD_DiffusionQuantificationCmdApps ON CACHE BOOL "Build commandline tools for diffusion quantification (IVIM, ADC, ...)" FORCE)
	-set(BUILD_DiffusionTractographyCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber tractography" FORCE)
	-set(BUILD_DiffusionTractographyEvaluationCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber tractography evaluation" FORCE)
	-set(BUILD_DiffusionConnectomicsCmdApps OFF CACHE BOOL "Build commandline tools for diffusion connectomics" FORCE)
	-set(BUILD_DiffusionPythonCmdApps OFF CACHE BOOL "Build commandline tools for diffusion with python" FORCE)
	-
	-# Build neither all plugins nor examples
	-set(MITK_BUILD_ALL_PLUGINS OFF CACHE BOOL "Build all MITK plugins" FORCE)
	-set(MITK_BUILD_EXAMPLES OFF CACHE BOOL "Build the MITK examples" FORCE)
	-set(BUILD_TESTING OFF CACHE BOOL "Build the MITK tests" FORCE)
	-
	-# Activate in-application help generation
	-set(MITK_DOXYGEN_GENERATE_QCH_FILES ON CACHE BOOL "Use doxygen to generate Qt compressed help files for MITK docs" FORCE)
	-set(BLUEBERRY_USE_QT_HELP ON CACHE BOOL "Enable support for integrating bundle documentation into Qt Help" FORCE)
	-
	-# Enable console window
	-set(MITK_SHOW_CONSOLE_WINDOW ON CACHE BOOL "Use this to enable or disable the console window when starting MITK GUI Applications" FORCE)
	-
	-set(MITK_VTK_DEBUG_LEAKS OFF CACHE BOOL "" FORCE)
	-set(CMAKE_BUILD_TYPE Release CACHE STRING "" FORCE)
	diff --git a/CMake/FindBetData.cmake b/CMake/FindBetData.cmake
	deleted file mode 100644
	index f15a41f9f2..0000000000
	--- a/CMake/FindBetData.cmake
	+++ /dev/null
	@@ -1,7 +0,0 @@
	-set(BetData_DIR ${MITK_SUPERBUILD_BINARY_DIR}/ep/src/BetData)
	-
	-if(EXISTS ${BetData_DIR})
	- set(BetData_FOUND TRUE)
	-else()
	- set(BetData_FOUND FALSE)
	-endif()
	diff --git a/CMake/PackageDepends/MITK_BetData_Config.cmake b/CMake/PackageDepends/MITK_BetData_Config.cmake
	deleted file mode 100644
	index e69de29bb2..0000000000
	diff --git a/CMakeExternals/BetData.cmake b/CMakeExternals/BetData.cmake
	deleted file mode 100644
	index f511435b0e..0000000000
	--- a/CMakeExternals/BetData.cmake
	+++ /dev/null
	@@ -1,37 +0,0 @@
	-#-----------------------------------------------------------------------------
	-# Brain Extraction Data
	-#-----------------------------------------------------------------------------
	-
	-if(MITK_USE_BetData)
	-
	-
	-# Sanity checks
	-if(DEFINED BetData_DIR AND NOT EXISTS ${BetData_DIR})
	- message(FATAL_ERROR "BetData_DIR variable is defined but corresponds to non-existing directory")
	-endif()
	-
	-set(proj BetData)
	-set(proj_DEPENDENCIES)
	-set(BetData_DEPENDS ${proj})
	-
	-if(NOT DEFINED BetData_DIR)
	-
	- set(BetData_DIR ${ep_prefix}/src/${proj}/)
	-
	- ExternalProject_Add(${proj}
	- URL http://mitk.org/download/data/MITK-BET-20180711.tar.gz
	- UPDATE_COMMAND ""
	- CONFIGURE_COMMAND ""
	- BUILD_COMMAND ""
	- INSTALL_COMMAND ""
	- DEPENDS ${proj_DEPENDENCIES}
	- )
	-
	- configure_file(${CMAKE_CURRENT_LIST_DIR}/${proj}.h.in ${CMAKE_BINARY_DIR}/${proj}.h)
	-
	-else()
	-
	- mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}")
	-endif()
	-
	-endif()
	diff --git a/CMakeExternals/BetData.h.in b/CMakeExternals/BetData.h.in
	deleted file mode 100644
	index 0287b03917..0000000000
	--- a/CMakeExternals/BetData.h.in
	+++ /dev/null
	@@ -1,31 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef BetData_h
	-#define BetData_h
	-
	-//#define BetData_DIR "@BetData_DIR@"
	-
	-namespace mitk
	-{
	-namespace bet
	-{
	-std::vector< std::string > relative_search_dirs = {"/","/bin/","/BetData/","/bin/BetData/"};
	-std::vector< std::string > absolute_search_dirs = {"@BetData_DIR@"};
	-}
	-}
	-
	-#endif
	diff --git a/CMakeExternals/ExternalProjectList.cmake b/CMakeExternals/ExternalProjectList.cmake
	index 9873030a41..a3fe925b3b 100644
	--- a/CMakeExternals/ExternalProjectList.cmake
	+++ b/CMakeExternals/ExternalProjectList.cmake
	@@ -1,44 +1,43 @@
	mitkFunctionAddExternalProject(NAME Poco ON COMPONENTS Foundation Net Util XML Zip)
	mitkFunctionAddExternalProject(NAME DCMTK ON DOC "EXPERIMENTAL, superbuild only: Use DCMTK in MITK")
	mitkFunctionAddExternalProject(NAME OpenIGTLink OFF)

	mitkFunctionAddExternalProject(NAME tinyxml ON ADVANCED)
	mitkFunctionAddExternalProject(NAME GDCM ON ADVANCED)
	mitkFunctionAddExternalProject(NAME GLUT OFF ADVANCED)
	mitkFunctionAddExternalProject(NAME Raptor2 OFF ADVANCED)
	mitkFunctionAddExternalProject(NAME Eigen ON ADVANCED DOC "Use the Eigen library")
	mitkFunctionAddExternalProject(NAME ANN ON ADVANCED DOC "Use Approximate Nearest Neighbor Library")
	mitkFunctionAddExternalProject(NAME CppUnit ON ADVANCED DOC "Use CppUnit for unit tests")

	mitkFunctionAddExternalProject(NAME PCRE OFF ADVANCED NO_PACKAGE)

	mitkFunctionAddExternalProject(NAME HDF5 ON ADVANCED)
	-mitkFunctionAddExternalProject(NAME BetData OFF ADVANCED)
	mitkFunctionAddExternalProject(NAME OpenMP ON)

	# -----------------------------------------
	# The following external projects must be
	# ordered according to their
	# inter-dependencies

	mitkFunctionAddExternalProject(NAME SWIG OFF ADVANCED NO_PACKAGE DEPENDS PCRE)
	mitkFunctionAddExternalProject(NAME Python OFF)
	mitkFunctionAddExternalProject(NAME OpenCV OFF)
	mitkFunctionAddExternalProject(NAME Vigra OFF DEPENDS HDF5)

	# These are "hard" dependencies and always set to ON
	mitkFunctionAddExternalProject(NAME ITK ON NO_CACHE DEPENDS HDF5)
	mitkFunctionAddExternalProject(NAME VTK ON NO_CACHE)
	mitkFunctionAddExternalProject(NAME Boost ON NO_CACHE)
	mitkFunctionAddExternalProject(NAME ZLIB OFF ADVANCED)
	mitkFunctionAddExternalProject(NAME cpprestsdk OFF DEPENDS Boost ZLIB ADVANCED)
	mitkFunctionAddExternalProject(NAME ACVD OFF DOC "Use Approximated Centroidal Voronoi Diagrams")
	mitkFunctionAddExternalProject(NAME CTK ON DEPENDS Qt5 DCMTK DOC "Use CTK in MITK")
	mitkFunctionAddExternalProject(NAME Rasqal OFF DEPENDS Raptor2 PCRE ADVANCED)
	mitkFunctionAddExternalProject(NAME Redland OFF DEPENDS Rasqal DOC "Use the Redland RDF library")
	mitkFunctionAddExternalProject(NAME DCMQI ON DEPENDS DCMTK ITK DOC "Use dcmqi in MITK")
	mitkFunctionAddExternalProject(NAME MatchPoint OFF ADVANCED DEPENDS ITK DOC "Use the MatchPoint translation image registration library")

	if(MITK_USE_Qt5)
	mitkFunctionAddExternalProject(NAME Qwt ON ADVANCED DEPENDS Qt5)
	endif()
	diff --git a/Modules/DiffusionImaging/CMakeLists.txt b/Modules/DiffusionImaging/CMakeLists.txt
	deleted file mode 100644
	index 0be1046bbc..0000000000
	--- a/Modules/DiffusionImaging/CMakeLists.txt
	+++ /dev/null
	@@ -1,14 +0,0 @@
	-set( diffusion_module_dirs
	- DiffusionCore
	- FiberTracking
	- Connectomics
	- Quantification
	- DiffusionIO
	- DiffusionCmdApps
	-)
	-
	-foreach(diffusion_module_dir ${diffusion_module_dirs})
	- add_subdirectory(${diffusion_module_dir})
	-endforeach()
	-
	-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/mitkDiffusionImagingConfigure.h.in ${CMAKE_CURRENT_BINARY_DIR}/DiffusionCore/mitkDiffusionImagingConfigure.h)
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/BrainParcellation/mitkCostFunctionBase.cpp b/Modules/DiffusionImaging/Connectomics/Algorithms/BrainParcellation/mitkCostFunctionBase.cpp
	deleted file mode 100644
	index a62ab39648..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/BrainParcellation/mitkCostFunctionBase.cpp
	+++ /dev/null
	@@ -1,178 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-//#include <mitkCostFunctionBase.h>
	-
	-//Itk Iterators
	-#include <itkNeighborhoodIterator.h>
	-#include <itkImageRegionIterator.h>
	-
	-//Set Functions
	-template <typename TPixel, unsigned int VImageDimension>
	-void mitk::CostFunctionBase<TPixel, VImageDimension>::SetRegion(std::pair<RegionType, int> regionPair)
	-{
	- m_RegionPair = regionPair;
	-}
	-
	-template <typename TPixel, unsigned int VImageDimension>
	-void mitk::CostFunctionBase<TPixel, VImageDimension>::SetImage(itk::Image<TPixel, VImageDimension> * image)
	-{
	- m_Image = image;
	-}
	-
	-//Other Functions
	-template < typename TPixel, unsigned int VImageDimension >
	-int mitk::CostFunctionBase<TPixel, VImageDimension>::RegionIsFullEnough ()
	-{
	- //Calculate the volume of the region cuboid
	- itk::Size<3> size = m_RegionPair.first.GetSize();
	- double volume = size[0] * size[1] * size[2];
	-
	- typedef itk::Image< int, VImageDimension > IntegerImageType;
	- itk::ImageRegionIterator<IntegerImageType> it_region(m_Image, m_RegionPair.first);
	-
	- double voxelsWithRegionValue(1); //Because the possible new voxel hasn't been set to the region value yet
	- double voxelsWithValueZero(0);
	-
	- for(it_region.GoToBegin(); !it_region.IsAtEnd(); ++it_region)
	- {
	- if (it_region.Value() == m_RegionPair.second)
	- {
	- voxelsWithRegionValue++;
	- }
	- if (it_region.Value() == 0)
	- {
	- voxelsWithValueZero++;
	- }
	- }
	-
	- double measurement = voxelsWithRegionValue / (volume - voxelsWithValueZero);
	-
	- if (measurement > 0.3)
	- {
	- return 1;
	- }
	- return 0;
	-}
	-
	-template < typename TPixel, unsigned int VImageDimension >
	-int mitk::CostFunctionBase<TPixel, VImageDimension>::SidesAreNotTooLong ()
	-{
	- itk::Size<3> size = m_RegionPair.first.GetSize();
	-
	- if (size[0] < size[1] + size[2] + 1 && size[1] < size[0] + size[2] + 1 && size[2] < size[0] + size[1] + 1)
	- {
	- return 1;
	- }
	- return 0;
	-}
	-
	-template < typename TPixel, unsigned int VImageDimension >
	-int mitk::CostFunctionBase<TPixel, VImageDimension>::COMLiesWithinParcel()
	-{
	- std::pair<RegionType, int> chosenRegion = m_RegionPair;
	-
	- typedef itk::Image< int, VImageDimension > IntegerImageType;
	- itk::ImageRegionIterator<IntegerImageType> it_region(m_Image, chosenRegion.first);
	- std::vector<double> centerOfMass;
	- centerOfMass = this->GetCenterOfMass();
	- typename IntegerImageType::IndexType indexCenterOfMass;
	- indexCenterOfMass.SetElement(0, centerOfMass[0] + 0.5);
	- indexCenterOfMass.SetElement(1, centerOfMass[1] + 0.5);
	- indexCenterOfMass.SetElement(2, centerOfMass[2] + 0.5);
	- it_region.SetIndex(indexCenterOfMass);
	-
	- if (it_region.Value() == chosenRegion.second \|\| it_region.Value() == 0)
	- {
	- return 1;
	- }
	- return 0;
	-}
	-
	-template < typename TPixel, unsigned int VImageDimension >
	-int mitk::CostFunctionBase<TPixel, VImageDimension>::CalculateCost()
	-{
	- int costFunctionValue(0);
	- std::vector<int> costVector;
	- costVector.push_back(this->RegionIsFullEnough());
	- costVector.push_back(this->SidesAreNotTooLong());
	- costVector.push_back(this->COMLiesWithinParcel());
	-
	- m_weight.clear();
	- m_weight.push_back(1); //weight for RegionIsFullEnough
	- m_weight.push_back(1); //weight for SidesAreNotTooLong
	- m_weight.push_back(0); //weight for COMLiesWithinParcel
	-
	- //Vector multiplication
	- for (std::size_t i = 0; i < costVector.size(); i++)
	- {
	- costFunctionValue += costVector[i]*m_weight[i];
	- }
	-
	- return costFunctionValue;
	-}
	-
	-template <typename TPixel, unsigned int VImageDimension>
	-std::vector<double> mitk::CostFunctionBase<TPixel, VImageDimension>::GetCenterOfMass()
	-{
	- //Count all tagged voxels in this region
	- itk::ImageRegionIterator<ImageType> it_region(m_Image, m_RegionPair.first);
	-
	- typedef itk::Image< TPixel, VImageDimension > ImageType;
	- int currentSizeOfRegion (0);
	- std::vector<typename ImageType::IndexType> indexVoxel;
	- std::vector<double> centerOfMass;
	- double xValue(0);
	- double yValue(0);
	- double zValue(0);
	-
	- for (it_region.GoToBegin(); !it_region.IsAtEnd(); ++it_region)
	- {
	- if(it_region.Value() == m_RegionPair.second)
	- {
	- indexVoxel.push_back(it_region.GetIndex());
	- currentSizeOfRegion++;
	- }
	- }
	-
	- xValue = 0;
	- yValue = 0;
	- zValue = 0;
	-
	- for (int i = 0; i < currentSizeOfRegion; i++)
	- {
	- xValue += indexVoxel[i][0];
	- yValue += indexVoxel[i][1];
	- zValue += indexVoxel[i][2];
	- }
	-
	- centerOfMass.push_back(xValue/currentSizeOfRegion);
	- centerOfMass.push_back(yValue/currentSizeOfRegion);
	- centerOfMass.push_back(zValue/currentSizeOfRegion);
	-
	- return centerOfMass;
	-}
	-
	-template <typename TPixel, unsigned int VImageDimension>
	-int mitk::CostFunctionBase<TPixel, VImageDimension>::MaximalValue()
	-{
	- int maximalValue(0);
	- for (std::size_t i = 0; i < m_weight.size(); i++)
	- {
	- maximalValue += m_weight[i];
	- }
	- return maximalValue;
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/BrainParcellation/mitkCostFunctionBase.h b/Modules/DiffusionImaging/Connectomics/Algorithms/BrainParcellation/mitkCostFunctionBase.h
	deleted file mode 100644
	index 2be9b702fd..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/BrainParcellation/mitkCostFunctionBase.h
	+++ /dev/null
	@@ -1,73 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef mitkCostFunctionBase_h
	-#define mitkCostFunctionBase_h
	-
	-//Which one do we really need?
	-//#include <berryISelectionListener.h>
	-#include <itkImage.h>
	-
	-#include <vector>
	-#include "mitkCommon.h"
	-#include "MitkConnectomicsExports.h"
	-
	-//To use pair
	-#include <utility>
	-
	-namespace mitk
	-{
	- template <typename TPixel, unsigned int VImageDimension>
	- class CostFunctionBase
	- {
	- public:
	- typedef itk::ImageRegion<3> RegionType;
	- typedef itk::Image< TPixel, VImageDimension > ImageType;
	- //Set Functions
	- void SetImage(itk::Image<TPixel, VImageDimension> *);
	- void SetRegion(std::pair<RegionType, int>);
	- //Main Function
	- /** \brief Checks if the functions RegionIsFullEnough, SidesAreNotTooLong and COMLiesWithinParcel all return value 1*/
	- int CalculateCost();
	- /** \brief Calculates the maximal possible value of the cost function*/
	- int MaximalValue();
	-
	- private:
	- ImageType * m_Image;
	- std::pair<RegionType, int> m_RegionPair;
	- //Functions to calculate cost
	- /** \brief Checks if the parcel fills out the region it lies within quit well
	- * This is to get a convex structure.
	- */
	- int RegionIsFullEnough ();
	- /** \brief Checks if the length of one direction is much longer than the length of the other two directions
	- * So we don't get parcels which just grow in one direction and look like a line.
	- */
	- int SidesAreNotTooLong ();
	- /** \brief Checks if the center of mass of a parcel lies within the parcel
	- * This is to avoid U-shaped parcels.
	- */
	- int COMLiesWithinParcel();
	- /** \brief Gives back the center of mass of a parcel as a vector*/
	- std::vector<double> GetCenterOfMass();
	-
	- std::vector<int> m_weight;
	- };
	-}
	-
	-#include "mitkCostFunctionBase.cpp"
	-
	-#endif /* mitkCostFunctionBase_h */
	\ No newline at end of file
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/BrainParcellation/mitkRandomParcellationGenerator.cpp b/Modules/DiffusionImaging/Connectomics/Algorithms/BrainParcellation/mitkRandomParcellationGenerator.cpp
	deleted file mode 100644
	index f6cfb9e35e..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/BrainParcellation/mitkRandomParcellationGenerator.cpp
	+++ /dev/null
	@@ -1,1189 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-//#include <mitkRandomParcellationGenerator.h>
	-
	-//To sort
	-#include <algorithm>
	-
	-//To use sqrt
	-#include <cmath>
	-
	-//Itk Iterators
	-#include <itkNeighborhoodIterator.h>
	-#include <itkImageRegionIterator.h>
	-
	-//for the use of abs()
	-#include <cstdlib>
	-
	-template <typename TPixel, unsigned int VImageDimension>
	-mitk::RandomParcellationGenerator<TPixel, VImageDimension>::RandomParcellationGenerator()
	- : m_RandGen(ItkRngType::New())
	-{
	-
	-}
	-
	-//Definition of the Set-Functions
	-template <typename TPixel, unsigned int VImageDimension>
	-void mitk::RandomParcellationGenerator<TPixel, VImageDimension>::SetImage(itk::Image<TPixel, VImageDimension> * image)
	-{
	- m_Image = image;
	-}
	-
	-template <typename TPixel, unsigned int VImageDimension>
	-void mitk::RandomParcellationGenerator<TPixel, VImageDimension>::SetNumberNodes(int numberNodes)
	-{
	- m_NumberNodes = numberNodes;
	-}
	-
	-template <typename TPixel, unsigned int VImageDimension>
	-void mitk::RandomParcellationGenerator<TPixel, VImageDimension>::SetVariablesForMerging (int givenSizeOfSmallestRegion, int desiredNumberOfParcels, int givenSizeOfSmallestRegionBeginning)
	-{
	- m_GivenSizeOfSmallestRegion = givenSizeOfSmallestRegion;
	- m_DesiredNumberOfParcels = desiredNumberOfParcels;
	- m_GivenSizeOfSmallestRegionBeginning = givenSizeOfSmallestRegionBeginning;
	-}
	-
	-template <typename TPixel, unsigned int VImageDimension>
	-void mitk::RandomParcellationGenerator<TPixel, VImageDimension>::SetBoolsForMerging(bool mergingWithNumberParcels, bool mergingWithSmallestParcel, bool justMergeSmallParcels)
	-{
	- m_MergingWithNumberParcels = mergingWithNumberParcels;
	- m_MergingWithSmallestParcel = mergingWithSmallestParcel;
	- m_JustMergeSmallParcels = justMergeSmallParcels;
	-}
	-
	-//Definition of other functions
	-
	-//Calculates the Center of mass (COM) and m_SizeOfRegions
	-template <typename TPixel, unsigned int VImageDimension>
	-std::vector<double> mitk::RandomParcellationGenerator<TPixel, VImageDimension>::GetCenterOfMass( itk::ImageRegionIterator<ImageType> it_region, int valueOfRegion, bool getSizeOfRegions)
	-{
	- //Counts all tagged voxels in this region
	-
	- typedef itk::Image< TPixel, VImageDimension > ImageType;
	- int currentSizeOfRegion (0);
	- std::vector<typename ImageType::IndexType> indexVoxel;
	- std::vector<double> centerOfMass;
	- double xValue(0);
	- double yValue(0);
	- double zValue(0);
	-
	- for (it_region.GoToBegin(); !it_region.IsAtEnd(); ++it_region)
	- {
	- if(it_region.Value() == valueOfRegion)
	- {
	- indexVoxel.push_back(it_region.GetIndex());
	- currentSizeOfRegion++;
	- }
	- }
	-
	- if (getSizeOfRegions == true)
	- {
	- m_SizeOfRegions.push_back(currentSizeOfRegion);
	- }
	-
	- xValue = 0;
	- yValue = 0;
	- zValue = 0;
	-
	- for (int i = 0; i < currentSizeOfRegion; i++)
	- {
	- xValue += indexVoxel[i][0];
	- yValue += indexVoxel[i][1];
	- zValue += indexVoxel[i][2];
	- }
	-
	- centerOfMass.push_back(xValue/currentSizeOfRegion);
	- centerOfMass.push_back(yValue/currentSizeOfRegion);
	- centerOfMass.push_back(zValue/currentSizeOfRegion);
	-
	- return centerOfMass;
	-}
	-
	-template <typename TPixel, unsigned int VImageDimension>
	-double mitk::RandomParcellationGenerator<TPixel, VImageDimension>::GetDistance( std::vector<double> centerOfMass, typename itk::Image< TPixel, VImageDimension >::IndexType indexNewVoxel)
	-{
	- double distancetemp(0);
	-
	- for (int i = 0; i < 3; i++)
	- {
	- distancetemp += (centerOfMass[i] - indexNewVoxel[i])*(centerOfMass[i] - indexNewVoxel[i]);
	- }
	- return sqrt(distancetemp);
	-}
	-
	-template <typename TPixel, unsigned int VImageDimension>
	-double mitk::RandomParcellationGenerator<TPixel, VImageDimension>::GetDistanceVector( std::vector<double> centerOfMass, std::vector<double> indexNewVoxel)
	-{
	- double distancetemp(0);
	-
	- for (int i = 0; i < 3; i++)
	- {
	- distancetemp += (centerOfMass[i] - indexNewVoxel[i])*(centerOfMass[i] - indexNewVoxel[i]);
	- }
	- return sqrt(distancetemp);
	-}
	-
	-
	-template < typename TPixel, unsigned int VImageDimension >
	-int mitk::RandomParcellationGenerator<TPixel, VImageDimension>::SmallestValue (std::vector<int> distance)
	-{
	- int distancemin;
	- distancemin = distance[0];
	-
	- for (std::size_t i = 1; i < distance.size(); i++)
	- {
	- if (distance[i] < distancemin)
	- {
	- distancemin = distance[i];
	- }
	- }
	- return distancemin;
	-}
	-
	-template < typename TPixel, unsigned int VImageDimension >
	-double mitk::RandomParcellationGenerator<TPixel, VImageDimension>::SmallestValue (std::vector<double> distance)
	-{
	- double distancemin;
	- distancemin = distance[0];
	-
	- for (std::size_t i = 1; i < distance.size(); i++)
	- {
	- if (distance[i] < distancemin)
	- {
	- distancemin = distance[i];
	- }
	- }
	- return distancemin;
	-}
	-
	-template < typename TPixel, unsigned int VImageDimension >
	-void mitk::RandomParcellationGenerator<TPixel, VImageDimension>::SetAppropriateValues()
	-{
	- typedef itk::Image< TPixel, VImageDimension > TemplateImageType;
	-
	- itk::ImageRegionIterator<TemplateImageType> it_image(m_Image, m_Image->GetLargestPossibleRegion());
	-
	- TPixel minimumValue, maximumValue;
	-
	- it_image.GoToBegin();
	- maximumValue = minimumValue = it_image.Value();
	-
	- for(it_image.GoToBegin(); !it_image.IsAtEnd(); ++it_image)
	- {
	- if ( it_image.Value() < minimumValue )
	- {
	- minimumValue = it_image.Value();
	- }
	- else
	- {
	- if ( it_image.Value() > maximumValue )
	- {
	- maximumValue = it_image.Value();
	- }
	- }
	- }
	-
	- int range = int ( maximumValue - minimumValue ); //needs to be castable to int
	- int offset = int ( minimumValue );
	-
	- if ( range < 0 ) //error
	- {
	- return;
	- }
	-
	- std::vector< std::size_t > histogram;
	- histogram.resize( range + 1, 0 );
	-
	- for(it_image.GoToBegin(); !it_image.IsAtEnd(); ++it_image)
	- {
	- histogram[ int ( it_image.Value() ) - offset ] += 1;
	- }
	-
	- int gapCounter = 0; //this variable will be used to count the empty labels
	-
	- //stores how much has to be subtracted from the image to remove gaps
	- std::vector< TPixel > subtractionStorage;
	- subtractionStorage.resize( range + 1, 0 );
	-
	- for( int index = 0; index <= range; index++ )
	- {
	- if( histogram[ index ] == 0 )
	- {
	- gapCounter++; //if the label is empty, increase gapCounter
	- }
	- else
	- {
	- subtractionStorage[ index ] = TPixel ( gapCounter );
	- }
	- }
	-
	- //remove gaps from label image
	- for(it_image.GoToBegin(); !it_image.IsAtEnd(); ++it_image)
	- {
	- it_image.Value() = it_image.Value() - subtractionStorage[ int ( it_image.Value() ) ];
	- }
	-}
	-
	-
	-
	-template < typename TPixel, unsigned int VImageDimension >
	-typename itk::Image< TPixel, VImageDimension >::RegionType mitk::RandomParcellationGenerator<TPixel, VImageDimension>::ExtendedRegion(typename itk::Image< TPixel, VImageDimension >::RegionType chosenRegion, typename ImageType::IndexType indexChosenVoxel)
	-{
	- itk::Size<3> size = chosenRegion.GetSize();
	- itk::Index<3> start = chosenRegion.GetIndex();
	- std::vector<int> greatestValues;
	- std::vector<int> smallestValues;
	-
	- for(int i = 0; i < 3; i++)
	- {
	- greatestValues.push_back(start[i] + size[i]);
	- smallestValues.push_back(start[i]);
	- }
	-
	- for(int i = 0; i < 3; i++)
	- {
	- if (indexChosenVoxel[i] == greatestValues[i])
	- {
	- size[i] += 1;
	- }
	- if (indexChosenVoxel[i] == smallestValues[i] - 1)
	- {
	- start[i] -= 1;
	- size[i] += 1;
	- }
	- }
	-
	- chosenRegion.SetSize(size);
	- chosenRegion.SetIndex(start);
	-
	- return chosenRegion;
	-}
	-
	-template < typename TPixel, unsigned int VImageDimension >
	-typename itk::Image< TPixel, VImageDimension >::RegionType mitk::RandomParcellationGenerator<TPixel, VImageDimension>::ExtendedRegionNotNeighbor(typename itk::Image< TPixel, VImageDimension >::RegionType chosenRegion, typename itk::Image< TPixel, VImageDimension >::RegionType smallestRegion)
	-{
	- itk::Size<3> sizeChosenRegion = chosenRegion.GetSize();
	- itk::Index<3> startChosenRegion = chosenRegion.GetIndex();
	- itk::Size<3> sizeSmallestRegion = smallestRegion.GetSize();
	- itk::Index<3> startSmallestRegion = smallestRegion.GetIndex();
	-
	- //size and start of the new merged region
	- itk::Size<3> size;
	- itk::Index<3> start;
	-
	- //Calculate the size of the merged region
	- for (int i = 0; i < 3; i++)
	- {
	- //Overlapping (start of ChosenRegion before start of SmallestRegion)
	- if ((startChosenRegion[i] + (itk::IndexValueType)sizeChosenRegion[i] > startSmallestRegion[i]) &&
	- (startChosenRegion[i] <= startSmallestRegion[i]))
	- {
	- //Not integrated
	- if (startSmallestRegion[i] + sizeSmallestRegion[i] > startChosenRegion[i] + sizeChosenRegion[i])
	- {
	- size[i] = abs(startSmallestRegion[i] - startChosenRegion[i]) + sizeSmallestRegion[i];
	- }
	- //Integrated
	- else
	- {
	- size[i] = std::max(sizeChosenRegion[i], sizeSmallestRegion[i]);
	- }
	- }
	-
	- //Overlapping (start of SmallestRegion before start of ChosenRegion)
	- if ((startSmallestRegion[i] + (itk::IndexValueType)sizeSmallestRegion[i] > startChosenRegion[i]) &&
	- (startChosenRegion[i] >= startSmallestRegion[i]))
	- {
	- //Not integrated
	- if (startChosenRegion[i] + sizeChosenRegion[i] > startSmallestRegion[i] + sizeSmallestRegion[i])
	- {
	- size[i] = abs(startSmallestRegion[i] - startChosenRegion[i]) + sizeChosenRegion[i];
	- }
	- //Integrated
	- else
	- {
	- size[i] = std::max(sizeChosenRegion[i], sizeSmallestRegion[i]);
	- }
	- }
	-
	- //No overlapping (right next to each other)
	- if ((startChosenRegion[i] + (itk::IndexValueType)sizeChosenRegion[i] == startSmallestRegion[i]) \|\|
	- (startSmallestRegion[i] + (itk::IndexValueType)sizeSmallestRegion[i] == startChosenRegion[i]))
	- {
	- size[i] = sizeChosenRegion[i] + sizeSmallestRegion[i];
	- }
	-
	- //Isolated
	- if ((startChosenRegion[i] + (itk::IndexValueType)sizeChosenRegion[i] < startSmallestRegion[i]) \|\|
	- (startSmallestRegion[i] + (itk::IndexValueType)sizeSmallestRegion[i] < startChosenRegion[i]))
	- {
	- if(startChosenRegion[i] + (itk::IndexValueType)sizeChosenRegion[i] < startSmallestRegion[i])
	- {
	- size[i] = abs(startChosenRegion[i] - startSmallestRegion[i]) +1;
	- }
	- if(startSmallestRegion[i] + (itk::IndexValueType)sizeSmallestRegion[i] < startChosenRegion[i])
	- {
	- size[i] = abs(startChosenRegion[i] - startSmallestRegion[i]) + sizeChosenRegion[i];
	- }
	- }
	- }
	-
	- //Calculate the start point of the new region, choose the smallest value respectively
	- for (int i = 0; i < 3; i++)
	- {
	- start[i] = std::min(startChosenRegion[i], startSmallestRegion[i]);
	- }
	-
	- chosenRegion.SetSize(size);
	- chosenRegion.SetIndex(start);
	-
	- return chosenRegion;
	-}
	-
	-//checks if a number is already an element of the vector
	-template < typename TPixel, unsigned int VImageDimension >
	-bool mitk::RandomParcellationGenerator<TPixel, VImageDimension>::IsUnique (int number, std::vector<int> vec)
	-{
	- for (std::size_t i = 0; i < vec.size(); i++)
	- {
	- if (vec[i] == number)
	- {
	- return false;
	- }
	- }
	- return true;
	-}
	-
	-template < typename TPixel, unsigned int VImageDimension >
	-void mitk::RandomParcellationGenerator<TPixel, VImageDimension>::GetRandomSeedVoxels()
	-{
	- typedef itk::Image< TPixel, VImageDimension > ImageType;
	-
	- RegionVoxelCounter<int, 3> counter;
	- counter.SetImage(m_Image);
	- counter.SetRegion(m_Image->GetLargestPossibleRegion());
	-
	- int numberVoxels = counter.VoxelWithValue(1);
	-
	- //Create vector with unique numbers
	-
	- std::vector<int> randomvector;
	- int randomnumber;
	-
	- //for-loop to get (m_NumberNodes) randomly chosen seed-points
	- for (int j = 0; j < m_NumberNodes; j++)
	- {
	- //m_RandGen->GetIntegerVariate() is the same as rand() but with an extended range
	- randomnumber = m_RandGen->GetIntegerVariate() % numberVoxels +1;
	-
	- //Bool-function (IsUnique)
	- if (this->IsUnique(randomnumber, randomvector))
	- {
	- randomvector.push_back(randomnumber);
	- }
	- else
	- {
	- j--;
	- }
	- }
	-
	- //sorts the numbers in randomvector according to their size
	- sort (randomvector.begin(), randomvector.end());
	-
	- //assign new values to the chosen voxels and build the regions
	-
	- itk::Size<3> originalSize;
	- originalSize.Fill(1);
	- itk::Index<3> originalStart;
	- typename ImageType::IndexType currentIndex;
	-
	- int valueCounter(0);
	- int regionNumber(0);
	- typename ImageType::RegionType tempRegion;
	- itk::ImageRegionIterator<ImageType> it_image(m_Image, m_Image->GetLargestPossibleRegion());
	-
	-
	- for (it_image.GoToBegin(); !it_image.IsAtEnd() && regionNumber < m_NumberNodes; ++it_image)
	- {
	- if (it_image.Value() >= 1)
	- {
	- valueCounter++;
	- if (valueCounter == randomvector[regionNumber])
	- {
	- it_image.Value() = regionNumber+3;
	-
	- //Build the Regions
	- currentIndex = it_image.GetIndex();
	- originalStart[0] = currentIndex[0];
	- originalStart[1] = currentIndex[1];
	- originalStart[2] = currentIndex[2];
	-
	- tempRegion.SetSize(originalSize);
	- tempRegion.SetIndex(originalStart);
	- std::pair<RegionType, int> tempPair (tempRegion, regionNumber+3);
	- m_OddRegions.push_back(tempPair);
	- regionNumber++;
	- }
	- }
	- }
	-}
	-
	-template < typename TPixel, unsigned int VImageDimension >
	-void mitk::RandomParcellationGenerator<TPixel, VImageDimension>::ParcelGrowthOverFaces()
	-{
	- typedef itk::Image< int, VImageDimension > IntegerImageType;
	- typedef itk::NeighborhoodIterator< IntegerImageType > NeighborhoodIteratorType;
	- typename NeighborhoodIteratorType::RadiusType radius;
	- radius.Fill(1);
	-
	- std::pair<RegionType, int> chosenRegion;
	- int thisRegion;
	- typename IntegerImageType::IndexType indexChosenVoxel;
	- std::vector<double> distance;
	- std::vector<int> possibleNeighbor;
	- int thisNeighbor;
	- std::vector<double> centerOfMass;
	- typename IntegerImageType::IndexType indexNewVoxel;
	- std::vector<typename IntegerImageType::IndexType> indexNewVoxelVector;
	- int numberAvailableVoxels(0);
	- bool validVoxelNotYetFound;
	- bool checkRegionsOfOddSize(true);
	- std::vector<std::pair<RegionType,int> > * possibleRegions = nullptr;
	- int costValue;
	-
	-
	- //As long as there are still non invalid regions (of even or odd size) add a voxel to them in each iteration step
	- while(m_OddRegions.size() != 0 \|\| m_EvenRegions.size() != 0)
	- {
	- //When we change from odd to even or vice versa
	- if (m_OddRegions.size() == 0)
	- {
	- checkRegionsOfOddSize = false;
	- possibleRegions = &m_EvenRegions;
	- }
	-
	- if (m_EvenRegions.size() == 0)
	- {
	- checkRegionsOfOddSize = true;
	- possibleRegions = &m_OddRegions;
	- }
	-
	- //All our smallest regions are contained in possibleRegions, choose one randomly and check whether we can expand it
	-
	- thisRegion = m_RandGen->GetIntegerVariate() % possibleRegions->size();
	- chosenRegion = (*possibleRegions)[thisRegion];
	-
	- //Calculate Center of mass (COM)
	- centerOfMass.clear();
	- itk::ImageRegionIterator<IntegerImageType> it_region(m_Image, chosenRegion.first);
	- centerOfMass = this->GetCenterOfMass(it_region, chosenRegion.second, false);
	-
	- numberAvailableVoxels = 0;
	- NeighborhoodIteratorType it_neighborhood(radius, m_Image, chosenRegion.first);
	-
	- //Check if there are any valid voxels which we can add to our chosen region
	-
	- for (it_neighborhood.GoToBegin(); !it_neighborhood.IsAtEnd(); ++it_neighborhood)
	- {
	- if (it_neighborhood.GetCenterPixel() == chosenRegion.second)
	- {
	- //Now the Neighborhood of a Parcel-Voxel is available
	- //Check if there is a valid voxel
	-
	- for (int k = 0; k <27; k++)
	- {
	- if (it_neighborhood.GetPixel(k) == 1 && (k == 4 \|\| k == 10 \|\| k == 12 \|\| k == 14 \|\| k == 16 \|\| k == 22) )
	- {
	- // Calculate the distance btw. the centerOfMass and the NewVoxel
	- indexNewVoxel = it_neighborhood.GetIndex(k);
	- indexNewVoxelVector.push_back(indexNewVoxel);
	-
	- distance.push_back(this->GetDistance(centerOfMass, indexNewVoxel));
	-
	- numberAvailableVoxels++;
	- }
	- }
	- }
	- }
	-
	- if (numberAvailableVoxels > 0)
	- {
	- validVoxelNotYetFound = true;
	- while (validVoxelNotYetFound && distance.size() > 0)
	- {
	- possibleNeighbor.clear();
	- //Find the possible neighbors with the smallest distance to the COM of the region
	-
	- for (std::size_t i = 0; i < distance.size(); i++)
	- {
	- if (distance[i] == this->SmallestValue(distance))
	- {
	- possibleNeighbor.push_back(i);
	- }
	- }
	-
	- //Choose a random voxel and check if it is valid
	- //Get the index of this voxel
	- thisNeighbor = m_RandGen->GetIntegerVariate() % possibleNeighbor.size();
	- indexChosenVoxel = indexNewVoxelVector[possibleNeighbor[thisNeighbor]];
	-
	- //Check if we now have to expand the region due to the possible new voxel
	- std::pair<RegionType, int> chosenRegionChanged;
	- chosenRegionChanged.first = this->ExtendedRegion(chosenRegion.first, indexChosenVoxel);
	- chosenRegionChanged.second = chosenRegion.second;
	-
	- //Constraints
	-
	- CostFunctionBase<TPixel, VImageDimension> costCalculator;
	- costCalculator.SetImage(m_Image);
	- costCalculator.SetRegion(chosenRegionChanged);
	- costValue = costCalculator.CalculateCost();
	-
	-
	- if(costValue >= costCalculator.MaximalValue())//Constraints are fulfilled
	- {
	- validVoxelNotYetFound = false;
	- chosenRegion = chosenRegionChanged;
	- }
	- else //Constraints are not fulfilled
	- {
	- validVoxelNotYetFound = true; //So we are still in the while loop
	- distance.erase(distance.begin() + possibleNeighbor[thisNeighbor]);
	- indexNewVoxelVector.erase(indexNewVoxelVector.begin() + possibleNeighbor[thisNeighbor]);
	-
	- if (distance.size() == 0)
	- {
	- if (checkRegionsOfOddSize == true)
	- {
	- m_InvalidRegions.push_back(chosenRegion);
	- m_OddRegions.erase(m_OddRegions.begin() + thisRegion);
	- }
	- else
	- {
	- m_InvalidRegions.push_back(chosenRegion);
	- m_EvenRegions.erase(m_EvenRegions.begin() + thisRegion);
	- }
	- }
	- }
	- }
	-
	-
	- if (distance.size() > 0)
	- {
	- //Change the value of the new voxel
	- itk::ImageRegionIterator<IntegerImageType> it_region(m_Image, m_Image->GetLargestPossibleRegion());
	- it_region.SetIndex(indexChosenVoxel);
	- it_region.Value() = chosenRegion.second;
	-
	- //Change from even to odd or vice versa
	- if (checkRegionsOfOddSize == true)
	- {
	- m_EvenRegions.push_back(chosenRegion);
	- m_OddRegions.erase(m_OddRegions.begin() + thisRegion);
	- }
	- else
	- {
	- m_OddRegions.push_back(chosenRegion);
	- m_EvenRegions.erase(m_EvenRegions.begin() + thisRegion);
	- }
	-
	- distance.clear();
	- indexNewVoxelVector.clear();
	- }
	- }
	- else
	- {
	- //The region can't be extended, put it into the m_InvalidRegions vector
	- m_InvalidRegions.push_back((*possibleRegions)[thisRegion]);
	- possibleRegions->erase(possibleRegions->begin() + thisRegion);
	- }
	- }
	-}
	-
	-template < typename TPixel, unsigned int VImageDimension >
	-void mitk::RandomParcellationGenerator<TPixel, VImageDimension>::FillOverEdgeOrVertex()
	-{
	- typedef itk::Image< int, VImageDimension > IntegerImageType;
	- typedef itk::NeighborhoodIterator< IntegerImageType > NeighborhoodIteratorType;
	- typename NeighborhoodIteratorType::RadiusType radius;
	- radius.Fill(1);
	- NeighborhoodIteratorType it_neighborhood(radius, m_Image, m_Image->GetLargestPossibleRegion());
	-
	- std::vector<int> valueOfRegions;
	- std::vector<int> sizeOfPossibleRegions;
	- std::vector<int> valueOfPossibleRegions;
	- std::vector<int> indexInvalidRegions;
	- std::vector<int> indexOfPossibleInvalidRegions;
	- std::vector<double> distance;
	- std::vector<int> possibleNeighbor;
	- typename IntegerImageType::IndexType indexNewVoxel;
	- std::vector<double> centerOfMass;
	- int thisNeighbor;
	- std::pair<RegionType, int> chosenRegion;
	- typename IntegerImageType::IndexType indexChosenVoxel;
	-
	- RegionVoxelCounter<int, VImageDimension> wholeImageCounter;
	- wholeImageCounter.SetImage(m_Image);
	- wholeImageCounter.SetRegion(m_Image->GetLargestPossibleRegion());
	- int voxelsWithValueOne = wholeImageCounter.VoxelWithValue(1);
	-
	- if (voxelsWithValueOne > 0)
	- {
	- std::stringstream message;
	- message << "Edge " << voxelsWithValueOne << endl;
	- MITK_DEBUG << message.str();
	- for (it_neighborhood.GoToBegin(); !it_neighborhood.IsAtEnd(); ++it_neighborhood)
	- {
	- if (it_neighborhood.GetCenterPixel() == 1) //Found Voxel with Value 1
	- {
	- m_SizeOfRegions.clear();
	- distance.clear();
	- valueOfRegions.clear();
	- possibleNeighbor.clear();
	- indexInvalidRegions.clear();
	- indexOfPossibleInvalidRegions.clear();
	- indexNewVoxel = it_neighborhood.GetIndex();
	-
	- //Add this voxel to a region
	- //first check if it shares an edge or vertex with (at least) one region
	- for (int k = 0; k <27; k++)
	- {
	- if (it_neighborhood.GetPixel(k) > 2)
	- {
	- for (std::size_t i = 0; i < m_InvalidRegions.size(); i++)
	- {
	- if (it_neighborhood.GetPixel(k) == m_InvalidRegions[i].second)
	- {
	- valueOfRegions.push_back(m_InvalidRegions[i].second);
	- itk::ImageRegionIterator<IntegerImageType> it_region(m_Image, m_InvalidRegions[i].first);
	-
	- //Gets center of mass and the m_SizeOfRegions
	- centerOfMass = this->GetCenterOfMass(it_region, m_InvalidRegions[i].second, true);
	- distance.push_back(this->GetDistance(centerOfMass, indexNewVoxel));
	- indexInvalidRegions.push_back(i);
	- break;
	- }
	- }
	- }
	- }
	- //Minimal distance
	- if (distance.size() != 0)
	- {
	- for (std::size_t i = 0; i < distance.size(); i++)
	- {
	- if (distance[i] == this->SmallestValue(distance))
	- {
	- possibleNeighbor.push_back(i);
	- }
	- }
	- distance.clear();
	-
	- //Check the Size of the Regions and get the smallest one!
	- //First get the regions with the same distance to COM
	- for (std::size_t i = 0; i < possibleNeighbor.size(); i++)
	- {
	- sizeOfPossibleRegions.push_back(m_SizeOfRegions[possibleNeighbor[i]]);
	- valueOfPossibleRegions.push_back(valueOfRegions[possibleNeighbor[i]]);
	- indexOfPossibleInvalidRegions.push_back(indexInvalidRegions[possibleNeighbor[i]]);
	- }
	- possibleNeighbor.clear();
	- indexInvalidRegions.clear();
	-
	- for (std::size_t i = 0; i < sizeOfPossibleRegions.size(); i++)
	- {
	- if (sizeOfPossibleRegions[i] == this->SmallestValue(sizeOfPossibleRegions))
	- {
	- possibleNeighbor.push_back(i);
	- }
	- }
	- sizeOfPossibleRegions.clear();
	-
	- thisNeighbor = m_RandGen->GetIntegerVariate() % possibleNeighbor.size();
	-
	- it_neighborhood.SetCenterPixel(valueOfPossibleRegions[thisNeighbor]);
	- valueOfPossibleRegions.clear();
	-
	- //region extansion if necessary
	- //first we need to get the right region
	- chosenRegion = m_InvalidRegions[indexOfPossibleInvalidRegions[thisNeighbor]];
	- indexChosenVoxel = it_neighborhood.GetIndex();
	-
	- m_InvalidRegions[indexOfPossibleInvalidRegions[thisNeighbor]].first = this->ExtendedRegion(chosenRegion.first, indexChosenVoxel);
	-
	- indexOfPossibleInvalidRegions.clear();
	-
	- }
	- }
	- }
	- }
	-}
	-
	-template < typename TPixel, unsigned int VImageDimension >
	-void mitk::RandomParcellationGenerator<TPixel, VImageDimension>::AllocateIsolatedVoxels()
	-{
	- typedef itk::Image< int, VImageDimension > IntegerImageType;
	-
	- std::vector<int> valueOfRegions;
	- std::vector<int> sizeOfPossibleRegions;
	- std::vector<int> valueOfPossibleRegions;
	- std::vector<int> indexInvalidRegions;
	- std::vector<int> indexOfPossibleInvalidRegions;
	- std::vector<double> distance;
	- std::vector<int> possibleNeighbor;
	- typename IntegerImageType::IndexType indexNewVoxel;
	- std::vector<double> centerOfMass;
	- int thisNeighbor;
	- std::pair<RegionType, int> chosenRegion;
	- typename IntegerImageType::IndexType indexChosenVoxel;
	-
	- RegionVoxelCounter<int, VImageDimension> wholeImageCounter;
	- wholeImageCounter.SetImage(m_Image);
	- wholeImageCounter.SetRegion(m_Image->GetLargestPossibleRegion());
	- int voxelsWithValueOne = wholeImageCounter.VoxelWithValue(1);
	-
	- if (voxelsWithValueOne > 0)
	- {
	- std::stringstream message;
	- message << "Isolated " << voxelsWithValueOne << endl;
	- MITK_DEBUG << message.str();
	- std::vector<std::vector<double> > comOfRegions;
	- m_SizeOfRegions.clear();
	-
	- //Calculate all center of mass
	- for (std::size_t i = 0; i < m_InvalidRegions.size(); i++)
	- {
	- valueOfRegions.push_back(m_InvalidRegions[i].second);
	- itk::ImageRegionIterator<IntegerImageType> it_region(m_Image, m_InvalidRegions[i].first);
	-
	- centerOfMass = this->GetCenterOfMass(it_region, m_InvalidRegions[i].second, true);
	- comOfRegions.push_back(centerOfMass);
	- }
	-
	- itk::ImageRegionIterator<IntegerImageType> it_region(m_Image, m_Image->GetLargestPossibleRegion());
	-
	- for (it_region.GoToBegin(); !it_region.IsAtEnd(); ++it_region)
	- {
	- if (it_region.Value() == 1) //Found Voxel with Value 1
	- {
	- indexNewVoxel = it_region.GetIndex();
	-
	- //distance calculation
	- for (std::size_t j = 0; j < m_InvalidRegions.size(); j++)
	- {
	- distance.push_back(this->GetDistance(comOfRegions[j], indexNewVoxel));
	- indexInvalidRegions.push_back(j);
	-
	- }
	-
	- //Minimal distance
	- if (distance.size() != 0)
	- {
	- for (std::size_t i = 0; i < distance.size(); i++)
	- {
	- if (distance[i] == this->SmallestValue(distance))
	- {
	- possibleNeighbor.push_back(i);
	- }
	- }
	- distance.clear();
	-
	- //Check the Size of the Regions and get the smallest one!
	- //First get the regions with the same distance to COM
	- for (std::size_t i = 0; i < possibleNeighbor.size(); i++)
	- {
	- sizeOfPossibleRegions.push_back(m_SizeOfRegions[possibleNeighbor[i]]);
	- valueOfPossibleRegions.push_back(valueOfRegions[possibleNeighbor[i]]);
	- indexOfPossibleInvalidRegions.push_back(indexInvalidRegions[possibleNeighbor[i]]);
	- }
	- possibleNeighbor.clear();
	- indexInvalidRegions.clear();
	-
	- for (std::size_t i = 0; i < sizeOfPossibleRegions.size(); i++)
	- {
	- if (sizeOfPossibleRegions[i] == this->SmallestValue(sizeOfPossibleRegions))
	- {
	- possibleNeighbor.push_back(i);
	- }
	- }
	- sizeOfPossibleRegions.clear();
	-
	- thisNeighbor = m_RandGen->GetIntegerVariate() % possibleNeighbor.size();
	-
	- it_region.Value() = valueOfPossibleRegions[thisNeighbor];
	- valueOfPossibleRegions.clear();
	- possibleNeighbor.clear();
	-
	- //region extansion if necessary
	- //first we need to get the right region
	- chosenRegion = m_InvalidRegions[indexOfPossibleInvalidRegions[thisNeighbor]];
	- indexChosenVoxel = it_region.GetIndex();
	- RegionType voxelRegion;
	- voxelRegion.SetIndex(indexChosenVoxel);
	- itk::Size<3> voxelSize;
	- voxelSize.Fill(1);
	- voxelRegion.SetSize(voxelSize);
	-
	- m_InvalidRegions[indexOfPossibleInvalidRegions[thisNeighbor]].first = this->ExtendedRegionNotNeighbor(chosenRegion.first, voxelRegion);
	-
	- indexOfPossibleInvalidRegions.clear();
	- }
	- }
	- }
	- }
	-}
	-
	-template < typename TPixel, unsigned int VImageDimension >
	-int mitk::RandomParcellationGenerator<TPixel, VImageDimension>::MergeParcels()
	-{
	- typedef itk::Image< int, VImageDimension > IntegerImageType;
	- typedef itk::NeighborhoodIterator< IntegerImageType > NeighborhoodIteratorType;
	- typename NeighborhoodIteratorType::RadiusType radius;
	- radius.Fill(1);
	-
	- //Calculate the m_SizeOfRegions
	- this->GetSizeOfRegions();
	-
	- int sizeOfSmallestRegion = this->SmallestValue(m_SizeOfRegions);
	-
	- std::vector<int> smallRegions;
	- std::vector<int> indexSmallRegions;
	- int thisIndex = 0;
	- int thisSmallRegion;
	- bool mergingStillPossible(true);
	- std::vector<int> smallDistances;
	- std::vector<double> centerOfMassPossibleRegion;
	- std::vector<std::vector<double> > comOfRegions;
	- std::vector<int> sizeSmallRegions;
	- std::vector<int> smallestRegions;
	- bool tooManyParcels(true);
	- int currentNumberOfParcels = m_NumberNodes;
	- int sizeNewParcel;
	- std::vector<double> costFunctionValue;
	- std::vector<double> smallestCostFunctionValues;
	- std::vector<int> valueOfPossibleRegions;
	- std::vector<double> distance;
	- std::pair<RegionType, int> chosenRegion;
	- std::vector<double> centerOfMass;
	- bool smallRegionFound(false);
	- bool hasNeighbors(false);
	-
	- while (sizeOfSmallestRegion < m_GivenSizeOfSmallestRegion && mergingStillPossible && tooManyParcels)
	- {
	- smallRegions.clear();
	- sizeSmallRegions.clear();
	- smallestRegions.clear();
	-
	- //Find all small Regions
	- for (std::size_t i = 0; i < m_SizeOfRegions.size(); i++)
	- {
	- if (m_SizeOfRegions[i] < m_GivenSizeOfSmallestRegion)
	- {
	- smallRegions.push_back(i);
	- sizeSmallRegions.push_back(m_SizeOfRegions[i]);
	- }
	- }
	-
	- //Find one of the smallest regions
	- for (std::size_t i = 0; i < sizeSmallRegions.size(); i++)
	- {
	- if (sizeSmallRegions[i] == this->SmallestValue(sizeSmallRegions))
	- {
	- smallestRegions.push_back(smallRegions[i]);
	- }
	- }
	-
	- if (smallestRegions.size() > 0 && this->SmallestValue(sizeSmallRegions) < m_GivenSizeOfSmallestRegionBeginning)
	- {
	- thisSmallRegion = rand() % smallestRegions.size();
	-
	- //Choose a random small region
	- //First check if it has direct neighbors
	- NeighborhoodIteratorType it_neighborhood(radius, m_Image, m_InvalidRegions[smallestRegions[thisSmallRegion]].first);
	- valueOfPossibleRegions.clear();
	- smallRegionFound = false;
	- hasNeighbors = false;
	-
	- for (it_neighborhood.GoToBegin(); !it_neighborhood.IsAtEnd(); ++it_neighborhood)
	- {
	- for (int k = 0; k <27; k++)
	- {
	- if ((k == 4 \|\| k == 10 \|\| k == 12 \|\| k == 14 \|\| k == 16 \|\| k == 22) &&//over faces
	- it_neighborhood.GetPixel(k) > 2 //found value which belongs to a region != the chosen region
	- && it_neighborhood.GetPixel(k) != m_InvalidRegions[smallestRegions[thisSmallRegion]].second)
	- {
	- hasNeighbors = true;
	- for (std::size_t i = 0; i < smallRegions.size(); i++)
	- {
	- if (it_neighborhood.GetPixel(k) == m_InvalidRegions[smallRegions[i]].second) //The value belongs to a small region
	- {
	- valueOfPossibleRegions.push_back(it_neighborhood.GetPixel(k));
	- smallRegionFound = true;
	- break;
	- }
	- }
	- }
	- }
	- }
	-
	- if (hasNeighbors == true)
	- {
	- if (smallRegionFound == true)//the region has direct neighbors
	- {
	- //valueOfPossibleRegions may contain some values, that are the same. Erase the duplicates and sort the vector.
	- std::sort(valueOfPossibleRegions.begin(), valueOfPossibleRegions.end());
	- valueOfPossibleRegions.erase(std::unique(valueOfPossibleRegions.begin(), valueOfPossibleRegions.end()), valueOfPossibleRegions.end());
	-
	- indexSmallRegions.clear();
	-
	- //Get the values of the possible regions!
	- for (std::size_t i = 0; i < valueOfPossibleRegions.size() ; i++)
	- {
	- for (std::size_t j = 0; j < m_InvalidRegions.size(); j++)
	- {
	- if (valueOfPossibleRegions[i] == m_InvalidRegions[j].second)
	- {
	- indexSmallRegions.push_back(j);
	- break;
	- }
	- }
	- }
	-
	- //take the region with the greatest value of the cost function
	- //the cost function depends on the distance (btw the 2 COMs) and the size of the merged parcel
	-
	- //First get all the distances
	- itk::ImageRegionIterator<IntegerImageType> it_regionSmallest(m_Image, m_InvalidRegions[smallestRegions[thisSmallRegion]].first);
	- std::vector<double> centerOfMassCurrentRegion = this->GetCenterOfMass(it_regionSmallest, m_InvalidRegions[smallestRegions[thisSmallRegion]].second, false);
	-
	- distance.clear();
	-
	- for (std::size_t i = 0; i < indexSmallRegions.size(); i++)
	- {
	- itk::ImageRegionIterator<IntegerImageType> it_region(m_Image, m_InvalidRegions[indexSmallRegions[i]].first);
	- centerOfMassPossibleRegion = this->GetCenterOfMass(it_region, m_InvalidRegions[indexSmallRegions[i]].second, false);
	- distance.push_back(this->GetDistanceVector(centerOfMassCurrentRegion, centerOfMassPossibleRegion));
	- }
	- smallDistances.clear();
	-
	- if (m_MergingWithSmallestParcel && m_JustMergeSmallParcels)
	- {
	- //If there are small Regions with equal distance btw the COMs choose a random one
	- for (std::size_t i = 0; i < distance.size(); i++)
	- {
	- if (distance[i] == this->SmallestValue(distance))
	- {
	- smallDistances.push_back(indexSmallRegions[i]);
	- }
	- }
	- thisIndex = smallDistances[rand() % smallDistances.size()];
	- }
	-
	- //Calculate the cost function values
	-
	- if (m_MergingWithNumberParcels \|\| (m_MergingWithSmallestParcel && !m_JustMergeSmallParcels))
	- {
	- costFunctionValue.clear();
	-
	- for (std::size_t i = 0; i < indexSmallRegions.size(); i++)
	- {
	- if (distance[i] == 0)
	- {
	- distance[i] = 0.01;
	- }
	- sizeNewParcel = (m_SizeOfRegions[smallestRegions[thisSmallRegion]] + m_SizeOfRegions[indexSmallRegions[i]]);
	-
	- costFunctionValue.push_back(-(1.0/distance[i]) - (1.0/sizeNewParcel)); //1, 2 or 3 at sizeNewParcel
	- }
	- smallestCostFunctionValues.clear();
	-
	- for (std::size_t i = 0; i < indexSmallRegions.size(); i++)
	- {
	- if (costFunctionValue[i] == this->SmallestValue(costFunctionValue))
	- {
	- smallestCostFunctionValues.push_back(indexSmallRegions[i]);
	- }
	- }
	- thisIndex = smallestCostFunctionValues[rand() % smallestCostFunctionValues.size()];
	- }
	-
	- //m_InvalidRegions[thisIndex].first is the region we want to merge with our current one
	-
	- //Colour the small parcel like the found one
	- for (it_regionSmallest.GoToBegin(); !it_regionSmallest.IsAtEnd(); ++it_regionSmallest)
	- {
	- if (it_regionSmallest.Value() == m_InvalidRegions[smallestRegions[thisSmallRegion]].second)
	- {
	- it_regionSmallest.Value() = m_InvalidRegions[thisIndex].second;
	- }
	- }
	-
	- //Expand the region of the new parcel if necessary!
	-
	- chosenRegion = m_InvalidRegions[thisIndex];
	- chosenRegion.first = this->ExtendedRegionNotNeighbor(chosenRegion.first, m_InvalidRegions[smallestRegions[thisSmallRegion]].first);
	- m_InvalidRegions[thisIndex] = chosenRegion;
	-
	- //Erase the smallest Region from m_InvalidRegions
	- m_InvalidRegions.erase(m_InvalidRegions.begin() + smallestRegions[thisSmallRegion]);
	- currentNumberOfParcels--;
	-
	- if (currentNumberOfParcels <= m_DesiredNumberOfParcels)
	- {
	- tooManyParcels = false;
	- }
	-
	- //m_SizeOfRegions changed, get the new one
	- this->GetSizeOfRegions();
	- }
	-
	- else //No merging possible, erase this small region from m_InvalidRegions and from m_SizeOfRegions
	- {
	- m_InvalidRegions.erase(m_InvalidRegions.begin() + smallestRegions[thisSmallRegion]);
	- currentNumberOfParcels--;
	- m_SizeOfFinishedRegions.push_back(m_SizeOfRegions[smallestRegions[thisSmallRegion]]);
	- m_SizeOfRegions.erase(m_SizeOfRegions.begin() + smallestRegions[thisSmallRegion]);
	-
	- if (currentNumberOfParcels <= m_DesiredNumberOfParcels)
	- {
	- tooManyParcels = false;
	- }
	- }
	- }
	- else //There are no 6-connected neighborhood-regions. Try to merge this small region to a near region (according to the Center of Mass)
	- {
	- comOfRegions.clear();
	- //Calculate the center of mass of all small regions
	- for (std::size_t i = 0; i < smallRegions.size(); i++)
	- {
	- itk::ImageRegionIterator<IntegerImageType> it_region(m_Image, m_InvalidRegions[smallRegions[i]].first);
	-
	- centerOfMass = this->GetCenterOfMass(it_region, m_InvalidRegions[smallRegions[i]].second, false);
	- comOfRegions.push_back(centerOfMass);
	- }
	-
	- //Calculate the distance between the center of mass of our small region and all other regions
	- itk::ImageRegionIterator<IntegerImageType> it_regionSmallest(m_Image, m_InvalidRegions[smallestRegions[thisSmallRegion]].first);
	- std::vector<double> centerOfMassCurrentRegion = this->GetCenterOfMass(it_regionSmallest, m_InvalidRegions[smallestRegions[thisSmallRegion]].second, false);
	-
	- distance.clear();
	-
	- for (std::size_t i = 0; i < smallRegions.size(); i++)
	- {
	- itk::ImageRegionIterator<IntegerImageType> it_region(m_Image, m_InvalidRegions[smallRegions[i]].first);
	- centerOfMassPossibleRegion = this->GetCenterOfMass(it_region, m_InvalidRegions[smallRegions[i]].second, false);
	- distance.push_back(this->GetDistanceVector(centerOfMassCurrentRegion, centerOfMassPossibleRegion));
	- }
	- smallDistances.clear();
	- std::vector<double> distanceWithoutZero = distance;
	- for (std::size_t i = 0; i < distanceWithoutZero.size(); i++)
	- {
	- if (distanceWithoutZero[i] == 0)
	- {
	- distanceWithoutZero.erase(distanceWithoutZero.begin() + i); //Our smallestRegion is calculated too, erase the zero entry
	- break;
	- }
	- }
	-
	- if (distanceWithoutZero.size() > 0)
	- {
	- //If there are small Regions with equal distance btw the COM's choose a random one
	- for (std::size_t i = 0; i < distance.size(); i++)
	- {
	- if (distance[i] == this->SmallestValue(distanceWithoutZero))
	- {
	- smallDistances.push_back(smallRegions[i]);
	- }
	- }
	-
	- thisIndex = smallDistances[rand() % smallDistances.size()];
	-
	- //Colour the small parcel like the found one
	- for (it_regionSmallest.GoToBegin(); !it_regionSmallest.IsAtEnd(); ++it_regionSmallest)
	- {
	- if (it_regionSmallest.Value() == m_InvalidRegions[smallestRegions[thisSmallRegion]].second)
	- {
	- it_regionSmallest.Value() = m_InvalidRegions[thisIndex].second;
	- }
	- }
	-
	- //Expand the region of the new parcel if necessary!
	- chosenRegion = m_InvalidRegions[thisIndex];
	- chosenRegion.first = this->ExtendedRegionNotNeighbor(chosenRegion.first , m_InvalidRegions[smallestRegions[thisSmallRegion]].first);
	- m_InvalidRegions[thisIndex] = chosenRegion;
	-
	- //Erase the smallest Region from m_InvalidRegions
	- m_InvalidRegions.erase(m_InvalidRegions.begin() + smallestRegions[thisSmallRegion]);
	- currentNumberOfParcels--;
	-
	- if (currentNumberOfParcels <= m_DesiredNumberOfParcels)
	- {
	- tooManyParcels = false;
	- }
	-
	- //m_SizeOfRegions changed, get the new one
	- this->GetSizeOfRegions();
	- }
	-
	- else//No merging possible, erase this small region from m_InvalidRegions and from m_SizeOfRegions
	- {
	- m_InvalidRegions.erase(m_InvalidRegions.begin() + smallestRegions[thisSmallRegion]);
	- currentNumberOfParcels--;
	- m_SizeOfFinishedRegions.push_back(m_SizeOfRegions[smallestRegions[thisSmallRegion]]);
	- m_SizeOfRegions.erase(m_SizeOfRegions.begin() + smallestRegions[thisSmallRegion]);
	-
	- if (currentNumberOfParcels <= m_DesiredNumberOfParcels)
	- {
	- tooManyParcels = false;
	- }
	- }
	- }
	- }
	- else //there are no parcels left to merge with
	- {
	- mergingStillPossible = false;
	- }
	- }
	- return (m_SizeOfFinishedRegions.size() + m_SizeOfRegions.size());
	-}
	-
	-template < typename TPixel, unsigned int VImageDimension >
	-void mitk::RandomParcellationGenerator<TPixel, VImageDimension>::GetSizeOfRegions()
	-{
	- m_SizeOfRegions.clear();
	- RegionVoxelCounter<int, VImageDimension> voxelCounter;
	- voxelCounter.SetImage(m_Image);
	- for (std::size_t i = 0; i < m_InvalidRegions.size(); i++)
	- {
	- voxelCounter.SetRegion(m_InvalidRegions[i].first);
	- m_SizeOfRegions.push_back(voxelCounter.VoxelWithValue(m_InvalidRegions[i].second));
	- }
	-}
	-
	-template < typename TPixel, unsigned int VImageDimension >
	-void mitk::RandomParcellationGenerator<TPixel, VImageDimension>::ShowSizeOfRegions()
	-{
	- RegionVoxelCounter<int, VImageDimension> voxelCounter;
	- voxelCounter.SetImage(m_Image);
	- std::stringstream message;
	- for (std::size_t i = 0; i < m_InvalidRegions.size(); i++)
	- {
	- voxelCounter.SetRegion(m_InvalidRegions[i].first);
	- m_SizeOfRegions.push_back(voxelCounter.VoxelWithValue(m_InvalidRegions[i].second));
	- message << voxelCounter.VoxelWithValue(m_InvalidRegions[i].second) << " , ";
	- }
	- MITK_DEBUG << message.str();
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/BrainParcellation/mitkRandomParcellationGenerator.h b/Modules/DiffusionImaging/Connectomics/Algorithms/BrainParcellation/mitkRandomParcellationGenerator.h
	deleted file mode 100644
	index 1ef283cb89..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/BrainParcellation/mitkRandomParcellationGenerator.h
	+++ /dev/null
	@@ -1,132 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef mitkRandomParcellationGenerator_h
	-#define mitkRandomParcellationGenerator_h
	-
	-#include<itkImage.h>
	-
	-#include "mitkCommon.h"
	-#include "MitkConnectomicsExports.h"
	-
	-// mitk
	-#include <mitkCostFunctionBase.h>
	-#include <mitkRegionVoxelCounter.h>
	-
	-//Itk Iterators
	-#include <itkNeighborhoodIterator.h>
	-#include <itkImageRegionIterator.h>
	-
	-#include <vector>
	-
	-//To use pair
	-#include <utility>
	-#include <itkMersenneTwisterRandomVariateGenerator.h>
	-
	-namespace mitk
	-{
	-
	- template <typename TPixel, unsigned int VImageDimension>
	- class RandomParcellationGenerator
	- {
	- public:
	- typedef itk::Image< TPixel, VImageDimension > ImageType;
	- typedef itk::Statistics::MersenneTwisterRandomVariateGenerator ItkRngType;
	-
	- RandomParcellationGenerator();
	-
	- //Set-Functions
	- void SetImage(itk::Image<TPixel, VImageDimension> *);
	- void SetNumberNodes(int inputNumberNodes);
	- void SetVariablesForMerging(int givenSizeOfSmallestRegion, int desiredNumberOfParcels, int givenSizeOfSmallestRegionBeginning);
	- void SetBoolsForMerging(bool mergingWithNumberParcels, bool mergingWithSmallestParcel, bool justMergeSmallParcels);
	-
	- //Main Functions
	-
	- /** \brief Sets randomly chosen seed voxels (1x1x1 regions) on the segmented image
	- * This is done by creating a vector with unique values, which represents the position of a voxel respectively.
	- * For this purpose we count all voxels with value one and choose random numbers.
	- */
	- void GetRandomSeedVoxels();
	- /** \brief Add appropriate voxels of the segmented part to a region (just 6-connected neighborhood)
	- * A voxel is appropriate if the cost function value is high enough. Several constraints have to be fulfilled for this purpose.
	- */
	- void ParcelGrowthOverFaces();
	- /** \brief Add voxels of the segmented part to an appropriate region (26-connected neighborhood)
	- * Checks which voxels still have value one and to which neighborhood-region each one should be added.
	- */
	- void FillOverEdgeOrVertex();
	- /** \brief Add voxels of the segmented part to an appropriate region (no neighbors necessary)
	- * Checks which voxels still have value one and calculates the distance to all parcels.
	- * Finally each voxel is added to the region with the smallest distance to it.
	- */
	- void AllocateIsolatedVoxels();
	- /** \brief Merge parcels according to a cost function
	- * Looks for the parcel with the smallest number of voxels.
	- * Then merges it to a neighborhood-parcel such that the cost function value is small enough.
	- * The new number of nodes is returned so we can show them on the GUI.
	- */
	- int MergeParcels();
	- /** \brief Changes the values of the nodes, such that no gaps exist and it starts with value 1*/
	- void SetAppropriateValues();
	- /** \brief Calculates and shows the size (number of voxels) of all regions on the console*/
	- void ShowSizeOfRegions();
	-
	- protected:
	- //Sub-Functions
	- /** \brief Gives back the center of mass and -if wanted- the size (number of voxels) of a parcel*/
	- std::vector<double> GetCenterOfMass( itk::ImageRegionIterator<ImageType> it_region, int valueOfRegion, bool getSizeOfRegions );
	- /** \brief Calculates the distance between two voxels, the position of the first one is given by an index and the position of the second one is given by a vector*/
	- double GetDistance( std::vector<double> centerOfMass, typename ImageType::IndexType indexNewVoxel);
	- /** \brief Calculates the distance between two voxels, both positions are given by vectors*/
	- double GetDistanceVector( std::vector<double> centerOfMass, std::vector<double> indexNewVoxel);
	- /** \brief Gives back the smallest value of an int-vector*/
	- int SmallestValue (std::vector<int> distance);
	- /** \brief Gives back the smallest value of a double-vector*/
	- double SmallestValue (std::vector<double> distance);
	- /** \brief Extends the region if the chosen voxel lies outside*/
	- typename ImageType::RegionType ExtendedRegion(typename ImageType::RegionType chosenRegion, typename ImageType::IndexType indexChosenVoxel);
	- /** \brief Extends the region of a parcel such that the second region lies within*/
	- typename ImageType::RegionType ExtendedRegionNotNeighbor(typename ImageType::RegionType chosenRegion, typename ImageType::RegionType smallestRegion);
	- /** \brief Checks if a number is an element of the vector already*/
	- bool IsUnique (int number, std::vector<int> vec);
	- /** \brief Calculates the size (number of voxels) of all regions*/
	- void GetSizeOfRegions();
	-
	- typedef itk::ImageRegion<3> RegionType;
	- //Start the algorithm ParcelGrowthOverFaces with m_OddRegions and transfer them to m_EvenRegions or m_InvalidRegions respectively
	- std::vector<std::pair<RegionType, int> > m_EvenRegions;
	- std::vector<std::pair<RegionType, int> > m_OddRegions;
	- std::vector<std::pair<RegionType, int> > m_InvalidRegions;
	- std::vector<int> m_SizeOfRegions;
	- //For merging; regions that can't be merged any more
	- std::vector<int> m_SizeOfFinishedRegions;
	-
	- ImageType * m_Image;
	- int m_NumberNodes;
	- int m_GivenSizeOfSmallestRegion;
	- int m_DesiredNumberOfParcels;
	- int m_GivenSizeOfSmallestRegionBeginning;
	- bool m_MergingWithNumberParcels;
	- bool m_MergingWithSmallestParcel;
	- bool m_JustMergeSmallParcels;
	- ItkRngType::Pointer m_RandGen;
	- };
	-}
	-
	-#include "mitkRandomParcellationGenerator.cpp"
	-
	-#endif /* mitkRandomParcellationGenerator_h */
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/BrainParcellation/mitkRegionVoxelCounter.cpp b/Modules/DiffusionImaging/Connectomics/Algorithms/BrainParcellation/mitkRegionVoxelCounter.cpp
	deleted file mode 100644
	index 9e7cd8e725..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/BrainParcellation/mitkRegionVoxelCounter.cpp
	+++ /dev/null
	@@ -1,61 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-//#include <mitkRegionVoxelCounter.h>
	-
	-//Itk Iterators
	-#include <itkNeighborhoodIterator.h>
	-#include <itkImageRegionIterator.h>
	-
	-//Set Functions
	-template <typename TPixel, unsigned int VImageDimension>
	-void mitk::RegionVoxelCounter<TPixel, VImageDimension>::SetRegion(typename ImageType::RegionType region)
	-{
	- m_Region = region;
	-}
	-
	-template <typename TPixel, unsigned int VImageDimension>
	-void mitk::RegionVoxelCounter<TPixel, VImageDimension>::SetImage(itk::Image<TPixel, VImageDimension> * image)
	-{
	- m_Image = image;
	-}
	-
	-//Other Functions
	-template <typename TPixel, unsigned int VImageDimension>
	-int mitk::RegionVoxelCounter<TPixel, VImageDimension>::VoxelWithValue(TPixel value)
	-{
	- itk::ImageRegionIterator<ImageType> it_region(m_Image, m_Region);
	- int counter(0);
	-
	- for (it_region.GoToBegin(); !it_region.IsAtEnd(); ++it_region)
	- {
	- if (it_region.Value() == value) //Found Voxel with chosen value
	- {
	- counter++;
	- }
	- }
	- return counter;
	-}
	-
	-template <typename TPixel, unsigned int VImageDimension>
	-double mitk::RegionVoxelCounter<TPixel, VImageDimension>::PercentageVoxelWithValueZeroExcluded(int value)
	-{
	- itk::Size<3> regionSize = m_Region.GetSize();
	- double volume = regionSize[0] * regionSize[1] * regionSize[2];
	-
	- double measurement = this->VoxelWithValue(value) / (volume - this->VoxelWithValue(0));
	- return measurement;
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/BrainParcellation/mitkRegionVoxelCounter.h b/Modules/DiffusionImaging/Connectomics/Algorithms/BrainParcellation/mitkRegionVoxelCounter.h
	deleted file mode 100644
	index e80a804613..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/BrainParcellation/mitkRegionVoxelCounter.h
	+++ /dev/null
	@@ -1,51 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef mitkRegionVoxelCounter_h
	-#define mitkRegionVoxelCounter_h
	-
	-#include<itkImage.h>
	-
	-#include "mitkCommon.h"
	-#include "MitkConnectomicsExports.h"
	-
	-namespace mitk
	-{
	-
	- template <typename TPixel, unsigned int VImageDimension>
	- class RegionVoxelCounter
	- {
	- public:
	- typedef itk::Image< TPixel, VImageDimension > ImageType;
	-
	- void SetRegion(typename ImageType::RegionType);
	- void SetImage(itk::Image<TPixel, VImageDimension> *);
	-
	- /** \brief Counts all voxels with the chosen value in the set region*/
	- int VoxelWithValue(TPixel value);
	- /** \brief Gives back the percentage of the number of voxels with the chosen value in comparison to the number of voxels with other values (except zero)*/
	- double PercentageVoxelWithValueZeroExcluded(int value);
	-
	- private:
	- typename ImageType::RegionType m_Region;
	- ImageType * m_Image;
	- };
	-
	-}
	-
	-#include "mitkRegionVoxelCounter.cpp"
	-
	-#endif /* mitkRegionVoxelCounter_h */
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/itkConnectomicsNetworkToConnectivityMatrixImageFilter.cpp b/Modules/DiffusionImaging/Connectomics/Algorithms/itkConnectomicsNetworkToConnectivityMatrixImageFilter.cpp
	deleted file mode 100644
	index 405bf202eb..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/itkConnectomicsNetworkToConnectivityMatrixImageFilter.cpp
	+++ /dev/null
	@@ -1,186 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef ITK_ConnectomicsNetworkToConnectivityMatrixImageFilter_CPP
	-#define ITK_ConnectomicsNetworkToConnectivityMatrixImageFilter_CPP
	-
	-#include <itkImageRegionIterator.h>
	-
	-#include <vector>
	-
	-itk::ConnectomicsNetworkToConnectivityMatrixImageFilter::ConnectomicsNetworkToConnectivityMatrixImageFilter()
	- : m_BinaryConnectivity(false)
	- , m_RescaleConnectivity(false)
	- , m_InputNetwork(nullptr)
	-{
	-}
	-
	-
	-itk::ConnectomicsNetworkToConnectivityMatrixImageFilter::~ConnectomicsNetworkToConnectivityMatrixImageFilter()
	-{
	-}
	-
	-void itk::ConnectomicsNetworkToConnectivityMatrixImageFilter::GenerateData()
	-{
	-
	- this->AllocateOutputs();
	-
	- OutputImageType::Pointer output = this->GetOutput();
	-
	- if(m_InputNetwork.IsNull())
	- {
	- MITK_ERROR << "Failed to generate data, no valid network was set.";
	- return;
	- }
	-
	- typedef mitk::ConnectomicsNetwork::NetworkType NetworkType;
	- typedef boost::graph_traits< NetworkType >::vertex_descriptor DescriptorType;
	- typedef boost::graph_traits< NetworkType >::vertex_iterator IteratorType;
	-
	- // prepare connectivity matrix for data
	- std::vector< std::vector< double > > connectivityMatrix;
	- int numberOfVertices = m_InputNetwork->GetNumberOfVertices();
	-
	- connectivityMatrix.resize( numberOfVertices );
	- for( int index(0); index < numberOfVertices; index++ )
	- {
	- connectivityMatrix[ index ].resize( numberOfVertices );
	- }
	-
	- // Create LabelToIndex translation
	- std::map< std::string, DescriptorType > labelToIndexMap;
	-
	- NetworkType boostGraph = *(m_InputNetwork->GetBoostGraph());
	-
	- // translate index to label
	- IteratorType iterator, end;
	- boost::tie(iterator, end) = boost::vertices( boostGraph );
	-
	- for ( ; iterator != end; ++iterator)
	- {
	- labelToIndexMap.insert(
	- std::pair< std::string, DescriptorType >(
	- boostGraph[ iterator ].label, iterator )
	- );
	- }
	-
	- std::vector< std::string > indexToLabel;
	-
	- // translate index to label
	- indexToLabel.resize( numberOfVertices );
	-
	- boost::tie(iterator, end) = boost::vertices( boostGraph );
	-
	- for ( ; iterator != end; ++iterator)
	- {
	- indexToLabel[ iterator ] = boostGraph[ iterator ].label;
	- }
	-
	- //translate label to position
	- std::vector< std::string > positionToLabelVector;
	- positionToLabelVector = indexToLabel;
	-
	- std::sort ( positionToLabelVector.begin(), positionToLabelVector.end() );
	-
	- for( int outerLoop( 0 ); outerLoop < numberOfVertices; outerLoop++ )
	- {
	- DescriptorType fromVertexDescriptor = labelToIndexMap.find( positionToLabelVector[ outerLoop ] )->second;
	- for( int innerLoop( outerLoop + 1 ); innerLoop < numberOfVertices; innerLoop++ )
	- {
	- DescriptorType toVertexDescriptor = labelToIndexMap.find( positionToLabelVector[ innerLoop ] )->second;
	-
	-
	- double fiber_count( 0 );
	-
	- if( boost::edge(toVertexDescriptor, fromVertexDescriptor, boostGraph ).second )
	- {
	- fiber_count = m_InputNetwork->GetEdge( fromVertexDescriptor , toVertexDescriptor ).fiber_count;
	- }
	- connectivityMatrix[outerLoop][innerLoop] = fiber_count;
	- connectivityMatrix[innerLoop][outerLoop] = fiber_count;
	- }
	- }
	-
	-
	- OutputImageType::SpacingType spacing;
	- spacing[0] = 1.0;
	- spacing[1] = 1.0;
	- OutputImageType::PointType origin;
	- origin[0] = 0.0;
	- origin[1] = 0.0;
	- OutputImageType::IndexType index;
	- index[0] = 0.0;
	- index[1] = 0.0;
	- OutputImageType::SizeType size;
	- size[0] = numberOfVertices;
	- size[1] = numberOfVertices;
	- OutputImageType::RegionType region;
	- region.SetIndex( index );
	- region.SetSize( size );
	-
	- output->SetSpacing( spacing ); // Set the image spacing
	- output->SetOrigin( origin ); // Set the image origin
	- output->SetRegions( region );
	- output->Allocate();
	- output->FillBuffer(0);
	-
	-
	- itk::ImageRegionIterator< OutputImageType > it_connect(output, output->GetLargestPossibleRegion());
	-
	- int counter( 0 );
	-
	- double rescaleFactor( 1.0 );
	- double rescaleMax( 255.0 );
	-
	- if( m_RescaleConnectivity )
	- {
	- rescaleFactor = rescaleMax / m_InputNetwork->GetMaximumWeight();
	- }
	-
	- // Colour pixels according to connectivity
	- if( m_BinaryConnectivity )
	- {
	- // binary connectivity
	- while( !it_connect.IsAtEnd() )
	- {
	- if( connectivityMatrix[ ( counter - counter % numberOfVertices ) / numberOfVertices][ counter % numberOfVertices ] )
	- {
	- it_connect.Set( 1 );
	- }
	- else
	- {
	- it_connect.Set( 0 );
	- }
	- ++it_connect;
	- counter++;
	- }
	- }
	- else
	- {
	- // if desired rescale to the 0-255 range
	- while( !it_connect.IsAtEnd() )
	- {
	- it_connect.Set( ( unsigned short ) (rescaleFactor *
	- connectivityMatrix[ ( counter - counter % numberOfVertices ) / numberOfVertices][ counter % numberOfVertices ])
	- );
	- ++it_connect;
	- counter++;
	- }
	- }
	-
	-}
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/itkConnectomicsNetworkToConnectivityMatrixImageFilter.h b/Modules/DiffusionImaging/Connectomics/Algorithms/itkConnectomicsNetworkToConnectivityMatrixImageFilter.h
	deleted file mode 100644
	index e6c19175d6..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/itkConnectomicsNetworkToConnectivityMatrixImageFilter.h
	+++ /dev/null
	@@ -1,81 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef ITK_ConnectomicsNetworkToConnectivityMatrixImageFilter_H
	-#define ITK_ConnectomicsNetworkToConnectivityMatrixImageFilter_H
	-
	-// ITK includes
	-#include <itkImageSource.h>
	-#include <itkImage.h>
	-
	-// MITK includes
	-#include "mitkConnectomicsNetwork.h"
	-
	-namespace itk
	-{
	-
	- class ConnectomicsNetworkToConnectivityMatrixImageFilter : public ImageSource< itk::Image< unsigned short, 2 > >
	- {
	-
	- public:
	- typedef ConnectomicsNetworkToConnectivityMatrixImageFilter Self;
	- typedef ProcessObject Superclass;
	- typedef SmartPointer< Self > Pointer;
	- typedef SmartPointer< const Self > ConstPointer;
	-
	- typedef itk::Image< unsigned short, 2 > OutputImageType;
	- typedef OutputImageType::PixelType OutPixelType;
	-
	- typedef mitk::ConnectomicsNetwork InputType;
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- itkTypeMacro( ConnectomicsNetworkToConnectivityMatrixImageFilter, ImageSource )
	-
	- / Get/Set m_BinaryConnectivity /
	- itkSetMacro( BinaryConnectivity, bool)
	- itkGetMacro( BinaryConnectivity, bool)
	-
	- / Get/Set m_RescaleConnectivity /
	- itkSetMacro( RescaleConnectivity, bool)
	- itkGetMacro( RescaleConnectivity, bool)
	-
	- itkSetMacro( InputNetwork, InputType::Pointer)
	-
	- void GenerateData() override;
	-
	- protected:
	-
	- ConnectomicsNetworkToConnectivityMatrixImageFilter();
	- virtual ~ConnectomicsNetworkToConnectivityMatrixImageFilter();
	-
	- /** Controls whether the connectivity matrix is binary */
	- bool m_BinaryConnectivity;
	- /** Controls whether the connectivity matrix entries are rescaled to lie between 0 and 255*/
	- bool m_RescaleConnectivity;
	-
	- InputType::Pointer m_InputNetwork;
	-
	- };
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkConnectomicsNetworkToConnectivityMatrixImageFilter.cpp"
	-#endif
	-
	-
	-#endif /* ITK_ConnectomicsNetworkToConnectivityMatrixImageFilter_H */
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsBetweennessHistogram.cpp b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsBetweennessHistogram.cpp
	deleted file mode 100644
	index 0654b735f3..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsBetweennessHistogram.cpp
	+++ /dev/null
	@@ -1,130 +0,0 @@
	-
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include<mitkConnectomicsBetweennessHistogram.h>
	-
	-#include <boost/numeric/conversion/converter.hpp>
	-
	-#include <mitkConnectomicsConstantsManager.h>
	-
	-mitk::ConnectomicsBetweennessHistogram::ConnectomicsBetweennessHistogram()
	-: m_Mode( UnweightedUndirectedMode )
	-, m_CentralityMap()
	-{
	- m_Subject = "Node Betweenness";
	-}
	-
	-mitk::ConnectomicsBetweennessHistogram::~ConnectomicsBetweennessHistogram()
	-{
	-}
	-
	-void mitk::ConnectomicsBetweennessHistogram::SetBetweennessCalculationMode(
	- const mitk::ConnectomicsBetweennessHistogram::BetweennessCalculationMode & mode )
	-{
	- m_Mode = mode;
	-}
	-
	-mitk::ConnectomicsBetweennessHistogram::BetweennessCalculationMode mitk::ConnectomicsBetweennessHistogram::GetBetweennessCalculationMode()
	-{
	- return m_Mode;
	-}
	-
	-void mitk::ConnectomicsBetweennessHistogram::ComputeFromConnectomicsNetwork( ConnectomicsNetwork* source )
	-{
	- NetworkType* boostGraph = source->GetBoostGraph();
	- IteratorType vertex_iterator_begin, vertex_iterator_end;
	-
	- m_CentralityMap.clear();
	- m_CentralityMap.resize( source->GetNumberOfVertices() );
	-
	- switch( m_Mode )
	- {
	- case UnweightedUndirectedMode:
	- {
	- CalculateUnweightedUndirectedBetweennessCentrality( boostGraph, vertex_iterator_begin, vertex_iterator_end );
	- break;
	- }
	- case WeightedUndirectedMode:
	- {
	- CalculateWeightedUndirectedBetweennessCentrality( boostGraph, vertex_iterator_begin, vertex_iterator_end );
	- break;
	- }
	- }
	-
	- ConvertCentralityMapToHistogram();
	-}
	-
	-void mitk::ConnectomicsBetweennessHistogram::CalculateUnweightedUndirectedBetweennessCentrality(
	- NetworkType* boostGraph, IteratorType /vertex_iterator_begin/, IteratorType /vertex_iterator_end/ )
	-{
	- boost::brandes_betweenness_centrality(
	- *boostGraph,
	- boost::centrality_map(
	- boost::make_iterator_property_map( m_CentralityMap.begin(), boost::get( &mitk::ConnectomicsNetwork::NetworkNode::id, *boostGraph ), double() )
	- ).vertex_index_map( boost::get( &mitk::ConnectomicsNetwork::NetworkNode::id, *boostGraph ) )
	- );
	-
	-}
	-
	-void mitk::ConnectomicsBetweennessHistogram::CalculateWeightedUndirectedBetweennessCentrality(
	- NetworkType* /boostGraph/, IteratorType /vertex_iterator_begin/, IteratorType /vertex_iterator_end/ )
	-{
	- MBI_WARN << mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_UNIMPLEMENTED_FEATURE;
	-}
	-
	-void mitk::ConnectomicsBetweennessHistogram::ConvertCentralityMapToHistogram()
	-{
	- double maximumFloat( 0.0 );
	-
	- for ( unsigned int index( 0 ); index < m_CentralityMap.size(); index++ )
	- {
	- if( m_CentralityMap[ index ] > maximumFloat )
	- {
	- maximumFloat = m_CentralityMap[ index ];
	- }
	- }
	-
	- // use the boost double to int converter
	- // it defaults to trunc
	- typedef boost::numeric::converter<int,double> Double2Int ;
	-
	- // for rounding, reduces the number of nodes classed as zero
	- maximumFloat += 0.5;
	-
	- int maximumInt( 0 );
	- try
	- {
	- maximumInt = Double2Int::convert( maximumFloat );
	- }
	- catch ( boost::numeric::positive_overflow const& )
	- {
	- MBI_WARN << mitk::ConnectomicsConstantsManager::CONNECTOMICS_ERROR_OUTSIDE_INTEGER_RANGE;
	- }
	-
	- m_HistogramVector.resize( maximumInt + 1 );
	-
	- for ( unsigned int index( 0 ); index < m_CentralityMap.size(); index++ )
	- {
	- int value( 0 );
	- value = Double2Int::convert( ( m_CentralityMap[index ] + 0.5 ) );
	- m_HistogramVector[ value ]++;
	- }
	-
	- UpdateYMax();
	-
	- m_Valid = true;
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsBetweennessHistogram.h b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsBetweennessHistogram.h
	deleted file mode 100644
	index 483ad42791..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsBetweennessHistogram.h
	+++ /dev/null
	@@ -1,90 +0,0 @@
	-
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef _MITK_ConnectomicsBetweennessHistogram_H
	-#define _MITK_ConnectomicsBetweennessHistogram_H
	-
	-#include<mitkConnectomicsHistogramBase.h>
	-
	-
	-#ifdef _MSC_VER
	-# pragma warning(push)
	-# pragma warning(disable: 4172)
	-#endif
	-
	-#include <boost/graph/betweenness_centrality.hpp>
	-
	-#ifdef _MSC_VER
	-# pragma warning(pop)
	-#endif
	-
	-namespace mitk {
	-
	- /**
	- * \brief A class to calculate and store the betweenness of each node */
	- class ConnectomicsBetweennessHistogram : public mitk::ConnectomicsHistogramBase
	- {
	-
	- public:
	-
	- /** Enum for different ways to calculate betweenness centrality */
	-
	- enum BetweennessCalculationMode
	- {
	- UnweightedUndirectedMode,
	- WeightedUndirectedMode
	- };
	-
	- ConnectomicsBetweennessHistogram();
	- ~ConnectomicsBetweennessHistogram() override;
	-
	- /** Set the calucaltion mode */
	- void SetBetweennessCalculationMode( const BetweennessCalculationMode & );
	-
	- /** Get the calculation mode */
	- BetweennessCalculationMode GetBetweennessCalculationMode();
	-
	- protected:
	-
	- /* Typedefs */
	- typedef mitk::ConnectomicsNetwork::NetworkType NetworkType;
	- typedef boost::graph_traits< NetworkType >::vertex_iterator IteratorType;
	- typedef std::vector< double > BCMapType;
	-
	- /** @brief Creates a new histogram from the network source. */
	- void ComputeFromConnectomicsNetwork( ConnectomicsNetwork* source ) override;
	-
	- /** Calculate betweenness centrality ignoring the weight of the edges */
	- void CalculateUnweightedUndirectedBetweennessCentrality( NetworkType*, IteratorType, IteratorType );
	-
	- /** Calculate betweenness centrality taking into consideration the weight of the edges */
	- void CalculateWeightedUndirectedBetweennessCentrality( NetworkType*, IteratorType, IteratorType );
	-
	- /** Converts the centrality map to a histogram by binning */
	- void ConvertCentralityMapToHistogram();
	-
	- /** Stores which mode has been selected for betweenness centrality calculation */
	- BetweennessCalculationMode m_Mode;
	-
	- /** Stores the betweenness centralities for each node */
	- BCMapType m_CentralityMap;
	- };
	-
	-}
	-
	-#endif /* _MITK_ConnectomicsBetweennessHistogram_H */
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsDegreeHistogram.cpp b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsDegreeHistogram.cpp
	deleted file mode 100644
	index e6440634c5..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsDegreeHistogram.cpp
	+++ /dev/null
	@@ -1,58 +0,0 @@
	-
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkConnectomicsDegreeHistogram.h>
	-
	-mitk::ConnectomicsDegreeHistogram::ConnectomicsDegreeHistogram()
	-{
	- m_Subject = "Node degree";
	-}
	-
	-mitk::ConnectomicsDegreeHistogram::~ConnectomicsDegreeHistogram()
	-{
	-}
	-
	-void mitk::ConnectomicsDegreeHistogram::ComputeFromConnectomicsNetwork( ConnectomicsNetwork* source )
	-{
	- std::vector< int > degreeOfNodesVector = source->GetDegreeOfNodes();
	-
	- int maximumDegree( 0 );
	-
	- for(unsigned int index( 0 ); index < degreeOfNodesVector.size(); index++ )
	- {
	- if( maximumDegree < degreeOfNodesVector[ index ] )
	- {
	- maximumDegree = degreeOfNodesVector[ index ];
	- }
	- }
	-
	- this->m_HistogramVector.resize( maximumDegree + 1 );
	-
	- for(unsigned int index( 0 ); index < m_HistogramVector.size(); index++ )
	- {
	- this->m_HistogramVector[ index ] = 0;
	- }
	- this->m_TopValue = maximumDegree;
	-
	- for(unsigned int index( 0 ); index < degreeOfNodesVector.size(); index++ )
	- {
	- this->m_HistogramVector[ degreeOfNodesVector[ index ] ]++;
	-
	- }
	- // successfully created a valid histogram
	- this->m_Valid = true;
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsDegreeHistogram.h b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsDegreeHistogram.h
	deleted file mode 100644
	index 1bd14462a5..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsDegreeHistogram.h
	+++ /dev/null
	@@ -1,47 +0,0 @@
	-
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef _MITK_ConnectomicsDegreeHistogram_H
	-#define _MITK_ConnectomicsDegreeHistogram_H
	-
	-#include<mitkConnectomicsHistogramBase.h>
	-
	-namespace mitk {
	-
	- /**
	- * \brief A class to calculate and store the degree of each node */
	- class ConnectomicsDegreeHistogram : public mitk::ConnectomicsHistogramBase
	- {
	-
	- public:
	-
	- ConnectomicsDegreeHistogram();
	- ~ConnectomicsDegreeHistogram() override;
	-
	-
	-
	- protected:
	-
	- /** @brief Creates a new histogram from the network source. */
	- void ComputeFromConnectomicsNetwork( ConnectomicsNetwork* source ) override;
	-
	- };
	-
	-}
	-
	-#endif /* _MITK_ConnectomicsDegreeHistogram_H */
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsHistogramBase.cpp b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsHistogramBase.cpp
	deleted file mode 100644
	index 44f18c5f0a..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsHistogramBase.cpp
	+++ /dev/null
	@@ -1,226 +0,0 @@
	-
	-
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkConnectomicsHistogramBase.h>
	-#include <mitkConnectomicsConstantsManager.h>
	-
	-#include <boost/numeric/conversion/converter.hpp>
	-
	-mitk::ConnectomicsHistogramBase::ConnectomicsHistogramBase()
	-: m_Valid( false )
	-, m_BaselineValue( 0 )
	-, m_TopValue( 1 )
	-, m_StartValue( 0 )
	-, m_Subject( "" )
	-{
	-}
	-
	-mitk::ConnectomicsHistogramBase::~ConnectomicsHistogramBase()
	-{
	-}
	-
	-
	-double mitk::ConnectomicsHistogramBase::GetYMin() const
	-{
	- return m_BaselineValue;
	-}
	-
	-double mitk::ConnectomicsHistogramBase::GetYMax() const
	-{
	- return m_TopValue;
	-}
	-
	-double mitk::ConnectomicsHistogramBase::GetMin() const
	-{
	- return this->GetXMin();
	-}
	-
	-double mitk::ConnectomicsHistogramBase::GetMax() const
	-{
	- return this->GetXMax();
	-}
	-
	-double mitk::ConnectomicsHistogramBase::GetXMin() const
	-{
	- return m_StartValue;
	-}
	-
	-double mitk::ConnectomicsHistogramBase::GetXMax() const
	-{
	- return ( m_StartValue + this->GetRange() );
	-}
	-
	-int mitk::ConnectomicsHistogramBase::GetRange() const
	-{
	- return m_HistogramVector.size();
	-}
	-
	-bool mitk::ConnectomicsHistogramBase::IsValid() const
	-{
	- return m_Valid;
	-}
	-
	-void mitk::ConnectomicsHistogramBase::PrintToConsole() const
	-{
	- MITK_INFO << "Histogram - Maximum " << this->GetYMax() << " Minimum " << this->GetYMin() << " Range " << this->GetRange();
	-
	- for(unsigned int index( 0 ); index < m_HistogramVector.size(); index++ )
	- {
	- MITK_INFO << " Bin: " << index << " Value: " << m_HistogramVector[ index ];
	- }
	-}
	-
	-std::string mitk::ConnectomicsHistogramBase::GetSubject() const
	-{
	- return m_Subject;
	-}
	-
	-void mitk::ConnectomicsHistogramBase::SetSubject( std::string subject )
	-{
	- m_Subject = subject;
	-}
	-
	-void mitk::ConnectomicsHistogramBase::ComputeFromBaseData( BaseData* source )
	-{
	- m_Valid = false;
	- m_HistogramVector.clear();
	-
	- //check if input is valid
	- if (source==nullptr)
	- { // empty base data
	- return;
	- }
	-
	- mitk::ConnectomicsNetwork* networkSource = dynamic_cast<mitk::ConnectomicsNetwork*>(source);
	-
	- if (networkSource==nullptr)
	- { // base data but no network
	- return;
	- }
	-
	- ComputeFromConnectomicsNetwork( networkSource );
	-}
	-
	-float mitk::ConnectomicsHistogramBase::GetRelativeBin( double start, double end ) const
	-{
	- // use the boost double to int converter
	- // it defaults to trunc
	- typedef boost::numeric::converter<int,double> Double2Int ;
	-
	- float result( 0.0 );
	-
	- if( !m_Valid )
	- {
	- MITK_ERROR << mitk::ConnectomicsConstantsManager::CONNECTOMICS_ERROR_TRIED_TO_ACCESS_INVALID_HISTOGRAM;
	- return result;
	- }
	-
	- if( ( start < 0.0 ) \|\|
	- ( end < 0.0 ) )
	- {
	- MITK_ERROR << mitk::ConnectomicsConstantsManager::CONNECTOMICS_ERROR_PASSED_NEGATIVE_INDEX_TO_HISTOGRAM;
	- return result;
	- }
	-
	- // calculate result
	- if( std::abs( end - start ) <= 1.0 )
	- { // if the bin size is one or less, we can do not need to interpolate
	-
	- unsigned int index( 0 );
	- try
	- {
	- // show the value for n between n - .5 and n + .5
	- double temp = ( start + end ) / 2.0;
	- index = Double2Int::convert( temp ); // By default throws positive_overflow()
	- }
	- catch ( boost::numeric::positive_overflow const& )
	- {
	- MBI_WARN << mitk::ConnectomicsConstantsManager::CONNECTOMICS_ERROR_OUTSIDE_INTEGER_RANGE;
	- }
	-
	- if( index < m_HistogramVector.size() )
	- {
	- result = m_HistogramVector[ index ];
	- }
	- else
	- {
	- MBI_WARN << mitk::ConnectomicsConstantsManager::CONNECTOMICS_ERROR_BEYOND_SCOPE <<
	- index << " on vector sized: " << m_HistogramVector.size();
	- }
	- }
	- else
	- { // if the bin size is more than one we need to interpolate
	-
	- unsigned int indexStart( 0 ), indexEnd( 0 );
	-
	- try
	- {
	- indexStart = Double2Int::convert( start );
	- indexEnd = Double2Int::convert( end );
	- }
	- catch ( boost::numeric::positive_overflow const& )
	- {
	- MBI_WARN << mitk::ConnectomicsConstantsManager::CONNECTOMICS_ERROR_OUTSIDE_INTEGER_RANGE;
	- }
	-
	- if( ( indexStart < m_HistogramVector.size() ) &&
	- ( indexEnd < m_HistogramVector.size() ) )
	- {
	- // add up weighted values and divide by range
	-
	- // add partial start and end bin
	-
	- double startPercentage = 1.0 - start + indexStart;
	- double endPercentage = end - indexEnd;
	-
	- result += startPercentage * m_HistogramVector[ indexStart ];
	- result += endPercentage * m_HistogramVector[ indexEnd ];
	-
	- // add whole inbetween bins
	- for( unsigned int tempIndex = indexStart + 1; tempIndex < indexEnd; tempIndex++ )
	- {
	- result += m_HistogramVector[ tempIndex ];
	- }
	- }
	- else
	- {
	- MBI_WARN << mitk::ConnectomicsConstantsManager::CONNECTOMICS_ERROR_BEYOND_SCOPE << indexStart << " to " <<
	- indexEnd << " on vector sized: " << m_HistogramVector.size();
	- }
	- }
	-
	- // normalizeresult by dividing through maximum degree
	- result = result / GetYMax();
	- return result;
	-}
	-
	-void mitk::ConnectomicsHistogramBase::UpdateYMax()
	-{
	- for ( unsigned int index( 0 ); index < m_HistogramVector.size(); index++ )
	- {
	- if( m_HistogramVector[ index ] > m_TopValue )
	- {
	- m_TopValue = m_HistogramVector[ index ];
	- }
	- }
	-}
	-
	-std::vector< double > mitk::ConnectomicsHistogramBase::GetHistogramVector()
	-{
	- return m_HistogramVector;
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsHistogramBase.h b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsHistogramBase.h
	deleted file mode 100644
	index 399b618589..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsHistogramBase.h
	+++ /dev/null
	@@ -1,101 +0,0 @@
	-
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_ConnectomicsHistogramBase_H
	-#define _MITK_ConnectomicsHistogramBase_H
	-
	-#include "mitkSimpleHistogram.h"
	-#include "mitkCommon.h"
	-
	-#include "mitkConnectomicsNetwork.h"
	-
	-namespace mitk {
	-
	- /**
	- * \brief Superclass for histograms working with connectomic networks
	- */
	-
	- class ConnectomicsHistogramBase : public mitk::SimpleHistogram
	- {
	-
	- public:
	-
	- ConnectomicsHistogramBase();
	- virtual ~ConnectomicsHistogramBase();
	-
	- /** @brief Returns the minimal y=f(x) value of the histogram. */
	- virtual double GetYMin() const;
	- /** @brief Returns the maximum y=f(x) value of the histogram. */
	- virtual double GetYMax() const;
	- /** @brief Returns the minimal x value of the histogram. */
	- virtual double GetXMin() const;
	- /** @brief Returns the maximum x value of the histogram. */
	- virtual double GetXMax() const;
	- /** @brief Returns the range of the histogram. */
	- virtual int GetRange() const;
	- /** @brief Update the Y maximum to the maximal value in the histogram */
	- virtual void UpdateYMax();
	- /** @brief Creates a new histogram from the source. */
	- void ComputeFromBaseData( BaseData* source ) override;
	- /** @brief Print values to console. */
	- virtual void PrintToConsole( ) const;
	- /** @brief Returns whether the histogram can be considered valid. */
	- virtual bool IsValid() const;
	- /** @brief Returns the subject of the histogram as a string. */
	- virtual std::string GetSubject() const;
	- /** @brief Set the subject of the histogram as a string. */
	- virtual void SetSubject( std::string );
	-
	- /** @brief Get bin height for the bin between start and end*/
	- float GetRelativeBin( double start, double end ) const override;
	-
	- /** @brief Get the double vector*/
	- virtual std::vector< double > GetHistogramVector();
	-
	- protected:
	-
	- // Functions
	-
	- /** @brief Creates a new histogram from the network source. */
	- virtual void ComputeFromConnectomicsNetwork( ConnectomicsNetwork* source ) = 0;
	- /** @brief Legacy method, do no use */
	- double GetMin() const override;
	- /** @brief Legacy method, do no use */
	- double GetMax() const override;
	-
	- // Variables
	-
	- /** @brief Is this a valid histogram*/
	- bool m_Valid;
	- /** @brief Which is the baseline value for the histogram
	- This value should be zero for all network histograms */
	- int m_BaselineValue;
	- /** @brief Which is the top value for the histogram */
	- int m_TopValue;
	- /** @brief Which is the starting x value for the histogram */
	- int m_StartValue;
	-
	- /** @brief We expect not continuous but discrete histograms */
	- std::vector< double > m_HistogramVector;
	-
	- /** @brief Subject of the histogram as a string. */
	- std::string m_Subject;
	- };
	-
	-}
	-
	-#endif /* _MITK_ConnectomicsHistogramBase_H */
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsHistogramCache.cpp b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsHistogramCache.cpp
	deleted file mode 100644
	index d553cb791a..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsHistogramCache.cpp
	+++ /dev/null
	@@ -1,95 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkConnectomicsHistogramCache.h"
	-
	-mitk::ConnectomicsHistogramCache::ConnectomicsHistogramCache()
	-{
	-}
	-
	-mitk::ConnectomicsHistogramCache::~ConnectomicsHistogramCache()
	-{
	-}
	-
	-mitk::ConnectomicsHistogramsContainer * mitk::ConnectomicsHistogramCache::operator[]( mitk::ConnectomicsNetwork::Pointer sp_NetworkData )
	-{
	- BaseData p_BaseData = dynamic_cast< BaseData >( sp_NetworkData.GetPointer() );
	-
	- if(!p_BaseData)
	- {
	- MITK_WARN << "ConnectomicsHistogramCache::operator[] with null connectomics network data called";
	- return nullptr;
	- }
	-
	- ConnectomicsHistogramsCacheElement *elementToUpdate = nullptr;
	-
	- bool first( true );
	-
	- bool found( false );
	-
	- for(auto iter = cache.begin(); iter != cache.end(); iter++)
	- {
	- ConnectomicsHistogramsCacheElement e = dynamic_cast<ConnectomicsHistogramsCacheElement >(*iter);
	- BaseData *p_tmp = e->baseData.Lock();
	-
	- if(p_tmp == p_BaseData)
	- {
	- if(!first)
	- {
	- cache.erase(iter);
	- cache.push_front(e);
	- }
	- if( p_BaseData->GetMTime() > e->m_LastUpdateTime.GetMTime())
	- {
	- // found but needs an update
	- found = true;
	- elementToUpdate = e;
	- break;
	- }
	-
	- // found but no update needed
	- return dynamic_cast<ConnectomicsHistogramsContainer*>( e->GetHistograms() );
	- }
	-
	- first = false;
	- }
	-
	- if( !found )
	- {
	- if (dynamic_cast<ConnectomicsNetwork*>(p_BaseData))
	- {
	- elementToUpdate = new ConnectomicsHistogramsCacheElement();
	- }
	- else
	- {
	- MITK_WARN << "not supported: " << p_BaseData->GetNameOfClass();
	- return nullptr;
	- }
	-
	- elementToUpdate->baseData = p_BaseData;
	- cache.push_front(elementToUpdate);
	- TrimCache();
	- }
	-
	- if(elementToUpdate)
	- {
	- elementToUpdate->ComputeFromBaseData(p_BaseData);
	- elementToUpdate->m_LastUpdateTime.Modified();
	- return dynamic_cast<ConnectomicsHistogramsContainer*>( elementToUpdate->GetHistograms() );
	- }
	- return nullptr;
	-}
	-
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsHistogramCache.h b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsHistogramCache.h
	deleted file mode 100644
	index 0400a6fb50..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsHistogramCache.h
	+++ /dev/null
	@@ -1,113 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef MITKCONNECTOMICSHISTOGRAMCACHE_H
	-#define MITKCONNECTOMICSHISTOGRAMCACHE_H
	-
	-#include "mitkSimpleHistogram.h"
	-#include "mitkConnectomicsNetwork.h"
	-
	-#include <mitkConnectomicsDegreeHistogram.h>
	-#include <mitkConnectomicsBetweennessHistogram.h>
	-#include <mitkConnectomicsShortestPathHistogram.h>
	-
	-#include <MitkConnectomicsExports.h>
	-
	-namespace mitk {
	-
	- /**
	- * @brief Provides a method to cache network histograms
	- */
	-
	- class ConnectomicsHistogramsContainer
	- {
	- public:
	-
	- void ComputeFromBaseData(BaseData* baseData)
	- {
	- m_BetweennessHistogram.ComputeFromBaseData(baseData);
	- m_DegreeHistogram.ComputeFromBaseData(baseData);
	- m_ShortestPathHistogram.ComputeFromBaseData(baseData);
	- }
	-
	- ConnectomicsBetweennessHistogram* GetBetweennessHistogram( )
	- {
	- return &m_BetweennessHistogram;
	- }
	-
	- ConnectomicsDegreeHistogram* GetDegreeHistogram( )
	- {
	- return &m_DegreeHistogram;
	- }
	-
	- ConnectomicsShortestPathHistogram* GetShortestPathHistogram( )
	- {
	- return &m_ShortestPathHistogram;
	- }
	-
	- ConnectomicsBetweennessHistogram m_BetweennessHistogram;
	- ConnectomicsDegreeHistogram m_DegreeHistogram;
	- ConnectomicsShortestPathHistogram m_ShortestPathHistogram;
	- };
	-
	- class MITKCONNECTOMICS_EXPORT ConnectomicsHistogramCache : public SimpleHistogramCache
	- {
	- public:
	-
	- ConnectomicsHistogramCache();
	- ~ConnectomicsHistogramCache();
	-
	- ConnectomicsHistogramsContainer *operator[]( ConnectomicsNetwork::Pointer sp_NetworkData);
	-
	-
	- protected:
	-
	- // purposely not implemented
	- SimpleHistogram *operator[](BaseData::Pointer sp_BaseData);
	-
	- };
	-
	-
	-
	- class ConnectomicsHistogramsCacheElement : public ConnectomicsHistogramCache::Element
	- {
	- public:
	-
	- void ComputeFromBaseData(BaseData* baseData) override
	- {
	- m_Container.ComputeFromBaseData(baseData);
	- }
	-
	- ConnectomicsHistogramsContainer* GetHistograms()
	- {
	- return &m_Container;
	- }
	-
	- ConnectomicsHistogramsContainer m_Container;
	-
	- private:
	- ConnectomicsHistogramBase* GetHistogram() override
	- {
	- return nullptr;
	- }
	- };
	-
	-
	-
	-}
	-
	-#endif // MITKCONNECTOMICSHISTOGRAMCACHE_H
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsNetworkConverter.cpp b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsNetworkConverter.cpp
	deleted file mode 100644
	index 4c6f7e505a..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsNetworkConverter.cpp
	+++ /dev/null
	@@ -1,71 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkConnectomicsNetworkConverter.h"
	-
	-mitk::ConnectomicsNetworkConverter::ConnectomicsNetworkConverter()
	-{
	-}
	-
	-mitk::ConnectomicsNetworkConverter::~ConnectomicsNetworkConverter()
	-{
	-}
	-
	-vnl_matrix<double> mitk::ConnectomicsNetworkConverter::GetNetworkAsVNLAdjacencyMatrix()
	-{
	- int numberOfNodes = boost::num_vertices( *(m_Network->GetBoostGraph()) );
	-
	- //initialize a matrix N by N
	- vnl_matrix<double> matrix(numberOfNodes, numberOfNodes, 0);
	-
	- //Define the vertex iterators
	- VertexIteratorType vi, vi_end;
	- for(boost::tie(vi, vi_end) = boost::vertices( *(m_Network->GetBoostGraph()) ); vi != vi_end; ++vi)
	- {
	- //Define the neighbor iterator
	- AdjacencyIteratorType neighbors, neighbors_end;
	- for(boost::tie(neighbors, neighbors_end) = boost::adjacent_vertices(vi, (m_Network->GetBoostGraph()) );
	- neighbors != neighbors_end; ++neighbors )
	- {
	- //Set the i,j element of the matrix to 1.
	- matrix.put(vi, neighbors, 1);
	- }
	- }
	- return matrix;
	-}
	-
	-vnl_matrix<double> mitk::ConnectomicsNetworkConverter::GetNetworkAsVNLDegreeMatrix()
	-{
	- int numberOfNodes = boost::num_vertices( *(m_Network->GetBoostGraph()) );
	-
	- vnl_matrix<double> matrix( numberOfNodes, numberOfNodes, 0);
	-
	- //Define the vertex iterators
	- VertexIteratorType vi, vi_end;
	- for(boost::tie(vi, vi_end) = boost::vertices( *(m_Network->GetBoostGraph()) ); vi != vi_end; ++vi)
	- {
	- double numberOfNeighbors = 0;
	- //Define the neighbor iterator
	- AdjacencyIteratorType neighbors, neighbors_end;
	- for( boost::tie(neighbors, neighbors_end) = adjacent_vertices(vi, (m_Network->GetBoostGraph()) );
	- neighbors != neighbors_end; ++neighbors )
	- {
	- numberOfNeighbors++;
	- }
	- matrix.put(vi, vi, numberOfNeighbors);
	- }
	- return matrix;
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsNetworkConverter.h b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsNetworkConverter.h
	deleted file mode 100644
	index 9c28b97ab2..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsNetworkConverter.h
	+++ /dev/null
	@@ -1,77 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef mitkConnectomicsNetworkConverter_h
	-#define mitkConnectomicsNetworkConverter_h
	-
	-#include <itkObject.h>
	-#include <itkObjectFactory.h>
	-#include <itkMacro.h>
	-
	-#include "mitkCommon.h"
	-
	-#include <MitkConnectomicsExports.h>
	-
	-#include <mitkConnectomicsNetwork.h>
	-
	-namespace mitk
	-{
	- /**
	- * \brief A class giving functions for conversion of connectomics networks into different formats */
	- class MITKCONNECTOMICS_EXPORT ConnectomicsNetworkConverter : public itk::Object
	- {
	- public:
	-
	- /** Standard class typedefs. */
	- /** Method for creation through the object factory. */
	-
	- mitkClassMacroItkParent(ConnectomicsNetworkConverter, itk::Object);
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- // Typedefs
	- typedef mitk::ConnectomicsNetwork::NetworkType NetworkType;
	- typedef mitk::ConnectomicsNetwork::VertexDescriptorType VertexDescriptorType;
	- typedef mitk::ConnectomicsNetwork::EdgeDescriptorType EdgeDescriptorType;
	- typedef boost::graph_traits<NetworkType>::vertex_iterator VertexIteratorType;
	- typedef boost::graph_traits<NetworkType>::adjacency_iterator AdjacencyIteratorType;
	- typedef std::map<EdgeDescriptorType, int> EdgeIndexStdMapType;
	- typedef boost::associative_property_map< EdgeIndexStdMapType > EdgeIndexMapType;
	- typedef boost::iterator_property_map< std::vector< double >::iterator, EdgeIndexMapType > EdgeIteratorPropertyMapType;
	- typedef boost::property_map< NetworkType, boost::vertex_index_t>::type VertexIndexMapType;
	- typedef boost::iterator_property_map< std::vector< double >::iterator, VertexIndexMapType > VertexIteratorPropertyMapType;
	-
	- //Macro
	- itkSetObjectMacro( Network, mitk::ConnectomicsNetwork );
	-
	- // Conversion Getters
	- vnl_matrix<double> GetNetworkAsVNLAdjacencyMatrix();
	- vnl_matrix<double> GetNetworkAsVNLDegreeMatrix();
	-
	- protected:
	-
	- //////////////////// Functions ///////////////////////
	- ConnectomicsNetworkConverter();
	- ~ConnectomicsNetworkConverter() override;
	-
	- /////////////////////// Variables ////////////////////////
	- // The connectomics network, which is converted
	- mitk::ConnectomicsNetwork::Pointer m_Network;
	- };
	-
	-}// end namespace mitk
	-
	-#endif // mitkConnectomicsNetworkConverter_h
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsNetworkCreator.cpp b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsNetworkCreator.cpp
	deleted file mode 100644
	index b10a18e921..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsNetworkCreator.cpp
	+++ /dev/null
	@@ -1,853 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkConnectomicsNetworkCreator.h"
	-
	-#include <sstream>
	-#include <vector>
	-
	-#include "mitkConnectomicsConstantsManager.h"
	-#include "mitkImageAccessByItk.h"
	-#include "mitkImageStatisticsHolder.h"
	-#include "mitkImageCast.h"
	-
	-#include "itkImageRegionIteratorWithIndex.h"
	-#include <mitkDiffusionFunctionCollection.h>
	-
	-// VTK
	-#include <vtkPolyData.h>
	-#include <vtkPolyLine.h>
	-#include <vtkCellArray.h>
	-
	-mitk::ConnectomicsNetworkCreator::ConnectomicsNetworkCreator()
	-: m_FiberBundle()
	-, m_Segmentation()
	-, m_ConNetwork( mitk::ConnectomicsNetwork::New() )
	-, idCounter(0)
	-, m_LabelToVertexMap()
	-, m_LabelToNodePropertyMap()
	-, allowLoops( false )
	-, m_UseCoMCoordinates( false )
	-, m_LabelsToCoordinatesMap()
	-, m_MappingStrategy( EndElementPositionAvoidingWhiteMatter )
	-, m_EndPointSearchRadius( 10.0 )
	-, m_ZeroLabelInvalid( true )
	-, m_AbortConnection( false )
	-{
	-}
	-
	-mitk::ConnectomicsNetworkCreator::ConnectomicsNetworkCreator( mitk::Image::Pointer segmentation, mitk::FiberBundle::Pointer fiberBundle )
	-: m_FiberBundle(fiberBundle)
	-, m_Segmentation(segmentation)
	-, m_ConNetwork( mitk::ConnectomicsNetwork::New() )
	-, idCounter(0)
	-, m_LabelToVertexMap()
	-, m_LabelToNodePropertyMap()
	-, allowLoops( false )
	-, m_LabelsToCoordinatesMap()
	-, m_MappingStrategy( EndElementPositionAvoidingWhiteMatter )
	-, m_EndPointSearchRadius( 10.0 )
	-, m_ZeroLabelInvalid( true )
	-, m_AbortConnection( false )
	-{
	- mitk::CastToItkImage( segmentation, m_SegmentationItk );
	-}
	-
	-mitk::ConnectomicsNetworkCreator::~ConnectomicsNetworkCreator()
	-{
	-}
	-
	-void mitk::ConnectomicsNetworkCreator::SetFiberBundle(mitk::FiberBundle::Pointer fiberBundle)
	-{
	- m_FiberBundle = fiberBundle;
	-}
	-
	-void mitk::ConnectomicsNetworkCreator::SetSegmentation(mitk::Image::Pointer segmentation)
	-{
	- m_Segmentation = segmentation;
	- mitk::CastToItkImage( segmentation, m_SegmentationItk );
	-}
	-
	-void mitk::ConnectomicsNetworkCreator::CreateNetworkFromFibersAndSegmentation()
	-{
	- //empty graph
	- m_ConNetwork = mitk::ConnectomicsNetwork::New();
	- m_LabelToVertexMap.clear();
	- m_LabelToNodePropertyMap.clear();
	- idCounter = 0;
	-
	- vtkSmartPointer<vtkPolyData> fiberPolyData = m_FiberBundle->GetFiberPolyData();
	-
	- int numFibers = m_FiberBundle->GetNumFibers();
	- for( int fiberID( 0 ); fiberID < numFibers; fiberID++ )
	- {
	- vtkCell* cell = fiberPolyData->GetCell(fiberID);
	- int numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- TractType::Pointer singleTract = TractType::New();
	- for( int pointInCellID( 0 ); pointInCellID < numPoints ; pointInCellID++)
	- {
	- // push back point
	- PointType point = mitk::imv::GetItkPoint( points->GetPoint( pointInCellID ) );
	- singleTract->InsertElement( singleTract->Size(), point );
	- }
	-
	- if ( singleTract && ( singleTract->Size() > 0 ) )
	- {
	- AddConnectionToNetwork(
	- ReturnAssociatedVertexPairForLabelPair(
	- ReturnLabelForFiberTract( singleTract, m_MappingStrategy )
	- ), m_FiberBundle->GetFiberWeight(fiberID)
	- );
	- m_AbortConnection = false;
	- }
	- }
	-
	- // Prune unconnected nodes
	- //m_ConNetwork->PruneUnconnectedSingleNodes();
	-
	- // provide network with geometry
	- m_ConNetwork->SetGeometry( dynamic_cast<mitk::BaseGeometry*>(m_Segmentation->GetGeometry()->Clone().GetPointer()) );
	- m_ConNetwork->UpdateBounds();
	- m_ConNetwork->SetIsModified( true );
	-
	- MBI_INFO << mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_INFO_NETWORK_CREATED;
	-}
	-
	-void mitk::ConnectomicsNetworkCreator::AddConnectionToNetwork(ConnectionType newConnection, double fiber_count)
	-{
	- if( m_AbortConnection )
	- {
	- MITK_DEBUG << "Connection aborted";
	- return;
	- }
	-
	- VertexType vertexA = newConnection.first;
	- VertexType vertexB = newConnection.second;
	-
	- // check for loops (if they are not allowed)
	- if( allowLoops \|\| !( vertexA == vertexB ) )
	- {
	- // If the connection already exists, increment weight, else create connection
	- if ( m_ConNetwork->EdgeExists( vertexA, vertexB ) )
	- {
	- m_ConNetwork->IncreaseEdgeWeight( vertexA, vertexB, fiber_count );
	- }
	- else
	- {
	- m_ConNetwork->AddEdge( vertexA, vertexB, fiber_count );
	- }
	- }
	-}
	-
	-
	-mitk::ConnectomicsNetworkCreator::VertexType mitk::ConnectomicsNetworkCreator::ReturnAssociatedVertexForLabel( ImageLabelType label )
	-{
	- if( m_ZeroLabelInvalid && ( label == 0 ) )
	- {
	- m_AbortConnection = true;
	- return ULONG_MAX;
	- }
	-
	- // if label is not known, create entry
	- if( ! ( m_LabelToVertexMap.count( label ) > 0 ) )
	- {
	- VertexType newVertex = m_ConNetwork->AddVertex( idCounter );
	- idCounter++;
	- SupplyVertexWithInformation(label, newVertex);
	- m_LabelToVertexMap.insert( std::pair< ImageLabelType, VertexType >( label, newVertex ) );
	- }
	-
	- //return associated vertex
	- return m_LabelToVertexMap.find( label )->second;
	-}
	-
	-mitk::ConnectomicsNetworkCreator::ConnectionType mitk::ConnectomicsNetworkCreator::ReturnAssociatedVertexPairForLabelPair( ImageLabelPairType labelpair )
	-{
	- //hand both labels through to the single label function
	- ConnectionType connection( ReturnAssociatedVertexForLabel(labelpair.first), ReturnAssociatedVertexForLabel(labelpair.second) );
	-
	- return connection;
	-}
	-
	-mitk::ConnectomicsNetworkCreator::ImageLabelPairType mitk::ConnectomicsNetworkCreator::ReturnLabelForFiberTract( TractType::Pointer singleTract, mitk::ConnectomicsNetworkCreator::MappingStrategy strategy)
	-{
	- switch( strategy )
	- {
	- case EndElementPosition:
	- {
	- return EndElementPositionLabel( singleTract );
	- }
	- case JustEndPointVerticesNoLabel:
	- {
	- return JustEndPointVerticesNoLabelTest( singleTract );
	- }
	- case EndElementPositionAvoidingWhiteMatter:
	- {
	- return EndElementPositionLabelAvoidingWhiteMatter( singleTract );
	- }
	- case PrecomputeAndDistance:
	- {
	- return PrecomputeVertexLocationsBySegmentation( singleTract );
	- }
	- }
	-
	- // To remove warnings, this code should never be reached
	- MBI_ERROR << mitk::ConnectomicsConstantsManager::CONNECTOMICS_ERROR_INVALID_MAPPING;
	- ImageLabelPairType nullPair( 0,0 );
	- return nullPair;
	-}
	-
	-mitk::ConnectomicsNetworkCreator::ImageLabelPairType mitk::ConnectomicsNetworkCreator::EndElementPositionLabel( TractType::Pointer singleTract )
	-{
	- ImageLabelPairType labelpair;
	-
	- {// Note: .fib image tracts are safed using index coordinates
	- mitk::Point3D firstElementFiberCoord, lastElementFiberCoord;
	- mitk::Point3D firstElementSegCoord, lastElementSegCoord;
	- itk::Index<3> firstElementSegIndex, lastElementSegIndex;
	-
	- if( singleTract->front().Size() != 3 )
	- {
	- MBI_ERROR << mitk::ConnectomicsConstantsManager::CONNECTOMICS_ERROR_INVALID_DIMENSION_NEED_3;
	- }
	- for( unsigned int index = 0; index < singleTract->front().Size(); index++ )
	- {
	- firstElementFiberCoord.SetElement( index, singleTract->front().GetElement( index ) );
	- lastElementFiberCoord.SetElement( index, singleTract->back().GetElement( index ) );
	- }
	-
	- // convert from fiber index coordinates to segmentation index coordinates
	- FiberToSegmentationCoords( firstElementFiberCoord, firstElementSegCoord );
	- FiberToSegmentationCoords( lastElementFiberCoord, lastElementSegCoord );
	-
	- for( int index = 0; index < 3; index++ )
	- {
	- firstElementSegIndex.SetElement( index, firstElementSegCoord.GetElement( index ) );
	- lastElementSegIndex.SetElement( index, lastElementSegCoord.GetElement( index ) );
	- }
	-
	- int firstLabel = m_SegmentationItk->GetPixel(firstElementSegIndex);
	- int lastLabel = m_SegmentationItk->GetPixel(lastElementSegIndex );
	-
	- labelpair.first = firstLabel;
	- labelpair.second = lastLabel;
	-
	- // Add property to property map
	- CreateNewNode( firstLabel, firstElementSegIndex, m_UseCoMCoordinates );
	- CreateNewNode( lastLabel, lastElementSegIndex, m_UseCoMCoordinates );
	- }
	-
	- return labelpair;
	-}
	-
	-mitk::ConnectomicsNetworkCreator::ImageLabelPairType mitk::ConnectomicsNetworkCreator::PrecomputeVertexLocationsBySegmentation( TractType::Pointer /singleTract/ )
	-{
	- ImageLabelPairType labelpair;
	-
	- return labelpair;
	-}
	-
	-mitk::ConnectomicsNetworkCreator::ImageLabelPairType mitk::ConnectomicsNetworkCreator::EndElementPositionLabelAvoidingWhiteMatter( TractType::Pointer singleTract )
	-{
	- ImageLabelPairType labelpair;
	-
	- {// Note: .fib image tracts are safed using index coordinates
	- mitk::Point3D firstElementFiberCoord, lastElementFiberCoord;
	- mitk::Point3D firstElementSegCoord, lastElementSegCoord;
	- itk::Index<3> firstElementSegIndex, lastElementSegIndex;
	-
	- if( singleTract->front().Size() != 3 )
	- {
	- MBI_ERROR << mitk::ConnectomicsConstantsManager::CONNECTOMICS_ERROR_INVALID_DIMENSION_NEED_3;
	- }
	- for( unsigned int index = 0; index < singleTract->front().Size(); index++ )
	- {
	- firstElementFiberCoord.SetElement( index, singleTract->front().GetElement( index ) );
	- lastElementFiberCoord.SetElement( index, singleTract->back().GetElement( index ) );
	- }
	-
	- // convert from fiber index coordinates to segmentation index coordinates
	- FiberToSegmentationCoords( firstElementFiberCoord, firstElementSegCoord );
	- FiberToSegmentationCoords( lastElementFiberCoord, lastElementSegCoord );
	-
	- for( int index = 0; index < 3; index++ )
	- {
	- firstElementSegIndex.SetElement( index, firstElementSegCoord.GetElement( index ) );
	- lastElementSegIndex.SetElement( index, lastElementSegCoord.GetElement( index ) );
	- }
	-
	- int firstLabel = m_SegmentationItk->GetPixel(firstElementSegIndex);
	- int lastLabel = m_SegmentationItk->GetPixel(lastElementSegIndex );
	-
	- // Check whether the labels belong to the white matter (which means, that the fibers ended early)
	- bool extendFront(false), extendEnd(false), retractFront(false), retractEnd(false);
	- extendFront = !IsNonWhiteMatterLabel( firstLabel );
	- extendEnd = !IsNonWhiteMatterLabel( lastLabel );
	- retractFront = IsBackgroundLabel( firstLabel );
	- retractEnd = IsBackgroundLabel( lastLabel );
	-
	- //if( extendFront \|\| extendEnd )
	- //{
	- //MBI_INFO << "Before Start: " << firstLabel << " at " << firstElementSegIndex[ 0 ] << " " << firstElementSegIndex[ 1 ] << " " << firstElementSegIndex[ 2 ] << " End: " << lastLabel << " at " << lastElementSegIndex[ 0 ] << " " << lastElementSegIndex[ 1 ] << " " << lastElementSegIndex[ 2 ];
	- //}
	- if ( extendFront )
	- {
	- std::vector< int > indexVectorOfPointsToUse;
	-
	- //Use first two points for direction
	- indexVectorOfPointsToUse.push_back( 1 );
	- indexVectorOfPointsToUse.push_back( 0 );
	-
	- // label and coordinate temp storage
	- int tempLabel( firstLabel );
	- itk::Index<3> tempIndex = firstElementSegIndex;
	-
	- LinearExtensionUntilGreyMatter( indexVectorOfPointsToUse, singleTract, tempLabel, tempIndex );
	-
	- firstLabel = tempLabel;
	- firstElementSegIndex = tempIndex;
	-
	- }
	-
	- if ( extendEnd )
	- {
	- std::vector< int > indexVectorOfPointsToUse;
	-
	- //Use last two points for direction
	- indexVectorOfPointsToUse.push_back( singleTract->Size() - 2 );
	- indexVectorOfPointsToUse.push_back( singleTract->Size() - 1 );
	-
	- // label and coordinate temp storage
	- int tempLabel( lastLabel );
	- itk::Index<3> tempIndex = lastElementSegIndex;
	-
	- LinearExtensionUntilGreyMatter( indexVectorOfPointsToUse, singleTract, tempLabel, tempIndex );
	-
	- lastLabel = tempLabel;
	- lastElementSegIndex = tempIndex;
	- }
	- if ( retractFront )
	- {
	- // label and coordinate temp storage
	- int tempLabel( firstLabel );
	- itk::Index<3> tempIndex = firstElementSegIndex;
	-
	- RetractionUntilBrainMatter( true, singleTract, tempLabel, tempIndex );
	-
	- firstLabel = tempLabel;
	- firstElementSegIndex = tempIndex;
	-
	- }
	-
	- if ( retractEnd )
	- {
	- // label and coordinate temp storage
	- int tempLabel( lastLabel );
	- itk::Index<3> tempIndex = lastElementSegIndex;
	-
	- RetractionUntilBrainMatter( false, singleTract, tempLabel, tempIndex );
	-
	- lastLabel = tempLabel;
	- lastElementSegIndex = tempIndex;
	- }
	- //if( extendFront \|\| extendEnd )
	- //{
	- // MBI_INFO << "After Start: " << firstLabel << " at " << firstElementSegIndex[ 0 ] << " " << firstElementSegIndex[ 1 ] << " " << firstElementSegIndex[ 2 ] << " End: " << lastLabel << " at " << lastElementSegIndex[ 0 ] << " " << lastElementSegIndex[ 1 ] << " " << lastElementSegIndex[ 2 ];
	- //}
	-
	- labelpair.first = firstLabel;
	- labelpair.second = lastLabel;
	-
	- // Add property to property map
	- CreateNewNode( firstLabel, firstElementSegIndex, m_UseCoMCoordinates );
	- CreateNewNode( lastLabel, lastElementSegIndex, m_UseCoMCoordinates );
	- }
	-
	- return labelpair;
	-}
	-
	-mitk::ConnectomicsNetworkCreator::ImageLabelPairType mitk::ConnectomicsNetworkCreator::JustEndPointVerticesNoLabelTest( TractType::Pointer singleTract )
	-{
	- ImageLabelPairType labelpair;
	-
	- {// Note: .fib image tracts are safed using index coordinates
	- mitk::Point3D firstElementFiberCoord, lastElementFiberCoord;
	- mitk::Point3D firstElementSegCoord, lastElementSegCoord;
	- itk::Index<3> firstElementSegIndex, lastElementSegIndex;
	-
	- if( singleTract->front().Size() != 3 )
	- {
	- MBI_ERROR << mitk::ConnectomicsConstantsManager::CONNECTOMICS_ERROR_INVALID_DIMENSION_NEED_3;
	- }
	- for( unsigned int index = 0; index < singleTract->front().Size(); index++ )
	- {
	- firstElementFiberCoord.SetElement( index, singleTract->front().GetElement( index ) );
	- lastElementFiberCoord.SetElement( index, singleTract->back().GetElement( index ) );
	- }
	-
	- // convert from fiber index coordinates to segmentation index coordinates
	- FiberToSegmentationCoords( firstElementFiberCoord, firstElementSegCoord );
	- FiberToSegmentationCoords( lastElementFiberCoord, lastElementSegCoord );
	-
	- for( int index = 0; index < 3; index++ )
	- {
	- firstElementSegIndex.SetElement( index, firstElementSegCoord.GetElement( index ) );
	- lastElementSegIndex.SetElement( index, lastElementSegCoord.GetElement( index ) );
	- }
	-
	- int firstLabel = 1 * firstElementSegIndex[ 0 ] + 1000 * firstElementSegIndex[ 1 ] + 1000000 * firstElementSegIndex[ 2 ];
	- int lastLabel = 1 * firstElementSegIndex[ 0 ] + 1000 * firstElementSegIndex[ 1 ] + 1000000 * firstElementSegIndex[ 2 ];
	-
	- labelpair.first = firstLabel;
	- labelpair.second = lastLabel;
	-
	- // Add property to property map
	- CreateNewNode( firstLabel, firstElementSegIndex, m_UseCoMCoordinates );
	- CreateNewNode( lastLabel, lastElementSegIndex, m_UseCoMCoordinates );
	- }
	-
	- return labelpair;
	-}
	-
	-void mitk::ConnectomicsNetworkCreator::SupplyVertexWithInformation( ImageLabelType& label, VertexType& vertex )
	-{ // supply a vertex with the additional information belonging to the label
	-
	- // TODO: Implement additional information acquisition
	-
	- m_ConNetwork->SetLabel( vertex, m_LabelToNodePropertyMap.find( label )->second.label );
	- m_ConNetwork->SetCoordinates( vertex, m_LabelToNodePropertyMap.find( label )->second.coordinates );
	-
	-}
	-
	-std::string mitk::ConnectomicsNetworkCreator::LabelToString( ImageLabelType& label )
	-{
	- int tempInt = (int) label;
	- std::stringstream ss;//create a stringstream
	- std::string tempString;
	- ss << tempInt;//add number to the stream
	- tempString = ss.str();
	- return tempString;//return a string with the contents of the stream
	-}
	-
	-mitk::ConnectomicsNetwork::Pointer mitk::ConnectomicsNetworkCreator::GetNetwork()
	-{
	- return m_ConNetwork;
	-}
	-
	-void mitk::ConnectomicsNetworkCreator::FiberToSegmentationCoords( mitk::Point3D& fiberCoord, mitk::Point3D& segCoord )
	-{
	- mitk::Point3D tempPoint;
	-
	- // convert from fiber index coordinates to segmentation index coordinates
	- m_FiberBundle->GetGeometry()->IndexToWorld( fiberCoord, tempPoint );
	- m_Segmentation->GetGeometry()->WorldToIndex( tempPoint, segCoord );
	-}
	-
	-void mitk::ConnectomicsNetworkCreator::SegmentationToFiberCoords( mitk::Point3D& segCoord, mitk::Point3D& fiberCoord )
	-{
	- mitk::Point3D tempPoint;
	-
	- // convert from fiber index coordinates to segmentation index coordinates
	- m_Segmentation->GetGeometry()->IndexToWorld( segCoord, tempPoint );
	- m_FiberBundle->GetGeometry()->WorldToIndex( tempPoint, fiberCoord );
	-}
	-
	-bool mitk::ConnectomicsNetworkCreator::IsNonWhiteMatterLabel( int labelInQuestion )
	-{
	- bool isWhite( false );
	-
	- isWhite = (
	- ( labelInQuestion == freesurfer_Left_Cerebral_White_Matter ) \|\|
	- ( labelInQuestion == freesurfer_Left_Cerebellum_White_Matter ) \|\|
	- ( labelInQuestion == freesurfer_Right_Cerebral_White_Matter ) \|\|
	- ( labelInQuestion == freesurfer_Right_Cerebellum_White_Matter )\|\|
	- ( labelInQuestion == freesurfer_Left_Cerebellum_Cortex ) \|\|
	- ( labelInQuestion == freesurfer_Right_Cerebellum_Cortex ) \|\|
	- ( labelInQuestion == freesurfer_Brain_Stem )
	- );
	-
	- return !isWhite;
	-}
	-
	-bool mitk::ConnectomicsNetworkCreator::IsBackgroundLabel( int labelInQuestion )
	-{
	- bool isBackground( false );
	-
	- isBackground = ( labelInQuestion == 0 );
	-
	- return isBackground;
	-}
	-
	-void mitk::ConnectomicsNetworkCreator::LinearExtensionUntilGreyMatter(
	- std::vector<int> & indexVectorOfPointsToUse,
	- TractType::Pointer singleTract,
	- int & label,
	- itk::Index<3> & mitkIndex )
	-{
	- if( indexVectorOfPointsToUse.size() > singleTract->Size() )
	- {
	- MBI_WARN << mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_MORE_POINTS_THAN_PRESENT;
	- return;
	- }
	-
	- if( indexVectorOfPointsToUse.size() < 2 )
	- {
	- MBI_WARN << mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_ESTIMATING_LESS_THAN_2;
	- return;
	- }
	-
	- for( unsigned int index( 0 ); index < indexVectorOfPointsToUse.size(); index++ )
	- {
	- if( indexVectorOfPointsToUse[ index ] < 0 )
	- {
	- MBI_WARN << mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_ESTIMATING_BEYOND_START;
	- return;
	- }
	- if( (unsigned int)indexVectorOfPointsToUse[ index ] > singleTract->Size() )
	- {
	- MBI_WARN << mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_ESTIMATING_BEYOND_END;
	- return;
	- }
	- }
	-
	- mitk::Point3D startPoint, endPoint;
	- std::vector< double > differenceVector;
	- differenceVector.resize( singleTract->front().Size() );
	-
	- {
	- // which points to use, currently only last two //TODO correct using all points
	- int endPointIndex = indexVectorOfPointsToUse.size() - 1;
	- int startPointIndex = indexVectorOfPointsToUse.size() - 2;
	-
	- // convert to segmentation coords
	- mitk::Point3D startFiber, endFiber;
	- for( unsigned int index = 0; index < singleTract->front().Size(); index++ )
	- {
	- endFiber.SetElement( index, singleTract->GetElement( indexVectorOfPointsToUse[ endPointIndex ] ).GetElement( index ) );
	- startFiber.SetElement( index, singleTract->GetElement( indexVectorOfPointsToUse[ startPointIndex ] ).GetElement( index ) );
	- }
	-
	- FiberToSegmentationCoords( endFiber, endPoint );
	- FiberToSegmentationCoords( startFiber, startPoint );
	-
	- // calculate straight line
	-
	- for( unsigned int index = 0; index < singleTract->front().Size(); index++ )
	- {
	- differenceVector[ index ] = endPoint.GetElement( index ) - startPoint.GetElement( index );
	- }
	-
	- // normalizing direction vector
	-
	- double length( 0.0 );
	- double sum( 0.0 );
	-
	- for( unsigned int index = 0; index < differenceVector.size() ; index++ )
	- {
	- sum = sum + differenceVector[ index ] * differenceVector[ index ];
	- }
	-
	- length = std::sqrt( sum );
	-
	- for( unsigned int index = 0; index < differenceVector.size() ; index++ )
	- {
	- differenceVector[ index ] = differenceVector[ index ] / length;
	- }
	-
	- // follow line until first non white matter label
	- itk::Index<3> tempIndex;
	- int tempLabel( label );
	-
	- bool keepOn( true );
	-
	- itk::ImageRegion<3> itkRegion = m_SegmentationItk->GetLargestPossibleRegion();
	-
	- for( int parameter( 0 ) ; keepOn ; parameter++ )
	- {
	- if( parameter > 1000 )
	- {
	- MBI_WARN << mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_DID_NOT_FIND_WHITE;
	- break;
	- }
	-
	- for( int index( 0 ); index < 3; index++ )
	- {
	- tempIndex.SetElement( index, endPoint.GetElement( index ) + parameter * differenceVector[ index ] );
	- }
	-
	- if( itkRegion.IsInside( tempIndex ) )
	- {
	- tempLabel = m_SegmentationItk->GetPixel( tempIndex );
	- }
	- else
	- {
	- tempLabel = -1;
	- }
	-
	- if( IsNonWhiteMatterLabel( tempLabel ) )
	- {
	- if( tempLabel < 1 )
	- {
	- keepOn = false;
	- //MBI_WARN << mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_NOT_EXTEND_TO_WHITE;
	- }
	- else
	- {
	- label = tempLabel;
	- mitkIndex = tempIndex;
	- keepOn = false;
	- }
	- }
	- }
	-
	- }
	-}
	-
	-void mitk::ConnectomicsNetworkCreator::RetractionUntilBrainMatter( bool retractFront, TractType::Pointer singleTract,
	- int & label, itk::Index<3> & mitkIndex )
	-{
	- int retractionStartIndex( singleTract->Size() - 1 );
	- int retractionStepIndexSize( -1 );
	- int retractionTerminationIndex( 0 );
	-
	- if( retractFront )
	- {
	- retractionStartIndex = 0;
	- retractionStepIndexSize = 1;
	- retractionTerminationIndex = singleTract->Size() - 1;
	- }
	-
	- int currentRetractionIndex = retractionStartIndex;
	-
	- bool keepRetracting( true );
	-
	- mitk::Point3D currentPoint, nextPoint;
	- std::vector< double > differenceVector;
	- differenceVector.resize( singleTract->front().Size() );
	-
	- while( keepRetracting && ( currentRetractionIndex != retractionTerminationIndex ) )
	- {
	- // convert to segmentation coords
	- mitk::Point3D currentPointFiberCoord, nextPointFiberCoord;
	- for( unsigned int index = 0; index < singleTract->front().Size(); index++ )
	- {
	- currentPointFiberCoord.SetElement( index, singleTract->GetElement( currentRetractionIndex ).GetElement( index ) );
	- nextPointFiberCoord.SetElement( index, singleTract->GetElement( currentRetractionIndex + retractionStepIndexSize ).GetElement( index ) );
	- }
	-
	- FiberToSegmentationCoords( currentPointFiberCoord, currentPoint );
	- FiberToSegmentationCoords( nextPointFiberCoord, nextPoint );
	-
	- // calculate straight line
	-
	- for( unsigned int index = 0; index < singleTract->front().Size(); index++ )
	- {
	- differenceVector[ index ] = nextPoint.GetElement( index ) - currentPoint.GetElement( index );
	- }
	-
	- // calculate length of direction vector
	-
	- double length( 0.0 );
	- double sum( 0.0 );
	-
	- for( unsigned int index = 0; index < differenceVector.size() ; index++ )
	- {
	- sum = sum + differenceVector[ index ] * differenceVector[ index ];
	- }
	-
	- length = std::sqrt( sum );
	-
	- // retract
	- itk::Index<3> tempIndex;
	- int tempLabel( label );
	-
	- for( int parameter( 0 ) ; parameter < length ; parameter++ )
	- {
	-
	- for( int index( 0 ); index < 3; index++ )
	- {
	- tempIndex.SetElement( index,
	- currentPoint.GetElement( index ) + ( 1.0 + parameter ) / ( 1.0 + length ) * differenceVector[ index ] );
	- }
	-
	- tempLabel = m_SegmentationItk->GetPixel( tempIndex );
	-
	- if( !IsBackgroundLabel( tempLabel ) )
	- {
	- // check whether result is within the search space
	- {
	- mitk::Point3D endPoint, foundPointSegmentation, foundPointFiber;
	- for( unsigned int index = 0; index < singleTract->front().Size(); index++ )
	- {
	- // this is in fiber (world) coordinates
	- endPoint.SetElement( index, singleTract->GetElement( retractionStartIndex ).GetElement( index ) );
	- }
	-
	- for( int index( 0 ); index < 3; index++ )
	- {
	- foundPointSegmentation.SetElement( index,
	- currentPoint.GetElement( index ) + ( 1.0 + parameter ) / ( 1.0 + length ) * differenceVector[ index ] );
	- }
	-
	- SegmentationToFiberCoords( foundPointSegmentation, foundPointFiber );
	-
	- std::vector< double > finalDistance;
	- finalDistance.resize( singleTract->front().Size() );
	- for( unsigned int index = 0; index < singleTract->front().Size(); index++ )
	- {
	- finalDistance[ index ] = foundPointFiber.GetElement( index ) - endPoint.GetElement( index );
	- }
	-
	- // calculate length of direction vector
	-
	- double finalLength( 0.0 );
	- double finalSum( 0.0 );
	-
	- for( unsigned int index = 0; index < finalDistance.size() ; index++ )
	- {
	- finalSum = finalSum + finalDistance[ index ] * finalDistance[ index ];
	- }
	- finalLength = std::sqrt( finalSum );
	-
	- if( finalLength > m_EndPointSearchRadius )
	- {
	- // the found point was not within the search space
	- return;
	- }
	- }
	-
	- label = tempLabel;
	- mitkIndex = tempIndex;
	- return;
	- }
	- // hit next point without finding brain matter
	- currentRetractionIndex = currentRetractionIndex + retractionStepIndexSize;
	- if( ( currentRetractionIndex < 1 ) \|\| ( (unsigned int)currentRetractionIndex > ( singleTract->Size() - 2 ) ) )
	- {
	- keepRetracting = false;
	- }
	- }
	- }
	-}
	-
	-void mitk::ConnectomicsNetworkCreator::CalculateCenterOfMass()
	-{
	-
	- const int dimensions = 3;
	- int max = m_Segmentation->GetStatistics()->GetScalarValueMax();
	- int min = m_Segmentation->GetStatistics()->GetScalarValueMin();
	-
	- int range = max - min +1;
	-
	- // each label owns a vector of coordinates
	- std::vector< std::vector< std::vector< double> > > coordinatesPerLabelVector;
	- coordinatesPerLabelVector.resize( range );
	-
	- itk::ImageRegionIteratorWithIndex<ITKImageType> it_itkImage( m_SegmentationItk, m_SegmentationItk->GetLargestPossibleRegion() );
	-
	- for( it_itkImage.GoToBegin(); !it_itkImage.IsAtEnd(); ++it_itkImage )
	- {
	- std::vector< double > coordinates;
	- coordinates.resize(dimensions);
	-
	- itk::Index< dimensions > index = it_itkImage.GetIndex();
	-
	- for( int loop(0); loop < dimensions; loop++)
	- {
	- coordinates.at( loop ) = index.GetElement( loop );
	- }
	-
	- // add the coordinates to the corresponding label vector
	- coordinatesPerLabelVector.at( it_itkImage.Value() - min ).push_back( coordinates );
	- }
	-
	- for(int currentIndex(0), currentLabel( min ); currentIndex < range; currentIndex++, currentLabel++ )
	- {
	- std::vector< double > currentCoordinates;
	- currentCoordinates.resize(dimensions);
	-
	- int numberOfPoints = coordinatesPerLabelVector.at( currentIndex ).size();
	-
	- std::vector< double > sumCoords;
	- sumCoords.resize( dimensions );
	-
	- for( int loop(0); loop < numberOfPoints; loop++ )
	- {
	- for( int loopDimension( 0 ); loopDimension < dimensions; loopDimension++ )
	- {
	- sumCoords.at( loopDimension ) += coordinatesPerLabelVector.at( currentIndex ).at( loop ).at( loopDimension );
	- }
	- }
	-
	- for( int loopDimension( 0 ); loopDimension < dimensions; loopDimension++ )
	- {
	- currentCoordinates.at( loopDimension ) = sumCoords.at( loopDimension ) / numberOfPoints;
	- }
	-
	- m_LabelsToCoordinatesMap.insert( std::pair< int, std::vector<double> >( currentLabel, currentCoordinates ) );
	- }
	-
	- //can now use center of mass coordinates
	- m_UseCoMCoordinates = true;
	-}
	-
	-std::vector< double > mitk::ConnectomicsNetworkCreator::GetCenterOfMass( int label )
	-{
	- // if label is not known, warn
	- if( ! ( m_LabelsToCoordinatesMap.count( label ) > 0 ) )
	- {
	- MITK_ERROR << "Label " << label << " not found. Could not return coordinates.";
	- std::vector< double > nullVector;
	- nullVector.resize(3);
	- return nullVector;
	- }
	-
	- //return associated coordinates
	- return m_LabelsToCoordinatesMap.find( label )->second;
	-}
	-
	-void mitk::ConnectomicsNetworkCreator::CreateNewNode( int label, itk::Index<3> index, bool useCoM )
	-{
	- // Only create node if it does not exist yet
	-
	- if( ! ( m_LabelToNodePropertyMap.count( label ) > 0 ) )
	- {
	- NetworkNode newNode;
	-
	- newNode.coordinates.resize( 3 );
	- if( !useCoM )
	- {
	- for( unsigned int loop = 0; loop < newNode.coordinates.size() ; loop++ )
	- {
	- newNode.coordinates[ loop ] = index[ loop ] ;
	- }
	- }
	- else
	- {
	- std::vector<double> labelCoords = GetCenterOfMass( label );
	- for( unsigned int loop = 0; loop < newNode.coordinates.size() ; loop++ )
	- {
	- newNode.coordinates[ loop ] = labelCoords.at( loop ) ;
	- }
	- }
	-
	- newNode.label = LabelToString( label );
	-
	- m_LabelToNodePropertyMap.insert( std::pair< ImageLabelType, NetworkNode >( label, newNode ) );
	- }
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsNetworkCreator.h b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsNetworkCreator.h
	deleted file mode 100644
	index 2b736f844a..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsNetworkCreator.h
	+++ /dev/null
	@@ -1,246 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef mitkConnectomicsNetworkCreator_h
	-#define mitkConnectomicsNetworkCreator_h
	-
	-#include <itkObject.h>
	-#include <itkObjectFactory.h>
	-#include <itkMacro.h>
	-
	-#include "mitkCommon.h"
	-#include "mitkImage.h"
	-
	-#include "mitkFiberBundle.h"
	-#include "mitkConnectomicsNetwork.h"
	-
	-#include <MitkConnectomicsExports.h>
	-
	-namespace mitk
	-{
	-
	- /**
	- * \brief Creates connectomics networks from fibers and parcellation
	- *
	- * This class needs a parcellation image and a fiber image to be set. Then you can create
	- * a connectomics network from the two, using different strategies.
	- */
	-
	- class MITKCONNECTOMICS_EXPORT ConnectomicsNetworkCreator : public itk::Object
	- {
	- public:
	-
	- /** Enum for different ways to create the mapping from fibers to network */
	-
	- enum MappingStrategy
	- {
	- EndElementPosition,
	- EndElementPositionAvoidingWhiteMatter,
	- JustEndPointVerticesNoLabel,
	- PrecomputeAndDistance
	- };
	-
	- /** Standard class typedefs. */
	- /** Method for creation through the object factory. */
	-
	- mitkClassMacroItkParent(ConnectomicsNetworkCreator, itk::Object);
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	-
	- / Type for Images /
	- typedef itk::Image<int, 3 > ITKImageType;
	-
	- / Types for the standardized Tract /
	- typedef itk::Point<float,3> PointType;
	- typedef itk::VectorContainer<unsigned int, PointType> TractType;
	- typedef itk::VectorContainer< unsigned int, TractType::Pointer > TractContainerType; //init via smartpointer
	-
	-
	- / Types for Network /
	- typedef mitk::ConnectomicsNetwork::VertexDescriptorType VertexType;
	- typedef mitk::ConnectomicsNetwork::EdgeDescriptorType EdgeType;
	- typedef mitk::ConnectomicsNetwork::NetworkNode NetworkNode;
	- typedef std::pair< VertexType, VertexType > ConnectionType;
	-
	- / Types for labels /
	- typedef int ImageLabelType;
	- typedef std::pair< ImageLabelType, ImageLabelType > ImageLabelPairType;
	-
	- /** Given a fiber bundle and a parcellation are set, this will create a network from both */
	- void CreateNetworkFromFibersAndSegmentation();
	- void SetFiberBundle(mitk::FiberBundle::Pointer fiberBundle);
	- void SetSegmentation(mitk::Image::Pointer segmentation);
	-
	- mitk::ConnectomicsNetwork::Pointer GetNetwork();
	-
	- itkSetMacro(MappingStrategy, MappingStrategy);
	- itkSetMacro(EndPointSearchRadius, double);
	- itkSetMacro(ZeroLabelInvalid, bool);
	-
	- /** \brief Calculate the locations of vertices
	- *
	- * Calculate the center of mass for each label and store the information. This will need a set parcellation image.
	- * Unless this function is called the first location where a label is encountered will be used. After calling this function
	- * the center of mass will be used instead.
	- */
	- void CalculateCenterOfMass();
	-
	- protected:
	-
	- //////////////////// Functions ///////////////////////
	- ConnectomicsNetworkCreator();
	- ConnectomicsNetworkCreator( mitk::Image::Pointer segmentation, mitk::FiberBundle::Pointer fiberBundle );
	- ~ConnectomicsNetworkCreator() override;
	-
	- /** Add a connection to the network */
	- void AddConnectionToNetwork(ConnectionType newConnection, double fiber_count);
	-
	- /** Determine if a label is already identified with a vertex, otherwise create a new one */
	- VertexType ReturnAssociatedVertexForLabel( ImageLabelType label );
	-
	- /** Return the vertexes associated with a pair of labels */
	- ConnectionType ReturnAssociatedVertexPairForLabelPair( ImageLabelPairType labelpair );
	-
	- /** Return the pair of labels which identify the areas connected by a single fiber */
	- ImageLabelPairType ReturnLabelForFiberTract( TractType::Pointer singleTract, MappingStrategy strategy );
	-
	- /** Assign the additional information which should be part of the vertex */
	- void SupplyVertexWithInformation( ImageLabelType& label, VertexType& vertex );
	-
	- /** Create a string from the label */
	- std::string LabelToString( ImageLabelType& label );
	-
	- /** Check whether the label in question belongs to white matter according to the freesurfer table */
	- bool IsNonWhiteMatterLabel( int labelInQuestion );
	-
	- /** Check whether the label in question belongs to background according to the freesurfer table */
	- bool IsBackgroundLabel( int labelInQuestion );
	-
	- /** Extend a straight line through the given points and look for the first non white matter label
	-
	- It will try extend in the direction of the points in the vector so a vector {B,C} will result in
	- extending from C in the direction C-B */
	- void LinearExtensionUntilGreyMatter( std::vector<int> & indexVectorOfPointsToUse, TractType::Pointer singleTract,
	- int & label, itk::Index<3> & mitkIndex );
	-
	- /** Retract fiber until the first brain matter label is hit
	-
	- The bool parameter controls whether the front or the end is retracted */
	- void RetractionUntilBrainMatter( bool retractFront, TractType::Pointer singleTract,
	- int & label, itk::Index<3> & mitkIndex );
	-
	- /** \brief Get the location of the center of mass for a specific label
	- * This can throw an exception if the label is not found.
	- */
	- std::vector< double > GetCenterOfMass( int label );
	-
	- /** \brief Creates a new node
	- *
	- * A new node will be created, using the label and either the supplied coordinates
	- * or the center of mass coordinates, depending on the supplied bool.
	- */
	- void CreateNewNode( int label, itk::Index<3>, bool useIndex );
	-
	- ///////// Mapping strategies //////////
	-
	- /** Use the position of the end and starting element only to map to labels
	-
	- Map a fiber to a vertex by taking the value of the parcellation image at the same world coordinates as the last
	- and first element of the tract.*/
	- ImageLabelPairType EndElementPositionLabel( TractType::Pointer singleTract );
	-
	- /** Map by distance between elements and vertices depending on their volume
	-
	- First go through the parcellation and compute the coordinates of the future vertices. Assign a radius according on their volume.
	- Then map an edge to a label by considering the nearest vertices and comparing the distance to them to their radii. */
	- ImageLabelPairType PrecomputeVertexLocationsBySegmentation( TractType::Pointer singleTract );
	-
	- /** Use the position of the end and starting element only to map to labels
	-
	- Just take first and last position, no labelling, nothing */
	- ImageLabelPairType JustEndPointVerticesNoLabelTest( TractType::Pointer singleTract );
	-
	- /** Use the position of the end and starting element unless it is in white matter, then search for nearby parcellation to map to labels
	-
	- Map a fiber to a vertex by taking the value of the parcellation image at the same world coordinates as the last
	- and first element of the tract. If this happens to be white matter, then try to extend the fiber in a line and
	- take the first non-white matter parcel, that is intersected. */
	- ImageLabelPairType EndElementPositionLabelAvoidingWhiteMatter( TractType::Pointer singleTract );
	-
	- ///////// Conversions //////////
	- /** Convert fiber index to segmentation index coordinates */
	- void FiberToSegmentationCoords( mitk::Point3D& fiberCoord, mitk::Point3D& segCoord );
	- /** Convert segmentation index to fiber index coordinates */
	- void SegmentationToFiberCoords( mitk::Point3D& segCoord, mitk::Point3D& fiberCoord );
	-
	- /////////////////////// Variables ////////////////////////
	- mitk::FiberBundle::Pointer m_FiberBundle;
	- mitk::Image::Pointer m_Segmentation;
	- ITKImageType::Pointer m_SegmentationItk;
	-
	- // the graph itself
	- mitk::ConnectomicsNetwork::Pointer m_ConNetwork;
	-
	- // the id counter
	- int idCounter;
	-
	- // the map mapping labels to vertices
	- std::map< ImageLabelType, VertexType > m_LabelToVertexMap;
	-
	- // mapping labels to additional information
	- std::map< ImageLabelType, NetworkNode > m_LabelToNodePropertyMap;
	-
	- // toggles whether edges between a node and itself can exist
	- bool allowLoops;
	-
	- // toggles whether to use the center of mass coordinates
	- bool m_UseCoMCoordinates;
	-
	- // stores the coordinates of labels
	- std::map< int, std::vector< double> > m_LabelsToCoordinatesMap;
	-
	- // the straty to use for mapping
	- MappingStrategy m_MappingStrategy;
	-
	- // search radius for finding a non white matter/background area. Should be in mm
	- double m_EndPointSearchRadius;
	-
	- // toggles whether a node with the label 0 may be present
	- bool m_ZeroLabelInvalid;
	-
	- // used internally to communicate a connection should not be added if the a problem
	- // is encountered while adding it
	- bool m_AbortConnection;
	-
	- //////////////////////// IDs ////////////////////////////
	-
	- // These IDs are the freesurfer ids used in parcellation
	-
	- static const int freesurfer_Left_Cerebral_White_Matter = 2;
	- static const int freesurfer_Left_Cerebellum_White_Matter = 7;
	- static const int freesurfer_Left_Cerebellum_Cortex = 8;
	- static const int freesurfer_Brain_Stem = 16;
	- static const int freesurfer_Right_Cerebral_White_Matter = 41;
	- static const int freesurfer_Right_Cerebellum_White_Matter = 46;
	- static const int freesurfer_Right_Cerebellum_Cortex = 47;
	-
	-
	- };
	-
	-}// end namespace mitk
	-
	-#endif // _mitkConnectomicsNetworkCreator_H_INCLUDED
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsNetworkThresholder.cpp b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsNetworkThresholder.cpp
	deleted file mode 100644
	index 28ebb35eb9..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsNetworkThresholder.cpp
	+++ /dev/null
	@@ -1,251 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkConnectomicsNetworkThresholder.h"
	-#include <mitkConnectomicsStatisticsCalculator.h>
	-#include "vnl/vnl_random.h"
	-
	-mitk::ConnectomicsNetworkThresholder::ConnectomicsNetworkThresholder()
	- : m_Network( nullptr )
	- , m_ThresholdingScheme( mitk::ConnectomicsNetworkThresholder::ThresholdBased )
	- , m_TargetThreshold( 0.0 )
	- , m_TargetDensity( 1.0 )
	-{
	-}
	-
	-mitk::ConnectomicsNetworkThresholder::~ConnectomicsNetworkThresholder()
	-{
	-}
	-
	-mitk::ConnectomicsNetwork::Pointer mitk::ConnectomicsNetworkThresholder::GetThresholdedNetwork()
	-{
	- mitk::ConnectomicsNetwork::Pointer result;
	-
	- if( ! CheckValidity() )
	- {
	- MITK_ERROR << "Aborting";
	- return m_Network;
	- }
	-
	- switch(m_ThresholdingScheme)
	- {
	- case RandomRemovalOfWeakest :
	- {
	- result = ThresholdByRandomRemoval( m_Network, m_TargetDensity );
	- break;
	- }
	- case LargestLowerThanDensity :
	- {
	- result = ThresholdBelowDensity( m_Network, m_TargetDensity );
	- break;
	- }
	- case ThresholdBased :
	- {
	- result = Threshold( m_Network, m_TargetThreshold );
	- break;
	- }
	- default :
	- {
	- MITK_ERROR << "Specified unknown Thresholding Scheme";
	- result = m_Network;
	- }
	- }
	-
	- return result;
	-}
	-
	-bool mitk::ConnectomicsNetworkThresholder::CheckValidity()
	-{
	- bool valid(true);
	-
	- if( m_Network.IsNull() )
	- {
	- valid = false;
	- MITK_ERROR << "Network is nullptr.";
	- }
	-
	- switch(m_ThresholdingScheme)
	- {
	- case RandomRemovalOfWeakest :
	- case LargestLowerThanDensity :
	- {
	- if( m_TargetDensity < 0.0 )
	- {
	- valid = false;
	- MITK_ERROR << "Target density is negative.";
	- }
	- if( m_TargetDensity > 1.0 )
	- {
	- valid = false;
	- MITK_ERROR << "Target density is larger than 1.";
	- }
	- break;
	- }
	- case ThresholdBased :
	- {
	- if( m_TargetThreshold < 0 )
	- {
	- valid = false;
	- MITK_ERROR << "Target threshold is negative.";
	- }
	- break;
	- }
	- default :
	- {
	- valid = false;
	- MITK_ERROR << "Specified unknown Thresholding Scheme";
	- }
	- }
	-
	- return valid;
	-}
	-
	-mitk::ConnectomicsNetwork::Pointer mitk::ConnectomicsNetworkThresholder::ThresholdByRandomRemoval( mitk::ConnectomicsNetwork::Pointer input, double targetDensity )
	-{
	- mitk::ConnectomicsNetwork::Pointer result = mitk::ConnectomicsNetwork::New();
	- result->ImportNetwort( input );
	-
	- mitk::ConnectomicsStatisticsCalculator::Pointer calculator = mitk::ConnectomicsStatisticsCalculator::New();
	-
	- calculator->SetNetwork( result );
	- calculator->Update();
	-
	- //the random number generator
	- vnl_random rng( (unsigned int) rand() );
	-
	- bool notBelow( targetDensity < calculator->GetConnectionDensity() );
	-
	- double minWeight( result->GetMaximumWeight() );
	- int count( 0 );
	-
	- while( notBelow )
	- {
	- // result = Threshold( result, loop );
	- std::vector< EdgeDescriptorType > candidateVector;
	- minWeight = result->GetMaximumWeight();
	- count = 0;
	-
	- // determine minimum weight and number of edges having that weight
	- NetworkType* boostGraph = result->GetBoostGraph();
	- EdgeIteratorType iterator, end;
	- // sets iterator to start end end to end
	- boost::tie(iterator, end) = boost::edges( *boostGraph );
	-
	- for ( ; iterator != end; ++iterator)
	- {
	- double tempWeight;
	-
	- // the value of an iterator is a descriptor
	- tempWeight = (boostGraph)[ iterator ].fiber_count;
	-
	- if( mitk::Equal( tempWeight, minWeight ) )
	- {
	- candidateVector.push_back( *iterator );
	- count++;
	- }
	- else if( tempWeight < minWeight )
	- {
	- candidateVector.clear();
	- candidateVector.push_back( *iterator );
	- minWeight = tempWeight;
	- count = 1;
	- }
	- }
	-
	- // Which to delete
	- int deleteNumber( rng.lrand32( count - 1 ) );
	-
	- boost::remove_edge( candidateVector.at( deleteNumber ), *boostGraph );
	-
	- calculator->SetNetwork( result );
	- calculator->Update();
	- notBelow = targetDensity < calculator->GetConnectionDensity();
	- }
	-
	- result->UpdateIDs();
	- return result;
	-}
	-
	-mitk::ConnectomicsNetwork::Pointer mitk::ConnectomicsNetworkThresholder::ThresholdBelowDensity( mitk::ConnectomicsNetwork::Pointer input, double targetDensity )
	-{
	- mitk::ConnectomicsNetwork::Pointer result = mitk::ConnectomicsNetwork::New();
	- result->ImportNetwort( input );
	-
	- mitk::ConnectomicsStatisticsCalculator::Pointer calculator = mitk::ConnectomicsStatisticsCalculator::New();
	-
	- calculator->SetNetwork( result );
	- calculator->Update();
	-
	- bool notBelow( targetDensity < calculator->GetConnectionDensity() );
	-
	- for( int loop( 1 ); notBelow; loop++ )
	- {
	- result = Threshold( result, loop );
	- calculator->SetNetwork( result );
	- calculator->Update();
	- notBelow = targetDensity < calculator->GetConnectionDensity();
	- }
	-
	- return result;
	-}
	-
	-mitk::ConnectomicsNetwork::Pointer mitk::ConnectomicsNetworkThresholder::Threshold( mitk::ConnectomicsNetwork::Pointer input, double targetThreshold )
	-{
	- mitk::ConnectomicsNetwork::Pointer result = mitk::ConnectomicsNetwork::New();
	- result->ImportNetwort( input );
	-
	- NetworkType* boostGraph = result->GetBoostGraph();
	-
	- EdgeIteratorType iterator, end;
	-
	- // set to true if iterators are invalidated by deleting an edge
	- bool edgeHasBeenRemoved( true );
	-
	- // if no edge has been removed in the last loop, we are done
	- while( edgeHasBeenRemoved )
	- {
	- edgeHasBeenRemoved = false;
	- // sets iterator to start and end to end
	- boost::tie(iterator, end) = boost::edges( *boostGraph );
	-
	- bool endReached( false );
	- while( !edgeHasBeenRemoved && !endReached )
	- {
	- if( iterator != end )
	- {
	- // If the edge is below the target threshold it is deleted
	- if( (boostGraph)[ iterator ].fiber_count < targetThreshold )
	- {
	- edgeHasBeenRemoved = true;
	- // this invalidates all iterators
	- boost::remove_edge( iterator, boostGraph );
	- }
	- else
	- {
	- ++iterator;
	- }
	- }
	- else
	- {
	- endReached = true;
	- }
	- }
	- }
	-
	- result->UpdateIDs();
	-
	- return result;
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsNetworkThresholder.h b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsNetworkThresholder.h
	deleted file mode 100644
	index 76d351c05a..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsNetworkThresholder.h
	+++ /dev/null
	@@ -1,111 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef mitkConnectomicsNetworkThresholder_h
	-#define mitkConnectomicsNetworkThresholder_h
	-
	-#include <itkObject.h>
	-#include <itkObjectFactory.h>
	-#include <itkMacro.h>
	-
	-#include "mitkCommon.h"
	-
	-#include <MitkConnectomicsExports.h>
	-
	-#include <mitkConnectomicsNetwork.h>
	-
	-namespace mitk
	-{
	- /**
	- * \brief A class for thresholding connectomics networks */
	- class MITKCONNECTOMICS_EXPORT ConnectomicsNetworkThresholder : public itk::Object
	- {
	- public:
	-
	- /** Standard class typedefs. */
	- /** Method for creation through the object factory. */
	-
	- mitkClassMacroItkParent(ConnectomicsNetworkThresholder, itk::Object);
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- // Typedefs
	- typedef mitk::ConnectomicsNetwork::NetworkType NetworkType;
	- typedef mitk::ConnectomicsNetwork::VertexDescriptorType VertexDescriptorType;
	- typedef mitk::ConnectomicsNetwork::EdgeDescriptorType EdgeDescriptorType;
	- typedef boost::graph_traits<NetworkType>::vertex_iterator VertexIteratorType;
	- typedef boost::graph_traits<NetworkType>::edge_iterator EdgeIteratorType;
	- typedef boost::graph_traits<NetworkType>::adjacency_iterator AdjacencyIteratorType;
	- typedef std::map<EdgeDescriptorType, int> EdgeIndexStdMapType;
	- typedef boost::associative_property_map< EdgeIndexStdMapType > EdgeIndexMapType;
	- typedef std::map<VertexDescriptorType, int> VertexIndexStdMapType;
	- typedef boost::associative_property_map< VertexIndexStdMapType > VertexIndexMapType;
	-
	- /** \brief Possible schemes for thresholding the network
	- *
	- * \li \c RandomRemovalOfWeakest: Randomly remove one of the weakest edges until a given density is reached
	- * \li \c LargestLowerThanDensity: Remove all edges of the lowest weight, repeat until below the specified density
	- * \li \c ThresholdBased: Remove all edges with a weight of threshold and lower. This will not take density information into account.
	- */
	- enum ThresholdingSchemes
	- {
	- RandomRemovalOfWeakest,
	- LargestLowerThanDensity,
	- ThresholdBased
	- };
	-
	- // Set/Get Macros
	- itkSetObjectMacro( Network, mitk::ConnectomicsNetwork );
	- itkSetMacro( ThresholdingScheme, ThresholdingSchemes );
	- itkSetMacro( TargetThreshold, double );
	- itkSetMacro( TargetDensity, double );
	-
	- itkGetObjectMacro( Network, mitk::ConnectomicsNetwork );
	- itkGetMacro( ThresholdingScheme, ThresholdingSchemes );
	- itkGetMacro( TargetThreshold, double );
	- itkGetMacro( TargetDensity, double );
	-
	- /** \brief Apply thresholding scheme and get resulting network */
	- mitk::ConnectomicsNetwork::Pointer GetThresholdedNetwork();
	-
	- protected:
	-
	- //////////////////// Functions ///////////////////////
	- ConnectomicsNetworkThresholder();
	- ~ConnectomicsNetworkThresholder() override;
	-
	- mitk::ConnectomicsNetwork::Pointer ThresholdByRandomRemoval( mitk::ConnectomicsNetwork::Pointer input, double targetDensity );
	- mitk::ConnectomicsNetwork::Pointer ThresholdBelowDensity( mitk::ConnectomicsNetwork::Pointer input, double targetDensity );
	- mitk::ConnectomicsNetwork::Pointer Threshold( mitk::ConnectomicsNetwork::Pointer input, double targetThreshold );
	- // Returns false if parameter combination is invalid
	- bool CheckValidity();
	-
	- /////////////////////// Variables ////////////////////////
	-
	- // The connectomics network, which is used for statistics calculation
	- mitk::ConnectomicsNetwork::Pointer m_Network;
	-
	- // The thresholding scheme to be used
	- ThresholdingSchemes m_ThresholdingScheme;
	-
	- double m_TargetThreshold;
	- double m_TargetDensity;
	-
	- };
	-
	-}// end namespace mitk
	-
	-#endif // mitkConnectomicsNetworkThresholder_h
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsShortestPathHistogram.cpp b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsShortestPathHistogram.cpp
	deleted file mode 100644
	index b8f321b01a..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsShortestPathHistogram.cpp
	+++ /dev/null
	@@ -1,193 +0,0 @@
	-
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include<mitkConnectomicsShortestPathHistogram.h>
	-
	-#ifdef _MSC_VER
	-# pragma warning(push)
	-# pragma warning(disable: 4172)
	-#endif
	-
	-#include <boost/graph/dijkstra_shortest_paths.hpp>
	-
	-#ifdef _MSC_VER
	-# pragma warning(pop)
	-#endif
	-
	-#include "mitkConnectomicsConstantsManager.h"
	-
	-mitk::ConnectomicsShortestPathHistogram::ConnectomicsShortestPathHistogram()
	-: m_Mode( UnweightedUndirectedMode )
	-, m_EverythingConnected( true )
	-{
	- m_Subject = "Shortest path";
	-}
	-
	-mitk::ConnectomicsShortestPathHistogram::~ConnectomicsShortestPathHistogram()
	-{
	-}
	-
	-void mitk::ConnectomicsShortestPathHistogram::SetShortestPathCalculationMode( const mitk::ConnectomicsShortestPathHistogram::ShortestPathCalculationMode & mode)
	-{
	- m_Mode = mode;
	-}
	-
	-mitk::ConnectomicsShortestPathHistogram::ShortestPathCalculationMode mitk::ConnectomicsShortestPathHistogram::GetShortestPathCalculationMode()
	-{
	- return m_Mode;
	-}
	-
	-void mitk::ConnectomicsShortestPathHistogram::ComputeFromConnectomicsNetwork( ConnectomicsNetwork* source )
	-{
	-
	- NetworkType* boostGraph = source->GetBoostGraph();
	-
	- switch( m_Mode )
	- {
	- case UnweightedUndirectedMode:
	- {
	- CalculateUnweightedUndirectedShortestPaths( boostGraph );
	- break;
	- }
	- case WeightedUndirectedMode:
	- {
	- CalculateWeightedUndirectedShortestPaths( boostGraph );
	- break;
	- }
	- }
	-
	- ConvertDistanceMapToHistogram();
	-}
	-
	-void mitk::ConnectomicsShortestPathHistogram::CalculateUnweightedUndirectedShortestPaths( NetworkType* boostGraph )
	-{
	- std::vector< DescriptorType > predecessorMap( boost::num_vertices( *boostGraph ) );
	- int numberOfNodes( boost::num_vertices( *boostGraph ) );
	-
	- m_DistanceMatrix.resize( numberOfNodes );
	- for(unsigned int index(0); index < m_DistanceMatrix.size(); index++ )
	- {
	- m_DistanceMatrix[ index ].resize( numberOfNodes );
	- }
	-
	- IteratorType iterator, end;
	- boost::tie(iterator, end) = boost::vertices( *boostGraph );
	-
	- for ( int index(0) ; iterator != end; ++iterator, index++)
	- {
	- boost::dijkstra_shortest_paths(boostGraph, iterator, boost::predecessor_map(&predecessorMap[ 0 ]).distance_map(&m_DistanceMatrix[ index ][ 0 ]).weight_map( boost::get( &mitk::ConnectomicsNetwork::NetworkEdge::edge_weight ,*boostGraph ) ) ) ;
	- }
	-}
	-
	-void mitk::ConnectomicsShortestPathHistogram::CalculateWeightedUndirectedShortestPaths( NetworkType* /boostGraph/ )
	-{
	- MBI_WARN << mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_UNIMPLEMENTED_FEATURE;
	-}
	-
	-void mitk::ConnectomicsShortestPathHistogram::ConvertDistanceMapToHistogram()
	-{
	- // get the longest path between any two nodes in the network
	- // we assume that no nodes are farther apart than there are nodes,
	- // this is to filter unconnected nodes
	- int longestPath( 0 );
	- int numberOfNodes( m_DistanceMatrix.size() );
	- m_EverythingConnected = true;
	-
	- for(unsigned int index(0); index < m_DistanceMatrix.size(); index++ )
	- {
	- for(unsigned int innerIndex(0); innerIndex < m_DistanceMatrix[ index ].size(); innerIndex++ )
	- {
	- if( m_DistanceMatrix[ index ][ innerIndex ] > longestPath )
	- {
	- if( m_DistanceMatrix[ index ][ innerIndex ] < numberOfNodes )
	- {
	- longestPath = m_DistanceMatrix[ index ][ innerIndex ];
	- }
	- else
	- {
	- // these nodes are not connected
	- m_EverythingConnected = false;
	- }
	- }
	- }
	- }
	-
	- m_HistogramVector.resize( longestPath + 1 );
	-
	- for(unsigned int index(0); index < m_DistanceMatrix.size(); index++ )
	- {
	- for( unsigned int innerIndex(0); innerIndex < m_DistanceMatrix[ index ].size(); innerIndex++ )
	- {
	- if( m_DistanceMatrix[ index ][ innerIndex ] < numberOfNodes )
	- {
	- m_HistogramVector[ m_DistanceMatrix[ index ][ innerIndex ] ]++;
	- }
	- }
	- }
	-
	- // correct for every path being counted twice
	-
	- for( unsigned int index(1); index < m_HistogramVector.size(); index++ )
	- {
	- m_HistogramVector[ index ] = m_HistogramVector[ index ] / 2;
	- }
	-
	- // correct for every node being distance zero to itself
	- if( m_HistogramVector[ 0 ] >= numberOfNodes )
	- {
	- m_HistogramVector[ 0 ] = m_HistogramVector[ 0 ] - numberOfNodes;
	- }
	- else
	- {
	- MBI_WARN << mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_ZERO_DISTANCE_NODES;
	- }
	-
	- UpdateYMax();
	-
	- this->m_Valid = true;
	-}
	-
	-double mitk::ConnectomicsShortestPathHistogram::GetEfficiency()
	-{
	- if( !this->m_Valid )
	- {
	- MBI_INFO << mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_CAN_NOT_COMPUTE_EFFICIENCY << mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_NETWORK_NOT_VALID;
	- return 0.0;
	- }
	-
	- if( !m_EverythingConnected )
	- { // efficiency of disconnected graphs is 0
	- MBI_INFO << mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_NETWORK_DISCONNECTED;
	- return 0.0;
	- }
	-
	- double efficiency( 0.0 );
	-
	- double overallDistance( 0.0 );
	- double numberOfPairs( 0.0 );
	- // add up all distances
	- for( unsigned int index(0); index < m_HistogramVector.size(); index++ )
	- {
	- overallDistance = overallDistance + m_HistogramVector[ index ] * index;
	- numberOfPairs = numberOfPairs + m_HistogramVector[ index ];
	- }
	-
	- // efficiency = 1 / averageDistance = 1 / ( overallDistance / numberofPairs )
	- efficiency = numberOfPairs / overallDistance;
	-
	- return efficiency;
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsShortestPathHistogram.h b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsShortestPathHistogram.h
	deleted file mode 100644
	index 84f83221da..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsShortestPathHistogram.h
	+++ /dev/null
	@@ -1,86 +0,0 @@
	-
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef _MITK_ConnectomicsShortestPathHistogram_H
	-#define _MITK_ConnectomicsShortestPathHistogram_H
	-
	-#include<mitkConnectomicsHistogramBase.h>
	-
	-#include <MitkConnectomicsExports.h>
	-
	-namespace mitk {
	-
	- /**
	- * \brief A class to calculate and store the shortest path between each pair of nodes */
	- class MITKCONNECTOMICS_EXPORT ConnectomicsShortestPathHistogram : public mitk::ConnectomicsHistogramBase
	- {
	-
	- public:
	-
	- /** Enum for different ways to calculate shortest paths */
	- enum ShortestPathCalculationMode
	- {
	- UnweightedUndirectedMode,
	- WeightedUndirectedMode
	- };
	-
	- ConnectomicsShortestPathHistogram();
	- ~ConnectomicsShortestPathHistogram() override;
	-
	- /** Set the calucaltion mode */
	- void SetShortestPathCalculationMode( const ShortestPathCalculationMode & );
	-
	- /** Get the calculation mode */
	- ShortestPathCalculationMode GetShortestPathCalculationMode();
	-
	- /** Get efficiency */
	- double GetEfficiency();
	-
	-
	- protected:
	-
	- /* Typedefs */
	- typedef mitk::ConnectomicsNetwork::NetworkType NetworkType;
	- typedef boost::graph_traits< NetworkType >::vertex_descriptor DescriptorType;
	- typedef boost::graph_traits< NetworkType >::vertex_iterator IteratorType;
	-
	- /** @brief Creates a new histogram from the network source. */
	- void ComputeFromConnectomicsNetwork( ConnectomicsNetwork* source ) override;
	-
	- /** Calculate shortest paths ignoring the weight of the edges */
	- void CalculateUnweightedUndirectedShortestPaths( NetworkType* boostGraph );
	-
	- /** Calculate shortest paths taking into consideration the weight of the edges */
	- void CalculateWeightedUndirectedShortestPaths( NetworkType* boostGraph );
	-
	- /** Converts the distance map to a histogram */
	- void ConvertDistanceMapToHistogram();
	-
	- /** Stores which mode has been selected for shortest path calculation */
	- ShortestPathCalculationMode m_Mode;
	-
	- /** Stores the shortest paths between the nodes */
	- std::vector< std::vector< int > > m_DistanceMatrix;
	-
	- /** Stores, whether the graph has disconnected components */
	- bool m_EverythingConnected;
	- };
	-
	-}
	-
	-#endif /* _MITK_ConnectomicsShortestPathHistogram_H */
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingCostFunctionBase.cpp b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingCostFunctionBase.cpp
	deleted file mode 100644
	index 7c5a03ce34..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingCostFunctionBase.cpp
	+++ /dev/null
	@@ -1,25 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkConnectomicsSimulatedAnnealingCostFunctionBase.h"
	-
	-mitk::ConnectomicsSimulatedAnnealingCostFunctionBase::ConnectomicsSimulatedAnnealingCostFunctionBase()
	-{
	-}
	-
	-mitk::ConnectomicsSimulatedAnnealingCostFunctionBase::~ConnectomicsSimulatedAnnealingCostFunctionBase()
	-{
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingCostFunctionBase.h b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingCostFunctionBase.h
	deleted file mode 100644
	index 8eb2e0286a..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingCostFunctionBase.h
	+++ /dev/null
	@@ -1,55 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef mitkConnectomicsSimulatedAnnealingCostFunctionBase_h
	-#define mitkConnectomicsSimulatedAnnealingCostFunctionBase_h
	-
	-#include <itkObject.h>
	-#include <itkObjectFactory.h>
	-#include <itkMacro.h>
	-
	-#include "mitkCommon.h"
	-
	-#include <MitkConnectomicsExports.h>
	-
	-namespace mitk
	-{
	- /**
	- * \brief A generic base class for cost functions for use in simulated annealing */
	- class MITKCONNECTOMICS_EXPORT ConnectomicsSimulatedAnnealingCostFunctionBase : public itk::Object
	- {
	- public:
	-
	- /** Standard class typedefs. */
	- /** Method for creation through the object factory. */
	-
	- mitkClassMacroItkParent(ConnectomicsSimulatedAnnealingCostFunctionBase, itk::Object);
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	-
	-
	- protected:
	-
	- //////////////////// Functions ///////////////////////
	- ConnectomicsSimulatedAnnealingCostFunctionBase();
	- ~ConnectomicsSimulatedAnnealingCostFunctionBase() override;
	-
	- };
	-
	-}// end namespace mitk
	-
	-#endif // mitkConnectomicsSimulatedAnnealingCostFunctionBase_h
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingCostFunctionModularity.cpp b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingCostFunctionModularity.cpp
	deleted file mode 100644
	index 16007f5385..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingCostFunctionModularity.cpp
	+++ /dev/null
	@@ -1,125 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkConnectomicsSimulatedAnnealingCostFunctionModularity.h"
	-
	-mitk::ConnectomicsSimulatedAnnealingCostFunctionModularity::ConnectomicsSimulatedAnnealingCostFunctionModularity()
	-{
	-}
	-
	-mitk::ConnectomicsSimulatedAnnealingCostFunctionModularity::~ConnectomicsSimulatedAnnealingCostFunctionModularity()
	-{
	-}
	-
	-double mitk::ConnectomicsSimulatedAnnealingCostFunctionModularity::Evaluate( mitk::ConnectomicsNetwork::Pointer network, ToModuleMapType* vertexToModuleMap ) const
	-{
	- double cost( 0.0 );
	- cost = 100.0 * ( 1.0 - CalculateModularity( network, vertexToModuleMap ) );
	- return cost;
	-}
	-
	-double mitk::ConnectomicsSimulatedAnnealingCostFunctionModularity::CalculateModularity( mitk::ConnectomicsNetwork::Pointer network, ToModuleMapType* vertexToModuleMap ) const
	-{
	- double modularity( 0.0 );
	- int numberOfModules = getNumberOfModules( vertexToModuleMap );
	-
	- if( network->GetNumberOfVertices() != (int)vertexToModuleMap->size() )
	- {
	- MBI_ERROR << "Number of vertices and vertex to module map size do not match!";
	- return modularity;
	- }
	-
	- int numberOfLinksInNetwork( 0 );
	- std::vector< int > numberOfLinksInModule, sumOfDegreesInModule;
	- numberOfLinksInModule.resize( numberOfModules, 0 );
	- sumOfDegreesInModule.resize( numberOfModules, 0 );
	- // get vector of all vertex descriptors in the network
	-
	- const std::vector< VertexDescriptorType > allNodesVector
	- = network->GetVectorOfAllVertexDescriptors();
	-
	- for( unsigned int nodeNumber( 0 ); nodeNumber < allNodesVector.size() ; nodeNumber++)
	- {
	- int correspondingModule = vertexToModuleMap->find( allNodesVector[ nodeNumber ] )->second;
	- const std::vector< VertexDescriptorType > adjacentNodexVector
	- = network->GetVectorOfAdjacentNodes( allNodesVector[ nodeNumber ] );
	- numberOfLinksInNetwork += adjacentNodexVector.size();
	- sumOfDegreesInModule[ correspondingModule ] += adjacentNodexVector.size();
	-
	- for( unsigned int adjacentNodeNumber( 0 ); adjacentNodeNumber < adjacentNodexVector.size() ; adjacentNodeNumber++)
	- {
	- if( correspondingModule == vertexToModuleMap->find( adjacentNodexVector[ adjacentNodeNumber ] )->second )
	- {
	- numberOfLinksInModule[ correspondingModule ]++;
	- }
	- }
	- }
	-
	- // the numbers for links have to be halved, as each edge was counted twice
	- numberOfLinksInNetwork = numberOfLinksInNetwork / 2;
	-
	- // if the network contains no links return 0
	- if( numberOfLinksInNetwork < 1)
	- {
	- return 0;
	- }
	-
	- for( int index( 0 ); index < numberOfModules ; index++)
	- {
	- numberOfLinksInModule[ index ] = numberOfLinksInModule[ index ] / 2;
	- }
	-
	- //Calculate modularity M:
	- //M = sum_{s=1}^{N_{M}} [ (l_{s} / L) - (d_{s} / ( 2L ))^2 ]
	- //where N_{M} is the number of modules
	- //L is the number of links in the network
	- //l_{s} is the number of links between nodes in the module
	- //s is the module
	- //d_{s} is the sum of degrees of the nodes in the module
	- //( taken from Guimera, R. AND Amaral, L. A. N.
	- // Cartography of complex networks: modules and universal roles
	- // Journal of Statistical Mechanics: Theory and Experiment, 2005, 2005, P02001 )
	-
	- for( int moduleID( 0 ); moduleID < numberOfModules; moduleID++ )
	- {
	- modularity += (((double) numberOfLinksInModule[ moduleID ]) / ((double) numberOfLinksInNetwork)) -
	- (
	- (((double) sumOfDegreesInModule[ moduleID ]) / ((double) 2 * numberOfLinksInNetwork) ) *
	- (((double) sumOfDegreesInModule[ moduleID ]) / ((double) 2 * numberOfLinksInNetwork) )
	- );
	- }
	-
	- return modularity;
	-}
	-
	-int mitk::ConnectomicsSimulatedAnnealingCostFunctionModularity::getNumberOfModules(
	- ToModuleMapType *vertexToModuleMap ) const
	-{
	- int maxModule( 0 );
	- auto iter = vertexToModuleMap->begin();
	- auto end = vertexToModuleMap->end();
	- while( iter != end )
	- {
	- if( iter->second > maxModule )
	- {
	- maxModule = iter->second;
	- }
	-
	- iter++;
	- }
	-
	- return maxModule + 1;
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingCostFunctionModularity.h b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingCostFunctionModularity.h
	deleted file mode 100644
	index ec968108ed..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingCostFunctionModularity.h
	+++ /dev/null
	@@ -1,63 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef mitkConnectomicsSimulatedAnnealingCostFunctionModularity_h
	-#define mitkConnectomicsSimulatedAnnealingCostFunctionModularity_h
	-
	-#include "mitkConnectomicsSimulatedAnnealingCostFunctionBase.h"
	-
	-#include "mitkConnectomicsNetwork.h"
	-
	-namespace mitk
	-{
	- /**
	- * \brief A cost function using the modularity of the network */
	- class MITKCONNECTOMICS_EXPORT ConnectomicsSimulatedAnnealingCostFunctionModularity : public mitk::ConnectomicsSimulatedAnnealingCostFunctionBase
	- {
	- public:
	-
	- typedef mitk::ConnectomicsNetwork::VertexDescriptorType VertexDescriptorType;
	- typedef std::map< VertexDescriptorType, int > ToModuleMapType;
	- typedef std::map< VertexDescriptorType, VertexDescriptorType > VertexToVertexMapType;
	-
	- /** Standard class typedefs. */
	- /** Method for creation through the object factory. */
	-
	- mitkClassMacro(ConnectomicsSimulatedAnnealingCostFunctionModularity, mitk::ConnectomicsSimulatedAnnealingCostFunctionBase);
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- // Evaluate the network according to the set cost function
	- double Evaluate( mitk::ConnectomicsNetwork::Pointer network, ToModuleMapType *vertexToModuleMap ) const;
	-
	- // Will calculate and return the modularity of the network
	- double CalculateModularity( mitk::ConnectomicsNetwork::Pointer network, ToModuleMapType *vertexToModuleMap ) const;
	-
	-
	- protected:
	-
	- // returns the number of modules
	- int getNumberOfModules( ToModuleMapType *vertexToModuleMap ) const;
	-
	- //////////////////// Functions ///////////////////////
	- ConnectomicsSimulatedAnnealingCostFunctionModularity();
	- ~ConnectomicsSimulatedAnnealingCostFunctionModularity() override;
	-
	- };
	-
	-}// end namespace mitk
	-
	-#endif // mitkConnectomicsSimulatedAnnealingCostFunctionModularity_h
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingManager.cpp b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingManager.cpp
	deleted file mode 100644
	index 520b474380..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingManager.cpp
	+++ /dev/null
	@@ -1,95 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkConnectomicsSimulatedAnnealingManager.h"
	-
	-//for random number generation
	-#include "vnl/vnl_random.h"
	-#include "vnl/vnl_math.h"
	-
	-mitk::ConnectomicsSimulatedAnnealingManager::ConnectomicsSimulatedAnnealingManager()
	-: m_Permutation( nullptr )
	-{
	-}
	-
	-mitk::ConnectomicsSimulatedAnnealingManager::~ConnectomicsSimulatedAnnealingManager()
	-{
	-}
	-
	-
	-bool mitk::ConnectomicsSimulatedAnnealingManager::AcceptChange( double costBefore, double costAfter, double temperature )
	-{
	- if( costAfter <= costBefore )
	- {// if cost is lower after
	- return true;
	- }
	-
	- //the random number generators
	- vnl_random rng( (unsigned int) rand() );
	-
	- //randomly generate threshold
	- const double threshold = rng.drand64( 0.0 , 1.0);
	-
	- //the likelihood of acceptance
	- double likelihood = std::exp( - ( costAfter - costBefore ) / temperature );
	-
	- if( threshold < likelihood )
	- {
	- return true;
	- }
	-
	- return false;
	-}
	-
	-void mitk::ConnectomicsSimulatedAnnealingManager::SetPermutation( mitk::ConnectomicsSimulatedAnnealingPermutationBase::Pointer permutation )
	-{
	- m_Permutation = permutation;
	-}
	-
	-void mitk::ConnectomicsSimulatedAnnealingManager::RunSimulatedAnnealing(
	- double temperature,
	- double stepSize
	- )
	-{
	- if( m_Permutation.IsNull() )
	- {
	- MBI_ERROR << "Trying to run simulated annealing on empty permutation.";
	- return;
	- }
	-
	- if( !m_Permutation->HasCostFunction() )
	- {
	- MBI_ERROR << "Trying to run simulated annealing on empty cost function.";
	- return;
	- }
	-
	- // Initialize the associated permutation
	- m_Permutation->Initialize();
	-
	-
	- for( double currentTemperature( temperature );
	- currentTemperature > 0.00001;
	- currentTemperature = currentTemperature / stepSize )
	- {
	- // Run Permutations at the current temperature
	- m_Permutation->Permutate( currentTemperature );
	-
	- }
	-
	- // Clean up result
	- m_Permutation->CleanUp();
	-
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingManager.h b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingManager.h
	deleted file mode 100644
	index f270b48570..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingManager.h
	+++ /dev/null
	@@ -1,68 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef mitkConnectomicsSimulatedAnnealingManager_h
	-#define mitkConnectomicsSimulatedAnnealingManager_h
	-
	-#include <itkObject.h>
	-#include <itkObjectFactory.h>
	-#include <itkMacro.h>
	-
	-#include "mitkCommon.h"
	-
	-#include <MitkConnectomicsExports.h>
	-
	-#include "mitkConnectomicsSimulatedAnnealingPermutationBase.h"
	-
	-namespace mitk
	-{
	- /**
	- * \brief A class allow generic simulated annealing by using classes derived from ConnectomicsSimulatedAnnealingPermutationBase */
	- class MITKCONNECTOMICS_EXPORT ConnectomicsSimulatedAnnealingManager : public itk::Object
	- {
	- public:
	-
	- /** Standard class typedefs. */
	- /** Method for creation through the object factory. */
	-
	- mitkClassMacroItkParent(ConnectomicsSimulatedAnnealingManager, itk::Object);
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- // Decide whether to accept the change or not
	- bool AcceptChange( double costBefore, double costAfter, double temperature );
	-
	- // Run the permutations at different temperatures, where t_n = t_n-1 / stepSize
	- void RunSimulatedAnnealing( double temperature, double stepSize );
	-
	- // Set the permutation to be used
	- void SetPermutation( mitk::ConnectomicsSimulatedAnnealingPermutationBase::Pointer permutation );
	-
	- protected:
	-
	- //////////////////// Functions ///////////////////////
	- ConnectomicsSimulatedAnnealingManager();
	- ~ConnectomicsSimulatedAnnealingManager() override;
	-
	- /////////////////////// Variables ////////////////////////
	- // The permutation assigned to the simulated annealing manager
	- mitk::ConnectomicsSimulatedAnnealingPermutationBase::Pointer m_Permutation;
	-
	- };
	-
	-}// end namespace mitk
	-
	-#endif // mitkConnectomicsSimulatedAnnealingManager_h
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingPermutationBase.cpp b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingPermutationBase.cpp
	deleted file mode 100644
	index 0eb0bc5474..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingPermutationBase.cpp
	+++ /dev/null
	@@ -1,44 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkConnectomicsSimulatedAnnealingPermutationBase.h"
	-
	-mitk::ConnectomicsSimulatedAnnealingPermutationBase::ConnectomicsSimulatedAnnealingPermutationBase()
	-: m_CostFunction( nullptr )
	-{
	-}
	-
	-mitk::ConnectomicsSimulatedAnnealingPermutationBase::~ConnectomicsSimulatedAnnealingPermutationBase()
	-{
	-}
	-
	-void mitk::ConnectomicsSimulatedAnnealingPermutationBase::SetCostFunction(
	- mitk::ConnectomicsSimulatedAnnealingCostFunctionBase::Pointer costFunction )
	-{
	- m_CostFunction = costFunction;
	-}
	-
	-bool mitk::ConnectomicsSimulatedAnnealingPermutationBase::HasCostFunction( )
	-{
	- bool hasCostFunction( false );
	-
	- if( m_CostFunction.IsNotNull() )
	- {
	- hasCostFunction = true;
	- }
	-
	- return hasCostFunction;
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingPermutationBase.h b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingPermutationBase.h
	deleted file mode 100644
	index 08276592c9..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingPermutationBase.h
	+++ /dev/null
	@@ -1,75 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef mitkConnectomicsSimulatedAnnealingPermutationBase_h
	-#define mitkConnectomicsSimulatedAnnealingPermutationBase_h
	-
	-#include <itkObject.h>
	-#include <itkObjectFactory.h>
	-#include <itkMacro.h>
	-
	-#include "mitkCommon.h"
	-
	-#include <MitkConnectomicsExports.h>
	-
	-#include "mitkConnectomicsSimulatedAnnealingCostFunctionBase.h"
	-
	-namespace mitk
	-{
	-
	- /**
	- * \brief Base class of a permutation to be used in simulated annealing */
	- class MITKCONNECTOMICS_EXPORT ConnectomicsSimulatedAnnealingPermutationBase : public itk::Object
	- {
	- public:
	-
	- /** Standard class typedefs. */
	- /** Method for creation through the object factory. */
	-
	- mitkClassMacroItkParent(ConnectomicsSimulatedAnnealingPermutationBase, itk::Object);
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- // Set the cost function
	- void SetCostFunction( mitk::ConnectomicsSimulatedAnnealingCostFunctionBase::Pointer costFunction );
	-
	- // Returns true if a cost function is assigned
	- bool HasCostFunction( );
	-
	- // Initialize the permutation
	- virtual void Initialize(){};
	-
	- // Do a permutation for a specific temperature
	- virtual void Permutate( double /temperature/ ){};
	-
	- // Do clean up necessary after a permutation
	- virtual void CleanUp(){};
	-
	- protected:
	-
	- //////////////////// Functions ///////////////////////
	- ConnectomicsSimulatedAnnealingPermutationBase();
	- ~ConnectomicsSimulatedAnnealingPermutationBase() override;
	-
	- /////////////////////// Variables ////////////////////////
	- // The cost function assigned to the permutation
	- mitk::ConnectomicsSimulatedAnnealingCostFunctionBase::Pointer m_CostFunction;
	-
	- };
	-
	-}// end namespace mitk
	-
	-#endif // mitkConnectomicsSimulatedAnnealingPermutationBase_h
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingPermutationModularity.cpp b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingPermutationModularity.cpp
	deleted file mode 100644
	index 543d76a7c8..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingPermutationModularity.cpp
	+++ /dev/null
	@@ -1,540 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkConnectomicsSimulatedAnnealingPermutationModularity.h"
	-#include "mitkConnectomicsSimulatedAnnealingCostFunctionModularity.h"
	-#include "mitkConnectomicsSimulatedAnnealingManager.h"
	-
	-//for random number generation
	-#include "vnl/vnl_random.h"
	-#include "vnl/vnl_math.h"
	-
	-mitk::ConnectomicsSimulatedAnnealingPermutationModularity::ConnectomicsSimulatedAnnealingPermutationModularity()
	-{
	-}
	-
	-mitk::ConnectomicsSimulatedAnnealingPermutationModularity::~ConnectomicsSimulatedAnnealingPermutationModularity()
	-{
	-}
	-
	-void mitk::ConnectomicsSimulatedAnnealingPermutationModularity::SetNetwork(
	- mitk::ConnectomicsNetwork::Pointer theNetwork )
	-{
	- m_Network = theNetwork;
	-}
	-
	-void mitk::ConnectomicsSimulatedAnnealingPermutationModularity::Initialize()
	-{
	- // create entry for every vertex
	- std::vector< VertexDescriptorType > vertexVector = m_Network->GetVectorOfAllVertexDescriptors();
	- const int vectorSize = vertexVector.size();
	-
	- for( int index( 0 ); index < vectorSize; index++)
	- {
	- m_BestSolution.insert( std::pair<VertexDescriptorType, int>( vertexVector[ index ], 0 ) );
	- }
	-
	- // initialize with random distribution of n modules
	- int n( 5 );
	- randomlyAssignNodesToModules( &m_BestSolution, n );
	-
	-}
	-
	-void mitk::ConnectomicsSimulatedAnnealingPermutationModularity::Permutate( double temperature )
	-{
	-
	- ToModuleMapType currentSolution = m_BestSolution;
	- ToModuleMapType currentBestSolution = m_BestSolution;
	-
	- int factor = 1;
	- int numberOfVertices = m_BestSolution.size();
	- int singleNodeMaxNumber = factor * numberOfVertices * numberOfVertices;
	- int moduleMaxNumber = factor * numberOfVertices;
	- double currentBestCost = Evaluate( &currentBestSolution );
	-
	- // do singleNodeMaxNumber node permutations and evaluate
	- for(int loop( 0 ); loop < singleNodeMaxNumber; loop++)
	- {
	- permutateMappingSingleNodeShift( &currentSolution, m_Network );
	- if( AcceptChange( currentBestCost, Evaluate( &currentSolution ), temperature ) )
	- {
	- currentBestSolution = currentSolution;
	- currentBestCost = Evaluate( &currentBestSolution );
	- }
	- }
	-
	- // do moduleMaxNumber module permutations
	- for(int loop( 0 ); loop < moduleMaxNumber; loop++)
	- {
	- permutateMappingModuleChange( &currentSolution, temperature, m_Network );
	- if( AcceptChange( currentBestCost, Evaluate( &currentSolution ), temperature ) )
	- {
	- currentBestSolution = currentSolution;
	- currentBestCost = Evaluate( &currentBestSolution );
	- }
	- }
	-
	- // store the best solution after the run
	- m_BestSolution = currentBestSolution;
	-}
	-
	-void mitk::ConnectomicsSimulatedAnnealingPermutationModularity::CleanUp()
	-{
	- // delete empty modules, if any
	- for( int loop( 0 ); loop < getNumberOfModules( &m_BestSolution ) ; loop++ )
	- {
	- if( getNumberOfVerticesInModule( &m_BestSolution, loop ) < 1 )
	- {
	- removeModule( &m_BestSolution, loop );
	- }
	- }
	-}
	-
	-void mitk::ConnectomicsSimulatedAnnealingPermutationModularity::permutateMappingSingleNodeShift(
	- ToModuleMapType *vertexToModuleMap, mitk::ConnectomicsNetwork::Pointer network )
	-{
	-
	- const int nodeCount = vertexToModuleMap->size();
	- const int moduleCount = getNumberOfModules( vertexToModuleMap );
	-
	- // the random number generators
	- vnl_random rng( (unsigned int) rand() );
	- unsigned long randomNode = rng.lrand32( nodeCount - 1 );
	- // move the node either to any existing module, or to its own
	- //unsigned long randomModule = rng.lrand32( moduleCount );
	- unsigned long randomModule = rng.lrand32( moduleCount - 1 );
	-
	- // do some sanity checks
	-
	- if ( nodeCount < 2 )
	- {
	- // no sense in doing anything
	- return;
	- }
	-
	- const std::vector< VertexDescriptorType > allNodesVector
	- = network->GetVectorOfAllVertexDescriptors();
	-
	- auto iter = vertexToModuleMap->find( allNodesVector[ randomNode ] );
	- const int previousModuleNumber = iter->second;
	-
	- // if we move the node to its own module, do nothing
	- if( previousModuleNumber == (long)randomModule )
	- {
	- return;
	- }
	-
	- iter->second = randomModule;
	-
	- if( getNumberOfVerticesInModule( vertexToModuleMap, previousModuleNumber ) < 1 )
	- {
	- removeModule( vertexToModuleMap, previousModuleNumber );
	- }
	-}
	-
	-void mitk::ConnectomicsSimulatedAnnealingPermutationModularity::permutateMappingModuleChange(
	- ToModuleMapType *vertexToModuleMap, double currentTemperature, mitk::ConnectomicsNetwork::Pointer network )
	-{
	- //the random number generators
	- vnl_random rng( (unsigned int) rand() );
	-
	- //randomly generate threshold
	- const double threshold = rng.drand64( 0.0 , 1.0);
	-
	- //for deciding whether to join two modules or split one
	- double splitThreshold = 0.5;
	-
	- //stores whether to join or two split
	- bool joinModules( false );
	-
	- //select random module
	- int numberOfModules = getNumberOfModules( vertexToModuleMap );
	- unsigned long randomModuleA = rng.lrand32( numberOfModules - 1 );
	-
	- //select the second module to join, if joining
	- unsigned long randomModuleB = rng.lrand32( numberOfModules - 1 );
	-
	- if( ( threshold < splitThreshold ) && ( randomModuleA != randomModuleB ) )
	- {
	- joinModules = true;
	- }
	-
	- if( joinModules )
	- {
	- // this being an kommutative operation, we will always join B to A
	- joinTwoModules( vertexToModuleMap, randomModuleA, randomModuleB );
	- //eliminate the empty module
	- removeModule( vertexToModuleMap, randomModuleB );
	-
	- }
	- else
	- {
	- //split module
	- splitModule( vertexToModuleMap, currentTemperature, network, randomModuleA );
	- }
	-
	-
	-}
	-
	-void mitk::ConnectomicsSimulatedAnnealingPermutationModularity::joinTwoModules(
	- ToModuleMapType *vertexToModuleMap, int moduleA, int moduleB )
	-{
	-
	- auto iter = vertexToModuleMap->begin();
	- auto end = vertexToModuleMap->end();
	-
	- while( iter != end )
	- {
	- // if vertex belongs to module B move it to A
	- if( iter->second == moduleB )
	- {
	- iter->second = moduleA;
	- }
	-
	- iter++;
	- }// end while( iter != end )
	-}
	-
	-void mitk::ConnectomicsSimulatedAnnealingPermutationModularity::splitModule(
	- ToModuleMapType *vertexToModuleMap, double currentTemperature, mitk::ConnectomicsNetwork::Pointer network, int moduleToSplit )
	-{
	-
	- if( m_Depth == 0 )
	- {
	- // do nothing
	- return;
	- }
	-
	- // if the module contains only one node, no more division is sensible
	- if( getNumberOfVerticesInModule( vertexToModuleMap, moduleToSplit ) < 2 )
	- {
	- // do nothing
	- return;
	- }
	-
	- // create subgraph of the module, that is to be splitted
	-
	- mitk::ConnectomicsNetwork::Pointer subNetwork = mitk::ConnectomicsNetwork::New();
	- VertexToVertexMapType graphToSubgraphVertexMap;
	- VertexToVertexMapType subgraphToGraphVertexMap;
	-
	-
	- extractModuleSubgraph( vertexToModuleMap, network, moduleToSplit, subNetwork, &graphToSubgraphVertexMap, &subgraphToGraphVertexMap );
	-
	-
	- // The submap
	- ToModuleMapType vertexToModuleSubMap;
	-
	- // run simulated annealing on the subgraph to determine how the module should be split
	- if( m_Depth > 0 && m_StepSize > 0 )
	- {
	- mitk::ConnectomicsSimulatedAnnealingManager::Pointer manager = mitk::ConnectomicsSimulatedAnnealingManager::New();
	- mitk::ConnectomicsSimulatedAnnealingPermutationModularity::Pointer permutation = mitk::ConnectomicsSimulatedAnnealingPermutationModularity::New();
	- mitk::ConnectomicsSimulatedAnnealingCostFunctionModularity::Pointer costFunction = mitk::ConnectomicsSimulatedAnnealingCostFunctionModularity::New();
	-
	- permutation->SetCostFunction( costFunction.GetPointer() );
	- permutation->SetNetwork( subNetwork );
	- permutation->SetDepth( m_Depth - 1 );
	- permutation->SetStepSize( m_StepSize * 2 );
	-
	- manager->SetPermutation( permutation.GetPointer() );
	-
	- manager->RunSimulatedAnnealing( currentTemperature, m_StepSize * 2 );
	-
	- vertexToModuleSubMap = permutation->GetMapping();
	- }
	-
	- // now carry the information over to the original map
	- std::vector< int > moduleTranslationVector;
	- moduleTranslationVector.resize( getNumberOfModules( &vertexToModuleSubMap ), 0 );
	- int originalNumber = getNumberOfModules( vertexToModuleMap );
	-
	- // the new parts are added at the end
	- for(unsigned int index( 0 ); index < moduleTranslationVector.size() ; index++)
	- {
	- moduleTranslationVector[ index ] = originalNumber + index;
	- }
	-
	- auto iter2 = vertexToModuleSubMap.begin();
	- auto end2 = vertexToModuleSubMap.end();
	-
	- while( iter2 != end2 )
	- {
	- // translate vertex descriptor from subgraph to graph
	- VertexDescriptorType key = subgraphToGraphVertexMap.find( iter2->first )->second;
	- // translate module number from subgraph to graph
	- int value = moduleTranslationVector[ iter2->second ];
	- // change the corresponding entry
	- vertexToModuleMap->find( key )->second = value;
	-
	- iter2++;
	- }
	-
	- // remove the now empty module, that was splitted
	- removeModule( vertexToModuleMap, moduleToSplit );
	-
	-}
	-
	-void mitk::ConnectomicsSimulatedAnnealingPermutationModularity::extractModuleSubgraph(
	- ToModuleMapType *vertexToModuleMap,
	- mitk::ConnectomicsNetwork::Pointer network,
	- int moduleToSplit,
	- mitk::ConnectomicsNetwork::Pointer subNetwork,
	- VertexToVertexMapType* graphToSubgraphVertexMap,
	- VertexToVertexMapType* subgraphToGraphVertexMap )
	-{
	- const std::vector< VertexDescriptorType > allNodesVector = network->GetVectorOfAllVertexDescriptors();
	-
	- // add vertices to subgraph
	- for( unsigned int nodeNumber( 0 ); nodeNumber < allNodesVector.size() ; nodeNumber++)
	- {
	-
	- if( moduleToSplit == vertexToModuleMap->find( allNodesVector[ nodeNumber ] )->second )
	- {
	- int id = network->GetNode( allNodesVector[ nodeNumber ] ).id;
	- VertexDescriptorType newVertex = subNetwork->AddVertex( id );
	-
	- graphToSubgraphVertexMap->insert(
	- std::pair<VertexDescriptorType, VertexDescriptorType>(
	- allNodesVector[ nodeNumber ], newVertex
	- )
	- );
	- subgraphToGraphVertexMap->insert(
	- std::pair<VertexDescriptorType, VertexDescriptorType>(
	- newVertex, allNodesVector[ nodeNumber ]
	- )
	- );
	- }
	- }
	-
	- // add edges to subgraph
	- auto iter = graphToSubgraphVertexMap->begin();
	- auto end = graphToSubgraphVertexMap->end();
	-
	- while( iter != end )
	- {
	- const std::vector< VertexDescriptorType > adjacentNodexVector
	- = network->GetVectorOfAdjacentNodes( iter->first );
	-
	- for( unsigned int adjacentNodeNumber( 0 ); adjacentNodeNumber < adjacentNodexVector.size() ; adjacentNodeNumber++)
	- {
	- // if the adjacent vertex is part of the subgraph,
	- // add edge, if it does not exist yet, else do nothing
	-
	- VertexDescriptorType adjacentVertex = adjacentNodexVector[ adjacentNodeNumber ];
	- if( graphToSubgraphVertexMap->count( adjacentVertex ) > 0 )
	- {
	- if( !subNetwork->EdgeExists( iter->second, graphToSubgraphVertexMap->find( adjacentVertex )->second ) )
	- { //edge exists in parent network, but not yet in sub network
	- const VertexDescriptorType vertexA = iter->second;
	- const VertexDescriptorType vertexB = graphToSubgraphVertexMap->find( adjacentVertex )->second;
	- const int sourceID = network->GetNode( vertexA ).id;
	- const int targetID = network->GetNode( vertexB ).id;
	- const double fiber_count = network->GetEdge( iter->first, graphToSubgraphVertexMap->find( adjacentVertex )->first ).fiber_count;
	- subNetwork->AddEdge( vertexA , vertexB, sourceID, targetID, fiber_count );
	- }
	- }
	- }
	- iter++;
	- }// end while( iter != end )
	-}
	-
	-int mitk::ConnectomicsSimulatedAnnealingPermutationModularity::getNumberOfModules(
	- ToModuleMapType *vertexToModuleMap ) const
	-{
	- int maxModule( 0 );
	- auto iter = vertexToModuleMap->begin();
	- auto end = vertexToModuleMap->end();
	- while( iter != end )
	- {
	- if( iter->second > maxModule )
	- {
	- maxModule = iter->second;
	- }
	-
	- iter++;
	- }
	-
	- return maxModule + 1;
	-}
	-
	-int mitk::ConnectomicsSimulatedAnnealingPermutationModularity::getNumberOfVerticesInModule(
	- ToModuleMapType *vertexToModuleMap, int module ) const
	-{
	- int number( 0 );
	- auto iter = vertexToModuleMap->begin();
	- auto end = vertexToModuleMap->end();
	- while( iter != end )
	- {
	- if( iter->second == module )
	- {
	- number++;
	- }
	-
	- iter++;
	- }
	-
	- return number;
	-}
	-
	-void mitk::ConnectomicsSimulatedAnnealingPermutationModularity::removeModule(
	- ToModuleMapType *vertexToModuleMap, int module )
	-{
	- int lastModuleNumber = getNumberOfModules( vertexToModuleMap ) - 1;
	- if( module == lastModuleNumber )
	- {
	- // no need to do anything, the last module is deleted "automatically"
	- return;
	- }
	-
	- if( getNumberOfVerticesInModule( vertexToModuleMap, module ) > 0 )
	- {
	- MBI_WARN << "Trying to remove non-empty module";
	- return;
	- }
	-
	- auto iter = vertexToModuleMap->begin();
	- auto end = vertexToModuleMap->end();
	- while( iter != end )
	- {
	- if( iter->second == lastModuleNumber )
	- {
	- // renumber last module to to-be-deleted module
	- iter->second = module;
	- }
	-
	- iter++;
	- }
	-}
	-
	-void mitk::ConnectomicsSimulatedAnnealingPermutationModularity::randomlyAssignNodesToModules(
	- ToModuleMapType *vertexToModuleMap, int numberOfIntendedModules )
	-{
	- // we make sure that each intended module contains at least one node
	- // thus if more modules are asked for than node exists we will only generate
	- // as many modules as there are nodes
	- if( numberOfIntendedModules > 0 &&
	- (unsigned int)numberOfIntendedModules > vertexToModuleMap->size() )
	- {
	- MBI_ERROR << "Tried to generate more modules than vertices were provided";
	- numberOfIntendedModules = vertexToModuleMap->size();
	- }
	-
	- //the random number generators
	- vnl_random rng( (unsigned int) rand() );
	-
	- std::vector< int > histogram;
	- std::vector< int > nodeList;
	-
	- histogram.resize( numberOfIntendedModules, 0 );
	- nodeList.resize( vertexToModuleMap->size(), 0 );
	-
	- int numberOfVertices = vertexToModuleMap->size();
	-
	- //randomly distribute nodes to modules
	- for( unsigned int nodeIndex( 0 ); nodeIndex < nodeList.size(); nodeIndex++ )
	- {
	- //select random module
	- nodeList[ nodeIndex ] = rng.lrand32( numberOfIntendedModules - 1 );
	-
	- histogram[ nodeList[ nodeIndex ] ]++;
	-
	- }
	-
	- // make sure no module contains no node, if one does assign it one of a random module
	- // that does contain at least two
	- for( unsigned int moduleIndex( 0 ); moduleIndex < histogram.size(); moduleIndex++ )
	- {
	- while( histogram[ moduleIndex ] == 0 )
	- {
	- int randomNodeIndex = rng.lrand32( numberOfVertices - 1 );
	- if( histogram[ nodeList[ randomNodeIndex ] ] > 1 )
	- {
	- histogram[ moduleIndex ]++;
	- histogram[ nodeList[ randomNodeIndex ] ]--;
	- nodeList[ randomNodeIndex ] = moduleIndex;
	- }
	- }
	- }
	-
	- auto iter = vertexToModuleMap->begin();
	- auto end = vertexToModuleMap->end();
	-
	- for( unsigned int index( 0 ); ( iter != end ) && ( index < nodeList.size() ); index++, iter++ )
	- {
	- iter->second = nodeList[ index ] ;
	- }
	-}
	-
	-void mitk::ConnectomicsSimulatedAnnealingPermutationModularity::SetMapping( ToModuleMapType mapping )
	-{
	- m_BestSolution = mapping;
	-}
	-
	-mitk::ConnectomicsSimulatedAnnealingPermutationModularity::ToModuleMapType
	-mitk::ConnectomicsSimulatedAnnealingPermutationModularity::GetMapping()
	-{
	- return m_BestSolution;
	-}
	-
	-double mitk::ConnectomicsSimulatedAnnealingPermutationModularity::Evaluate( ToModuleMapType* mapping ) const
	-{
	- mitk::ConnectomicsSimulatedAnnealingCostFunctionModularity* costMapping =
	- dynamic_cast<mitk::ConnectomicsSimulatedAnnealingCostFunctionModularity*>( m_CostFunction.GetPointer() );
	- if( costMapping )
	- {
	- return costMapping->Evaluate( m_Network, mapping );
	- }
	- else
	- {
	- return 0;
	- }
	-}
	-
	-bool mitk::ConnectomicsSimulatedAnnealingPermutationModularity::AcceptChange( double costBefore, double costAfter, double temperature ) const
	-{
	- if( costAfter <= costBefore )
	- {// if cost is lower after
	- return true;
	- }
	-
	- //the random number generators
	- vnl_random rng( (unsigned int) rand() );
	-
	- //randomly generate threshold
	- const double threshold = rng.drand64( 0.0 , 1.0);
	-
	- //the likelihood of acceptance
	- double likelihood = std::exp( - ( costAfter - costBefore ) / temperature );
	-
	- if( threshold < likelihood )
	- {
	- return true;
	- }
	-
	- return false;
	-}
	-
	-
	-void mitk::ConnectomicsSimulatedAnnealingPermutationModularity::SetDepth( int depth )
	-{
	- m_Depth = depth;
	-}
	-
	-void mitk::ConnectomicsSimulatedAnnealingPermutationModularity::SetStepSize( double size )
	-{
	- m_StepSize = size;
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingPermutationModularity.h b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingPermutationModularity.h
	deleted file mode 100644
	index 99368e9436..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSimulatedAnnealingPermutationModularity.h
	+++ /dev/null
	@@ -1,140 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef mitkConnectomicsSimulatedAnnealingPermutationModularity_h
	-#define mitkConnectomicsSimulatedAnnealingPermutationModularity_h
	-
	-#include "mitkConnectomicsSimulatedAnnealingPermutationBase.h"
	-
	-#include "mitkConnectomicsNetwork.h"
	-
	-namespace mitk
	-{
	- /**
	- * \brief A class providing permutations for the calculation of modularity using simulated annealing */
	- class MITKCONNECTOMICS_EXPORT ConnectomicsSimulatedAnnealingPermutationModularity : public mitk::ConnectomicsSimulatedAnnealingPermutationBase
	- {
	- public:
	-
	- typedef mitk::ConnectomicsNetwork::VertexDescriptorType VertexDescriptorType;
	- typedef std::map< VertexDescriptorType, int > ToModuleMapType;
	- typedef std::map< VertexDescriptorType, VertexDescriptorType > VertexToVertexMapType;
	-
	- /** Standard class typedefs. */
	- /** Method for creation through the object factory. */
	-
	- mitkClassMacroItkParent(ConnectomicsSimulatedAnnealingPermutationModularity, itk::Object);
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- // Initialize the permutation
	- void Initialize() override;
	-
	- // Do a permutation for a specific temperature
	- void Permutate( double temperature ) override;
	-
	- // Do clean up necessary after a permutation
	- void CleanUp() override;
	-
	- // set the network permutation is to be run upon
	- void SetNetwork( mitk::ConnectomicsNetwork::Pointer theNetwork );
	-
	- // Get the number of modules the graph has ( highest number - 1 )
	- int getNumberOfModules( ToModuleMapType *vertexToModuleMap ) const;
	-
	- // Get the number of vertices belonging to a given module
	- int getNumberOfVerticesInModule( ToModuleMapType *vertexToModuleMap, int module ) const;
	-
	- // Set the mapping
	- void SetMapping( ToModuleMapType mapping );
	-
	- // Get the mapping
	- ToModuleMapType GetMapping();
	-
	- // Set depth
	- void SetDepth( int depth );
	-
	- // Set stepSize
	- void SetStepSize( double size );
	-
	- protected:
	-
	- //////////////////// Functions ///////////////////////
	- ConnectomicsSimulatedAnnealingPermutationModularity();
	- ~ConnectomicsSimulatedAnnealingPermutationModularity() override;
	-
	- // This function moves one single node from a module to another
	- void permutateMappingSingleNodeShift(
	- ToModuleMapType *vertexToModuleMap,
	- mitk::ConnectomicsNetwork::Pointer network );
	-
	- // This function splits and joins modules
	- void permutateMappingModuleChange(
	- ToModuleMapType *vertexToModuleMap,
	- double currentTemperature,
	- mitk::ConnectomicsNetwork::Pointer network );
	-
	- // join the two given modules to a single one
	- void joinTwoModules( ToModuleMapType *vertexToModuleMap, int moduleA, int moduleB );
	-
	- // split the given module recursively up to a certain level
	- // first randomly assigns nodes and then starts another simulated annealing
	- // on the sub network, as long as depthOfModuleChange > 0
	- void splitModule(
	- ToModuleMapType *vertexToModuleMap,
	- double currentTemperature,
	- mitk::ConnectomicsNetwork::Pointer network,
	- int moduleToSplit );
	-
	- // Extract the subgraph of a network containing all nodes
	- // of a given module and the egdes between them
	- void extractModuleSubgraph(
	- ToModuleMapType *vertexToModuleMap,
	- mitk::ConnectomicsNetwork::Pointer network,
	- int moduleToSplit,
	- mitk::ConnectomicsNetwork::Pointer subNetwork,
	- VertexToVertexMapType* graphToSubgraphVertexMap,
	- VertexToVertexMapType* subgraphToGraphVertexMap );
	-
	- // Remove empty modules by moving all nodes of the highest module to the given module
	- void removeModule( ToModuleMapType *vertexToModuleMap, int module );
	-
	- // Randomly assign nodes to modules, this makes sure each module contains at least one node
	- // as long as numberOfIntendedModules < number of nodes
	- void randomlyAssignNodesToModules(ToModuleMapType *vertexToModuleMap, int numberOfIntendedModules );
	-
	- // Evaluate mapping using a modularity cost function
	- double Evaluate( ToModuleMapType* mapping ) const;
	-
	- // Whether to accept the permutation
	- bool AcceptChange( double costBefore, double costAfter, double temperature ) const;
	-
	- // the current best solution
	- ToModuleMapType m_BestSolution;
	-
	- // the network
	- mitk::ConnectomicsNetwork::Pointer m_Network;
	-
	- // How many levels of recursive calls can be gone down
	- int m_Depth;
	-
	- // The step size for recursive configuring of simulated annealing manager
	- double m_StepSize;
	- };
	-
	-}// end namespace mitk
	-
	-#endif // mitkConnectomicsSimulatedAnnealingPermutationModularity_h
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsStatisticsCalculator.cpp b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsStatisticsCalculator.cpp
	deleted file mode 100644
	index b7d9b44a40..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsStatisticsCalculator.cpp
	+++ /dev/null
	@@ -1,749 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkConnectomicsStatisticsCalculator.h"
	-#include "mitkConnectomicsNetworkConverter.h"
	-
	-#include <numeric>
	-
	-#include <boost/graph/clustering_coefficient.hpp>
	-
	-#ifdef _MSC_VER
	-# pragma warning(push)
	-# pragma warning(disable: 4172)
	-#endif
	-#include <boost/graph/connected_components.hpp>
	-#include <boost/graph/betweenness_centrality.hpp>
	-
	-#ifdef _MSC_VER
	-# pragma warning(pop)
	-#endif
	-
	-#include <boost/graph/visitors.hpp>
	-
	-#include "vnl/algo/vnl_symmetric_eigensystem.h"
	-
	-template<typename GraphType>
	-class all_pairs_shortest_recorder : public boost::default_bfs_visitor
	-{
	-public:
	- typedef typename boost::graph_traits<GraphType>::vertex_descriptor VertexType;
	- typedef typename boost::graph_traits<GraphType>::edge_descriptor EdgeType;
	-
	- all_pairs_shortest_recorder(int* dist, int &max, unsigned int &size)
	- {
	- d = dist;
	- ecc = &max;
	- component_size = &size;
	- }
	-
	- void tree_edge(EdgeType edge, const GraphType& graph) {
	- VertexType u = boost::source(edge, graph);
	- VertexType v = boost::target(edge, graph);
	- d[v] = d[u] + 1;
	- *ecc = d[v];
	- component_size = component_size + 1;
	- }
	-private:
	- int* d;
	- int* ecc;
	- unsigned int* component_size;
	-};
	-
	-mitk::ConnectomicsStatisticsCalculator::ConnectomicsStatisticsCalculator()
	- : m_Network( nullptr )
	- , m_NumberOfVertices( 0 )
	- , m_NumberOfEdges( 0 )
	- , m_AverageDegree( 0.0 )
	- , m_ConnectionDensity( 0.0 )
	- , m_NumberOfConnectedComponents( 0 )
	- , m_AverageComponentSize( 0.0 )
	- , m_Components(0)
	- , m_LargestComponentSize( 0 )
	- , m_HopPlotExponent( 0.0 )
	- , m_EffectiveHopDiameter( 0.0 )
	- , m_VectorOfClusteringCoefficientsC( 0 )
	- , m_VectorOfClusteringCoefficientsD( 0 )
	- , m_VectorOfClusteringCoefficientsE( 0 )
	- , m_AverageClusteringCoefficientsC( 0.0 )
	- , m_AverageClusteringCoefficientsD( 0.0 )
	- , m_AverageClusteringCoefficientsE( 0.0 )
	- , m_VectorOfVertexBetweennessCentralities( 0 )
	- , m_PropertyMapOfVertexBetweennessCentralities( )
	- , m_AverageVertexBetweennessCentrality( 0.0 )
	- , m_VectorOfEdgeBetweennessCentralities( 0 )
	- , m_PropertyMapOfEdgeBetweennessCentralities( )
	- , m_AverageEdgeBetweennessCentrality( 0.0 )
	- , m_NumberOfIsolatedPoints( 0 )
	- , m_RatioOfIsolatedPoints( 0.0 )
	- , m_NumberOfEndPoints( 0 )
	- , m_RatioOfEndPoints( 0.0 )
	- , m_VectorOfEccentrities( 0 )
	- , m_VectorOfEccentrities90( 0 )
	- , m_VectorOfAveragePathLengths( 0.0 )
	- , m_Diameter( 0 )
	- , m_Diameter90( 0 )
	- , m_Radius( 0 )
	- , m_Radius90( 0 )
	- , m_AverageEccentricity( 0.0 )
	- , m_AverageEccentricity90( 0.0 )
	- , m_AveragePathLength( 0.0 )
	- , m_NumberOfCentralPoints( 0 )
	- , m_RatioOfCentralPoints( 0.0 )
	- , m_VectorOfSortedEigenValues( 0 )
	- , m_SpectralRadius( 0.0 )
	- , m_SecondLargestEigenValue( 0.0 )
	- , m_AdjacencyTrace( 0.0 )
	- , m_AdjacencyEnergy( 0.0 )
	- , m_VectorOfSortedLaplacianEigenValues( 0 )
	- , m_LaplacianTrace( 0.0 )
	- , m_LaplacianEnergy( 0.0 )
	- , m_LaplacianSpectralGap( 0.0 )
	- , m_VectorOfSortedNormalizedLaplacianEigenValues( 0 )
	- , m_NormalizedLaplacianTrace( 0.0 )
	- , m_NormalizedLaplacianEnergy( 0.0 )
	- , m_NormalizedLaplacianNumberOf2s( 0 )
	- , m_NormalizedLaplacianNumberOf1s( 0 )
	- , m_NormalizedLaplacianNumberOf0s( 0 )
	- , m_NormalizedLaplacianLowerSlope( 0.0 )
	- , m_NormalizedLaplacianUpperSlope( 0.0 )
	- , m_SmallWorldness( 0.0 )
	-{
	-}
	-
	-mitk::ConnectomicsStatisticsCalculator::~ConnectomicsStatisticsCalculator()
	-{
	-}
	-
	-void mitk::ConnectomicsStatisticsCalculator::Update()
	-{
	- CalculateNumberOfVertices();
	- CalculateNumberOfEdges();
	- CalculateAverageDegree();
	- CalculateConnectionDensity();
	- CalculateNumberOfConnectedComponents();
	- CalculateAverageComponentSize();
	- CalculateLargestComponentSize();
	- CalculateRatioOfNodesInLargestComponent();
	- CalculateHopPlotValues();
	- CalculateClusteringCoefficients();
	- CalculateBetweennessCentrality();
	- CalculateIsolatedAndEndPoints();
	- CalculateShortestPathMetrics();
	- CalculateSpectralMetrics();
	- CalculateLaplacianMetrics();
	- CalculateNormalizedLaplacianMetrics();
	- CalculateSmallWorldness();
	-}
	-
	-void mitk::ConnectomicsStatisticsCalculator::CalculateNumberOfVertices()
	-{
	- m_NumberOfVertices = boost::num_vertices( *(m_Network->GetBoostGraph()) );
	-}
	-
	-void mitk::ConnectomicsStatisticsCalculator::CalculateNumberOfEdges()
	-{
	- m_NumberOfEdges = boost::num_edges( *(m_Network->GetBoostGraph()) );
	-}
	-
	-void mitk::ConnectomicsStatisticsCalculator::CalculateAverageDegree()
	-{
	- m_AverageDegree = ( ( (double) m_NumberOfEdges * 2.0 ) / (double) m_NumberOfVertices );
	-}
	-
	-void mitk::ConnectomicsStatisticsCalculator::CalculateConnectionDensity()
	-{
	- double numberOfPossibleEdges = (double) m_NumberOfVertices * ( (double) m_NumberOfVertices - 1 ) / 2;
	-
	- m_ConnectionDensity = (double) m_NumberOfEdges / numberOfPossibleEdges;
	-}
	-
	-void mitk::ConnectomicsStatisticsCalculator::CalculateNumberOfConnectedComponents()
	-{
	- m_Components.resize( m_NumberOfVertices );
	- m_NumberOfConnectedComponents = boost::connected_components( *(m_Network->GetBoostGraph()), &m_Components[0] );
	-}
	-
	-void mitk::ConnectomicsStatisticsCalculator::CalculateAverageComponentSize()
	-{
	- m_AverageComponentSize = (double) m_NumberOfVertices / (double) m_NumberOfConnectedComponents ;
	-}
	-
	-void mitk::ConnectomicsStatisticsCalculator::CalculateLargestComponentSize()
	-{
	- m_LargestComponentSize = 0;
	- std::vector<unsigned int> bins( m_NumberOfConnectedComponents );
	-
	- for(unsigned int i=0; i < m_NumberOfVertices; i++)
	- {
	- bins[ m_Components[i] ]++;
	- }
	-
	- for(unsigned int i=0; i < m_NumberOfConnectedComponents; i++)
	- {
	- if (bins[i] > m_LargestComponentSize )
	- {
	- m_LargestComponentSize = bins[i];
	- }
	- }
	-}
	-
	-void mitk::ConnectomicsStatisticsCalculator::CalculateRatioOfNodesInLargestComponent()
	-{
	- m_RatioOfNodesInLargestComponent = (double) m_LargestComponentSize / (double) m_NumberOfVertices ;
	-}
	-
	-void mitk::ConnectomicsStatisticsCalculator::CalculateHopPlotValues()
	-{
	- std::vector<int> bins( m_NumberOfVertices );
	-
	- VertexIteratorType vi, vi_end;
	- unsigned int index( 0 );
	-
	- for( boost::tie( vi, vi_end ) = boost::vertices( *(m_Network->GetBoostGraph()) ); vi != vi_end; ++vi)
	- {
	- std::vector<int> distances(m_NumberOfVertices, 0);
	- int max_distance = 0;
	- VertexDescriptorType src = *vi;
	- distances[src] = 0;
	- unsigned int size = 0;
	-
	- boost::breadth_first_search(*(m_Network->GetBoostGraph()), src,
	- visitor(all_pairs_shortest_recorder< NetworkType >
	- (&distances[0], max_distance, size)));
	-
	- for(index=0; index < distances.size(); index++)
	- {
	- if(distances[index] > 0)
	- {
	- bins[distances[index]]++;
	- }
	- }
	- }
	-
	- bins[0] = m_NumberOfVertices;
	- for(index=1; index < bins.size(); index++)
	- {
	- bins[index] = bins[index] + bins[index-1];
	- }
	-
	- int counter = 0;
	- double C=0, D=0, E=0, F=0;
	-
	- for (unsigned int i=1; i<bins.size()-1; i++)
	- {
	- counter ++;
	- if(fabs(log(double(bins[i+1])) - log(double(bins[i]))) < 0.0000001)
	- {
	- break;
	- }
	- }
	-
	- for (int i=1; i<=counter; i++)
	- {
	- double x = log(double(i));
	- double y = log(double(bins[i]));
	- C += x;
	- D += y;
	- E += x * y;
	- F += x * x;
	- }
	- double b = (DF - CE)/(Fcounter - CC);
	- m_HopPlotExponent = (E - b*C)/F;
	-
	- m_EffectiveHopDiameter =
	- std::pow( ( m_NumberOfVertices * m_NumberOfVertices )
	- / ( m_NumberOfVertices + 2 * m_NumberOfEdges ), 1.0 / m_HopPlotExponent );
	-}
	-
	-void mitk::ConnectomicsStatisticsCalculator::CalculateClusteringCoefficients()
	-{
	- VertexIteratorType vi, vi_end;
	- std::vector<double> m_VectorOfClusteringCoefficientsC;
	- std::vector<double> m_VectorOfClusteringCoefficientsD;
	- std::vector<double> m_VectorOfClusteringCoefficientsE;
	- typedef std::set<VertexDescriptorType> NeighborSetType;
	- typedef NetworkType::out_edge_iterator OutEdgeIterType;
	-
	- for(boost::tie(vi,vi_end) = boost::vertices( *(m_Network->GetBoostGraph()) ); vi!=vi_end; ++vi)
	- {
	- // Get the list of vertices which are in the neighborhood of vi.
	- std::pair<AdjacencyIteratorType, AdjacencyIteratorType> adjacent =
	- boost::adjacent_vertices(vi, (m_Network->GetBoostGraph()) );
	-
	- //Populate a set with the neighbors of vi
	- NeighborSetType neighbors;
	- for(; adjacent.first!=adjacent.second; ++adjacent.first)
	- {
	- neighbors.insert(*adjacent.first);
	- }
	-
	- // Now, count the edges between vertices in the neighborhood.
	- unsigned int neighborhood_edge_count = 0;
	- if(neighbors.size() > 0)
	- {
	- NeighborSetType::iterator iter;
	- for(iter = neighbors.begin(); iter != neighbors.end(); ++iter)
	- {
	- std::pair<OutEdgeIterType, OutEdgeIterType> oe = out_edges(iter, (m_Network->GetBoostGraph()) );
	- for(; oe.first != oe.second; ++oe.first)
	- {
	- if(neighbors.find(target(oe.first, (m_Network->GetBoostGraph()) )) != neighbors.end())
	- {
	- ++neighborhood_edge_count;
	- }
	- }
	- }
	- neighborhood_edge_count /= 2;
	- }
	- //Clustering Coefficienct C,E
	- if(neighbors.size() > 1)
	- {
	- double num = neighborhood_edge_count;
	- double denum = neighbors.size() * (neighbors.size()-1)/2;
	- m_VectorOfClusteringCoefficientsC.push_back( num / denum);
	- m_VectorOfClusteringCoefficientsE.push_back( num / denum);
	- }
	- else
	- {
	- m_VectorOfClusteringCoefficientsC.push_back(0.0);
	- }
	-
	- //Clustering Coefficienct D
	- if(neighbors.size() > 0)
	- {
	- double num = neighbors.size() + neighborhood_edge_count;
	- double denum = ( (neighbors.size()+1) * neighbors.size()) / 2;
	- m_VectorOfClusteringCoefficientsD.push_back( num / denum);
	- }
	- else
	- {
	- m_VectorOfClusteringCoefficientsD.push_back(0.0);
	- }
	- }
	-
	- // Average Clustering coefficienies:
	- m_AverageClusteringCoefficientsC = std::accumulate(m_VectorOfClusteringCoefficientsC.begin(),
	- m_VectorOfClusteringCoefficientsC.end(),
	- 0.0) / m_NumberOfVertices;
	-
	- m_AverageClusteringCoefficientsD = std::accumulate(m_VectorOfClusteringCoefficientsD.begin(),
	- m_VectorOfClusteringCoefficientsD.end(),
	- 0.0) / m_NumberOfVertices;
	-
	- m_AverageClusteringCoefficientsE = std::accumulate(m_VectorOfClusteringCoefficientsE.begin(),
	- m_VectorOfClusteringCoefficientsE.end(),
	- 0.0) / m_VectorOfClusteringCoefficientsE.size();
	-}
	-
	-void mitk::ConnectomicsStatisticsCalculator::CalculateBetweennessCentrality()
	-{
	- // std::map used for convenient initialization
	- EdgeIndexStdMapType stdEdgeIndex;
	- // associative property map needed for iterator property map-wrapper
	- EdgeIndexMapType edgeIndex(stdEdgeIndex);
	-
	- EdgeIteratorType iterator, end;
	-
	- // sets iterator to start end end to end
	- boost::tie(iterator, end) = boost::edges( *(m_Network->GetBoostGraph()) );
	-
	- int i(0);
	- for ( ; iterator != end; ++iterator, ++i)
	- {
	- stdEdgeIndex.insert(std::pair< EdgeDescriptorType, int >( *iterator, i));
	- }
	-
	- // Define EdgeCentralityMap
	- m_VectorOfEdgeBetweennessCentralities.resize( m_NumberOfEdges, 0.0);
	- // Create the external property map
	- m_PropertyMapOfEdgeBetweennessCentralities = EdgeIteratorPropertyMapType(m_VectorOfEdgeBetweennessCentralities.begin(), edgeIndex);
	-
	- // Define VertexCentralityMap
	- VertexIndexMapType vertexIndex = get(boost::vertex_index, *(m_Network->GetBoostGraph()) );
	- m_VectorOfVertexBetweennessCentralities.resize( m_NumberOfVertices, 0.0);
	- // Create the external property map
	- m_PropertyMapOfVertexBetweennessCentralities = VertexIteratorPropertyMapType(m_VectorOfVertexBetweennessCentralities.begin(), vertexIndex);
	-
	- boost::brandes_betweenness_centrality( *(m_Network->GetBoostGraph()),
	- m_PropertyMapOfVertexBetweennessCentralities, m_PropertyMapOfEdgeBetweennessCentralities );
	-
	- m_AverageVertexBetweennessCentrality = std::accumulate(m_VectorOfVertexBetweennessCentralities.begin(),
	- m_VectorOfVertexBetweennessCentralities.end(),
	- 0.0) / (double) m_NumberOfVertices;
	-
	- m_AverageEdgeBetweennessCentrality = std::accumulate(m_VectorOfEdgeBetweennessCentralities.begin(),
	- m_VectorOfEdgeBetweennessCentralities.end(),
	- 0.0) / (double) m_NumberOfEdges;
	-}
	-
	-void mitk::ConnectomicsStatisticsCalculator::CalculateIsolatedAndEndPoints()
	-{
	- m_NumberOfIsolatedPoints = 0;
	- m_NumberOfEndPoints = 0;
	-
	- VertexIteratorType vi, vi_end;
	- for( boost::tie(vi,vi_end) = boost::vertices( *(m_Network->GetBoostGraph()) ); vi!=vi_end; ++vi)
	- {
	- int degree = boost::out_degree(vi, (m_Network->GetBoostGraph()) );
	- if(degree == 0)
	- {
	- m_NumberOfIsolatedPoints++;
	- }
	- else if (degree == 1)
	- {
	- m_NumberOfEndPoints++;
	- }
	- }
	-
	- m_RatioOfEndPoints = (double) m_NumberOfEndPoints / (double) m_NumberOfVertices;
	- m_RatioOfIsolatedPoints = (double) m_NumberOfIsolatedPoints / (double) m_NumberOfVertices;
	-}
	-
	-
	-/**
	-* Calculates Shortest Path Related metrics of the graph. The
	-* function runs a BFS from each node to find out the shortest
	-* distances to other nodes in the graph. The maximum of this distance
	-* is called the eccentricity of that node. The maximum eccentricity
	-* in the graph is called diameter and the minimum eccentricity is
	-* called the radius of the graph. Central points are those nodes
	-* having eccentricity equals to radius.
	-*/
	-void mitk::ConnectomicsStatisticsCalculator::CalculateShortestPathMetrics()
	-{
	- //for all vertices:
	- VertexIteratorType vi, vi_end;
	-
	- //store the eccentricities in a vector.
	- m_VectorOfEccentrities.resize( m_NumberOfVertices );
	- m_VectorOfEccentrities90.resize( m_NumberOfVertices );
	- m_VectorOfAveragePathLengths.resize( m_NumberOfVertices );
	-
	- //assign diameter and radius while iterating over the ecccencirities.
	- m_Diameter = 0;
	- m_Diameter90 = 0;
	- m_Radius = std::numeric_limits<unsigned int>::max();
	- m_Radius90 = std::numeric_limits<unsigned int>::max();
	- m_AverageEccentricity = 0.0;
	- m_AverageEccentricity90 = 0.0;
	- m_AveragePathLength = 0.0;
	-
	- //The size of the giant connected component so far.
	- unsigned int giant_component_size = 0;
	- VertexDescriptorType radius_src(0);
	-
	- //Loop over the vertices
	- for( boost::tie(vi, vi_end) = boost::vertices( *(m_Network->GetBoostGraph()) ); vi!=vi_end; ++vi)
	- {
	- //We are going to start a BFS, initialize the neccessary
	- //structures for that. Store the distances of nodes from the
	- //source in distance vector. The maximum distance is stored in
	- //max. The BFS will start from the node that vi is pointing, that
	- //is the src is *vi. We also init the distance of the src node to
	- //itself to 0. size gives the number of nodes discovered during
	- //this BFS.
	- std::vector<int> distances( m_NumberOfVertices );
	- int max_distance = 0;
	- VertexDescriptorType src = *vi;
	- distances[src] = 0;
	- unsigned int size = 0;
	-
	- breadth_first_search(*(m_Network->GetBoostGraph()), src,
	- visitor(all_pairs_shortest_recorder<NetworkType>
	- (&distances[0], max_distance, size)));
	- // vertex vi has eccentricity equal to max_distance
	- m_VectorOfEccentrities[src] = max_distance;
	-
	- //check whether there is any change in the diameter or the radius.
	- //note that the diameter we are calculating here is also the
	- //diameter of the giant connected component!
	- if(m_VectorOfEccentrities[src] > m_Diameter)
	- {
	- m_Diameter = m_VectorOfEccentrities[src];
	- }
	-
	- //The radius should be calculated on the largest connected
	- //component, otherwise it is very likely that radius will be 1.
	- //We change the value of the radius only if this is the giant
	- //connected component so far. After all the eccentricities are
	- //found we should loop over this connected component and find the
	- //minimum eccentricity which is the radius. So we keep the src
	- //node, so that we can find the connected component later on.
	- if(size > giant_component_size)
	- {
	- giant_component_size = size;
	- radius_src = src;
	- }
	-
	- //Calculate in how many hops we can reach 90 percent of the
	- //nodes. We store the number of hops we can reach in h hops in the
	- //bucket vector. That is bucket[h] gives the number of nodes
	- //reachable in exactly h hops. sum of bucket[i<h] gives the number
	- //of nodes that are reachable in less than h hops. We also
	- //calculate sum of the distances from this node to every single
	- //other node in the graph.
	- int reachable90 = std::ceil((double)size * 0.9);
	- std::vector <int> bucket (max_distance+1);
	- int counter = 0;
	- for(unsigned int i=0; i<distances.size(); i++)
	- {
	- if(distances[i]>0)
	- {
	- bucket[distances[i]]++;
	- m_VectorOfAveragePathLengths[src] += distances[i];
	- counter ++;
	- }
	- }
	- if(counter > 0)
	- {
	- m_VectorOfAveragePathLengths[src] = m_VectorOfAveragePathLengths[src] / counter;
	- }
	-
	- int eccentricity90 = 0;
	- while(reachable90 > 0)
	- {
	- eccentricity90 ++;
	- reachable90 = reachable90 - bucket[eccentricity90];
	- }
	- // vertex vi has eccentricity90 equal to eccentricity90
	- m_VectorOfEccentrities90[src] = eccentricity90;
	- if(m_VectorOfEccentrities90[src] > m_Diameter90)
	- {
	- m_Diameter90 = m_VectorOfEccentrities90[src];
	- }
	- }
	-
	- //We are going to calculate the radius now. We stored the src node
	- //that when we start a BFS gives the giant connected component, and
	- //we have the eccentricities calculated. Iterate over the nodes of
	- //this giant component and find the minimum eccentricity.
	- std::vector<int> component( m_NumberOfVertices );
	- boost::connected_components( *(m_Network->GetBoostGraph()), &component[0]);
	- for (unsigned int i=0; i<component.size(); i++)
	- {
	- //If we are in the same component and the radius is not the
	- //minimum so far store the eccentricity as the radius.
	- if( component[i] == component[radius_src])
	- {
	- if(m_Radius > m_VectorOfEccentrities[i])
	- {
	- m_Radius = m_VectorOfEccentrities[i];
	- }
	- if(m_Radius90 > m_VectorOfEccentrities90[i])
	- {
	- m_Radius90 = m_VectorOfEccentrities90[i];
	- }
	- }
	- }
	-
	- m_AverageEccentricity = std::accumulate(m_VectorOfEccentrities.begin(),
	- m_VectorOfEccentrities.end(), 0.0) / m_NumberOfVertices;
	-
	- m_AverageEccentricity90 = std::accumulate(m_VectorOfEccentrities90.begin(),
	- m_VectorOfEccentrities90.end(), 0.0) / m_NumberOfVertices;
	-
	- m_AveragePathLength = std::accumulate(m_VectorOfAveragePathLengths.begin(),
	- m_VectorOfAveragePathLengths.end(), 0.0) / m_NumberOfVertices;
	-
	- //calculate Number of Central Points, nodes having eccentricity = radius.
	- m_NumberOfCentralPoints = 0;
	- for (boost::tie(vi, vi_end) = boost::vertices( *(m_Network->GetBoostGraph()) ); vi != vi_end; ++vi)
	- {
	- if(m_VectorOfEccentrities[*vi] == m_Radius)
	- {
	- m_NumberOfCentralPoints++;
	- }
	- }
	- m_RatioOfCentralPoints = (double)m_NumberOfCentralPoints / m_NumberOfVertices;
	-}
	-
	-void mitk::ConnectomicsStatisticsCalculator::CalculateSpectralMetrics()
	-{
	- mitk::ConnectomicsNetworkConverter::Pointer converter = mitk::ConnectomicsNetworkConverter::New();
	- converter->SetNetwork( m_Network );
	- vnl_matrix<double> adjacencyMatrix = converter->GetNetworkAsVNLAdjacencyMatrix();
	-
	- vnl_symmetric_eigensystem<double> eigenSystem(adjacencyMatrix);
	-
	- m_AdjacencyTrace = 0;
	- m_AdjacencyEnergy = 0;
	- m_VectorOfSortedEigenValues.clear();
	-
	- for(unsigned int i=0; i < m_NumberOfVertices; ++i)
	- {
	- double value = std::fabs(eigenSystem.get_eigenvalue(i));
	- m_VectorOfSortedEigenValues.push_back(value);
	- m_AdjacencyTrace += value;
	- m_AdjacencyEnergy += value * value;
	- }
	-
	- std::sort(m_VectorOfSortedEigenValues.begin(), m_VectorOfSortedEigenValues.end());
	-
	- m_SpectralRadius = m_VectorOfSortedEigenValues[ m_NumberOfVertices - 1];
	- m_SecondLargestEigenValue = m_VectorOfSortedEigenValues[ m_NumberOfVertices - 2];
	-}
	-
	-void mitk::ConnectomicsStatisticsCalculator::CalculateLaplacianMetrics()
	-{
	- mitk::ConnectomicsNetworkConverter::Pointer converter = mitk::ConnectomicsNetworkConverter::New();
	- converter->SetNetwork( m_Network );
	- vnl_matrix<double> adjacencyMatrix = converter->GetNetworkAsVNLAdjacencyMatrix();
	- vnl_matrix<double> laplacianMatrix ( m_NumberOfVertices, m_NumberOfVertices, 0);
	- vnl_matrix<double> degreeMatrix = converter->GetNetworkAsVNLDegreeMatrix();
	-
	- m_VectorOfSortedLaplacianEigenValues.clear();
	- laplacianMatrix = degreeMatrix - adjacencyMatrix;
	- int numberOfConnectedComponents = 0;
	- vnl_symmetric_eigensystem <double> laplacianEigenSystem( laplacianMatrix );
	- m_LaplacianEnergy = 0;
	- m_LaplacianTrace = 0;
	- for(unsigned int i(0); i < m_NumberOfVertices; ++i)
	- {
	- double value = std::fabs( laplacianEigenSystem.get_eigenvalue(i) );
	- m_VectorOfSortedLaplacianEigenValues.push_back( value );
	- m_LaplacianTrace += value;
	- m_LaplacianEnergy += value * value;
	- if ( std::fabs( value ) < mitk::eps )
	- {
	- numberOfConnectedComponents++;
	- }
	- }
	-
	- std::sort(m_VectorOfSortedLaplacianEigenValues.begin(), m_VectorOfSortedLaplacianEigenValues.end());
	- for(unsigned int i(0); i < m_VectorOfSortedLaplacianEigenValues.size(); ++i)
	- {
	- if(m_VectorOfSortedLaplacianEigenValues[i] > mitk::eps )
	- {
	- m_LaplacianSpectralGap = m_VectorOfSortedLaplacianEigenValues[i];
	- break;
	- }
	- }
	-}
	-
	-void mitk::ConnectomicsStatisticsCalculator::CalculateNormalizedLaplacianMetrics()
	-{
	- vnl_matrix<double> normalizedLaplacianMatrix(m_NumberOfVertices, m_NumberOfVertices, 0);
	- EdgeIteratorType ei, ei_end;
	- VertexDescriptorType sourceVertex, destinationVertex;
	- int sourceIndex, destinationIndex;
	- VertexIndexMapType vertexIndexMap = boost::get(boost::vertex_index, *(m_Network->GetBoostGraph()) );
	- m_VectorOfSortedNormalizedLaplacianEigenValues.clear();
	-
	- // Normalized laplacian matrix
	- for( boost::tie(ei, ei_end) = boost::edges( *(m_Network->GetBoostGraph()) ); ei != ei_end; ++ei)
	- {
	- sourceVertex = boost::source(ei, (m_Network->GetBoostGraph()) );
	- sourceIndex = vertexIndexMap[sourceVertex];
	-
	- destinationVertex = boost::target(ei, (m_Network->GetBoostGraph()) );
	- destinationIndex = vertexIndexMap[destinationVertex];
	- int sourceDegree = boost::out_degree(sourceVertex, *(m_Network->GetBoostGraph()) );
	- int destinationDegree = boost::out_degree(destinationVertex, *(m_Network->GetBoostGraph()) );
	-
	- normalizedLaplacianMatrix.put(
	- sourceIndex, destinationIndex, -1 / (sqrt(double(sourceDegree * destinationDegree))));
	- normalizedLaplacianMatrix.put(
	- destinationIndex, sourceIndex, -1 / (sqrt(double(sourceDegree * destinationDegree))));
	- }
	-
	- VertexIteratorType vi, vi_end;
	- for(boost::tie(vi, vi_end)=boost::vertices( *(m_Network->GetBoostGraph()) ); vi!=vi_end; ++vi)
	- {
	- if(boost::out_degree(vi, (m_Network->GetBoostGraph()) ) > 0)
	- {
	- normalizedLaplacianMatrix.put(vertexIndexMap[vi], vertexIndexMap[vi], 1);
	- }
	- }
	- //End of normalized laplacian matrix definition
	-
	- vnl_symmetric_eigensystem <double>
	- normalizedLaplacianEigensystem(normalizedLaplacianMatrix);
	-
	- double N1=0, C1=0, D1=0, E1=0, F1=0, b1=0;
	- double N2=0, C2=0, D2=0, E2=0, F2=0, b2=0;
	- m_NormalizedLaplacianNumberOf2s = 0;
	- m_NormalizedLaplacianNumberOf1s = 0;
	- m_NormalizedLaplacianNumberOf0s = 0;
	- m_NormalizedLaplacianTrace = 0;
	- m_NormalizedLaplacianEnergy = 0;
	-
	- for(unsigned int i(0); i< m_NumberOfVertices; ++i)
	- {
	- double eigenValue = std::fabs(normalizedLaplacianEigensystem.get_eigenvalue(i));
	- m_VectorOfSortedNormalizedLaplacianEigenValues.push_back(eigenValue);
	- m_NormalizedLaplacianTrace += eigenValue;
	- m_NormalizedLaplacianEnergy += eigenValue * eigenValue;
	-
	- //0
	- if(eigenValue < mitk::eps)
	- {
	- m_NormalizedLaplacianNumberOf0s++;
	- }
	-
	- //Between 0 and 1.
	- else if(eigenValue > mitk::eps && eigenValue< 1 - mitk::eps)
	- {
	- C1 += i;
	- D1 += eigenValue;
	- E1 += i * eigenValue;
	- F1 += i * i;
	- N1 ++;
	- }
	-
	- //1
	- else if(std::fabs( std::fabs(eigenValue) - 1) < mitk::eps)
	- {
	- m_NormalizedLaplacianNumberOf1s++;
	- }
	-
	- //Between 1 and 2
	- else if(std::fabs(eigenValue) > 1+mitk::eps && std::fabs(eigenValue)< 2 - mitk::eps)
	- {
	- C2 += i;
	- D2 += eigenValue;
	- E2 += i * eigenValue;
	- F2 += i * i;
	- N2 ++;
	- }
	-
	- //2
	- else if(std::fabs( std::fabs(eigenValue) - 2) < mitk::eps)
	- {
	- m_NormalizedLaplacianNumberOf2s++;
	- }
	- }
	-
	- b1 = (D1F1 - C1E1)/(F1N1 - C1C1);
	- m_NormalizedLaplacianLowerSlope = (E1 - b1*C1)/F1;
	-
	- b2 = (D2F2 - C2E2)/(F2N2 - C2C2);
	- m_NormalizedLaplacianUpperSlope = (E2 - b2*C2)/F2;
	-}
	-
	-void mitk::ConnectomicsStatisticsCalculator::CalculateSmallWorldness()
	-{
	- double k( this->GetAverageDegree() );
	- double N( this->GetNumberOfVertices() );
	- // The clustering coefficient of an Erdos-Reny network is equivalent to
	- // the likelihood two random nodes are connected
	- double gamma = this->GetAverageClusteringCoefficientsC() / ( k / N );
	- //The mean path length of an Erdos-Reny network is approximately
	- // ln( #vertices ) / ln( average degree )
	- double lambda = this->GetAveragePathLength() / ( std::log( N ) / std::log( k ) );
	-
	- m_SmallWorldness = gamma / lambda;
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsStatisticsCalculator.h b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsStatisticsCalculator.h
	deleted file mode 100644
	index 75635ffa12..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsStatisticsCalculator.h
	+++ /dev/null
	@@ -1,243 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef mitkConnectomicsStatisticsCalculator_h
	-#define mitkConnectomicsStatisticsCalculator_h
	-
	-#include <itkObject.h>
	-#include <itkObjectFactory.h>
	-#include <itkMacro.h>
	-
	-#include "mitkCommon.h"
	-
	-#include <MitkConnectomicsExports.h>
	-
	-#include <mitkConnectomicsNetwork.h>
	-
	-namespace mitk
	-{
	- /**
	- * \brief A class giving functions for calculating a variety of network indices */
	- class MITKCONNECTOMICS_EXPORT ConnectomicsStatisticsCalculator : public itk::Object
	- {
	- public:
	-
	- /** Standard class typedefs. */
	- /** Method for creation through the object factory. */
	-
	- mitkClassMacroItkParent(ConnectomicsStatisticsCalculator, itk::Object);
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- // Typedefs
	- typedef mitk::ConnectomicsNetwork::NetworkType NetworkType;
	- typedef mitk::ConnectomicsNetwork::VertexDescriptorType VertexDescriptorType;
	- typedef mitk::ConnectomicsNetwork::EdgeDescriptorType EdgeDescriptorType;
	- typedef boost::graph_traits<NetworkType>::vertex_iterator VertexIteratorType;
	- typedef boost::graph_traits<NetworkType>::edge_iterator EdgeIteratorType;
	- typedef boost::graph_traits<NetworkType>::adjacency_iterator AdjacencyIteratorType;
	- typedef std::map<EdgeDescriptorType, int> EdgeIndexStdMapType;
	- typedef boost::associative_property_map< EdgeIndexStdMapType > EdgeIndexMapType;
	- typedef boost::iterator_property_map< std::vector< double >::iterator, EdgeIndexMapType > EdgeIteratorPropertyMapType;
	- typedef boost::property_map< NetworkType, boost::vertex_index_t>::type VertexIndexMapType;
	- typedef boost::iterator_property_map< std::vector< double >::iterator, VertexIndexMapType > VertexIteratorPropertyMapType;
	-
	- // Set/Get Macros
	- itkSetObjectMacro( Network, mitk::ConnectomicsNetwork );
	- itkGetMacro( NumberOfVertices, unsigned int );
	- itkGetMacro( NumberOfEdges, unsigned int );
	- itkGetMacro( AverageDegree, double );
	- itkGetMacro( ConnectionDensity, double );
	- itkGetMacro( NumberOfConnectedComponents, unsigned int );
	- itkGetMacro( AverageComponentSize, double );
	- itkGetMacro( Components, std::vector< int > );
	- itkGetMacro( LargestComponentSize, unsigned int );
	- itkGetMacro( RatioOfNodesInLargestComponent, double );
	- itkGetMacro( HopPlotExponent, double );
	- itkGetMacro( EffectiveHopDiameter, double );
	- itkGetMacro( VectorOfClusteringCoefficientsC, std::vector< double > );
	- itkGetMacro( VectorOfClusteringCoefficientsD, std::vector< double > );
	- itkGetMacro( VectorOfClusteringCoefficientsE, std::vector< double > );
	- itkGetMacro( AverageClusteringCoefficientsC, double );
	- itkGetMacro( AverageClusteringCoefficientsD, double );
	- itkGetMacro( AverageClusteringCoefficientsE, double );
	- itkGetMacro( VectorOfVertexBetweennessCentralities, std::vector< double > );
	- itkGetMacro( PropertyMapOfVertexBetweennessCentralities, VertexIteratorPropertyMapType );
	- itkGetMacro( AverageVertexBetweennessCentrality, double );
	- itkGetMacro( VectorOfEdgeBetweennessCentralities, std::vector< double > );
	- itkGetMacro( PropertyMapOfEdgeBetweennessCentralities, EdgeIteratorPropertyMapType );
	- itkGetMacro( AverageEdgeBetweennessCentrality, double );
	- itkGetMacro( NumberOfIsolatedPoints, unsigned int );
	- itkGetMacro( RatioOfIsolatedPoints, double );
	- itkGetMacro( NumberOfEndPoints, unsigned int );
	- itkGetMacro( RatioOfEndPoints, double );
	- itkGetMacro( VectorOfEccentrities, std::vector< unsigned int > );
	- itkGetMacro( VectorOfEccentrities90, std::vector< unsigned int > );
	- itkGetMacro( VectorOfAveragePathLengths, std::vector< double > );
	- itkGetMacro( Diameter, unsigned int );
	- itkGetMacro( Diameter90, unsigned int );
	- itkGetMacro( Radius, unsigned int );
	- itkGetMacro( Radius90, unsigned int );
	- itkGetMacro( AverageEccentricity, double );
	- itkGetMacro( AverageEccentricity90, double );
	- itkGetMacro( AveragePathLength, double );
	- itkGetMacro( NumberOfCentralPoints, unsigned int );
	- itkGetMacro( RatioOfCentralPoints, double );
	- itkGetMacro( VectorOfSortedEigenValues, std::vector< double > );
	- itkGetMacro( SpectralRadius, double );
	- itkGetMacro( SecondLargestEigenValue, double );
	- itkGetMacro( AdjacencyTrace, double );
	- itkGetMacro( AdjacencyEnergy, double );
	- itkGetMacro( VectorOfSortedLaplacianEigenValues, std::vector< double > );
	- itkGetMacro( LaplacianTrace, double );
	- itkGetMacro( LaplacianEnergy, double );
	- itkGetMacro( LaplacianSpectralGap, double );
	- itkGetMacro( VectorOfSortedNormalizedLaplacianEigenValues, std::vector< double > );
	- itkGetMacro( NormalizedLaplacianTrace, double );
	- itkGetMacro( NormalizedLaplacianEnergy, double );
	- itkGetMacro( NormalizedLaplacianNumberOf2s, unsigned int );
	- itkGetMacro( NormalizedLaplacianNumberOf1s, unsigned int );
	- itkGetMacro( NormalizedLaplacianNumberOf0s, unsigned int );
	- itkGetMacro( NormalizedLaplacianLowerSlope, double );
	- itkGetMacro( NormalizedLaplacianUpperSlope, double );
	- itkGetMacro( SmallWorldness, double );
	-
	- void Update();
	-
	- protected:
	-
	- //////////////////// Functions ///////////////////////
	- ConnectomicsStatisticsCalculator();
	- ~ConnectomicsStatisticsCalculator() override;
	-
	- void CalculateNumberOfVertices();
	-
	- void CalculateNumberOfEdges();
	-
	- void CalculateAverageDegree();
	-
	- void CalculateConnectionDensity();
	-
	- void CalculateNumberOfConnectedComponents();
	-
	- void CalculateAverageComponentSize();
	-
	- void CalculateLargestComponentSize();
	-
	- void CalculateRatioOfNodesInLargestComponent();
	-
	- void CalculateHopPlotValues();
	-
	- /**
	- * \brief Calculate the different clustering coefficients
	- *
	- * The clustering coefficient (cc) measures how strong the tendency to form cliques
	- * is in the network. Groups of nodes, that are highly interconnected.
	- *
	- * CC C - Percentage of connections between nodes connected with the given node
	- * CC D - Same as C, but including the connections with the given node
	- * CC E - Same as C, but not counting isolated nodes when averaging
	- */
	- void CalculateClusteringCoefficients();
	-
	- void CalculateBetweennessCentrality();
	-
	- void CalculateIsolatedAndEndPoints();
	-
	- void CalculateShortestPathMetrics();
	-
	- void CalculateSpectralMetrics();
	-
	- void CalculateLaplacianMetrics();
	-
	- void CalculateNormalizedLaplacianMetrics();
	-
	- /**
	- * \brief Calculate the small worldness of the network.
	- *
	- * This will compare the clustering coefficient and mean path length of the network
	- * to an Erdos-Reny network of the same number of nodes and edges.
	- */
	- void CalculateSmallWorldness();
	-
	- /////////////////////// Variables ////////////////////////
	-
	- // The connectomics network, which is used for statistics calculation
	- mitk::ConnectomicsNetwork::Pointer m_Network;
	-
	- // Statistics
	- unsigned int m_NumberOfVertices;
	- unsigned int m_NumberOfEdges;
	- double m_AverageDegree;
	- double m_ConnectionDensity;
	- unsigned int m_NumberOfConnectedComponents;
	- double m_AverageComponentSize;
	- std::vector< int > m_Components;
	- unsigned int m_LargestComponentSize;
	- double m_RatioOfNodesInLargestComponent;
	- double m_HopPlotExponent;
	- double m_EffectiveHopDiameter;
	- std::vector< double > m_VectorOfClusteringCoefficientsC;
	- std::vector< double > m_VectorOfClusteringCoefficientsD;
	- std::vector< double > m_VectorOfClusteringCoefficientsE;
	- double m_AverageClusteringCoefficientsC;
	- double m_AverageClusteringCoefficientsD;
	- double m_AverageClusteringCoefficientsE;
	- std::vector< double > m_VectorOfVertexBetweennessCentralities;
	- VertexIteratorPropertyMapType m_PropertyMapOfVertexBetweennessCentralities;
	- double m_AverageVertexBetweennessCentrality;
	- std::vector< double > m_VectorOfEdgeBetweennessCentralities;
	- EdgeIteratorPropertyMapType m_PropertyMapOfEdgeBetweennessCentralities;
	- double m_AverageEdgeBetweennessCentrality;
	- unsigned int m_NumberOfIsolatedPoints;
	- double m_RatioOfIsolatedPoints;
	- unsigned int m_NumberOfEndPoints;
	- double m_RatioOfEndPoints;
	- std::vector< unsigned int > m_VectorOfEccentrities;
	- std::vector< unsigned int > m_VectorOfEccentrities90;
	- std::vector< double > m_VectorOfAveragePathLengths;
	- unsigned int m_Diameter;
	- unsigned int m_Diameter90;
	- unsigned int m_Radius;
	- unsigned int m_Radius90;
	- double m_AverageEccentricity;
	- double m_AverageEccentricity90;
	- double m_AveragePathLength;
	- unsigned int m_NumberOfCentralPoints;
	- double m_RatioOfCentralPoints;
	- std::vector<double> m_VectorOfSortedEigenValues;
	- double m_SpectralRadius;
	- double m_SecondLargestEigenValue;
	- double m_AdjacencyTrace;
	- double m_AdjacencyEnergy;
	- std::vector<double> m_VectorOfSortedLaplacianEigenValues;
	- double m_LaplacianTrace;
	- double m_LaplacianEnergy;
	- double m_LaplacianSpectralGap;
	- std::vector<double> m_VectorOfSortedNormalizedLaplacianEigenValues;
	- double m_NormalizedLaplacianTrace;
	- double m_NormalizedLaplacianEnergy;
	- unsigned int m_NormalizedLaplacianNumberOf2s;
	- unsigned int m_NormalizedLaplacianNumberOf1s;
	- unsigned int m_NormalizedLaplacianNumberOf0s;
	- double m_NormalizedLaplacianLowerSlope;
	- double m_NormalizedLaplacianUpperSlope;
	- double m_SmallWorldness;
	- };
	-
	-}// end namespace mitk
	-
	-#endif // mitkConnectomicsStatisticsCalculator_h
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSyntheticNetworkGenerator.cpp b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSyntheticNetworkGenerator.cpp
	deleted file mode 100644
	index 9cd2c7e8dc..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSyntheticNetworkGenerator.cpp
	+++ /dev/null
	@@ -1,353 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkConnectomicsSyntheticNetworkGenerator.h"
	-
	-#include <sstream>
	-#include <vector>
	-
	-#include "mitkConnectomicsConstantsManager.h"
	-#include <mitkConnectomicsNetworkProperties.h>
	-
	-#include <vtkMatrix4x4.h>
	-
	-//for random number generation
	-#include "vnl/vnl_random.h"
	-#include "vnl/vnl_math.h"
	-
	-mitk::ConnectomicsSyntheticNetworkGenerator::ConnectomicsSyntheticNetworkGenerator()
	-: m_LastGenerationWasSuccess( false )
	-{
	-}
	-
	-mitk::ConnectomicsSyntheticNetworkGenerator::~ConnectomicsSyntheticNetworkGenerator()
	-{
	-}
	-
	-mitk::ConnectomicsNetwork::Pointer mitk::ConnectomicsSyntheticNetworkGenerator::CreateSyntheticNetwork(int networkTypeId, int paramterOne, double parameterTwo)
	-{
	- mitk::ConnectomicsNetwork::Pointer network = mitk::ConnectomicsNetwork::New();
	-
	- m_LastGenerationWasSuccess = false;
	- // give the network an artificial geometry
	- network->SetGeometry( this->GenerateDefaultGeometry() );
	-
	- switch (networkTypeId) {
	- case 0:
	- GenerateSyntheticCubeNetwork( network, paramterOne, parameterTwo );
	- break;
	- case 1:
	- GenerateSyntheticCenterToSurfaceNetwork( network, paramterOne, parameterTwo );
	- break;
	- case 2:
	- GenerateSyntheticRandomNetwork( network, paramterOne, parameterTwo );
	- break;
	- case 3:
	- //GenerateSyntheticScaleFreeNetwork( network, 1000 );
	- break;
	- case 4:
	- //GenerateSyntheticSmallWorldNetwork( network, 1000 );
	- break;
	- default:
	- MBI_ERROR << "Unrecognized Network ID";
	- }
	-
	- network->UpdateBounds();
	- network->SetProperty(connectomicsDataAdditionalHeaderInformation.c_str(), mitk::StringProperty::New("Synthetic Network"));
	-
	- return network;
	-
	-}
	-
	-mitk::Geometry3D::Pointer mitk::ConnectomicsSyntheticNetworkGenerator::GenerateDefaultGeometry()
	-{
	- mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New();
	-
	- double zero( 0.0 );
	- double one( 1.0 );
	- // origin = {0,0,0}
	- mitk::Point3D origin;
	-
	- origin[0] = zero;
	- origin[1] = zero;
	- origin[2] = zero;
	- geometry->SetOrigin(origin);
	-
	- // spacing = {1,1,1}
	- ScalarType spacing[3];
	- spacing[0] = one;
	- spacing[1] = one;
	- spacing[2] = one;
	- geometry->SetSpacing(spacing);
	-
	- // transform
	- vtkMatrix4x4* transformMatrix = vtkMatrix4x4::New();
	- transformMatrix->SetElement(0,0,one);
	- transformMatrix->SetElement(1,0,zero);
	- transformMatrix->SetElement(2,0,zero);
	- transformMatrix->SetElement(0,1,zero);
	- transformMatrix->SetElement(1,1,one);
	- transformMatrix->SetElement(2,1,zero);
	- transformMatrix->SetElement(0,2,zero);
	- transformMatrix->SetElement(1,2,zero);
	- transformMatrix->SetElement(2,2,one);
	-
	- transformMatrix->SetElement(0,3,origin[0]);
	- transformMatrix->SetElement(1,3,origin[1]);
	- transformMatrix->SetElement(2,3,origin[2]);
	- transformMatrix->SetElement(3,3,1);
	- geometry->SetIndexToWorldTransformByVtkMatrix( transformMatrix );
	-
	- geometry->SetImageGeometry(true);
	-
	- return geometry;
	-}
	-
	-void mitk::ConnectomicsSyntheticNetworkGenerator::GenerateSyntheticCubeNetwork(
	- mitk::ConnectomicsNetwork::Pointer network, int cubeExtent, double distance )
	-{
	- // map for storing the conversion from indices to vertex descriptor
	- std::map< int, mitk::ConnectomicsNetwork::VertexDescriptorType > idToVertexMap;
	-
	- int vertexID(0);
	- for( int loopX( 0 ); loopX < cubeExtent; loopX++ )
	- {
	- for( int loopY( 0 ); loopY < cubeExtent; loopY++ )
	- {
	- for( int loopZ( 0 ); loopZ < cubeExtent; loopZ++ )
	- {
	- std::vector< float > position;
	- std::string label;
	- std::stringstream labelStream;
	- labelStream << vertexID;
	- label = labelStream.str();
	-
	- position.push_back( loopX * distance );
	- position.push_back( loopY * distance );
	- position.push_back( loopZ * distance );
	-
	- mitk::ConnectomicsNetwork::VertexDescriptorType newVertex = network->AddVertex( vertexID );
	- network->SetLabel( newVertex, label );
	- network->SetCoordinates( newVertex, position );
	-
	- if ( idToVertexMap.count( vertexID ) > 0 )
	- {
	- MITK_ERROR << "Aborting network creation, duplicate vertex ID generated.";
	- m_LastGenerationWasSuccess = false;
	- return;
	- }
	- idToVertexMap.insert( std::pair< int, mitk::ConnectomicsNetwork::VertexDescriptorType >( vertexID, newVertex) );
	-
	- vertexID++;
	- }
	- }
	- }
	-
	- int edgeID(0), edgeSourceID(0), edgeTargetID(0);
	- // uniform weight of one
	- int edgeWeight(1);
	-
	- mitk::ConnectomicsNetwork::VertexDescriptorType source;
	- mitk::ConnectomicsNetwork::VertexDescriptorType target;
	-
	- for( int loopX( 0 ); loopX < cubeExtent; loopX++ )
	- {
	- for( int loopY( 0 ); loopY < cubeExtent; loopY++ )
	- {
	- for( int loopZ( 0 ); loopZ < cubeExtent; loopZ++ )
	- {
	- // to avoid creating an edge twice (this being an undirected graph) we only generate
	- // edges in three directions, the others will be supplied by the corresponding nodes
	- if( loopX != 0 )
	- {
	- edgeTargetID = edgeSourceID - cubeExtent * cubeExtent;
	-
	- source = idToVertexMap.find( edgeSourceID )->second;
	- target = idToVertexMap.find( edgeTargetID )->second;
	- network->AddEdge( source, target, edgeSourceID, edgeTargetID, edgeWeight);
	-
	- edgeID++;
	- }
	- if( loopY != 0 )
	- {
	- edgeTargetID = edgeSourceID - cubeExtent;
	-
	- source = idToVertexMap.find( edgeSourceID )->second;
	- target = idToVertexMap.find( edgeTargetID )->second;
	- network->AddEdge( source, target, edgeSourceID, edgeTargetID, edgeWeight);
	-
	- edgeID++;
	- }
	- if( loopZ != 0 )
	- {
	- edgeTargetID = edgeSourceID - 1;
	-
	- source = idToVertexMap.find( edgeSourceID )->second;
	- target = idToVertexMap.find( edgeTargetID )->second;
	- network->AddEdge( source, target, edgeSourceID, edgeTargetID, edgeWeight);
	-
	- edgeID++;
	- }
	-
	- edgeSourceID++;
	- } // end for( int loopZ( 0 ); loopZ < cubeExtent; loopZ++ )
	- } // end for( int loopY( 0 ); loopY < cubeExtent; loopY++ )
	- } // end for( int loopX( 0 ); loopX < cubeExtent; loopX++ )
	- m_LastGenerationWasSuccess = true;
	-}
	-
	-void mitk::ConnectomicsSyntheticNetworkGenerator::GenerateSyntheticCenterToSurfaceNetwork(
	- mitk::ConnectomicsNetwork::Pointer network, int numberOfPoints, double radius )
	-{
	-
	- vnl_random rng( (unsigned int) rand() );
	-
	- mitk::ConnectomicsNetwork::VertexDescriptorType centerVertex;
	- int vertexID(0);
	- { //add center vertex
	- std::vector< float > position;
	- std::string label;
	- std::stringstream labelStream;
	- labelStream << vertexID;
	- label = labelStream.str();
	-
	- position.push_back( 0 );
	- position.push_back( 0 );
	- position.push_back( 0 );
	-
	- centerVertex = network->AddVertex( vertexID );
	- network->SetLabel( centerVertex, label );
	- network->SetCoordinates( centerVertex, position );
	- }//end add center vertex
	-
	- // uniform weight of one
	- int edgeWeight(1);
	-
	- //add vertices on sphere surface
	- for( int loopID( 1 ); loopID < numberOfPoints; loopID++ )
	- {
	-
	- std::vector< float > position;
	- std::string label;
	- std::stringstream labelStream;
	- labelStream << loopID;
	- label = labelStream.str();
	-
	- //generate random, uniformly distributed points on a sphere surface
	- const double uVariable = rng.drand64( 0.0 , 1.0);
	- const double vVariable = rng.drand64( 0.0 , 1.0);
	- const double phi = 2 * vnl_math::pi * uVariable;
	- const double theta = std::acos( 2 * vVariable - 1 );
	-
	- double xpos = radius * std::cos( phi ) * std::sin( theta );
	- double ypos = radius * std::sin( phi ) * std::sin( theta );
	- double zpos = radius * std::cos( theta );
	-
	- position.push_back( xpos );
	- position.push_back( ypos );
	- position.push_back( zpos );
	-
	- mitk::ConnectomicsNetwork::VertexDescriptorType newVertex = network->AddVertex( loopID );
	- network->SetLabel( newVertex, label );
	- network->SetCoordinates( newVertex, position );
	-
	- network->AddEdge( newVertex, centerVertex, loopID, 0, edgeWeight);
	- }
	- m_LastGenerationWasSuccess = true;
	-}
	-
	-void mitk::ConnectomicsSyntheticNetworkGenerator::GenerateSyntheticRandomNetwork(
	- mitk::ConnectomicsNetwork::Pointer network, int numberOfPoints, double threshold )
	-{
	- // as the surface is proportional to the square of the radius the density stays the same
	- double radius = 5 * std::sqrt( (float) numberOfPoints );
	-
	- vnl_random rng( (unsigned int) rand() );
	-
	- // map for storing the conversion from indices to vertex descriptor
	- std::map< int, mitk::ConnectomicsNetwork::VertexDescriptorType > idToVertexMap;
	-
	- //add vertices on sphere surface
	- for( int loopID( 0 ); loopID < numberOfPoints; loopID++ )
	- {
	-
	- std::vector< float > position;
	- std::string label;
	- std::stringstream labelStream;
	- labelStream << loopID;
	- label = labelStream.str();
	-
	- //generate random, uniformly distributed points on a sphere surface
	- const double uVariable = rng.drand64( 0.0 , 1.0);
	- const double vVariable = rng.drand64( 0.0 , 1.0);
	- const double phi = 2 * vnl_math::pi * uVariable;
	- const double theta = std::acos( 2 * vVariable - 1 );
	-
	- double xpos = radius * std::cos( phi ) * std::sin( theta );
	- double ypos = radius * std::sin( phi ) * std::sin( theta );
	- double zpos = radius * std::cos( theta );
	-
	- position.push_back( xpos );
	- position.push_back( ypos );
	- position.push_back( zpos );
	-
	- mitk::ConnectomicsNetwork::VertexDescriptorType newVertex = network->AddVertex( loopID );
	- network->SetLabel( newVertex, label );
	- network->SetCoordinates( newVertex, position );
	-
	- if ( idToVertexMap.count( loopID ) > 0 )
	- {
	- MITK_ERROR << "Aborting network creation, duplicate vertex ID generated.";
	- m_LastGenerationWasSuccess = false;
	- return;
	- }
	- idToVertexMap.insert( std::pair< int, mitk::ConnectomicsNetwork::VertexDescriptorType >( loopID, newVertex) );
	- }
	-
	- int edgeID(0);
	- // uniform weight of one
	- int edgeWeight(1);
	-
	- mitk::ConnectomicsNetwork::VertexDescriptorType source;
	- mitk::ConnectomicsNetwork::VertexDescriptorType target;
	-
	- for( int loopID( 0 ); loopID < numberOfPoints; loopID++ )
	- {
	- // to avoid creating an edge twice (this being an undirected graph) we only
	- // potentially generate edges with all nodes with a bigger ID
	- for( int innerLoopID( loopID ); innerLoopID < numberOfPoints; innerLoopID++ )
	- {
	- if( rng.drand64( 0.0 , 1.0) > threshold)
	- {
	- // do nothing
	- }
	- else
	- {
	- source = idToVertexMap.find( loopID )->second;
	- target = idToVertexMap.find( innerLoopID )->second;
	- network->AddEdge( source, target, loopID, innerLoopID, edgeWeight);
	-
	- edgeID++;
	- }
	- } // end for( int innerLoopID( loopID ); innerLoopID < numberOfPoints; innerLoopID++ )
	- } // end for( int loopID( 0 ); loopID < numberOfPoints; loopID++ )
	- m_LastGenerationWasSuccess = true;
	-}
	-
	-bool mitk::ConnectomicsSyntheticNetworkGenerator::WasGenerationSuccessfull()
	-{
	- return m_LastGenerationWasSuccess;
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSyntheticNetworkGenerator.h b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSyntheticNetworkGenerator.h
	deleted file mode 100644
	index ed5d96eab7..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkConnectomicsSyntheticNetworkGenerator.h
	+++ /dev/null
	@@ -1,88 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef mitkConnectomicsSyntheticNetworkGenerator_h
	-#define mitkConnectomicsSyntheticNetworkGenerator_h
	-
	-#include <itkObject.h>
	-#include <itkObjectFactory.h>
	-#include <itkMacro.h>
	-
	-#include "mitkCommon.h"
	-#include "mitkImage.h"
	-
	-#include "mitkConnectomicsNetwork.h"
	-
	-#include <MitkConnectomicsExports.h>
	-
	-namespace mitk
	-{
	-
	- /**
	- * \brief A class to generate synthetic networks */
	- class MITKCONNECTOMICS_EXPORT ConnectomicsSyntheticNetworkGenerator : public itk::Object
	- {
	- public:
	-
	- /** Standard class typedefs. */
	- /** Method for creation through the object factory. */
	-
	- mitkClassMacroItkParent(ConnectomicsSyntheticNetworkGenerator, itk::Object);
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Create Synthetic Networks */
	- mitk::ConnectomicsNetwork::Pointer CreateSyntheticNetwork(int networkTypeId, int paramterOne, double parameterTwo);
	-
	- /** Return whether the last attempted network generation was a success*/
	- bool WasGenerationSuccessfull();
	-
	- protected:
	-
	- //////////////////// Functions ///////////////////////
	- ConnectomicsSyntheticNetworkGenerator();
	- ~ConnectomicsSyntheticNetworkGenerator() override;
	-
	- /** Generate a default geometry for synthetic images */
	- mitk::Geometry3D::Pointer GenerateDefaultGeometry();
	-
	- /** Generate a synthetic cube (regular lattice) network */
	- void GenerateSyntheticCubeNetwork( mitk::ConnectomicsNetwork::Pointer network, int cubeExtent, double distance );
	-
	- /** Generate a highly heterogenic network
	- *
	- * This is achieved by generating a center vertex and vertices on
	- * a sphere surface, which are all only connected to the center
	- * vertex. */
	- void GenerateSyntheticCenterToSurfaceNetwork(
	- mitk::ConnectomicsNetwork::Pointer network, int numberOfPoints, double radius );
	-
	- /** Generate a random network without specific characteristics
	- *
	- * This is achieved by generating vertices and then deciding whether to
	- * specific vertices are connected by comparing a random number to the threshold */
	- void GenerateSyntheticRandomNetwork(
	- mitk::ConnectomicsNetwork::Pointer network, int numberOfPoints, double threshold );
	-
	- /////////////////////// Variables ////////////////////////
	-
	- /** Store whether the network generated last was generated properly */
	- bool m_LastGenerationWasSuccess;
	- };
	-
	-}// end namespace mitk
	-
	-#endif // _mitkConnectomicsSyntheticNetworkGenerator_H_INCLUDED
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkCorrelationCalculator.h b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkCorrelationCalculator.h
	deleted file mode 100644
	index f7c29d0137..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkCorrelationCalculator.h
	+++ /dev/null
	@@ -1,173 +0,0 @@
	-
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_CORRELATIONCALCULATOR_H
	-#define _MITK_CORRELATIONCALCULATOR_H
	-
	-#include "mitkCommon.h"
	-#include <itkObject.h>
	-#include <mitkImage.h>
	-#include <vnl/vnl_matrix.h>
	-#include <mitkConnectomicsNetwork.h>
	-
	-namespace mitk {
	-
	- /**
	- * \brief Class to calculate covariance and correlation
	- *
	- * In addition to static functions to calculate covariance and correlation,
	- * this class offers capability to set a time series image and optionally a
	- * parcellation image and calculate a correlation matrix.
	- *
	- * Whole correlation only needs a time series image and will return a
	- * #voxel x #voxel matrix where each voxel's time series is correlated
	- * against the time series of each other voxel.
	- *
	- * Parcel correlation will compute an average time series for each parcel
	- * of a parcellation image and create a #parcel x #parcel correlation matrix.
	- *
	- * Please note that time series images are assumed to be 4D and parcellation
	- * images integer valued and 3D.
	- */
	-
	- template< class T >
	- class CorrelationCalculator : public itk::Object
	- {
	-
	- public:
	-
	- // Standard macros
	- mitkClassMacroItkParent(CorrelationCalculator, itk::Object);
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /**
	- * @brief The ParcelMode enum defines how to define the correlation between two parcels
	- *
	- * Available choices are:
	- * <ol>
	- * <li> UseAverageTimeSeries - Average time series across the parcel, correlate average time series between parcels
	- * <li> UseMaximumCorrelation - Correlate all voxels of the parcels with each other, use maximum correlation
	- * <li> UseAverageCorrelation - Correlate all voxels of the parcels with each other, use average correlation
	- * </ol>
	- */
	- enum ParcelMode
	- {
	- UseAverageTimeSeries,
	- UseMaximumCorrelation,
	- UseAverageCorrelation
	- };
	-
	- /**
	- * @brief Calculate and return the pearson correlation coefficient for two vectors of data
	- *
	- * This function expects two vectors of the same length and data type and calculates the
	- * pearson correlation coefficient.
	- *
	- * @param one first data vector
	- * @param two second data vector
	- * @return pearson correlation coefficent
	- */
	- static double CalculatePearsonCorrelationCoefficient( const std::vector<T>& one, const std::vector<T>& two );
	-
	- /**
	- * @brief Calculates the covariance of two vectors of data
	- *
	- * Expects two vectors of the same length and data type and returns the covariance of the two.
	- * Variance can be calculated by providing the same data vector twice.
	- *
	- * @param one first data vector
	- * @param two second data vector
	- * @return covariance of the two
	- */
	- static double CalculateCovariance( const std::vector<T>& one, const std::vector<T>& two );
	-
	- /**
	- * @brief Extracts the average time series from a roi defined by the parcellation image
	- *
	- * This function requires a parcellation image and a time series image to be set and registered to each other.
	- * For each voxel in the time series image it will check whether it is inside the specified parcel of the
	- * parcellation image. All inside voxels will be averaged for all time steps and an average time series
	- * is returned.
	- *
	- * Calculates and saves the averages for all parcellations, to speed up consecutive calls.
	- *
	- * @param parcelValue the voxel value of the roi in the parcellation image.
	- * @return vector of the average values of the roi for each timestep
	- */
	- std::vector< double > ExtractAverageTimeSeriesOfParcel( int parcelValue );
	-
	- /**
	- * @brief Create a #voxel x #voxel correlation matrix
	- */
	- void DoWholeCorrelation();
	-
	- /**
	- * @brief Create a #parcel x #parcel correlation matrix
	- */
	- void DoParcelCorrelation( ParcelMode mode = UseAverageTimeSeries );
	-
	- /**
	- * @brief Marks average time series as invalid and calls superclass modified
	- */
	- virtual void Modified();
	-
	- const vnl_matrix< double >* GetCorrelationMatrix() const;
	- const std::map< unsigned int, int >* GetLabelOrderMap() const;
	- mitk::ConnectomicsNetwork::Pointer GetConnectomicsNetwork();
	-
	- // Get/Set macros
	- itkSetMacro(ParcellationImage, mitk::Image::Pointer)
	- itkSetMacro(TimeSeriesImage, mitk::Image::Pointer)
	-
	- protected:
	-
	- // intentionally not accessible, use our non-const Modified function instead
	- void Modified() const override;
	-
	- CorrelationCalculator();
	- ~CorrelationCalculator() override;
	-
	- template< typename TPixel, unsigned int VImageDimension >
	- void ExtractAllAverageTimeSeries( itk::Image< TPixel, VImageDimension>* itkTimeSeriesImage );
	-
	- void ExtractCenterOfMassForParcels();
	-
	-
	- double GetParcelCorrelation(const int& parcelA,const int& parcelB, ParcelMode& mode) const;
	-
	- // Member variables
	- bool m_InvalidTimeSeries;
	-
	- mitk::Image::Pointer m_ParcellationImage;
	- mitk::Image::Pointer m_TimeSeriesImage;
	-
	- std::map< int, std::vector<double> > m_AverageTimeSeries;
	- std::map< int, std::vector<std::vector< T > > > m_ParcelTimeSeries;
	-
	- std::map< int, mitk::Point3D > m_ParcelCenterOfMass;
	-
	- vnl_matrix< double > m_CorrelationMatrix;
	-
	- std::map< unsigned int, int > m_LabelOrderMap;
	- };
	-
	-}
	-
	-#include <mitkCorrelationCalculator.txx>
	-
	-#endif /* _MITK_CORRELATIONCALCULATOR_H */
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkCorrelationCalculator.txx b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkCorrelationCalculator.txx
	deleted file mode 100644
	index f5f6044a0d..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkCorrelationCalculator.txx
	+++ /dev/null
	@@ -1,454 +0,0 @@
	-
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_CORRELATIONCALCULATOR_TXX
	-#define _MITK_CORRELATIONCALCULATOR_TXX
	-
	-#include <algorithm>
	-#include <numeric>
	-#include <mitkLogMacros.h>
	-#include <mitkLog.h>
	-#include <mitkImageCast.h>
	-#include <mitkImageAccessByItk.h>
	-#include <mitkImagePixelReadAccessor.h>
	-
	-#include <itkImageRegionConstIteratorWithIndex.h>
	-
	-template< class T >
	-mitk::CorrelationCalculator<T>::CorrelationCalculator()
	- : m_InvalidTimeSeries( true )
	- , m_ParcellationImage( nullptr )
	- , m_TimeSeriesImage( nullptr )
	-{
	-}
	-
	-template< class T >
	-mitk::CorrelationCalculator<T>::~CorrelationCalculator()
	-{
	-}
	-
	-template< class T >
	-double mitk::CorrelationCalculator<T>::CalculatePearsonCorrelationCoefficient( const std::vector<T>& one, const std::vector<T>& two )
	-{
	- double standardDevOne( std::sqrt(CalculateCovariance( one, one )) );
	- double standardDevTwo( std::sqrt(CalculateCovariance( two, two )) );
	-
	- return CalculateCovariance(one, two) / (standardDevOne * standardDevTwo);
	-
	-}
	-
	-template< class T >
	-double mitk::CorrelationCalculator<T>::CalculateCovariance( const std::vector<T>& one, const std::vector<T>& two )
	-{
	- if( one.size() != two.size() )
	- {
	- MITK_WARN << "Expect two same length vectors for covariance.";
	- return 0;
	- }
	-
	- double meanOne( std::accumulate( one.begin(), one.end(), 0.0 ) / double(one.size()) );
	- double meanTwo( std::accumulate( two.begin(), two.end(), 0.0 ) / double(two.size()) );
	-
	- double sum( 0.0 );
	-
	- for(unsigned int index(0); index < one.size(); ++index)
	- {
	- sum += (one[index] - meanOne ) * (two[index] - meanTwo);
	- }
	-
	- double n( one.size() );
	-
	- return sum/n;
	-}
	-
	-template< class T >
	-std::vector< double > mitk::CorrelationCalculator<T>::ExtractAverageTimeSeriesOfParcel( int parcelValue )
	-{
	- if( this->m_InvalidTimeSeries)
	- {
	- this->ExtractAllAverageTimeSeries();
	- this->m_InvalidTimeSeries = false;
	- }
	-
	- std::vector< double > result;
	-
	- if( m_AverageTimeSeries.count(parcelValue) > 0 )
	- {
	- result = m_AverageTimeSeries.find(parcelValue)->second;
	- }
	-
	- return result;
	-}
	-
	-template< class T >
	-void mitk::CorrelationCalculator<T>::DoWholeCorrelation( )
	-{
	- if(this->m_TimeSeriesImage->GetDimension() != 4 )
	- {
	- MITK_ERROR << "Expect 3D+t timeseries image.";
	- return;
	- }
	- // calculate numbe of voxels
	- unsigned int numberOfVoxels(1);
	- unsigned int dim[3];
	- for(unsigned int loop(0); loop < 3; ++loop)
	- {
	- numberOfVoxels *= this->m_TimeSeriesImage->GetDimension( loop );
	- dim[loop] = this->m_TimeSeriesImage->GetDimension( loop );
	- }
	- m_CorrelationMatrix = vnl_matrix<double>(numberOfVoxels, numberOfVoxels);
	- unsigned int numberOfSteps( this->m_TimeSeriesImage->GetDimension( 3 ));
	-
	- //iterate over all voxels and calculate correlation
	- for( unsigned int i( 0 ); i < numberOfVoxels; ++i )
	- {
	- for( unsigned int j(0); j < i; ++j)
	- {
	- std::vector< T > one, two;
	- one.resize(numberOfSteps);
	- two.resize(numberOfSteps);
	-
	- mitk::ImagePixelReadAccessor<T, 4> readAccess(m_TimeSeriesImage);
	-
	- itk::Index<4> idx_i;
	- itk::Index<4> idx_j;
	-
	- idx_i[2] = (i / (dim[0] * dim[1])) % dim[2];
	- idx_i[1] = (i / dim[0]) % dim[1];
	- idx_i[0] = i % dim[0];
	-
	- idx_j[2] = (j / (dim[0] * dim[1])) % dim[2];
	- idx_j[1] = (j / dim[0]) % dim[1];
	- idx_j[0] = j % dim[0];
	-
	- for(unsigned int timestep(0); timestep < numberOfSteps; ++timestep)
	- {
	- idx_i[3] = timestep;
	- idx_j[3] = timestep;
	- one[timestep] = readAccess.GetPixelByIndex(idx_i);
	- two[timestep] = readAccess.GetPixelByIndex(idx_j);
	- }
	-
	- m_CorrelationMatrix[i][j] = mitk::CorrelationCalculator<T>::CalculatePearsonCorrelationCoefficient( one, two );
	- m_CorrelationMatrix[j][i] = m_CorrelationMatrix[i][j];
	- }
	- m_CorrelationMatrix[i][i] = 1;
	- }
	-}
	-
	-template< class T >
	-void mitk::CorrelationCalculator<T>::DoParcelCorrelation( typename mitk::CorrelationCalculator<T>::ParcelMode mode )
	-{
	- this->ExtractCenterOfMassForParcels();
	-
	- m_CorrelationMatrix = vnl_matrix<double>(m_ParcelCenterOfMass.size(), m_ParcelCenterOfMass.size());
	-
	-
	- AccessFixedDimensionByItk(this->m_TimeSeriesImage, ExtractAllAverageTimeSeries, 4);
	-
	- // fill matrix
	- unsigned int i(0);
	- for( std::map< int, std::vector<double> >::const_iterator it(m_AverageTimeSeries.begin()); it != m_AverageTimeSeries.end(); ++it, ++i)
	- {
	- unsigned int j(0);
	- for(std::map< int, std::vector<double> >::const_iterator inner_it(m_AverageTimeSeries.begin()); inner_it != it; ++inner_it, ++j)
	- {
	- switch( mode )
	- {
	- case UseAverageTimeSeries :
	- m_CorrelationMatrix[i][j] = mitk::CorrelationCalculator<double>::CalculatePearsonCorrelationCoefficient( it->second, inner_it->second );
	- break;
	- case UseMaximumCorrelation :
	- m_CorrelationMatrix[i][j] = mitk::CorrelationCalculator<T>::GetParcelCorrelation(it->first, inner_it->first, mode);
	- break;
	- case UseAverageCorrelation :
	- m_CorrelationMatrix[i][j] = mitk::CorrelationCalculator<T>::GetParcelCorrelation(it->first, inner_it->first, mode);
	- break;
	- default:
	- mitkThrow() << "No valid parcel correlation mode selected";
	- }
	- m_CorrelationMatrix[j][i] = m_CorrelationMatrix[i][j];
	- }
	-
	- m_CorrelationMatrix[i][i] = 1;
	- m_LabelOrderMap.insert(std::pair< unsigned int, int >(i, it->first));
	- }
	-}
	-
	-template< class T >
	-double mitk::CorrelationCalculator<T>::GetParcelCorrelation(const int& parcelA, const int& parcelB, typename mitk::CorrelationCalculator<T>::ParcelMode& mode) const
	-{
	- double result(0.0);
	-
	- if(m_ParcelTimeSeries.count(parcelA) < 1 \|\| m_ParcelTimeSeries.count(parcelB) < 1)
	- {
	- MITK_ERROR << "Tried to calculate correlation between at least one non-existent parcel " << parcelA << " and " << parcelB;
	- return result;
	- }
	- std::vector< std::vector< T > > parcelATimeSeriesVector = m_ParcelTimeSeries.find( parcelA )->second;
	- std::vector< std::vector< T > > parcelBTimeSeriesVector = m_ParcelTimeSeries.find( parcelB )->second;
	-
	- switch( mode )
	- {
	- case UseAverageTimeSeries :
	- {
	- mitkThrow() << "Wrong function called for this mode.";
	- break;
	- }
	- case UseMaximumCorrelation :
	- {
	- for(unsigned int i(0); i < parcelATimeSeriesVector.size(); ++i)
	- {
	- for(unsigned int j(0); j < parcelBTimeSeriesVector.size(); ++j)
	- {
	- double corr =
	- mitk::CorrelationCalculator<T>::CalculatePearsonCorrelationCoefficient(
	- parcelATimeSeriesVector[i], parcelBTimeSeriesVector[j]
	- );
	- if( corr > result )
	- {
	- result = corr;
	- }
	- }
	- }
	- break;
	- }
	- case UseAverageCorrelation :
	- {
	- double corr(0.0);
	- for(unsigned int i(0); i < parcelATimeSeriesVector.size(); ++i)
	- {
	- for(unsigned int j(0); j < parcelBTimeSeriesVector.size(); ++j)
	- {
	- corr +=
	- mitk::CorrelationCalculator<T>::CalculatePearsonCorrelationCoefficient(
	- parcelATimeSeriesVector[i], parcelBTimeSeriesVector[j]
	- );
	- }
	- }
	- result = corr / double( parcelATimeSeriesVector.size() * parcelBTimeSeriesVector.size() );
	- break;
	- }
	- default:
	- {
	- mitkThrow() << "No valid parcel correlation mode selected";
	- }
	- }
	-
	- return result;
	-}
	-
	-template< class T >
	-void mitk::CorrelationCalculator<T>::Modified( ) const
	-{
	- Superclass::Modified();
	-}
	-
	-template< class T >
	-void mitk::CorrelationCalculator<T>::Modified( )
	-{
	- Superclass::Modified();
	- this->m_InvalidTimeSeries = true;
	-}
	-
	-template< class T>
	-template< typename TPixel, unsigned int VImageDimension >
	-void mitk::CorrelationCalculator<T>::ExtractAllAverageTimeSeries( itk::Image<TPixel, VImageDimension>* itkTimeSeriesImage )
	-{
	- // storage contains for each parcel value a vector of length time steps,
	- // which manages the pixel value vectors for each time step
	- std::map< int, std::vector< std::vector< T > > > storage;
	-
	- itk::ImageRegionConstIteratorWithIndex< itk::Image<TPixel, VImageDimension> > it_itkTimeSeriesImage(
	- itkTimeSeriesImage, itkTimeSeriesImage->GetLargestPossibleRegion() );
	-
	- unsigned int timesteps( itkTimeSeriesImage->GetLargestPossibleRegion().GetSize()[3] );
	-
	- for( it_itkTimeSeriesImage.GoToBegin(); !it_itkTimeSeriesImage.IsAtEnd(); ++it_itkTimeSeriesImage )
	- {
	- itk::Index< 4 > itkIndex = it_itkTimeSeriesImage.GetIndex();
	- itk::Index< 3 > itkIndex3D;
	- for(unsigned int axis( 0 ); axis < 3; ++axis )
	- {
	- itkIndex3D.SetElement( axis, itkIndex.GetElement(axis) );
	- }
	-
	- mitk::Point3D tempPoint;
	-
	- m_TimeSeriesImage->GetGeometry()->IndexToWorld( itkIndex3D, tempPoint );
	- mitk::ImagePixelReadAccessor<int, 3> readAccess(m_ParcellationImage);
	- int value( std::floor( readAccess.GetPixelByWorldCoordinates( tempPoint ) + 0.5 ) );
	-
	- if(storage.count(value) == 0)
	- {
	- std::vector< std::vector< T > > temp;
	- temp.resize( timesteps );
	- storage.insert(std::pair< int, std::vector< std::vector< T > > >(value, temp));
	- }
	-
	- storage[value][ itkIndex.GetElement( 3 ) ].push_back( it_itkTimeSeriesImage.Value() );
	- }
	-
	- // store means
	- for( typename std::map< int, std::vector< std::vector< T > > >::iterator it = storage.begin(); it != storage.end(); ++it )
	- {
	- std::vector< double > means;
	- means.resize( timesteps );
	- for(unsigned int loop(0); loop < timesteps; ++loop)
	- {
	- means[loop] = std::accumulate( it->second[loop].begin(), it->second[loop].end(), 0.0 ) / double(it->second[loop].size());
	- }
	- m_AverageTimeSeries.insert( std::pair< int, std::vector< double > >(it->first, means) );
	-
	- // reorder the information in storage for m_ParcelTimeSeries
	- // time series of each voxel by their parcellation value
	- std::vector< std::vector< T > > vectorOfTimeSeriesVectors;
	- vectorOfTimeSeriesVectors.resize(it->second[0].size());
	- for(unsigned int loop(0); loop < vectorOfTimeSeriesVectors.size(); ++loop)
	- {
	- vectorOfTimeSeriesVectors[loop].resize(timesteps);
	- }
	-
	- for(unsigned int step(0); step < timesteps; ++step)
	- {
	- for(unsigned int number(0); number < vectorOfTimeSeriesVectors.size(); ++number)
	- {
	- vectorOfTimeSeriesVectors[number][step] = it->second[step][number];
	- }
	- }
	- m_ParcelTimeSeries.insert(std::pair< int, std::vector< std::vector< T > > >(it->first, vectorOfTimeSeriesVectors));
	- }
	-}
	-
	-template< class T >
	-void mitk::CorrelationCalculator<T>::ExtractCenterOfMassForParcels()
	-{
	- itk::Image< int, 3 >::Pointer itkParcelImage;
	- mitk::CastToItkImage( m_ParcellationImage, itkParcelImage );
	-
	- itk::ImageRegionConstIteratorWithIndex< itk::Image<int, 3> > it_itkParcelImage(
	- itkParcelImage, itkParcelImage->GetLargestPossibleRegion() );
	-
	- std::map< int, std::vector< mitk::Point3D > > storage;
	-
	- for( it_itkParcelImage.GoToBegin(); !it_itkParcelImage.IsAtEnd(); ++it_itkParcelImage )
	- {
	- mitk::Point3D tempPoint;
	-
	- m_ParcellationImage->GetGeometry()->IndexToWorld( it_itkParcelImage.GetIndex(), tempPoint );
	-
	- if( storage.count( it_itkParcelImage.Value() ) == 1 )
	- {
	- storage[ it_itkParcelImage.Value() ].push_back( tempPoint );
	- }
	- else
	- {
	- storage.insert( std::pair< int, std::vector< mitk::Point3D > >(
	- it_itkParcelImage.Value(), std::vector< mitk::Point3D >( 1, tempPoint ) ));
	- }
	- }
	-
	- for( std::map< int, std::vector< mitk::Point3D > >::iterator it( storage.begin() ); it != storage.end(); ++it )
	- {
	- itk::Vector< int, 3 > tempVector( 0 );
	-
	- for( unsigned int loop(0); loop < it->second.size(); ++loop)
	- {
	- for(unsigned int index(0); index < 3; ++index)
	- {
	- tempVector[index] = tempVector[index] + it->second[loop][index];
	- }
	- }
	-
	- mitk::Point3D tempPoint;
	-
	- for( unsigned int loop(0); loop < 3; ++loop )
	- {
	- tempPoint.SetElement(loop, tempVector.GetElement(loop) / it->second.size());
	- }
	-
	- m_ParcelCenterOfMass.insert( std::pair< int, mitk::Point3D >(it->first, tempPoint) );
	- }
	-}
	-
	-template< class T >
	-const vnl_matrix< double >* mitk::CorrelationCalculator<T>::GetCorrelationMatrix() const
	-{
	- return &m_CorrelationMatrix;
	-}
	-
	-template< class T >
	-const std::map< unsigned int, int >* mitk::CorrelationCalculator<T>::GetLabelOrderMap() const
	-{
	- return &m_LabelOrderMap;
	-}
	-
	-template< class T >
	-mitk::ConnectomicsNetwork::Pointer mitk::CorrelationCalculator<T>::GetConnectomicsNetwork()
	-{
	- mitk::ConnectomicsNetwork::NetworkType* boostGraph = new mitk::ConnectomicsNetwork::NetworkType;
	-
	- std::map< int, mitk::ConnectomicsNetwork::VertexDescriptorType > idToVertexMap;
	-
	- // fill nodes
	- unsigned int numberOfNodes( m_CorrelationMatrix.columns() );
	-
	- for(unsigned int loop(0); loop < numberOfNodes; ++loop )
	- {
	- idToVertexMap.insert( std::pair< int, mitk::ConnectomicsNetwork::VertexDescriptorType >(loop, boost::add_vertex( *boostGraph )) );
	- }
	-
	- if( m_ParcelCenterOfMass.size() > 0)
	- {
	- std::map< int, mitk::Point3D >::const_iterator it = m_ParcelCenterOfMass.begin();
	- for(unsigned int loop(0); (loop < numberOfNodes) && (it != m_ParcelCenterOfMass.end()); ++loop, ++it )
	- {
	- (*boostGraph)[ idToVertexMap[loop] ].id = idToVertexMap[loop];
	- (*boostGraph)[ idToVertexMap[loop] ].label = std::to_string( it->first );
	- (*boostGraph)[ idToVertexMap[loop] ].coordinates.resize(3);
	- for(unsigned int dimension(0); dimension < 3; ++dimension)
	- {
	- (*boostGraph)[ idToVertexMap[loop] ].coordinates[dimension] = it->second[dimension];
	- }
	- }
	- }
	-
	- //fill edges
	- for( unsigned int i(0); i < numberOfNodes; ++i)
	- {
	- for(unsigned int j(0); j < i; ++j)
	- {
	- mitk::ConnectomicsNetwork::VertexDescriptorType vertexA = idToVertexMap[i];
	- mitk::ConnectomicsNetwork::VertexDescriptorType vertexB = idToVertexMap[j];
	- boost::add_edge( vertexA, vertexB, *boostGraph );
	- (boostGraph)[ boost::edge(vertexA, vertexB, boostGraph ).first ].sourceId = (*boostGraph)[vertexA].id;
	- (boostGraph)[ boost::edge(vertexA, vertexB, boostGraph ).first ].targetId = (*boostGraph)[vertexB].id;
	- (boostGraph)[ boost::edge(vertexA, vertexB, boostGraph ).first ].fiber_count = 1;
	- (boostGraph)[ boost::edge(vertexA, vertexB, boostGraph ).first ].edge_weight = m_CorrelationMatrix[i][j];
	- }
	- }
	-
	- // create data node
	- mitk::ConnectomicsNetwork::Pointer network = mitk::ConnectomicsNetwork::New();
	- network->SetBoostGraph( boostGraph );
	- network->SetGeometry( dynamic_cast<mitk::BaseGeometry*>(m_TimeSeriesImage->GetGeometry()->Clone().GetPointer()) );
	- network->UpdateBounds();
	- network->SetIsModified( true );
	- return network;
	-}
	-
	-#endif /* _MITK_CORRELATIONCALCULATOR_TXX */
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkFreeSurferParcellationTranslator.cpp b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkFreeSurferParcellationTranslator.cpp
	deleted file mode 100644
	index 68b7e3656c..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkFreeSurferParcellationTranslator.cpp
	+++ /dev/null
	@@ -1,3919 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkLookupTableProperty.h>
	-#include <mitkRenderingModeProperty.h>
	-#include <mitkTransferFunctionProperty.h>
	-#include "mitkFreeSurferParcellationTranslator.h"
	-
	-using namespace mitk;
	-
	-/########### Static Members ###########/
	-LookupTable::Pointer FreeSurferParcellationTranslator::m_LookupTable = FreeSurferParcellationTranslator::CreateLookupTable();
	-const FreeSurferParcellationTranslator::NameTable FreeSurferParcellationTranslator::m_NameTable = FreeSurferParcellationTranslator::CreateNameTable();
	-TransferFunction::Pointer FreeSurferParcellationTranslator::m_TransferFunction = FreeSurferParcellationTranslator::CreateTransferFunction();
	-
	-
	-/########### Constructors ###########/
	-FreeSurferParcellationTranslator::FreeSurferParcellationTranslator()
	-{
	-}
	-FreeSurferParcellationTranslator::~FreeSurferParcellationTranslator()
	-{
	-}
	-
	-
	-/########### Methods ###########/
	-// Assign the lookup table to the given node
	-void FreeSurferParcellationTranslator::AssignLookupTable(DataNode::Pointer node) const
	-{
	- LookupTableProperty::Pointer lookupTableProp = LookupTableProperty::New( this->GetLookupTable() );
	- node->SetProperty( "LookupTable", lookupTableProp );
	-}
	-// Assign the color transfer function to the given node
	-void FreeSurferParcellationTranslator::AssignTransferFunction(DataNode::Pointer node) const
	-{
	- TransferFunctionProperty::Pointer transferFunctionProp = TransferFunctionProperty::New( this->GetTransferFunction() );
	- node->SetProperty( "Image Rendering.Transfer Function", transferFunctionProp );
	-}
	-// Get the label assigned to the given name
	-const std::string FreeSurferParcellationTranslator::GetLabel(const std::string& name) const
	-{
	- NameTable::const_iterator iter;
	- for( iter = m_NameTable.begin(); iter != m_NameTable.end(); ++iter )
	- {
	- if( iter->second == name )
	- return iter->first;
	- }
	- return "0";
	-}
	-// Get the label assigned to the given name as integer
	-int FreeSurferParcellationTranslator::GetLabelAsNumber(const std::string &name) const
	-{
	- return std::atoi(this->GetLabel( name ).c_str()) ;
	-}
	-// Return the lookup table
	-LookupTable::Pointer FreeSurferParcellationTranslator::GetLookupTable() const
	-{
	- return m_LookupTable;
	-}
	-// Get the name assigned to the given label
	-const std::string FreeSurferParcellationTranslator::GetName(const std::string & label) const
	-{
	- auto endIter = this->m_NameTable.end();
	- auto iter = this->m_NameTable.find( label );
	- if( iter != endIter )
	- {
	- return iter->second;
	- }
	- else
	- {
	- return "Unknown area or outside the cerebrum.";
	- }
	-}
	-// Get the name assigned to the given label
	-const std::string FreeSurferParcellationTranslator::GetName(int label) const
	-{
	- std::stringstream ss;//create a stringstream
	- ss << label;//add number to the stream
	- return this->GetName( ss.str() );
	-}
	-// Get the transfer function
	-TransferFunction::Pointer FreeSurferParcellationTranslator::GetTransferFunction() const
	-{
	- return m_TransferFunction;
	-}
	-
	-LookupTable::Pointer FreeSurferParcellationTranslator::CreateLookupTable()
	-{
	- vtkSmartPointer<vtkLookupTable> table = vtkSmartPointer<vtkLookupTable>::New();
	- table->SetRange(0.0, 14175.0);
	- table->SetNumberOfTableValues( 14176.0 ); // Count of the overall range (0 - 14175)
	- table->Build();
	- table->SetTableValue( 0.0, 0, 0, 0, 0);
	- table->SetTableValue( 1.0, 0.27451, 0.509804, 0.705882 );
	- table->SetTableValue( 2.0, 0.960784, 0.960784, 0.960784 );
	- table->SetTableValue( 3.0, 0.803922, 0.243137, 0.305882 );
	- table->SetTableValue( 4.0, 0.470588, 0.0705882, 0.52549 );
	- table->SetTableValue( 5.0, 0.768627, 0.227451, 0.980392 );
	- table->SetTableValue( 6.0, 0, 0.580392, 0 );
	- table->SetTableValue( 7.0, 0.862745, 0.972549, 0.643137 );
	- table->SetTableValue( 8.0, 0.901961, 0.580392, 0.133333 );
	- table->SetTableValue( 9.0, 0, 0.462745, 0.054902 );
	- table->SetTableValue( 10.0, 0, 0.462745, 0.054902 );
	- table->SetTableValue( 11.0, 0.478431, 0.729412, 0.862745 );
	- table->SetTableValue( 12.0, 0.92549, 0.0509804, 0.690196 );
	- table->SetTableValue( 13.0, 0.0470588, 0.188235, 1 );
	- table->SetTableValue( 14.0, 0.8, 0.713725, 0.556863 );
	- table->SetTableValue( 15.0, 0.164706, 0.8, 0.643137 );
	- table->SetTableValue( 16.0, 0.466667, 0.623529, 0.690196 );
	- table->SetTableValue( 17.0, 0.862745, 0.847059, 0.0784314 );
	- table->SetTableValue( 18.0, 0.403922, 1, 1 );
	- table->SetTableValue( 19.0, 0.313725, 0.768627, 0.384314 );
	- table->SetTableValue( 20.0, 0.235294, 0.227451, 0.823529 );
	- table->SetTableValue( 21.0, 0.235294, 0.227451, 0.823529 );
	- table->SetTableValue( 22.0, 0.235294, 0.227451, 0.823529 );
	- table->SetTableValue( 23.0, 0.235294, 0.227451, 0.823529 );
	- table->SetTableValue( 24.0, 0.235294, 0.235294, 0.235294 );
	- table->SetTableValue( 25.0, 1, 0.647059, 0 );
	- table->SetTableValue( 26.0, 1, 0.647059, 0 );
	- table->SetTableValue( 27.0, 0, 1, 0.498039 );
	- table->SetTableValue( 28.0, 0.647059, 0.164706, 0.164706 );
	- table->SetTableValue( 29.0, 0.529412, 0.807843, 0.921569 );
	- table->SetTableValue( 30.0, 0.627451, 0.12549, 0.941176 );
	- table->SetTableValue( 31.0, 0, 0.784314, 0.784314 );
	- table->SetTableValue( 32.0, 0.392157, 0.196078, 0.392157 );
	- table->SetTableValue( 33.0, 0.529412, 0.196078, 0.290196 );
	- table->SetTableValue( 34.0, 0.478431, 0.529412, 0.196078 );
	- table->SetTableValue( 35.0, 0.2, 0.196078, 0.529412 );
	- table->SetTableValue( 36.0, 0.290196, 0.607843, 0.235294 );
	- table->SetTableValue( 37.0, 0.470588, 0.243137, 0.168627 );
	- table->SetTableValue( 38.0, 0.290196, 0.607843, 0.235294 );
	- table->SetTableValue( 39.0, 0.478431, 0.529412, 0.196078 );
	- table->SetTableValue( 40.0, 0.27451, 0.509804, 0.705882 );
	- table->SetTableValue( 41.0, 0, 0.882353, 0 );
	- table->SetTableValue( 42.0, 0.803922, 0.243137, 0.305882 );
	- table->SetTableValue( 43.0, 0.470588, 0.0705882, 0.52549 );
	- table->SetTableValue( 44.0, 0.768627, 0.227451, 0.980392 );
	- table->SetTableValue( 45.0, 0, 0.580392, 0 );
	- table->SetTableValue( 46.0, 0.862745, 0.972549, 0.643137 );
	- table->SetTableValue( 47.0, 0.901961, 0.580392, 0.133333 );
	- table->SetTableValue( 48.0, 0, 0.462745, 0.054902 );
	- table->SetTableValue( 49.0, 0, 0.462745, 0.054902 );
	- table->SetTableValue( 50.0, 0.478431, 0.729412, 0.862745 );
	- table->SetTableValue( 51.0, 0.92549, 0.0509804, 0.690196 );
	- table->SetTableValue( 52.0, 0.0509804, 0.188235, 1 );
	- table->SetTableValue( 53.0, 0.862745, 0.847059, 0.0784314 );
	- table->SetTableValue( 54.0, 0.403922, 1, 1 );
	- table->SetTableValue( 55.0, 0.313725, 0.768627, 0.384314 );
	- table->SetTableValue( 56.0, 0.235294, 0.227451, 0.823529 );
	- table->SetTableValue( 57.0, 1, 0.647059, 0 );
	- table->SetTableValue( 58.0, 1, 0.647059, 0 );
	- table->SetTableValue( 59.0, 0, 1, 0.498039 );
	- table->SetTableValue( 60.0, 0.647059, 0.164706, 0.164706 );
	- table->SetTableValue( 61.0, 0.529412, 0.807843, 0.921569 );
	- table->SetTableValue( 62.0, 0.627451, 0.12549, 0.941176 );
	- table->SetTableValue( 63.0, 0, 0.784314, 0.866667 );
	- table->SetTableValue( 64.0, 0.392157, 0.196078, 0.392157 );
	- table->SetTableValue( 65.0, 0.529412, 0.196078, 0.290196 );
	- table->SetTableValue( 66.0, 0.478431, 0.529412, 0.196078 );
	- table->SetTableValue( 67.0, 0.2, 0.196078, 0.529412 );
	- table->SetTableValue( 68.0, 0.290196, 0.607843, 0.235294 );
	- table->SetTableValue( 69.0, 0.470588, 0.243137, 0.168627 );
	- table->SetTableValue( 70.0, 0.290196, 0.607843, 0.235294 );
	- table->SetTableValue( 71.0, 0.478431, 0.529412, 0.196078 );
	- table->SetTableValue( 72.0, 0.470588, 0.745098, 0.588235 );
	- table->SetTableValue( 73.0, 0.478431, 0.529412, 0.196078 );
	- table->SetTableValue( 74.0, 0.478431, 0.529412, 0.196078 );
	- table->SetTableValue( 77.0, 0.784314, 0.27451, 1 );
	- table->SetTableValue( 78.0, 1, 0.580392, 0.0392157 );
	- table->SetTableValue( 79.0, 1, 0.580392, 0.0392157 );
	- table->SetTableValue( 80.0, 0.643137, 0.423529, 0.886275 );
	- table->SetTableValue( 81.0, 0.643137, 0.423529, 0.886275 );
	- table->SetTableValue( 82.0, 0.643137, 0.423529, 0.886275 );
	- table->SetTableValue( 83.0, 1, 0.854902, 0.72549 );
	- table->SetTableValue( 84.0, 1, 0.854902, 0.72549 );
	- table->SetTableValue( 85.0, 0.917647, 0.662745, 0.117647 );
	- table->SetTableValue( 192.0, 0.980392, 1, 0.196078 );
	- table->SetTableValue( 86.0, 0.784314, 0.470588, 1 );
	- table->SetTableValue( 87.0, 0.784314, 0.47451, 1 );
	- table->SetTableValue( 88.0, 0.784314, 0.478431, 1 );
	- table->SetTableValue( 96.0, 0.803922, 0.0392157, 0.490196 );
	- table->SetTableValue( 97.0, 0.803922, 0.0392157, 0.490196 );
	- table->SetTableValue( 98.0, 0.627451, 0.12549, 0.941176 );
	- table->SetTableValue( 100.0, 0.486275, 0.54902, 0.698039 );
	- table->SetTableValue( 101.0, 0.490196, 0.54902, 0.698039 );
	- table->SetTableValue( 102.0, 0.494118, 0.54902, 0.698039 );
	- table->SetTableValue( 103.0, 0.498039, 0.54902, 0.698039 );
	- table->SetTableValue( 104.0, 0.486275, 0.552941, 0.698039 );
	- table->SetTableValue( 105.0, 0.486275, 0.556863, 0.698039 );
	- table->SetTableValue( 106.0, 0.486275, 0.560784, 0.698039 );
	- table->SetTableValue( 107.0, 0.486275, 0.564706, 0.698039 );
	- table->SetTableValue( 108.0, 0.486275, 0.54902, 0.701961 );
	- table->SetTableValue( 109.0, 0.486275, 0.54902, 0.698039 );
	- table->SetTableValue( 110.0, 0.490196, 0.54902, 0.698039 );
	- table->SetTableValue( 111.0, 0.494118, 0.54902, 0.698039 );
	- table->SetTableValue( 112.0, 0.498039, 0.54902, 0.698039 );
	- table->SetTableValue( 113.0, 0.486275, 0.552941, 0.698039 );
	- table->SetTableValue( 114.0, 0.486275, 0.556863, 0.698039 );
	- table->SetTableValue( 115.0, 0.486275, 0.560784, 0.698039 );
	- table->SetTableValue( 116.0, 0.486275, 0.564706, 0.698039 );
	- table->SetTableValue( 117.0, 0.486275, 0.54902, 0.701961 );
	- table->SetTableValue( 118.0, 1, 0.0784314, 0.576471 );
	- table->SetTableValue( 119.0, 0.803922, 0.701961, 0.545098 );
	- table->SetTableValue( 120.0, 0.933333, 0.933333, 0.819608 );
	- table->SetTableValue( 121.0, 0.784314, 0.784314, 0.784314 );
	- table->SetTableValue( 122.0, 0.290196, 1, 0.290196 );
	- table->SetTableValue( 123.0, 0.933333, 0, 0 );
	- table->SetTableValue( 124.0, 0, 0, 0.545098 );
	- table->SetTableValue( 125.0, 0.678431, 1, 0.184314 );
	- table->SetTableValue( 126.0, 0.521569, 0.796078, 0.898039 );
	- table->SetTableValue( 127.0, 0.101961, 0.929412, 0.223529 );
	- table->SetTableValue( 128.0, 0.133333, 0.545098, 0.133333 );
	- table->SetTableValue( 129.0, 0.117647, 0.564706, 1 );
	- table->SetTableValue( 130.0, 0.576471, 0.0745098, 0.678431 );
	- table->SetTableValue( 131.0, 0.933333, 0.231373, 0.231373 );
	- table->SetTableValue( 132.0, 0.866667, 0.152941, 0.784314 );
	- table->SetTableValue( 133.0, 0.933333, 0.682353, 0.933333 );
	- table->SetTableValue( 134.0, 1, 0, 0 );
	- table->SetTableValue( 135.0, 0.282353, 0.239216, 0.545098 );
	- table->SetTableValue( 136.0, 0.0823529, 0.152941, 0.517647 );
	- table->SetTableValue( 137.0, 0.0823529, 0.152941, 0.517647 );
	- table->SetTableValue( 138.0, 0.254902, 0.529412, 0.0784314 );
	- table->SetTableValue( 139.0, 0.254902, 0.529412, 0.0784314 );
	- table->SetTableValue( 140.0, 0.52549, 0.0156863, 0.627451 );
	- table->SetTableValue( 142.0, 0.866667, 0.886275, 0.266667 );
	- table->SetTableValue( 143.0, 1, 1, 0.996078 );
	- table->SetTableValue( 144.0, 0.203922, 0.819608, 0.886275 );
	- table->SetTableValue( 145.0, 0.937255, 0.627451, 0.87451 );
	- table->SetTableValue( 146.0, 0.27451, 0.509804, 0.705882 );
	- table->SetTableValue( 147.0, 0.27451, 0.509804, 0.709804 );
	- table->SetTableValue( 148.0, 0.545098, 0.47451, 0.368627 );
	- table->SetTableValue( 149.0, 0.878431, 0.878431, 0.878431 );
	- table->SetTableValue( 150.0, 1, 0, 0 );
	- table->SetTableValue( 151.0, 0.803922, 0.803922, 0 );
	- table->SetTableValue( 152.0, 0.933333, 0.933333, 0.819608 );
	- table->SetTableValue( 153.0, 0.545098, 0.47451, 0.368627 );
	- table->SetTableValue( 154.0, 0.933333, 0.231373, 0.231373 );
	- table->SetTableValue( 155.0, 0.933333, 0.231373, 0.231373 );
	- table->SetTableValue( 156.0, 0.933333, 0.231373, 0.231373 );
	- table->SetTableValue( 157.0, 0.243137, 0.0392157, 0.803922 );
	- table->SetTableValue( 158.0, 0.243137, 0.0392157, 0.803922 );
	- table->SetTableValue( 159.0, 0, 0.462745, 0.054902 );
	- table->SetTableValue( 160.0, 0, 0.462745, 0.054902 );
	- table->SetTableValue( 161.0, 0.862745, 0.847059, 0.0823529 );
	- table->SetTableValue( 162.0, 0.862745, 0.847059, 0.0823529 );
	- table->SetTableValue( 163.0, 0.478431, 0.729412, 0.862745 );
	- table->SetTableValue( 164.0, 0.478431, 0.729412, 0.862745 );
	- table->SetTableValue( 165.0, 1, 0.647059, 0 );
	- table->SetTableValue( 166.0, 0.054902, 0.188235, 1 );
	- table->SetTableValue( 167.0, 0.65098, 0.164706, 0.164706 );
	- table->SetTableValue( 168.0, 0.47451, 0.0705882, 0.52549 );
	- table->SetTableValue( 169.0, 0.92549, 0.0509804, 0.498039 );
	- table->SetTableValue( 176.0, 0.92549, 0.0509804, 0.494118 );
	- table->SetTableValue( 170.0, 0.466667, 0.623529, 0.690196 );
	- table->SetTableValue( 171.0, 0.466667, 0, 0.690196 );
	- table->SetTableValue( 172.0, 0.466667, 0.392157, 0.690196 );
	- table->SetTableValue( 173.0, 0.466667, 0.784314, 0.690196 );
	- table->SetTableValue( 174.0, 0.466667, 0.623529, 0.392157 );
	- table->SetTableValue( 175.0, 0.466667, 0.623529, 0.784314 );
	- table->SetTableValue( 180.0, 0.286275, 0.239216, 0.545098 );
	- table->SetTableValue( 181.0, 0.286275, 0.243137, 0.545098 );
	- table->SetTableValue( 193.0, 0, 0.768627, 1 );
	- table->SetTableValue( 194.0, 1, 0.643137, 0.643137 );
	- table->SetTableValue( 195.0, 0.768627, 0.768627, 0 );
	- table->SetTableValue( 196.0, 0, 0.392157, 1 );
	- table->SetTableValue( 197.0, 0.501961, 0.768627, 0.643137 );
	- table->SetTableValue( 198.0, 0, 0.494118, 0.294118 );
	- table->SetTableValue( 199.0, 0.501961, 0.376471, 0.25098 );
	- table->SetTableValue( 200.0, 0, 0.196078, 0.501961 );
	- table->SetTableValue( 201.0, 1, 0.8, 0.6 );
	- table->SetTableValue( 202.0, 1, 0.501961, 0.501961 );
	- table->SetTableValue( 203.0, 1, 1, 0 );
	- table->SetTableValue( 204.0, 0.25098, 0, 0.25098 );
	- table->SetTableValue( 205.0, 0, 0, 1 );
	- table->SetTableValue( 206.0, 1, 0, 0 );
	- table->SetTableValue( 207.0, 0.501961, 0.501961, 1 );
	- table->SetTableValue( 208.0, 0, 0.501961, 0 );
	- table->SetTableValue( 209.0, 0.768627, 0.627451, 0.501961 );
	- table->SetTableValue( 210.0, 0.12549, 0.784314, 1 );
	- table->SetTableValue( 211.0, 0.501961, 1, 0.501961 );
	- table->SetTableValue( 212.0, 0.8, 0.6, 0.8 );
	- table->SetTableValue( 213.0, 0.47451, 0.0666667, 0.533333 );
	- table->SetTableValue( 214.0, 0.501961, 0, 0 );
	- table->SetTableValue( 215.0, 0.501961, 0.12549, 1 );
	- table->SetTableValue( 216.0, 1, 0.8, 0.4 );
	- table->SetTableValue( 217.0, 0.501961, 0.501961, 0.501961 );
	- table->SetTableValue( 218.0, 0.407843, 1, 1 );
	- table->SetTableValue( 219.0, 0, 0.886275, 0 );
	- table->SetTableValue( 220.0, 0.803922, 0.247059, 0.305882 );
	- table->SetTableValue( 221.0, 0.772549, 0.227451, 0.980392 );
	- table->SetTableValue( 222.0, 0.129412, 0.588235, 0.980392 );
	- table->SetTableValue( 223.0, 0.886275, 0, 0 );
	- table->SetTableValue( 224.0, 0.392157, 0.392157, 0.392157 );
	- table->SetTableValue( 225.0, 0.772549, 0.588235, 0.980392 );
	- table->SetTableValue( 226.0, 0.666667, 0.666667, 1 );
	- table->SetTableValue( 250.0, 1, 0, 0 );
	- table->SetTableValue( 251.0, 0, 0, 0.25098 );
	- table->SetTableValue( 252.0, 0, 0, 0.439216 );
	- table->SetTableValue( 253.0, 0, 0, 0.627451 );
	- table->SetTableValue( 254.0, 0, 0, 0.815686 );
	- table->SetTableValue( 255.0, 0, 0, 1 );
	- table->SetTableValue( 256.0, 0, 0, 0, 0);
	- table->SetTableValue( 331.0, 1, 0, 0 );
	- table->SetTableValue( 332.0, 1, 0.313725, 0 );
	- table->SetTableValue( 333.0, 1, 0.627451, 0 );
	- table->SetTableValue( 334.0, 1, 1, 0 );
	- table->SetTableValue( 335.0, 0, 1, 0 );
	- table->SetTableValue( 336.0, 1, 0, 0.627451 );
	- table->SetTableValue( 337.0, 1, 0, 1 );
	- table->SetTableValue( 338.0, 1, 0.196078, 0.313725 );
	- table->SetTableValue( 339.0, 0.313725, 1, 0.196078 );
	- table->SetTableValue( 340.0, 0.627451, 1, 0.196078 );
	- table->SetTableValue( 341.0, 0.627451, 0.784314, 1 );
	- table->SetTableValue( 342.0, 0, 1, 0.627451 );
	- table->SetTableValue( 343.0, 0, 0, 1 );
	- table->SetTableValue( 344.0, 0.313725, 0.196078, 1 );
	- table->SetTableValue( 345.0, 0.627451, 0, 1 );
	- table->SetTableValue( 346.0, 1, 0.823529, 0 );
	- table->SetTableValue( 347.0, 0, 0.627451, 1 );
	- table->SetTableValue( 348.0, 1, 0.784314, 0.313725 );
	- table->SetTableValue( 349.0, 1, 0.784314, 0.627451 );
	- table->SetTableValue( 350.0, 1, 0.313725, 0.784314 );
	- table->SetTableValue( 351.0, 1, 0.627451, 0.784314 );
	- table->SetTableValue( 352.0, 0.117647, 1, 0.313725 );
	- table->SetTableValue( 353.0, 0.313725, 0.784314, 1 );
	- table->SetTableValue( 354.0, 0.313725, 1, 0.784314 );
	- table->SetTableValue( 355.0, 0.764706, 1, 0.784314 );
	- table->SetTableValue( 356.0, 0.470588, 0.784314, 0.0784314 );
	- table->SetTableValue( 357.0, 0.666667, 0.0392157, 0.784314 );
	- table->SetTableValue( 358.0, 0.0784314, 0.509804, 0.705882 );
	- table->SetTableValue( 359.0, 0.0784314, 0.705882, 0.509804 );
	- table->SetTableValue( 400.0, 0.807843, 0.243137, 0.305882 );
	- table->SetTableValue( 401.0, 0.47451, 0.0705882, 0.52549 );
	- table->SetTableValue( 402.0, 0.780392, 0.227451, 0.980392 );
	- table->SetTableValue( 403.0, 0.00392157, 0.580392, 0 );
	- table->SetTableValue( 404.0, 0.866667, 0.972549, 0.643137 );
	- table->SetTableValue( 405.0, 0.905882, 0.580392, 0.133333 );
	- table->SetTableValue( 406.0, 0.00392157, 0.462745, 0.054902 );
	- table->SetTableValue( 407.0, 0.470588, 0.462745, 0.054902 );
	- table->SetTableValue( 408.0, 0.482353, 0.729412, 0.866667 );
	- table->SetTableValue( 409.0, 0.933333, 0.0509804, 0.694118 );
	- table->SetTableValue( 410.0, 0.482353, 0.729412, 0.862745 );
	- table->SetTableValue( 411.0, 0.541176, 0.0509804, 0.807843 );
	- table->SetTableValue( 412.0, 0.933333, 0.509804, 0.690196 );
	- table->SetTableValue( 413.0, 0.854902, 0.901961, 0.298039 );
	- table->SetTableValue( 414.0, 0.14902, 0.835294, 0.690196 );
	- table->SetTableValue( 415.0, 0.00392157, 0.882353, 0.690196 );
	- table->SetTableValue( 416.0, 0.00392157, 0.882353, 0.690196 );
	- table->SetTableValue( 417.0, 0.784314, 0.00784314, 0.392157 );
	- table->SetTableValue( 418.0, 0.784314, 0.00784314, 0.392157 );
	- table->SetTableValue( 419.0, 0.0196078, 0.784314, 0.352941 );
	- table->SetTableValue( 420.0, 0.0196078, 0.784314, 0.352941 );
	- table->SetTableValue( 421.0, 0.392157, 0.0196078, 0.784314 );
	- table->SetTableValue( 422.0, 0.0980392, 1, 0.392157 );
	- table->SetTableValue( 423.0, 0.0980392, 1, 0.392157 );
	- table->SetTableValue( 424.0, 0.901961, 0.027451, 0.392157 );
	- table->SetTableValue( 425.0, 0.901961, 0.027451, 0.392157 );
	- table->SetTableValue( 426.0, 0.392157, 0.0196078, 0.784314 );
	- table->SetTableValue( 427.0, 0.588235, 0.0392157, 0.784314 );
	- table->SetTableValue( 428.0, 0.588235, 0.0392157, 0.784314 );
	- table->SetTableValue( 429.0, 0.686275, 0.0392157, 0.690196 );
	- table->SetTableValue( 430.0, 0.686275, 0.0392157, 0.690196 );
	- table->SetTableValue( 431.0, 0.0392157, 0.392157, 1 );
	- table->SetTableValue( 432.0, 0.0392157, 0.392157, 1 );
	- table->SetTableValue( 433.0, 0.588235, 0.176471, 0.27451 );
	- table->SetTableValue( 434.0, 0.588235, 0.176471, 0.27451 );
	- table->SetTableValue( 435.0, 0.176471, 0.784314, 0.0588235 );
	- table->SetTableValue( 436.0, 0.176471, 0.784314, 0.0588235 );
	- table->SetTableValue( 437.0, 0.890196, 0.176471, 0.392157 );
	- table->SetTableValue( 438.0, 0.890196, 0.176471, 0.392157 );
	- table->SetTableValue( 439.0, 0.890196, 0.176471, 0.392157 );
	- table->SetTableValue( 498.0, 0.560784, 0.737255, 0.560784 );
	- table->SetTableValue( 499.0, 1, 0.972549, 0.862745 );
	- table->SetTableValue( 500.0, 0.0666667, 0.333333, 0.533333 );
	- table->SetTableValue( 501.0, 0.466667, 0.733333, 0.4 );
	- table->SetTableValue( 502.0, 0.8, 0.266667, 0.133333 );
	- table->SetTableValue( 503.0, 0.8, 0, 1 );
	- table->SetTableValue( 504.0, 0.866667, 0.733333, 0.0666667 );
	- table->SetTableValue( 505.0, 0.6, 0.866667, 0.933333 );
	- table->SetTableValue( 506.0, 0.2, 0.0666667, 0.0666667 );
	- table->SetTableValue( 507.0, 0, 0.466667, 0.333333 );
	- table->SetTableValue( 508.0, 0.0784314, 0.392157, 0.784314 );
	- table->SetTableValue( 550.0, 0.0666667, 0.333333, 0.537255 );
	- table->SetTableValue( 551.0, 0.466667, 0.733333, 0.403922 );
	- table->SetTableValue( 552.0, 0.8, 0.266667, 0.137255 );
	- table->SetTableValue( 553.0, 0.8, 0, 0.996078 );
	- table->SetTableValue( 554.0, 0.866667, 0.733333, 0.0627451 );
	- table->SetTableValue( 555.0, 0.6, 0.866667, 0.937255 );
	- table->SetTableValue( 556.0, 0.2, 0.0666667, 0.0705882 );
	- table->SetTableValue( 557.0, 0, 0.466667, 0.337255 );
	- table->SetTableValue( 558.0, 0.0784314, 0.392157, 0.788235 );
	- table->SetTableValue( 600.0, 0.996078, 0.996078, 0.996078 );
	- table->SetTableValue( 601.0, 0.27451, 0.509804, 0.705882 );
	- table->SetTableValue( 602.0, 0.960784, 0.960784, 0.960784 );
	- table->SetTableValue( 603.0, 0.803922, 0.243137, 0.305882 );
	- table->SetTableValue( 604.0, 0.470588, 0.0705882, 0.52549 );
	- table->SetTableValue( 605.0, 0.768627, 0.227451, 0.980392 );
	- table->SetTableValue( 606.0, 0, 0.580392, 0 );
	- table->SetTableValue( 607.0, 0.862745, 0.972549, 0.643137 );
	- table->SetTableValue( 608.0, 0.901961, 0.580392, 0.133333 );
	- table->SetTableValue( 609.0, 0, 0.462745, 0.054902 );
	- table->SetTableValue( 610.0, 0, 0.462745, 0.054902 );
	- table->SetTableValue( 611.0, 0.478431, 0.729412, 0.862745 );
	- table->SetTableValue( 612.0, 0.92549, 0.0509804, 0.690196 );
	- table->SetTableValue( 613.0, 0.0470588, 0.188235, 1 );
	- table->SetTableValue( 614.0, 0.8, 0.713725, 0.556863 );
	- table->SetTableValue( 615.0, 0.164706, 0.8, 0.643137 );
	- table->SetTableValue( 616.0, 0.466667, 0.623529, 0.690196 );
	- table->SetTableValue( 617.0, 0.862745, 0.847059, 0.0784314 );
	- table->SetTableValue( 618.0, 0.403922, 1, 1 );
	- table->SetTableValue( 619.0, 0.313725, 0.768627, 0.384314 );
	- table->SetTableValue( 620.0, 0.235294, 0.227451, 0.823529 );
	- table->SetTableValue( 621.0, 0.235294, 0.227451, 0.823529 );
	- table->SetTableValue( 622.0, 0.235294, 0.227451, 0.823529 );
	- table->SetTableValue( 623.0, 0.235294, 0.227451, 0.823529 );
	- table->SetTableValue( 624.0, 0.235294, 0.235294, 0.235294 );
	- table->SetTableValue( 625.0, 1, 0.647059, 0 );
	- table->SetTableValue( 626.0, 1, 0.647059, 0 );
	- table->SetTableValue( 627.0, 0, 1, 0.498039 );
	- table->SetTableValue( 628.0, 0.647059, 0.164706, 0.164706 );
	- table->SetTableValue( 640.0, 0.8, 0, 0 );
	- table->SetTableValue( 641.0, 1, 0, 0 );
	- table->SetTableValue( 642.0, 0, 0, 1 );
	- table->SetTableValue( 643.0, 0.117647, 0.564706, 1 );
	- table->SetTableValue( 644.0, 0.392157, 0.831373, 0.929412 );
	- table->SetTableValue( 645.0, 0.854902, 0.647059, 0.12549 );
	- table->SetTableValue( 646.0, 1, 0.843137, 0 );
	- table->SetTableValue( 647.0, 1, 1, 0.65098 );
	- table->SetTableValue( 648.0, 0.6, 0, 0.8 );
	- table->SetTableValue( 649.0, 0.6, 0.552941, 0.819608 );
	- table->SetTableValue( 650.0, 0.8, 0.8, 1 );
	- table->SetTableValue( 651.0, 0.121569, 0.831373, 0.760784 );
	- table->SetTableValue( 652.0, 0.0117647, 1, 0.929412 );
	- table->SetTableValue( 653.0, 0.8, 1, 1 );
	- table->SetTableValue( 654.0, 0.337255, 0.290196, 0.576471 );
	- table->SetTableValue( 655.0, 0.447059, 0.447059, 0.745098 );
	- table->SetTableValue( 656.0, 0.721569, 0.698039, 1 );
	- table->SetTableValue( 657.0, 0.494118, 0.541176, 0.145098 );
	- table->SetTableValue( 658.0, 0.741176, 0.772549, 0.458824 );
	- table->SetTableValue( 659.0, 0.941176, 0.901961, 0.54902 );
	- table->SetTableValue( 660.0, 0.8, 0, 0 );
	- table->SetTableValue( 661.0, 1, 0, 0 );
	- table->SetTableValue( 662.0, 0, 0, 1 );
	- table->SetTableValue( 663.0, 0.117647, 0.564706, 1 );
	- table->SetTableValue( 664.0, 0.392157, 0.831373, 0.929412 );
	- table->SetTableValue( 665.0, 0.854902, 0.647059, 0.12549 );
	- table->SetTableValue( 666.0, 1, 0.843137, 0 );
	- table->SetTableValue( 667.0, 1, 1, 0.65098 );
	- table->SetTableValue( 668.0, 0.6, 0, 0.8 );
	- table->SetTableValue( 669.0, 0.6, 0.552941, 0.819608 );
	- table->SetTableValue( 670.0, 0.8, 0.8, 1 );
	- table->SetTableValue( 671.0, 0.121569, 0.831373, 0.760784 );
	- table->SetTableValue( 672.0, 0.0117647, 1, 0.929412 );
	- table->SetTableValue( 673.0, 0.8, 1, 1 );
	- table->SetTableValue( 674.0, 0.337255, 0.290196, 0.576471 );
	- table->SetTableValue( 675.0, 0.447059, 0.447059, 0.745098 );
	- table->SetTableValue( 676.0, 0.721569, 0.698039, 1 );
	- table->SetTableValue( 677.0, 0.494118, 0.541176, 0.145098 );
	- table->SetTableValue( 678.0, 0.741176, 0.772549, 0.458824 );
	- table->SetTableValue( 679.0, 0.941176, 0.901961, 0.54902 );
	- table->SetTableValue( 701.0, 0.470588, 0.0705882, 0.52549 );
	- table->SetTableValue( 702.0, 0.803922, 0.243137, 0.305882 );
	- table->SetTableValue( 703.0, 0, 0.882353, 0 );
	- table->SetTableValue( 999.0, 1, 0.392157, 0.392157 );
	- table->SetTableValue( 1000.0, 0.0980392, 0.0196078, 0.0980392 );
	- table->SetTableValue( 1001.0, 0.0980392, 0.392157, 0.156863 );
	- table->SetTableValue( 1002.0, 0.490196, 0.392157, 0.627451 );
	- table->SetTableValue( 1003.0, 0.392157, 0.0980392, 0 );
	- table->SetTableValue( 1004.0, 0.470588, 0.27451, 0.196078 );
	- table->SetTableValue( 1005.0, 0.862745, 0.0784314, 0.392157 );
	- table->SetTableValue( 1006.0, 0.862745, 0.0784314, 0.0392157 );
	- table->SetTableValue( 1007.0, 0.705882, 0.862745, 0.54902 );
	- table->SetTableValue( 1008.0, 0.862745, 0.235294, 0.862745 );
	- table->SetTableValue( 1009.0, 0.705882, 0.156863, 0.470588 );
	- table->SetTableValue( 1010.0, 0.54902, 0.0784314, 0.54902 );
	- table->SetTableValue( 1011.0, 0.0784314, 0.117647, 0.54902 );
	- table->SetTableValue( 1012.0, 0.137255, 0.294118, 0.196078 );
	- table->SetTableValue( 1013.0, 0.882353, 0.54902, 0.54902 );
	- table->SetTableValue( 1014.0, 0.784314, 0.137255, 0.294118 );
	- table->SetTableValue( 1015.0, 0.627451, 0.392157, 0.196078 );
	- table->SetTableValue( 1016.0, 0.0784314, 0.862745, 0.235294 );
	- table->SetTableValue( 1017.0, 0.235294, 0.862745, 0.235294 );
	- table->SetTableValue( 1018.0, 0.862745, 0.705882, 0.54902 );
	- table->SetTableValue( 1019.0, 0.0784314, 0.392157, 0.196078 );
	- table->SetTableValue( 1020.0, 0.862745, 0.235294, 0.0784314 );
	- table->SetTableValue( 1021.0, 0.470588, 0.392157, 0.235294 );
	- table->SetTableValue( 1022.0, 0.862745, 0.0784314, 0.0784314 );
	- table->SetTableValue( 1023.0, 0.862745, 0.705882, 0.862745 );
	- table->SetTableValue( 1024.0, 0.235294, 0.0784314, 0.862745 );
	- table->SetTableValue( 1025.0, 0.627451, 0.54902, 0.705882 );
	- table->SetTableValue( 1026.0, 0.313725, 0.0784314, 0.54902 );
	- table->SetTableValue( 1027.0, 0.294118, 0.196078, 0.490196 );
	- table->SetTableValue( 1028.0, 0.0784314, 0.862745, 0.627451 );
	- table->SetTableValue( 1029.0, 0.0784314, 0.705882, 0.54902 );
	- table->SetTableValue( 1030.0, 0.54902, 0.862745, 0.862745 );
	- table->SetTableValue( 1031.0, 0.313725, 0.627451, 0.0784314 );
	- table->SetTableValue( 1032.0, 0.392157, 0, 0.392157 );
	- table->SetTableValue( 1033.0, 0.27451, 0.27451, 0.27451 );
	- table->SetTableValue( 1034.0, 0.588235, 0.588235, 0.784314 );
	- table->SetTableValue( 1035.0, 1, 0.752941, 0.12549 );
	- table->SetTableValue( 2000.0, 0.0980392, 0.0196078, 0.0980392 );
	- table->SetTableValue( 2001.0, 0.0980392, 0.392157, 0.156863 );
	- table->SetTableValue( 2002.0, 0.490196, 0.392157, 0.627451 );
	- table->SetTableValue( 2003.0, 0.392157, 0.0980392, 0 );
	- table->SetTableValue( 2004.0, 0.470588, 0.27451, 0.196078 );
	- table->SetTableValue( 2005.0, 0.862745, 0.0784314, 0.392157 );
	- table->SetTableValue( 2006.0, 0.862745, 0.0784314, 0.0392157 );
	- table->SetTableValue( 2007.0, 0.705882, 0.862745, 0.54902 );
	- table->SetTableValue( 2008.0, 0.862745, 0.235294, 0.862745 );
	- table->SetTableValue( 2009.0, 0.705882, 0.156863, 0.470588 );
	- table->SetTableValue( 2010.0, 0.54902, 0.0784314, 0.54902 );
	- table->SetTableValue( 2011.0, 0.0784314, 0.117647, 0.54902 );
	- table->SetTableValue( 2012.0, 0.137255, 0.294118, 0.196078 );
	- table->SetTableValue( 2013.0, 0.882353, 0.54902, 0.54902 );
	- table->SetTableValue( 2014.0, 0.784314, 0.137255, 0.294118 );
	- table->SetTableValue( 2015.0, 0.627451, 0.392157, 0.196078 );
	- table->SetTableValue( 2016.0, 0.0784314, 0.862745, 0.235294 );
	- table->SetTableValue( 2017.0, 0.235294, 0.862745, 0.235294 );
	- table->SetTableValue( 2018.0, 0.862745, 0.705882, 0.54902 );
	- table->SetTableValue( 2019.0, 0.0784314, 0.392157, 0.196078 );
	- table->SetTableValue( 2020.0, 0.862745, 0.235294, 0.0784314 );
	- table->SetTableValue( 2021.0, 0.470588, 0.392157, 0.235294 );
	- table->SetTableValue( 2022.0, 0.862745, 0.0784314, 0.0784314 );
	- table->SetTableValue( 2023.0, 0.862745, 0.705882, 0.862745 );
	- table->SetTableValue( 2024.0, 0.235294, 0.0784314, 0.862745 );
	- table->SetTableValue( 2025.0, 0.627451, 0.54902, 0.705882 );
	- table->SetTableValue( 2026.0, 0.313725, 0.0784314, 0.54902 );
	- table->SetTableValue( 2027.0, 0.294118, 0.196078, 0.490196 );
	- table->SetTableValue( 2028.0, 0.0784314, 0.862745, 0.627451 );
	- table->SetTableValue( 2029.0, 0.0784314, 0.705882, 0.54902 );
	- table->SetTableValue( 2030.0, 0.54902, 0.862745, 0.862745 );
	- table->SetTableValue( 2031.0, 0.313725, 0.627451, 0.0784314 );
	- table->SetTableValue( 2032.0, 0.392157, 0, 0.392157 );
	- table->SetTableValue( 2033.0, 0.27451, 0.27451, 0.27451 );
	- table->SetTableValue( 2034.0, 0.588235, 0.588235, 0.784314 );
	- table->SetTableValue( 2035.0, 1, 0.752941, 0.12549 );
	- table->SetTableValue( 3000.0, 0.901961, 0.980392, 0.901961 );
	- table->SetTableValue( 3001.0, 0.901961, 0.607843, 0.843137 );
	- table->SetTableValue( 3002.0, 0.509804, 0.607843, 0.372549 );
	- table->SetTableValue( 3003.0, 0.607843, 0.901961, 1 );
	- table->SetTableValue( 3004.0, 0.529412, 0.72549, 0.803922 );
	- table->SetTableValue( 3005.0, 0.137255, 0.921569, 0.607843 );
	- table->SetTableValue( 3006.0, 0.137255, 0.921569, 0.960784 );
	- table->SetTableValue( 3007.0, 0.294118, 0.137255, 0.45098 );
	- table->SetTableValue( 3008.0, 0.137255, 0.764706, 0.137255 );
	- table->SetTableValue( 3009.0, 0.294118, 0.843137, 0.529412 );
	- table->SetTableValue( 3010.0, 0.45098, 0.921569, 0.45098 );
	- table->SetTableValue( 3011.0, 0.921569, 0.882353, 0.45098 );
	- table->SetTableValue( 3012.0, 0.862745, 0.705882, 0.803922 );
	- table->SetTableValue( 3013.0, 0.117647, 0.45098, 0.45098 );
	- table->SetTableValue( 3014.0, 0.215686, 0.862745, 0.705882 );
	- table->SetTableValue( 3015.0, 0.372549, 0.607843, 0.803922 );
	- table->SetTableValue( 3016.0, 0.921569, 0.137255, 0.764706 );
	- table->SetTableValue( 3017.0, 0.764706, 0.137255, 0.764706 );
	- table->SetTableValue( 3018.0, 0.137255, 0.294118, 0.45098 );
	- table->SetTableValue( 3019.0, 0.921569, 0.607843, 0.803922 );
	- table->SetTableValue( 3020.0, 0.137255, 0.764706, 0.921569 );
	- table->SetTableValue( 3021.0, 0.529412, 0.607843, 0.764706 );
	- table->SetTableValue( 3022.0, 0.137255, 0.921569, 0.921569 );
	- table->SetTableValue( 3023.0, 0.137255, 0.294118, 0.137255 );
	- table->SetTableValue( 3024.0, 0.764706, 0.921569, 0.137255 );
	- table->SetTableValue( 3025.0, 0.372549, 0.45098, 0.294118 );
	- table->SetTableValue( 3026.0, 0.686275, 0.921569, 0.45098 );
	- table->SetTableValue( 3027.0, 0.705882, 0.803922, 0.509804 );
	- table->SetTableValue( 3028.0, 0.921569, 0.137255, 0.372549 );
	- table->SetTableValue( 3029.0, 0.921569, 0.294118, 0.45098 );
	- table->SetTableValue( 3030.0, 0.45098, 0.137255, 0.137255 );
	- table->SetTableValue( 3031.0, 0.686275, 0.372549, 0.921569 );
	- table->SetTableValue( 3032.0, 0.607843, 1, 0.607843 );
	- table->SetTableValue( 3033.0, 0.72549, 0.72549, 0.72549 );
	- table->SetTableValue( 3034.0, 0.411765, 0.411765, 0.215686 );
	- table->SetTableValue( 3035.0, 0.996078, 0.74902, 0.121569 );
	- table->SetTableValue( 4000.0, 0.901961, 0.980392, 0.901961 );
	- table->SetTableValue( 4001.0, 0.901961, 0.607843, 0.843137 );
	- table->SetTableValue( 4002.0, 0.509804, 0.607843, 0.372549 );
	- table->SetTableValue( 4003.0, 0.607843, 0.901961, 1 );
	- table->SetTableValue( 4004.0, 0.529412, 0.72549, 0.803922 );
	- table->SetTableValue( 4005.0, 0.137255, 0.921569, 0.607843 );
	- table->SetTableValue( 4006.0, 0.137255, 0.921569, 0.960784 );
	- table->SetTableValue( 4007.0, 0.294118, 0.137255, 0.45098 );
	- table->SetTableValue( 4008.0, 0.137255, 0.764706, 0.137255 );
	- table->SetTableValue( 4009.0, 0.294118, 0.843137, 0.529412 );
	- table->SetTableValue( 4010.0, 0.45098, 0.921569, 0.45098 );
	- table->SetTableValue( 4011.0, 0.921569, 0.882353, 0.45098 );
	- table->SetTableValue( 4012.0, 0.862745, 0.705882, 0.803922 );
	- table->SetTableValue( 4013.0, 0.117647, 0.45098, 0.45098 );
	- table->SetTableValue( 4014.0, 0.215686, 0.862745, 0.705882 );
	- table->SetTableValue( 4015.0, 0.372549, 0.607843, 0.803922 );
	- table->SetTableValue( 4016.0, 0.921569, 0.137255, 0.764706 );
	- table->SetTableValue( 4017.0, 0.764706, 0.137255, 0.764706 );
	- table->SetTableValue( 4018.0, 0.137255, 0.294118, 0.45098 );
	- table->SetTableValue( 4019.0, 0.921569, 0.607843, 0.803922 );
	- table->SetTableValue( 4020.0, 0.137255, 0.764706, 0.921569 );
	- table->SetTableValue( 4021.0, 0.529412, 0.607843, 0.764706 );
	- table->SetTableValue( 4022.0, 0.137255, 0.921569, 0.921569 );
	- table->SetTableValue( 4023.0, 0.137255, 0.294118, 0.137255 );
	- table->SetTableValue( 4024.0, 0.764706, 0.921569, 0.137255 );
	- table->SetTableValue( 4025.0, 0.372549, 0.45098, 0.294118 );
	- table->SetTableValue( 4026.0, 0.686275, 0.921569, 0.45098 );
	- table->SetTableValue( 4027.0, 0.705882, 0.803922, 0.509804 );
	- table->SetTableValue( 4028.0, 0.921569, 0.137255, 0.372549 );
	- table->SetTableValue( 4029.0, 0.921569, 0.294118, 0.45098 );
	- table->SetTableValue( 4030.0, 0.45098, 0.137255, 0.137255 );
	- table->SetTableValue( 4031.0, 0.686275, 0.372549, 0.921569 );
	- table->SetTableValue( 4032.0, 0.607843, 1, 0.607843 );
	- table->SetTableValue( 4033.0, 0.72549, 0.72549, 0.72549 );
	- table->SetTableValue( 4034.0, 0.411765, 0.411765, 0.215686 );
	- table->SetTableValue( 4035.0, 0.996078, 0.74902, 0.121569 );
	- table->SetTableValue( 1100.0, 0, 0, 0, 0);
	- table->SetTableValue( 1101.0, 0.196078, 0.196078, 0.196078 );
	- table->SetTableValue( 1102.0, 0.705882, 0.0784314, 0.117647 );
	- table->SetTableValue( 1103.0, 0.235294, 0.0980392, 0.0980392 );
	- table->SetTableValue( 1104.0, 0.0980392, 0.235294, 0.235294 );
	- table->SetTableValue( 1200.0, 0.0980392, 0.235294, 0.239216 );
	- table->SetTableValue( 1201.0, 0.0980392, 0.352941, 0.235294 );
	- table->SetTableValue( 1202.0, 0.0980392, 0.470588, 0.235294 );
	- table->SetTableValue( 1205.0, 0.0980392, 0.588235, 0.235294 );
	- table->SetTableValue( 1206.0, 0.0980392, 0.705882, 0.235294 );
	- table->SetTableValue( 1207.0, 0.0980392, 0.823529, 0.235294 );
	- table->SetTableValue( 1210.0, 0.0980392, 0.588235, 0.352941 );
	- table->SetTableValue( 1211.0, 0.0980392, 0.705882, 0.352941 );
	- table->SetTableValue( 1212.0, 0.0980392, 0.823529, 0.352941 );
	- table->SetTableValue( 1105.0, 0.705882, 0.0784314, 0.0784314 );
	- table->SetTableValue( 1106.0, 0.862745, 0.0784314, 0.392157 );
	- table->SetTableValue( 1107.0, 0.54902, 0.235294, 0.235294 );
	- table->SetTableValue( 1108.0, 0.705882, 0.862745, 0.54902 );
	- table->SetTableValue( 1109.0, 0.54902, 0.392157, 0.705882 );
	- table->SetTableValue( 1110.0, 0.705882, 0.0784314, 0.54902 );
	- table->SetTableValue( 1111.0, 0.54902, 0.0784314, 0.54902 );
	- table->SetTableValue( 1112.0, 0.0823529, 0.0392157, 0.0392157 );
	- table->SetTableValue( 1113.0, 0.882353, 0.54902, 0.54902 );
	- table->SetTableValue( 1114.0, 0.0901961, 0.235294, 0.705882 );
	- table->SetTableValue( 1115.0, 0.705882, 0.235294, 0.705882 );
	- table->SetTableValue( 1116.0, 0.0784314, 0.862745, 0.235294 );
	- table->SetTableValue( 1117.0, 0.235294, 0.0784314, 0.54902 );
	- table->SetTableValue( 1118.0, 0.862745, 0.705882, 0.54902 );
	- table->SetTableValue( 1119.0, 0.254902, 0.392157, 0.0784314 );
	- table->SetTableValue( 1120.0, 0.862745, 0.235294, 0.0784314 );
	- table->SetTableValue( 1121.0, 0.235294, 0.392157, 0.235294 );
	- table->SetTableValue( 1122.0, 0.0784314, 0.235294, 0.862745 );
	- table->SetTableValue( 1123.0, 0.392157, 0.392157, 0.235294 );
	- table->SetTableValue( 1124.0, 0.862745, 0.705882, 0.862745 );
	- table->SetTableValue( 1125.0, 0.0784314, 0.705882, 0.54902 );
	- table->SetTableValue( 1126.0, 0.235294, 0.54902, 0.705882 );
	- table->SetTableValue( 1127.0, 0.0980392, 0.0784314, 0.54902 );
	- table->SetTableValue( 1128.0, 0.0784314, 0.235294, 0.392157 );
	- table->SetTableValue( 1129.0, 0.235294, 0.862745, 0.0784314 );
	- table->SetTableValue( 1130.0, 0.235294, 0.0784314, 0.862745 );
	- table->SetTableValue( 1131.0, 0.862745, 0.862745, 0.392157 );
	- table->SetTableValue( 1132.0, 0.705882, 0.235294, 0.235294 );
	- table->SetTableValue( 1133.0, 0.235294, 0.235294, 0.862745 );
	- table->SetTableValue( 1134.0, 0.862745, 0.235294, 0.862745 );
	- table->SetTableValue( 1135.0, 0.254902, 0.862745, 0.235294 );
	- table->SetTableValue( 1136.0, 0.0980392, 0.54902, 0.0784314 );
	- table->SetTableValue( 1137.0, 0.0509804, 0, 0.980392 );
	- table->SetTableValue( 1138.0, 0.239216, 0.0784314, 0.862745 );
	- table->SetTableValue( 1139.0, 0.239216, 0.0784314, 0.235294 );
	- table->SetTableValue( 1140.0, 0.239216, 0.235294, 0.392157 );
	- table->SetTableValue( 1141.0, 0.0980392, 0.0980392, 0.0980392 );
	- table->SetTableValue( 1142.0, 0.54902, 0.0784314, 0.235294 );
	- table->SetTableValue( 1143.0, 0.862745, 0.705882, 0.0784314 );
	- table->SetTableValue( 1144.0, 0.247059, 0.705882, 0.705882 );
	- table->SetTableValue( 1145.0, 0.866667, 0.0784314, 0.0392157 );
	- table->SetTableValue( 1146.0, 0.0823529, 0.862745, 0.0784314 );
	- table->SetTableValue( 1147.0, 0.717647, 0.392157, 0.0784314 );
	- table->SetTableValue( 1148.0, 0.866667, 0.0784314, 0.392157 );
	- table->SetTableValue( 1149.0, 0.866667, 0.235294, 0.54902 );
	- table->SetTableValue( 1150.0, 0.866667, 0.0784314, 0.862745 );
	- table->SetTableValue( 1151.0, 0.239216, 0.862745, 0.862745 );
	- table->SetTableValue( 1152.0, 0.392157, 0.784314, 0.784314 );
	- table->SetTableValue( 1153.0, 0.0392157, 0.784314, 0.784314 );
	- table->SetTableValue( 1154.0, 0.866667, 0.862745, 0.0784314 );
	- table->SetTableValue( 1155.0, 0.552941, 0.0784314, 0.392157 );
	- table->SetTableValue( 1156.0, 0.239216, 0.862745, 0.392157 );
	- table->SetTableValue( 1157.0, 0.0823529, 0.862745, 0.235294 );
	- table->SetTableValue( 1158.0, 0.552941, 0.235294, 0.0784314 );
	- table->SetTableValue( 1159.0, 0.560784, 0.0784314, 0.862745 );
	- table->SetTableValue( 1160.0, 0.239216, 0.0784314, 0.705882 );
	- table->SetTableValue( 1161.0, 0.396078, 0.235294, 0.862745 );
	- table->SetTableValue( 1162.0, 0.0823529, 0.0784314, 0.54902 );
	- table->SetTableValue( 1163.0, 0.866667, 0.54902, 0.0784314 );
	- table->SetTableValue( 1164.0, 0.552941, 0.392157, 0.862745 );
	- table->SetTableValue( 1165.0, 0.396078, 0.0784314, 0.0784314 );
	- table->SetTableValue( 1166.0, 0.866667, 0.392157, 0.0784314 );
	- table->SetTableValue( 1167.0, 0.709804, 0.784314, 0.0784314 );
	- table->SetTableValue( 1168.0, 0.0823529, 0.705882, 0.54902 );
	- table->SetTableValue( 1169.0, 0.396078, 0.392157, 0.705882 );
	- table->SetTableValue( 1170.0, 0.709804, 0.862745, 0.0784314 );
	- table->SetTableValue( 1171.0, 0.0823529, 0.54902, 0.784314 );
	- table->SetTableValue( 1172.0, 0.0823529, 0.0784314, 0.941176 );
	- table->SetTableValue( 1173.0, 0.0823529, 0.0784314, 0.784314 );
	- table->SetTableValue( 1174.0, 0.239216, 0.705882, 0.235294 );
	- table->SetTableValue( 1175.0, 0.239216, 0.705882, 0.980392 );
	- table->SetTableValue( 1176.0, 0.0823529, 0.0784314, 0.235294 );
	- table->SetTableValue( 1177.0, 0.396078, 0.235294, 0.235294 );
	- table->SetTableValue( 1178.0, 0.0823529, 0.862745, 0.862745 );
	- table->SetTableValue( 1179.0, 0.0823529, 0.705882, 0.705882 );
	- table->SetTableValue( 1180.0, 0.87451, 0.862745, 0.235294 );
	- table->SetTableValue( 1181.0, 0.866667, 0.235294, 0.235294 );
	- table->SetTableValue( 2100.0, 0, 0, 0, 0);
	- table->SetTableValue( 2101.0, 0.196078, 0.196078, 0.196078 );
	- table->SetTableValue( 2102.0, 0.705882, 0.0784314, 0.117647 );
	- table->SetTableValue( 2103.0, 0.235294, 0.0980392, 0.0980392 );
	- table->SetTableValue( 2104.0, 0.0980392, 0.235294, 0.235294 );
	- table->SetTableValue( 2105.0, 0.705882, 0.0784314, 0.0784314 );
	- table->SetTableValue( 2106.0, 0.862745, 0.0784314, 0.392157 );
	- table->SetTableValue( 2107.0, 0.54902, 0.235294, 0.235294 );
	- table->SetTableValue( 2108.0, 0.705882, 0.862745, 0.54902 );
	- table->SetTableValue( 2109.0, 0.54902, 0.392157, 0.705882 );
	- table->SetTableValue( 2110.0, 0.705882, 0.0784314, 0.54902 );
	- table->SetTableValue( 2111.0, 0.54902, 0.0784314, 0.54902 );
	- table->SetTableValue( 2112.0, 0.0823529, 0.0392157, 0.0392157 );
	- table->SetTableValue( 2113.0, 0.882353, 0.54902, 0.54902 );
	- table->SetTableValue( 2114.0, 0.0901961, 0.235294, 0.705882 );
	- table->SetTableValue( 2115.0, 0.705882, 0.235294, 0.705882 );
	- table->SetTableValue( 2116.0, 0.0784314, 0.862745, 0.235294 );
	- table->SetTableValue( 2117.0, 0.235294, 0.0784314, 0.54902 );
	- table->SetTableValue( 2118.0, 0.862745, 0.705882, 0.54902 );
	- table->SetTableValue( 2119.0, 0.254902, 0.392157, 0.0784314 );
	- table->SetTableValue( 2120.0, 0.862745, 0.235294, 0.0784314 );
	- table->SetTableValue( 2121.0, 0.235294, 0.392157, 0.235294 );
	- table->SetTableValue( 2122.0, 0.0784314, 0.235294, 0.862745 );
	- table->SetTableValue( 2123.0, 0.392157, 0.392157, 0.235294 );
	- table->SetTableValue( 2124.0, 0.862745, 0.705882, 0.862745 );
	- table->SetTableValue( 2125.0, 0.0784314, 0.705882, 0.54902 );
	- table->SetTableValue( 2126.0, 0.235294, 0.54902, 0.705882 );
	- table->SetTableValue( 2127.0, 0.0980392, 0.0784314, 0.54902 );
	- table->SetTableValue( 2128.0, 0.0784314, 0.235294, 0.392157 );
	- table->SetTableValue( 2129.0, 0.235294, 0.862745, 0.0784314 );
	- table->SetTableValue( 2130.0, 0.235294, 0.0784314, 0.862745 );
	- table->SetTableValue( 2131.0, 0.862745, 0.862745, 0.392157 );
	- table->SetTableValue( 2132.0, 0.705882, 0.235294, 0.235294 );
	- table->SetTableValue( 2133.0, 0.235294, 0.235294, 0.862745 );
	- table->SetTableValue( 2134.0, 0.862745, 0.235294, 0.862745 );
	- table->SetTableValue( 2135.0, 0.254902, 0.862745, 0.235294 );
	- table->SetTableValue( 2136.0, 0.0980392, 0.54902, 0.0784314 );
	- table->SetTableValue( 2137.0, 0.0509804, 0, 0.980392 );
	- table->SetTableValue( 2138.0, 0.239216, 0.0784314, 0.862745 );
	- table->SetTableValue( 2139.0, 0.239216, 0.0784314, 0.235294 );
	- table->SetTableValue( 2140.0, 0.239216, 0.235294, 0.392157 );
	- table->SetTableValue( 2141.0, 0.0980392, 0.0980392, 0.0980392 );
	- table->SetTableValue( 2142.0, 0.54902, 0.0784314, 0.235294 );
	- table->SetTableValue( 2143.0, 0.862745, 0.705882, 0.0784314 );
	- table->SetTableValue( 2144.0, 0.247059, 0.705882, 0.705882 );
	- table->SetTableValue( 2145.0, 0.866667, 0.0784314, 0.0392157 );
	- table->SetTableValue( 2146.0, 0.0823529, 0.862745, 0.0784314 );
	- table->SetTableValue( 2147.0, 0.717647, 0.392157, 0.0784314 );
	- table->SetTableValue( 2148.0, 0.866667, 0.0784314, 0.392157 );
	- table->SetTableValue( 2149.0, 0.866667, 0.235294, 0.54902 );
	- table->SetTableValue( 2150.0, 0.866667, 0.0784314, 0.862745 );
	- table->SetTableValue( 2151.0, 0.239216, 0.862745, 0.862745 );
	- table->SetTableValue( 2152.0, 0.392157, 0.784314, 0.784314 );
	- table->SetTableValue( 2153.0, 0.0392157, 0.784314, 0.784314 );
	- table->SetTableValue( 2154.0, 0.866667, 0.862745, 0.0784314 );
	- table->SetTableValue( 2155.0, 0.552941, 0.0784314, 0.392157 );
	- table->SetTableValue( 2156.0, 0.239216, 0.862745, 0.392157 );
	- table->SetTableValue( 2157.0, 0.0823529, 0.862745, 0.235294 );
	- table->SetTableValue( 2158.0, 0.552941, 0.235294, 0.0784314 );
	- table->SetTableValue( 2159.0, 0.560784, 0.0784314, 0.862745 );
	- table->SetTableValue( 2160.0, 0.239216, 0.0784314, 0.705882 );
	- table->SetTableValue( 2161.0, 0.396078, 0.235294, 0.862745 );
	- table->SetTableValue( 2162.0, 0.0823529, 0.0784314, 0.54902 );
	- table->SetTableValue( 2163.0, 0.866667, 0.54902, 0.0784314 );
	- table->SetTableValue( 2164.0, 0.552941, 0.392157, 0.862745 );
	- table->SetTableValue( 2165.0, 0.396078, 0.0784314, 0.0784314 );
	- table->SetTableValue( 2166.0, 0.866667, 0.392157, 0.0784314 );
	- table->SetTableValue( 2167.0, 0.709804, 0.784314, 0.0784314 );
	- table->SetTableValue( 2168.0, 0.0823529, 0.705882, 0.54902 );
	- table->SetTableValue( 2169.0, 0.396078, 0.392157, 0.705882 );
	- table->SetTableValue( 2170.0, 0.709804, 0.862745, 0.0784314 );
	- table->SetTableValue( 2171.0, 0.0823529, 0.54902, 0.784314 );
	- table->SetTableValue( 2172.0, 0.0823529, 0.0784314, 0.941176 );
	- table->SetTableValue( 2173.0, 0.0823529, 0.0784314, 0.784314 );
	- table->SetTableValue( 2174.0, 0.239216, 0.705882, 0.235294 );
	- table->SetTableValue( 2175.0, 0.239216, 0.705882, 0.980392 );
	- table->SetTableValue( 2176.0, 0.0823529, 0.0784314, 0.235294 );
	- table->SetTableValue( 2177.0, 0.396078, 0.235294, 0.235294 );
	- table->SetTableValue( 2178.0, 0.0823529, 0.862745, 0.862745 );
	- table->SetTableValue( 2179.0, 0.0823529, 0.705882, 0.705882 );
	- table->SetTableValue( 2180.0, 0.87451, 0.862745, 0.235294 );
	- table->SetTableValue( 2181.0, 0.866667, 0.235294, 0.235294 );
	- table->SetTableValue( 2200.0, 0.0980392, 0.235294, 0.239216 );
	- table->SetTableValue( 2201.0, 0.0980392, 0.352941, 0.235294 );
	- table->SetTableValue( 2202.0, 0.0980392, 0.470588, 0.235294 );
	- table->SetTableValue( 2205.0, 0.0980392, 0.588235, 0.235294 );
	- table->SetTableValue( 2206.0, 0.0980392, 0.705882, 0.235294 );
	- table->SetTableValue( 2207.0, 0.0980392, 0.823529, 0.235294 );
	- table->SetTableValue( 2210.0, 0.0980392, 0.588235, 0.352941 );
	- table->SetTableValue( 2211.0, 0.0980392, 0.705882, 0.352941 );
	- table->SetTableValue( 2212.0, 0.0980392, 0.823529, 0.352941 );
	- table->SetTableValue( 3100.0, 0, 0, 0, 0);
	- table->SetTableValue( 3101.0, 0.196078, 0.196078, 0.196078 );
	- table->SetTableValue( 3102.0, 0.705882, 0.0784314, 0.117647 );
	- table->SetTableValue( 3103.0, 0.235294, 0.0980392, 0.0980392 );
	- table->SetTableValue( 3104.0, 0.0980392, 0.235294, 0.235294 );
	- table->SetTableValue( 3105.0, 0.705882, 0.0784314, 0.0784314 );
	- table->SetTableValue( 3106.0, 0.862745, 0.0784314, 0.392157 );
	- table->SetTableValue( 3107.0, 0.54902, 0.235294, 0.235294 );
	- table->SetTableValue( 3108.0, 0.705882, 0.862745, 0.54902 );
	- table->SetTableValue( 3109.0, 0.54902, 0.392157, 0.705882 );
	- table->SetTableValue( 3110.0, 0.705882, 0.0784314, 0.54902 );
	- table->SetTableValue( 3111.0, 0.54902, 0.0784314, 0.54902 );
	- table->SetTableValue( 3112.0, 0.0823529, 0.0392157, 0.0392157 );
	- table->SetTableValue( 3113.0, 0.882353, 0.54902, 0.54902 );
	- table->SetTableValue( 3114.0, 0.0901961, 0.235294, 0.705882 );
	- table->SetTableValue( 3115.0, 0.705882, 0.235294, 0.705882 );
	- table->SetTableValue( 3116.0, 0.0784314, 0.862745, 0.235294 );
	- table->SetTableValue( 3117.0, 0.235294, 0.0784314, 0.54902 );
	- table->SetTableValue( 3118.0, 0.862745, 0.705882, 0.54902 );
	- table->SetTableValue( 3119.0, 0.254902, 0.392157, 0.0784314 );
	- table->SetTableValue( 3120.0, 0.862745, 0.235294, 0.0784314 );
	- table->SetTableValue( 3121.0, 0.235294, 0.392157, 0.235294 );
	- table->SetTableValue( 3122.0, 0.0784314, 0.235294, 0.862745 );
	- table->SetTableValue( 3123.0, 0.392157, 0.392157, 0.235294 );
	- table->SetTableValue( 3124.0, 0.862745, 0.705882, 0.862745 );
	- table->SetTableValue( 3125.0, 0.0784314, 0.705882, 0.54902 );
	- table->SetTableValue( 3126.0, 0.235294, 0.54902, 0.705882 );
	- table->SetTableValue( 3127.0, 0.0980392, 0.0784314, 0.54902 );
	- table->SetTableValue( 3128.0, 0.0784314, 0.235294, 0.392157 );
	- table->SetTableValue( 3129.0, 0.235294, 0.862745, 0.0784314 );
	- table->SetTableValue( 3130.0, 0.235294, 0.0784314, 0.862745 );
	- table->SetTableValue( 3131.0, 0.862745, 0.862745, 0.392157 );
	- table->SetTableValue( 3132.0, 0.705882, 0.235294, 0.235294 );
	- table->SetTableValue( 3133.0, 0.235294, 0.235294, 0.862745 );
	- table->SetTableValue( 3134.0, 0.862745, 0.235294, 0.862745 );
	- table->SetTableValue( 3135.0, 0.254902, 0.862745, 0.235294 );
	- table->SetTableValue( 3136.0, 0.0980392, 0.54902, 0.0784314 );
	- table->SetTableValue( 3137.0, 0.0509804, 0, 0.980392 );
	- table->SetTableValue( 3138.0, 0.239216, 0.0784314, 0.862745 );
	- table->SetTableValue( 3139.0, 0.239216, 0.0784314, 0.235294 );
	- table->SetTableValue( 3140.0, 0.239216, 0.235294, 0.392157 );
	- table->SetTableValue( 3141.0, 0.0980392, 0.0980392, 0.0980392 );
	- table->SetTableValue( 3142.0, 0.54902, 0.0784314, 0.235294 );
	- table->SetTableValue( 3143.0, 0.862745, 0.705882, 0.0784314 );
	- table->SetTableValue( 3144.0, 0.247059, 0.705882, 0.705882 );
	- table->SetTableValue( 3145.0, 0.866667, 0.0784314, 0.0392157 );
	- table->SetTableValue( 3146.0, 0.0823529, 0.862745, 0.0784314 );
	- table->SetTableValue( 3147.0, 0.717647, 0.392157, 0.0784314 );
	- table->SetTableValue( 3148.0, 0.866667, 0.0784314, 0.392157 );
	- table->SetTableValue( 3149.0, 0.866667, 0.235294, 0.54902 );
	- table->SetTableValue( 3150.0, 0.866667, 0.0784314, 0.862745 );
	- table->SetTableValue( 3151.0, 0.239216, 0.862745, 0.862745 );
	- table->SetTableValue( 3152.0, 0.392157, 0.784314, 0.784314 );
	- table->SetTableValue( 3153.0, 0.0392157, 0.784314, 0.784314 );
	- table->SetTableValue( 3154.0, 0.866667, 0.862745, 0.0784314 );
	- table->SetTableValue( 3155.0, 0.552941, 0.0784314, 0.392157 );
	- table->SetTableValue( 3156.0, 0.239216, 0.862745, 0.392157 );
	- table->SetTableValue( 3157.0, 0.0823529, 0.862745, 0.235294 );
	- table->SetTableValue( 3158.0, 0.552941, 0.235294, 0.0784314 );
	- table->SetTableValue( 3159.0, 0.560784, 0.0784314, 0.862745 );
	- table->SetTableValue( 3160.0, 0.239216, 0.0784314, 0.705882 );
	- table->SetTableValue( 3161.0, 0.396078, 0.235294, 0.862745 );
	- table->SetTableValue( 3162.0, 0.0823529, 0.0784314, 0.54902 );
	- table->SetTableValue( 3163.0, 0.866667, 0.54902, 0.0784314 );
	- table->SetTableValue( 3164.0, 0.552941, 0.392157, 0.862745 );
	- table->SetTableValue( 3165.0, 0.396078, 0.0784314, 0.0784314 );
	- table->SetTableValue( 3166.0, 0.866667, 0.392157, 0.0784314 );
	- table->SetTableValue( 3167.0, 0.709804, 0.784314, 0.0784314 );
	- table->SetTableValue( 3168.0, 0.0823529, 0.705882, 0.54902 );
	- table->SetTableValue( 3169.0, 0.396078, 0.392157, 0.705882 );
	- table->SetTableValue( 3170.0, 0.709804, 0.862745, 0.0784314 );
	- table->SetTableValue( 3171.0, 0.0823529, 0.54902, 0.784314 );
	- table->SetTableValue( 3172.0, 0.0823529, 0.0784314, 0.941176 );
	- table->SetTableValue( 3173.0, 0.0823529, 0.0784314, 0.784314 );
	- table->SetTableValue( 3174.0, 0.239216, 0.705882, 0.235294 );
	- table->SetTableValue( 3175.0, 0.239216, 0.705882, 0.980392 );
	- table->SetTableValue( 3176.0, 0.0823529, 0.0784314, 0.235294 );
	- table->SetTableValue( 3177.0, 0.396078, 0.235294, 0.235294 );
	- table->SetTableValue( 3178.0, 0.0823529, 0.862745, 0.862745 );
	- table->SetTableValue( 3179.0, 0.0823529, 0.705882, 0.705882 );
	- table->SetTableValue( 3180.0, 0.87451, 0.862745, 0.235294 );
	- table->SetTableValue( 3181.0, 0.866667, 0.235294, 0.235294 );
	- table->SetTableValue( 4100.0, 0, 0, 0, 0);
	- table->SetTableValue( 4101.0, 0.196078, 0.196078, 0.196078 );
	- table->SetTableValue( 4102.0, 0.705882, 0.0784314, 0.117647 );
	- table->SetTableValue( 4103.0, 0.235294, 0.0980392, 0.0980392 );
	- table->SetTableValue( 4104.0, 0.0980392, 0.235294, 0.235294 );
	- table->SetTableValue( 4105.0, 0.705882, 0.0784314, 0.0784314 );
	- table->SetTableValue( 4106.0, 0.862745, 0.0784314, 0.392157 );
	- table->SetTableValue( 4107.0, 0.54902, 0.235294, 0.235294 );
	- table->SetTableValue( 4108.0, 0.705882, 0.862745, 0.54902 );
	- table->SetTableValue( 4109.0, 0.54902, 0.392157, 0.705882 );
	- table->SetTableValue( 4110.0, 0.705882, 0.0784314, 0.54902 );
	- table->SetTableValue( 4111.0, 0.54902, 0.0784314, 0.54902 );
	- table->SetTableValue( 4112.0, 0.0823529, 0.0392157, 0.0392157 );
	- table->SetTableValue( 4113.0, 0.882353, 0.54902, 0.54902 );
	- table->SetTableValue( 4114.0, 0.0901961, 0.235294, 0.705882 );
	- table->SetTableValue( 4115.0, 0.705882, 0.235294, 0.705882 );
	- table->SetTableValue( 4116.0, 0.0784314, 0.862745, 0.235294 );
	- table->SetTableValue( 4117.0, 0.235294, 0.0784314, 0.54902 );
	- table->SetTableValue( 4118.0, 0.862745, 0.705882, 0.54902 );
	- table->SetTableValue( 4119.0, 0.254902, 0.392157, 0.0784314 );
	- table->SetTableValue( 4120.0, 0.862745, 0.235294, 0.0784314 );
	- table->SetTableValue( 4121.0, 0.235294, 0.392157, 0.235294 );
	- table->SetTableValue( 4122.0, 0.0784314, 0.235294, 0.862745 );
	- table->SetTableValue( 4123.0, 0.392157, 0.392157, 0.235294 );
	- table->SetTableValue( 4124.0, 0.862745, 0.705882, 0.862745 );
	- table->SetTableValue( 4125.0, 0.0784314, 0.705882, 0.54902 );
	- table->SetTableValue( 4126.0, 0.235294, 0.54902, 0.705882 );
	- table->SetTableValue( 4127.0, 0.0980392, 0.0784314, 0.54902 );
	- table->SetTableValue( 4128.0, 0.0784314, 0.235294, 0.392157 );
	- table->SetTableValue( 4129.0, 0.235294, 0.862745, 0.0784314 );
	- table->SetTableValue( 4130.0, 0.235294, 0.0784314, 0.862745 );
	- table->SetTableValue( 4131.0, 0.862745, 0.862745, 0.392157 );
	- table->SetTableValue( 4132.0, 0.705882, 0.235294, 0.235294 );
	- table->SetTableValue( 4133.0, 0.235294, 0.235294, 0.862745 );
	- table->SetTableValue( 4134.0, 0.862745, 0.235294, 0.862745 );
	- table->SetTableValue( 4135.0, 0.254902, 0.862745, 0.235294 );
	- table->SetTableValue( 4136.0, 0.0980392, 0.54902, 0.0784314 );
	- table->SetTableValue( 4137.0, 0.0509804, 0, 0.980392 );
	- table->SetTableValue( 4138.0, 0.239216, 0.0784314, 0.862745 );
	- table->SetTableValue( 4139.0, 0.239216, 0.0784314, 0.235294 );
	- table->SetTableValue( 4140.0, 0.239216, 0.235294, 0.392157 );
	- table->SetTableValue( 4141.0, 0.0980392, 0.0980392, 0.0980392 );
	- table->SetTableValue( 4142.0, 0.54902, 0.0784314, 0.235294 );
	- table->SetTableValue( 4143.0, 0.862745, 0.705882, 0.0784314 );
	- table->SetTableValue( 4144.0, 0.247059, 0.705882, 0.705882 );
	- table->SetTableValue( 4145.0, 0.866667, 0.0784314, 0.0392157 );
	- table->SetTableValue( 4146.0, 0.0823529, 0.862745, 0.0784314 );
	- table->SetTableValue( 4147.0, 0.717647, 0.392157, 0.0784314 );
	- table->SetTableValue( 4148.0, 0.866667, 0.0784314, 0.392157 );
	- table->SetTableValue( 4149.0, 0.866667, 0.235294, 0.54902 );
	- table->SetTableValue( 4150.0, 0.866667, 0.0784314, 0.862745 );
	- table->SetTableValue( 4151.0, 0.239216, 0.862745, 0.862745 );
	- table->SetTableValue( 4152.0, 0.392157, 0.784314, 0.784314 );
	- table->SetTableValue( 4153.0, 0.0392157, 0.784314, 0.784314 );
	- table->SetTableValue( 4154.0, 0.866667, 0.862745, 0.0784314 );
	- table->SetTableValue( 4155.0, 0.552941, 0.0784314, 0.392157 );
	- table->SetTableValue( 4156.0, 0.239216, 0.862745, 0.392157 );
	- table->SetTableValue( 4157.0, 0.0823529, 0.862745, 0.235294 );
	- table->SetTableValue( 4158.0, 0.552941, 0.235294, 0.0784314 );
	- table->SetTableValue( 4159.0, 0.560784, 0.0784314, 0.862745 );
	- table->SetTableValue( 4160.0, 0.239216, 0.0784314, 0.705882 );
	- table->SetTableValue( 4161.0, 0.396078, 0.235294, 0.862745 );
	- table->SetTableValue( 4162.0, 0.0823529, 0.0784314, 0.54902 );
	- table->SetTableValue( 4163.0, 0.866667, 0.54902, 0.0784314 );
	- table->SetTableValue( 4164.0, 0.552941, 0.392157, 0.862745 );
	- table->SetTableValue( 4165.0, 0.396078, 0.0784314, 0.0784314 );
	- table->SetTableValue( 4166.0, 0.866667, 0.392157, 0.0784314 );
	- table->SetTableValue( 4167.0, 0.709804, 0.784314, 0.0784314 );
	- table->SetTableValue( 4168.0, 0.0823529, 0.705882, 0.54902 );
	- table->SetTableValue( 4169.0, 0.396078, 0.392157, 0.705882 );
	- table->SetTableValue( 4170.0, 0.709804, 0.862745, 0.0784314 );
	- table->SetTableValue( 4171.0, 0.0823529, 0.54902, 0.784314 );
	- table->SetTableValue( 4172.0, 0.0823529, 0.0784314, 0.941176 );
	- table->SetTableValue( 4173.0, 0.0823529, 0.0784314, 0.784314 );
	- table->SetTableValue( 4174.0, 0.239216, 0.705882, 0.235294 );
	- table->SetTableValue( 4175.0, 0.239216, 0.705882, 0.980392 );
	- table->SetTableValue( 4176.0, 0.0823529, 0.0784314, 0.235294 );
	- table->SetTableValue( 4177.0, 0.396078, 0.235294, 0.235294 );
	- table->SetTableValue( 4178.0, 0.0823529, 0.862745, 0.862745 );
	- table->SetTableValue( 4179.0, 0.0823529, 0.705882, 0.705882 );
	- table->SetTableValue( 4180.0, 0.87451, 0.862745, 0.235294 );
	- table->SetTableValue( 4181.0, 0.866667, 0.235294, 0.235294 );
	- table->SetTableValue( 5001.0, 0.0784314, 0.117647, 0.156863 );
	- table->SetTableValue( 5002.0, 0.0784314, 0.117647, 0.156863 );
	- table->SetTableValue( 5100.0, 0.8, 0.4, 0.4 );
	- table->SetTableValue( 5101.0, 0.8, 0.4, 0.4 );
	- table->SetTableValue( 5102.0, 1, 1, 0.4 );
	- table->SetTableValue( 5103.0, 0.6, 0.8, 0 );
	- table->SetTableValue( 5104.0, 0, 0.6, 0.6 );
	- table->SetTableValue( 5105.0, 0.8, 0.6, 1 );
	- table->SetTableValue( 5106.0, 1, 0.6, 0.2 );
	- table->SetTableValue( 5107.0, 0.8, 0.8, 0.8 );
	- table->SetTableValue( 5108.0, 0.6, 1, 1 );
	- table->SetTableValue( 5109.0, 0.4, 0.6, 1 );
	- table->SetTableValue( 5110.0, 1, 1, 0.4 );
	- table->SetTableValue( 5111.0, 0.6, 0.8, 0 );
	- table->SetTableValue( 5112.0, 0, 0.6, 0.6 );
	- table->SetTableValue( 5113.0, 0.8, 0.6, 1 );
	- table->SetTableValue( 5114.0, 1, 0.6, 0.2 );
	- table->SetTableValue( 5115.0, 0.8, 0.8, 0.8 );
	- table->SetTableValue( 5116.0, 0.6, 1, 1 );
	- table->SetTableValue( 5117.0, 0.4, 0.6, 1 );
	- table->SetTableValue( 5200.0, 0.8, 0.4, 0.4 );
	- table->SetTableValue( 5201.0, 0.8, 0.4, 0.4 );
	- table->SetTableValue( 5202.0, 1, 1, 0.4 );
	- table->SetTableValue( 5203.0, 0.6, 0.8, 0 );
	- table->SetTableValue( 5204.0, 0, 0.6, 0.6 );
	- table->SetTableValue( 5205.0, 0.8, 0.6, 1 );
	- table->SetTableValue( 5206.0, 1, 0.6, 0.2 );
	- table->SetTableValue( 5207.0, 0.8, 0.8, 0.8 );
	- table->SetTableValue( 5208.0, 0.6, 1, 1 );
	- table->SetTableValue( 5209.0, 0.4, 0.6, 1 );
	- table->SetTableValue( 5210.0, 1, 1, 0.4 );
	- table->SetTableValue( 5211.0, 0.6, 0.8, 0 );
	- table->SetTableValue( 5212.0, 0, 0.6, 0.6 );
	- table->SetTableValue( 5213.0, 0.8, 0.6, 1 );
	- table->SetTableValue( 5214.0, 1, 0.6, 0.2 );
	- table->SetTableValue( 5215.0, 0.8, 0.8, 0.8 );
	- table->SetTableValue( 5216.0, 0.6, 1, 1 );
	- table->SetTableValue( 5217.0, 0.4, 0.6, 1 );
	- table->SetTableValue( 6000.0, 0, 1, 0 );
	- table->SetTableValue( 6001.0, 1, 1, 0 );
	- table->SetTableValue( 6002.0, 0, 1, 1 );
	- table->SetTableValue( 6003.0, 0, 0, 1 );
	- table->SetTableValue( 6010.0, 0.92549, 0.0627451, 0.905882 );
	- table->SetTableValue( 6020.0, 0.929412, 0.0705882, 0.909804 );
	- table->SetTableValue( 6030.0, 0.92549, 0.0509804, 0.890196 );
	- table->SetTableValue( 6040.0, 0.92549, 0.0666667, 0.894118 );
	- table->SetTableValue( 6050.0, 0.00392157, 1, 0.00392157 );
	- table->SetTableValue( 6060.0, 0.00784314, 1, 0.00392157 );
	- table->SetTableValue( 6070.0, 0.92549, 0.054902, 0.901961 );
	- table->SetTableValue( 6080.0, 0.929412, 0.054902, 0.901961 );
	- table->SetTableValue( 7001.0, 0.282353, 0.517647, 0.709804 );
	- table->SetTableValue( 7002.0, 0.952941, 0.952941, 0.952941 );
	- table->SetTableValue( 7003.0, 0.811765, 0.247059, 0.309804 );
	- table->SetTableValue( 7004.0, 0.47451, 0.0784314, 0.529412 );
	- table->SetTableValue( 7005.0, 0.772549, 0.235294, 0.972549 );
	- table->SetTableValue( 7006.0, 0.00784314, 0.584314, 0.00784314 );
	- table->SetTableValue( 7007.0, 0.866667, 0.976471, 0.65098 );
	- table->SetTableValue( 7008.0, 0.909804, 0.572549, 0.137255 );
	- table->SetTableValue( 7009.0, 0.0784314, 0.235294, 0.470588 );
	- table->SetTableValue( 7010.0, 0.980392, 0.980392, 0 );
	- table->SetTableValue( 7011.0, 0.478431, 0.733333, 0.870588 );
	- table->SetTableValue( 7012.0, 0.929412, 0.0470588, 0.694118 );
	- table->SetTableValue( 7013.0, 0.0392157, 0.192157, 1 );
	- table->SetTableValue( 7014.0, 0.803922, 0.721569, 0.564706 );
	- table->SetTableValue( 7015.0, 0.176471, 0.803922, 0.647059 );
	- table->SetTableValue( 7016.0, 0.458824, 0.627451, 0.686275 );
	- table->SetTableValue( 7017.0, 0.866667, 0.85098, 0.0823529 );
	- table->SetTableValue( 7018.0, 0.0784314, 0.235294, 0.470588 );
	- table->SetTableValue( 7019.0, 0.552941, 0.0823529, 0.392157 );
	- table->SetTableValue( 7020.0, 0.882353, 0.54902, 0.552941 );
	- table->SetTableValue( 7100.0, 0.164706, 0.788235, 0.658824 );
	- table->SetTableValue( 7101.0, 0.658824, 0.407843, 0.635294 );
	- table->SetTableValue( 8001.0, 0.290196, 0.509804, 0.709804 );
	- table->SetTableValue( 8002.0, 0.94902, 0.945098, 0.941176 );
	- table->SetTableValue( 8003.0, 0.807843, 0.254902, 0.305882 );
	- table->SetTableValue( 8004.0, 0.470588, 0.0823529, 0.521569 );
	- table->SetTableValue( 8005.0, 0.764706, 0.239216, 0.964706 );
	- table->SetTableValue( 8006.0, 0.0117647, 0.576471, 0.0235294 );
	- table->SetTableValue( 8007.0, 0.862745, 0.984314, 0.639216 );
	- table->SetTableValue( 8008.0, 0.909804, 0.572549, 0.129412 );
	- table->SetTableValue( 8009.0, 0.0156863, 0.447059, 0.054902 );
	- table->SetTableValue( 8010.0, 0.47451, 0.721569, 0.862745 );
	- table->SetTableValue( 8011.0, 0.921569, 0.0431373, 0.686275 );
	- table->SetTableValue( 8012.0, 0.0470588, 0.180392, 0.980392 );
	- table->SetTableValue( 8013.0, 0.796078, 0.713725, 0.560784 );
	- table->SetTableValue( 8014.0, 0.164706, 0.8, 0.654902 );
	- table->SetTableValue( 9000.0, 0.117647, 0.0196078, 0.117647 );
	- table->SetTableValue( 9001.0, 0.117647, 0.392157, 0.176471 );
	- table->SetTableValue( 9002.0, 0.509804, 0.392157, 0.647059 );
	- table->SetTableValue( 9003.0, 0.411765, 0.0980392, 0.0196078 );
	- table->SetTableValue( 9004.0, 0.490196, 0.27451, 0.215686 );
	- table->SetTableValue( 9005.0, 0.882353, 0.0784314, 0.411765 );
	- table->SetTableValue( 9006.0, 0.882353, 0.0784314, 0.0588235 );
	- table->SetTableValue( 9500.0, 0.117647, 0.215686, 0.117647 );
	- table->SetTableValue( 9501.0, 0.117647, 0.588235, 0.176471 );
	- table->SetTableValue( 9502.0, 0.509804, 0.588235, 0.647059 );
	- table->SetTableValue( 9503.0, 0.411765, 0.294118, 0.0196078 );
	- table->SetTableValue( 9504.0, 0.490196, 0.470588, 0.215686 );
	- table->SetTableValue( 9505.0, 0.882353, 0.27451, 0.411765 );
	- table->SetTableValue( 9506.0, 0.882353, 0.27451, 0.0588235 );
	- table->SetTableValue( 11100.0, 0, 0, 0, 0);
	- table->SetTableValue( 11101.0, 0.0901961, 0.862745, 0.235294 );
	- table->SetTableValue( 11102.0, 0.0901961, 0.235294, 0.705882 );
	- table->SetTableValue( 11103.0, 0.247059, 0.392157, 0.235294 );
	- table->SetTableValue( 11104.0, 0.247059, 0.0784314, 0.862745 );
	- table->SetTableValue( 11105.0, 0.0509804, 0, 0.980392 );
	- table->SetTableValue( 11106.0, 0.101961, 0.235294, 0 );
	- table->SetTableValue( 11107.0, 0.101961, 0.235294, 0.294118 );
	- table->SetTableValue( 11108.0, 0.101961, 0.235294, 0.588235 );
	- table->SetTableValue( 11109.0, 0.0980392, 0.235294, 0.980392 );
	- table->SetTableValue( 11110.0, 0.235294, 0.0980392, 0.0980392 );
	- table->SetTableValue( 11111.0, 0.705882, 0.0784314, 0.0784314 );
	- table->SetTableValue( 11112.0, 0.862745, 0.0784314, 0.392157 );
	- table->SetTableValue( 11113.0, 0.54902, 0.235294, 0.235294 );
	- table->SetTableValue( 11114.0, 0.705882, 0.862745, 0.54902 );
	- table->SetTableValue( 11115.0, 0.54902, 0.392157, 0.705882 );
	- table->SetTableValue( 11116.0, 0.705882, 0.0784314, 0.54902 );
	- table->SetTableValue( 11117.0, 0.0901961, 0.0392157, 0.0392157 );
	- table->SetTableValue( 11118.0, 0.882353, 0.54902, 0.54902 );
	- table->SetTableValue( 11119.0, 0.705882, 0.235294, 0.705882 );
	- table->SetTableValue( 11120.0, 0.0784314, 0.862745, 0.235294 );
	- table->SetTableValue( 11121.0, 0.235294, 0.0784314, 0.54902 );
	- table->SetTableValue( 11122.0, 0.862745, 0.705882, 0.54902 );
	- table->SetTableValue( 11123.0, 0.254902, 0.392157, 0.0784314 );
	- table->SetTableValue( 11124.0, 0.862745, 0.235294, 0.0784314 );
	- table->SetTableValue( 11125.0, 0.0784314, 0.235294, 0.862745 );
	- table->SetTableValue( 11126.0, 0.392157, 0.392157, 0.235294 );
	- table->SetTableValue( 11127.0, 0.862745, 0.705882, 0.862745 );
	- table->SetTableValue( 11128.0, 0.0784314, 0.705882, 0.54902 );
	- table->SetTableValue( 11129.0, 0.235294, 0.54902, 0.705882 );
	- table->SetTableValue( 11130.0, 0.0980392, 0.0784314, 0.54902 );
	- table->SetTableValue( 11131.0, 0.0784314, 0.235294, 0.392157 );
	- table->SetTableValue( 11132.0, 0.235294, 0.862745, 0.0784314 );
	- table->SetTableValue( 11133.0, 0.235294, 0.235294, 0.862745 );
	- table->SetTableValue( 11134.0, 0.862745, 0.235294, 0.862745 );
	- table->SetTableValue( 11135.0, 0.254902, 0.862745, 0.235294 );
	- table->SetTableValue( 11136.0, 0.0980392, 0.54902, 0.0784314 );
	- table->SetTableValue( 11137.0, 0.862745, 0.862745, 0.392157 );
	- table->SetTableValue( 11138.0, 0.705882, 0.235294, 0.235294 );
	- table->SetTableValue( 11139.0, 0.239216, 0.0784314, 0.862745 );
	- table->SetTableValue( 11140.0, 0.239216, 0.0784314, 0.235294 );
	- table->SetTableValue( 11141.0, 0.239216, 0.235294, 0.392157 );
	- table->SetTableValue( 11142.0, 0.0980392, 0.0980392, 0.0980392 );
	- table->SetTableValue( 11143.0, 0.54902, 0.0784314, 0.235294 );
	- table->SetTableValue( 11144.0, 0.862745, 0.705882, 0.0784314 );
	- table->SetTableValue( 11145.0, 0.247059, 0.705882, 0.705882 );
	- table->SetTableValue( 11146.0, 0.866667, 0.0784314, 0.0392157 );
	- table->SetTableValue( 11147.0, 0.866667, 0.0784314, 0.392157 );
	- table->SetTableValue( 11148.0, 0.866667, 0.235294, 0.54902 );
	- table->SetTableValue( 11149.0, 0.866667, 0.0784314, 0.862745 );
	- table->SetTableValue( 11150.0, 0.239216, 0.862745, 0.862745 );
	- table->SetTableValue( 11151.0, 0.392157, 0.784314, 0.784314 );
	- table->SetTableValue( 11152.0, 0.0392157, 0.784314, 0.784314 );
	- table->SetTableValue( 11153.0, 0.866667, 0.862745, 0.0784314 );
	- table->SetTableValue( 11154.0, 0.552941, 0.0784314, 0.392157 );
	- table->SetTableValue( 11155.0, 0.239216, 0.862745, 0.392157 );
	- table->SetTableValue( 11156.0, 0.552941, 0.235294, 0.0784314 );
	- table->SetTableValue( 11157.0, 0.560784, 0.0784314, 0.862745 );
	- table->SetTableValue( 11158.0, 0.396078, 0.235294, 0.862745 );
	- table->SetTableValue( 11159.0, 0.0823529, 0.0784314, 0.54902 );
	- table->SetTableValue( 11160.0, 0.239216, 0.0784314, 0.705882 );
	- table->SetTableValue( 11161.0, 0.866667, 0.54902, 0.0784314 );
	- table->SetTableValue( 11162.0, 0.552941, 0.392157, 0.862745 );
	- table->SetTableValue( 11163.0, 0.866667, 0.392157, 0.0784314 );
	- table->SetTableValue( 11164.0, 0.709804, 0.784314, 0.0784314 );
	- table->SetTableValue( 11165.0, 0.396078, 0.0784314, 0.0784314 );
	- table->SetTableValue( 11166.0, 0.396078, 0.392157, 0.705882 );
	- table->SetTableValue( 11167.0, 0.709804, 0.862745, 0.0784314 );
	- table->SetTableValue( 11168.0, 0.0823529, 0.54902, 0.784314 );
	- table->SetTableValue( 11169.0, 0.0823529, 0.0784314, 0.941176 );
	- table->SetTableValue( 11170.0, 0.0823529, 0.0784314, 0.784314 );
	- table->SetTableValue( 11171.0, 0.0823529, 0.0784314, 0.235294 );
	- table->SetTableValue( 11172.0, 0.396078, 0.235294, 0.235294 );
	- table->SetTableValue( 11173.0, 0.0823529, 0.705882, 0.705882 );
	- table->SetTableValue( 11174.0, 0.87451, 0.862745, 0.235294 );
	- table->SetTableValue( 11175.0, 0.866667, 0.235294, 0.235294 );
	- table->SetTableValue( 12100.0, 0, 0, 0, 0);
	- table->SetTableValue( 12101.0, 0.0901961, 0.862745, 0.235294 );
	- table->SetTableValue( 12102.0, 0.0901961, 0.235294, 0.705882 );
	- table->SetTableValue( 12103.0, 0.247059, 0.392157, 0.235294 );
	- table->SetTableValue( 12104.0, 0.247059, 0.0784314, 0.862745 );
	- table->SetTableValue( 12105.0, 0.0509804, 0, 0.980392 );
	- table->SetTableValue( 12106.0, 0.101961, 0.235294, 0 );
	- table->SetTableValue( 12107.0, 0.101961, 0.235294, 0.294118 );
	- table->SetTableValue( 12108.0, 0.101961, 0.235294, 0.588235 );
	- table->SetTableValue( 12109.0, 0.0980392, 0.235294, 0.980392 );
	- table->SetTableValue( 12110.0, 0.235294, 0.0980392, 0.0980392 );
	- table->SetTableValue( 12111.0, 0.705882, 0.0784314, 0.0784314 );
	- table->SetTableValue( 12112.0, 0.862745, 0.0784314, 0.392157 );
	- table->SetTableValue( 12113.0, 0.54902, 0.235294, 0.235294 );
	- table->SetTableValue( 12114.0, 0.705882, 0.862745, 0.54902 );
	- table->SetTableValue( 12115.0, 0.54902, 0.392157, 0.705882 );
	- table->SetTableValue( 12116.0, 0.705882, 0.0784314, 0.54902 );
	- table->SetTableValue( 12117.0, 0.0901961, 0.0392157, 0.0392157 );
	- table->SetTableValue( 12118.0, 0.882353, 0.54902, 0.54902 );
	- table->SetTableValue( 12119.0, 0.705882, 0.235294, 0.705882 );
	- table->SetTableValue( 12120.0, 0.0784314, 0.862745, 0.235294 );
	- table->SetTableValue( 12121.0, 0.235294, 0.0784314, 0.54902 );
	- table->SetTableValue( 12122.0, 0.862745, 0.705882, 0.54902 );
	- table->SetTableValue( 12123.0, 0.254902, 0.392157, 0.0784314 );
	- table->SetTableValue( 12124.0, 0.862745, 0.235294, 0.0784314 );
	- table->SetTableValue( 12125.0, 0.0784314, 0.235294, 0.862745 );
	- table->SetTableValue( 12126.0, 0.392157, 0.392157, 0.235294 );
	- table->SetTableValue( 12127.0, 0.862745, 0.705882, 0.862745 );
	- table->SetTableValue( 12128.0, 0.0784314, 0.705882, 0.54902 );
	- table->SetTableValue( 12129.0, 0.235294, 0.54902, 0.705882 );
	- table->SetTableValue( 12130.0, 0.0980392, 0.0784314, 0.54902 );
	- table->SetTableValue( 12131.0, 0.0784314, 0.235294, 0.392157 );
	- table->SetTableValue( 12132.0, 0.235294, 0.862745, 0.0784314 );
	- table->SetTableValue( 12133.0, 0.235294, 0.235294, 0.862745 );
	- table->SetTableValue( 12134.0, 0.862745, 0.235294, 0.862745 );
	- table->SetTableValue( 12135.0, 0.254902, 0.862745, 0.235294 );
	- table->SetTableValue( 12136.0, 0.0980392, 0.54902, 0.0784314 );
	- table->SetTableValue( 12137.0, 0.862745, 0.862745, 0.392157 );
	- table->SetTableValue( 12138.0, 0.705882, 0.235294, 0.235294 );
	- table->SetTableValue( 12139.0, 0.239216, 0.0784314, 0.862745 );
	- table->SetTableValue( 12140.0, 0.239216, 0.0784314, 0.235294 );
	- table->SetTableValue( 12141.0, 0.239216, 0.235294, 0.392157 );
	- table->SetTableValue( 12142.0, 0.0980392, 0.0980392, 0.0980392 );
	- table->SetTableValue( 12143.0, 0.54902, 0.0784314, 0.235294 );
	- table->SetTableValue( 12144.0, 0.862745, 0.705882, 0.0784314 );
	- table->SetTableValue( 12145.0, 0.247059, 0.705882, 0.705882 );
	- table->SetTableValue( 12146.0, 0.866667, 0.0784314, 0.0392157 );
	- table->SetTableValue( 12147.0, 0.866667, 0.0784314, 0.392157 );
	- table->SetTableValue( 12148.0, 0.866667, 0.235294, 0.54902 );
	- table->SetTableValue( 12149.0, 0.866667, 0.0784314, 0.862745 );
	- table->SetTableValue( 12150.0, 0.239216, 0.862745, 0.862745 );
	- table->SetTableValue( 12151.0, 0.392157, 0.784314, 0.784314 );
	- table->SetTableValue( 12152.0, 0.0392157, 0.784314, 0.784314 );
	- table->SetTableValue( 12153.0, 0.866667, 0.862745, 0.0784314 );
	- table->SetTableValue( 12154.0, 0.552941, 0.0784314, 0.392157 );
	- table->SetTableValue( 12155.0, 0.239216, 0.862745, 0.392157 );
	- table->SetTableValue( 12156.0, 0.552941, 0.235294, 0.0784314 );
	- table->SetTableValue( 12157.0, 0.560784, 0.0784314, 0.862745 );
	- table->SetTableValue( 12158.0, 0.396078, 0.235294, 0.862745 );
	- table->SetTableValue( 12159.0, 0.0823529, 0.0784314, 0.54902 );
	- table->SetTableValue( 12160.0, 0.239216, 0.0784314, 0.705882 );
	- table->SetTableValue( 12161.0, 0.866667, 0.54902, 0.0784314 );
	- table->SetTableValue( 12162.0, 0.552941, 0.392157, 0.862745 );
	- table->SetTableValue( 12163.0, 0.866667, 0.392157, 0.0784314 );
	- table->SetTableValue( 12164.0, 0.709804, 0.784314, 0.0784314 );
	- table->SetTableValue( 12165.0, 0.396078, 0.0784314, 0.0784314 );
	- table->SetTableValue( 12166.0, 0.396078, 0.392157, 0.705882 );
	- table->SetTableValue( 12167.0, 0.709804, 0.862745, 0.0784314 );
	- table->SetTableValue( 12168.0, 0.0823529, 0.54902, 0.784314 );
	- table->SetTableValue( 12169.0, 0.0823529, 0.0784314, 0.941176 );
	- table->SetTableValue( 12170.0, 0.0823529, 0.0784314, 0.784314 );
	- table->SetTableValue( 12171.0, 0.0823529, 0.0784314, 0.235294 );
	- table->SetTableValue( 12172.0, 0.396078, 0.235294, 0.235294 );
	- table->SetTableValue( 12173.0, 0.0823529, 0.705882, 0.705882 );
	- table->SetTableValue( 12174.0, 0.87451, 0.862745, 0.235294 );
	- table->SetTableValue( 12175.0, 0.866667, 0.235294, 0.235294 );
	- table->SetTableValue( 13100.0, 0, 0, 0, 0);
	- table->SetTableValue( 13101.0, 0.0901961, 0.862745, 0.235294 );
	- table->SetTableValue( 13102.0, 0.0901961, 0.235294, 0.705882 );
	- table->SetTableValue( 13103.0, 0.247059, 0.392157, 0.235294 );
	- table->SetTableValue( 13104.0, 0.247059, 0.0784314, 0.862745 );
	- table->SetTableValue( 13105.0, 0.0509804, 0, 0.980392 );
	- table->SetTableValue( 13106.0, 0.101961, 0.235294, 0 );
	- table->SetTableValue( 13107.0, 0.101961, 0.235294, 0.294118 );
	- table->SetTableValue( 13108.0, 0.101961, 0.235294, 0.588235 );
	- table->SetTableValue( 13109.0, 0.0980392, 0.235294, 0.980392 );
	- table->SetTableValue( 13110.0, 0.235294, 0.0980392, 0.0980392 );
	- table->SetTableValue( 13111.0, 0.705882, 0.0784314, 0.0784314 );
	- table->SetTableValue( 13112.0, 0.862745, 0.0784314, 0.392157 );
	- table->SetTableValue( 13113.0, 0.54902, 0.235294, 0.235294 );
	- table->SetTableValue( 13114.0, 0.705882, 0.862745, 0.54902 );
	- table->SetTableValue( 13115.0, 0.54902, 0.392157, 0.705882 );
	- table->SetTableValue( 13116.0, 0.705882, 0.0784314, 0.54902 );
	- table->SetTableValue( 13117.0, 0.0901961, 0.0392157, 0.0392157 );
	- table->SetTableValue( 13118.0, 0.882353, 0.54902, 0.54902 );
	- table->SetTableValue( 13119.0, 0.705882, 0.235294, 0.705882 );
	- table->SetTableValue( 13120.0, 0.0784314, 0.862745, 0.235294 );
	- table->SetTableValue( 13121.0, 0.235294, 0.0784314, 0.54902 );
	- table->SetTableValue( 13122.0, 0.862745, 0.705882, 0.54902 );
	- table->SetTableValue( 13123.0, 0.254902, 0.392157, 0.0784314 );
	- table->SetTableValue( 13124.0, 0.862745, 0.235294, 0.0784314 );
	- table->SetTableValue( 13125.0, 0.0784314, 0.235294, 0.862745 );
	- table->SetTableValue( 13126.0, 0.392157, 0.392157, 0.235294 );
	- table->SetTableValue( 13127.0, 0.862745, 0.705882, 0.862745 );
	- table->SetTableValue( 13128.0, 0.0784314, 0.705882, 0.54902 );
	- table->SetTableValue( 13129.0, 0.235294, 0.54902, 0.705882 );
	- table->SetTableValue( 13130.0, 0.0980392, 0.0784314, 0.54902 );
	- table->SetTableValue( 13131.0, 0.0784314, 0.235294, 0.392157 );
	- table->SetTableValue( 13132.0, 0.235294, 0.862745, 0.0784314 );
	- table->SetTableValue( 13133.0, 0.235294, 0.235294, 0.862745 );
	- table->SetTableValue( 13134.0, 0.862745, 0.235294, 0.862745 );
	- table->SetTableValue( 13135.0, 0.254902, 0.862745, 0.235294 );
	- table->SetTableValue( 13136.0, 0.0980392, 0.54902, 0.0784314 );
	- table->SetTableValue( 13137.0, 0.862745, 0.862745, 0.392157 );
	- table->SetTableValue( 13138.0, 0.705882, 0.235294, 0.235294 );
	- table->SetTableValue( 13139.0, 0.239216, 0.0784314, 0.862745 );
	- table->SetTableValue( 13140.0, 0.239216, 0.0784314, 0.235294 );
	- table->SetTableValue( 13141.0, 0.239216, 0.235294, 0.392157 );
	- table->SetTableValue( 13142.0, 0.0980392, 0.0980392, 0.0980392 );
	- table->SetTableValue( 13143.0, 0.54902, 0.0784314, 0.235294 );
	- table->SetTableValue( 13144.0, 0.862745, 0.705882, 0.0784314 );
	- table->SetTableValue( 13145.0, 0.247059, 0.705882, 0.705882 );
	- table->SetTableValue( 13146.0, 0.866667, 0.0784314, 0.0392157 );
	- table->SetTableValue( 13147.0, 0.866667, 0.0784314, 0.392157 );
	- table->SetTableValue( 13148.0, 0.866667, 0.235294, 0.54902 );
	- table->SetTableValue( 13149.0, 0.866667, 0.0784314, 0.862745 );
	- table->SetTableValue( 13150.0, 0.239216, 0.862745, 0.862745 );
	- table->SetTableValue( 13151.0, 0.392157, 0.784314, 0.784314 );
	- table->SetTableValue( 13152.0, 0.0392157, 0.784314, 0.784314 );
	- table->SetTableValue( 13153.0, 0.866667, 0.862745, 0.0784314 );
	- table->SetTableValue( 13154.0, 0.552941, 0.0784314, 0.392157 );
	- table->SetTableValue( 13155.0, 0.239216, 0.862745, 0.392157 );
	- table->SetTableValue( 13156.0, 0.552941, 0.235294, 0.0784314 );
	- table->SetTableValue( 13157.0, 0.560784, 0.0784314, 0.862745 );
	- table->SetTableValue( 13158.0, 0.396078, 0.235294, 0.862745 );
	- table->SetTableValue( 13159.0, 0.0823529, 0.0784314, 0.54902 );
	- table->SetTableValue( 13160.0, 0.239216, 0.0784314, 0.705882 );
	- table->SetTableValue( 13161.0, 0.866667, 0.54902, 0.0784314 );
	- table->SetTableValue( 13162.0, 0.552941, 0.392157, 0.862745 );
	- table->SetTableValue( 13163.0, 0.866667, 0.392157, 0.0784314 );
	- table->SetTableValue( 13164.0, 0.709804, 0.784314, 0.0784314 );
	- table->SetTableValue( 13165.0, 0.396078, 0.0784314, 0.0784314 );
	- table->SetTableValue( 13166.0, 0.396078, 0.392157, 0.705882 );
	- table->SetTableValue( 13167.0, 0.709804, 0.862745, 0.0784314 );
	- table->SetTableValue( 13168.0, 0.0823529, 0.54902, 0.784314 );
	- table->SetTableValue( 13169.0, 0.0823529, 0.0784314, 0.941176 );
	- table->SetTableValue( 13170.0, 0.0823529, 0.0784314, 0.784314 );
	- table->SetTableValue( 13171.0, 0.0823529, 0.0784314, 0.235294 );
	- table->SetTableValue( 13172.0, 0.396078, 0.235294, 0.235294 );
	- table->SetTableValue( 13173.0, 0.0823529, 0.705882, 0.705882 );
	- table->SetTableValue( 13174.0, 0.87451, 0.862745, 0.235294 );
	- table->SetTableValue( 13175.0, 0.866667, 0.235294, 0.235294 );
	- table->SetTableValue( 14100.0, 0, 0, 0, 0);
	- table->SetTableValue( 14101.0, 0.0901961, 0.862745, 0.235294 );
	- table->SetTableValue( 14102.0, 0.0901961, 0.235294, 0.705882 );
	- table->SetTableValue( 14103.0, 0.247059, 0.392157, 0.235294 );
	- table->SetTableValue( 14104.0, 0.247059, 0.0784314, 0.862745 );
	- table->SetTableValue( 14105.0, 0.0509804, 0, 0.980392 );
	- table->SetTableValue( 14106.0, 0.101961, 0.235294, 0 );
	- table->SetTableValue( 14107.0, 0.101961, 0.235294, 0.294118 );
	- table->SetTableValue( 14108.0, 0.101961, 0.235294, 0.588235 );
	- table->SetTableValue( 14109.0, 0.0980392, 0.235294, 0.980392 );
	- table->SetTableValue( 14110.0, 0.235294, 0.0980392, 0.0980392 );
	- table->SetTableValue( 14111.0, 0.705882, 0.0784314, 0.0784314 );
	- table->SetTableValue( 14112.0, 0.862745, 0.0784314, 0.392157 );
	- table->SetTableValue( 14113.0, 0.54902, 0.235294, 0.235294 );
	- table->SetTableValue( 14114.0, 0.705882, 0.862745, 0.54902 );
	- table->SetTableValue( 14115.0, 0.54902, 0.392157, 0.705882 );
	- table->SetTableValue( 14116.0, 0.705882, 0.0784314, 0.54902 );
	- table->SetTableValue( 14117.0, 0.0901961, 0.0392157, 0.0392157 );
	- table->SetTableValue( 14118.0, 0.882353, 0.54902, 0.54902 );
	- table->SetTableValue( 14119.0, 0.705882, 0.235294, 0.705882 );
	- table->SetTableValue( 14120.0, 0.0784314, 0.862745, 0.235294 );
	- table->SetTableValue( 14121.0, 0.235294, 0.0784314, 0.54902 );
	- table->SetTableValue( 14122.0, 0.862745, 0.705882, 0.54902 );
	- table->SetTableValue( 14123.0, 0.254902, 0.392157, 0.0784314 );
	- table->SetTableValue( 14124.0, 0.862745, 0.235294, 0.0784314 );
	- table->SetTableValue( 14125.0, 0.0784314, 0.235294, 0.862745 );
	- table->SetTableValue( 14126.0, 0.392157, 0.392157, 0.235294 );
	- table->SetTableValue( 14127.0, 0.862745, 0.705882, 0.862745 );
	- table->SetTableValue( 14128.0, 0.0784314, 0.705882, 0.54902 );
	- table->SetTableValue( 14129.0, 0.235294, 0.54902, 0.705882 );
	- table->SetTableValue( 14130.0, 0.0980392, 0.0784314, 0.54902 );
	- table->SetTableValue( 14131.0, 0.0784314, 0.235294, 0.392157 );
	- table->SetTableValue( 14132.0, 0.235294, 0.862745, 0.0784314 );
	- table->SetTableValue( 14133.0, 0.235294, 0.235294, 0.862745 );
	- table->SetTableValue( 14134.0, 0.862745, 0.235294, 0.862745 );
	- table->SetTableValue( 14135.0, 0.254902, 0.862745, 0.235294 );
	- table->SetTableValue( 14136.0, 0.0980392, 0.54902, 0.0784314 );
	- table->SetTableValue( 14137.0, 0.862745, 0.862745, 0.392157 );
	- table->SetTableValue( 14138.0, 0.705882, 0.235294, 0.235294 );
	- table->SetTableValue( 14139.0, 0.239216, 0.0784314, 0.862745 );
	- table->SetTableValue( 14140.0, 0.239216, 0.0784314, 0.235294 );
	- table->SetTableValue( 14141.0, 0.239216, 0.235294, 0.392157 );
	- table->SetTableValue( 14142.0, 0.0980392, 0.0980392, 0.0980392 );
	- table->SetTableValue( 14143.0, 0.54902, 0.0784314, 0.235294 );
	- table->SetTableValue( 14144.0, 0.862745, 0.705882, 0.0784314 );
	- table->SetTableValue( 14145.0, 0.247059, 0.705882, 0.705882 );
	- table->SetTableValue( 14146.0, 0.866667, 0.0784314, 0.0392157 );
	- table->SetTableValue( 14147.0, 0.866667, 0.0784314, 0.392157 );
	- table->SetTableValue( 14148.0, 0.866667, 0.235294, 0.54902 );
	- table->SetTableValue( 14149.0, 0.866667, 0.0784314, 0.862745 );
	- table->SetTableValue( 14150.0, 0.239216, 0.862745, 0.862745 );
	- table->SetTableValue( 14151.0, 0.392157, 0.784314, 0.784314 );
	- table->SetTableValue( 14152.0, 0.0392157, 0.784314, 0.784314 );
	- table->SetTableValue( 14153.0, 0.866667, 0.862745, 0.0784314 );
	- table->SetTableValue( 14154.0, 0.552941, 0.0784314, 0.392157 );
	- table->SetTableValue( 14155.0, 0.239216, 0.862745, 0.392157 );
	- table->SetTableValue( 14156.0, 0.552941, 0.235294, 0.0784314 );
	- table->SetTableValue( 14157.0, 0.560784, 0.0784314, 0.862745 );
	- table->SetTableValue( 14158.0, 0.396078, 0.235294, 0.862745 );
	- table->SetTableValue( 14159.0, 0.0823529, 0.0784314, 0.54902 );
	- table->SetTableValue( 14160.0, 0.239216, 0.0784314, 0.705882 );
	- table->SetTableValue( 14161.0, 0.866667, 0.54902, 0.0784314 );
	- table->SetTableValue( 14162.0, 0.552941, 0.392157, 0.862745 );
	- table->SetTableValue( 14163.0, 0.866667, 0.392157, 0.0784314 );
	- table->SetTableValue( 14164.0, 0.709804, 0.784314, 0.0784314 );
	- table->SetTableValue( 14165.0, 0.396078, 0.0784314, 0.0784314 );
	- table->SetTableValue( 14166.0, 0.396078, 0.392157, 0.705882 );
	- table->SetTableValue( 14167.0, 0.709804, 0.862745, 0.0784314 );
	- table->SetTableValue( 14168.0, 0.0823529, 0.54902, 0.784314 );
	- table->SetTableValue( 14169.0, 0.0823529, 0.0784314, 0.941176 );
	- table->SetTableValue( 14170.0, 0.0823529, 0.0784314, 0.784314 );
	- table->SetTableValue( 14171.0, 0.0823529, 0.0784314, 0.235294 );
	- table->SetTableValue( 14172.0, 0.396078, 0.235294, 0.235294 );
	- table->SetTableValue( 14173.0, 0.0823529, 0.705882, 0.705882 );
	- table->SetTableValue( 14174.0, 0.87451, 0.862745, 0.235294 );
	- table->SetTableValue( 14175.0, 0.866667, 0.235294, 0.235294 );
	- mitk::LookupTable::Pointer lookupTable = mitk::LookupTable::New();
	- lookupTable->SetVtkLookupTable( table );
	- return lookupTable;
	-}
	-
	-TransferFunction::Pointer FreeSurferParcellationTranslator::CreateTransferFunction()
	-{
	- mitk::TransferFunction::Pointer transferFunction = mitk::TransferFunction::New();
	- transferFunction->AddRGBPoint( 1.0, 0.27451, 0.509804, 0.705882 );
	- transferFunction->AddRGBPoint( 2.0, 0.960784, 0.960784, 0.960784 );
	- transferFunction->AddRGBPoint( 3.0, 0.803922, 0.243137, 0.305882 );
	- transferFunction->AddRGBPoint( 4.0, 0.470588, 0.0705882, 0.52549 );
	- transferFunction->AddRGBPoint( 5.0, 0.768627, 0.227451, 0.980392 );
	- transferFunction->AddRGBPoint( 6.0, 0, 0.580392, 0 );
	- transferFunction->AddRGBPoint( 7.0, 0.862745, 0.972549, 0.643137 );
	- transferFunction->AddRGBPoint( 8.0, 0.901961, 0.580392, 0.133333 );
	- transferFunction->AddRGBPoint( 9.0, 0, 0.462745, 0.054902 );
	- transferFunction->AddRGBPoint( 10.0, 0, 0.462745, 0.054902 );
	- transferFunction->AddRGBPoint( 11.0, 0.478431, 0.729412, 0.862745 );
	- transferFunction->AddRGBPoint( 12.0, 0.92549, 0.0509804, 0.690196 );
	- transferFunction->AddRGBPoint( 13.0, 0.0470588, 0.188235, 1 );
	- transferFunction->AddRGBPoint( 14.0, 0.8, 0.713725, 0.556863 );
	- transferFunction->AddRGBPoint( 15.0, 0.164706, 0.8, 0.643137 );
	- transferFunction->AddRGBPoint( 16.0, 0.466667, 0.623529, 0.690196 );
	- transferFunction->AddRGBPoint( 17.0, 0.862745, 0.847059, 0.0784314 );
	- transferFunction->AddRGBPoint( 18.0, 0.403922, 1, 1 );
	- transferFunction->AddRGBPoint( 19.0, 0.313725, 0.768627, 0.384314 );
	- transferFunction->AddRGBPoint( 20.0, 0.235294, 0.227451, 0.823529 );
	- transferFunction->AddRGBPoint( 21.0, 0.235294, 0.227451, 0.823529 );
	- transferFunction->AddRGBPoint( 22.0, 0.235294, 0.227451, 0.823529 );
	- transferFunction->AddRGBPoint( 23.0, 0.235294, 0.227451, 0.823529 );
	- transferFunction->AddRGBPoint( 24.0, 0.235294, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 25.0, 1, 0.647059, 0 );
	- transferFunction->AddRGBPoint( 26.0, 1, 0.647059, 0 );
	- transferFunction->AddRGBPoint( 27.0, 0, 1, 0.498039 );
	- transferFunction->AddRGBPoint( 28.0, 0.647059, 0.164706, 0.164706 );
	- transferFunction->AddRGBPoint( 29.0, 0.529412, 0.807843, 0.921569 );
	- transferFunction->AddRGBPoint( 30.0, 0.627451, 0.12549, 0.941176 );
	- transferFunction->AddRGBPoint( 31.0, 0, 0.784314, 0.784314 );
	- transferFunction->AddRGBPoint( 32.0, 0.392157, 0.196078, 0.392157 );
	- transferFunction->AddRGBPoint( 33.0, 0.529412, 0.196078, 0.290196 );
	- transferFunction->AddRGBPoint( 34.0, 0.478431, 0.529412, 0.196078 );
	- transferFunction->AddRGBPoint( 35.0, 0.2, 0.196078, 0.529412 );
	- transferFunction->AddRGBPoint( 36.0, 0.290196, 0.607843, 0.235294 );
	- transferFunction->AddRGBPoint( 37.0, 0.470588, 0.243137, 0.168627 );
	- transferFunction->AddRGBPoint( 38.0, 0.290196, 0.607843, 0.235294 );
	- transferFunction->AddRGBPoint( 39.0, 0.478431, 0.529412, 0.196078 );
	- transferFunction->AddRGBPoint( 40.0, 0.27451, 0.509804, 0.705882 );
	- transferFunction->AddRGBPoint( 41.0, 0, 0.882353, 0 );
	- transferFunction->AddRGBPoint( 42.0, 0.803922, 0.243137, 0.305882 );
	- transferFunction->AddRGBPoint( 43.0, 0.470588, 0.0705882, 0.52549 );
	- transferFunction->AddRGBPoint( 44.0, 0.768627, 0.227451, 0.980392 );
	- transferFunction->AddRGBPoint( 45.0, 0, 0.580392, 0 );
	- transferFunction->AddRGBPoint( 46.0, 0.862745, 0.972549, 0.643137 );
	- transferFunction->AddRGBPoint( 47.0, 0.901961, 0.580392, 0.133333 );
	- transferFunction->AddRGBPoint( 48.0, 0, 0.462745, 0.054902 );
	- transferFunction->AddRGBPoint( 49.0, 0, 0.462745, 0.054902 );
	- transferFunction->AddRGBPoint( 50.0, 0.478431, 0.729412, 0.862745 );
	- transferFunction->AddRGBPoint( 51.0, 0.92549, 0.0509804, 0.690196 );
	- transferFunction->AddRGBPoint( 52.0, 0.0509804, 0.188235, 1 );
	- transferFunction->AddRGBPoint( 53.0, 0.862745, 0.847059, 0.0784314 );
	- transferFunction->AddRGBPoint( 54.0, 0.403922, 1, 1 );
	- transferFunction->AddRGBPoint( 55.0, 0.313725, 0.768627, 0.384314 );
	- transferFunction->AddRGBPoint( 56.0, 0.235294, 0.227451, 0.823529 );
	- transferFunction->AddRGBPoint( 57.0, 1, 0.647059, 0 );
	- transferFunction->AddRGBPoint( 58.0, 1, 0.647059, 0 );
	- transferFunction->AddRGBPoint( 59.0, 0, 1, 0.498039 );
	- transferFunction->AddRGBPoint( 60.0, 0.647059, 0.164706, 0.164706 );
	- transferFunction->AddRGBPoint( 61.0, 0.529412, 0.807843, 0.921569 );
	- transferFunction->AddRGBPoint( 62.0, 0.627451, 0.12549, 0.941176 );
	- transferFunction->AddRGBPoint( 63.0, 0, 0.784314, 0.866667 );
	- transferFunction->AddRGBPoint( 64.0, 0.392157, 0.196078, 0.392157 );
	- transferFunction->AddRGBPoint( 65.0, 0.529412, 0.196078, 0.290196 );
	- transferFunction->AddRGBPoint( 66.0, 0.478431, 0.529412, 0.196078 );
	- transferFunction->AddRGBPoint( 67.0, 0.2, 0.196078, 0.529412 );
	- transferFunction->AddRGBPoint( 68.0, 0.290196, 0.607843, 0.235294 );
	- transferFunction->AddRGBPoint( 69.0, 0.470588, 0.243137, 0.168627 );
	- transferFunction->AddRGBPoint( 70.0, 0.290196, 0.607843, 0.235294 );
	- transferFunction->AddRGBPoint( 71.0, 0.478431, 0.529412, 0.196078 );
	- transferFunction->AddRGBPoint( 72.0, 0.470588, 0.745098, 0.588235 );
	- transferFunction->AddRGBPoint( 73.0, 0.478431, 0.529412, 0.196078 );
	- transferFunction->AddRGBPoint( 74.0, 0.478431, 0.529412, 0.196078 );
	- transferFunction->AddRGBPoint( 77.0, 0.784314, 0.27451, 1 );
	- transferFunction->AddRGBPoint( 78.0, 1, 0.580392, 0.0392157 );
	- transferFunction->AddRGBPoint( 79.0, 1, 0.580392, 0.0392157 );
	- transferFunction->AddRGBPoint( 80.0, 0.643137, 0.423529, 0.886275 );
	- transferFunction->AddRGBPoint( 81.0, 0.643137, 0.423529, 0.886275 );
	- transferFunction->AddRGBPoint( 82.0, 0.643137, 0.423529, 0.886275 );
	- transferFunction->AddRGBPoint( 83.0, 1, 0.854902, 0.72549 );
	- transferFunction->AddRGBPoint( 84.0, 1, 0.854902, 0.72549 );
	- transferFunction->AddRGBPoint( 85.0, 0.917647, 0.662745, 0.117647 );
	- transferFunction->AddRGBPoint( 192.0, 0.980392, 1, 0.196078 );
	- transferFunction->AddRGBPoint( 86.0, 0.784314, 0.470588, 1 );
	- transferFunction->AddRGBPoint( 87.0, 0.784314, 0.47451, 1 );
	- transferFunction->AddRGBPoint( 88.0, 0.784314, 0.478431, 1 );
	- transferFunction->AddRGBPoint( 96.0, 0.803922, 0.0392157, 0.490196 );
	- transferFunction->AddRGBPoint( 97.0, 0.803922, 0.0392157, 0.490196 );
	- transferFunction->AddRGBPoint( 98.0, 0.627451, 0.12549, 0.941176 );
	- transferFunction->AddRGBPoint( 100.0, 0.486275, 0.54902, 0.698039 );
	- transferFunction->AddRGBPoint( 101.0, 0.490196, 0.54902, 0.698039 );
	- transferFunction->AddRGBPoint( 102.0, 0.494118, 0.54902, 0.698039 );
	- transferFunction->AddRGBPoint( 103.0, 0.498039, 0.54902, 0.698039 );
	- transferFunction->AddRGBPoint( 104.0, 0.486275, 0.552941, 0.698039 );
	- transferFunction->AddRGBPoint( 105.0, 0.486275, 0.556863, 0.698039 );
	- transferFunction->AddRGBPoint( 106.0, 0.486275, 0.560784, 0.698039 );
	- transferFunction->AddRGBPoint( 107.0, 0.486275, 0.564706, 0.698039 );
	- transferFunction->AddRGBPoint( 108.0, 0.486275, 0.54902, 0.701961 );
	- transferFunction->AddRGBPoint( 109.0, 0.486275, 0.54902, 0.698039 );
	- transferFunction->AddRGBPoint( 110.0, 0.490196, 0.54902, 0.698039 );
	- transferFunction->AddRGBPoint( 111.0, 0.494118, 0.54902, 0.698039 );
	- transferFunction->AddRGBPoint( 112.0, 0.498039, 0.54902, 0.698039 );
	- transferFunction->AddRGBPoint( 113.0, 0.486275, 0.552941, 0.698039 );
	- transferFunction->AddRGBPoint( 114.0, 0.486275, 0.556863, 0.698039 );
	- transferFunction->AddRGBPoint( 115.0, 0.486275, 0.560784, 0.698039 );
	- transferFunction->AddRGBPoint( 116.0, 0.486275, 0.564706, 0.698039 );
	- transferFunction->AddRGBPoint( 117.0, 0.486275, 0.54902, 0.701961 );
	- transferFunction->AddRGBPoint( 118.0, 1, 0.0784314, 0.576471 );
	- transferFunction->AddRGBPoint( 119.0, 0.803922, 0.701961, 0.545098 );
	- transferFunction->AddRGBPoint( 120.0, 0.933333, 0.933333, 0.819608 );
	- transferFunction->AddRGBPoint( 121.0, 0.784314, 0.784314, 0.784314 );
	- transferFunction->AddRGBPoint( 122.0, 0.290196, 1, 0.290196 );
	- transferFunction->AddRGBPoint( 123.0, 0.933333, 0, 0 );
	- transferFunction->AddRGBPoint( 124.0, 0, 0, 0.545098 );
	- transferFunction->AddRGBPoint( 125.0, 0.678431, 1, 0.184314 );
	- transferFunction->AddRGBPoint( 126.0, 0.521569, 0.796078, 0.898039 );
	- transferFunction->AddRGBPoint( 127.0, 0.101961, 0.929412, 0.223529 );
	- transferFunction->AddRGBPoint( 128.0, 0.133333, 0.545098, 0.133333 );
	- transferFunction->AddRGBPoint( 129.0, 0.117647, 0.564706, 1 );
	- transferFunction->AddRGBPoint( 130.0, 0.576471, 0.0745098, 0.678431 );
	- transferFunction->AddRGBPoint( 131.0, 0.933333, 0.231373, 0.231373 );
	- transferFunction->AddRGBPoint( 132.0, 0.866667, 0.152941, 0.784314 );
	- transferFunction->AddRGBPoint( 133.0, 0.933333, 0.682353, 0.933333 );
	- transferFunction->AddRGBPoint( 134.0, 1, 0, 0 );
	- transferFunction->AddRGBPoint( 135.0, 0.282353, 0.239216, 0.545098 );
	- transferFunction->AddRGBPoint( 136.0, 0.0823529, 0.152941, 0.517647 );
	- transferFunction->AddRGBPoint( 137.0, 0.0823529, 0.152941, 0.517647 );
	- transferFunction->AddRGBPoint( 138.0, 0.254902, 0.529412, 0.0784314 );
	- transferFunction->AddRGBPoint( 139.0, 0.254902, 0.529412, 0.0784314 );
	- transferFunction->AddRGBPoint( 140.0, 0.52549, 0.0156863, 0.627451 );
	- transferFunction->AddRGBPoint( 142.0, 0.866667, 0.886275, 0.266667 );
	- transferFunction->AddRGBPoint( 143.0, 1, 1, 0.996078 );
	- transferFunction->AddRGBPoint( 144.0, 0.203922, 0.819608, 0.886275 );
	- transferFunction->AddRGBPoint( 145.0, 0.937255, 0.627451, 0.87451 );
	- transferFunction->AddRGBPoint( 146.0, 0.27451, 0.509804, 0.705882 );
	- transferFunction->AddRGBPoint( 147.0, 0.27451, 0.509804, 0.709804 );
	- transferFunction->AddRGBPoint( 148.0, 0.545098, 0.47451, 0.368627 );
	- transferFunction->AddRGBPoint( 149.0, 0.878431, 0.878431, 0.878431 );
	- transferFunction->AddRGBPoint( 150.0, 1, 0, 0 );
	- transferFunction->AddRGBPoint( 151.0, 0.803922, 0.803922, 0 );
	- transferFunction->AddRGBPoint( 152.0, 0.933333, 0.933333, 0.819608 );
	- transferFunction->AddRGBPoint( 153.0, 0.545098, 0.47451, 0.368627 );
	- transferFunction->AddRGBPoint( 154.0, 0.933333, 0.231373, 0.231373 );
	- transferFunction->AddRGBPoint( 155.0, 0.933333, 0.231373, 0.231373 );
	- transferFunction->AddRGBPoint( 156.0, 0.933333, 0.231373, 0.231373 );
	- transferFunction->AddRGBPoint( 157.0, 0.243137, 0.0392157, 0.803922 );
	- transferFunction->AddRGBPoint( 158.0, 0.243137, 0.0392157, 0.803922 );
	- transferFunction->AddRGBPoint( 159.0, 0, 0.462745, 0.054902 );
	- transferFunction->AddRGBPoint( 160.0, 0, 0.462745, 0.054902 );
	- transferFunction->AddRGBPoint( 161.0, 0.862745, 0.847059, 0.0823529 );
	- transferFunction->AddRGBPoint( 162.0, 0.862745, 0.847059, 0.0823529 );
	- transferFunction->AddRGBPoint( 163.0, 0.478431, 0.729412, 0.862745 );
	- transferFunction->AddRGBPoint( 164.0, 0.478431, 0.729412, 0.862745 );
	- transferFunction->AddRGBPoint( 165.0, 1, 0.647059, 0 );
	- transferFunction->AddRGBPoint( 166.0, 0.054902, 0.188235, 1 );
	- transferFunction->AddRGBPoint( 167.0, 0.65098, 0.164706, 0.164706 );
	- transferFunction->AddRGBPoint( 168.0, 0.47451, 0.0705882, 0.52549 );
	- transferFunction->AddRGBPoint( 169.0, 0.92549, 0.0509804, 0.498039 );
	- transferFunction->AddRGBPoint( 176.0, 0.92549, 0.0509804, 0.494118 );
	- transferFunction->AddRGBPoint( 170.0, 0.466667, 0.623529, 0.690196 );
	- transferFunction->AddRGBPoint( 171.0, 0.466667, 0, 0.690196 );
	- transferFunction->AddRGBPoint( 172.0, 0.466667, 0.392157, 0.690196 );
	- transferFunction->AddRGBPoint( 173.0, 0.466667, 0.784314, 0.690196 );
	- transferFunction->AddRGBPoint( 174.0, 0.466667, 0.623529, 0.392157 );
	- transferFunction->AddRGBPoint( 175.0, 0.466667, 0.623529, 0.784314 );
	- transferFunction->AddRGBPoint( 180.0, 0.286275, 0.239216, 0.545098 );
	- transferFunction->AddRGBPoint( 181.0, 0.286275, 0.243137, 0.545098 );
	- transferFunction->AddRGBPoint( 193.0, 0, 0.768627, 1 );
	- transferFunction->AddRGBPoint( 194.0, 1, 0.643137, 0.643137 );
	- transferFunction->AddRGBPoint( 195.0, 0.768627, 0.768627, 0 );
	- transferFunction->AddRGBPoint( 196.0, 0, 0.392157, 1 );
	- transferFunction->AddRGBPoint( 197.0, 0.501961, 0.768627, 0.643137 );
	- transferFunction->AddRGBPoint( 198.0, 0, 0.494118, 0.294118 );
	- transferFunction->AddRGBPoint( 199.0, 0.501961, 0.376471, 0.25098 );
	- transferFunction->AddRGBPoint( 200.0, 0, 0.196078, 0.501961 );
	- transferFunction->AddRGBPoint( 201.0, 1, 0.8, 0.6 );
	- transferFunction->AddRGBPoint( 202.0, 1, 0.501961, 0.501961 );
	- transferFunction->AddRGBPoint( 203.0, 1, 1, 0 );
	- transferFunction->AddRGBPoint( 204.0, 0.25098, 0, 0.25098 );
	- transferFunction->AddRGBPoint( 205.0, 0, 0, 1 );
	- transferFunction->AddRGBPoint( 206.0, 1, 0, 0 );
	- transferFunction->AddRGBPoint( 207.0, 0.501961, 0.501961, 1 );
	- transferFunction->AddRGBPoint( 208.0, 0, 0.501961, 0 );
	- transferFunction->AddRGBPoint( 209.0, 0.768627, 0.627451, 0.501961 );
	- transferFunction->AddRGBPoint( 210.0, 0.12549, 0.784314, 1 );
	- transferFunction->AddRGBPoint( 211.0, 0.501961, 1, 0.501961 );
	- transferFunction->AddRGBPoint( 212.0, 0.8, 0.6, 0.8 );
	- transferFunction->AddRGBPoint( 213.0, 0.47451, 0.0666667, 0.533333 );
	- transferFunction->AddRGBPoint( 214.0, 0.501961, 0, 0 );
	- transferFunction->AddRGBPoint( 215.0, 0.501961, 0.12549, 1 );
	- transferFunction->AddRGBPoint( 216.0, 1, 0.8, 0.4 );
	- transferFunction->AddRGBPoint( 217.0, 0.501961, 0.501961, 0.501961 );
	- transferFunction->AddRGBPoint( 218.0, 0.407843, 1, 1 );
	- transferFunction->AddRGBPoint( 219.0, 0, 0.886275, 0 );
	- transferFunction->AddRGBPoint( 220.0, 0.803922, 0.247059, 0.305882 );
	- transferFunction->AddRGBPoint( 221.0, 0.772549, 0.227451, 0.980392 );
	- transferFunction->AddRGBPoint( 222.0, 0.129412, 0.588235, 0.980392 );
	- transferFunction->AddRGBPoint( 223.0, 0.886275, 0, 0 );
	- transferFunction->AddRGBPoint( 224.0, 0.392157, 0.392157, 0.392157 );
	- transferFunction->AddRGBPoint( 225.0, 0.772549, 0.588235, 0.980392 );
	- transferFunction->AddRGBPoint( 226.0, 0.666667, 0.666667, 1 );
	- transferFunction->AddRGBPoint( 250.0, 1, 0, 0 );
	- transferFunction->AddRGBPoint( 251.0, 0, 0, 0.25098 );
	- transferFunction->AddRGBPoint( 252.0, 0, 0, 0.439216 );
	- transferFunction->AddRGBPoint( 253.0, 0, 0, 0.627451 );
	- transferFunction->AddRGBPoint( 254.0, 0, 0, 0.815686 );
	- transferFunction->AddRGBPoint( 255.0, 0, 0, 1 );
	- transferFunction->AddRGBPoint( 331.0, 1, 0, 0 );
	- transferFunction->AddRGBPoint( 332.0, 1, 0.313725, 0 );
	- transferFunction->AddRGBPoint( 333.0, 1, 0.627451, 0 );
	- transferFunction->AddRGBPoint( 334.0, 1, 1, 0 );
	- transferFunction->AddRGBPoint( 335.0, 0, 1, 0 );
	- transferFunction->AddRGBPoint( 336.0, 1, 0, 0.627451 );
	- transferFunction->AddRGBPoint( 337.0, 1, 0, 1 );
	- transferFunction->AddRGBPoint( 338.0, 1, 0.196078, 0.313725 );
	- transferFunction->AddRGBPoint( 339.0, 0.313725, 1, 0.196078 );
	- transferFunction->AddRGBPoint( 340.0, 0.627451, 1, 0.196078 );
	- transferFunction->AddRGBPoint( 341.0, 0.627451, 0.784314, 1 );
	- transferFunction->AddRGBPoint( 342.0, 0, 1, 0.627451 );
	- transferFunction->AddRGBPoint( 343.0, 0, 0, 1 );
	- transferFunction->AddRGBPoint( 344.0, 0.313725, 0.196078, 1 );
	- transferFunction->AddRGBPoint( 345.0, 0.627451, 0, 1 );
	- transferFunction->AddRGBPoint( 346.0, 1, 0.823529, 0 );
	- transferFunction->AddRGBPoint( 347.0, 0, 0.627451, 1 );
	- transferFunction->AddRGBPoint( 348.0, 1, 0.784314, 0.313725 );
	- transferFunction->AddRGBPoint( 349.0, 1, 0.784314, 0.627451 );
	- transferFunction->AddRGBPoint( 350.0, 1, 0.313725, 0.784314 );
	- transferFunction->AddRGBPoint( 351.0, 1, 0.627451, 0.784314 );
	- transferFunction->AddRGBPoint( 352.0, 0.117647, 1, 0.313725 );
	- transferFunction->AddRGBPoint( 353.0, 0.313725, 0.784314, 1 );
	- transferFunction->AddRGBPoint( 354.0, 0.313725, 1, 0.784314 );
	- transferFunction->AddRGBPoint( 355.0, 0.764706, 1, 0.784314 );
	- transferFunction->AddRGBPoint( 356.0, 0.470588, 0.784314, 0.0784314 );
	- transferFunction->AddRGBPoint( 357.0, 0.666667, 0.0392157, 0.784314 );
	- transferFunction->AddRGBPoint( 358.0, 0.0784314, 0.509804, 0.705882 );
	- transferFunction->AddRGBPoint( 359.0, 0.0784314, 0.705882, 0.509804 );
	- transferFunction->AddRGBPoint( 400.0, 0.807843, 0.243137, 0.305882 );
	- transferFunction->AddRGBPoint( 401.0, 0.47451, 0.0705882, 0.52549 );
	- transferFunction->AddRGBPoint( 402.0, 0.780392, 0.227451, 0.980392 );
	- transferFunction->AddRGBPoint( 403.0, 0.00392157, 0.580392, 0 );
	- transferFunction->AddRGBPoint( 404.0, 0.866667, 0.972549, 0.643137 );
	- transferFunction->AddRGBPoint( 405.0, 0.905882, 0.580392, 0.133333 );
	- transferFunction->AddRGBPoint( 406.0, 0.00392157, 0.462745, 0.054902 );
	- transferFunction->AddRGBPoint( 407.0, 0.470588, 0.462745, 0.054902 );
	- transferFunction->AddRGBPoint( 408.0, 0.482353, 0.729412, 0.866667 );
	- transferFunction->AddRGBPoint( 409.0, 0.933333, 0.0509804, 0.694118 );
	- transferFunction->AddRGBPoint( 410.0, 0.482353, 0.729412, 0.862745 );
	- transferFunction->AddRGBPoint( 411.0, 0.541176, 0.0509804, 0.807843 );
	- transferFunction->AddRGBPoint( 412.0, 0.933333, 0.509804, 0.690196 );
	- transferFunction->AddRGBPoint( 413.0, 0.854902, 0.901961, 0.298039 );
	- transferFunction->AddRGBPoint( 414.0, 0.14902, 0.835294, 0.690196 );
	- transferFunction->AddRGBPoint( 415.0, 0.00392157, 0.882353, 0.690196 );
	- transferFunction->AddRGBPoint( 416.0, 0.00392157, 0.882353, 0.690196 );
	- transferFunction->AddRGBPoint( 417.0, 0.784314, 0.00784314, 0.392157 );
	- transferFunction->AddRGBPoint( 418.0, 0.784314, 0.00784314, 0.392157 );
	- transferFunction->AddRGBPoint( 419.0, 0.0196078, 0.784314, 0.352941 );
	- transferFunction->AddRGBPoint( 420.0, 0.0196078, 0.784314, 0.352941 );
	- transferFunction->AddRGBPoint( 421.0, 0.392157, 0.0196078, 0.784314 );
	- transferFunction->AddRGBPoint( 422.0, 0.0980392, 1, 0.392157 );
	- transferFunction->AddRGBPoint( 423.0, 0.0980392, 1, 0.392157 );
	- transferFunction->AddRGBPoint( 424.0, 0.901961, 0.027451, 0.392157 );
	- transferFunction->AddRGBPoint( 425.0, 0.901961, 0.027451, 0.392157 );
	- transferFunction->AddRGBPoint( 426.0, 0.392157, 0.0196078, 0.784314 );
	- transferFunction->AddRGBPoint( 427.0, 0.588235, 0.0392157, 0.784314 );
	- transferFunction->AddRGBPoint( 428.0, 0.588235, 0.0392157, 0.784314 );
	- transferFunction->AddRGBPoint( 429.0, 0.686275, 0.0392157, 0.690196 );
	- transferFunction->AddRGBPoint( 430.0, 0.686275, 0.0392157, 0.690196 );
	- transferFunction->AddRGBPoint( 431.0, 0.0392157, 0.392157, 1 );
	- transferFunction->AddRGBPoint( 432.0, 0.0392157, 0.392157, 1 );
	- transferFunction->AddRGBPoint( 433.0, 0.588235, 0.176471, 0.27451 );
	- transferFunction->AddRGBPoint( 434.0, 0.588235, 0.176471, 0.27451 );
	- transferFunction->AddRGBPoint( 435.0, 0.176471, 0.784314, 0.0588235 );
	- transferFunction->AddRGBPoint( 436.0, 0.176471, 0.784314, 0.0588235 );
	- transferFunction->AddRGBPoint( 437.0, 0.890196, 0.176471, 0.392157 );
	- transferFunction->AddRGBPoint( 438.0, 0.890196, 0.176471, 0.392157 );
	- transferFunction->AddRGBPoint( 439.0, 0.890196, 0.176471, 0.392157 );
	- transferFunction->AddRGBPoint( 498.0, 0.560784, 0.737255, 0.560784 );
	- transferFunction->AddRGBPoint( 499.0, 1, 0.972549, 0.862745 );
	- transferFunction->AddRGBPoint( 500.0, 0.0666667, 0.333333, 0.533333 );
	- transferFunction->AddRGBPoint( 501.0, 0.466667, 0.733333, 0.4 );
	- transferFunction->AddRGBPoint( 502.0, 0.8, 0.266667, 0.133333 );
	- transferFunction->AddRGBPoint( 503.0, 0.8, 0, 1 );
	- transferFunction->AddRGBPoint( 504.0, 0.866667, 0.733333, 0.0666667 );
	- transferFunction->AddRGBPoint( 505.0, 0.6, 0.866667, 0.933333 );
	- transferFunction->AddRGBPoint( 506.0, 0.2, 0.0666667, 0.0666667 );
	- transferFunction->AddRGBPoint( 507.0, 0, 0.466667, 0.333333 );
	- transferFunction->AddRGBPoint( 508.0, 0.0784314, 0.392157, 0.784314 );
	- transferFunction->AddRGBPoint( 550.0, 0.0666667, 0.333333, 0.537255 );
	- transferFunction->AddRGBPoint( 551.0, 0.466667, 0.733333, 0.403922 );
	- transferFunction->AddRGBPoint( 552.0, 0.8, 0.266667, 0.137255 );
	- transferFunction->AddRGBPoint( 553.0, 0.8, 0, 0.996078 );
	- transferFunction->AddRGBPoint( 554.0, 0.866667, 0.733333, 0.0627451 );
	- transferFunction->AddRGBPoint( 555.0, 0.6, 0.866667, 0.937255 );
	- transferFunction->AddRGBPoint( 556.0, 0.2, 0.0666667, 0.0705882 );
	- transferFunction->AddRGBPoint( 557.0, 0, 0.466667, 0.337255 );
	- transferFunction->AddRGBPoint( 558.0, 0.0784314, 0.392157, 0.788235 );
	- transferFunction->AddRGBPoint( 600.0, 0.996078, 0.996078, 0.996078 );
	- transferFunction->AddRGBPoint( 601.0, 0.27451, 0.509804, 0.705882 );
	- transferFunction->AddRGBPoint( 602.0, 0.960784, 0.960784, 0.960784 );
	- transferFunction->AddRGBPoint( 603.0, 0.803922, 0.243137, 0.305882 );
	- transferFunction->AddRGBPoint( 604.0, 0.470588, 0.0705882, 0.52549 );
	- transferFunction->AddRGBPoint( 605.0, 0.768627, 0.227451, 0.980392 );
	- transferFunction->AddRGBPoint( 606.0, 0, 0.580392, 0 );
	- transferFunction->AddRGBPoint( 607.0, 0.862745, 0.972549, 0.643137 );
	- transferFunction->AddRGBPoint( 608.0, 0.901961, 0.580392, 0.133333 );
	- transferFunction->AddRGBPoint( 609.0, 0, 0.462745, 0.054902 );
	- transferFunction->AddRGBPoint( 610.0, 0, 0.462745, 0.054902 );
	- transferFunction->AddRGBPoint( 611.0, 0.478431, 0.729412, 0.862745 );
	- transferFunction->AddRGBPoint( 612.0, 0.92549, 0.0509804, 0.690196 );
	- transferFunction->AddRGBPoint( 613.0, 0.0470588, 0.188235, 1 );
	- transferFunction->AddRGBPoint( 614.0, 0.8, 0.713725, 0.556863 );
	- transferFunction->AddRGBPoint( 615.0, 0.164706, 0.8, 0.643137 );
	- transferFunction->AddRGBPoint( 616.0, 0.466667, 0.623529, 0.690196 );
	- transferFunction->AddRGBPoint( 617.0, 0.862745, 0.847059, 0.0784314 );
	- transferFunction->AddRGBPoint( 618.0, 0.403922, 1, 1 );
	- transferFunction->AddRGBPoint( 619.0, 0.313725, 0.768627, 0.384314 );
	- transferFunction->AddRGBPoint( 620.0, 0.235294, 0.227451, 0.823529 );
	- transferFunction->AddRGBPoint( 621.0, 0.235294, 0.227451, 0.823529 );
	- transferFunction->AddRGBPoint( 622.0, 0.235294, 0.227451, 0.823529 );
	- transferFunction->AddRGBPoint( 623.0, 0.235294, 0.227451, 0.823529 );
	- transferFunction->AddRGBPoint( 624.0, 0.235294, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 625.0, 1, 0.647059, 0 );
	- transferFunction->AddRGBPoint( 626.0, 1, 0.647059, 0 );
	- transferFunction->AddRGBPoint( 627.0, 0, 1, 0.498039 );
	- transferFunction->AddRGBPoint( 628.0, 0.647059, 0.164706, 0.164706 );
	- transferFunction->AddRGBPoint( 640.0, 0.8, 0, 0 );
	- transferFunction->AddRGBPoint( 641.0, 1, 0, 0 );
	- transferFunction->AddRGBPoint( 642.0, 0, 0, 1 );
	- transferFunction->AddRGBPoint( 643.0, 0.117647, 0.564706, 1 );
	- transferFunction->AddRGBPoint( 644.0, 0.392157, 0.831373, 0.929412 );
	- transferFunction->AddRGBPoint( 645.0, 0.854902, 0.647059, 0.12549 );
	- transferFunction->AddRGBPoint( 646.0, 1, 0.843137, 0 );
	- transferFunction->AddRGBPoint( 647.0, 1, 1, 0.65098 );
	- transferFunction->AddRGBPoint( 648.0, 0.6, 0, 0.8 );
	- transferFunction->AddRGBPoint( 649.0, 0.6, 0.552941, 0.819608 );
	- transferFunction->AddRGBPoint( 650.0, 0.8, 0.8, 1 );
	- transferFunction->AddRGBPoint( 651.0, 0.121569, 0.831373, 0.760784 );
	- transferFunction->AddRGBPoint( 652.0, 0.0117647, 1, 0.929412 );
	- transferFunction->AddRGBPoint( 653.0, 0.8, 1, 1 );
	- transferFunction->AddRGBPoint( 654.0, 0.337255, 0.290196, 0.576471 );
	- transferFunction->AddRGBPoint( 655.0, 0.447059, 0.447059, 0.745098 );
	- transferFunction->AddRGBPoint( 656.0, 0.721569, 0.698039, 1 );
	- transferFunction->AddRGBPoint( 657.0, 0.494118, 0.541176, 0.145098 );
	- transferFunction->AddRGBPoint( 658.0, 0.741176, 0.772549, 0.458824 );
	- transferFunction->AddRGBPoint( 659.0, 0.941176, 0.901961, 0.54902 );
	- transferFunction->AddRGBPoint( 660.0, 0.8, 0, 0 );
	- transferFunction->AddRGBPoint( 661.0, 1, 0, 0 );
	- transferFunction->AddRGBPoint( 662.0, 0, 0, 1 );
	- transferFunction->AddRGBPoint( 663.0, 0.117647, 0.564706, 1 );
	- transferFunction->AddRGBPoint( 664.0, 0.392157, 0.831373, 0.929412 );
	- transferFunction->AddRGBPoint( 665.0, 0.854902, 0.647059, 0.12549 );
	- transferFunction->AddRGBPoint( 666.0, 1, 0.843137, 0 );
	- transferFunction->AddRGBPoint( 667.0, 1, 1, 0.65098 );
	- transferFunction->AddRGBPoint( 668.0, 0.6, 0, 0.8 );
	- transferFunction->AddRGBPoint( 669.0, 0.6, 0.552941, 0.819608 );
	- transferFunction->AddRGBPoint( 670.0, 0.8, 0.8, 1 );
	- transferFunction->AddRGBPoint( 671.0, 0.121569, 0.831373, 0.760784 );
	- transferFunction->AddRGBPoint( 672.0, 0.0117647, 1, 0.929412 );
	- transferFunction->AddRGBPoint( 673.0, 0.8, 1, 1 );
	- transferFunction->AddRGBPoint( 674.0, 0.337255, 0.290196, 0.576471 );
	- transferFunction->AddRGBPoint( 675.0, 0.447059, 0.447059, 0.745098 );
	- transferFunction->AddRGBPoint( 676.0, 0.721569, 0.698039, 1 );
	- transferFunction->AddRGBPoint( 677.0, 0.494118, 0.541176, 0.145098 );
	- transferFunction->AddRGBPoint( 678.0, 0.741176, 0.772549, 0.458824 );
	- transferFunction->AddRGBPoint( 679.0, 0.941176, 0.901961, 0.54902 );
	- transferFunction->AddRGBPoint( 701.0, 0.470588, 0.0705882, 0.52549 );
	- transferFunction->AddRGBPoint( 702.0, 0.803922, 0.243137, 0.305882 );
	- transferFunction->AddRGBPoint( 703.0, 0, 0.882353, 0 );
	- transferFunction->AddRGBPoint( 999.0, 1, 0.392157, 0.392157 );
	- transferFunction->AddRGBPoint( 1000.0, 0.0980392, 0.0196078, 0.0980392 );
	- transferFunction->AddRGBPoint( 1001.0, 0.0980392, 0.392157, 0.156863 );
	- transferFunction->AddRGBPoint( 1002.0, 0.490196, 0.392157, 0.627451 );
	- transferFunction->AddRGBPoint( 1003.0, 0.392157, 0.0980392, 0 );
	- transferFunction->AddRGBPoint( 1004.0, 0.470588, 0.27451, 0.196078 );
	- transferFunction->AddRGBPoint( 1005.0, 0.862745, 0.0784314, 0.392157 );
	- transferFunction->AddRGBPoint( 1006.0, 0.862745, 0.0784314, 0.0392157 );
	- transferFunction->AddRGBPoint( 1007.0, 0.705882, 0.862745, 0.54902 );
	- transferFunction->AddRGBPoint( 1008.0, 0.862745, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 1009.0, 0.705882, 0.156863, 0.470588 );
	- transferFunction->AddRGBPoint( 1010.0, 0.54902, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 1011.0, 0.0784314, 0.117647, 0.54902 );
	- transferFunction->AddRGBPoint( 1012.0, 0.137255, 0.294118, 0.196078 );
	- transferFunction->AddRGBPoint( 1013.0, 0.882353, 0.54902, 0.54902 );
	- transferFunction->AddRGBPoint( 1014.0, 0.784314, 0.137255, 0.294118 );
	- transferFunction->AddRGBPoint( 1015.0, 0.627451, 0.392157, 0.196078 );
	- transferFunction->AddRGBPoint( 1016.0, 0.0784314, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 1017.0, 0.235294, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 1018.0, 0.862745, 0.705882, 0.54902 );
	- transferFunction->AddRGBPoint( 1019.0, 0.0784314, 0.392157, 0.196078 );
	- transferFunction->AddRGBPoint( 1020.0, 0.862745, 0.235294, 0.0784314 );
	- transferFunction->AddRGBPoint( 1021.0, 0.470588, 0.392157, 0.235294 );
	- transferFunction->AddRGBPoint( 1022.0, 0.862745, 0.0784314, 0.0784314 );
	- transferFunction->AddRGBPoint( 1023.0, 0.862745, 0.705882, 0.862745 );
	- transferFunction->AddRGBPoint( 1024.0, 0.235294, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 1025.0, 0.627451, 0.54902, 0.705882 );
	- transferFunction->AddRGBPoint( 1026.0, 0.313725, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 1027.0, 0.294118, 0.196078, 0.490196 );
	- transferFunction->AddRGBPoint( 1028.0, 0.0784314, 0.862745, 0.627451 );
	- transferFunction->AddRGBPoint( 1029.0, 0.0784314, 0.705882, 0.54902 );
	- transferFunction->AddRGBPoint( 1030.0, 0.54902, 0.862745, 0.862745 );
	- transferFunction->AddRGBPoint( 1031.0, 0.313725, 0.627451, 0.0784314 );
	- transferFunction->AddRGBPoint( 1032.0, 0.392157, 0, 0.392157 );
	- transferFunction->AddRGBPoint( 1033.0, 0.27451, 0.27451, 0.27451 );
	- transferFunction->AddRGBPoint( 1034.0, 0.588235, 0.588235, 0.784314 );
	- transferFunction->AddRGBPoint( 1035.0, 1, 0.752941, 0.12549 );
	- transferFunction->AddRGBPoint( 2000.0, 0.0980392, 0.0196078, 0.0980392 );
	- transferFunction->AddRGBPoint( 2001.0, 0.0980392, 0.392157, 0.156863 );
	- transferFunction->AddRGBPoint( 2002.0, 0.490196, 0.392157, 0.627451 );
	- transferFunction->AddRGBPoint( 2003.0, 0.392157, 0.0980392, 0 );
	- transferFunction->AddRGBPoint( 2004.0, 0.470588, 0.27451, 0.196078 );
	- transferFunction->AddRGBPoint( 2005.0, 0.862745, 0.0784314, 0.392157 );
	- transferFunction->AddRGBPoint( 2006.0, 0.862745, 0.0784314, 0.0392157 );
	- transferFunction->AddRGBPoint( 2007.0, 0.705882, 0.862745, 0.54902 );
	- transferFunction->AddRGBPoint( 2008.0, 0.862745, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 2009.0, 0.705882, 0.156863, 0.470588 );
	- transferFunction->AddRGBPoint( 2010.0, 0.54902, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 2011.0, 0.0784314, 0.117647, 0.54902 );
	- transferFunction->AddRGBPoint( 2012.0, 0.137255, 0.294118, 0.196078 );
	- transferFunction->AddRGBPoint( 2013.0, 0.882353, 0.54902, 0.54902 );
	- transferFunction->AddRGBPoint( 2014.0, 0.784314, 0.137255, 0.294118 );
	- transferFunction->AddRGBPoint( 2015.0, 0.627451, 0.392157, 0.196078 );
	- transferFunction->AddRGBPoint( 2016.0, 0.0784314, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 2017.0, 0.235294, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 2018.0, 0.862745, 0.705882, 0.54902 );
	- transferFunction->AddRGBPoint( 2019.0, 0.0784314, 0.392157, 0.196078 );
	- transferFunction->AddRGBPoint( 2020.0, 0.862745, 0.235294, 0.0784314 );
	- transferFunction->AddRGBPoint( 2021.0, 0.470588, 0.392157, 0.235294 );
	- transferFunction->AddRGBPoint( 2022.0, 0.862745, 0.0784314, 0.0784314 );
	- transferFunction->AddRGBPoint( 2023.0, 0.862745, 0.705882, 0.862745 );
	- transferFunction->AddRGBPoint( 2024.0, 0.235294, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 2025.0, 0.627451, 0.54902, 0.705882 );
	- transferFunction->AddRGBPoint( 2026.0, 0.313725, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 2027.0, 0.294118, 0.196078, 0.490196 );
	- transferFunction->AddRGBPoint( 2028.0, 0.0784314, 0.862745, 0.627451 );
	- transferFunction->AddRGBPoint( 2029.0, 0.0784314, 0.705882, 0.54902 );
	- transferFunction->AddRGBPoint( 2030.0, 0.54902, 0.862745, 0.862745 );
	- transferFunction->AddRGBPoint( 2031.0, 0.313725, 0.627451, 0.0784314 );
	- transferFunction->AddRGBPoint( 2032.0, 0.392157, 0, 0.392157 );
	- transferFunction->AddRGBPoint( 2033.0, 0.27451, 0.27451, 0.27451 );
	- transferFunction->AddRGBPoint( 2034.0, 0.588235, 0.588235, 0.784314 );
	- transferFunction->AddRGBPoint( 2035.0, 1, 0.752941, 0.12549 );
	- transferFunction->AddRGBPoint( 3000.0, 0.901961, 0.980392, 0.901961 );
	- transferFunction->AddRGBPoint( 3001.0, 0.901961, 0.607843, 0.843137 );
	- transferFunction->AddRGBPoint( 3002.0, 0.509804, 0.607843, 0.372549 );
	- transferFunction->AddRGBPoint( 3003.0, 0.607843, 0.901961, 1 );
	- transferFunction->AddRGBPoint( 3004.0, 0.529412, 0.72549, 0.803922 );
	- transferFunction->AddRGBPoint( 3005.0, 0.137255, 0.921569, 0.607843 );
	- transferFunction->AddRGBPoint( 3006.0, 0.137255, 0.921569, 0.960784 );
	- transferFunction->AddRGBPoint( 3007.0, 0.294118, 0.137255, 0.45098 );
	- transferFunction->AddRGBPoint( 3008.0, 0.137255, 0.764706, 0.137255 );
	- transferFunction->AddRGBPoint( 3009.0, 0.294118, 0.843137, 0.529412 );
	- transferFunction->AddRGBPoint( 3010.0, 0.45098, 0.921569, 0.45098 );
	- transferFunction->AddRGBPoint( 3011.0, 0.921569, 0.882353, 0.45098 );
	- transferFunction->AddRGBPoint( 3012.0, 0.862745, 0.705882, 0.803922 );
	- transferFunction->AddRGBPoint( 3013.0, 0.117647, 0.45098, 0.45098 );
	- transferFunction->AddRGBPoint( 3014.0, 0.215686, 0.862745, 0.705882 );
	- transferFunction->AddRGBPoint( 3015.0, 0.372549, 0.607843, 0.803922 );
	- transferFunction->AddRGBPoint( 3016.0, 0.921569, 0.137255, 0.764706 );
	- transferFunction->AddRGBPoint( 3017.0, 0.764706, 0.137255, 0.764706 );
	- transferFunction->AddRGBPoint( 3018.0, 0.137255, 0.294118, 0.45098 );
	- transferFunction->AddRGBPoint( 3019.0, 0.921569, 0.607843, 0.803922 );
	- transferFunction->AddRGBPoint( 3020.0, 0.137255, 0.764706, 0.921569 );
	- transferFunction->AddRGBPoint( 3021.0, 0.529412, 0.607843, 0.764706 );
	- transferFunction->AddRGBPoint( 3022.0, 0.137255, 0.921569, 0.921569 );
	- transferFunction->AddRGBPoint( 3023.0, 0.137255, 0.294118, 0.137255 );
	- transferFunction->AddRGBPoint( 3024.0, 0.764706, 0.921569, 0.137255 );
	- transferFunction->AddRGBPoint( 3025.0, 0.372549, 0.45098, 0.294118 );
	- transferFunction->AddRGBPoint( 3026.0, 0.686275, 0.921569, 0.45098 );
	- transferFunction->AddRGBPoint( 3027.0, 0.705882, 0.803922, 0.509804 );
	- transferFunction->AddRGBPoint( 3028.0, 0.921569, 0.137255, 0.372549 );
	- transferFunction->AddRGBPoint( 3029.0, 0.921569, 0.294118, 0.45098 );
	- transferFunction->AddRGBPoint( 3030.0, 0.45098, 0.137255, 0.137255 );
	- transferFunction->AddRGBPoint( 3031.0, 0.686275, 0.372549, 0.921569 );
	- transferFunction->AddRGBPoint( 3032.0, 0.607843, 1, 0.607843 );
	- transferFunction->AddRGBPoint( 3033.0, 0.72549, 0.72549, 0.72549 );
	- transferFunction->AddRGBPoint( 3034.0, 0.411765, 0.411765, 0.215686 );
	- transferFunction->AddRGBPoint( 3035.0, 0.996078, 0.74902, 0.121569 );
	- transferFunction->AddRGBPoint( 4000.0, 0.901961, 0.980392, 0.901961 );
	- transferFunction->AddRGBPoint( 4001.0, 0.901961, 0.607843, 0.843137 );
	- transferFunction->AddRGBPoint( 4002.0, 0.509804, 0.607843, 0.372549 );
	- transferFunction->AddRGBPoint( 4003.0, 0.607843, 0.901961, 1 );
	- transferFunction->AddRGBPoint( 4004.0, 0.529412, 0.72549, 0.803922 );
	- transferFunction->AddRGBPoint( 4005.0, 0.137255, 0.921569, 0.607843 );
	- transferFunction->AddRGBPoint( 4006.0, 0.137255, 0.921569, 0.960784 );
	- transferFunction->AddRGBPoint( 4007.0, 0.294118, 0.137255, 0.45098 );
	- transferFunction->AddRGBPoint( 4008.0, 0.137255, 0.764706, 0.137255 );
	- transferFunction->AddRGBPoint( 4009.0, 0.294118, 0.843137, 0.529412 );
	- transferFunction->AddRGBPoint( 4010.0, 0.45098, 0.921569, 0.45098 );
	- transferFunction->AddRGBPoint( 4011.0, 0.921569, 0.882353, 0.45098 );
	- transferFunction->AddRGBPoint( 4012.0, 0.862745, 0.705882, 0.803922 );
	- transferFunction->AddRGBPoint( 4013.0, 0.117647, 0.45098, 0.45098 );
	- transferFunction->AddRGBPoint( 4014.0, 0.215686, 0.862745, 0.705882 );
	- transferFunction->AddRGBPoint( 4015.0, 0.372549, 0.607843, 0.803922 );
	- transferFunction->AddRGBPoint( 4016.0, 0.921569, 0.137255, 0.764706 );
	- transferFunction->AddRGBPoint( 4017.0, 0.764706, 0.137255, 0.764706 );
	- transferFunction->AddRGBPoint( 4018.0, 0.137255, 0.294118, 0.45098 );
	- transferFunction->AddRGBPoint( 4019.0, 0.921569, 0.607843, 0.803922 );
	- transferFunction->AddRGBPoint( 4020.0, 0.137255, 0.764706, 0.921569 );
	- transferFunction->AddRGBPoint( 4021.0, 0.529412, 0.607843, 0.764706 );
	- transferFunction->AddRGBPoint( 4022.0, 0.137255, 0.921569, 0.921569 );
	- transferFunction->AddRGBPoint( 4023.0, 0.137255, 0.294118, 0.137255 );
	- transferFunction->AddRGBPoint( 4024.0, 0.764706, 0.921569, 0.137255 );
	- transferFunction->AddRGBPoint( 4025.0, 0.372549, 0.45098, 0.294118 );
	- transferFunction->AddRGBPoint( 4026.0, 0.686275, 0.921569, 0.45098 );
	- transferFunction->AddRGBPoint( 4027.0, 0.705882, 0.803922, 0.509804 );
	- transferFunction->AddRGBPoint( 4028.0, 0.921569, 0.137255, 0.372549 );
	- transferFunction->AddRGBPoint( 4029.0, 0.921569, 0.294118, 0.45098 );
	- transferFunction->AddRGBPoint( 4030.0, 0.45098, 0.137255, 0.137255 );
	- transferFunction->AddRGBPoint( 4031.0, 0.686275, 0.372549, 0.921569 );
	- transferFunction->AddRGBPoint( 4032.0, 0.607843, 1, 0.607843 );
	- transferFunction->AddRGBPoint( 4033.0, 0.72549, 0.72549, 0.72549 );
	- transferFunction->AddRGBPoint( 4034.0, 0.411765, 0.411765, 0.215686 );
	- transferFunction->AddRGBPoint( 4035.0, 0.996078, 0.74902, 0.121569 );
	- transferFunction->AddRGBPoint( 1101.0, 0.196078, 0.196078, 0.196078 );
	- transferFunction->AddRGBPoint( 1102.0, 0.705882, 0.0784314, 0.117647 );
	- transferFunction->AddRGBPoint( 1103.0, 0.235294, 0.0980392, 0.0980392 );
	- transferFunction->AddRGBPoint( 1104.0, 0.0980392, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 1200.0, 0.0980392, 0.235294, 0.239216 );
	- transferFunction->AddRGBPoint( 1201.0, 0.0980392, 0.352941, 0.235294 );
	- transferFunction->AddRGBPoint( 1202.0, 0.0980392, 0.470588, 0.235294 );
	- transferFunction->AddRGBPoint( 1205.0, 0.0980392, 0.588235, 0.235294 );
	- transferFunction->AddRGBPoint( 1206.0, 0.0980392, 0.705882, 0.235294 );
	- transferFunction->AddRGBPoint( 1207.0, 0.0980392, 0.823529, 0.235294 );
	- transferFunction->AddRGBPoint( 1210.0, 0.0980392, 0.588235, 0.352941 );
	- transferFunction->AddRGBPoint( 1211.0, 0.0980392, 0.705882, 0.352941 );
	- transferFunction->AddRGBPoint( 1212.0, 0.0980392, 0.823529, 0.352941 );
	- transferFunction->AddRGBPoint( 1105.0, 0.705882, 0.0784314, 0.0784314 );
	- transferFunction->AddRGBPoint( 1106.0, 0.862745, 0.0784314, 0.392157 );
	- transferFunction->AddRGBPoint( 1107.0, 0.54902, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 1108.0, 0.705882, 0.862745, 0.54902 );
	- transferFunction->AddRGBPoint( 1109.0, 0.54902, 0.392157, 0.705882 );
	- transferFunction->AddRGBPoint( 1110.0, 0.705882, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 1111.0, 0.54902, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 1112.0, 0.0823529, 0.0392157, 0.0392157 );
	- transferFunction->AddRGBPoint( 1113.0, 0.882353, 0.54902, 0.54902 );
	- transferFunction->AddRGBPoint( 1114.0, 0.0901961, 0.235294, 0.705882 );
	- transferFunction->AddRGBPoint( 1115.0, 0.705882, 0.235294, 0.705882 );
	- transferFunction->AddRGBPoint( 1116.0, 0.0784314, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 1117.0, 0.235294, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 1118.0, 0.862745, 0.705882, 0.54902 );
	- transferFunction->AddRGBPoint( 1119.0, 0.254902, 0.392157, 0.0784314 );
	- transferFunction->AddRGBPoint( 1120.0, 0.862745, 0.235294, 0.0784314 );
	- transferFunction->AddRGBPoint( 1121.0, 0.235294, 0.392157, 0.235294 );
	- transferFunction->AddRGBPoint( 1122.0, 0.0784314, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 1123.0, 0.392157, 0.392157, 0.235294 );
	- transferFunction->AddRGBPoint( 1124.0, 0.862745, 0.705882, 0.862745 );
	- transferFunction->AddRGBPoint( 1125.0, 0.0784314, 0.705882, 0.54902 );
	- transferFunction->AddRGBPoint( 1126.0, 0.235294, 0.54902, 0.705882 );
	- transferFunction->AddRGBPoint( 1127.0, 0.0980392, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 1128.0, 0.0784314, 0.235294, 0.392157 );
	- transferFunction->AddRGBPoint( 1129.0, 0.235294, 0.862745, 0.0784314 );
	- transferFunction->AddRGBPoint( 1130.0, 0.235294, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 1131.0, 0.862745, 0.862745, 0.392157 );
	- transferFunction->AddRGBPoint( 1132.0, 0.705882, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 1133.0, 0.235294, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 1134.0, 0.862745, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 1135.0, 0.254902, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 1136.0, 0.0980392, 0.54902, 0.0784314 );
	- transferFunction->AddRGBPoint( 1137.0, 0.0509804, 0, 0.980392 );
	- transferFunction->AddRGBPoint( 1138.0, 0.239216, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 1139.0, 0.239216, 0.0784314, 0.235294 );
	- transferFunction->AddRGBPoint( 1140.0, 0.239216, 0.235294, 0.392157 );
	- transferFunction->AddRGBPoint( 1141.0, 0.0980392, 0.0980392, 0.0980392 );
	- transferFunction->AddRGBPoint( 1142.0, 0.54902, 0.0784314, 0.235294 );
	- transferFunction->AddRGBPoint( 1143.0, 0.862745, 0.705882, 0.0784314 );
	- transferFunction->AddRGBPoint( 1144.0, 0.247059, 0.705882, 0.705882 );
	- transferFunction->AddRGBPoint( 1145.0, 0.866667, 0.0784314, 0.0392157 );
	- transferFunction->AddRGBPoint( 1146.0, 0.0823529, 0.862745, 0.0784314 );
	- transferFunction->AddRGBPoint( 1147.0, 0.717647, 0.392157, 0.0784314 );
	- transferFunction->AddRGBPoint( 1148.0, 0.866667, 0.0784314, 0.392157 );
	- transferFunction->AddRGBPoint( 1149.0, 0.866667, 0.235294, 0.54902 );
	- transferFunction->AddRGBPoint( 1150.0, 0.866667, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 1151.0, 0.239216, 0.862745, 0.862745 );
	- transferFunction->AddRGBPoint( 1152.0, 0.392157, 0.784314, 0.784314 );
	- transferFunction->AddRGBPoint( 1153.0, 0.0392157, 0.784314, 0.784314 );
	- transferFunction->AddRGBPoint( 1154.0, 0.866667, 0.862745, 0.0784314 );
	- transferFunction->AddRGBPoint( 1155.0, 0.552941, 0.0784314, 0.392157 );
	- transferFunction->AddRGBPoint( 1156.0, 0.239216, 0.862745, 0.392157 );
	- transferFunction->AddRGBPoint( 1157.0, 0.0823529, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 1158.0, 0.552941, 0.235294, 0.0784314 );
	- transferFunction->AddRGBPoint( 1159.0, 0.560784, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 1160.0, 0.239216, 0.0784314, 0.705882 );
	- transferFunction->AddRGBPoint( 1161.0, 0.396078, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 1162.0, 0.0823529, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 1163.0, 0.866667, 0.54902, 0.0784314 );
	- transferFunction->AddRGBPoint( 1164.0, 0.552941, 0.392157, 0.862745 );
	- transferFunction->AddRGBPoint( 1165.0, 0.396078, 0.0784314, 0.0784314 );
	- transferFunction->AddRGBPoint( 1166.0, 0.866667, 0.392157, 0.0784314 );
	- transferFunction->AddRGBPoint( 1167.0, 0.709804, 0.784314, 0.0784314 );
	- transferFunction->AddRGBPoint( 1168.0, 0.0823529, 0.705882, 0.54902 );
	- transferFunction->AddRGBPoint( 1169.0, 0.396078, 0.392157, 0.705882 );
	- transferFunction->AddRGBPoint( 1170.0, 0.709804, 0.862745, 0.0784314 );
	- transferFunction->AddRGBPoint( 1171.0, 0.0823529, 0.54902, 0.784314 );
	- transferFunction->AddRGBPoint( 1172.0, 0.0823529, 0.0784314, 0.941176 );
	- transferFunction->AddRGBPoint( 1173.0, 0.0823529, 0.0784314, 0.784314 );
	- transferFunction->AddRGBPoint( 1174.0, 0.239216, 0.705882, 0.235294 );
	- transferFunction->AddRGBPoint( 1175.0, 0.239216, 0.705882, 0.980392 );
	- transferFunction->AddRGBPoint( 1176.0, 0.0823529, 0.0784314, 0.235294 );
	- transferFunction->AddRGBPoint( 1177.0, 0.396078, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 1178.0, 0.0823529, 0.862745, 0.862745 );
	- transferFunction->AddRGBPoint( 1179.0, 0.0823529, 0.705882, 0.705882 );
	- transferFunction->AddRGBPoint( 1180.0, 0.87451, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 1181.0, 0.866667, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 2101.0, 0.196078, 0.196078, 0.196078 );
	- transferFunction->AddRGBPoint( 2102.0, 0.705882, 0.0784314, 0.117647 );
	- transferFunction->AddRGBPoint( 2103.0, 0.235294, 0.0980392, 0.0980392 );
	- transferFunction->AddRGBPoint( 2104.0, 0.0980392, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 2105.0, 0.705882, 0.0784314, 0.0784314 );
	- transferFunction->AddRGBPoint( 2106.0, 0.862745, 0.0784314, 0.392157 );
	- transferFunction->AddRGBPoint( 2107.0, 0.54902, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 2108.0, 0.705882, 0.862745, 0.54902 );
	- transferFunction->AddRGBPoint( 2109.0, 0.54902, 0.392157, 0.705882 );
	- transferFunction->AddRGBPoint( 2110.0, 0.705882, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 2111.0, 0.54902, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 2112.0, 0.0823529, 0.0392157, 0.0392157 );
	- transferFunction->AddRGBPoint( 2113.0, 0.882353, 0.54902, 0.54902 );
	- transferFunction->AddRGBPoint( 2114.0, 0.0901961, 0.235294, 0.705882 );
	- transferFunction->AddRGBPoint( 2115.0, 0.705882, 0.235294, 0.705882 );
	- transferFunction->AddRGBPoint( 2116.0, 0.0784314, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 2117.0, 0.235294, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 2118.0, 0.862745, 0.705882, 0.54902 );
	- transferFunction->AddRGBPoint( 2119.0, 0.254902, 0.392157, 0.0784314 );
	- transferFunction->AddRGBPoint( 2120.0, 0.862745, 0.235294, 0.0784314 );
	- transferFunction->AddRGBPoint( 2121.0, 0.235294, 0.392157, 0.235294 );
	- transferFunction->AddRGBPoint( 2122.0, 0.0784314, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 2123.0, 0.392157, 0.392157, 0.235294 );
	- transferFunction->AddRGBPoint( 2124.0, 0.862745, 0.705882, 0.862745 );
	- transferFunction->AddRGBPoint( 2125.0, 0.0784314, 0.705882, 0.54902 );
	- transferFunction->AddRGBPoint( 2126.0, 0.235294, 0.54902, 0.705882 );
	- transferFunction->AddRGBPoint( 2127.0, 0.0980392, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 2128.0, 0.0784314, 0.235294, 0.392157 );
	- transferFunction->AddRGBPoint( 2129.0, 0.235294, 0.862745, 0.0784314 );
	- transferFunction->AddRGBPoint( 2130.0, 0.235294, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 2131.0, 0.862745, 0.862745, 0.392157 );
	- transferFunction->AddRGBPoint( 2132.0, 0.705882, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 2133.0, 0.235294, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 2134.0, 0.862745, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 2135.0, 0.254902, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 2136.0, 0.0980392, 0.54902, 0.0784314 );
	- transferFunction->AddRGBPoint( 2137.0, 0.0509804, 0, 0.980392 );
	- transferFunction->AddRGBPoint( 2138.0, 0.239216, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 2139.0, 0.239216, 0.0784314, 0.235294 );
	- transferFunction->AddRGBPoint( 2140.0, 0.239216, 0.235294, 0.392157 );
	- transferFunction->AddRGBPoint( 2141.0, 0.0980392, 0.0980392, 0.0980392 );
	- transferFunction->AddRGBPoint( 2142.0, 0.54902, 0.0784314, 0.235294 );
	- transferFunction->AddRGBPoint( 2143.0, 0.862745, 0.705882, 0.0784314 );
	- transferFunction->AddRGBPoint( 2144.0, 0.247059, 0.705882, 0.705882 );
	- transferFunction->AddRGBPoint( 2145.0, 0.866667, 0.0784314, 0.0392157 );
	- transferFunction->AddRGBPoint( 2146.0, 0.0823529, 0.862745, 0.0784314 );
	- transferFunction->AddRGBPoint( 2147.0, 0.717647, 0.392157, 0.0784314 );
	- transferFunction->AddRGBPoint( 2148.0, 0.866667, 0.0784314, 0.392157 );
	- transferFunction->AddRGBPoint( 2149.0, 0.866667, 0.235294, 0.54902 );
	- transferFunction->AddRGBPoint( 2150.0, 0.866667, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 2151.0, 0.239216, 0.862745, 0.862745 );
	- transferFunction->AddRGBPoint( 2152.0, 0.392157, 0.784314, 0.784314 );
	- transferFunction->AddRGBPoint( 2153.0, 0.0392157, 0.784314, 0.784314 );
	- transferFunction->AddRGBPoint( 2154.0, 0.866667, 0.862745, 0.0784314 );
	- transferFunction->AddRGBPoint( 2155.0, 0.552941, 0.0784314, 0.392157 );
	- transferFunction->AddRGBPoint( 2156.0, 0.239216, 0.862745, 0.392157 );
	- transferFunction->AddRGBPoint( 2157.0, 0.0823529, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 2158.0, 0.552941, 0.235294, 0.0784314 );
	- transferFunction->AddRGBPoint( 2159.0, 0.560784, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 2160.0, 0.239216, 0.0784314, 0.705882 );
	- transferFunction->AddRGBPoint( 2161.0, 0.396078, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 2162.0, 0.0823529, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 2163.0, 0.866667, 0.54902, 0.0784314 );
	- transferFunction->AddRGBPoint( 2164.0, 0.552941, 0.392157, 0.862745 );
	- transferFunction->AddRGBPoint( 2165.0, 0.396078, 0.0784314, 0.0784314 );
	- transferFunction->AddRGBPoint( 2166.0, 0.866667, 0.392157, 0.0784314 );
	- transferFunction->AddRGBPoint( 2167.0, 0.709804, 0.784314, 0.0784314 );
	- transferFunction->AddRGBPoint( 2168.0, 0.0823529, 0.705882, 0.54902 );
	- transferFunction->AddRGBPoint( 2169.0, 0.396078, 0.392157, 0.705882 );
	- transferFunction->AddRGBPoint( 2170.0, 0.709804, 0.862745, 0.0784314 );
	- transferFunction->AddRGBPoint( 2171.0, 0.0823529, 0.54902, 0.784314 );
	- transferFunction->AddRGBPoint( 2172.0, 0.0823529, 0.0784314, 0.941176 );
	- transferFunction->AddRGBPoint( 2173.0, 0.0823529, 0.0784314, 0.784314 );
	- transferFunction->AddRGBPoint( 2174.0, 0.239216, 0.705882, 0.235294 );
	- transferFunction->AddRGBPoint( 2175.0, 0.239216, 0.705882, 0.980392 );
	- transferFunction->AddRGBPoint( 2176.0, 0.0823529, 0.0784314, 0.235294 );
	- transferFunction->AddRGBPoint( 2177.0, 0.396078, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 2178.0, 0.0823529, 0.862745, 0.862745 );
	- transferFunction->AddRGBPoint( 2179.0, 0.0823529, 0.705882, 0.705882 );
	- transferFunction->AddRGBPoint( 2180.0, 0.87451, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 2181.0, 0.866667, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 2200.0, 0.0980392, 0.235294, 0.239216 );
	- transferFunction->AddRGBPoint( 2201.0, 0.0980392, 0.352941, 0.235294 );
	- transferFunction->AddRGBPoint( 2202.0, 0.0980392, 0.470588, 0.235294 );
	- transferFunction->AddRGBPoint( 2205.0, 0.0980392, 0.588235, 0.235294 );
	- transferFunction->AddRGBPoint( 2206.0, 0.0980392, 0.705882, 0.235294 );
	- transferFunction->AddRGBPoint( 2207.0, 0.0980392, 0.823529, 0.235294 );
	- transferFunction->AddRGBPoint( 2210.0, 0.0980392, 0.588235, 0.352941 );
	- transferFunction->AddRGBPoint( 2211.0, 0.0980392, 0.705882, 0.352941 );
	- transferFunction->AddRGBPoint( 2212.0, 0.0980392, 0.823529, 0.352941 );
	- transferFunction->AddRGBPoint( 3101.0, 0.196078, 0.196078, 0.196078 );
	- transferFunction->AddRGBPoint( 3102.0, 0.705882, 0.0784314, 0.117647 );
	- transferFunction->AddRGBPoint( 3103.0, 0.235294, 0.0980392, 0.0980392 );
	- transferFunction->AddRGBPoint( 3104.0, 0.0980392, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 3105.0, 0.705882, 0.0784314, 0.0784314 );
	- transferFunction->AddRGBPoint( 3106.0, 0.862745, 0.0784314, 0.392157 );
	- transferFunction->AddRGBPoint( 3107.0, 0.54902, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 3108.0, 0.705882, 0.862745, 0.54902 );
	- transferFunction->AddRGBPoint( 3109.0, 0.54902, 0.392157, 0.705882 );
	- transferFunction->AddRGBPoint( 3110.0, 0.705882, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 3111.0, 0.54902, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 3112.0, 0.0823529, 0.0392157, 0.0392157 );
	- transferFunction->AddRGBPoint( 3113.0, 0.882353, 0.54902, 0.54902 );
	- transferFunction->AddRGBPoint( 3114.0, 0.0901961, 0.235294, 0.705882 );
	- transferFunction->AddRGBPoint( 3115.0, 0.705882, 0.235294, 0.705882 );
	- transferFunction->AddRGBPoint( 3116.0, 0.0784314, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 3117.0, 0.235294, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 3118.0, 0.862745, 0.705882, 0.54902 );
	- transferFunction->AddRGBPoint( 3119.0, 0.254902, 0.392157, 0.0784314 );
	- transferFunction->AddRGBPoint( 3120.0, 0.862745, 0.235294, 0.0784314 );
	- transferFunction->AddRGBPoint( 3121.0, 0.235294, 0.392157, 0.235294 );
	- transferFunction->AddRGBPoint( 3122.0, 0.0784314, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 3123.0, 0.392157, 0.392157, 0.235294 );
	- transferFunction->AddRGBPoint( 3124.0, 0.862745, 0.705882, 0.862745 );
	- transferFunction->AddRGBPoint( 3125.0, 0.0784314, 0.705882, 0.54902 );
	- transferFunction->AddRGBPoint( 3126.0, 0.235294, 0.54902, 0.705882 );
	- transferFunction->AddRGBPoint( 3127.0, 0.0980392, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 3128.0, 0.0784314, 0.235294, 0.392157 );
	- transferFunction->AddRGBPoint( 3129.0, 0.235294, 0.862745, 0.0784314 );
	- transferFunction->AddRGBPoint( 3130.0, 0.235294, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 3131.0, 0.862745, 0.862745, 0.392157 );
	- transferFunction->AddRGBPoint( 3132.0, 0.705882, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 3133.0, 0.235294, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 3134.0, 0.862745, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 3135.0, 0.254902, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 3136.0, 0.0980392, 0.54902, 0.0784314 );
	- transferFunction->AddRGBPoint( 3137.0, 0.0509804, 0, 0.980392 );
	- transferFunction->AddRGBPoint( 3138.0, 0.239216, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 3139.0, 0.239216, 0.0784314, 0.235294 );
	- transferFunction->AddRGBPoint( 3140.0, 0.239216, 0.235294, 0.392157 );
	- transferFunction->AddRGBPoint( 3141.0, 0.0980392, 0.0980392, 0.0980392 );
	- transferFunction->AddRGBPoint( 3142.0, 0.54902, 0.0784314, 0.235294 );
	- transferFunction->AddRGBPoint( 3143.0, 0.862745, 0.705882, 0.0784314 );
	- transferFunction->AddRGBPoint( 3144.0, 0.247059, 0.705882, 0.705882 );
	- transferFunction->AddRGBPoint( 3145.0, 0.866667, 0.0784314, 0.0392157 );
	- transferFunction->AddRGBPoint( 3146.0, 0.0823529, 0.862745, 0.0784314 );
	- transferFunction->AddRGBPoint( 3147.0, 0.717647, 0.392157, 0.0784314 );
	- transferFunction->AddRGBPoint( 3148.0, 0.866667, 0.0784314, 0.392157 );
	- transferFunction->AddRGBPoint( 3149.0, 0.866667, 0.235294, 0.54902 );
	- transferFunction->AddRGBPoint( 3150.0, 0.866667, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 3151.0, 0.239216, 0.862745, 0.862745 );
	- transferFunction->AddRGBPoint( 3152.0, 0.392157, 0.784314, 0.784314 );
	- transferFunction->AddRGBPoint( 3153.0, 0.0392157, 0.784314, 0.784314 );
	- transferFunction->AddRGBPoint( 3154.0, 0.866667, 0.862745, 0.0784314 );
	- transferFunction->AddRGBPoint( 3155.0, 0.552941, 0.0784314, 0.392157 );
	- transferFunction->AddRGBPoint( 3156.0, 0.239216, 0.862745, 0.392157 );
	- transferFunction->AddRGBPoint( 3157.0, 0.0823529, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 3158.0, 0.552941, 0.235294, 0.0784314 );
	- transferFunction->AddRGBPoint( 3159.0, 0.560784, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 3160.0, 0.239216, 0.0784314, 0.705882 );
	- transferFunction->AddRGBPoint( 3161.0, 0.396078, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 3162.0, 0.0823529, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 3163.0, 0.866667, 0.54902, 0.0784314 );
	- transferFunction->AddRGBPoint( 3164.0, 0.552941, 0.392157, 0.862745 );
	- transferFunction->AddRGBPoint( 3165.0, 0.396078, 0.0784314, 0.0784314 );
	- transferFunction->AddRGBPoint( 3166.0, 0.866667, 0.392157, 0.0784314 );
	- transferFunction->AddRGBPoint( 3167.0, 0.709804, 0.784314, 0.0784314 );
	- transferFunction->AddRGBPoint( 3168.0, 0.0823529, 0.705882, 0.54902 );
	- transferFunction->AddRGBPoint( 3169.0, 0.396078, 0.392157, 0.705882 );
	- transferFunction->AddRGBPoint( 3170.0, 0.709804, 0.862745, 0.0784314 );
	- transferFunction->AddRGBPoint( 3171.0, 0.0823529, 0.54902, 0.784314 );
	- transferFunction->AddRGBPoint( 3172.0, 0.0823529, 0.0784314, 0.941176 );
	- transferFunction->AddRGBPoint( 3173.0, 0.0823529, 0.0784314, 0.784314 );
	- transferFunction->AddRGBPoint( 3174.0, 0.239216, 0.705882, 0.235294 );
	- transferFunction->AddRGBPoint( 3175.0, 0.239216, 0.705882, 0.980392 );
	- transferFunction->AddRGBPoint( 3176.0, 0.0823529, 0.0784314, 0.235294 );
	- transferFunction->AddRGBPoint( 3177.0, 0.396078, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 3178.0, 0.0823529, 0.862745, 0.862745 );
	- transferFunction->AddRGBPoint( 3179.0, 0.0823529, 0.705882, 0.705882 );
	- transferFunction->AddRGBPoint( 3180.0, 0.87451, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 3181.0, 0.866667, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 4101.0, 0.196078, 0.196078, 0.196078 );
	- transferFunction->AddRGBPoint( 4102.0, 0.705882, 0.0784314, 0.117647 );
	- transferFunction->AddRGBPoint( 4103.0, 0.235294, 0.0980392, 0.0980392 );
	- transferFunction->AddRGBPoint( 4104.0, 0.0980392, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 4105.0, 0.705882, 0.0784314, 0.0784314 );
	- transferFunction->AddRGBPoint( 4106.0, 0.862745, 0.0784314, 0.392157 );
	- transferFunction->AddRGBPoint( 4107.0, 0.54902, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 4108.0, 0.705882, 0.862745, 0.54902 );
	- transferFunction->AddRGBPoint( 4109.0, 0.54902, 0.392157, 0.705882 );
	- transferFunction->AddRGBPoint( 4110.0, 0.705882, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 4111.0, 0.54902, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 4112.0, 0.0823529, 0.0392157, 0.0392157 );
	- transferFunction->AddRGBPoint( 4113.0, 0.882353, 0.54902, 0.54902 );
	- transferFunction->AddRGBPoint( 4114.0, 0.0901961, 0.235294, 0.705882 );
	- transferFunction->AddRGBPoint( 4115.0, 0.705882, 0.235294, 0.705882 );
	- transferFunction->AddRGBPoint( 4116.0, 0.0784314, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 4117.0, 0.235294, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 4118.0, 0.862745, 0.705882, 0.54902 );
	- transferFunction->AddRGBPoint( 4119.0, 0.254902, 0.392157, 0.0784314 );
	- transferFunction->AddRGBPoint( 4120.0, 0.862745, 0.235294, 0.0784314 );
	- transferFunction->AddRGBPoint( 4121.0, 0.235294, 0.392157, 0.235294 );
	- transferFunction->AddRGBPoint( 4122.0, 0.0784314, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 4123.0, 0.392157, 0.392157, 0.235294 );
	- transferFunction->AddRGBPoint( 4124.0, 0.862745, 0.705882, 0.862745 );
	- transferFunction->AddRGBPoint( 4125.0, 0.0784314, 0.705882, 0.54902 );
	- transferFunction->AddRGBPoint( 4126.0, 0.235294, 0.54902, 0.705882 );
	- transferFunction->AddRGBPoint( 4127.0, 0.0980392, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 4128.0, 0.0784314, 0.235294, 0.392157 );
	- transferFunction->AddRGBPoint( 4129.0, 0.235294, 0.862745, 0.0784314 );
	- transferFunction->AddRGBPoint( 4130.0, 0.235294, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 4131.0, 0.862745, 0.862745, 0.392157 );
	- transferFunction->AddRGBPoint( 4132.0, 0.705882, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 4133.0, 0.235294, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 4134.0, 0.862745, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 4135.0, 0.254902, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 4136.0, 0.0980392, 0.54902, 0.0784314 );
	- transferFunction->AddRGBPoint( 4137.0, 0.0509804, 0, 0.980392 );
	- transferFunction->AddRGBPoint( 4138.0, 0.239216, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 4139.0, 0.239216, 0.0784314, 0.235294 );
	- transferFunction->AddRGBPoint( 4140.0, 0.239216, 0.235294, 0.392157 );
	- transferFunction->AddRGBPoint( 4141.0, 0.0980392, 0.0980392, 0.0980392 );
	- transferFunction->AddRGBPoint( 4142.0, 0.54902, 0.0784314, 0.235294 );
	- transferFunction->AddRGBPoint( 4143.0, 0.862745, 0.705882, 0.0784314 );
	- transferFunction->AddRGBPoint( 4144.0, 0.247059, 0.705882, 0.705882 );
	- transferFunction->AddRGBPoint( 4145.0, 0.866667, 0.0784314, 0.0392157 );
	- transferFunction->AddRGBPoint( 4146.0, 0.0823529, 0.862745, 0.0784314 );
	- transferFunction->AddRGBPoint( 4147.0, 0.717647, 0.392157, 0.0784314 );
	- transferFunction->AddRGBPoint( 4148.0, 0.866667, 0.0784314, 0.392157 );
	- transferFunction->AddRGBPoint( 4149.0, 0.866667, 0.235294, 0.54902 );
	- transferFunction->AddRGBPoint( 4150.0, 0.866667, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 4151.0, 0.239216, 0.862745, 0.862745 );
	- transferFunction->AddRGBPoint( 4152.0, 0.392157, 0.784314, 0.784314 );
	- transferFunction->AddRGBPoint( 4153.0, 0.0392157, 0.784314, 0.784314 );
	- transferFunction->AddRGBPoint( 4154.0, 0.866667, 0.862745, 0.0784314 );
	- transferFunction->AddRGBPoint( 4155.0, 0.552941, 0.0784314, 0.392157 );
	- transferFunction->AddRGBPoint( 4156.0, 0.239216, 0.862745, 0.392157 );
	- transferFunction->AddRGBPoint( 4157.0, 0.0823529, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 4158.0, 0.552941, 0.235294, 0.0784314 );
	- transferFunction->AddRGBPoint( 4159.0, 0.560784, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 4160.0, 0.239216, 0.0784314, 0.705882 );
	- transferFunction->AddRGBPoint( 4161.0, 0.396078, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 4162.0, 0.0823529, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 4163.0, 0.866667, 0.54902, 0.0784314 );
	- transferFunction->AddRGBPoint( 4164.0, 0.552941, 0.392157, 0.862745 );
	- transferFunction->AddRGBPoint( 4165.0, 0.396078, 0.0784314, 0.0784314 );
	- transferFunction->AddRGBPoint( 4166.0, 0.866667, 0.392157, 0.0784314 );
	- transferFunction->AddRGBPoint( 4167.0, 0.709804, 0.784314, 0.0784314 );
	- transferFunction->AddRGBPoint( 4168.0, 0.0823529, 0.705882, 0.54902 );
	- transferFunction->AddRGBPoint( 4169.0, 0.396078, 0.392157, 0.705882 );
	- transferFunction->AddRGBPoint( 4170.0, 0.709804, 0.862745, 0.0784314 );
	- transferFunction->AddRGBPoint( 4171.0, 0.0823529, 0.54902, 0.784314 );
	- transferFunction->AddRGBPoint( 4172.0, 0.0823529, 0.0784314, 0.941176 );
	- transferFunction->AddRGBPoint( 4173.0, 0.0823529, 0.0784314, 0.784314 );
	- transferFunction->AddRGBPoint( 4174.0, 0.239216, 0.705882, 0.235294 );
	- transferFunction->AddRGBPoint( 4175.0, 0.239216, 0.705882, 0.980392 );
	- transferFunction->AddRGBPoint( 4176.0, 0.0823529, 0.0784314, 0.235294 );
	- transferFunction->AddRGBPoint( 4177.0, 0.396078, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 4178.0, 0.0823529, 0.862745, 0.862745 );
	- transferFunction->AddRGBPoint( 4179.0, 0.0823529, 0.705882, 0.705882 );
	- transferFunction->AddRGBPoint( 4180.0, 0.87451, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 4181.0, 0.866667, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 5001.0, 0.0784314, 0.117647, 0.156863 );
	- transferFunction->AddRGBPoint( 5002.0, 0.0784314, 0.117647, 0.156863 );
	- transferFunction->AddRGBPoint( 5100.0, 0.8, 0.4, 0.4 );
	- transferFunction->AddRGBPoint( 5101.0, 0.8, 0.4, 0.4 );
	- transferFunction->AddRGBPoint( 5102.0, 1, 1, 0.4 );
	- transferFunction->AddRGBPoint( 5103.0, 0.6, 0.8, 0 );
	- transferFunction->AddRGBPoint( 5104.0, 0, 0.6, 0.6 );
	- transferFunction->AddRGBPoint( 5105.0, 0.8, 0.6, 1 );
	- transferFunction->AddRGBPoint( 5106.0, 1, 0.6, 0.2 );
	- transferFunction->AddRGBPoint( 5107.0, 0.8, 0.8, 0.8 );
	- transferFunction->AddRGBPoint( 5108.0, 0.6, 1, 1 );
	- transferFunction->AddRGBPoint( 5109.0, 0.4, 0.6, 1 );
	- transferFunction->AddRGBPoint( 5110.0, 1, 1, 0.4 );
	- transferFunction->AddRGBPoint( 5111.0, 0.6, 0.8, 0 );
	- transferFunction->AddRGBPoint( 5112.0, 0, 0.6, 0.6 );
	- transferFunction->AddRGBPoint( 5113.0, 0.8, 0.6, 1 );
	- transferFunction->AddRGBPoint( 5114.0, 1, 0.6, 0.2 );
	- transferFunction->AddRGBPoint( 5115.0, 0.8, 0.8, 0.8 );
	- transferFunction->AddRGBPoint( 5116.0, 0.6, 1, 1 );
	- transferFunction->AddRGBPoint( 5117.0, 0.4, 0.6, 1 );
	- transferFunction->AddRGBPoint( 5200.0, 0.8, 0.4, 0.4 );
	- transferFunction->AddRGBPoint( 5201.0, 0.8, 0.4, 0.4 );
	- transferFunction->AddRGBPoint( 5202.0, 1, 1, 0.4 );
	- transferFunction->AddRGBPoint( 5203.0, 0.6, 0.8, 0 );
	- transferFunction->AddRGBPoint( 5204.0, 0, 0.6, 0.6 );
	- transferFunction->AddRGBPoint( 5205.0, 0.8, 0.6, 1 );
	- transferFunction->AddRGBPoint( 5206.0, 1, 0.6, 0.2 );
	- transferFunction->AddRGBPoint( 5207.0, 0.8, 0.8, 0.8 );
	- transferFunction->AddRGBPoint( 5208.0, 0.6, 1, 1 );
	- transferFunction->AddRGBPoint( 5209.0, 0.4, 0.6, 1 );
	- transferFunction->AddRGBPoint( 5210.0, 1, 1, 0.4 );
	- transferFunction->AddRGBPoint( 5211.0, 0.6, 0.8, 0 );
	- transferFunction->AddRGBPoint( 5212.0, 0, 0.6, 0.6 );
	- transferFunction->AddRGBPoint( 5213.0, 0.8, 0.6, 1 );
	- transferFunction->AddRGBPoint( 5214.0, 1, 0.6, 0.2 );
	- transferFunction->AddRGBPoint( 5215.0, 0.8, 0.8, 0.8 );
	- transferFunction->AddRGBPoint( 5216.0, 0.6, 1, 1 );
	- transferFunction->AddRGBPoint( 5217.0, 0.4, 0.6, 1 );
	- transferFunction->AddRGBPoint( 6000.0, 0, 1, 0 );
	- transferFunction->AddRGBPoint( 6001.0, 1, 1, 0 );
	- transferFunction->AddRGBPoint( 6002.0, 0, 1, 1 );
	- transferFunction->AddRGBPoint( 6003.0, 0, 0, 1 );
	- transferFunction->AddRGBPoint( 6010.0, 0.92549, 0.0627451, 0.905882 );
	- transferFunction->AddRGBPoint( 6020.0, 0.929412, 0.0705882, 0.909804 );
	- transferFunction->AddRGBPoint( 6030.0, 0.92549, 0.0509804, 0.890196 );
	- transferFunction->AddRGBPoint( 6040.0, 0.92549, 0.0666667, 0.894118 );
	- transferFunction->AddRGBPoint( 6050.0, 0.00392157, 1, 0.00392157 );
	- transferFunction->AddRGBPoint( 6060.0, 0.00784314, 1, 0.00392157 );
	- transferFunction->AddRGBPoint( 6070.0, 0.92549, 0.054902, 0.901961 );
	- transferFunction->AddRGBPoint( 6080.0, 0.929412, 0.054902, 0.901961 );
	- transferFunction->AddRGBPoint( 7001.0, 0.282353, 0.517647, 0.709804 );
	- transferFunction->AddRGBPoint( 7002.0, 0.952941, 0.952941, 0.952941 );
	- transferFunction->AddRGBPoint( 7003.0, 0.811765, 0.247059, 0.309804 );
	- transferFunction->AddRGBPoint( 7004.0, 0.47451, 0.0784314, 0.529412 );
	- transferFunction->AddRGBPoint( 7005.0, 0.772549, 0.235294, 0.972549 );
	- transferFunction->AddRGBPoint( 7006.0, 0.00784314, 0.584314, 0.00784314 );
	- transferFunction->AddRGBPoint( 7007.0, 0.866667, 0.976471, 0.65098 );
	- transferFunction->AddRGBPoint( 7008.0, 0.909804, 0.572549, 0.137255 );
	- transferFunction->AddRGBPoint( 7009.0, 0.0784314, 0.235294, 0.470588 );
	- transferFunction->AddRGBPoint( 7010.0, 0.980392, 0.980392, 0 );
	- transferFunction->AddRGBPoint( 7011.0, 0.478431, 0.733333, 0.870588 );
	- transferFunction->AddRGBPoint( 7012.0, 0.929412, 0.0470588, 0.694118 );
	- transferFunction->AddRGBPoint( 7013.0, 0.0392157, 0.192157, 1 );
	- transferFunction->AddRGBPoint( 7014.0, 0.803922, 0.721569, 0.564706 );
	- transferFunction->AddRGBPoint( 7015.0, 0.176471, 0.803922, 0.647059 );
	- transferFunction->AddRGBPoint( 7016.0, 0.458824, 0.627451, 0.686275 );
	- transferFunction->AddRGBPoint( 7017.0, 0.866667, 0.85098, 0.0823529 );
	- transferFunction->AddRGBPoint( 7018.0, 0.0784314, 0.235294, 0.470588 );
	- transferFunction->AddRGBPoint( 7019.0, 0.552941, 0.0823529, 0.392157 );
	- transferFunction->AddRGBPoint( 7020.0, 0.882353, 0.54902, 0.552941 );
	- transferFunction->AddRGBPoint( 7100.0, 0.164706, 0.788235, 0.658824 );
	- transferFunction->AddRGBPoint( 7101.0, 0.658824, 0.407843, 0.635294 );
	- transferFunction->AddRGBPoint( 8001.0, 0.290196, 0.509804, 0.709804 );
	- transferFunction->AddRGBPoint( 8002.0, 0.94902, 0.945098, 0.941176 );
	- transferFunction->AddRGBPoint( 8003.0, 0.807843, 0.254902, 0.305882 );
	- transferFunction->AddRGBPoint( 8004.0, 0.470588, 0.0823529, 0.521569 );
	- transferFunction->AddRGBPoint( 8005.0, 0.764706, 0.239216, 0.964706 );
	- transferFunction->AddRGBPoint( 8006.0, 0.0117647, 0.576471, 0.0235294 );
	- transferFunction->AddRGBPoint( 8007.0, 0.862745, 0.984314, 0.639216 );
	- transferFunction->AddRGBPoint( 8008.0, 0.909804, 0.572549, 0.129412 );
	- transferFunction->AddRGBPoint( 8009.0, 0.0156863, 0.447059, 0.054902 );
	- transferFunction->AddRGBPoint( 8010.0, 0.47451, 0.721569, 0.862745 );
	- transferFunction->AddRGBPoint( 8011.0, 0.921569, 0.0431373, 0.686275 );
	- transferFunction->AddRGBPoint( 8012.0, 0.0470588, 0.180392, 0.980392 );
	- transferFunction->AddRGBPoint( 8013.0, 0.796078, 0.713725, 0.560784 );
	- transferFunction->AddRGBPoint( 8014.0, 0.164706, 0.8, 0.654902 );
	- transferFunction->AddRGBPoint( 9000.0, 0.117647, 0.0196078, 0.117647 );
	- transferFunction->AddRGBPoint( 9001.0, 0.117647, 0.392157, 0.176471 );
	- transferFunction->AddRGBPoint( 9002.0, 0.509804, 0.392157, 0.647059 );
	- transferFunction->AddRGBPoint( 9003.0, 0.411765, 0.0980392, 0.0196078 );
	- transferFunction->AddRGBPoint( 9004.0, 0.490196, 0.27451, 0.215686 );
	- transferFunction->AddRGBPoint( 9005.0, 0.882353, 0.0784314, 0.411765 );
	- transferFunction->AddRGBPoint( 9006.0, 0.882353, 0.0784314, 0.0588235 );
	- transferFunction->AddRGBPoint( 9500.0, 0.117647, 0.215686, 0.117647 );
	- transferFunction->AddRGBPoint( 9501.0, 0.117647, 0.588235, 0.176471 );
	- transferFunction->AddRGBPoint( 9502.0, 0.509804, 0.588235, 0.647059 );
	- transferFunction->AddRGBPoint( 9503.0, 0.411765, 0.294118, 0.0196078 );
	- transferFunction->AddRGBPoint( 9504.0, 0.490196, 0.470588, 0.215686 );
	- transferFunction->AddRGBPoint( 9505.0, 0.882353, 0.27451, 0.411765 );
	- transferFunction->AddRGBPoint( 9506.0, 0.882353, 0.27451, 0.0588235 );
	- transferFunction->AddRGBPoint( 11101.0, 0.0901961, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 11102.0, 0.0901961, 0.235294, 0.705882 );
	- transferFunction->AddRGBPoint( 11103.0, 0.247059, 0.392157, 0.235294 );
	- transferFunction->AddRGBPoint( 11104.0, 0.247059, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 11105.0, 0.0509804, 0, 0.980392 );
	- transferFunction->AddRGBPoint( 11106.0, 0.101961, 0.235294, 0 );
	- transferFunction->AddRGBPoint( 11107.0, 0.101961, 0.235294, 0.294118 );
	- transferFunction->AddRGBPoint( 11108.0, 0.101961, 0.235294, 0.588235 );
	- transferFunction->AddRGBPoint( 11109.0, 0.0980392, 0.235294, 0.980392 );
	- transferFunction->AddRGBPoint( 11110.0, 0.235294, 0.0980392, 0.0980392 );
	- transferFunction->AddRGBPoint( 11111.0, 0.705882, 0.0784314, 0.0784314 );
	- transferFunction->AddRGBPoint( 11112.0, 0.862745, 0.0784314, 0.392157 );
	- transferFunction->AddRGBPoint( 11113.0, 0.54902, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 11114.0, 0.705882, 0.862745, 0.54902 );
	- transferFunction->AddRGBPoint( 11115.0, 0.54902, 0.392157, 0.705882 );
	- transferFunction->AddRGBPoint( 11116.0, 0.705882, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 11117.0, 0.0901961, 0.0392157, 0.0392157 );
	- transferFunction->AddRGBPoint( 11118.0, 0.882353, 0.54902, 0.54902 );
	- transferFunction->AddRGBPoint( 11119.0, 0.705882, 0.235294, 0.705882 );
	- transferFunction->AddRGBPoint( 11120.0, 0.0784314, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 11121.0, 0.235294, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 11122.0, 0.862745, 0.705882, 0.54902 );
	- transferFunction->AddRGBPoint( 11123.0, 0.254902, 0.392157, 0.0784314 );
	- transferFunction->AddRGBPoint( 11124.0, 0.862745, 0.235294, 0.0784314 );
	- transferFunction->AddRGBPoint( 11125.0, 0.0784314, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 11126.0, 0.392157, 0.392157, 0.235294 );
	- transferFunction->AddRGBPoint( 11127.0, 0.862745, 0.705882, 0.862745 );
	- transferFunction->AddRGBPoint( 11128.0, 0.0784314, 0.705882, 0.54902 );
	- transferFunction->AddRGBPoint( 11129.0, 0.235294, 0.54902, 0.705882 );
	- transferFunction->AddRGBPoint( 11130.0, 0.0980392, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 11131.0, 0.0784314, 0.235294, 0.392157 );
	- transferFunction->AddRGBPoint( 11132.0, 0.235294, 0.862745, 0.0784314 );
	- transferFunction->AddRGBPoint( 11133.0, 0.235294, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 11134.0, 0.862745, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 11135.0, 0.254902, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 11136.0, 0.0980392, 0.54902, 0.0784314 );
	- transferFunction->AddRGBPoint( 11137.0, 0.862745, 0.862745, 0.392157 );
	- transferFunction->AddRGBPoint( 11138.0, 0.705882, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 11139.0, 0.239216, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 11140.0, 0.239216, 0.0784314, 0.235294 );
	- transferFunction->AddRGBPoint( 11141.0, 0.239216, 0.235294, 0.392157 );
	- transferFunction->AddRGBPoint( 11142.0, 0.0980392, 0.0980392, 0.0980392 );
	- transferFunction->AddRGBPoint( 11143.0, 0.54902, 0.0784314, 0.235294 );
	- transferFunction->AddRGBPoint( 11144.0, 0.862745, 0.705882, 0.0784314 );
	- transferFunction->AddRGBPoint( 11145.0, 0.247059, 0.705882, 0.705882 );
	- transferFunction->AddRGBPoint( 11146.0, 0.866667, 0.0784314, 0.0392157 );
	- transferFunction->AddRGBPoint( 11147.0, 0.866667, 0.0784314, 0.392157 );
	- transferFunction->AddRGBPoint( 11148.0, 0.866667, 0.235294, 0.54902 );
	- transferFunction->AddRGBPoint( 11149.0, 0.866667, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 11150.0, 0.239216, 0.862745, 0.862745 );
	- transferFunction->AddRGBPoint( 11151.0, 0.392157, 0.784314, 0.784314 );
	- transferFunction->AddRGBPoint( 11152.0, 0.0392157, 0.784314, 0.784314 );
	- transferFunction->AddRGBPoint( 11153.0, 0.866667, 0.862745, 0.0784314 );
	- transferFunction->AddRGBPoint( 11154.0, 0.552941, 0.0784314, 0.392157 );
	- transferFunction->AddRGBPoint( 11155.0, 0.239216, 0.862745, 0.392157 );
	- transferFunction->AddRGBPoint( 11156.0, 0.552941, 0.235294, 0.0784314 );
	- transferFunction->AddRGBPoint( 11157.0, 0.560784, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 11158.0, 0.396078, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 11159.0, 0.0823529, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 11160.0, 0.239216, 0.0784314, 0.705882 );
	- transferFunction->AddRGBPoint( 11161.0, 0.866667, 0.54902, 0.0784314 );
	- transferFunction->AddRGBPoint( 11162.0, 0.552941, 0.392157, 0.862745 );
	- transferFunction->AddRGBPoint( 11163.0, 0.866667, 0.392157, 0.0784314 );
	- transferFunction->AddRGBPoint( 11164.0, 0.709804, 0.784314, 0.0784314 );
	- transferFunction->AddRGBPoint( 11165.0, 0.396078, 0.0784314, 0.0784314 );
	- transferFunction->AddRGBPoint( 11166.0, 0.396078, 0.392157, 0.705882 );
	- transferFunction->AddRGBPoint( 11167.0, 0.709804, 0.862745, 0.0784314 );
	- transferFunction->AddRGBPoint( 11168.0, 0.0823529, 0.54902, 0.784314 );
	- transferFunction->AddRGBPoint( 11169.0, 0.0823529, 0.0784314, 0.941176 );
	- transferFunction->AddRGBPoint( 11170.0, 0.0823529, 0.0784314, 0.784314 );
	- transferFunction->AddRGBPoint( 11171.0, 0.0823529, 0.0784314, 0.235294 );
	- transferFunction->AddRGBPoint( 11172.0, 0.396078, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 11173.0, 0.0823529, 0.705882, 0.705882 );
	- transferFunction->AddRGBPoint( 11174.0, 0.87451, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 11175.0, 0.866667, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 12101.0, 0.0901961, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 12102.0, 0.0901961, 0.235294, 0.705882 );
	- transferFunction->AddRGBPoint( 12103.0, 0.247059, 0.392157, 0.235294 );
	- transferFunction->AddRGBPoint( 12104.0, 0.247059, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 12105.0, 0.0509804, 0, 0.980392 );
	- transferFunction->AddRGBPoint( 12106.0, 0.101961, 0.235294, 0 );
	- transferFunction->AddRGBPoint( 12107.0, 0.101961, 0.235294, 0.294118 );
	- transferFunction->AddRGBPoint( 12108.0, 0.101961, 0.235294, 0.588235 );
	- transferFunction->AddRGBPoint( 12109.0, 0.0980392, 0.235294, 0.980392 );
	- transferFunction->AddRGBPoint( 12110.0, 0.235294, 0.0980392, 0.0980392 );
	- transferFunction->AddRGBPoint( 12111.0, 0.705882, 0.0784314, 0.0784314 );
	- transferFunction->AddRGBPoint( 12112.0, 0.862745, 0.0784314, 0.392157 );
	- transferFunction->AddRGBPoint( 12113.0, 0.54902, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 12114.0, 0.705882, 0.862745, 0.54902 );
	- transferFunction->AddRGBPoint( 12115.0, 0.54902, 0.392157, 0.705882 );
	- transferFunction->AddRGBPoint( 12116.0, 0.705882, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 12117.0, 0.0901961, 0.0392157, 0.0392157 );
	- transferFunction->AddRGBPoint( 12118.0, 0.882353, 0.54902, 0.54902 );
	- transferFunction->AddRGBPoint( 12119.0, 0.705882, 0.235294, 0.705882 );
	- transferFunction->AddRGBPoint( 12120.0, 0.0784314, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 12121.0, 0.235294, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 12122.0, 0.862745, 0.705882, 0.54902 );
	- transferFunction->AddRGBPoint( 12123.0, 0.254902, 0.392157, 0.0784314 );
	- transferFunction->AddRGBPoint( 12124.0, 0.862745, 0.235294, 0.0784314 );
	- transferFunction->AddRGBPoint( 12125.0, 0.0784314, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 12126.0, 0.392157, 0.392157, 0.235294 );
	- transferFunction->AddRGBPoint( 12127.0, 0.862745, 0.705882, 0.862745 );
	- transferFunction->AddRGBPoint( 12128.0, 0.0784314, 0.705882, 0.54902 );
	- transferFunction->AddRGBPoint( 12129.0, 0.235294, 0.54902, 0.705882 );
	- transferFunction->AddRGBPoint( 12130.0, 0.0980392, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 12131.0, 0.0784314, 0.235294, 0.392157 );
	- transferFunction->AddRGBPoint( 12132.0, 0.235294, 0.862745, 0.0784314 );
	- transferFunction->AddRGBPoint( 12133.0, 0.235294, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 12134.0, 0.862745, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 12135.0, 0.254902, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 12136.0, 0.0980392, 0.54902, 0.0784314 );
	- transferFunction->AddRGBPoint( 12137.0, 0.862745, 0.862745, 0.392157 );
	- transferFunction->AddRGBPoint( 12138.0, 0.705882, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 12139.0, 0.239216, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 12140.0, 0.239216, 0.0784314, 0.235294 );
	- transferFunction->AddRGBPoint( 12141.0, 0.239216, 0.235294, 0.392157 );
	- transferFunction->AddRGBPoint( 12142.0, 0.0980392, 0.0980392, 0.0980392 );
	- transferFunction->AddRGBPoint( 12143.0, 0.54902, 0.0784314, 0.235294 );
	- transferFunction->AddRGBPoint( 12144.0, 0.862745, 0.705882, 0.0784314 );
	- transferFunction->AddRGBPoint( 12145.0, 0.247059, 0.705882, 0.705882 );
	- transferFunction->AddRGBPoint( 12146.0, 0.866667, 0.0784314, 0.0392157 );
	- transferFunction->AddRGBPoint( 12147.0, 0.866667, 0.0784314, 0.392157 );
	- transferFunction->AddRGBPoint( 12148.0, 0.866667, 0.235294, 0.54902 );
	- transferFunction->AddRGBPoint( 12149.0, 0.866667, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 12150.0, 0.239216, 0.862745, 0.862745 );
	- transferFunction->AddRGBPoint( 12151.0, 0.392157, 0.784314, 0.784314 );
	- transferFunction->AddRGBPoint( 12152.0, 0.0392157, 0.784314, 0.784314 );
	- transferFunction->AddRGBPoint( 12153.0, 0.866667, 0.862745, 0.0784314 );
	- transferFunction->AddRGBPoint( 12154.0, 0.552941, 0.0784314, 0.392157 );
	- transferFunction->AddRGBPoint( 12155.0, 0.239216, 0.862745, 0.392157 );
	- transferFunction->AddRGBPoint( 12156.0, 0.552941, 0.235294, 0.0784314 );
	- transferFunction->AddRGBPoint( 12157.0, 0.560784, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 12158.0, 0.396078, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 12159.0, 0.0823529, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 12160.0, 0.239216, 0.0784314, 0.705882 );
	- transferFunction->AddRGBPoint( 12161.0, 0.866667, 0.54902, 0.0784314 );
	- transferFunction->AddRGBPoint( 12162.0, 0.552941, 0.392157, 0.862745 );
	- transferFunction->AddRGBPoint( 12163.0, 0.866667, 0.392157, 0.0784314 );
	- transferFunction->AddRGBPoint( 12164.0, 0.709804, 0.784314, 0.0784314 );
	- transferFunction->AddRGBPoint( 12165.0, 0.396078, 0.0784314, 0.0784314 );
	- transferFunction->AddRGBPoint( 12166.0, 0.396078, 0.392157, 0.705882 );
	- transferFunction->AddRGBPoint( 12167.0, 0.709804, 0.862745, 0.0784314 );
	- transferFunction->AddRGBPoint( 12168.0, 0.0823529, 0.54902, 0.784314 );
	- transferFunction->AddRGBPoint( 12169.0, 0.0823529, 0.0784314, 0.941176 );
	- transferFunction->AddRGBPoint( 12170.0, 0.0823529, 0.0784314, 0.784314 );
	- transferFunction->AddRGBPoint( 12171.0, 0.0823529, 0.0784314, 0.235294 );
	- transferFunction->AddRGBPoint( 12172.0, 0.396078, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 12173.0, 0.0823529, 0.705882, 0.705882 );
	- transferFunction->AddRGBPoint( 12174.0, 0.87451, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 12175.0, 0.866667, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 13101.0, 0.0901961, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 13102.0, 0.0901961, 0.235294, 0.705882 );
	- transferFunction->AddRGBPoint( 13103.0, 0.247059, 0.392157, 0.235294 );
	- transferFunction->AddRGBPoint( 13104.0, 0.247059, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 13105.0, 0.0509804, 0, 0.980392 );
	- transferFunction->AddRGBPoint( 13106.0, 0.101961, 0.235294, 0 );
	- transferFunction->AddRGBPoint( 13107.0, 0.101961, 0.235294, 0.294118 );
	- transferFunction->AddRGBPoint( 13108.0, 0.101961, 0.235294, 0.588235 );
	- transferFunction->AddRGBPoint( 13109.0, 0.0980392, 0.235294, 0.980392 );
	- transferFunction->AddRGBPoint( 13110.0, 0.235294, 0.0980392, 0.0980392 );
	- transferFunction->AddRGBPoint( 13111.0, 0.705882, 0.0784314, 0.0784314 );
	- transferFunction->AddRGBPoint( 13112.0, 0.862745, 0.0784314, 0.392157 );
	- transferFunction->AddRGBPoint( 13113.0, 0.54902, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 13114.0, 0.705882, 0.862745, 0.54902 );
	- transferFunction->AddRGBPoint( 13115.0, 0.54902, 0.392157, 0.705882 );
	- transferFunction->AddRGBPoint( 13116.0, 0.705882, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 13117.0, 0.0901961, 0.0392157, 0.0392157 );
	- transferFunction->AddRGBPoint( 13118.0, 0.882353, 0.54902, 0.54902 );
	- transferFunction->AddRGBPoint( 13119.0, 0.705882, 0.235294, 0.705882 );
	- transferFunction->AddRGBPoint( 13120.0, 0.0784314, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 13121.0, 0.235294, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 13122.0, 0.862745, 0.705882, 0.54902 );
	- transferFunction->AddRGBPoint( 13123.0, 0.254902, 0.392157, 0.0784314 );
	- transferFunction->AddRGBPoint( 13124.0, 0.862745, 0.235294, 0.0784314 );
	- transferFunction->AddRGBPoint( 13125.0, 0.0784314, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 13126.0, 0.392157, 0.392157, 0.235294 );
	- transferFunction->AddRGBPoint( 13127.0, 0.862745, 0.705882, 0.862745 );
	- transferFunction->AddRGBPoint( 13128.0, 0.0784314, 0.705882, 0.54902 );
	- transferFunction->AddRGBPoint( 13129.0, 0.235294, 0.54902, 0.705882 );
	- transferFunction->AddRGBPoint( 13130.0, 0.0980392, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 13131.0, 0.0784314, 0.235294, 0.392157 );
	- transferFunction->AddRGBPoint( 13132.0, 0.235294, 0.862745, 0.0784314 );
	- transferFunction->AddRGBPoint( 13133.0, 0.235294, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 13134.0, 0.862745, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 13135.0, 0.254902, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 13136.0, 0.0980392, 0.54902, 0.0784314 );
	- transferFunction->AddRGBPoint( 13137.0, 0.862745, 0.862745, 0.392157 );
	- transferFunction->AddRGBPoint( 13138.0, 0.705882, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 13139.0, 0.239216, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 13140.0, 0.239216, 0.0784314, 0.235294 );
	- transferFunction->AddRGBPoint( 13141.0, 0.239216, 0.235294, 0.392157 );
	- transferFunction->AddRGBPoint( 13142.0, 0.0980392, 0.0980392, 0.0980392 );
	- transferFunction->AddRGBPoint( 13143.0, 0.54902, 0.0784314, 0.235294 );
	- transferFunction->AddRGBPoint( 13144.0, 0.862745, 0.705882, 0.0784314 );
	- transferFunction->AddRGBPoint( 13145.0, 0.247059, 0.705882, 0.705882 );
	- transferFunction->AddRGBPoint( 13146.0, 0.866667, 0.0784314, 0.0392157 );
	- transferFunction->AddRGBPoint( 13147.0, 0.866667, 0.0784314, 0.392157 );
	- transferFunction->AddRGBPoint( 13148.0, 0.866667, 0.235294, 0.54902 );
	- transferFunction->AddRGBPoint( 13149.0, 0.866667, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 13150.0, 0.239216, 0.862745, 0.862745 );
	- transferFunction->AddRGBPoint( 13151.0, 0.392157, 0.784314, 0.784314 );
	- transferFunction->AddRGBPoint( 13152.0, 0.0392157, 0.784314, 0.784314 );
	- transferFunction->AddRGBPoint( 13153.0, 0.866667, 0.862745, 0.0784314 );
	- transferFunction->AddRGBPoint( 13154.0, 0.552941, 0.0784314, 0.392157 );
	- transferFunction->AddRGBPoint( 13155.0, 0.239216, 0.862745, 0.392157 );
	- transferFunction->AddRGBPoint( 13156.0, 0.552941, 0.235294, 0.0784314 );
	- transferFunction->AddRGBPoint( 13157.0, 0.560784, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 13158.0, 0.396078, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 13159.0, 0.0823529, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 13160.0, 0.239216, 0.0784314, 0.705882 );
	- transferFunction->AddRGBPoint( 13161.0, 0.866667, 0.54902, 0.0784314 );
	- transferFunction->AddRGBPoint( 13162.0, 0.552941, 0.392157, 0.862745 );
	- transferFunction->AddRGBPoint( 13163.0, 0.866667, 0.392157, 0.0784314 );
	- transferFunction->AddRGBPoint( 13164.0, 0.709804, 0.784314, 0.0784314 );
	- transferFunction->AddRGBPoint( 13165.0, 0.396078, 0.0784314, 0.0784314 );
	- transferFunction->AddRGBPoint( 13166.0, 0.396078, 0.392157, 0.705882 );
	- transferFunction->AddRGBPoint( 13167.0, 0.709804, 0.862745, 0.0784314 );
	- transferFunction->AddRGBPoint( 13168.0, 0.0823529, 0.54902, 0.784314 );
	- transferFunction->AddRGBPoint( 13169.0, 0.0823529, 0.0784314, 0.941176 );
	- transferFunction->AddRGBPoint( 13170.0, 0.0823529, 0.0784314, 0.784314 );
	- transferFunction->AddRGBPoint( 13171.0, 0.0823529, 0.0784314, 0.235294 );
	- transferFunction->AddRGBPoint( 13172.0, 0.396078, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 13173.0, 0.0823529, 0.705882, 0.705882 );
	- transferFunction->AddRGBPoint( 13174.0, 0.87451, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 13175.0, 0.866667, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 14101.0, 0.0901961, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 14102.0, 0.0901961, 0.235294, 0.705882 );
	- transferFunction->AddRGBPoint( 14103.0, 0.247059, 0.392157, 0.235294 );
	- transferFunction->AddRGBPoint( 14104.0, 0.247059, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 14105.0, 0.0509804, 0, 0.980392 );
	- transferFunction->AddRGBPoint( 14106.0, 0.101961, 0.235294, 0 );
	- transferFunction->AddRGBPoint( 14107.0, 0.101961, 0.235294, 0.294118 );
	- transferFunction->AddRGBPoint( 14108.0, 0.101961, 0.235294, 0.588235 );
	- transferFunction->AddRGBPoint( 14109.0, 0.0980392, 0.235294, 0.980392 );
	- transferFunction->AddRGBPoint( 14110.0, 0.235294, 0.0980392, 0.0980392 );
	- transferFunction->AddRGBPoint( 14111.0, 0.705882, 0.0784314, 0.0784314 );
	- transferFunction->AddRGBPoint( 14112.0, 0.862745, 0.0784314, 0.392157 );
	- transferFunction->AddRGBPoint( 14113.0, 0.54902, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 14114.0, 0.705882, 0.862745, 0.54902 );
	- transferFunction->AddRGBPoint( 14115.0, 0.54902, 0.392157, 0.705882 );
	- transferFunction->AddRGBPoint( 14116.0, 0.705882, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 14117.0, 0.0901961, 0.0392157, 0.0392157 );
	- transferFunction->AddRGBPoint( 14118.0, 0.882353, 0.54902, 0.54902 );
	- transferFunction->AddRGBPoint( 14119.0, 0.705882, 0.235294, 0.705882 );
	- transferFunction->AddRGBPoint( 14120.0, 0.0784314, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 14121.0, 0.235294, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 14122.0, 0.862745, 0.705882, 0.54902 );
	- transferFunction->AddRGBPoint( 14123.0, 0.254902, 0.392157, 0.0784314 );
	- transferFunction->AddRGBPoint( 14124.0, 0.862745, 0.235294, 0.0784314 );
	- transferFunction->AddRGBPoint( 14125.0, 0.0784314, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 14126.0, 0.392157, 0.392157, 0.235294 );
	- transferFunction->AddRGBPoint( 14127.0, 0.862745, 0.705882, 0.862745 );
	- transferFunction->AddRGBPoint( 14128.0, 0.0784314, 0.705882, 0.54902 );
	- transferFunction->AddRGBPoint( 14129.0, 0.235294, 0.54902, 0.705882 );
	- transferFunction->AddRGBPoint( 14130.0, 0.0980392, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 14131.0, 0.0784314, 0.235294, 0.392157 );
	- transferFunction->AddRGBPoint( 14132.0, 0.235294, 0.862745, 0.0784314 );
	- transferFunction->AddRGBPoint( 14133.0, 0.235294, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 14134.0, 0.862745, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 14135.0, 0.254902, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 14136.0, 0.0980392, 0.54902, 0.0784314 );
	- transferFunction->AddRGBPoint( 14137.0, 0.862745, 0.862745, 0.392157 );
	- transferFunction->AddRGBPoint( 14138.0, 0.705882, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 14139.0, 0.239216, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 14140.0, 0.239216, 0.0784314, 0.235294 );
	- transferFunction->AddRGBPoint( 14141.0, 0.239216, 0.235294, 0.392157 );
	- transferFunction->AddRGBPoint( 14142.0, 0.0980392, 0.0980392, 0.0980392 );
	- transferFunction->AddRGBPoint( 14143.0, 0.54902, 0.0784314, 0.235294 );
	- transferFunction->AddRGBPoint( 14144.0, 0.862745, 0.705882, 0.0784314 );
	- transferFunction->AddRGBPoint( 14145.0, 0.247059, 0.705882, 0.705882 );
	- transferFunction->AddRGBPoint( 14146.0, 0.866667, 0.0784314, 0.0392157 );
	- transferFunction->AddRGBPoint( 14147.0, 0.866667, 0.0784314, 0.392157 );
	- transferFunction->AddRGBPoint( 14148.0, 0.866667, 0.235294, 0.54902 );
	- transferFunction->AddRGBPoint( 14149.0, 0.866667, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 14150.0, 0.239216, 0.862745, 0.862745 );
	- transferFunction->AddRGBPoint( 14151.0, 0.392157, 0.784314, 0.784314 );
	- transferFunction->AddRGBPoint( 14152.0, 0.0392157, 0.784314, 0.784314 );
	- transferFunction->AddRGBPoint( 14153.0, 0.866667, 0.862745, 0.0784314 );
	- transferFunction->AddRGBPoint( 14154.0, 0.552941, 0.0784314, 0.392157 );
	- transferFunction->AddRGBPoint( 14155.0, 0.239216, 0.862745, 0.392157 );
	- transferFunction->AddRGBPoint( 14156.0, 0.552941, 0.235294, 0.0784314 );
	- transferFunction->AddRGBPoint( 14157.0, 0.560784, 0.0784314, 0.862745 );
	- transferFunction->AddRGBPoint( 14158.0, 0.396078, 0.235294, 0.862745 );
	- transferFunction->AddRGBPoint( 14159.0, 0.0823529, 0.0784314, 0.54902 );
	- transferFunction->AddRGBPoint( 14160.0, 0.239216, 0.0784314, 0.705882 );
	- transferFunction->AddRGBPoint( 14161.0, 0.866667, 0.54902, 0.0784314 );
	- transferFunction->AddRGBPoint( 14162.0, 0.552941, 0.392157, 0.862745 );
	- transferFunction->AddRGBPoint( 14163.0, 0.866667, 0.392157, 0.0784314 );
	- transferFunction->AddRGBPoint( 14164.0, 0.709804, 0.784314, 0.0784314 );
	- transferFunction->AddRGBPoint( 14165.0, 0.396078, 0.0784314, 0.0784314 );
	- transferFunction->AddRGBPoint( 14166.0, 0.396078, 0.392157, 0.705882 );
	- transferFunction->AddRGBPoint( 14167.0, 0.709804, 0.862745, 0.0784314 );
	- transferFunction->AddRGBPoint( 14168.0, 0.0823529, 0.54902, 0.784314 );
	- transferFunction->AddRGBPoint( 14169.0, 0.0823529, 0.0784314, 0.941176 );
	- transferFunction->AddRGBPoint( 14170.0, 0.0823529, 0.0784314, 0.784314 );
	- transferFunction->AddRGBPoint( 14171.0, 0.0823529, 0.0784314, 0.235294 );
	- transferFunction->AddRGBPoint( 14172.0, 0.396078, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 14173.0, 0.0823529, 0.705882, 0.705882 );
	- transferFunction->AddRGBPoint( 14174.0, 0.87451, 0.862745, 0.235294 );
	- transferFunction->AddRGBPoint( 14175.0, 0.866667, 0.235294, 0.235294 );
	- transferFunction->AddRGBPoint( 0.0, 0.0, 0.0, 0.0 );
	- transferFunction->AddRGBPoint( 256.0, 0.0, 0.0, 0.0 );
	- transferFunction->AddRGBPoint( 1100.0, 0.0, 0.0, 0.0 );
	- transferFunction->AddRGBPoint( 2100.0, 0.0, 0.0, 0.0 );
	- transferFunction->AddRGBPoint( 3100.0, 0.0, 0.0, 0.0 );
	- transferFunction->AddRGBPoint( 4100.0, 0.0, 0.0, 0.0 );
	- transferFunction->AddRGBPoint( 11100.0, 0.0, 0.0, 0.0 );
	- transferFunction->AddRGBPoint( 12100.0, 0.0, 0.0, 0.0 );
	- transferFunction->AddRGBPoint( 13100.0, 0.0, 0.0, 0.0 );
	- transferFunction->AddRGBPoint( 14100.0, 0.0, 0.0, 0.0 );
	- return transferFunction;
	-}
	-
	-FreeSurferParcellationTranslator::NameTable FreeSurferParcellationTranslator::CreateNameTable()
	-{
	- mitk::FreeSurferParcellationTranslator::NameTable nameTable;
	- nameTable["0"] = "Unknown";
	- nameTable["1"] = "Left-Cerebral-Exterior";
	- nameTable["2"] = "Left-Cerebral-White-Matter";
	- nameTable["3"] = "Left-Cerebral-Cortex";
	- nameTable["4"] = "Left-Lateral-Ventricle";
	- nameTable["5"] = "Left-Inf-Lat-Vent";
	- nameTable["6"] = "Left-Cerebellum-Exterior";
	- nameTable["7"] = "Left-Cerebellum-White-Matter";
	- nameTable["8"] = "Left-Cerebellum-Cortex";
	- nameTable["9"] = "Left-Thalamus";
	- nameTable["10"] = "Left-Thalamus-Proper";
	- nameTable["11"] = "Left-Caudate";
	- nameTable["12"] = "Left-Putamen";
	- nameTable["13"] = "Left-Pallidum";
	- nameTable["14"] = "3rd-Ventricle";
	- nameTable["15"] = "4th-Ventricle";
	- nameTable["16"] = "Brain-Stem";
	- nameTable["17"] = "Left-Hippocampus";
	- nameTable["18"] = "Left-Amygdala";
	- nameTable["19"] = "Left-Insula";
	- nameTable["20"] = "Left-Operculum";
	- nameTable["21"] = "Line-1";
	- nameTable["22"] = "Line-2";
	- nameTable["23"] = "Line-3";
	- nameTable["24"] = "CSF";
	- nameTable["25"] = "Left-Lesion";
	- nameTable["26"] = "Left-Accumbens-area";
	- nameTable["27"] = "Left-Substancia-Nigra";
	- nameTable["28"] = "Left-VentralDC";
	- nameTable["29"] = "Left-undetermined";
	- nameTable["30"] = "Left-vessel";
	- nameTable["31"] = "Left-choroid-plexus";
	- nameTable["32"] = "Left-F3orb";
	- nameTable["33"] = "Left-lOg";
	- nameTable["34"] = "Left-aOg";
	- nameTable["35"] = "Left-mOg";
	- nameTable["36"] = "Left-pOg";
	- nameTable["37"] = "Left-Stellate";
	- nameTable["38"] = "Left-Porg";
	- nameTable["39"] = "Left-Aorg";
	- nameTable["40"] = "Right-Cerebral-Exterior";
	- nameTable["41"] = "Right-Cerebral-White-Matter";
	- nameTable["42"] = "Right-Cerebral-Cortex";
	- nameTable["43"] = "Right-Lateral-Ventricle";
	- nameTable["44"] = "Right-Inf-Lat-Vent";
	- nameTable["45"] = "Right-Cerebellum-Exterior";
	- nameTable["46"] = "Right-Cerebellum-White-Matter";
	- nameTable["47"] = "Right-Cerebellum-Cortex";
	- nameTable["48"] = "Right-Thalamus";
	- nameTable["49"] = "Right-Thalamus-Proper";
	- nameTable["50"] = "Right-Caudate";
	- nameTable["51"] = "Right-Putamen";
	- nameTable["52"] = "Right-Pallidum";
	- nameTable["53"] = "Right-Hippocampus";
	- nameTable["54"] = "Right-Amygdala";
	- nameTable["55"] = "Right-Insula";
	- nameTable["56"] = "Right-Operculum";
	- nameTable["57"] = "Right-Lesion";
	- nameTable["58"] = "Right-Accumbens-area";
	- nameTable["59"] = "Right-Substancia-Nigra";
	- nameTable["60"] = "Right-VentralDC";
	- nameTable["61"] = "Right-undetermined";
	- nameTable["62"] = "Right-vessel";
	- nameTable["63"] = "Right-choroid-plexus";
	- nameTable["64"] = "Right-F3orb";
	- nameTable["65"] = "Right-lOg";
	- nameTable["66"] = "Right-aOg";
	- nameTable["67"] = "Right-mOg";
	- nameTable["68"] = "Right-pOg";
	- nameTable["69"] = "Right-Stellate";
	- nameTable["70"] = "Right-Porg";
	- nameTable["71"] = "Right-Aorg";
	- nameTable["72"] = "5th-Ventricle";
	- nameTable["73"] = "Left-Interior";
	- nameTable["74"] = "Right-Interior";
	- nameTable["77"] = "WM-hypointensities";
	- nameTable["78"] = "Left-WM-hypointensities";
	- nameTable["79"] = "Right-WM-hypointensities";
	- nameTable["80"] = "non-WM-hypointensities";
	- nameTable["81"] = "Left-non-WM-hypointensities";
	- nameTable["82"] = "Right-non-WM-hypointensities";
	- nameTable["83"] = "Left-F1";
	- nameTable["84"] = "Right-F1";
	- nameTable["85"] = "Optic-Chiasm";
	- nameTable["192"] = "Corpus_Callosum";
	- nameTable["86"] = "Left_future_WMSA";
	- nameTable["87"] = "Right_future_WMSA";
	- nameTable["88"] = "future_WMSA";
	- nameTable["96"] = "Left-Amygdala-Anterior";
	- nameTable["97"] = "Right-Amygdala-Anterior";
	- nameTable["98"] = "Dura";
	- nameTable["100"] = "Left-wm-intensity-abnormality";
	- nameTable["101"] = "Left-caudate-intensity-abnormality";
	- nameTable["102"] = "Left-putamen-intensity-abnormality";
	- nameTable["103"] = "Left-accumbens-intensity-abnormality";
	- nameTable["104"] = "Left-pallidum-intensity-abnormality";
	- nameTable["105"] = "Left-amygdala-intensity-abnormality";
	- nameTable["106"] = "Left-hippocampus-intensity-abnormality";
	- nameTable["107"] = "Left-thalamus-intensity-abnormality";
	- nameTable["108"] = "Left-VDC-intensity-abnormality";
	- nameTable["109"] = "Right-wm-intensity-abnormality";
	- nameTable["110"] = "Right-caudate-intensity-abnormality";
	- nameTable["111"] = "Right-putamen-intensity-abnormality";
	- nameTable["112"] = "Right-accumbens-intensity-abnormality";
	- nameTable["113"] = "Right-pallidum-intensity-abnormality";
	- nameTable["114"] = "Right-amygdala-intensity-abnormality";
	- nameTable["115"] = "Right-hippocampus-intensity-abnormality";
	- nameTable["116"] = "Right-thalamus-intensity-abnormality";
	- nameTable["117"] = "Right-VDC-intensity-abnormality";
	- nameTable["118"] = "Epidermis";
	- nameTable["119"] = "Conn-Tissue";
	- nameTable["120"] = "SC-Fat-Muscle";
	- nameTable["121"] = "Cranium";
	- nameTable["122"] = "CSF-SA";
	- nameTable["123"] = "Muscle";
	- nameTable["124"] = "Ear";
	- nameTable["125"] = "Adipose";
	- nameTable["126"] = "Spinal-Cord";
	- nameTable["127"] = "Soft-Tissue";
	- nameTable["128"] = "Nerve";
	- nameTable["129"] = "Bone";
	- nameTable["130"] = "Air";
	- nameTable["131"] = "Orbital-Fat";
	- nameTable["132"] = "Tongue";
	- nameTable["133"] = "Nasal-Structures";
	- nameTable["134"] = "Globe";
	- nameTable["135"] = "Teeth";
	- nameTable["136"] = "Left-Caudate-Putamen";
	- nameTable["137"] = "Right-Caudate-Putamen";
	- nameTable["138"] = "Left-Claustrum";
	- nameTable["139"] = "Right-Claustrum";
	- nameTable["140"] = "Cornea";
	- nameTable["142"] = "Diploe";
	- nameTable["143"] = "Vitreous-Humor";
	- nameTable["144"] = "Lens";
	- nameTable["145"] = "Aqueous-Humor";
	- nameTable["146"] = "Outer-Table";
	- nameTable["147"] = "Inner-Table";
	- nameTable["148"] = "Periosteum";
	- nameTable["149"] = "Endosteum";
	- nameTable["150"] = "R-C-S";
	- nameTable["151"] = "Iris";
	- nameTable["152"] = "SC-Adipose-Muscle";
	- nameTable["153"] = "SC-Tissue";
	- nameTable["154"] = "Orbital-Adipose";
	- nameTable["155"] = "Left-IntCapsule-Ant";
	- nameTable["156"] = "Right-IntCapsule-Ant";
	- nameTable["157"] = "Left-IntCapsule-Pos";
	- nameTable["158"] = "Right-IntCapsule-Pos";
	- nameTable["159"] = "Left-Cerebral-WM-unmyelinated";
	- nameTable["160"] = "Right-Cerebral-WM-unmyelinated";
	- nameTable["161"] = "Left-Cerebral-WM-myelinated";
	- nameTable["162"] = "Right-Cerebral-WM-myelinated";
	- nameTable["163"] = "Left-Subcortical-Gray-Matter";
	- nameTable["164"] = "Right-Subcortical-Gray-Matter";
	- nameTable["165"] = "Skull";
	- nameTable["166"] = "Posterior-fossa";
	- nameTable["167"] = "Scalp";
	- nameTable["168"] = "Hematoma";
	- nameTable["169"] = "Left-Basal-Ganglia";
	- nameTable["176"] = "Right-Basal-Ganglia";
	- nameTable["170"] = "brainstem";
	- nameTable["171"] = "DCG";
	- nameTable["172"] = "Vermis";
	- nameTable["173"] = "Midbrain";
	- nameTable["174"] = "Pons";
	- nameTable["175"] = "Medulla";
	- nameTable["180"] = "Left-Cortical-Dysplasia";
	- nameTable["181"] = "Right-Cortical-Dysplasia";
	- nameTable["193"] = "Left-hippocampal_fissure";
	- nameTable["194"] = "Left-CADG-head";
	- nameTable["195"] = "Left-subiculum";
	- nameTable["196"] = "Left-fimbria";
	- nameTable["197"] = "Right-hippocampal_fissure";
	- nameTable["198"] = "Right-CADG-head";
	- nameTable["199"] = "Right-subiculum";
	- nameTable["200"] = "Right-fimbria";
	- nameTable["201"] = "alveus";
	- nameTable["202"] = "perforant_pathway";
	- nameTable["203"] = "parasubiculum";
	- nameTable["204"] = "presubiculum";
	- nameTable["205"] = "subiculum";
	- nameTable["206"] = "CA1";
	- nameTable["207"] = "CA2";
	- nameTable["208"] = "CA3";
	- nameTable["209"] = "CA4";
	- nameTable["210"] = "GC-ML-DG";
	- nameTable["211"] = "HATA";
	- nameTable["212"] = "fimbria";
	- nameTable["213"] = "lateral_ventricle";
	- nameTable["214"] = "molecular_layer_HP";
	- nameTable["215"] = "hippocampal_fissure";
	- nameTable["216"] = "entorhinal_cortex";
	- nameTable["217"] = "molecular_layer_subiculum";
	- nameTable["218"] = "Amygdala";
	- nameTable["219"] = "Cerebral_White_Matter";
	- nameTable["220"] = "Cerebral_Cortex";
	- nameTable["221"] = "Inf_Lat_Vent";
	- nameTable["222"] = "Perirhinal";
	- nameTable["223"] = "Cerebral_White_Matter_Edge";
	- nameTable["224"] = "Background";
	- nameTable["225"] = "Ectorhinal";
	- nameTable["226"] = "HP_tail";
	- nameTable["250"] = "Fornix";
	- nameTable["251"] = "CC_Posterior";
	- nameTable["252"] = "CC_Mid_Posterior";
	- nameTable["253"] = "CC_Central";
	- nameTable["254"] = "CC_Mid_Anterior";
	- nameTable["255"] = "CC_Anterior";
	- nameTable["256"] = "Voxel-Unchanged";
	- nameTable["331"] = "Aorta";
	- nameTable["332"] = "Left-Common-IliacA";
	- nameTable["333"] = "Right-Common-IliacA";
	- nameTable["334"] = "Left-External-IliacA";
	- nameTable["335"] = "Right-External-IliacA";
	- nameTable["336"] = "Left-Internal-IliacA";
	- nameTable["337"] = "Right-Internal-IliacA";
	- nameTable["338"] = "Left-Lateral-SacralA";
	- nameTable["339"] = "Right-Lateral-SacralA";
	- nameTable["340"] = "Left-ObturatorA";
	- nameTable["341"] = "Right-ObturatorA";
	- nameTable["342"] = "Left-Internal-PudendalA";
	- nameTable["343"] = "Right-Internal-PudendalA";
	- nameTable["344"] = "Left-UmbilicalA";
	- nameTable["345"] = "Right-UmbilicalA";
	- nameTable["346"] = "Left-Inf-RectalA";
	- nameTable["347"] = "Right-Inf-RectalA";
	- nameTable["348"] = "Left-Common-IliacV";
	- nameTable["349"] = "Right-Common-IliacV";
	- nameTable["350"] = "Left-External-IliacV";
	- nameTable["351"] = "Right-External-IliacV";
	- nameTable["352"] = "Left-Internal-IliacV";
	- nameTable["353"] = "Right-Internal-IliacV";
	- nameTable["354"] = "Left-ObturatorV";
	- nameTable["355"] = "Right-ObturatorV";
	- nameTable["356"] = "Left-Internal-PudendalV";
	- nameTable["357"] = "Right-Internal-PudendalV";
	- nameTable["358"] = "Pos-Lymph";
	- nameTable["359"] = "Neg-Lymph";
	- nameTable["400"] = "V1";
	- nameTable["401"] = "V2";
	- nameTable["402"] = "BA44";
	- nameTable["403"] = "BA45";
	- nameTable["404"] = "BA4a";
	- nameTable["405"] = "BA4p";
	- nameTable["406"] = "BA6";
	- nameTable["407"] = "BA2";
	- nameTable["408"] = "BA1_old";
	- nameTable["409"] = "BAun2";
	- nameTable["410"] = "BA1";
	- nameTable["411"] = "BA2b";
	- nameTable["412"] = "BA3a";
	- nameTable["413"] = "BA3b";
	- nameTable["414"] = "MT";
	- nameTable["415"] = "AIPS_AIP_l";
	- nameTable["416"] = "AIPS_AIP_r";
	- nameTable["417"] = "AIPS_VIP_l";
	- nameTable["418"] = "AIPS_VIP_r";
	- nameTable["419"] = "IPL_PFcm_l";
	- nameTable["420"] = "IPL_PFcm_r";
	- nameTable["421"] = "IPL_PF_l";
	- nameTable["422"] = "IPL_PFm_l";
	- nameTable["423"] = "IPL_PFm_r";
	- nameTable["424"] = "IPL_PFop_l";
	- nameTable["425"] = "IPL_PFop_r";
	- nameTable["426"] = "IPL_PF_r";
	- nameTable["427"] = "IPL_PFt_l";
	- nameTable["428"] = "IPL_PFt_r";
	- nameTable["429"] = "IPL_PGa_l";
	- nameTable["430"] = "IPL_PGa_r";
	- nameTable["431"] = "IPL_PGp_l";
	- nameTable["432"] = "IPL_PGp_r";
	- nameTable["433"] = "Visual_V3d_l";
	- nameTable["434"] = "Visual_V3d_r";
	- nameTable["435"] = "Visual_V4_l";
	- nameTable["436"] = "Visual_V4_r";
	- nameTable["437"] = "Visual_V5_b";
	- nameTable["438"] = "Visual_VP_l";
	- nameTable["439"] = "Visual_VP_r";
	- nameTable["498"] = "wmsa";
	- nameTable["499"] = "other_wmsa";
	- nameTable["500"] = "right_CA2_3";
	- nameTable["501"] = "right_alveus";
	- nameTable["502"] = "right_CA1";
	- nameTable["503"] = "right_fimbria";
	- nameTable["504"] = "right_presubiculum";
	- nameTable["505"] = "right_hippocampal_fissure";
	- nameTable["506"] = "right_CA4_DG";
	- nameTable["507"] = "right_subiculum";
	- nameTable["508"] = "right_fornix";
	- nameTable["550"] = "left_CA2_3";
	- nameTable["551"] = "left_alveus";
	- nameTable["552"] = "left_CA1";
	- nameTable["553"] = "left_fimbria";
	- nameTable["554"] = "left_presubiculum";
	- nameTable["555"] = "left_hippocampal_fissure";
	- nameTable["556"] = "left_CA4_DG";
	- nameTable["557"] = "left_subiculum";
	- nameTable["558"] = "left_fornix";
	- nameTable["600"] = "Tumor";
	- nameTable["601"] = "Cbm_Left_I_IV";
	- nameTable["602"] = "Cbm_Right_I_IV";
	- nameTable["603"] = "Cbm_Left_V";
	- nameTable["604"] = "Cbm_Right_V";
	- nameTable["605"] = "Cbm_Left_VI";
	- nameTable["606"] = "Cbm_Vermis_VI";
	- nameTable["607"] = "Cbm_Right_VI";
	- nameTable["608"] = "Cbm_Left_CrusI";
	- nameTable["609"] = "Cbm_Vermis_CrusI";
	- nameTable["610"] = "Cbm_Right_CrusI";
	- nameTable["611"] = "Cbm_Left_CrusII";
	- nameTable["612"] = "Cbm_Vermis_CrusII";
	- nameTable["613"] = "Cbm_Right_CrusII";
	- nameTable["614"] = "Cbm_Left_VIIb";
	- nameTable["615"] = "Cbm_Vermis_VIIb";
	- nameTable["616"] = "Cbm_Right_VIIb";
	- nameTable["617"] = "Cbm_Left_VIIIa";
	- nameTable["618"] = "Cbm_Vermis_VIIIa";
	- nameTable["619"] = "Cbm_Right_VIIIa";
	- nameTable["620"] = "Cbm_Left_VIIIb";
	- nameTable["621"] = "Cbm_Vermis_VIIIb";
	- nameTable["622"] = "Cbm_Right_VIIIb";
	- nameTable["623"] = "Cbm_Left_IX";
	- nameTable["624"] = "Cbm_Vermis_IX";
	- nameTable["625"] = "Cbm_Right_IX";
	- nameTable["626"] = "Cbm_Left_X";
	- nameTable["627"] = "Cbm_Vermis_X";
	- nameTable["628"] = "Cbm_Right_X";
	- nameTable["640"] = "Cbm_Right_I_V_med";
	- nameTable["641"] = "Cbm_Right_I_V_mid";
	- nameTable["642"] = "Cbm_Right_VI_med";
	- nameTable["643"] = "Cbm_Right_VI_mid";
	- nameTable["644"] = "Cbm_Right_VI_lat";
	- nameTable["645"] = "Cbm_Right_CrusI_med";
	- nameTable["646"] = "Cbm_Right_CrusI_mid";
	- nameTable["647"] = "Cbm_Right_CrusI_lat";
	- nameTable["648"] = "Cbm_Right_CrusII_med";
	- nameTable["649"] = "Cbm_Right_CrusII_mid";
	- nameTable["650"] = "Cbm_Right_CrusII_lat";
	- nameTable["651"] = "Cbm_Right_7med";
	- nameTable["652"] = "Cbm_Right_7mid";
	- nameTable["653"] = "Cbm_Right_7lat";
	- nameTable["654"] = "Cbm_Right_8med";
	- nameTable["655"] = "Cbm_Right_8mid";
	- nameTable["656"] = "Cbm_Right_8lat";
	- nameTable["657"] = "Cbm_Right_PUNs";
	- nameTable["658"] = "Cbm_Right_TONs";
	- nameTable["659"] = "Cbm_Right_FLOs";
	- nameTable["660"] = "Cbm_Left_I_V_med";
	- nameTable["661"] = "Cbm_Left_I_V_mid";
	- nameTable["662"] = "Cbm_Left_VI_med";
	- nameTable["663"] = "Cbm_Left_VI_mid";
	- nameTable["664"] = "Cbm_Left_VI_lat";
	- nameTable["665"] = "Cbm_Left_CrusI_med";
	- nameTable["666"] = "Cbm_Left_CrusI_mid";
	- nameTable["667"] = "Cbm_Left_CrusI_lat";
	- nameTable["668"] = "Cbm_Left_CrusII_med";
	- nameTable["669"] = "Cbm_Left_CrusII_mid";
	- nameTable["670"] = "Cbm_Left_CrusII_lat";
	- nameTable["671"] = "Cbm_Left_7med";
	- nameTable["672"] = "Cbm_Left_7mid";
	- nameTable["673"] = "Cbm_Left_7lat";
	- nameTable["674"] = "Cbm_Left_8med";
	- nameTable["675"] = "Cbm_Left_8mid";
	- nameTable["676"] = "Cbm_Left_8lat";
	- nameTable["677"] = "Cbm_Left_PUNs";
	- nameTable["678"] = "Cbm_Left_TONs";
	- nameTable["679"] = "Cbm_Left_FLOs";
	- nameTable["701"] = "CSF-FSL-FAST";
	- nameTable["702"] = "GrayMatter-FSL-FAST";
	- nameTable["703"] = "WhiteMatter-FSL-FAST";
	- nameTable["999"] = "SUSPICIOUS";
	- nameTable["1000"] = "ctx-lh-unknown";
	- nameTable["1001"] = "ctx-lh-bankssts";
	- nameTable["1002"] = "ctx-lh-caudalanteriorcingulate";
	- nameTable["1003"] = "ctx-lh-caudalmiddlefrontal";
	- nameTable["1004"] = "ctx-lh-corpuscallosum";
	- nameTable["1005"] = "ctx-lh-cuneus";
	- nameTable["1006"] = "ctx-lh-entorhinal";
	- nameTable["1007"] = "ctx-lh-fusiform";
	- nameTable["1008"] = "ctx-lh-inferiorparietal";
	- nameTable["1009"] = "ctx-lh-inferiortemporal";
	- nameTable["1010"] = "ctx-lh-isthmuscingulate";
	- nameTable["1011"] = "ctx-lh-lateraloccipital";
	- nameTable["1012"] = "ctx-lh-lateralorbitofrontal";
	- nameTable["1013"] = "ctx-lh-lingual";
	- nameTable["1014"] = "ctx-lh-medialorbitofrontal";
	- nameTable["1015"] = "ctx-lh-middletemporal";
	- nameTable["1016"] = "ctx-lh-parahippocampal";
	- nameTable["1017"] = "ctx-lh-paracentral";
	- nameTable["1018"] = "ctx-lh-parsopercularis";
	- nameTable["1019"] = "ctx-lh-parsorbitalis";
	- nameTable["1020"] = "ctx-lh-parstriangularis";
	- nameTable["1021"] = "ctx-lh-pericalcarine";
	- nameTable["1022"] = "ctx-lh-postcentral";
	- nameTable["1023"] = "ctx-lh-posteriorcingulate";
	- nameTable["1024"] = "ctx-lh-precentral";
	- nameTable["1025"] = "ctx-lh-precuneus";
	- nameTable["1026"] = "ctx-lh-rostralanteriorcingulate";
	- nameTable["1027"] = "ctx-lh-rostralmiddlefrontal";
	- nameTable["1028"] = "ctx-lh-superiorfrontal";
	- nameTable["1029"] = "ctx-lh-superiorparietal";
	- nameTable["1030"] = "ctx-lh-superiortemporal";
	- nameTable["1031"] = "ctx-lh-supramarginal";
	- nameTable["1032"] = "ctx-lh-frontalpole";
	- nameTable["1033"] = "ctx-lh-temporalpole";
	- nameTable["1034"] = "ctx-lh-transversetemporal";
	- nameTable["1035"] = "ctx-lh-insula";
	- nameTable["2000"] = "ctx-rh-unknown";
	- nameTable["2001"] = "ctx-rh-bankssts";
	- nameTable["2002"] = "ctx-rh-caudalanteriorcingulate";
	- nameTable["2003"] = "ctx-rh-caudalmiddlefrontal";
	- nameTable["2004"] = "ctx-rh-corpuscallosum";
	- nameTable["2005"] = "ctx-rh-cuneus";
	- nameTable["2006"] = "ctx-rh-entorhinal";
	- nameTable["2007"] = "ctx-rh-fusiform";
	- nameTable["2008"] = "ctx-rh-inferiorparietal";
	- nameTable["2009"] = "ctx-rh-inferiortemporal";
	- nameTable["2010"] = "ctx-rh-isthmuscingulate";
	- nameTable["2011"] = "ctx-rh-lateraloccipital";
	- nameTable["2012"] = "ctx-rh-lateralorbitofrontal";
	- nameTable["2013"] = "ctx-rh-lingual";
	- nameTable["2014"] = "ctx-rh-medialorbitofrontal";
	- nameTable["2015"] = "ctx-rh-middletemporal";
	- nameTable["2016"] = "ctx-rh-parahippocampal";
	- nameTable["2017"] = "ctx-rh-paracentral";
	- nameTable["2018"] = "ctx-rh-parsopercularis";
	- nameTable["2019"] = "ctx-rh-parsorbitalis";
	- nameTable["2020"] = "ctx-rh-parstriangularis";
	- nameTable["2021"] = "ctx-rh-pericalcarine";
	- nameTable["2022"] = "ctx-rh-postcentral";
	- nameTable["2023"] = "ctx-rh-posteriorcingulate";
	- nameTable["2024"] = "ctx-rh-precentral";
	- nameTable["2025"] = "ctx-rh-precuneus";
	- nameTable["2026"] = "ctx-rh-rostralanteriorcingulate";
	- nameTable["2027"] = "ctx-rh-rostralmiddlefrontal";
	- nameTable["2028"] = "ctx-rh-superiorfrontal";
	- nameTable["2029"] = "ctx-rh-superiorparietal";
	- nameTable["2030"] = "ctx-rh-superiortemporal";
	- nameTable["2031"] = "ctx-rh-supramarginal";
	- nameTable["2032"] = "ctx-rh-frontalpole";
	- nameTable["2033"] = "ctx-rh-temporalpole";
	- nameTable["2034"] = "ctx-rh-transversetemporal";
	- nameTable["2035"] = "ctx-rh-insula";
	- nameTable["3000"] = "wm-lh-unknown";
	- nameTable["3001"] = "wm-lh-bankssts";
	- nameTable["3002"] = "wm-lh-caudalanteriorcingulate";
	- nameTable["3003"] = "wm-lh-caudalmiddlefrontal";
	- nameTable["3004"] = "wm-lh-corpuscallosum";
	- nameTable["3005"] = "wm-lh-cuneus";
	- nameTable["3006"] = "wm-lh-entorhinal";
	- nameTable["3007"] = "wm-lh-fusiform";
	- nameTable["3008"] = "wm-lh-inferiorparietal";
	- nameTable["3009"] = "wm-lh-inferiortemporal";
	- nameTable["3010"] = "wm-lh-isthmuscingulate";
	- nameTable["3011"] = "wm-lh-lateraloccipital";
	- nameTable["3012"] = "wm-lh-lateralorbitofrontal";
	- nameTable["3013"] = "wm-lh-lingual";
	- nameTable["3014"] = "wm-lh-medialorbitofrontal";
	- nameTable["3015"] = "wm-lh-middletemporal";
	- nameTable["3016"] = "wm-lh-parahippocampal";
	- nameTable["3017"] = "wm-lh-paracentral";
	- nameTable["3018"] = "wm-lh-parsopercularis";
	- nameTable["3019"] = "wm-lh-parsorbitalis";
	- nameTable["3020"] = "wm-lh-parstriangularis";
	- nameTable["3021"] = "wm-lh-pericalcarine";
	- nameTable["3022"] = "wm-lh-postcentral";
	- nameTable["3023"] = "wm-lh-posteriorcingulate";
	- nameTable["3024"] = "wm-lh-precentral";
	- nameTable["3025"] = "wm-lh-precuneus";
	- nameTable["3026"] = "wm-lh-rostralanteriorcingulate";
	- nameTable["3027"] = "wm-lh-rostralmiddlefrontal";
	- nameTable["3028"] = "wm-lh-superiorfrontal";
	- nameTable["3029"] = "wm-lh-superiorparietal";
	- nameTable["3030"] = "wm-lh-superiortemporal";
	- nameTable["3031"] = "wm-lh-supramarginal";
	- nameTable["3032"] = "wm-lh-frontalpole";
	- nameTable["3033"] = "wm-lh-temporalpole";
	- nameTable["3034"] = "wm-lh-transversetemporal";
	- nameTable["3035"] = "wm-lh-insula";
	- nameTable["4000"] = "wm-rh-unknown";
	- nameTable["4001"] = "wm-rh-bankssts";
	- nameTable["4002"] = "wm-rh-caudalanteriorcingulate";
	- nameTable["4003"] = "wm-rh-caudalmiddlefrontal";
	- nameTable["4004"] = "wm-rh-corpuscallosum";
	- nameTable["4005"] = "wm-rh-cuneus";
	- nameTable["4006"] = "wm-rh-entorhinal";
	- nameTable["4007"] = "wm-rh-fusiform";
	- nameTable["4008"] = "wm-rh-inferiorparietal";
	- nameTable["4009"] = "wm-rh-inferiortemporal";
	- nameTable["4010"] = "wm-rh-isthmuscingulate";
	- nameTable["4011"] = "wm-rh-lateraloccipital";
	- nameTable["4012"] = "wm-rh-lateralorbitofrontal";
	- nameTable["4013"] = "wm-rh-lingual";
	- nameTable["4014"] = "wm-rh-medialorbitofrontal";
	- nameTable["4015"] = "wm-rh-middletemporal";
	- nameTable["4016"] = "wm-rh-parahippocampal";
	- nameTable["4017"] = "wm-rh-paracentral";
	- nameTable["4018"] = "wm-rh-parsopercularis";
	- nameTable["4019"] = "wm-rh-parsorbitalis";
	- nameTable["4020"] = "wm-rh-parstriangularis";
	- nameTable["4021"] = "wm-rh-pericalcarine";
	- nameTable["4022"] = "wm-rh-postcentral";
	- nameTable["4023"] = "wm-rh-posteriorcingulate";
	- nameTable["4024"] = "wm-rh-precentral";
	- nameTable["4025"] = "wm-rh-precuneus";
	- nameTable["4026"] = "wm-rh-rostralanteriorcingulate";
	- nameTable["4027"] = "wm-rh-rostralmiddlefrontal";
	- nameTable["4028"] = "wm-rh-superiorfrontal";
	- nameTable["4029"] = "wm-rh-superiorparietal";
	- nameTable["4030"] = "wm-rh-superiortemporal";
	- nameTable["4031"] = "wm-rh-supramarginal";
	- nameTable["4032"] = "wm-rh-frontalpole";
	- nameTable["4033"] = "wm-rh-temporalpole";
	- nameTable["4034"] = "wm-rh-transversetemporal";
	- nameTable["4035"] = "wm-rh-insula";
	- nameTable["1100"] = "ctx-lh-Unknown";
	- nameTable["1101"] = "ctx-lh-Corpus_callosum";
	- nameTable["1102"] = "ctx-lh-G_and_S_Insula_ONLY_AVERAGE";
	- nameTable["1103"] = "ctx-lh-G_cingulate-Isthmus";
	- nameTable["1104"] = "ctx-lh-G_cingulate-Main_part";
	- nameTable["1200"] = "ctx-lh-G_cingulate-caudal_ACC";
	- nameTable["1201"] = "ctx-lh-G_cingulate-rostral_ACC";
	- nameTable["1202"] = "ctx-lh-G_cingulate-posterior";
	- nameTable["1205"] = "ctx-lh-S_cingulate-caudal_ACC";
	- nameTable["1206"] = "ctx-lh-S_cingulate-rostral_ACC";
	- nameTable["1207"] = "ctx-lh-S_cingulate-posterior";
	- nameTable["1210"] = "ctx-lh-S_pericallosal-caudal";
	- nameTable["1211"] = "ctx-lh-S_pericallosal-rostral";
	- nameTable["1212"] = "ctx-lh-S_pericallosal-posterior";
	- nameTable["1105"] = "ctx-lh-G_cuneus";
	- nameTable["1106"] = "ctx-lh-G_frontal_inf-Opercular_part";
	- nameTable["1107"] = "ctx-lh-G_frontal_inf-Orbital_part";
	- nameTable["1108"] = "ctx-lh-G_frontal_inf-Triangular_part";
	- nameTable["1109"] = "ctx-lh-G_frontal_middle";
	- nameTable["1110"] = "ctx-lh-G_frontal_superior";
	- nameTable["1111"] = "ctx-lh-G_frontomarginal";
	- nameTable["1112"] = "ctx-lh-G_insular_long";
	- nameTable["1113"] = "ctx-lh-G_insular_short";
	- nameTable["1114"] = "ctx-lh-G_and_S_occipital_inferior";
	- nameTable["1115"] = "ctx-lh-G_occipital_middle";
	- nameTable["1116"] = "ctx-lh-G_occipital_superior";
	- nameTable["1117"] = "ctx-lh-G_occipit-temp_lat-Or_fusiform";
	- nameTable["1118"] = "ctx-lh-G_occipit-temp_med-Lingual_part";
	- nameTable["1119"] = "ctx-lh-G_occipit-temp_med-Parahippocampal_part";
	- nameTable["1120"] = "ctx-lh-G_orbital";
	- nameTable["1121"] = "ctx-lh-G_paracentral";
	- nameTable["1122"] = "ctx-lh-G_parietal_inferior-Angular_part";
	- nameTable["1123"] = "ctx-lh-G_parietal_inferior-Supramarginal_part";
	- nameTable["1124"] = "ctx-lh-G_parietal_superior";
	- nameTable["1125"] = "ctx-lh-G_postcentral";
	- nameTable["1126"] = "ctx-lh-G_precentral";
	- nameTable["1127"] = "ctx-lh-G_precuneus";
	- nameTable["1128"] = "ctx-lh-G_rectus";
	- nameTable["1129"] = "ctx-lh-G_subcallosal";
	- nameTable["1130"] = "ctx-lh-G_subcentral";
	- nameTable["1131"] = "ctx-lh-G_temporal_inferior";
	- nameTable["1132"] = "ctx-lh-G_temporal_middle";
	- nameTable["1133"] = "ctx-lh-G_temp_sup-G_temp_transv_and_interm_S";
	- nameTable["1134"] = "ctx-lh-G_temp_sup-Lateral_aspect";
	- nameTable["1135"] = "ctx-lh-G_temp_sup-Planum_polare";
	- nameTable["1136"] = "ctx-lh-G_temp_sup-Planum_tempolare";
	- nameTable["1137"] = "ctx-lh-G_and_S_transverse_frontopolar";
	- nameTable["1138"] = "ctx-lh-Lat_Fissure-ant_sgt-ramus_horizontal";
	- nameTable["1139"] = "ctx-lh-Lat_Fissure-ant_sgt-ramus_vertical";
	- nameTable["1140"] = "ctx-lh-Lat_Fissure-post_sgt";
	- nameTable["1141"] = "ctx-lh-Medial_wall";
	- nameTable["1142"] = "ctx-lh-Pole_occipital";
	- nameTable["1143"] = "ctx-lh-Pole_temporal";
	- nameTable["1144"] = "ctx-lh-S_calcarine";
	- nameTable["1145"] = "ctx-lh-S_central";
	- nameTable["1146"] = "ctx-lh-S_central_insula";
	- nameTable["1147"] = "ctx-lh-S_cingulate-Main_part_and_Intracingulate";
	- nameTable["1148"] = "ctx-lh-S_cingulate-Marginalis_part";
	- nameTable["1149"] = "ctx-lh-S_circular_insula_anterior";
	- nameTable["1150"] = "ctx-lh-S_circular_insula_inferior";
	- nameTable["1151"] = "ctx-lh-S_circular_insula_superior";
	- nameTable["1152"] = "ctx-lh-S_collateral_transverse_ant";
	- nameTable["1153"] = "ctx-lh-S_collateral_transverse_post";
	- nameTable["1154"] = "ctx-lh-S_frontal_inferior";
	- nameTable["1155"] = "ctx-lh-S_frontal_middle";
	- nameTable["1156"] = "ctx-lh-S_frontal_superior";
	- nameTable["1157"] = "ctx-lh-S_frontomarginal";
	- nameTable["1158"] = "ctx-lh-S_intermedius_primus-Jensen";
	- nameTable["1159"] = "ctx-lh-S_intraparietal-and_Parietal_transverse";
	- nameTable["1160"] = "ctx-lh-S_occipital_anterior";
	- nameTable["1161"] = "ctx-lh-S_occipital_middle_and_Lunatus";
	- nameTable["1162"] = "ctx-lh-S_occipital_superior_and_transversalis";
	- nameTable["1163"] = "ctx-lh-S_occipito-temporal_lateral";
	- nameTable["1164"] = "ctx-lh-S_occipito-temporal_medial_and_S_Lingual";
	- nameTable["1165"] = "ctx-lh-S_orbital-H_shapped";
	- nameTable["1166"] = "ctx-lh-S_orbital_lateral";
	- nameTable["1167"] = "ctx-lh-S_orbital_medial-Or_olfactory";
	- nameTable["1168"] = "ctx-lh-S_paracentral";
	- nameTable["1169"] = "ctx-lh-S_parieto_occipital";
	- nameTable["1170"] = "ctx-lh-S_pericallosal";
	- nameTable["1171"] = "ctx-lh-S_postcentral";
	- nameTable["1172"] = "ctx-lh-S_precentral-Inferior-part";
	- nameTable["1173"] = "ctx-lh-S_precentral-Superior-part";
	- nameTable["1174"] = "ctx-lh-S_subcentral_ant";
	- nameTable["1175"] = "ctx-lh-S_subcentral_post";
	- nameTable["1176"] = "ctx-lh-S_suborbital";
	- nameTable["1177"] = "ctx-lh-S_subparietal";
	- nameTable["1178"] = "ctx-lh-S_supracingulate";
	- nameTable["1179"] = "ctx-lh-S_temporal_inferior";
	- nameTable["1180"] = "ctx-lh-S_temporal_superior";
	- nameTable["1181"] = "ctx-lh-S_temporal_transverse";
	- nameTable["2100"] = "ctx-rh-Unknown";
	- nameTable["2101"] = "ctx-rh-Corpus_callosum";
	- nameTable["2102"] = "ctx-rh-G_and_S_Insula_ONLY_AVERAGE";
	- nameTable["2103"] = "ctx-rh-G_cingulate-Isthmus";
	- nameTable["2104"] = "ctx-rh-G_cingulate-Main_part";
	- nameTable["2105"] = "ctx-rh-G_cuneus";
	- nameTable["2106"] = "ctx-rh-G_frontal_inf-Opercular_part";
	- nameTable["2107"] = "ctx-rh-G_frontal_inf-Orbital_part";
	- nameTable["2108"] = "ctx-rh-G_frontal_inf-Triangular_part";
	- nameTable["2109"] = "ctx-rh-G_frontal_middle";
	- nameTable["2110"] = "ctx-rh-G_frontal_superior";
	- nameTable["2111"] = "ctx-rh-G_frontomarginal";
	- nameTable["2112"] = "ctx-rh-G_insular_long";
	- nameTable["2113"] = "ctx-rh-G_insular_short";
	- nameTable["2114"] = "ctx-rh-G_and_S_occipital_inferior";
	- nameTable["2115"] = "ctx-rh-G_occipital_middle";
	- nameTable["2116"] = "ctx-rh-G_occipital_superior";
	- nameTable["2117"] = "ctx-rh-G_occipit-temp_lat-Or_fusiform";
	- nameTable["2118"] = "ctx-rh-G_occipit-temp_med-Lingual_part";
	- nameTable["2119"] = "ctx-rh-G_occipit-temp_med-Parahippocampal_part";
	- nameTable["2120"] = "ctx-rh-G_orbital";
	- nameTable["2121"] = "ctx-rh-G_paracentral";
	- nameTable["2122"] = "ctx-rh-G_parietal_inferior-Angular_part";
	- nameTable["2123"] = "ctx-rh-G_parietal_inferior-Supramarginal_part";
	- nameTable["2124"] = "ctx-rh-G_parietal_superior";
	- nameTable["2125"] = "ctx-rh-G_postcentral";
	- nameTable["2126"] = "ctx-rh-G_precentral";
	- nameTable["2127"] = "ctx-rh-G_precuneus";
	- nameTable["2128"] = "ctx-rh-G_rectus";
	- nameTable["2129"] = "ctx-rh-G_subcallosal";
	- nameTable["2130"] = "ctx-rh-G_subcentral";
	- nameTable["2131"] = "ctx-rh-G_temporal_inferior";
	- nameTable["2132"] = "ctx-rh-G_temporal_middle";
	- nameTable["2133"] = "ctx-rh-G_temp_sup-G_temp_transv_and_interm_S";
	- nameTable["2134"] = "ctx-rh-G_temp_sup-Lateral_aspect";
	- nameTable["2135"] = "ctx-rh-G_temp_sup-Planum_polare";
	- nameTable["2136"] = "ctx-rh-G_temp_sup-Planum_tempolare";
	- nameTable["2137"] = "ctx-rh-G_and_S_transverse_frontopolar";
	- nameTable["2138"] = "ctx-rh-Lat_Fissure-ant_sgt-ramus_horizontal";
	- nameTable["2139"] = "ctx-rh-Lat_Fissure-ant_sgt-ramus_vertical";
	- nameTable["2140"] = "ctx-rh-Lat_Fissure-post_sgt";
	- nameTable["2141"] = "ctx-rh-Medial_wall";
	- nameTable["2142"] = "ctx-rh-Pole_occipital";
	- nameTable["2143"] = "ctx-rh-Pole_temporal";
	- nameTable["2144"] = "ctx-rh-S_calcarine";
	- nameTable["2145"] = "ctx-rh-S_central";
	- nameTable["2146"] = "ctx-rh-S_central_insula";
	- nameTable["2147"] = "ctx-rh-S_cingulate-Main_part_and_Intracingulate";
	- nameTable["2148"] = "ctx-rh-S_cingulate-Marginalis_part";
	- nameTable["2149"] = "ctx-rh-S_circular_insula_anterior";
	- nameTable["2150"] = "ctx-rh-S_circular_insula_inferior";
	- nameTable["2151"] = "ctx-rh-S_circular_insula_superior";
	- nameTable["2152"] = "ctx-rh-S_collateral_transverse_ant";
	- nameTable["2153"] = "ctx-rh-S_collateral_transverse_post";
	- nameTable["2154"] = "ctx-rh-S_frontal_inferior";
	- nameTable["2155"] = "ctx-rh-S_frontal_middle";
	- nameTable["2156"] = "ctx-rh-S_frontal_superior";
	- nameTable["2157"] = "ctx-rh-S_frontomarginal";
	- nameTable["2158"] = "ctx-rh-S_intermedius_primus-Jensen";
	- nameTable["2159"] = "ctx-rh-S_intraparietal-and_Parietal_transverse";
	- nameTable["2160"] = "ctx-rh-S_occipital_anterior";
	- nameTable["2161"] = "ctx-rh-S_occipital_middle_and_Lunatus";
	- nameTable["2162"] = "ctx-rh-S_occipital_superior_and_transversalis";
	- nameTable["2163"] = "ctx-rh-S_occipito-temporal_lateral";
	- nameTable["2164"] = "ctx-rh-S_occipito-temporal_medial_and_S_Lingual";
	- nameTable["2165"] = "ctx-rh-S_orbital-H_shapped";
	- nameTable["2166"] = "ctx-rh-S_orbital_lateral";
	- nameTable["2167"] = "ctx-rh-S_orbital_medial-Or_olfactory";
	- nameTable["2168"] = "ctx-rh-S_paracentral";
	- nameTable["2169"] = "ctx-rh-S_parieto_occipital";
	- nameTable["2170"] = "ctx-rh-S_pericallosal";
	- nameTable["2171"] = "ctx-rh-S_postcentral";
	- nameTable["2172"] = "ctx-rh-S_precentral-Inferior-part";
	- nameTable["2173"] = "ctx-rh-S_precentral-Superior-part";
	- nameTable["2174"] = "ctx-rh-S_subcentral_ant";
	- nameTable["2175"] = "ctx-rh-S_subcentral_post";
	- nameTable["2176"] = "ctx-rh-S_suborbital";
	- nameTable["2177"] = "ctx-rh-S_subparietal";
	- nameTable["2178"] = "ctx-rh-S_supracingulate";
	- nameTable["2179"] = "ctx-rh-S_temporal_inferior";
	- nameTable["2180"] = "ctx-rh-S_temporal_superior";
	- nameTable["2181"] = "ctx-rh-S_temporal_transverse";
	- nameTable["2200"] = "ctx-rh-G_cingulate-caudal_ACC";
	- nameTable["2201"] = "ctx-rh-G_cingulate-rostral_ACC";
	- nameTable["2202"] = "ctx-rh-G_cingulate-posterior";
	- nameTable["2205"] = "ctx-rh-S_cingulate-caudal_ACC";
	- nameTable["2206"] = "ctx-rh-S_cingulate-rostral_ACC";
	- nameTable["2207"] = "ctx-rh-S_cingulate-posterior";
	- nameTable["2210"] = "ctx-rh-S_pericallosal-caudal";
	- nameTable["2211"] = "ctx-rh-S_pericallosal-rostral";
	- nameTable["2212"] = "ctx-rh-S_pericallosal-posterior";
	- nameTable["3100"] = "wm-lh-Unknown";
	- nameTable["3101"] = "wm-lh-Corpus_callosum";
	- nameTable["3102"] = "wm-lh-G_and_S_Insula_ONLY_AVERAGE";
	- nameTable["3103"] = "wm-lh-G_cingulate-Isthmus";
	- nameTable["3104"] = "wm-lh-G_cingulate-Main_part";
	- nameTable["3105"] = "wm-lh-G_cuneus";
	- nameTable["3106"] = "wm-lh-G_frontal_inf-Opercular_part";
	- nameTable["3107"] = "wm-lh-G_frontal_inf-Orbital_part";
	- nameTable["3108"] = "wm-lh-G_frontal_inf-Triangular_part";
	- nameTable["3109"] = "wm-lh-G_frontal_middle";
	- nameTable["3110"] = "wm-lh-G_frontal_superior";
	- nameTable["3111"] = "wm-lh-G_frontomarginal";
	- nameTable["3112"] = "wm-lh-G_insular_long";
	- nameTable["3113"] = "wm-lh-G_insular_short";
	- nameTable["3114"] = "wm-lh-G_and_S_occipital_inferior";
	- nameTable["3115"] = "wm-lh-G_occipital_middle";
	- nameTable["3116"] = "wm-lh-G_occipital_superior";
	- nameTable["3117"] = "wm-lh-G_occipit-temp_lat-Or_fusiform";
	- nameTable["3118"] = "wm-lh-G_occipit-temp_med-Lingual_part";
	- nameTable["3119"] = "wm-lh-G_occipit-temp_med-Parahippocampal_part";
	- nameTable["3120"] = "wm-lh-G_orbital";
	- nameTable["3121"] = "wm-lh-G_paracentral";
	- nameTable["3122"] = "wm-lh-G_parietal_inferior-Angular_part";
	- nameTable["3123"] = "wm-lh-G_parietal_inferior-Supramarginal_part";
	- nameTable["3124"] = "wm-lh-G_parietal_superior";
	- nameTable["3125"] = "wm-lh-G_postcentral";
	- nameTable["3126"] = "wm-lh-G_precentral";
	- nameTable["3127"] = "wm-lh-G_precuneus";
	- nameTable["3128"] = "wm-lh-G_rectus";
	- nameTable["3129"] = "wm-lh-G_subcallosal";
	- nameTable["3130"] = "wm-lh-G_subcentral";
	- nameTable["3131"] = "wm-lh-G_temporal_inferior";
	- nameTable["3132"] = "wm-lh-G_temporal_middle";
	- nameTable["3133"] = "wm-lh-G_temp_sup-G_temp_transv_and_interm_S";
	- nameTable["3134"] = "wm-lh-G_temp_sup-Lateral_aspect";
	- nameTable["3135"] = "wm-lh-G_temp_sup-Planum_polare";
	- nameTable["3136"] = "wm-lh-G_temp_sup-Planum_tempolare";
	- nameTable["3137"] = "wm-lh-G_and_S_transverse_frontopolar";
	- nameTable["3138"] = "wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal";
	- nameTable["3139"] = "wm-lh-Lat_Fissure-ant_sgt-ramus_vertical";
	- nameTable["3140"] = "wm-lh-Lat_Fissure-post_sgt";
	- nameTable["3141"] = "wm-lh-Medial_wall";
	- nameTable["3142"] = "wm-lh-Pole_occipital";
	- nameTable["3143"] = "wm-lh-Pole_temporal";
	- nameTable["3144"] = "wm-lh-S_calcarine";
	- nameTable["3145"] = "wm-lh-S_central";
	- nameTable["3146"] = "wm-lh-S_central_insula";
	- nameTable["3147"] = "wm-lh-S_cingulate-Main_part_and_Intracingulate";
	- nameTable["3148"] = "wm-lh-S_cingulate-Marginalis_part";
	- nameTable["3149"] = "wm-lh-S_circular_insula_anterior";
	- nameTable["3150"] = "wm-lh-S_circular_insula_inferior";
	- nameTable["3151"] = "wm-lh-S_circular_insula_superior";
	- nameTable["3152"] = "wm-lh-S_collateral_transverse_ant";
	- nameTable["3153"] = "wm-lh-S_collateral_transverse_post";
	- nameTable["3154"] = "wm-lh-S_frontal_inferior";
	- nameTable["3155"] = "wm-lh-S_frontal_middle";
	- nameTable["3156"] = "wm-lh-S_frontal_superior";
	- nameTable["3157"] = "wm-lh-S_frontomarginal";
	- nameTable["3158"] = "wm-lh-S_intermedius_primus-Jensen";
	- nameTable["3159"] = "wm-lh-S_intraparietal-and_Parietal_transverse";
	- nameTable["3160"] = "wm-lh-S_occipital_anterior";
	- nameTable["3161"] = "wm-lh-S_occipital_middle_and_Lunatus";
	- nameTable["3162"] = "wm-lh-S_occipital_superior_and_transversalis";
	- nameTable["3163"] = "wm-lh-S_occipito-temporal_lateral";
	- nameTable["3164"] = "wm-lh-S_occipito-temporal_medial_and_S_Lingual";
	- nameTable["3165"] = "wm-lh-S_orbital-H_shapped";
	- nameTable["3166"] = "wm-lh-S_orbital_lateral";
	- nameTable["3167"] = "wm-lh-S_orbital_medial-Or_olfactory";
	- nameTable["3168"] = "wm-lh-S_paracentral";
	- nameTable["3169"] = "wm-lh-S_parieto_occipital";
	- nameTable["3170"] = "wm-lh-S_pericallosal";
	- nameTable["3171"] = "wm-lh-S_postcentral";
	- nameTable["3172"] = "wm-lh-S_precentral-Inferior-part";
	- nameTable["3173"] = "wm-lh-S_precentral-Superior-part";
	- nameTable["3174"] = "wm-lh-S_subcentral_ant";
	- nameTable["3175"] = "wm-lh-S_subcentral_post";
	- nameTable["3176"] = "wm-lh-S_suborbital";
	- nameTable["3177"] = "wm-lh-S_subparietal";
	- nameTable["3178"] = "wm-lh-S_supracingulate";
	- nameTable["3179"] = "wm-lh-S_temporal_inferior";
	- nameTable["3180"] = "wm-lh-S_temporal_superior";
	- nameTable["3181"] = "wm-lh-S_temporal_transverse";
	- nameTable["4100"] = "wm-rh-Unknown";
	- nameTable["4101"] = "wm-rh-Corpus_callosum";
	- nameTable["4102"] = "wm-rh-G_and_S_Insula_ONLY_AVERAGE";
	- nameTable["4103"] = "wm-rh-G_cingulate-Isthmus";
	- nameTable["4104"] = "wm-rh-G_cingulate-Main_part";
	- nameTable["4105"] = "wm-rh-G_cuneus";
	- nameTable["4106"] = "wm-rh-G_frontal_inf-Opercular_part";
	- nameTable["4107"] = "wm-rh-G_frontal_inf-Orbital_part";
	- nameTable["4108"] = "wm-rh-G_frontal_inf-Triangular_part";
	- nameTable["4109"] = "wm-rh-G_frontal_middle";
	- nameTable["4110"] = "wm-rh-G_frontal_superior";
	- nameTable["4111"] = "wm-rh-G_frontomarginal";
	- nameTable["4112"] = "wm-rh-G_insular_long";
	- nameTable["4113"] = "wm-rh-G_insular_short";
	- nameTable["4114"] = "wm-rh-G_and_S_occipital_inferior";
	- nameTable["4115"] = "wm-rh-G_occipital_middle";
	- nameTable["4116"] = "wm-rh-G_occipital_superior";
	- nameTable["4117"] = "wm-rh-G_occipit-temp_lat-Or_fusiform";
	- nameTable["4118"] = "wm-rh-G_occipit-temp_med-Lingual_part";
	- nameTable["4119"] = "wm-rh-G_occipit-temp_med-Parahippocampal_part";
	- nameTable["4120"] = "wm-rh-G_orbital";
	- nameTable["4121"] = "wm-rh-G_paracentral";
	- nameTable["4122"] = "wm-rh-G_parietal_inferior-Angular_part";
	- nameTable["4123"] = "wm-rh-G_parietal_inferior-Supramarginal_part";
	- nameTable["4124"] = "wm-rh-G_parietal_superior";
	- nameTable["4125"] = "wm-rh-G_postcentral";
	- nameTable["4126"] = "wm-rh-G_precentral";
	- nameTable["4127"] = "wm-rh-G_precuneus";
	- nameTable["4128"] = "wm-rh-G_rectus";
	- nameTable["4129"] = "wm-rh-G_subcallosal";
	- nameTable["4130"] = "wm-rh-G_subcentral";
	- nameTable["4131"] = "wm-rh-G_temporal_inferior";
	- nameTable["4132"] = "wm-rh-G_temporal_middle";
	- nameTable["4133"] = "wm-rh-G_temp_sup-G_temp_transv_and_interm_S";
	- nameTable["4134"] = "wm-rh-G_temp_sup-Lateral_aspect";
	- nameTable["4135"] = "wm-rh-G_temp_sup-Planum_polare";
	- nameTable["4136"] = "wm-rh-G_temp_sup-Planum_tempolare";
	- nameTable["4137"] = "wm-rh-G_and_S_transverse_frontopolar";
	- nameTable["4138"] = "wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal";
	- nameTable["4139"] = "wm-rh-Lat_Fissure-ant_sgt-ramus_vertical";
	- nameTable["4140"] = "wm-rh-Lat_Fissure-post_sgt";
	- nameTable["4141"] = "wm-rh-Medial_wall";
	- nameTable["4142"] = "wm-rh-Pole_occipital";
	- nameTable["4143"] = "wm-rh-Pole_temporal";
	- nameTable["4144"] = "wm-rh-S_calcarine";
	- nameTable["4145"] = "wm-rh-S_central";
	- nameTable["4146"] = "wm-rh-S_central_insula";
	- nameTable["4147"] = "wm-rh-S_cingulate-Main_part_and_Intracingulate";
	- nameTable["4148"] = "wm-rh-S_cingulate-Marginalis_part";
	- nameTable["4149"] = "wm-rh-S_circular_insula_anterior";
	- nameTable["4150"] = "wm-rh-S_circular_insula_inferior";
	- nameTable["4151"] = "wm-rh-S_circular_insula_superior";
	- nameTable["4152"] = "wm-rh-S_collateral_transverse_ant";
	- nameTable["4153"] = "wm-rh-S_collateral_transverse_post";
	- nameTable["4154"] = "wm-rh-S_frontal_inferior";
	- nameTable["4155"] = "wm-rh-S_frontal_middle";
	- nameTable["4156"] = "wm-rh-S_frontal_superior";
	- nameTable["4157"] = "wm-rh-S_frontomarginal";
	- nameTable["4158"] = "wm-rh-S_intermedius_primus-Jensen";
	- nameTable["4159"] = "wm-rh-S_intraparietal-and_Parietal_transverse";
	- nameTable["4160"] = "wm-rh-S_occipital_anterior";
	- nameTable["4161"] = "wm-rh-S_occipital_middle_and_Lunatus";
	- nameTable["4162"] = "wm-rh-S_occipital_superior_and_transversalis";
	- nameTable["4163"] = "wm-rh-S_occipito-temporal_lateral";
	- nameTable["4164"] = "wm-rh-S_occipito-temporal_medial_and_S_Lingual";
	- nameTable["4165"] = "wm-rh-S_orbital-H_shapped";
	- nameTable["4166"] = "wm-rh-S_orbital_lateral";
	- nameTable["4167"] = "wm-rh-S_orbital_medial-Or_olfactory";
	- nameTable["4168"] = "wm-rh-S_paracentral";
	- nameTable["4169"] = "wm-rh-S_parieto_occipital";
	- nameTable["4170"] = "wm-rh-S_pericallosal";
	- nameTable["4171"] = "wm-rh-S_postcentral";
	- nameTable["4172"] = "wm-rh-S_precentral-Inferior-part";
	- nameTable["4173"] = "wm-rh-S_precentral-Superior-part";
	- nameTable["4174"] = "wm-rh-S_subcentral_ant";
	- nameTable["4175"] = "wm-rh-S_subcentral_post";
	- nameTable["4176"] = "wm-rh-S_suborbital";
	- nameTable["4177"] = "wm-rh-S_subparietal";
	- nameTable["4178"] = "wm-rh-S_supracingulate";
	- nameTable["4179"] = "wm-rh-S_temporal_inferior";
	- nameTable["4180"] = "wm-rh-S_temporal_superior";
	- nameTable["4181"] = "wm-rh-S_temporal_transverse";
	- nameTable["5001"] = "Left-UnsegmentedWhiteMatter";
	- nameTable["5002"] = "Right-UnsegmentedWhiteMatter";
	- nameTable["5100"] = "fmajor";
	- nameTable["5101"] = "fminor";
	- nameTable["5102"] = "lh.atr";
	- nameTable["5103"] = "lh.cab";
	- nameTable["5104"] = "lh.ccg";
	- nameTable["5105"] = "lh.cst";
	- nameTable["5106"] = "lh.ilf";
	- nameTable["5107"] = "lh.slfp";
	- nameTable["5108"] = "lh.slft";
	- nameTable["5109"] = "lh.unc";
	- nameTable["5110"] = "rh.atr";
	- nameTable["5111"] = "rh.cab";
	- nameTable["5112"] = "rh.ccg";
	- nameTable["5113"] = "rh.cst";
	- nameTable["5114"] = "rh.ilf";
	- nameTable["5115"] = "rh.slfp";
	- nameTable["5116"] = "rh.slft";
	- nameTable["5117"] = "rh.unc";
	- nameTable["5200"] = "CC-ForcepsMajor";
	- nameTable["5201"] = "CC-ForcepsMinor";
	- nameTable["5202"] = "LAntThalRadiation";
	- nameTable["5203"] = "LCingulumAngBundle";
	- nameTable["5204"] = "LCingulumCingGyrus";
	- nameTable["5205"] = "LCorticospinalTract";
	- nameTable["5206"] = "LInfLongFas";
	- nameTable["5207"] = "LSupLongFasParietal";
	- nameTable["5208"] = "LSupLongFasTemporal";
	- nameTable["5209"] = "LUncinateFas";
	- nameTable["5210"] = "RAntThalRadiation";
	- nameTable["5211"] = "RCingulumAngBundle";
	- nameTable["5212"] = "RCingulumCingGyrus";
	- nameTable["5213"] = "RCorticospinalTract";
	- nameTable["5214"] = "RInfLongFas";
	- nameTable["5215"] = "RSupLongFasParietal";
	- nameTable["5216"] = "RSupLongFasTemporal";
	- nameTable["5217"] = "RUncinateFas";
	- nameTable["6000"] = "CST-orig";
	- nameTable["6001"] = "CST-hammer";
	- nameTable["6002"] = "CST-CVS";
	- nameTable["6003"] = "CST-flirt";
	- nameTable["6010"] = "Left-SLF1";
	- nameTable["6020"] = "Right-SLF1";
	- nameTable["6030"] = "Left-SLF3";
	- nameTable["6040"] = "Right-SLF3";
	- nameTable["6050"] = "Left-CST";
	- nameTable["6060"] = "Right-CST";
	- nameTable["6070"] = "Left-SLF2";
	- nameTable["6080"] = "Right-SLF2";
	- nameTable["7001"] = "Lateral-nucleus";
	- nameTable["7002"] = "Basolateral-nucleus";
	- nameTable["7003"] = "Basal-nucleus";
	- nameTable["7004"] = "Centromedial-nucleus";
	- nameTable["7005"] = "Central-nucleus";
	- nameTable["7006"] = "Medial-nucleus";
	- nameTable["7007"] = "Cortical-nucleus";
	- nameTable["7008"] = "Accessory-Basal-nucleus";
	- nameTable["7009"] = "Corticoamygdaloid-transitio";
	- nameTable["7010"] = "Anterior-amygdaloid-area-AAA";
	- nameTable["7011"] = "Fusion-amygdala-HP-FAH";
	- nameTable["7012"] = "Hippocampal-amygdala-transition-HATA";
	- nameTable["7013"] = "Endopiriform-nucleus";
	- nameTable["7014"] = "Lateral-nucleus-olfactory-tract";
	- nameTable["7015"] = "Paralaminar-nucleus";
	- nameTable["7016"] = "Intercalated-nucleus";
	- nameTable["7017"] = "Prepiriform-cortex";
	- nameTable["7018"] = "Periamygdaloid-cortex";
	- nameTable["7019"] = "Envelope-Amygdala";
	- nameTable["7020"] = "Extranuclear-Amydala";
	- nameTable["7100"] = "Brainstem-inferior-colliculus";
	- nameTable["7101"] = "Brainstem-cochlear-nucleus";
	- nameTable["8001"] = "Thalamus-Anterior";
	- nameTable["8002"] = "Thalamus-Ventral-anterior";
	- nameTable["8003"] = "Thalamus-Lateral-dorsal";
	- nameTable["8004"] = "Thalamus-Lateral-posterior";
	- nameTable["8005"] = "Thalamus-Ventral-lateral";
	- nameTable["8006"] = "Thalamus-Ventral-posterior-medial";
	- nameTable["8007"] = "Thalamus-Ventral-posterior-lateral";
	- nameTable["8008"] = "Thalamus-intralaminar";
	- nameTable["8009"] = "Thalamus-centromedian";
	- nameTable["8010"] = "Thalamus-mediodorsal";
	- nameTable["8011"] = "Thalamus-medial";
	- nameTable["8012"] = "Thalamus-pulvinar";
	- nameTable["8013"] = "Thalamus-lateral-geniculate";
	- nameTable["8014"] = "Thalamus-medial-geniculate";
	- nameTable["9000"] = "ctx-lh-prefrontal";
	- nameTable["9001"] = "ctx-lh-primary-motor";
	- nameTable["9002"] = "ctx-lh-premotor";
	- nameTable["9003"] = "ctx-lh-temporal";
	- nameTable["9004"] = "ctx-lh-posterior-parietal";
	- nameTable["9005"] = "ctx-lh-prim-sec-somatosensory";
	- nameTable["9006"] = "ctx-lh-occipital";
	- nameTable["9500"] = "ctx-rh-prefrontal";
	- nameTable["9501"] = "ctx-rh-primary-motor";
	- nameTable["9502"] = "ctx-rh-premotor";
	- nameTable["9503"] = "ctx-rh-temporal";
	- nameTable["9504"] = "ctx-rh-posterior-parietal";
	- nameTable["9505"] = "ctx-rh-prim-sec-somatosensory";
	- nameTable["9506"] = "ctx-rh-occipital";
	- nameTable["11100"] = "ctx_lh_Unknown";
	- nameTable["11101"] = "ctx_lh_G_and_S_frontomargin";
	- nameTable["11102"] = "ctx_lh_G_and_S_occipital_inf";
	- nameTable["11103"] = "ctx_lh_G_and_S_paracentral";
	- nameTable["11104"] = "ctx_lh_G_and_S_subcentral";
	- nameTable["11105"] = "ctx_lh_G_and_S_transv_frontopol";
	- nameTable["11106"] = "ctx_lh_G_and_S_cingul-Ant";
	- nameTable["11107"] = "ctx_lh_G_and_S_cingul-Mid-Ant";
	- nameTable["11108"] = "ctx_lh_G_and_S_cingul-Mid-Post";
	- nameTable["11109"] = "ctx_lh_G_cingul-Post-dorsal";
	- nameTable["11110"] = "ctx_lh_G_cingul-Post-ventral";
	- nameTable["11111"] = "ctx_lh_G_cuneus";
	- nameTable["11112"] = "ctx_lh_G_front_inf-Opercular";
	- nameTable["11113"] = "ctx_lh_G_front_inf-Orbital";
	- nameTable["11114"] = "ctx_lh_G_front_inf-Triangul";
	- nameTable["11115"] = "ctx_lh_G_front_middle";
	- nameTable["11116"] = "ctx_lh_G_front_sup";
	- nameTable["11117"] = "ctx_lh_G_Ins_lg_and_S_cent_ins";
	- nameTable["11118"] = "ctx_lh_G_insular_short";
	- nameTable["11119"] = "ctx_lh_G_occipital_middle";
	- nameTable["11120"] = "ctx_lh_G_occipital_sup";
	- nameTable["11121"] = "ctx_lh_G_oc-temp_lat-fusifor";
	- nameTable["11122"] = "ctx_lh_G_oc-temp_med-Lingual";
	- nameTable["11123"] = "ctx_lh_G_oc-temp_med-Parahip";
	- nameTable["11124"] = "ctx_lh_G_orbital";
	- nameTable["11125"] = "ctx_lh_G_pariet_inf-Angular";
	- nameTable["11126"] = "ctx_lh_G_pariet_inf-Supramar";
	- nameTable["11127"] = "ctx_lh_G_parietal_sup";
	- nameTable["11128"] = "ctx_lh_G_postcentral";
	- nameTable["11129"] = "ctx_lh_G_precentral";
	- nameTable["11130"] = "ctx_lh_G_precuneus";
	- nameTable["11131"] = "ctx_lh_G_rectus";
	- nameTable["11132"] = "ctx_lh_G_subcallosal";
	- nameTable["11133"] = "ctx_lh_G_temp_sup-G_T_transv";
	- nameTable["11134"] = "ctx_lh_G_temp_sup-Lateral";
	- nameTable["11135"] = "ctx_lh_G_temp_sup-Plan_polar";
	- nameTable["11136"] = "ctx_lh_G_temp_sup-Plan_tempo";
	- nameTable["11137"] = "ctx_lh_G_temporal_inf";
	- nameTable["11138"] = "ctx_lh_G_temporal_middle";
	- nameTable["11139"] = "ctx_lh_Lat_Fis-ant-Horizont";
	- nameTable["11140"] = "ctx_lh_Lat_Fis-ant-Vertical";
	- nameTable["11141"] = "ctx_lh_Lat_Fis-post";
	- nameTable["11142"] = "ctx_lh_Medial_wall";
	- nameTable["11143"] = "ctx_lh_Pole_occipital";
	- nameTable["11144"] = "ctx_lh_Pole_temporal";
	- nameTable["11145"] = "ctx_lh_S_calcarine";
	- nameTable["11146"] = "ctx_lh_S_central";
	- nameTable["11147"] = "ctx_lh_S_cingul-Marginalis";
	- nameTable["11148"] = "ctx_lh_S_circular_insula_ant";
	- nameTable["11149"] = "ctx_lh_S_circular_insula_inf";
	- nameTable["11150"] = "ctx_lh_S_circular_insula_sup";
	- nameTable["11151"] = "ctx_lh_S_collat_transv_ant";
	- nameTable["11152"] = "ctx_lh_S_collat_transv_post";
	- nameTable["11153"] = "ctx_lh_S_front_inf";
	- nameTable["11154"] = "ctx_lh_S_front_middle";
	- nameTable["11155"] = "ctx_lh_S_front_sup";
	- nameTable["11156"] = "ctx_lh_S_interm_prim-Jensen";
	- nameTable["11157"] = "ctx_lh_S_intrapariet_and_P_trans";
	- nameTable["11158"] = "ctx_lh_S_oc_middle_and_Lunatus";
	- nameTable["11159"] = "ctx_lh_S_oc_sup_and_transversal";
	- nameTable["11160"] = "ctx_lh_S_occipital_ant";
	- nameTable["11161"] = "ctx_lh_S_oc-temp_lat";
	- nameTable["11162"] = "ctx_lh_S_oc-temp_med_and_Lingual";
	- nameTable["11163"] = "ctx_lh_S_orbital_lateral";
	- nameTable["11164"] = "ctx_lh_S_orbital_med-olfact";
	- nameTable["11165"] = "ctx_lh_S_orbital-H_Shaped";
	- nameTable["11166"] = "ctx_lh_S_parieto_occipital";
	- nameTable["11167"] = "ctx_lh_S_pericallosal";
	- nameTable["11168"] = "ctx_lh_S_postcentral";
	- nameTable["11169"] = "ctx_lh_S_precentral-inf-part";
	- nameTable["11170"] = "ctx_lh_S_precentral-sup-part";
	- nameTable["11171"] = "ctx_lh_S_suborbital";
	- nameTable["11172"] = "ctx_lh_S_subparietal";
	- nameTable["11173"] = "ctx_lh_S_temporal_inf";
	- nameTable["11174"] = "ctx_lh_S_temporal_sup";
	- nameTable["11175"] = "ctx_lh_S_temporal_transverse";
	- nameTable["12100"] = "ctx_rh_Unknown";
	- nameTable["12101"] = "ctx_rh_G_and_S_frontomargin";
	- nameTable["12102"] = "ctx_rh_G_and_S_occipital_inf";
	- nameTable["12103"] = "ctx_rh_G_and_S_paracentral";
	- nameTable["12104"] = "ctx_rh_G_and_S_subcentral";
	- nameTable["12105"] = "ctx_rh_G_and_S_transv_frontopol";
	- nameTable["12106"] = "ctx_rh_G_and_S_cingul-Ant";
	- nameTable["12107"] = "ctx_rh_G_and_S_cingul-Mid-Ant";
	- nameTable["12108"] = "ctx_rh_G_and_S_cingul-Mid-Post";
	- nameTable["12109"] = "ctx_rh_G_cingul-Post-dorsal";
	- nameTable["12110"] = "ctx_rh_G_cingul-Post-ventral";
	- nameTable["12111"] = "ctx_rh_G_cuneus";
	- nameTable["12112"] = "ctx_rh_G_front_inf-Opercular";
	- nameTable["12113"] = "ctx_rh_G_front_inf-Orbital";
	- nameTable["12114"] = "ctx_rh_G_front_inf-Triangul";
	- nameTable["12115"] = "ctx_rh_G_front_middle";
	- nameTable["12116"] = "ctx_rh_G_front_sup";
	- nameTable["12117"] = "ctx_rh_G_Ins_lg_and_S_cent_ins";
	- nameTable["12118"] = "ctx_rh_G_insular_short";
	- nameTable["12119"] = "ctx_rh_G_occipital_middle";
	- nameTable["12120"] = "ctx_rh_G_occipital_sup";
	- nameTable["12121"] = "ctx_rh_G_oc-temp_lat-fusifor";
	- nameTable["12122"] = "ctx_rh_G_oc-temp_med-Lingual";
	- nameTable["12123"] = "ctx_rh_G_oc-temp_med-Parahip";
	- nameTable["12124"] = "ctx_rh_G_orbital";
	- nameTable["12125"] = "ctx_rh_G_pariet_inf-Angular";
	- nameTable["12126"] = "ctx_rh_G_pariet_inf-Supramar";
	- nameTable["12127"] = "ctx_rh_G_parietal_sup";
	- nameTable["12128"] = "ctx_rh_G_postcentral";
	- nameTable["12129"] = "ctx_rh_G_precentral";
	- nameTable["12130"] = "ctx_rh_G_precuneus";
	- nameTable["12131"] = "ctx_rh_G_rectus";
	- nameTable["12132"] = "ctx_rh_G_subcallosal";
	- nameTable["12133"] = "ctx_rh_G_temp_sup-G_T_transv";
	- nameTable["12134"] = "ctx_rh_G_temp_sup-Lateral";
	- nameTable["12135"] = "ctx_rh_G_temp_sup-Plan_polar";
	- nameTable["12136"] = "ctx_rh_G_temp_sup-Plan_tempo";
	- nameTable["12137"] = "ctx_rh_G_temporal_inf";
	- nameTable["12138"] = "ctx_rh_G_temporal_middle";
	- nameTable["12139"] = "ctx_rh_Lat_Fis-ant-Horizont";
	- nameTable["12140"] = "ctx_rh_Lat_Fis-ant-Vertical";
	- nameTable["12141"] = "ctx_rh_Lat_Fis-post";
	- nameTable["12142"] = "ctx_rh_Medial_wall";
	- nameTable["12143"] = "ctx_rh_Pole_occipital";
	- nameTable["12144"] = "ctx_rh_Pole_temporal";
	- nameTable["12145"] = "ctx_rh_S_calcarine";
	- nameTable["12146"] = "ctx_rh_S_central";
	- nameTable["12147"] = "ctx_rh_S_cingul-Marginalis";
	- nameTable["12148"] = "ctx_rh_S_circular_insula_ant";
	- nameTable["12149"] = "ctx_rh_S_circular_insula_inf";
	- nameTable["12150"] = "ctx_rh_S_circular_insula_sup";
	- nameTable["12151"] = "ctx_rh_S_collat_transv_ant";
	- nameTable["12152"] = "ctx_rh_S_collat_transv_post";
	- nameTable["12153"] = "ctx_rh_S_front_inf";
	- nameTable["12154"] = "ctx_rh_S_front_middle";
	- nameTable["12155"] = "ctx_rh_S_front_sup";
	- nameTable["12156"] = "ctx_rh_S_interm_prim-Jensen";
	- nameTable["12157"] = "ctx_rh_S_intrapariet_and_P_trans";
	- nameTable["12158"] = "ctx_rh_S_oc_middle_and_Lunatus";
	- nameTable["12159"] = "ctx_rh_S_oc_sup_and_transversal";
	- nameTable["12160"] = "ctx_rh_S_occipital_ant";
	- nameTable["12161"] = "ctx_rh_S_oc-temp_lat";
	- nameTable["12162"] = "ctx_rh_S_oc-temp_med_and_Lingual";
	- nameTable["12163"] = "ctx_rh_S_orbital_lateral";
	- nameTable["12164"] = "ctx_rh_S_orbital_med-olfact";
	- nameTable["12165"] = "ctx_rh_S_orbital-H_Shaped";
	- nameTable["12166"] = "ctx_rh_S_parieto_occipital";
	- nameTable["12167"] = "ctx_rh_S_pericallosal";
	- nameTable["12168"] = "ctx_rh_S_postcentral";
	- nameTable["12169"] = "ctx_rh_S_precentral-inf-part";
	- nameTable["12170"] = "ctx_rh_S_precentral-sup-part";
	- nameTable["12171"] = "ctx_rh_S_suborbital";
	- nameTable["12172"] = "ctx_rh_S_subparietal";
	- nameTable["12173"] = "ctx_rh_S_temporal_inf";
	- nameTable["12174"] = "ctx_rh_S_temporal_sup";
	- nameTable["12175"] = "ctx_rh_S_temporal_transverse";
	- nameTable["13100"] = "wm_lh_Unknown";
	- nameTable["13101"] = "wm_lh_G_and_S_frontomargin";
	- nameTable["13102"] = "wm_lh_G_and_S_occipital_inf";
	- nameTable["13103"] = "wm_lh_G_and_S_paracentral";
	- nameTable["13104"] = "wm_lh_G_and_S_subcentral";
	- nameTable["13105"] = "wm_lh_G_and_S_transv_frontopol";
	- nameTable["13106"] = "wm_lh_G_and_S_cingul-Ant";
	- nameTable["13107"] = "wm_lh_G_and_S_cingul-Mid-Ant";
	- nameTable["13108"] = "wm_lh_G_and_S_cingul-Mid-Post";
	- nameTable["13109"] = "wm_lh_G_cingul-Post-dorsal";
	- nameTable["13110"] = "wm_lh_G_cingul-Post-ventral";
	- nameTable["13111"] = "wm_lh_G_cuneus";
	- nameTable["13112"] = "wm_lh_G_front_inf-Opercular";
	- nameTable["13113"] = "wm_lh_G_front_inf-Orbital";
	- nameTable["13114"] = "wm_lh_G_front_inf-Triangul";
	- nameTable["13115"] = "wm_lh_G_front_middle";
	- nameTable["13116"] = "wm_lh_G_front_sup";
	- nameTable["13117"] = "wm_lh_G_Ins_lg_and_S_cent_ins";
	- nameTable["13118"] = "wm_lh_G_insular_short";
	- nameTable["13119"] = "wm_lh_G_occipital_middle";
	- nameTable["13120"] = "wm_lh_G_occipital_sup";
	- nameTable["13121"] = "wm_lh_G_oc-temp_lat-fusifor";
	- nameTable["13122"] = "wm_lh_G_oc-temp_med-Lingual";
	- nameTable["13123"] = "wm_lh_G_oc-temp_med-Parahip";
	- nameTable["13124"] = "wm_lh_G_orbital";
	- nameTable["13125"] = "wm_lh_G_pariet_inf-Angular";
	- nameTable["13126"] = "wm_lh_G_pariet_inf-Supramar";
	- nameTable["13127"] = "wm_lh_G_parietal_sup";
	- nameTable["13128"] = "wm_lh_G_postcentral";
	- nameTable["13129"] = "wm_lh_G_precentral";
	- nameTable["13130"] = "wm_lh_G_precuneus";
	- nameTable["13131"] = "wm_lh_G_rectus";
	- nameTable["13132"] = "wm_lh_G_subcallosal";
	- nameTable["13133"] = "wm_lh_G_temp_sup-G_T_transv";
	- nameTable["13134"] = "wm_lh_G_temp_sup-Lateral";
	- nameTable["13135"] = "wm_lh_G_temp_sup-Plan_polar";
	- nameTable["13136"] = "wm_lh_G_temp_sup-Plan_tempo";
	- nameTable["13137"] = "wm_lh_G_temporal_inf";
	- nameTable["13138"] = "wm_lh_G_temporal_middle";
	- nameTable["13139"] = "wm_lh_Lat_Fis-ant-Horizont";
	- nameTable["13140"] = "wm_lh_Lat_Fis-ant-Vertical";
	- nameTable["13141"] = "wm_lh_Lat_Fis-post";
	- nameTable["13142"] = "wm_lh_Medial_wall";
	- nameTable["13143"] = "wm_lh_Pole_occipital";
	- nameTable["13144"] = "wm_lh_Pole_temporal";
	- nameTable["13145"] = "wm_lh_S_calcarine";
	- nameTable["13146"] = "wm_lh_S_central";
	- nameTable["13147"] = "wm_lh_S_cingul-Marginalis";
	- nameTable["13148"] = "wm_lh_S_circular_insula_ant";
	- nameTable["13149"] = "wm_lh_S_circular_insula_inf";
	- nameTable["13150"] = "wm_lh_S_circular_insula_sup";
	- nameTable["13151"] = "wm_lh_S_collat_transv_ant";
	- nameTable["13152"] = "wm_lh_S_collat_transv_post";
	- nameTable["13153"] = "wm_lh_S_front_inf";
	- nameTable["13154"] = "wm_lh_S_front_middle";
	- nameTable["13155"] = "wm_lh_S_front_sup";
	- nameTable["13156"] = "wm_lh_S_interm_prim-Jensen";
	- nameTable["13157"] = "wm_lh_S_intrapariet_and_P_trans";
	- nameTable["13158"] = "wm_lh_S_oc_middle_and_Lunatus";
	- nameTable["13159"] = "wm_lh_S_oc_sup_and_transversal";
	- nameTable["13160"] = "wm_lh_S_occipital_ant";
	- nameTable["13161"] = "wm_lh_S_oc-temp_lat";
	- nameTable["13162"] = "wm_lh_S_oc-temp_med_and_Lingual";
	- nameTable["13163"] = "wm_lh_S_orbital_lateral";
	- nameTable["13164"] = "wm_lh_S_orbital_med-olfact";
	- nameTable["13165"] = "wm_lh_S_orbital-H_Shaped";
	- nameTable["13166"] = "wm_lh_S_parieto_occipital";
	- nameTable["13167"] = "wm_lh_S_pericallosal";
	- nameTable["13168"] = "wm_lh_S_postcentral";
	- nameTable["13169"] = "wm_lh_S_precentral-inf-part";
	- nameTable["13170"] = "wm_lh_S_precentral-sup-part";
	- nameTable["13171"] = "wm_lh_S_suborbital";
	- nameTable["13172"] = "wm_lh_S_subparietal";
	- nameTable["13173"] = "wm_lh_S_temporal_inf";
	- nameTable["13174"] = "wm_lh_S_temporal_sup";
	- nameTable["13175"] = "wm_lh_S_temporal_transverse";
	- nameTable["14100"] = "wm_rh_Unknown";
	- nameTable["14101"] = "wm_rh_G_and_S_frontomargin";
	- nameTable["14102"] = "wm_rh_G_and_S_occipital_inf";
	- nameTable["14103"] = "wm_rh_G_and_S_paracentral";
	- nameTable["14104"] = "wm_rh_G_and_S_subcentral";
	- nameTable["14105"] = "wm_rh_G_and_S_transv_frontopol";
	- nameTable["14106"] = "wm_rh_G_and_S_cingul-Ant";
	- nameTable["14107"] = "wm_rh_G_and_S_cingul-Mid-Ant";
	- nameTable["14108"] = "wm_rh_G_and_S_cingul-Mid-Post";
	- nameTable["14109"] = "wm_rh_G_cingul-Post-dorsal";
	- nameTable["14110"] = "wm_rh_G_cingul-Post-ventral";
	- nameTable["14111"] = "wm_rh_G_cuneus";
	- nameTable["14112"] = "wm_rh_G_front_inf-Opercular";
	- nameTable["14113"] = "wm_rh_G_front_inf-Orbital";
	- nameTable["14114"] = "wm_rh_G_front_inf-Triangul";
	- nameTable["14115"] = "wm_rh_G_front_middle";
	- nameTable["14116"] = "wm_rh_G_front_sup";
	- nameTable["14117"] = "wm_rh_G_Ins_lg_and_S_cent_ins";
	- nameTable["14118"] = "wm_rh_G_insular_short";
	- nameTable["14119"] = "wm_rh_G_occipital_middle";
	- nameTable["14120"] = "wm_rh_G_occipital_sup";
	- nameTable["14121"] = "wm_rh_G_oc-temp_lat-fusifor";
	- nameTable["14122"] = "wm_rh_G_oc-temp_med-Lingual";
	- nameTable["14123"] = "wm_rh_G_oc-temp_med-Parahip";
	- nameTable["14124"] = "wm_rh_G_orbital";
	- nameTable["14125"] = "wm_rh_G_pariet_inf-Angular";
	- nameTable["14126"] = "wm_rh_G_pariet_inf-Supramar";
	- nameTable["14127"] = "wm_rh_G_parietal_sup";
	- nameTable["14128"] = "wm_rh_G_postcentral";
	- nameTable["14129"] = "wm_rh_G_precentral";
	- nameTable["14130"] = "wm_rh_G_precuneus";
	- nameTable["14131"] = "wm_rh_G_rectus";
	- nameTable["14132"] = "wm_rh_G_subcallosal";
	- nameTable["14133"] = "wm_rh_G_temp_sup-G_T_transv";
	- nameTable["14134"] = "wm_rh_G_temp_sup-Lateral";
	- nameTable["14135"] = "wm_rh_G_temp_sup-Plan_polar";
	- nameTable["14136"] = "wm_rh_G_temp_sup-Plan_tempo";
	- nameTable["14137"] = "wm_rh_G_temporal_inf";
	- nameTable["14138"] = "wm_rh_G_temporal_middle";
	- nameTable["14139"] = "wm_rh_Lat_Fis-ant-Horizont";
	- nameTable["14140"] = "wm_rh_Lat_Fis-ant-Vertical";
	- nameTable["14141"] = "wm_rh_Lat_Fis-post";
	- nameTable["14142"] = "wm_rh_Medial_wall";
	- nameTable["14143"] = "wm_rh_Pole_occipital";
	- nameTable["14144"] = "wm_rh_Pole_temporal";
	- nameTable["14145"] = "wm_rh_S_calcarine";
	- nameTable["14146"] = "wm_rh_S_central";
	- nameTable["14147"] = "wm_rh_S_cingul-Marginalis";
	- nameTable["14148"] = "wm_rh_S_circular_insula_ant";
	- nameTable["14149"] = "wm_rh_S_circular_insula_inf";
	- nameTable["14150"] = "wm_rh_S_circular_insula_sup";
	- nameTable["14151"] = "wm_rh_S_collat_transv_ant";
	- nameTable["14152"] = "wm_rh_S_collat_transv_post";
	- nameTable["14153"] = "wm_rh_S_front_inf";
	- nameTable["14154"] = "wm_rh_S_front_middle";
	- nameTable["14155"] = "wm_rh_S_front_sup";
	- nameTable["14156"] = "wm_rh_S_interm_prim-Jensen";
	- nameTable["14157"] = "wm_rh_S_intrapariet_and_P_trans";
	- nameTable["14158"] = "wm_rh_S_oc_middle_and_Lunatus";
	- nameTable["14159"] = "wm_rh_S_oc_sup_and_transversal";
	- nameTable["14160"] = "wm_rh_S_occipital_ant";
	- nameTable["14161"] = "wm_rh_S_oc-temp_lat";
	- nameTable["14162"] = "wm_rh_S_oc-temp_med_and_Lingual";
	- nameTable["14163"] = "wm_rh_S_orbital_lateral";
	- nameTable["14164"] = "wm_rh_S_orbital_med-olfact";
	- nameTable["14165"] = "wm_rh_S_orbital-H_Shaped";
	- nameTable["14166"] = "wm_rh_S_parieto_occipital";
	- nameTable["14167"] = "wm_rh_S_pericallosal";
	- nameTable["14168"] = "wm_rh_S_postcentral";
	- nameTable["14169"] = "wm_rh_S_precentral-inf-part";
	- nameTable["14170"] = "wm_rh_S_precentral-sup-part";
	- nameTable["14171"] = "wm_rh_S_suborbital";
	- nameTable["14172"] = "wm_rh_S_subparietal";
	- nameTable["14173"] = "wm_rh_S_temporal_inf";
	- nameTable["14174"] = "wm_rh_S_temporal_sup";
	- nameTable["14175"] = "wm_rh_S_temporal_transverse";
	- return nameTable;
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkFreeSurferParcellationTranslator.h b/Modules/DiffusionImaging/Connectomics/Algorithms/mitkFreeSurferParcellationTranslator.h
	deleted file mode 100644
	index 900f07b74d..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Algorithms/mitkFreeSurferParcellationTranslator.h
	+++ /dev/null
	@@ -1,111 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef mitkFreeSurferParcellationTranslator_h
	-#define mitkFreeSurferParcellationTranslator_h
	-
	-// MITK
	-#include <MitkConnectomicsExports.h>
	-#include <itkObject.h>
	-#include <mitkDataNode.h>
	-#include <mitkLookupTable.h>
	-#include <mitkTransferFunction.h>
	-// VTK
	-#include <vtkSmartPointer.h>
	-
	-using namespace mitk;
	-
	-namespace mitk
	-{
	- /**
	- * @brief The mitkFreeSurferParcellationTranslator class
	- *
	- * This class provides a ready to use lookup table for freesurfer processed images and further functions e.g. to get the name assigned to a given label.
	- * Additional you can assign the lookup table or transferfunction by using the AssignLookupTable(DataNode* node) or AssignTransferfunction(DataNode* node) methods.
	- *
	- */
	- class MITKCONNECTOMICS_EXPORT FreeSurferParcellationTranslator : public itk::Object
	- {
	- /########### Constructors, Typedefs and Enumerations ###########/
	- public:
	- typedef std::map<std::string, std::string> NameTable;
	- mitkClassMacroItkParent( FreeSurferParcellationTranslator, itk::Object )
	- itkNewMacro( FreeSurferParcellationTranslator )
	- protected:
	- FreeSurferParcellationTranslator();
	- ~FreeSurferParcellationTranslator() override;
	-
	-
	- /########### Methods ###########/
	- public:
	- /**
	- * @brief Assign the lookup table to the given node
	- * @param node the lookup table should be assigned to
	- */
	- virtual void AssignLookupTable( DataNode::Pointer node ) const;
	- /**
	- * @brief Assign the color transfer function to the given node
	- * @param node the transferfunction should be assigned to
	- */
	- virtual void AssignTransferFunction( DataNode::Pointer node ) const;
	- /**
	- * @brief Get the label assigned to the given name
	- * @param name the label should be assigned to
	- * @return label
	- */
	- virtual const std::string GetLabel( const std::string & name ) const;
	- /**
	- * @brief Get the label assigned to the given name
	- * @param name the label should be assigned to
	- * @return label
	- */
	- virtual int GetLabelAsNumber( const std::string & name ) const;
	- /**
	- * @brief Return the lookup table
	- * @return lookup table
	- */
	- virtual LookupTable::Pointer GetLookupTable() const;
	- /**
	- * @brief Get the name assigned to the given label
	- * @param label
	- * @return name
	- */
	- virtual const std::string GetName( const std::string & label ) const;
	- /**
	- * @brief Get the name assigned to the given label
	- * @param label
	- * @return name
	- */
	- virtual const std::string GetName( int label ) const;
	- /**
	- * @brief Get the transfer function
	- * @return transfer function
	- */
	- virtual TransferFunction::Pointer GetTransferFunction() const;
	- private:
	- static LookupTable::Pointer CreateLookupTable();
	- static TransferFunction::Pointer CreateTransferFunction();
	- static NameTable CreateNameTable();
	-
	-
	- /########### Static Members ###########/
	- private:
	- static LookupTable::Pointer m_LookupTable;
	- static TransferFunction::Pointer m_TransferFunction;
	- static const NameTable m_NameTable;
	- };
	-}
	-#endif // mitkFreeSurferParcellationTranslator_h
	diff --git a/Modules/DiffusionImaging/Connectomics/CMakeLists.txt b/Modules/DiffusionImaging/Connectomics/CMakeLists.txt
	deleted file mode 100644
	index 3099bee377..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/CMakeLists.txt
	+++ /dev/null
	@@ -1,8 +0,0 @@
	-MITK_CREATE_MODULE(
	- SUBPROJECTS MITK-DTI
	- INCLUDE_DIRS Algorithms Algorithms/BrainParcellation IODataStructures Rendering ${CMAKE_CURRENT_BINARY_DIR}
	- DEPENDS MitkDiffusionCore MitkFiberTracking
	- PACKAGE_DEPENDS VTK\|vtkInfovisLayout
	-)
	-
	-add_subdirectory(Testing)
	diff --git a/Modules/DiffusionImaging/Connectomics/Documentation/doxygen/ConnectomicsRenderingProperties.dox b/Modules/DiffusionImaging/Connectomics/Documentation/doxygen/ConnectomicsRenderingProperties.dox
	deleted file mode 100644
	index d39c849f01..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Documentation/doxygen/ConnectomicsRenderingProperties.dox
	+++ /dev/null
	@@ -1,5 +0,0 @@
	-/**
	-\page ConnectomicsRenderingPropertiesPage Connectomics Rendering Properties
	-
	-The MITK connectomics module offers several different ways of visualizing connectomics network information. The corresponding properties are documented in \ref mitkConnectomicsRenderingProperties.h .
	-*/
	\ No newline at end of file
	diff --git a/Modules/DiffusionImaging/Connectomics/IODataStructures/mitkConnectomicsConstantsManager.cpp b/Modules/DiffusionImaging/Connectomics/IODataStructures/mitkConnectomicsConstantsManager.cpp
	deleted file mode 100644
	index 6101002cdd..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/IODataStructures/mitkConnectomicsConstantsManager.cpp
	+++ /dev/null
	@@ -1,62 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-//#ifndef _MITK_ConnectomicsConstantsManager_CPP
	-//#define _MITK_ConnectomicsConstantsManager_CPP
	-
	-#include "mitkConnectomicsConstantsManager.h"
	-
	-//============== String and other constants ===================
	-
	-//==== Error messages ====
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_ERROR_TRIED_TO_ACCESS_INVALID_HISTOGRAM = "Tried to access invalid histogram.";
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_ERROR_PASSED_NEGATIVE_INDEX_TO_HISTOGRAM = "Passed negative index to histogram.";
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_ERROR_OUTSIDE_INTEGER_RANGE = "Tried to access histogram vector outside integer range.";
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_ERROR_BEYOND_SCOPE = "Tried to access histogram vector for value beyond scope: ";
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_ERROR_INVALID_MAPPING = "Invalid mapping strategy selected.";
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_ERROR_INVALID_DIMENSION_NEED_3 = "Invalid dimension, need dimension 3.";
	-
	-//==== Warnings ====
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_ZERO_DISTANCE_NODES = "There are nodes which are not distance 0 to themselves.";
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_UNIMPLEMENTED_FEATURE = "You are trying to use an as of yet unimplemented feature.";
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_MORE_POINTS_THAN_PRESENT = "Trying to estimate using more points than are present.";
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_ESTIMATING_LESS_THAN_2 = "Trying to estimate using less than two points.";
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_ESTIMATING_BEYOND_END = "Trying to estimate using points beyond track end.";
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_ESTIMATING_BEYOND_START = "Trying to estimate using points beyond track start.";
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_DID_NOT_FIND_WHITE = "Did not find a non white matter label.";
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_NOT_EXTEND_TO_WHITE = "Could not extend to non white matter.";
	-
	-//==== Information ====
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_INFO_NETWORK_CREATED = "Network has been created.";
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_NETWORK_NOT_VALID = "Network not valid.";
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_NETWORK_DISCONNECTED = "Network is disconnected.";
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_WARNING_CAN_NOT_COMPUTE_EFFICIENCY = "Can not compute efficiency. ";
	-
	-//==== GUI ====
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_DASH = "-";
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_CONNECTOMICS = "Connectomics";
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_CONNECTOMICS_CREATION = "Connectomics Creation";
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_SELECTION_WARNING = "Please load and select exactly one parcellation image and one fiber image before starting network creation.";
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_FMRI_CORRELATION_SELECTION_WARNING = "Please load and select either only one time series image or one parcellation image and one time series image before starting correlation analysis.";
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_ONLY_PARCELLATION_SELECTION_WARNING = "Please load and select one parcellation image.";
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_PERFORMING_IMAGE_PROCESSING_FOR_IMAGE = "Performing image processing for image ";
	-
	-//==== Properties ====
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_PROPERTY_DEFAULT_RGBA_NAME = "rgbaImage";
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_PROPERTY_NAME = "name";
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_PROPERTY_VOLUMERENDERING = "volumerendering";
	-const char* mitk::ConnectomicsConstantsManager::CONNECTOMICS_PROPERTY_DEFAULT_CNF_NAME = "Connectomics network";
	-
	-//#endif /* _MITK_ConnectomicsConstantsManager_CPP */
	diff --git a/Modules/DiffusionImaging/Connectomics/IODataStructures/mitkConnectomicsConstantsManager.h b/Modules/DiffusionImaging/Connectomics/IODataStructures/mitkConnectomicsConstantsManager.h
	deleted file mode 100644
	index 7efe3405ec..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/IODataStructures/mitkConnectomicsConstantsManager.h
	+++ /dev/null
	@@ -1,87 +0,0 @@
	-
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_ConnectomicsConstantsManager_H
	-#define _MITK_ConnectomicsConstantsManager_H
	-
	-#include <MitkConnectomicsExports.h>
	-
	-namespace mitk
	-{
	-
	- /** \brief The XML consts for reading and writing
	- */
	-
	- class MITKCONNECTOMICS_EXPORT ConnectomicsConstantsManager
	- {
	- public:
	-
	- //============== String and other constants ===================
	-
	- //==== Error messages ====
	- static const char* CONNECTOMICS_ERROR_TRIED_TO_ACCESS_INVALID_HISTOGRAM;
	- static const char* CONNECTOMICS_ERROR_PASSED_NEGATIVE_INDEX_TO_HISTOGRAM;
	- static const char* CONNECTOMICS_ERROR_OUTSIDE_INTEGER_RANGE;
	- static const char* CONNECTOMICS_ERROR_BEYOND_SCOPE;
	- static const char* CONNECTOMICS_ERROR_INVALID_MAPPING;
	- static const char* CONNECTOMICS_ERROR_INVALID_DIMENSION_NEED_3;
	-
	- //==== Warnings ====
	- static const char* CONNECTOMICS_WARNING_ZERO_DISTANCE_NODES;
	- static const char* CONNECTOMICS_WARNING_UNIMPLEMENTED_FEATURE;
	- static const char* CONNECTOMICS_WARNING_MORE_POINTS_THAN_PRESENT;
	- static const char* CONNECTOMICS_WARNING_ESTIMATING_LESS_THAN_2;
	- static const char* CONNECTOMICS_WARNING_ESTIMATING_BEYOND_END;
	- static const char* CONNECTOMICS_WARNING_ESTIMATING_BEYOND_START;
	- static const char* CONNECTOMICS_WARNING_DID_NOT_FIND_WHITE;
	- static const char* CONNECTOMICS_WARNING_NOT_EXTEND_TO_WHITE;
	-
	- //==== Information ====
	- static const char* CONNECTOMICS_WARNING_INFO_NETWORK_CREATED;
	- static const char* CONNECTOMICS_WARNING_NETWORK_NOT_VALID;
	- static const char* CONNECTOMICS_WARNING_NETWORK_DISCONNECTED;
	- static const char* CONNECTOMICS_WARNING_CAN_NOT_COMPUTE_EFFICIENCY;
	-
	- //==== GUI ====
	- static const char* CONNECTOMICS_GUI_DASH;
	- static const char* CONNECTOMICS_GUI_CONNECTOMICS;
	- static const char* CONNECTOMICS_GUI_CONNECTOMICS_CREATION;
	- static const char* CONNECTOMICS_GUI_SELECTION_WARNING;
	- static const char* CONNECTOMICS_GUI_FMRI_CORRELATION_SELECTION_WARNING;
	- static const char* CONNECTOMICS_GUI_ONLY_PARCELLATION_SELECTION_WARNING;
	- static const char* CONNECTOMICS_GUI_PERFORMING_IMAGE_PROCESSING_FOR_IMAGE;
	-
	- //==== Properties ====
	- static const char* CONNECTOMICS_PROPERTY_DEFAULT_RGBA_NAME;
	- static const char* CONNECTOMICS_PROPERTY_NAME;
	- static const char* CONNECTOMICS_PROPERTY_VOLUMERENDERING;
	- static const char* CONNECTOMICS_PROPERTY_DEFAULT_CNF_NAME;
	-
	-
	- private:
	- ConnectomicsConstantsManager();
	- ~ConnectomicsConstantsManager();
	-
	- };
	-
	-} //namespace MITK
	-
	-// include cpp
	-
	-//#include <mitkConnectomicsConstantsManager.cpp>
	-
	-#endif /* _MITK_ConnectomicsConstantsManager_H */
	diff --git a/Modules/DiffusionImaging/Connectomics/IODataStructures/mitkConnectomicsNetwork.cpp b/Modules/DiffusionImaging/Connectomics/IODataStructures/mitkConnectomicsNetwork.cpp
	deleted file mode 100644
	index 75ab9332cf..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/IODataStructures/mitkConnectomicsNetwork.cpp
	+++ /dev/null
	@@ -1,782 +0,0 @@
	-
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkConnectomicsNetwork.h"
	-#include <mitkConnectomicsStatisticsCalculator.h>
	-
	-#include <boost/graph/clustering_coefficient.hpp>
	-
	-#ifdef _MSC_VER
	-# pragma warning(push)
	-# pragma warning(disable: 4172)
	-#endif
	-
	-#include <boost/graph/betweenness_centrality.hpp>
	-
	-#ifdef _MSC_VER
	-# pragma warning(pop)
	-#endif
	-
	-/* Constructor and Destructor */
	-mitk::ConnectomicsNetwork::ConnectomicsNetwork()
	-: m_IsModified( false )
	-{
	-}
	-
	-mitk::ConnectomicsNetwork::~ConnectomicsNetwork()
	-{
	-}
	-
	-/* Wrapper methods */
	-
	-bool mitk::ConnectomicsNetwork::EdgeExists(
	- mitk::ConnectomicsNetwork::VertexDescriptorType vertexA, mitk::ConnectomicsNetwork::VertexDescriptorType vertexB ) const
	-{
	- return boost::edge(vertexA, vertexB, m_Network ).second;
	-}
	-
	-void mitk::ConnectomicsNetwork::IncreaseEdgeWeight(mitk::ConnectomicsNetwork::VertexDescriptorType vertexA, mitk::ConnectomicsNetwork::VertexDescriptorType vertexB , double fiber_count)
	-{
	- m_Network[ boost::edge(vertexA, vertexB, m_Network ).first ].fiber_count += fiber_count;
	-
	- SetIsModified( true );
	-}
	-
	-void mitk::ConnectomicsNetwork::AddEdge(mitk::ConnectomicsNetwork::VertexDescriptorType vertexA,
	- mitk::ConnectomicsNetwork::VertexDescriptorType vertexB
	- , double fiber_count)
	-{
	- AddEdge(vertexA, vertexB, m_Network[ vertexA ].id, m_Network[ vertexB ].id, fiber_count );
	-}
	-
	-void mitk::ConnectomicsNetwork::AddEdge(
	- mitk::ConnectomicsNetwork::VertexDescriptorType vertexA,
	- mitk::ConnectomicsNetwork::VertexDescriptorType vertexB,
	- int sourceID, int targetID, double fiber_count, double edge_weight )
	-{
	- boost::add_edge( vertexA, vertexB, m_Network );
	- m_Network[ boost::edge(vertexA, vertexB, m_Network ).first ].sourceId = sourceID;
	- m_Network[ boost::edge(vertexA, vertexB, m_Network ).first ].targetId = targetID;
	- m_Network[ boost::edge(vertexA, vertexB, m_Network ).first ].fiber_count = fiber_count;
	- m_Network[ boost::edge(vertexA, vertexB, m_Network ).first ].edge_weight = edge_weight;
	-
	- SetIsModified( true );
	-}
	-
	-mitk::ConnectomicsNetwork::VertexDescriptorType mitk::ConnectomicsNetwork::AddVertex( int id )
	-{
	- VertexDescriptorType vertex = boost::add_vertex( m_Network );
	- m_Network[vertex].id = id;
	-
	- SetIsModified( true );
	-
	- return vertex;
	-}
	-
	-void mitk::ConnectomicsNetwork::SetLabel(
	- mitk::ConnectomicsNetwork::VertexDescriptorType vertex, std::string inLabel )
	-{
	- m_Network[vertex].label = inLabel;
	-
	- SetIsModified( true );
	-}
	-
	-void mitk::ConnectomicsNetwork::SetCoordinates(
	- mitk::ConnectomicsNetwork::VertexDescriptorType vertex, std::vector< float > inCoordinates )
	-{
	- m_Network[vertex].coordinates = inCoordinates;
	-
	- SetIsModified( true );
	-}
	-
	-void mitk::ConnectomicsNetwork::clear()
	-{
	- m_Network.clear();
	-
	- SetIsModified( true );
	-}
	-
	-/* Superclass methods, that need to be implemented */
	-void mitk::ConnectomicsNetwork::UpdateOutputInformation()
	-{
	-
	-}
	-void mitk::ConnectomicsNetwork::SetRequestedRegionToLargestPossibleRegion()
	-{
	-
	-}
	-bool mitk::ConnectomicsNetwork::RequestedRegionIsOutsideOfTheBufferedRegion()
	-{
	- return false;
	-}
	-bool mitk::ConnectomicsNetwork::VerifyRequestedRegion()
	-{
	- return true;
	-}
	-void mitk::ConnectomicsNetwork::SetRequestedRegion(const itk::DataObject * /data/ )
	-{
	-
	-}
	-
	-
	-
	-std::vector< mitk::ConnectomicsNetwork::NetworkNode >
	-mitk::ConnectomicsNetwork::GetVectorOfAllNodes() const
	-{
	- boost::graph_traits<NetworkType>::vertex_iterator iterator, end;
	-
	- // sets iterator to start end end to end
	- boost::tie(iterator, end) = boost::vertices( m_Network );
	-
	- std::vector< NetworkNode > vectorOfNodes;
	-
	- for ( ; iterator != end; ++iterator)
	- {
	- NetworkNode tempNode;
	-
	- // the value of an iterator is a descriptor
	- tempNode = m_Network[ *iterator ];
	-
	- vectorOfNodes.push_back( tempNode );
	- }
	-
	- return vectorOfNodes;
	-}
	-
	-std::vector< mitk::ConnectomicsNetwork::VertexDescriptorType >
	-mitk::ConnectomicsNetwork::GetVectorOfAllVertexDescriptors() const
	-{
	- boost::graph_traits<NetworkType>::vertex_iterator iterator, end;
	-
	- // sets iterator to start end end to end
	- boost::tie(iterator, end) = boost::vertices( m_Network );
	-
	- std::vector< VertexDescriptorType > vectorOfDescriptors;
	-
	- for ( ; iterator != end; ++iterator)
	- {
	- vectorOfDescriptors.push_back( *iterator );
	- }
	-
	- return vectorOfDescriptors;
	-}
	-
	-std::vector< std::pair<
	-std::pair< mitk::ConnectomicsNetwork::NetworkNode, mitk::ConnectomicsNetwork::NetworkNode >
	-, mitk::ConnectomicsNetwork::NetworkEdge > >
	-mitk::ConnectomicsNetwork::GetVectorOfAllEdges() const
	-{
	- boost::graph_traits<NetworkType>::edge_iterator iterator, end;
	-
	- // sets iterator to start end end to end
	- boost::tie(iterator, end) = boost::edges( m_Network );
	-
	- std::vector<
	- std::pair<
	- std::pair< NetworkNode, NetworkNode >
	- , NetworkEdge
	- >
	- > vectorOfEdges;
	-
	- for ( ; iterator != end; ++iterator)
	- {
	- NetworkNode sourceNode, targetNode;
	- NetworkEdge tempEdge;
	-
	- // the value of an iterator is a descriptor
	- tempEdge = m_Network[ *iterator ];
	- sourceNode = m_Network[ boost::source( *iterator, m_Network ) ];
	- targetNode = m_Network[ boost::target( *iterator, m_Network ) ];
	-
	- std::pair< NetworkNode, NetworkNode > nodePair( sourceNode, targetNode );
	- std::pair< std::pair< NetworkNode, NetworkNode > , NetworkEdge > edgePair( nodePair, tempEdge);
	- vectorOfEdges.push_back( edgePair );
	- }
	-
	- return vectorOfEdges;
	-}
	-
	-int mitk::ConnectomicsNetwork::GetNumberOfVertices() const
	-{
	- return boost::num_vertices( m_Network );
	-}
	-
	-int mitk::ConnectomicsNetwork::GetNumberOfEdges() const
	-{
	- return boost::num_edges( m_Network );
	-}
	-
	-double mitk::ConnectomicsNetwork::GetMaximumWeight() const
	-{
	- int maxWeight( 0 );
	-
	- boost::graph_traits<NetworkType>::edge_iterator iterator, end;
	-
	- // sets iterator to start end end to end
	- boost::tie(iterator, end) = boost::edges( m_Network );
	-
	- for ( ; iterator != end; ++iterator)
	- {
	- int tempWeight;
	-
	- // the value of an iterator is a descriptor
	- tempWeight = m_Network[ *iterator ].fiber_count;
	-
	- if( tempWeight > maxWeight )
	- {
	- maxWeight = tempWeight;
	- }
	- }
	-
	- return maxWeight;
	-}
	-
	-int mitk::ConnectomicsNetwork::GetNumberOfSelfLoops()
	-{
	- int noOfSelfLoops( 0 );
	-
	- std::vector< std::pair< std::pair< NetworkNode, NetworkNode > , NetworkEdge > >
	- edgeVector = GetVectorOfAllEdges();
	-
	- for( unsigned int index = 0; index < edgeVector.size() ; index++ )
	- {
	- double sourceX, sourceY, sourceZ, targetX, targetY, targetZ;
	-
	- sourceX = edgeVector[ index ].first.first.coordinates[0] ;
	- sourceY = edgeVector[ index ].first.first.coordinates[1] ;
	- sourceZ = edgeVector[ index ].first.first.coordinates[2] ;
	- targetX = edgeVector[ index ].first.second.coordinates[0] ;
	- targetY = edgeVector[ index ].first.second.coordinates[1] ;
	- targetZ = edgeVector[ index ].first.second.coordinates[2] ;
	-
	- // if the coordinates are the same
	- if(
	- sourceX > ( targetX - 0.01 ) &&
	- sourceX < ( targetX + 0.01 ) &&
	- sourceY > ( targetY - 0.01 ) &&
	- sourceY < ( targetY + 0.01 ) &&
	- sourceZ > ( targetZ - 0.01 ) &&
	- sourceZ < ( targetZ + 0.01 )
	- )
	- {
	- noOfSelfLoops++;
	- }
	- }
	-
	- return noOfSelfLoops;
	-}
	-
	-double mitk::ConnectomicsNetwork::GetAverageDegree()
	-{
	- double vertices = (double) GetNumberOfVertices();
	- double edges = (double) GetNumberOfEdges();
	-
	- return ( ( edges * 2.0 ) / vertices );
	-}
	-
	-double mitk::ConnectomicsNetwork::GetConnectionDensity()
	-{
	- double vertices = (double) GetNumberOfVertices();
	- double edges = (double) GetNumberOfEdges();
	- double numberOfPossibleEdges = vertices * ( vertices - 1 ) / 2 ;
	-
	- return ( edges / numberOfPossibleEdges );
	-}
	-
	-std::vector< int > mitk::ConnectomicsNetwork::GetDegreeOfNodes( ) const
	-{
	- std::vector< int > vectorOfDegree;
	-
	- boost::graph_traits<NetworkType>::vertex_iterator iterator, end;
	-
	- // sets iterator to start end end to end
	- boost::tie( iterator, end ) = boost::vertices( m_Network );
	-
	- vectorOfDegree.resize( this->GetNumberOfVertices() );
	-
	- for ( ; iterator != end; ++iterator)
	- {
	- // the value of an iterator is a descriptor
	- vectorOfDegree[ m_Network[ iterator ].id ] = GetVectorOfAdjacentNodes( iterator ).size();
	- }
	- return vectorOfDegree;
	-}
	-
	-std::vector< mitk::ConnectomicsNetwork::VertexDescriptorType >
	-mitk::ConnectomicsNetwork::GetVectorOfAdjacentNodes( mitk::ConnectomicsNetwork::VertexDescriptorType vertex ) const
	-{
	- std::vector< mitk::ConnectomicsNetwork::VertexDescriptorType > vectorOfAdjacentNodes;
	-
	- boost::graph_traits<NetworkType>::adjacency_iterator adjIter, adjEnd;
	-
	- boost::tie( adjIter, adjEnd ) = boost::adjacent_vertices( vertex, m_Network);
	-
	- for ( ; adjIter != adjEnd; ++adjIter)
	- {
	- vectorOfAdjacentNodes.push_back( *adjIter );
	- }
	-
	- return vectorOfAdjacentNodes;
	-}
	-
	-int mitk::ConnectomicsNetwork::GetMaximumDegree() const
	-{
	- int maximumDegree( 0 );
	-
	- std::vector< int > vectorOfDegree = GetDegreeOfNodes();
	-
	- for( unsigned int index( 0 ); index < vectorOfDegree.size(); ++index )
	- {
	- if( maximumDegree < vectorOfDegree[ index ] )
	- {
	- maximumDegree = vectorOfDegree[ index ];
	- }
	- }
	-
	- return maximumDegree;
	-}
	-
	-std::vector< double > mitk::ConnectomicsNetwork::GetLocalClusteringCoefficients( ) const
	-{
	- std::vector< double > vectorOfClusteringCoefficients;
	-
	- typedef boost::graph_traits<NetworkType>::vertex_iterator vertexIter;
	-
	- vectorOfClusteringCoefficients.resize( this->GetNumberOfVertices() );
	-
	- std::pair<vertexIter, vertexIter> vertexPair;
	-
	- //for every vertex calculate the clustering coefficient
	- int size = vectorOfClusteringCoefficients.size();
	- for (vertexPair = vertices(m_Network); vertexPair.first != vertexPair.second; ++vertexPair.first)
	- {
	- int index = m_Network[ *vertexPair.first ].id;
	-
	- if( index > size )
	- {
	- MITK_ERROR << "Trying to access out of bounds clustering coefficient";
	- continue;
	- }
	-
	- vectorOfClusteringCoefficients[ index ] =
	- boost::clustering_coefficient(m_Network,*vertexPair.first) ;
	- }
	-
	- return vectorOfClusteringCoefficients;
	-}
	-
	-std::vector< double > mitk::ConnectomicsNetwork::GetClusteringCoefficientsByDegree( )
	-{
	- std::vector< double > vectorOfClusteringCoefficients = GetLocalClusteringCoefficients();
	- std::vector< int > vectorOfDegree = GetDegreeOfNodes();
	-
	- std::vector< double > vectorOfClusteringCoefficientsByDegree;
	- vectorOfClusteringCoefficientsByDegree.resize( GetMaximumDegree() + 1, 0 );
	-
	- // c_{mean}(k) = frac{1}_{N_{k}} sum_{i in Y(k)} c_{i}
	- // where N_{k} is the number of vertices of degree k
	- // Y(k) is the set of vertices of degree k
	- // c_{i} is the local clustering coefficient of vertex i
	- for( unsigned int degree( 0 ); degree < vectorOfClusteringCoefficientsByDegree.size(); ++degree )
	- {
	- vectorOfClusteringCoefficientsByDegree[ degree ] = 0;
	- int n_k( 0 );
	- for( unsigned int index( 0 ); index < vectorOfDegree.size(); ++index )
	- {
	- if( degree == (unsigned int)vectorOfDegree[ index ] )
	- {// if in Y( degree )
	- vectorOfClusteringCoefficientsByDegree[ degree ] += vectorOfClusteringCoefficients[ index ];
	- n_k++;
	- }
	- }
	- if( n_k != 0 )
	- {
	- vectorOfClusteringCoefficientsByDegree[ degree ] =
	- vectorOfClusteringCoefficientsByDegree[ degree ] / n_k;
	- }
	- }
	-
	- return vectorOfClusteringCoefficientsByDegree;
	-}
	-
	-double mitk::ConnectomicsNetwork::GetGlobalClusteringCoefficient( )
	-{
	- double globalClusteringCoefficient( 0.0 );
	-
	- std::vector< double > vectorOfClusteringCoefficientsByDegree = GetClusteringCoefficientsByDegree();
	- std::vector< int > vectorOfDegree = GetDegreeOfNodes();
	- std::vector< int > degreeDistribution;
	- degreeDistribution.resize( vectorOfClusteringCoefficientsByDegree.size(), 0 );
	-
	- int normalizationParameter( 0 );
	-
	- for( unsigned int index( 0 ); index < vectorOfDegree.size(); ++index )
	- {
	- degreeDistribution[ vectorOfDegree[ index ] ]++;
	- normalizationParameter++;
	- }
	- // c_{mean} = sum_{k} P_{k} c_{mean}(k)
	- // where P_{k} is the degree distribution
	- // k is the degree
	- for( unsigned int degree( 0 ); degree < degreeDistribution.size(); ++degree )
	- {
	- globalClusteringCoefficient +=
	- degreeDistribution[ degree ] / ( (double) normalizationParameter)
	- * vectorOfClusteringCoefficientsByDegree[ degree ];
	- }
	-
	- return globalClusteringCoefficient;
	-}
	-
	-mitk::ConnectomicsNetwork::NetworkType* mitk::ConnectomicsNetwork::GetBoostGraph()
	-{
	- return &m_Network;
	-}
	-
	-void mitk::ConnectomicsNetwork::SetBoostGraph( NetworkType* newGraph )
	-{
	- this->clear();
	-
	- m_Network = *newGraph;
	- this->SetIsModified( true );
	-}
	-
	-void mitk::ConnectomicsNetwork::ImportNetwort( mitk::ConnectomicsNetwork::Pointer source )
	-{
	- typedef std::vector< std::pair< std::pair< NetworkNode, NetworkNode >, NetworkEdge > > EdgeVectorType;
	- typedef std::vector< NetworkNode > VertexVectorType;
	-
	- this->clear();
	-
	- this->SetGeometry( source->GetGeometry());
	- VertexVectorType vertexVector = source->GetVectorOfAllNodes();
	- EdgeVectorType edgeVector = source->GetVectorOfAllEdges();
	- std::map< int, VertexDescriptorType > idToVertexMap;
	-
	- for( unsigned int loop(0); loop < vertexVector.size(); loop++ )
	- {
	- VertexDescriptorType newVertex = this->AddVertex( vertexVector[ loop ].id );
	- this->SetLabel( newVertex, vertexVector[ loop ].label );
	- this->SetCoordinates( newVertex, vertexVector[ loop ].coordinates );
	-
	- if ( idToVertexMap.count( vertexVector[ loop ].id ) > 0 )
	- {
	- MITK_ERROR << "Aborting network import, duplicate vertex ID discovered.";
	- return;
	- }
	- idToVertexMap.insert( std::pair< int, VertexDescriptorType >( vertexVector[ loop ].id, newVertex) );
	- }
	-
	- for( unsigned int loop(0); loop < edgeVector.size(); loop++ )
	- {
	- VertexDescriptorType source = idToVertexMap.find( edgeVector[ loop ].second.sourceId )->second;
	- VertexDescriptorType target = idToVertexMap.find( edgeVector[ loop ].second.targetId )->second;
	-
	- this->AddEdge( source, target, edgeVector[ loop ].second.sourceId, edgeVector[ loop ].second.targetId, edgeVector[ loop ].second.fiber_count);
	- }
	-
	- this->SetIsModified( true );
	-}
	-
	-bool mitk::ConnectomicsNetwork::GetIsModified() const
	-{
	- return m_IsModified;
	-}
	-
	-
	-void mitk::ConnectomicsNetwork::SetIsModified( bool value)
	-{
	- m_IsModified = value;
	-}
	-
	-
	-mitk::ConnectomicsNetwork::NetworkNode mitk::ConnectomicsNetwork::GetNode( VertexDescriptorType vertex ) const
	-{
	- return m_Network[ vertex ];
	-}
	-
	-
	-mitk::ConnectomicsNetwork::NetworkEdge mitk::ConnectomicsNetwork::GetEdge( VertexDescriptorType vertexA, VertexDescriptorType vertexB ) const
	-{
	- if( EdgeExists(vertexA, vertexB) )
	- {
	- return m_Network[ boost::edge(vertexA, vertexB, m_Network ).first ];
	- }
	- else
	- {
	- mitkThrow() << "Edge does not exist";
	- }
	-}
	-
	-void mitk::ConnectomicsNetwork::UpdateBounds( )
	-{
	- float min = itk::NumericTraits<float>::min();
	- float max = itk::NumericTraits<float>::max();
	- float bounds[] = {max, min, max, min, max, min};
	-
	- std::vector< mitk::ConnectomicsNetwork::NetworkNode > nodeVector = this->GetVectorOfAllNodes();
	-
	- if( nodeVector.size() == 0 )
	- {
	- bounds[0] = 0;
	- bounds[1] = 1;
	- bounds[2] = 0;
	- bounds[3] = 1;
	- bounds[4] = 0;
	- bounds[5] = 1;
	- }
	-
	- // for each direction, make certain the point is in between
	- for(auto & elem : nodeVector)
	- {
	- for( unsigned int direction(0); direction < elem.coordinates.size(); direction++ )
	- {
	- if( elem.coordinates.at(direction) < bounds[ 2 * direction ] )
	- {
	- bounds[ 2 * direction ] = elem.coordinates.at(direction);
	- }
	-
	- if( elem.coordinates.at(direction) > bounds[ 2 * direction + 1] )
	- {
	- bounds[ 2 * direction + 1] = elem.coordinates.at(direction);
	- }
	- }
	- }
	-
	-
	- // provide some border margin
	- for(int i=0; i<=4; i+=2)
	- {
	- bounds[i] -=10;
	- }
	-
	- for(int i=1; i<=5; i+=2)
	- {
	- bounds[i] +=10;
	- }
	-
	- this->GetGeometry()->SetFloatBounds(bounds);
	- this->GetTimeGeometry()->Update();
	-}
	-
	-void mitk::ConnectomicsNetwork::PruneUnconnectedSingleNodes()
	-{
	- boost::graph_traits<NetworkType>::vertex_iterator iterator, end;
	-
	- // set to true if iterators are invalidated by deleting a vertex
	- bool vertexHasBeenRemoved( true );
	-
	- // if no vertex has been removed in the last loop, we are done
	- while( vertexHasBeenRemoved )
	- {
	- vertexHasBeenRemoved = false;
	- // sets iterator to start and end to end
	- boost::tie(iterator, end) = boost::vertices( m_Network );
	-
	- for ( ; iterator != end && !vertexHasBeenRemoved; ++iterator)
	- {
	- // If the node has no adjacent vertices it should be deleted
	- if( GetVectorOfAdjacentNodes( *iterator ).size() == 0 )
	- {
	- vertexHasBeenRemoved = true;
	- // this invalidates all iterators
	- boost::remove_vertex( *iterator, m_Network );
	- }
	- }
	- }
	-
	- UpdateIDs();
	-}
	-
	-void mitk::ConnectomicsNetwork::UpdateIDs()
	-{
	- boost::graph_traits<NetworkType>::vertex_iterator v_i, v_end;
	- boost::graph_traits<NetworkType>::edge_iterator e_i, e_end;
	-
	- // update node ids
	- boost::tie( v_i, v_end ) = boost::vertices( m_Network );
	-
	- for ( ; v_i != v_end; ++v_i)
	- {
	- m_Network[v_i].id = v_i;
	- }
	-
	- // update edge information
	- boost::tie(e_i, e_end) = boost::edges( m_Network );
	-
	- for ( ; e_i != e_end; ++e_i)
	- {
	- m_Network[ e_i ].sourceId = m_Network[ boost::source( e_i, m_Network ) ].id;
	- m_Network[ e_i ].targetId = m_Network[ boost::target( e_i, m_Network ) ].id;
	- }
	- this->SetIsModified( true );
	-}
	-
	-std::vector< double > mitk::ConnectomicsNetwork::GetNodeBetweennessVector() const
	-{
	- std::vector< double > betweennessVector;
	-
	- betweennessVector.clear();
	- betweennessVector.resize( this->GetNumberOfVertices() );
	-
	- boost::brandes_betweenness_centrality(
	- m_Network,
	- boost::centrality_map(
	- boost::make_iterator_property_map( betweennessVector.begin(), boost::get( &NetworkNode::id, m_Network ), double() )
	- ).vertex_index_map( boost::get( &NetworkNode::id, m_Network ) )
	- );
	-
	- return betweennessVector;
	-}
	-
	-std::vector< double > mitk::ConnectomicsNetwork::GetEdgeBetweennessVector() const
	-{
	- // std::map used for convenient initialization
	- typedef std::map<EdgeDescriptorType, int> EdgeIndexStdMap;
	- EdgeIndexStdMap stdEdgeIndex;
	- // associative property map needed for iterator property map-wrapper
	- typedef boost::associative_property_map< EdgeIndexStdMap > EdgeIndexMap;
	- EdgeIndexMap edgeIndex(stdEdgeIndex);
	-
	- boost::graph_traits<NetworkType>::edge_iterator iterator, end;
	-
	- // sets iterator to start end end to end
	- boost::tie(iterator, end) = boost::edges( m_Network );
	-
	- int i(0);
	- for ( ; iterator != end; ++iterator, ++i)
	- {
	- stdEdgeIndex.insert(std::pair< EdgeDescriptorType, int >( *iterator, i));
	- }
	-
	- // Define EdgeCentralityMap
	- std::vector< double > edgeBetweennessVector(boost::num_edges( m_Network ), 0.0);
	- // Create the external property map
	- boost::iterator_property_map< std::vector< double >::iterator, EdgeIndexMap >
	- e_centrality_map(edgeBetweennessVector.begin(), edgeIndex);
	-
	- // Define VertexCentralityMap
	- typedef boost::property_map< NetworkType, boost::vertex_index_t>::type VertexIndexMap;
	- VertexIndexMap vertexIndex = get(boost::vertex_index, m_Network );
	- std::vector< double > betweennessVector(boost::num_vertices( m_Network ), 0.0);
	- // Create the external property map
	- boost::iterator_property_map< std::vector< double >::iterator, VertexIndexMap >
	- v_centrality_map(betweennessVector.begin(), vertexIndex);
	-
	- boost::brandes_betweenness_centrality( m_Network, v_centrality_map, e_centrality_map );
	-
	- return edgeBetweennessVector;
	-}
	-
	-std::vector< double > mitk::ConnectomicsNetwork::GetShortestDistanceVectorFromLabel( std::string targetLabel ) const
	-{
	- std::vector< VertexDescriptorType > predecessorMap( boost::num_vertices( m_Network ) );
	- int numberOfNodes( boost::num_vertices( m_Network ) );
	-
	- std::vector< double > distanceMatrix;
	- distanceMatrix.resize( numberOfNodes );
	-
	- boost::graph_traits<NetworkType>::vertex_iterator iterator, end;
	- boost::tie(iterator, end) = boost::vertices( m_Network );
	-
	- while( (iterator != end) && (m_Network[ *iterator ].label != targetLabel) )
	- {
	- ++iterator;
	- }
	-
	- if( iterator == end )
	- {
	- MITK_WARN << "Label not found";
	- return distanceMatrix;
	- }
	-
	- boost::dijkstra_shortest_paths(m_Network, *iterator, boost::predecessor_map(&predecessorMap[ 0 ]).distance_map(&distanceMatrix[ 0 ]).weight_map( boost::get( &NetworkEdge::edge_weight ,m_Network ) ) ) ;
	-
	- return distanceMatrix;
	-}
	-
	-bool mitk::ConnectomicsNetwork::CheckForLabel( std::string targetLabel ) const
	-{
	- boost::graph_traits<NetworkType>::vertex_iterator iterator, end;
	- boost::tie(iterator, end) = boost::vertices( m_Network );
	-
	- while( (iterator != end) && (m_Network[ *iterator ].label != targetLabel) )
	- {
	- ++iterator;
	- }
	-
	- if( iterator == end )
	- {
	- return false;
	- }
	-
	- return true;
	-}
	-
	-bool mitk::Equal( mitk::ConnectomicsNetwork* leftHandSide, mitk::ConnectomicsNetwork* rightHandSide, mitk::ScalarType eps, bool verbose )
	-{
	- bool noDifferenceFound = true;
	-
	- if( rightHandSide == nullptr )
	- {
	- if(verbose)
	- {
	- MITK_INFO << "[Equal( ConnectomicsNetwork, ConnectomicsNetwork )] rightHandSide nullptr.";
	- }
	- return false;
	- }
	-
	- if( leftHandSide == nullptr )
	- {
	- if(verbose)
	- {
	- MITK_INFO << "[Equal( ConnectomicsNetwork, ConnectomicsNetwork )] leftHandSide nullptr.";
	- }
	- return false;
	- }
	-
	- mitk::ConnectomicsStatisticsCalculator::Pointer calculatorLeft = mitk::ConnectomicsStatisticsCalculator::New();
	- mitk::ConnectomicsStatisticsCalculator::Pointer calculatorRight = mitk::ConnectomicsStatisticsCalculator::New();
	-
	- calculatorLeft->SetNetwork( leftHandSide );
	- calculatorRight->SetNetwork( rightHandSide );
	- calculatorLeft->Update();
	- calculatorRight->Update();
	-
	- if( ! mitk::Equal( calculatorLeft->GetNumberOfVertices(), calculatorRight->GetNumberOfVertices(), eps ) )
	- {
	- if(verbose)
	- MITK_INFO << "[Equal( ConnectomicsNetwork, ConnectomicsNetwork )] Number of vertices not equal. " << calculatorLeft->GetNumberOfVertices() << " vs " << calculatorRight->GetNumberOfVertices();
	- noDifferenceFound = false;
	- }
	-
	- if( ! mitk::Equal( calculatorLeft->GetNumberOfEdges(), calculatorRight->GetNumberOfEdges(), eps ) )
	- {
	- if(verbose)
	- MITK_INFO << "[Equal( ConnectomicsNetwork, ConnectomicsNetwork )] Number of edges not equal. " << calculatorLeft->GetNumberOfEdges() << " vs " << calculatorRight->GetNumberOfEdges();
	- noDifferenceFound = false;
	- }
	-
	- if( ! mitk::Equal( calculatorLeft->GetSmallWorldness(), calculatorRight->GetSmallWorldness(), eps ) )
	- {
	- if(verbose)
	- MITK_INFO << "[Equal( ConnectomicsNetwork, ConnectomicsNetwork )] Small worldness not equal. " << calculatorLeft->GetSmallWorldness() << " vs " << calculatorRight->GetSmallWorldness();
	- noDifferenceFound = false;
	- }
	-
	- return noDifferenceFound;
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/IODataStructures/mitkConnectomicsNetwork.h b/Modules/DiffusionImaging/Connectomics/IODataStructures/mitkConnectomicsNetwork.h
	deleted file mode 100644
	index d78fc95fe2..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/IODataStructures/mitkConnectomicsNetwork.h
	+++ /dev/null
	@@ -1,238 +0,0 @@
	-
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef _MITK_ConnectomicsNetwork_H
	-#define _MITK_ConnectomicsNetwork_H
	-
	-#include <MitkConnectomicsExports.h>
	-
	-#include "mitkBaseData.h"
	-
	-#ifndef Q_MOC_RUN
	-#include <boost/graph/adjacency_list.hpp>
	-#endif
	-
	-namespace mitk {
	-
	- /**
	- * \brief Connectomics Network Class
	- *
	- * This class is designed to represent a connectomics network (brain network). It encapsulates a
	- * boost adjacency list and provides additional capabilities. The information contained in the nodes and edges is:
	- *
	- * Network Node:
	- * <ul>
	- * <li> int ID - The id of the node
	- * <li> string label - The label of the node, this can be any string, such as an anatomical label
	- * <li> vector<float> coordinates - The coordinates the node should be displayed at
	- * </ul>
	- *
	- * Network Edge:
	- * <ul>
	- * <li> int sourceId - The Id of the source node
	- * <li> int targetId - The Id of the target node
	- * <li> int weight - Weight of the edge as int (used for counting fibers)
	- * <li> double edge_weight - Used for boost and algorithms, should be between 0 and 1
	- * </ul>
	- */
	- class MITKCONNECTOMICS_EXPORT ConnectomicsNetwork : public BaseData
	- {
	- public:
	- /** Structs for the graph */
	-
	- /** The Node */
	- struct NetworkNode
	- {
	- int id;
	- std::string label;
	- std::vector< float > coordinates;
	- };
	-
	- /** The Edge */
	- struct NetworkEdge
	- {
	- int sourceId;
	- int targetId;
	- double fiber_count; // For now the number of times it was present
	- double edge_weight; // For boost, currently set to 1 by default for unweighted calculations
	- };
	-
	- / Typedefs /
	- //typedef boost::adjacency_list< boost::listS, boost::listS, boost::undirectedS, NetworkNode, NetworkEdge > NetworkType;
	- typedef boost::adjacency_list< boost::vecS, boost::vecS, boost::undirectedS, NetworkNode, NetworkEdge > NetworkType;
	- typedef boost::graph_traits<NetworkType>::vertex_descriptor VertexDescriptorType;
	- typedef boost::graph_traits<NetworkType>::edge_descriptor EdgeDescriptorType;
	-
	- // virtual methods that need to be implemented
	- void UpdateOutputInformation() override;
	- void SetRequestedRegionToLargestPossibleRegion() override;
	- bool RequestedRegionIsOutsideOfTheBufferedRegion() override;
	- bool VerifyRequestedRegion() override;
	- void SetRequestedRegion(const itk::DataObject * ) override;
	-
	-
	- // Macros
	- mitkClassMacro( ConnectomicsNetwork, BaseData );
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- ////////////////// Interface ///////////////////
	- /** return whether an edge exists between the two given vertices */
	- bool EdgeExists( VertexDescriptorType vertexA, VertexDescriptorType vertexB ) const;
	-
	- /** increase the weight of an edge between the two given vertices */
	- void IncreaseEdgeWeight( VertexDescriptorType vertexA, VertexDescriptorType vertexB, double fiber_count );
	-
	- /** add an edge between two given vertices */
	- void AddEdge( VertexDescriptorType vertexA, VertexDescriptorType vertexB, double fiber_count);
	-
	- /** add an edge between two given vertices ( with a specific weight ) */
	- void AddEdge(VertexDescriptorType vertexA, VertexDescriptorType vertexB, int sourceID, int targetID, double fiber_count, double edge_weight = 1.0 );
	-
	- /** add a vertex with a specified id */
	- VertexDescriptorType AddVertex( int id);
	-
	- /** set the label of a vertex */
	- void SetLabel( VertexDescriptorType vertex, std::string inLabel );
	-
	- /** set the coordinates of a vertex */
	- void SetCoordinates( VertexDescriptorType vertex, std::vector< float > inCoordinates );
	-
	- /** clear the graph */
	- void clear();
	-
	- /** return the node struct for a given node descriptor */
	- NetworkNode GetNode( VertexDescriptorType vertex ) const;
	-
	- /** return the edge struct for two given node descriptors */
	- NetworkEdge GetEdge( VertexDescriptorType vertexA, VertexDescriptorType vertexB ) const;
	-
	- /** get vector containing all the nodes of the network */
	- std::vector< NetworkNode > GetVectorOfAllNodes() const;
	-
	- /** get vector containing all the vertex descriptors of the network */
	- std::vector< VertexDescriptorType > GetVectorOfAllVertexDescriptors() const;
	-
	- /** get vector containing the descriptors of nodes adjacent to the vertex denoted by the given descriptor */
	- std::vector< VertexDescriptorType > GetVectorOfAdjacentNodes( VertexDescriptorType vertex ) const;
	-
	- /** get vector containing all the edges of the network and the connected nodes */
	- std::vector< std::pair< std::pair< NetworkNode, NetworkNode > , NetworkEdge > > GetVectorOfAllEdges() const;
	-
	- /** get overall number of vertices in the network */
	- int GetNumberOfVertices() const;
	-
	- /** get overall number of edges in the network */
	- int GetNumberOfEdges() const;
	-
	- /** get number of vertices, that are connected to themselves */
	- int GetNumberOfSelfLoops();
	-
	- /** get number of vertices, that are connected to themselves */
	- double GetAverageDegree();
	-
	- /** get number of edges divided by number of possible edges */
	- double GetConnectionDensity();
	-
	- /** Get the maximum weight of all edges */
	- double GetMaximumWeight() const;
	-
	- /** Get a vector in the format vector[ vertexID ] = degree */
	- std::vector< int > GetDegreeOfNodes( ) const;
	-
	- /** Get the maximum degree of all nodes */
	- int GetMaximumDegree() const;
	-
	- /** Get a vector in the format vector[ vertexID ] = clustering coefficient */
	- std::vector< double > GetLocalClusteringCoefficients( ) const;
	-
	- /** Get a vector in the format vector[ degree ] = average clustering coefficient */
	- std::vector< double > GetClusteringCoefficientsByDegree( );
	-
	- /** Get the global clustering coefficient */
	- double GetGlobalClusteringCoefficient( );
	-
	- /** Get the betweenness centrality for each vertex in form of a vector of length (number vertices)*/
	- std::vector< double > GetNodeBetweennessVector() const;
	-
	- /** Get the betweenness centrality for each edge in form of a vector of length (number edges)*/
	- std::vector< double > GetEdgeBetweennessVector() const;
	-
	- /** Check whether a vertex with the specified label exists*/
	- bool CheckForLabel( std::string targetLabel ) const;
	-
	- /** Get the shortest distance from a specified vertex to all other vertices in form of a vector of length (number vertices)*/
	- std::vector< double > GetShortestDistanceVectorFromLabel( std::string targetLabel ) const;
	-
	- /** Access boost graph directly */
	- NetworkType* GetBoostGraph();
	-
	- /** Set the boost graph directly */
	- void SetBoostGraph( NetworkType* newGraph );
	-
	- void ImportNetwort( mitk::ConnectomicsNetwork::Pointer source );
	-
	- /** Get the modified flag */
	- bool GetIsModified() const;
	-
	- /** Set the modified flag */
	- void SetIsModified( bool );
	-
	- /** Update the bounds of the geometry to fit the network */
	- void UpdateBounds( );
	-
	- /** Remove nodes not connected to any other node */
	- void PruneUnconnectedSingleNodes();
	-
	- /** This function will relabel all vertices and edges in a continuous manner
	- *
	- * Mainly important after removing vertices, to make sure that the ids run continuously from
	- * 0 to number of vertices - 1 and edge target and source ids match the corresponding node.
	- */
	- void UpdateIDs();
	-
	- protected:
	- ConnectomicsNetwork();
	- ~ConnectomicsNetwork() override;
	-
	- NetworkType m_Network;
	-
	- /// Flag which indicates whether the network has been modified since the last check
	- ///
	- /// mainly for rendering purposes
	-
	- bool m_IsModified;
	-
	- private:
	-
	- };
	-
	- /**
	- * \brief Returns true if the networks are considered equal.
	- *
	- * For now two networks are considered equal if they are equal in the following properties:
	- * - Number of nodes
	- * - Number of edges
	- * - Smallworldness
	- */
	-
	- MITKCONNECTOMICS_EXPORT bool Equal( mitk::ConnectomicsNetwork* leftHandSide, mitk::ConnectomicsNetwork* rightHandSide, mitk::ScalarType eps, bool verbose);
	-
	-} // namespace mitk
	-
	-#endif /* _MITK_ConnectomicsNetwork_H */
	diff --git a/Modules/DiffusionImaging/Connectomics/IODataStructures/mitkConnectomicsNetworkProperties.h b/Modules/DiffusionImaging/Connectomics/IODataStructures/mitkConnectomicsNetworkProperties.h
	deleted file mode 100644
	index 16c529a3bf..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/IODataStructures/mitkConnectomicsNetworkProperties.h
	+++ /dev/null
	@@ -1,43 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef ConnectomicsNetworkProperties_H_HEADER_INCLUDED
	-#define ConnectomicsNetworkProperties_H_HEADER_INCLUDED
	-
	-#include <cstring>
	-#include "mitkProperties.h"
	-#include "mitkStringProperty.h"
	-
	-namespace mitk {
	-
	- /** \file mitkConnectomicsNetworkProperties.h
	- * \brief This file defines the data properties for connectomics networks in MITK.
	- *
	- * This file collects and explains the properties which can be used store additional
	- * information in connectomics networks.
	- */
	-
	- /**
	- * \brief Additional header information
	- *
	- * This property contains a string with additional information which can be stored
	- * as a header in file formats which support it.
	- */
	- const std::string connectomicsDataAdditionalHeaderInformation = "Connectomics.Data.AdditionalHeaderInformation";
	-} // namespace mitk
	-
	-#endif //ConnectomicsNetworkProperties_H_HEADER_INCLUDED
	diff --git a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsEnumerationSubclassesSerializer.cpp b/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsEnumerationSubclassesSerializer.cpp
	deleted file mode 100644
	index a7e018ddc5..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsEnumerationSubclassesSerializer.cpp
	+++ /dev/null
	@@ -1,79 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef mitkConnectomicsEnumerationSubclassesSerializer_h_included
	-#define mitkConnectomicsEnumerationSubclassesSerializer_h_included
	-
	-#include "mitkEnumerationPropertySerializer.h"
	-
	-#include "mitkConnectomicsRenderingEdgeColorParameterProperty.h"
	-#include "mitkConnectomicsRenderingEdgeFilteringProperty.h"
	-#include "mitkConnectomicsRenderingEdgeRadiusParameterProperty.h"
	-#include "mitkConnectomicsRenderingEdgeThresholdParameterProperty.h"
	-#include "mitkConnectomicsRenderingNodeColorParameterProperty.h"
	-#include "mitkConnectomicsRenderingNodeFilteringProperty.h"
	-#include "mitkConnectomicsRenderingNodeRadiusParameterProperty.h"
	-#include "mitkConnectomicsRenderingNodeThresholdParameterProperty.h"
	-#include "mitkConnectomicsRenderingSchemeProperty.h"
	-
	-#include <MitkConnectomicsExports.h>
	-
	-#define MITK_REGISTER_ENUM_SUB_SERIALIZER(classname) \
	- \
	-namespace mitk \
	-{ \
	- \
	-class MITKCONNECTOMICS_EXPORT classname ## Serializer : public EnumerationPropertySerializer \
	-{ \
	- public: \
	- \
	- mitkClassMacro( classname ## Serializer, EnumerationPropertySerializer ) \
	- itkFactorylessNewMacro(Self) \
	- itkCloneMacro(Self) \
	- \
	- virtual BaseProperty::Pointer Deserialize(TiXmlElement* element) \
	- { \
	- if (!element) return nullptr; \
	- const char* sa( element->Attribute("value") ); \
	- \
	- std::string s(sa?sa:""); \
	- classname::Pointer property = classname::New(); \
	- property->SetValue( s ); \
	- \
	- return property.GetPointer(); \
	- } \
	- \
	- protected: \
	- \
	- classname ## Serializer () {} \
	- virtual ~classname ## Serializer () {} \
	-}; \
	- \
	-} \
	- \
	-MITK_REGISTER_SERIALIZER( classname ## Serializer );
	-
	-MITK_REGISTER_ENUM_SUB_SERIALIZER(ConnectomicsRenderingEdgeColorParameterProperty);
	-MITK_REGISTER_ENUM_SUB_SERIALIZER(ConnectomicsRenderingEdgeFilteringProperty);
	-MITK_REGISTER_ENUM_SUB_SERIALIZER(ConnectomicsRenderingEdgeRadiusParameterProperty);
	-MITK_REGISTER_ENUM_SUB_SERIALIZER(ConnectomicsRenderingEdgeThresholdParameterProperty);
	-MITK_REGISTER_ENUM_SUB_SERIALIZER(ConnectomicsRenderingNodeColorParameterProperty);
	-MITK_REGISTER_ENUM_SUB_SERIALIZER(ConnectomicsRenderingNodeFilteringProperty);
	-MITK_REGISTER_ENUM_SUB_SERIALIZER(ConnectomicsRenderingNodeRadiusParameterProperty);
	-MITK_REGISTER_ENUM_SUB_SERIALIZER(ConnectomicsRenderingNodeThresholdParameterProperty);
	-MITK_REGISTER_ENUM_SUB_SERIALIZER(ConnectomicsRenderingSchemeProperty);
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsNetworkMapper3D.cpp b/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsNetworkMapper3D.cpp
	deleted file mode 100644
	index aaa528bf49..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsNetworkMapper3D.cpp
	+++ /dev/null
	@@ -1,830 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkConnectomicsNetworkMapper3D.h"
	-
	-#include "vtkGlyph3D.h"
	-#include "vtkGlyphSource2D.h"
	-#include "vtkGraphLayout.h"
	-#include "vtkGraphToPolyData.h"
	-#include <vtkMutableUndirectedGraph.h>
	-#include <vtkPassThroughLayoutStrategy.h>
	-#include <vtkPoints.h>
	-
	-#include "mitkConnectomicsRenderingEdgeColorParameterProperty.h"
	-#include "mitkConnectomicsRenderingEdgeFilteringProperty.h"
	-#include "mitkConnectomicsRenderingEdgeRadiusParameterProperty.h"
	-#include "mitkConnectomicsRenderingEdgeThresholdParameterProperty.h"
	-#include "mitkConnectomicsRenderingNodeColorParameterProperty.h"
	-#include "mitkConnectomicsRenderingNodeFilteringProperty.h"
	-#include "mitkConnectomicsRenderingNodeRadiusParameterProperty.h"
	-#include "mitkConnectomicsRenderingNodeThresholdParameterProperty.h"
	-#include "mitkConnectomicsRenderingProperties.h"
	-#include "mitkConnectomicsRenderingSchemeProperty.h"
	-#include <mbilog.h>
	-#include <mitkManualPlacementAnnotationRenderer.h>
	-#include <vtkIndent.h>
	-
	-#include <string>
	-
	-#include <algorithm>
	-
	-mitk::ConnectomicsNetworkMapper3D::ConnectomicsNetworkMapper3D()
	-{
	- m_NetworkAssembly = vtkPropAssembly::New();
	- m_Translator = mitk::FreeSurferParcellationTranslator::New();
	-}
	-
	-mitk::ConnectomicsNetworkMapper3D::~ConnectomicsNetworkMapper3D()
	-{
	- m_NetworkAssembly->Delete();
	-}
	-
	-void mitk::ConnectomicsNetworkMapper3D::GenerateDataForRenderer(mitk::BaseRenderer *renderer)
	-{
	- if (this->GetInput() == nullptr)
	- {
	- m_TextOverlay3D->UnRegisterMicroservice();
	- return;
	- }
	-
	- bool propertiesHaveChanged = this->PropertiesChanged();
	-
	- if (this->GetInput()->GetIsModified() \|\| propertiesHaveChanged)
	- {
	- m_NetworkAssembly->Delete();
	- m_NetworkAssembly = vtkPropAssembly::New();
	-
	- // Here is the part where a graph is given and converted to points and connections between points...
	- std::vector<mitk::ConnectomicsNetwork::NetworkNode> vectorOfNodes = this->GetInput()->GetVectorOfAllNodes();
	- std::vector<std::pair<std::pair<mitk::ConnectomicsNetwork::NetworkNode, mitk::ConnectomicsNetwork::NetworkNode>,
	- mitk::ConnectomicsNetwork::NetworkEdge>>
	- vectorOfEdges = this->GetInput()->GetVectorOfAllEdges();
	-
	- // Decide on the style of rendering due to property
	- if (m_ChosenRenderingScheme == connectomicsRenderingMITKScheme)
	- {
	- mitk::Point3D tempWorldPoint, tempCNFGeometryPoint;
	-
	- ////// Prepare BalloonWidgets/Overlays: ////////////////////
	- if ((m_ChosenNodeLabel == "" \|\| m_ChosenNodeLabel == "-1") && m_TextOverlay3D)
	- {
	- m_TextOverlay3D->UnRegisterMicroservice();
	- GetDataNode()->SetProperty(
	- connectomicsRenderingBalloonTextName.c_str(), mitk::StringProperty::New(""), nullptr);
	- GetDataNode()->SetProperty(
	- connectomicsRenderingBalloonNodeStatsName.c_str(), mitk::StringProperty::New(""), nullptr);
	- }
	-
	- //////////////////////Prepare coloring and radius////////////
	- std::vector<double> vectorOfNodeRadiusParameterValues;
	- vectorOfNodeRadiusParameterValues.resize(vectorOfNodes.size());
	- double maxNodeRadiusParameterValue(
	- FillNodeParameterVector(&vectorOfNodeRadiusParameterValues, m_NodeRadiusParameter));
	-
	- std::vector<double> vectorOfNodeColorParameterValues;
	- vectorOfNodeColorParameterValues.resize(vectorOfNodes.size());
	- double maxNodeColorParameterValue(
	- FillNodeParameterVector(&vectorOfNodeColorParameterValues, m_NodeColorParameter));
	-
	- std::vector<double> vectorOfEdgeRadiusParameterValues;
	- vectorOfEdgeRadiusParameterValues.resize(vectorOfEdges.size());
	- double maxEdgeRadiusParameterValue(
	- FillEdgeParameterVector(&vectorOfEdgeRadiusParameterValues, m_EdgeRadiusParameter));
	-
	- std::vector<double> vectorOfEdgeColorParameterValues;
	- vectorOfEdgeColorParameterValues.resize(vectorOfEdges.size());
	- double maxEdgeColorParameterValue(
	- FillEdgeParameterVector(&vectorOfEdgeColorParameterValues, m_EdgeColorParameter));
	-
	- //////////////////////Prepare Filtering//////////////////////
	- // true will be rendered
	- std::vector<bool> vectorOfNodeFilterBools(vectorOfNodes.size(), true);
	- if (m_ChosenNodeFilter == connectomicsRenderingNodeThresholdingFilter)
	- {
	- FillNodeFilterBoolVector(&vectorOfNodeFilterBools, m_NodeThresholdParameter);
	- }
	-
	- std::vector<bool> vectorOfEdgeFilterBools(vectorOfEdges.size(), true);
	- if (m_ChosenEdgeFilter == connectomicsRenderingEdgeThresholdFilter)
	- {
	- FillEdgeFilterBoolVector(&vectorOfEdgeFilterBools, m_EdgeThresholdParameter);
	- }
	-
	- //////////////////////Create Spheres/////////////////////////
	- std::stringstream
	- nodeLabelStream; // local stream variable to hold csv list of node label names and node label numbers.
	-
	- for (unsigned int i = 0; i < vectorOfNodes.size(); i++)
	- {
	- vtkSmartPointer<vtkSphereSource> sphereSource = vtkSmartPointer<vtkSphereSource>::New();
	-
	- for (unsigned int dimension = 0; dimension < 3; dimension++)
	- {
	- tempCNFGeometryPoint.SetElement(dimension, vectorOfNodes[i].coordinates[dimension]);
	- }
	-
	- GetDataNode()->GetData()->GetGeometry()->IndexToWorld(tempCNFGeometryPoint, tempWorldPoint);
	-
	- sphereSource->SetCenter(tempWorldPoint[0], tempWorldPoint[1], tempWorldPoint[2]);
	-
	- // determine radius
	- double radiusFactor = vectorOfNodeRadiusParameterValues[i] / maxNodeRadiusParameterValue;
	-
	- double radius = m_NodeRadiusStart + (m_NodeRadiusEnd - m_NodeRadiusStart) * radiusFactor;
	- sphereSource->SetRadius(radius);
	-
	- vtkSmartPointer<vtkPolyDataMapper> mapper = vtkSmartPointer<vtkPolyDataMapper>::New();
	- mapper->SetInputConnection(sphereSource->GetOutputPort());
	-
	- vtkSmartPointer<vtkActor> actor = vtkSmartPointer<vtkActor>::New();
	- actor->SetMapper(mapper);
	-
	- // determine color
	- double colorFactor = vectorOfNodeColorParameterValues[i] / maxNodeColorParameterValue;
	-
	- double redStart = m_NodeColorStart.GetElement(0);
	- double greenStart = m_NodeColorStart.GetElement(1);
	- double blueStart = m_NodeColorStart.GetElement(2);
	- double redEnd = m_NodeColorEnd.GetElement(0);
	- double greenEnd = m_NodeColorEnd.GetElement(1);
	- double blueEnd = m_NodeColorEnd.GetElement(2);
	-
	- double red = redStart + (redEnd - redStart) * colorFactor;
	- double green = greenStart + (greenEnd - greenStart) * colorFactor;
	- double blue = blueStart + (blueEnd - blueStart) * colorFactor;
	-
	- actor->GetProperty()->SetColor(red, green, blue);
	-
	- // append to csv list of nodelabels.
	- nodeLabelStream << m_Translator->GetName(std::stoi(vectorOfNodes[i].label)) << ": " << vectorOfNodes[i].label
	- << ",";
	-
	- if (vectorOfNodeFilterBools[i])
	- {
	- if (vectorOfNodes[i].label == m_ChosenNodeLabel)
	- { // if chosen and enabled, show information in Balloon or TextOverlay:
	- // What to show:
	- std::stringstream balloonStringstream;
	- balloonStringstream << "Node id: " << vectorOfNodes[i].id << "\nlabel: " << vectorOfNodes[i].label
	- << "\nname: " << m_Translator->GetName(std::stoi(vectorOfNodes[i].label)) << std::endl;
	- m_BalloonText = balloonStringstream.str();
	- GetDataNode()->SetProperty(
	- connectomicsRenderingBalloonTextName.c_str(), mitk::StringProperty::New(m_BalloonText.c_str()), nullptr);
	-
	- std::stringstream balloonNodeStatsStream;
	- balloonNodeStatsStream << "Coordinates: (" << vectorOfNodes[i].coordinates[0] << " ; "
	- << vectorOfNodes[i].coordinates[1] << " ; " << vectorOfNodes[i].coordinates[2]
	- << " )"
	- << "\nDegree: " << (this->GetInput()->GetDegreeOfNodes()).at(vectorOfNodes[i].id)
	- << "\nBetweenness centrality: "
	- << (this->GetInput()->GetNodeBetweennessVector()).at(vectorOfNodes[i].id)
	- << "\nClustering coefficient: "
	- << (this->GetInput()->GetLocalClusteringCoefficients()).at(vectorOfNodes[i].id)
	- << std::endl;
	- m_BalloonNodeStats = balloonNodeStatsStream.str();
	- GetDataNode()->SetProperty(connectomicsRenderingBalloonNodeStatsName.c_str(),
	- mitk::StringProperty::New(m_BalloonNodeStats.c_str()),
	- nullptr);
	-
	- // Where to show:
	- float r[3];
	- r[0] = vectorOfNodes[i].coordinates[0];
	- r[1] = vectorOfNodes[i].coordinates[1];
	- r[2] = vectorOfNodes[i].coordinates[2];
	- mitk::Point3D BalloonAnchor(r);
	- mitk::Point3D BalloonAnchorWorldCoord(r);
	- GetDataNode()->GetData()->GetGeometry()->IndexToWorld(BalloonAnchor, BalloonAnchorWorldCoord);
	-
	- // How to show:
	- if (m_ChosenNodeLabel != "-1")
	- {
	- if (m_TextOverlay3D != nullptr)
	- {
	- m_TextOverlay3D->UnRegisterMicroservice();
	- }
	- m_TextOverlay3D = mitk::TextAnnotation3D::New();
	-
	- mitk::ManualPlacementAnnotationRenderer::AddAnnotation(m_TextOverlay3D.GetPointer(), renderer);
	- m_TextOverlay3D->SetFontSize(2);
	- m_TextOverlay3D->SetColor(0.96, 0.69, 0.01);
	- m_TextOverlay3D->SetOpacity(0.81);
	- m_TextOverlay3D->SetPosition3D(BalloonAnchorWorldCoord);
	- m_TextOverlay3D->SetText("...." + m_BalloonText);
	- m_TextOverlay3D->SetForceInForeground(true); // TODO: does not work anymore.
	- m_TextOverlay3D->SetVisibility(GetDataNode()->IsVisible(renderer));
	- // Colorize chosen node:
	- actor->GetProperty()->SetColor(1.0, 0.69, 0.01);
	- }
	- }
	- m_NetworkAssembly->AddPart(actor);
	- }
	- }
	- m_AllNodeLabels = nodeLabelStream.str(); // Store all Node Names and Node Labels in 1 Property.
	- m_AllNodeLabels.erase(m_AllNodeLabels.rfind(","), 1); // remove trailing ,.
	- GetDataNode()->SetProperty(connectomicsRenderingBalloonAllNodeLabelsName.c_str(),
	- mitk::StringProperty::New(m_AllNodeLabels.c_str()),
	- nullptr);
	-
	- //////////////////////Create Tubes/////////////////////////
	- for (unsigned int i = 0; i < vectorOfEdges.size(); i++)
	- {
	- vtkSmartPointer<vtkLineSource> lineSource = vtkSmartPointer<vtkLineSource>::New();
	-
	- for (unsigned int dimension = 0; dimension < 3; dimension++)
	- {
	- tempCNFGeometryPoint[dimension] = vectorOfEdges[i].first.first.coordinates[dimension];
	- }
	-
	- GetDataNode()->GetData()->GetGeometry()->IndexToWorld(tempCNFGeometryPoint, tempWorldPoint);
	-
	- lineSource->SetPoint1(tempWorldPoint[0], tempWorldPoint[1], tempWorldPoint[2]);
	-
	- for (unsigned int dimension = 0; dimension < 3; dimension++)
	- {
	- tempCNFGeometryPoint[dimension] = vectorOfEdges[i].first.second.coordinates[dimension];
	- }
	-
	- GetDataNode()->GetData()->GetGeometry()->IndexToWorld(tempCNFGeometryPoint, tempWorldPoint);
	-
	- lineSource->SetPoint2(tempWorldPoint[0], tempWorldPoint[1], tempWorldPoint[2]);
	-
	- vtkSmartPointer<vtkTubeFilter> tubes = vtkSmartPointer<vtkTubeFilter>::New();
	- tubes->SetInputConnection(lineSource->GetOutputPort());
	- tubes->SetNumberOfSides(12);
	-
	- // determine radius
	- double radiusFactor = vectorOfEdgeRadiusParameterValues[i] / maxEdgeRadiusParameterValue;
	-
	- double radius = m_EdgeRadiusStart + (m_EdgeRadiusEnd - m_EdgeRadiusStart) * radiusFactor;
	- tubes->SetRadius(radius);
	-
	- // originally we used a logarithmic scaling,
	- // double radiusFactor = 1.0 + ((double) vectorOfEdges[i].second.weight) / 10.0 ;
	- // tubes->SetRadius( std::log10( radiusFactor ) );
	-
	- vtkSmartPointer<vtkPolyDataMapper> mapper2 = vtkSmartPointer<vtkPolyDataMapper>::New();
	- mapper2->SetInputConnection(tubes->GetOutputPort());
	-
	- vtkSmartPointer<vtkActor> actor = vtkSmartPointer<vtkActor>::New();
	- actor->SetMapper(mapper2);
	-
	- // determine color
	- double colorFactor = vectorOfEdgeColorParameterValues[i] / maxEdgeColorParameterValue;
	-
	- double redStart = m_EdgeColorStart.GetElement(0);
	- double greenStart = m_EdgeColorStart.GetElement(1);
	- double blueStart = m_EdgeColorStart.GetElement(2);
	- double redEnd = m_EdgeColorEnd.GetElement(0);
	- double greenEnd = m_EdgeColorEnd.GetElement(1);
	- double blueEnd = m_EdgeColorEnd.GetElement(2);
	-
	- double red = redStart + (redEnd - redStart) * colorFactor;
	- double green = greenStart + (greenEnd - greenStart) * colorFactor;
	- double blue = blueStart + (blueEnd - blueStart) * colorFactor;
	-
	- actor->GetProperty()->SetColor(red, green, blue);
	-
	- if (vectorOfEdgeFilterBools[i])
	- {
	- m_NetworkAssembly->AddPart(actor);
	- }
	- }
	- }
	- else if (m_ChosenRenderingScheme == connectomicsRenderingVTKScheme)
	- {
	- vtkSmartPointer<vtkMutableUndirectedGraph> graph = vtkSmartPointer<vtkMutableUndirectedGraph>::New();
	-
	- std::vector<vtkIdType> networkToVTKvector;
	- networkToVTKvector.resize(vectorOfNodes.size());
	-
	- for (unsigned int i = 0; i < vectorOfNodes.size(); i++)
	- {
	- networkToVTKvector[vectorOfNodes[i].id] = graph->AddVertex();
	- }
	-
	- for (unsigned int i = 0; i < vectorOfEdges.size(); i++)
	- {
	- graph->AddEdge(networkToVTKvector[vectorOfEdges[i].first.first.id],
	- networkToVTKvector[vectorOfEdges[i].first.second.id]);
	- }
	-
	- vtkSmartPointer<vtkPoints> points = vtkSmartPointer<vtkPoints>::New();
	- for (unsigned int i = 0; i < vectorOfNodes.size(); i++)
	- {
	- double x = vectorOfNodes[i].coordinates[0];
	- double y = vectorOfNodes[i].coordinates[1];
	- double z = vectorOfNodes[i].coordinates[2];
	- points->InsertNextPoint(x, y, z);
	- }
	-
	- graph->SetPoints(points);
	-
	- vtkGraphLayout *layout = vtkGraphLayout::New();
	- layout->SetInputData(graph);
	- vtkPassThroughLayoutStrategy *ptls = vtkPassThroughLayoutStrategy::New();
	- layout->SetLayoutStrategy(ptls);
	-
	- vtkGraphToPolyData *graphToPoly = vtkGraphToPolyData::New();
	- graphToPoly->SetInputConnection(layout->GetOutputPort());
	-
	- // Create the standard VTK polydata mapper and actor
	- // for the connections (edges) in the tree.
	- vtkPolyDataMapper *edgeMapper = vtkPolyDataMapper::New();
	- edgeMapper->SetInputConnection(graphToPoly->GetOutputPort());
	- vtkActor *edgeActor = vtkActor::New();
	- edgeActor->SetMapper(edgeMapper);
	- edgeActor->GetProperty()->SetColor(0.0, 0.5, 1.0);
	-
	- // Glyph the points of the tree polydata to create
	- // VTK_VERTEX cells at each vertex in the tree.
	- vtkGlyph3D *vertGlyph = vtkGlyph3D::New();
	- vertGlyph->SetInputConnection(0, graphToPoly->GetOutputPort());
	- vtkGlyphSource2D *glyphSource = vtkGlyphSource2D::New();
	- glyphSource->SetGlyphTypeToVertex();
	- vertGlyph->SetInputConnection(1, glyphSource->GetOutputPort());
	-
	- // Create a mapper for the vertices, and tell the mapper
	- // to use the specified color array.
	- vtkPolyDataMapper *vertMapper = vtkPolyDataMapper::New();
	- vertMapper->SetInputConnection(vertGlyph->GetOutputPort());
	- /*if (colorArray)
	- {
	- vertMapper->SetScalarModeToUsePointFieldData();
	- vertMapper->SelectColorArray(colorArray);
	- vertMapper->SetScalarRange(colorRange);
	- }*/
	-
	- // Create an actor for the vertices. Move the actor forward
	- // in the z direction so it is drawn on top of the edge actor.
	- vtkActor *vertActor = vtkActor::New();
	- vertActor->SetMapper(vertMapper);
	- vertActor->GetProperty()->SetPointSize(5);
	- vertActor->SetPosition(0, 0, 0.001);
	- // vtkProp3D.h: virtual void SetPosition(double,double,double):
	- // Set/Get/Add the position of the Prop3D in world coordinates.
	- m_NetworkAssembly->AddPart(edgeActor);
	- m_NetworkAssembly->AddPart(vertActor);
	- }
	-
	- (static_cast<mitk::ConnectomicsNetwork *>(GetDataNode()->GetData()))->SetIsModified(false);
	- }
	-}
	-
	-const mitk::ConnectomicsNetwork *mitk::ConnectomicsNetworkMapper3D::GetInput()
	-{
	- return static_cast<const mitk::ConnectomicsNetwork *>(GetDataNode()->GetData());
	-}
	-
	-void mitk::ConnectomicsNetworkMapper3D::SetDefaultProperties(DataNode node, BaseRenderer renderer, bool overwrite)
	-{
	- // Initialize enumeration properties
	- mitk::ConnectomicsRenderingSchemeProperty::Pointer connectomicsRenderingScheme =
	- mitk::ConnectomicsRenderingSchemeProperty::New();
	- mitk::ConnectomicsRenderingEdgeFilteringProperty::Pointer connectomicsRenderingEdgeFiltering =
	- mitk::ConnectomicsRenderingEdgeFilteringProperty::New();
	- mitk::ConnectomicsRenderingNodeFilteringProperty::Pointer connectomicsRenderingNodeFiltering =
	- mitk::ConnectomicsRenderingNodeFilteringProperty::New();
	-
	- mitk::ConnectomicsRenderingNodeColorParameterProperty::Pointer connectomicsRenderingNodeGradientColorParameter =
	- mitk::ConnectomicsRenderingNodeColorParameterProperty::New();
	- mitk::ConnectomicsRenderingNodeRadiusParameterProperty::Pointer connectomicsRenderingNodeRadiusParameter =
	- mitk::ConnectomicsRenderingNodeRadiusParameterProperty::New();
	- mitk::ConnectomicsRenderingEdgeColorParameterProperty::Pointer connectomicsRenderingEdgeGradientColorParameter =
	- mitk::ConnectomicsRenderingEdgeColorParameterProperty::New();
	- mitk::ConnectomicsRenderingEdgeRadiusParameterProperty::Pointer connectomicsRenderingEdgeRadiusParameter =
	- mitk::ConnectomicsRenderingEdgeRadiusParameterProperty::New();
	-
	- mitk::ConnectomicsRenderingNodeThresholdParameterProperty::Pointer connectomicsRenderingNodeThresholdParameter =
	- mitk::ConnectomicsRenderingNodeThresholdParameterProperty::New();
	- mitk::ConnectomicsRenderingEdgeThresholdParameterProperty::Pointer connectomicsRenderingEdgeThresholdParameter =
	- mitk::ConnectomicsRenderingEdgeThresholdParameterProperty::New();
	-
	- mitk::StringProperty::Pointer balloonText = mitk::StringProperty::New();
	-
	- // set the properties
	- node->AddProperty(connectomicsRenderingSchemePropertyName.c_str(), connectomicsRenderingScheme, renderer, overwrite);
	-
	- node->AddProperty(
	- connectomicsRenderingEdgeFilteringPropertyName.c_str(), connectomicsRenderingEdgeFiltering, renderer, overwrite);
	- node->AddProperty(connectomicsRenderingEdgeThresholdFilterParameterName.c_str(),
	- connectomicsRenderingEdgeThresholdParameter,
	- renderer,
	- overwrite);
	- node->AddProperty(connectomicsRenderingEdgeThresholdFilterThresholdName.c_str(),
	- connectomicsRenderingEdgeThresholdFilterThresholdDefault,
	- renderer,
	- overwrite);
	-
	- node->AddProperty(
	- connectomicsRenderingNodeFilteringPropertyName.c_str(), connectomicsRenderingNodeFiltering, renderer, overwrite);
	- node->AddProperty(connectomicsRenderingNodeThresholdFilterParameterName.c_str(),
	- connectomicsRenderingNodeThresholdParameter,
	- renderer,
	- overwrite);
	- node->AddProperty(connectomicsRenderingNodeThresholdFilterThresholdName.c_str(),
	- connectomicsRenderingNodeThresholdFilterThresholdDefault,
	- renderer,
	- overwrite);
	-
	- node->AddProperty(connectomicsRenderingNodeGradientStartColorName.c_str(),
	- connectomicsRenderingNodeGradientStartColorDefault,
	- renderer,
	- overwrite);
	- node->AddProperty(connectomicsRenderingNodeGradientEndColorName.c_str(),
	- connectomicsRenderingNodeGradientEndColorDefault,
	- renderer,
	- overwrite);
	- node->AddProperty(connectomicsRenderingNodeGradientColorParameterName.c_str(),
	- connectomicsRenderingNodeGradientColorParameter,
	- renderer,
	- overwrite);
	-
	- node->AddProperty(
	- connectomicsRenderingNodeRadiusStartName.c_str(), connectomicsRenderingNodeRadiusStartDefault, renderer, overwrite);
	- node->AddProperty(
	- connectomicsRenderingNodeRadiusEndName.c_str(), connectomicsRenderingNodeRadiusEndDefault, renderer, overwrite);
	- node->AddProperty(connectomicsRenderingNodeRadiusParameterName.c_str(),
	- connectomicsRenderingNodeRadiusParameter,
	- renderer,
	- overwrite);
	-
	- node->AddProperty(
	- connectomicsRenderingNodeChosenNodeName.c_str(), connectomicsRenderingNodeChosenNodeDefault, renderer, overwrite);
	-
	- node->AddProperty(connectomicsRenderingEdgeGradientStartColorName.c_str(),
	- connectomicsRenderingEdgeGradientStartColorDefault,
	- renderer,
	- overwrite);
	- node->AddProperty(connectomicsRenderingEdgeGradientEndColorName.c_str(),
	- connectomicsRenderingEdgeGradientEndColorDefault,
	- renderer,
	- overwrite);
	- node->AddProperty(connectomicsRenderingEdgeGradientColorParameterName.c_str(),
	- connectomicsRenderingEdgeGradientColorParameter,
	- renderer,
	- overwrite);
	-
	- node->AddProperty(
	- connectomicsRenderingEdgeRadiusStartName.c_str(), connectomicsRenderingEdgeRadiusStartDefault, renderer, overwrite);
	- node->AddProperty(
	- connectomicsRenderingEdgeRadiusEndName.c_str(), connectomicsRenderingEdgeRadiusEndDefault, renderer, overwrite);
	- node->AddProperty(connectomicsRenderingEdgeRadiusParameterName.c_str(),
	- connectomicsRenderingEdgeRadiusParameter,
	- renderer,
	- overwrite);
	-
	- node->AddProperty(connectomicsRenderingBalloonTextName.c_str(),
	- balloonText,
	- nullptr,
	- overwrite); // renderer=nullptr: Property is renderer independent.
	-
	- Superclass::SetDefaultProperties(node, renderer, overwrite);
	-}
	-
	-void mitk::ConnectomicsNetworkMapper3D::UpdateVtkObjects()
	-{
	- // TODO: implement
	-}
	-
	-vtkProp mitk::ConnectomicsNetworkMapper3D::GetVtkProp(mitk::BaseRenderer /renderer/)
	-{
	- return m_NetworkAssembly;
	-}
	-
	-bool mitk::ConnectomicsNetworkMapper3D::PropertiesChanged()
	-{
	- mitk::ConnectomicsRenderingSchemeProperty renderingScheme = static_cast<mitk::ConnectomicsRenderingSchemeProperty >(
	- this->GetDataNode()->GetProperty(connectomicsRenderingSchemePropertyName.c_str()));
	- mitk::ConnectomicsRenderingEdgeFilteringProperty *edgeFilter =
	- static_cast<mitk::ConnectomicsRenderingEdgeFilteringProperty *>(
	- this->GetDataNode()->GetProperty(connectomicsRenderingEdgeFilteringPropertyName.c_str()));
	- mitk::FloatProperty edgeThreshold = static_cast<mitk::FloatProperty >(
	- this->GetDataNode()->GetProperty(connectomicsRenderingEdgeThresholdFilterThresholdName.c_str()));
	- mitk::ConnectomicsRenderingNodeFilteringProperty *nodeFilter =
	- static_cast<mitk::ConnectomicsRenderingNodeFilteringProperty *>(
	- this->GetDataNode()->GetProperty(connectomicsRenderingNodeFilteringPropertyName.c_str()));
	-
	- mitk::ConnectomicsRenderingNodeThresholdParameterProperty *nodeThresholdParameter =
	- static_cast<mitk::ConnectomicsRenderingNodeThresholdParameterProperty *>(
	- this->GetDataNode()->GetProperty(connectomicsRenderingNodeThresholdFilterParameterName.c_str()));
	- mitk::ConnectomicsRenderingEdgeThresholdParameterProperty *edgeThresholdParameter =
	- static_cast<mitk::ConnectomicsRenderingEdgeThresholdParameterProperty *>(
	- this->GetDataNode()->GetProperty(connectomicsRenderingEdgeThresholdFilterParameterName.c_str()));
	-
	- mitk::FloatProperty nodeThreshold = static_cast<mitk::FloatProperty >(
	- this->GetDataNode()->GetProperty(connectomicsRenderingNodeThresholdFilterThresholdName.c_str()));
	- mitk::ColorProperty nodeColorStart = static_cast<mitk::ColorProperty >(
	- this->GetDataNode()->GetProperty(connectomicsRenderingNodeGradientStartColorName.c_str()));
	- mitk::ColorProperty nodeColorEnd = static_cast<mitk::ColorProperty >(
	- this->GetDataNode()->GetProperty(connectomicsRenderingNodeGradientEndColorName.c_str()));
	- mitk::FloatProperty nodeRadiusStart = static_cast<mitk::FloatProperty >(
	- this->GetDataNode()->GetProperty(connectomicsRenderingNodeRadiusStartName.c_str()));
	- mitk::FloatProperty nodeRadiusEnd = static_cast<mitk::FloatProperty >(
	- this->GetDataNode()->GetProperty(connectomicsRenderingNodeRadiusEndName.c_str()));
	- mitk::StringProperty chosenNode = static_cast<mitk::StringProperty >(
	- this->GetDataNode()->GetProperty(connectomicsRenderingNodeChosenNodeName.c_str()));
	- mitk::ColorProperty edgeColorStart = static_cast<mitk::ColorProperty >(
	- this->GetDataNode()->GetProperty(connectomicsRenderingEdgeGradientStartColorName.c_str()));
	- mitk::ColorProperty edgeColorEnd = static_cast<mitk::ColorProperty >(
	- this->GetDataNode()->GetProperty(connectomicsRenderingEdgeGradientEndColorName.c_str()));
	- mitk::FloatProperty edgeRadiusStart = static_cast<mitk::FloatProperty >(
	- this->GetDataNode()->GetProperty(connectomicsRenderingEdgeRadiusStartName.c_str()));
	- mitk::FloatProperty edgeRadiusEnd = static_cast<mitk::FloatProperty >(
	- this->GetDataNode()->GetProperty(connectomicsRenderingEdgeRadiusEndName.c_str()));
	- mitk::ConnectomicsRenderingNodeColorParameterProperty *nodeColorParameter =
	- static_cast<mitk::ConnectomicsRenderingNodeColorParameterProperty *>(
	- this->GetDataNode()->GetProperty(connectomicsRenderingNodeGradientColorParameterName.c_str()));
	- mitk::ConnectomicsRenderingNodeRadiusParameterProperty *nodeRadiusParameter =
	- static_cast<mitk::ConnectomicsRenderingNodeRadiusParameterProperty *>(
	- this->GetDataNode()->GetProperty(connectomicsRenderingNodeRadiusParameterName.c_str()));
	- mitk::ConnectomicsRenderingEdgeColorParameterProperty *edgeColorParameter =
	- static_cast<mitk::ConnectomicsRenderingEdgeColorParameterProperty *>(
	- this->GetDataNode()->GetProperty(connectomicsRenderingEdgeGradientColorParameterName.c_str()));
	- mitk::ConnectomicsRenderingEdgeRadiusParameterProperty *edgeRadiusParameter =
	- static_cast<mitk::ConnectomicsRenderingEdgeRadiusParameterProperty *>(
	- this->GetDataNode()->GetProperty(connectomicsRenderingEdgeRadiusParameterName.c_str()));
	-
	- if (m_ChosenRenderingScheme != renderingScheme->GetValueAsString() \|\|
	- m_ChosenEdgeFilter != edgeFilter->GetValueAsString() \|\| m_EdgeThreshold != edgeThreshold->GetValue() \|\|
	- m_EdgeThresholdParameter != edgeThresholdParameter->GetValueAsString() \|\|
	- m_ChosenNodeFilter != nodeFilter->GetValueAsString() \|\| m_NodeThreshold != nodeThreshold->GetValue() \|\|
	- m_NodeThresholdParameter != nodeThresholdParameter->GetValueAsString() \|\|
	- m_NodeColorStart != nodeColorStart->GetValue() \|\| m_NodeColorEnd != nodeColorEnd->GetValue() \|\|
	- m_NodeRadiusStart != nodeRadiusStart->GetValue() \|\| m_NodeRadiusEnd != nodeRadiusEnd->GetValue() \|\|
	- m_ChosenNodeLabel != chosenNode->GetValueAsString() \|\| m_EdgeColorStart != edgeColorStart->GetValue() \|\|
	- m_EdgeColorEnd != edgeColorEnd->GetValue() \|\| m_EdgeRadiusStart != edgeRadiusStart->GetValue() \|\|
	- m_EdgeRadiusEnd != edgeRadiusEnd->GetValue() \|\| m_NodeColorParameter != nodeColorParameter->GetValueAsString() \|\|
	- m_NodeRadiusParameter != nodeRadiusParameter->GetValueAsString() \|\|
	- m_EdgeColorParameter != edgeColorParameter->GetValueAsString() \|\|
	- m_EdgeRadiusParameter != edgeRadiusParameter->GetValueAsString())
	- {
	- m_ChosenRenderingScheme = renderingScheme->GetValueAsString();
	- m_ChosenEdgeFilter = edgeFilter->GetValueAsString();
	- m_EdgeThreshold = edgeThreshold->GetValue();
	- m_EdgeThresholdParameter = edgeThresholdParameter->GetValueAsString();
	- m_ChosenNodeFilter = nodeFilter->GetValueAsString();
	- m_NodeThreshold = nodeThreshold->GetValue();
	- m_NodeThresholdParameter = nodeThresholdParameter->GetValueAsString();
	- m_NodeColorStart = nodeColorStart->GetValue();
	- m_NodeColorEnd = nodeColorEnd->GetValue();
	- m_NodeRadiusStart = nodeRadiusStart->GetValue();
	- m_NodeRadiusEnd = nodeRadiusEnd->GetValue();
	- m_ChosenNodeLabel = chosenNode->GetValueAsString();
	- m_EdgeColorStart = edgeColorStart->GetValue();
	- m_EdgeColorEnd = edgeColorEnd->GetValue();
	- m_EdgeRadiusStart = edgeRadiusStart->GetValue();
	- m_EdgeRadiusEnd = edgeRadiusEnd->GetValue();
	- m_NodeColorParameter = nodeColorParameter->GetValueAsString();
	- m_NodeRadiusParameter = nodeRadiusParameter->GetValueAsString();
	- m_EdgeColorParameter = edgeColorParameter->GetValueAsString();
	- m_EdgeRadiusParameter = edgeRadiusParameter->GetValueAsString();
	-
	- return true;
	- }
	-
	- return false;
	-}
	-
	-double mitk::ConnectomicsNetworkMapper3D::FillNodeParameterVector(std::vector<double> *parameterVector,
	- std::string parameterName)
	-{
	- int end(parameterVector->size());
	-
	- // constant parameter - uniform style
	- if (parameterName == connectomicsRenderingNodeParameterConstant)
	- {
	- for (int index(0); index < end; index++)
	- {
	- parameterVector->at(index) = 1.0;
	- }
	- return 1.0;
	- }
	-
	- double maximum(0.0);
	-
	- // using the degree as parameter
	- if (parameterName == connectomicsRenderingNodeParameterDegree)
	- {
	- std::vector<int> vectorOfDegree = this->GetInput()->GetDegreeOfNodes();
	- for (int index(0); index < end; index++)
	- {
	- parameterVector->at(index) = vectorOfDegree[index];
	- }
	- maximum = *std::max_element(parameterVector->begin(), parameterVector->end());
	- }
	-
	- // using betweenness centrality as parameter
	- if (parameterName == connectomicsRenderingNodeParameterBetweenness)
	- {
	- std::vector<double> vectorOfBetweenness = this->GetInput()->GetNodeBetweennessVector();
	- for (int index(0); index < end; index++)
	- {
	- parameterVector->at(index) = vectorOfBetweenness[index];
	- }
	- maximum = *std::max_element(parameterVector->begin(), parameterVector->end());
	- }
	-
	- // using clustering coefficient as parameter
	- if (parameterName == connectomicsRenderingNodeParameterClustering)
	- {
	- const std::vector<double> vectorOfClustering = this->GetInput()->GetLocalClusteringCoefficients();
	- for (int index(0); index < end; index++)
	- {
	- parameterVector->at(index) = vectorOfClustering[index];
	- }
	- maximum = *std::max_element(parameterVector->begin(), parameterVector->end());
	- }
	-
	- // using distance to a specific node as parameter
	- if (parameterName == connectomicsRenderingNodeParameterColoringShortestPath)
	- {
	- bool labelFound(this->GetInput()->CheckForLabel(m_ChosenNodeLabel));
	- // check whether the chosen node is valid
	- if (!labelFound)
	- {
	- MITK_WARN << "Node chosen for rendering is not valid.";
	- for (int index(0); index < end; index++)
	- {
	- parameterVector->at(index) = 1.0;
	- }
	- return 1.0;
	- }
	- else
	- {
	- const std::vector<double> distanceVector =
	- this->GetInput()->GetShortestDistanceVectorFromLabel(m_ChosenNodeLabel);
	- for (int index(0); index < end; index++)
	- {
	- parameterVector->at(index) = distanceVector[index];
	- }
	- maximum = *std::max_element(parameterVector->begin(), parameterVector->end());
	- }
	- }
	-
	- // if the maximum is nearly zero
	- if (std::abs(maximum) < mitk::eps)
	- {
	- maximum = 1.0;
	- }
	-
	- return maximum;
	-}
	-
	-double mitk::ConnectomicsNetworkMapper3D::FillEdgeParameterVector(std::vector<double> *parameterVector,
	- std::string parameterName)
	-{
	- int end(parameterVector->size());
	-
	- // constant parameter - uniform style
	- if (parameterName == connectomicsRenderingEdgeParameterConstant)
	- {
	- for (int index(0); index < end; index++)
	- {
	- parameterVector->at(index) = 1.0;
	- }
	- return 1.0;
	- }
	-
	- double maximum(0.0);
	-
	- // using the weight as parameter
	- if (parameterName == connectomicsRenderingEdgeParameterWeight)
	- {
	- std::vector<std::pair<std::pair<mitk::ConnectomicsNetwork::NetworkNode, mitk::ConnectomicsNetwork::NetworkNode>,
	- mitk::ConnectomicsNetwork::NetworkEdge>>
	- vectorOfEdges = this->GetInput()->GetVectorOfAllEdges();
	- for (int index(0); index < end; index++)
	- {
	- parameterVector->at(index) = vectorOfEdges[index].second.fiber_count;
	- }
	- maximum = *std::max_element(parameterVector->begin(), parameterVector->end());
	- }
	-
	- // using the edge centrality as parameter
	- if (parameterName == connectomicsRenderingEdgeParameterCentrality)
	- {
	- const std::vector<double> vectorOfCentrality = this->GetInput()->GetEdgeBetweennessVector();
	- for (int index(0); index < end; index++)
	- {
	- parameterVector->at(index) = vectorOfCentrality[index];
	- }
	- maximum = *std::max_element(parameterVector->begin(), parameterVector->end());
	- }
	-
	- // if the maximum is nearly zero
	- if (std::abs(maximum) < mitk::eps)
	- {
	- maximum = 1.0;
	- }
	-
	- return maximum;
	-}
	-
	-void mitk::ConnectomicsNetworkMapper3D::FillNodeFilterBoolVector(std::vector<bool> *boolVector,
	- std::string parameterName)
	-{
	- std::vector<double> parameterVector;
	- parameterVector.resize(boolVector->size());
	- int end(parameterVector.size());
	-
	- // using the degree as parameter
	- if (parameterName == connectomicsRenderingNodeParameterDegree)
	- {
	- std::vector<int> vectorOfDegree = this->GetInput()->GetDegreeOfNodes();
	- for (int index(0); index < end; index++)
	- {
	- parameterVector.at(index) = vectorOfDegree[index];
	- }
	- }
	-
	- // using betweenness centrality as parameter
	- if (parameterName == connectomicsRenderingNodeParameterBetweenness)
	- {
	- std::vector<double> vectorOfBetweenness = this->GetInput()->GetNodeBetweennessVector();
	- for (int index(0); index < end; index++)
	- {
	- parameterVector.at(index) = vectorOfBetweenness[index];
	- }
	- }
	-
	- // using clustering coefficient as parameter
	- if (parameterName == connectomicsRenderingNodeParameterClustering)
	- {
	- const std::vector<double> vectorOfClustering = this->GetInput()->GetLocalClusteringCoefficients();
	- for (int index(0); index < end; index++)
	- {
	- parameterVector.at(index) = vectorOfClustering[index];
	- }
	- }
	-
	- for (int index(0), end(boolVector->size()); index < end; index++)
	- {
	- if (parameterVector.at(index) >= m_NodeThreshold)
	- {
	- boolVector->at(index) = true;
	- }
	- else
	- {
	- boolVector->at(index) = false;
	- }
	- }
	- return;
	-}
	-
	-void mitk::ConnectomicsNetworkMapper3D::FillEdgeFilterBoolVector(std::vector<bool> *boolVector,
	- std::string parameterName)
	-{
	- std::vector<double> parameterVector;
	- parameterVector.resize(boolVector->size());
	- int end(parameterVector.size());
	-
	- // using the weight as parameter
	- if (parameterName == connectomicsRenderingEdgeParameterWeight)
	- {
	- std::vector<std::pair<std::pair<mitk::ConnectomicsNetwork::NetworkNode, mitk::ConnectomicsNetwork::NetworkNode>,
	- mitk::ConnectomicsNetwork::NetworkEdge>>
	- vectorOfEdges = this->GetInput()->GetVectorOfAllEdges();
	-
	- for (int index(0); index < end; index++)
	- {
	- parameterVector.at(index) = vectorOfEdges[index].second.fiber_count;
	- }
	- }
	-
	- // using the edge centrality as parameter
	- if (parameterName == connectomicsRenderingEdgeParameterCentrality)
	- {
	- const std::vector<double> vectorOfCentrality = this->GetInput()->GetEdgeBetweennessVector();
	- for (int index(0); index < end; index++)
	- {
	- parameterVector.at(index) = vectorOfCentrality[index];
	- }
	- }
	-
	- for (int index(0), end(boolVector->size()); index < end; index++)
	- {
	- if (parameterVector.at(index) >= m_EdgeThreshold)
	- {
	- boolVector->at(index) = true;
	- }
	- else
	- {
	- boolVector->at(index) = false;
	- }
	- }
	- return;
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsNetworkMapper3D.h b/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsNetworkMapper3D.h
	deleted file mode 100644
	index f796dc604e..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsNetworkMapper3D.h
	+++ /dev/null
	@@ -1,145 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef ConnectomicsNetworkMapper3D_H_HEADER_INCLUDED
	-#define ConnectomicsNetworkMapper3D_H_HEADER_INCLUDED
	-
	-// VTK includes
	-
	-#include "vtkPropAssembly.h"
	-#include <vtkSmartPointer.h>
	-
	-// MITK includes
	-// base class
	-#include "mitkVtkMapper.h"
	-
	-// data type
	-
	-#include "mitkConnectomicsNetwork.h"
	-
	-#include <vtkActor.h>
	-
	-#include <vtkCellArray.h>
	-#include <vtkCellData.h>
	-#include <vtkDoubleArray.h>
	-#include <vtkLineSource.h>
	-#include <vtkPoints.h>
	-#include <vtkPolyData.h>
	-#include <vtkPolyLine.h>
	-#include <vtkProperty.h>
	-#include <vtkSphereSource.h>
	-
	-#include <vtkPolyDataMapper.h>
	-#include <vtkTubeFilter.h>
	-
	-#include <vtkRenderWindow.h>
	-#include <vtkRenderWindowInteractor.h>
	-#include <vtkRenderer.h>
	-
	-#include <vtkInteractorStyleTrackball.h>
	-#include <vtkInteractorStyleTrackballCamera.h>
	-
	-#include "mitkFreeSurferParcellationTranslator.h"
	-#include "mitkTextAnnotation2D.h"
	-#include "mitkTextAnnotation3D.h"
	-#include "mitkVtkInteractorStyle.h"
	-#include <mitkManualPlacementAnnotationRenderer.h>
	-#include <vtkActor2D.h>
	-#include <vtkPolyDataMapper2D.h>
	-#include <vtkProperty2D.h>
	-#include <vtkRegularPolygonSource.h>
	-
	-#include <iostream>
	-#include <string>
	-#include <vector>
	-
	-#include <MitkConnectomicsExports.h>
	-
	-namespace mitk
	-{
	- /**
	- * \brief Mapper for Networks
	- * \ingroup Mapper
	- */
	-
	- class MITKCONNECTOMICS_EXPORT ConnectomicsNetworkMapper3D : public VtkMapper
	- {
	- public:
	- mitkClassMacro(ConnectomicsNetworkMapper3D, VtkMapper);
	- itkFactorylessNewMacro(Self) itkCloneMacro(Self)
	-
	- vtkProp *GetVtkProp(
	- mitk::BaseRenderer *renderer) override; // looks like deprecated.. should be replaced bz GetViewProp()
	- static void SetDefaultProperties(DataNode node, BaseRenderer renderer = nullptr, bool overwrite = false);
	-
	- void GenerateDataForRenderer(mitk::BaseRenderer *renderer) override;
	-
	- virtual const mitk::ConnectomicsNetwork *GetInput();
	-
	- protected:
	- ConnectomicsNetworkMapper3D();
	- ~ConnectomicsNetworkMapper3D() override;
	-
	- void UpdateVtkObjects();
	-
	- vtkPropAssembly *m_NetworkAssembly;
	-
	- /**
	- * \brief Returns true if the properties have changed since the last data generation
	- */
	- bool PropertiesChanged();
	-
	- // Create vectors for customizing color and radius and return maximum
	- double FillNodeParameterVector(std::vector<double> *parameterVector, std::string parameterName);
	- double FillEdgeParameterVector(std::vector<double> *parameterVector, std::string parameterName);
	-
	- void FillNodeFilterBoolVector(std::vector<bool> *boolVector, std::string parameterName);
	- void FillEdgeFilterBoolVector(std::vector<bool> *boolVector, std::string parameterName);
	-
	- // Property storing members
	- std::string m_ChosenRenderingScheme;
	- std::string m_ChosenEdgeFilter;
	- std::string m_EdgeThresholdParameter;
	- double m_EdgeThreshold;
	- std::string m_ChosenNodeFilter;
	- std::string m_NodeThresholdParameter;
	- double m_NodeThreshold;
	- mitk::Color m_NodeColorStart;
	- mitk::Color m_NodeColorEnd;
	- double m_NodeRadiusStart;
	- double m_NodeRadiusEnd;
	- std::string m_ChosenNodeLabel;
	- mitk::Color m_EdgeColorStart;
	- mitk::Color m_EdgeColorEnd;
	- double m_EdgeRadiusStart;
	- double m_EdgeRadiusEnd;
	- std::string m_NodeRadiusParameter;
	- std::string m_NodeColorParameter;
	- std::string m_EdgeRadiusParameter;
	- std::string m_EdgeColorParameter;
	-
	- // Balloons
	- std::string m_BalloonText;
	- std::string m_BalloonNodeStats;
	- mitk::FreeSurferParcellationTranslator::Pointer m_Translator;
	- std::string m_AllNodeLabels;
	-
	- mitk::TextAnnotation3D::Pointer m_TextOverlay3D;
	- };
	-
	-} // namespace mitk
	-
	-#endif /* ConnectomicsNetworkMapper3D_H_HEADER_INCLUDED */
	diff --git a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingEdgeColorParameterProperty.cpp b/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingEdgeColorParameterProperty.cpp
	deleted file mode 100644
	index 8dc1881b2b..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingEdgeColorParameterProperty.cpp
	+++ /dev/null
	@@ -1,70 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkConnectomicsRenderingEdgeColorParameterProperty.h"
	-#include "mitkConnectomicsRenderingProperties.h"
	-
	-#define EDGE_COLOR_CONSTANT 0
	-#define EDGE_COLOR_WEIGHT 1
	-#define EDGE_COLOR_CENTRALITY 2
	-
	-mitk::ConnectomicsRenderingEdgeColorParameterProperty::ConnectomicsRenderingEdgeColorParameterProperty( )
	-{
	- AddRenderingEdgeColorParameters();
	- SetValue( EDGE_COLOR_CONSTANT );
	-}
	-
	-
	-mitk::ConnectomicsRenderingEdgeColorParameterProperty::ConnectomicsRenderingEdgeColorParameterProperty( const IdType& value )
	-{
	- AddRenderingEdgeColorParameters();
	- if ( IsValidEnumerationValue( value ) )
	- {
	- SetValue( value ) ;
	- }
	- else
	- {
	- SetValue( EDGE_COLOR_CONSTANT );
	- }
	-}
	-
	-mitk::ConnectomicsRenderingEdgeColorParameterProperty::ConnectomicsRenderingEdgeColorParameterProperty( const std::string& value )
	-{
	- AddRenderingEdgeColorParameters();
	- if ( IsValidEnumerationValue( value ) )
	- {
	- SetValue( value );
	- }
	- else
	- {
	- SetValue( EDGE_COLOR_CONSTANT );
	- }
	-}
	-
	-
	-
	-void mitk::ConnectomicsRenderingEdgeColorParameterProperty::AddRenderingEdgeColorParameters()
	-{
	- AddEnum( connectomicsRenderingEdgeParameterConstant , EDGE_COLOR_CONSTANT );
	- AddEnum( connectomicsRenderingEdgeParameterWeight , EDGE_COLOR_WEIGHT );
	- AddEnum( connectomicsRenderingEdgeParameterCentrality , EDGE_COLOR_CENTRALITY );
	-}
	-
	-
	-bool mitk::ConnectomicsRenderingEdgeColorParameterProperty::AddEnum( const std::string& name, const IdType& id )
	-{
	- return Superclass::AddEnum( name, id );
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingEdgeColorParameterProperty.h b/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingEdgeColorParameterProperty.h
	deleted file mode 100644
	index 00fe003fc1..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingEdgeColorParameterProperty.h
	+++ /dev/null
	@@ -1,95 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_CONNECTOMICS_RENDERING_EDGE_COLOR_PARAMETER_PROPERTY__H_
	-#define _MITK_CONNECTOMICS_RENDERING_EDGE_COLOR_PARAMETER_PROPERTY__H_
	-
	-#include "mitkEnumerationProperty.h"
	-#include <MitkConnectomicsExports.h>
	-
	-namespace mitk
	-{
	-
	-#ifdef _MSC_VER
	-# pragma warning(push)
	-# pragma warning(disable: 4522)
	-#endif
	-
	-/**
	- * Encapsulates the enumeration of different rendering schemes for connectomics networks
	- */
	-class MITKCONNECTOMICS_EXPORT ConnectomicsRenderingEdgeColorParameterProperty : public EnumerationProperty
	-{
	-public:
	-
	- mitkClassMacro( ConnectomicsRenderingEdgeColorParameterProperty, EnumerationProperty );
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- mitkNewMacro1Param(ConnectomicsRenderingEdgeColorParameterProperty, const IdType&);
	-
	- mitkNewMacro1Param(ConnectomicsRenderingEdgeColorParameterProperty, const std::string&);
	-
	- using BaseProperty::operator=;
	-
	-protected:
	-
	- /**
	- * Constructor. Sets the representation to a default value of 0
	- */
	- ConnectomicsRenderingEdgeColorParameterProperty( );
	-
	- /**
	- * Constructor. Sets the parameter to the given value. If it is not
	- * valid, the value is set to 0
	- * @param value the integer representation of the parameter
	- */
	- ConnectomicsRenderingEdgeColorParameterProperty( const IdType& value );
	-
	- /**
	- * Constructor. Sets the parameter to the given value. If it is not
	- * valid, the value is set to 0
	- * @param value the string representation of the parameter
	- */
	- ConnectomicsRenderingEdgeColorParameterProperty( const std::string& value );
	-
	- /**
	- * this function is overridden as protected, so that the user may not add
	- * additional enumerations.
	- */
	- bool AddEnum( const std::string& name, const IdType& id ) override;
	-
	- /**
	- * Adds the enumeration types as defined by vtk to the list of known
	- * enumeration values.
	- */
	- virtual void AddRenderingEdgeColorParameters();
	-
	-private:
	-
	- // purposely not implemented
	- ConnectomicsRenderingEdgeColorParameterProperty(const ConnectomicsRenderingEdgeColorParameterProperty&);
	- ConnectomicsRenderingEdgeColorParameterProperty& operator=(const ConnectomicsRenderingEdgeColorParameterProperty&);
	-};
	-
	-#ifdef _MSC_VER
	-# pragma warning(pop)
	-#endif
	-
	-} // end of namespace mitk
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingEdgeFilteringProperty.cpp b/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingEdgeFilteringProperty.cpp
	deleted file mode 100644
	index dd2630ed13..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingEdgeFilteringProperty.cpp
	+++ /dev/null
	@@ -1,70 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkConnectomicsRenderingEdgeFilteringProperty.h"
	-#include "mitkConnectomicsRenderingProperties.h"
	-
	-#define NO_FILTER 0
	-#define SHORTEST_PATH_FILTER 1
	-#define THRESHOLDING_FILTER 2
	-
	-mitk::ConnectomicsRenderingEdgeFilteringProperty::ConnectomicsRenderingEdgeFilteringProperty( )
	-{
	- AddRenderingFilter();
	- SetValue( NO_FILTER );
	-}
	-
	-
	-mitk::ConnectomicsRenderingEdgeFilteringProperty::ConnectomicsRenderingEdgeFilteringProperty( const IdType& value )
	-{
	- AddRenderingFilter();
	- if ( IsValidEnumerationValue( value ) )
	- {
	- SetValue( value ) ;
	- }
	- else
	- {
	- SetValue( NO_FILTER );
	- }
	-}
	-
	-mitk::ConnectomicsRenderingEdgeFilteringProperty::ConnectomicsRenderingEdgeFilteringProperty( const std::string& value )
	-{
	- AddRenderingFilter();
	- if ( IsValidEnumerationValue( value ) )
	- {
	- SetValue( value );
	- }
	- else
	- {
	- SetValue( NO_FILTER );
	- }
	-}
	-
	-
	-
	-void mitk::ConnectomicsRenderingEdgeFilteringProperty::AddRenderingFilter()
	-{
	- AddEnum( connectomicsRenderingEdgeNoFilter, NO_FILTER );
	- //AddEnum( connectomicsRenderingEdgeShortestPathFilter, SHORTEST_PATH_FILTER );
	- AddEnum( connectomicsRenderingEdgeThresholdFilter, THRESHOLDING_FILTER );
	-}
	-
	-
	-bool mitk::ConnectomicsRenderingEdgeFilteringProperty::AddEnum( const std::string& name, const IdType& id )
	-{
	- return Superclass::AddEnum( name, id );
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingEdgeFilteringProperty.h b/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingEdgeFilteringProperty.h
	deleted file mode 100644
	index 9de719dcb6..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingEdgeFilteringProperty.h
	+++ /dev/null
	@@ -1,95 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_CONNECTOMICS_RENDERING_EDGE_FILTERING_PROPERTY__H_
	-#define _MITK_CONNECTOMICS_RENDERING_EDGE_FILTERING_PROPERTY__H_
	-
	-#include "mitkEnumerationProperty.h"
	-#include <MitkConnectomicsExports.h>
	-
	-namespace mitk
	-{
	-
	-#ifdef _MSC_VER
	-# pragma warning(push)
	-# pragma warning(disable: 4522)
	-#endif
	-
	-/**
	- * Encapsulates the enumeration of different edge filtering options for rendering connectomics networks
	- */
	-class MITKCONNECTOMICS_EXPORT ConnectomicsRenderingEdgeFilteringProperty : public EnumerationProperty
	-{
	-public:
	-
	- mitkClassMacro( ConnectomicsRenderingEdgeFilteringProperty, EnumerationProperty );
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- mitkNewMacro1Param(ConnectomicsRenderingEdgeFilteringProperty, const IdType&);
	-
	- mitkNewMacro1Param(ConnectomicsRenderingEdgeFilteringProperty, const std::string&);
	-
	- using BaseProperty::operator=;
	-
	-protected:
	-
	- /**
	- * Constructor. Sets the representation to a default value of 0
	- */
	- ConnectomicsRenderingEdgeFilteringProperty( );
	-
	- /**
	- * Constructor. Sets the filter to the given value. If it is not
	- * valid, the value is set to 0
	- * @param value the integer representation of the filter
	- */
	- ConnectomicsRenderingEdgeFilteringProperty( const IdType& value );
	-
	- /**
	- * Constructor. Sets the filter to the given value. If it is not
	- * valid, the value is set to 0
	- * @param value the string representation of the filter
	- */
	- ConnectomicsRenderingEdgeFilteringProperty( const std::string& value );
	-
	- /**
	- * this function is overridden as protected, so that the user may not add
	- * additional enumerations.
	- */
	- bool AddEnum( const std::string& name, const IdType& id ) override;
	-
	- /**
	- * Adds the enumeration types as defined by vtk to the list of known
	- * enumeration values.
	- */
	- virtual void AddRenderingFilter();
	-
	-private:
	-
	- // purposely not implemented
	- ConnectomicsRenderingEdgeFilteringProperty(const ConnectomicsRenderingEdgeFilteringProperty&);
	- ConnectomicsRenderingEdgeFilteringProperty& operator=(const ConnectomicsRenderingEdgeFilteringProperty&);
	-};
	-
	-#ifdef _MSC_VER
	-# pragma warning(pop)
	-#endif
	-
	-} // end of namespace mitk
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingEdgeRadiusParameterProperty.cpp b/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingEdgeRadiusParameterProperty.cpp
	deleted file mode 100644
	index c71385669a..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingEdgeRadiusParameterProperty.cpp
	+++ /dev/null
	@@ -1,70 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkConnectomicsRenderingEdgeRadiusParameterProperty.h"
	-#include "mitkConnectomicsRenderingProperties.h"
	-
	-#define EDGE_RADIUS_CONSTANT 0
	-#define EDGE_RADIUS_WEIGHT 1
	-#define EDGE_RADIUS_CENTRALITY 2
	-
	-mitk::ConnectomicsRenderingEdgeRadiusParameterProperty::ConnectomicsRenderingEdgeRadiusParameterProperty( )
	-{
	- AddRenderingEdgeRadiusParameters();
	- SetValue( EDGE_RADIUS_CONSTANT );
	-}
	-
	-
	-mitk::ConnectomicsRenderingEdgeRadiusParameterProperty::ConnectomicsRenderingEdgeRadiusParameterProperty( const IdType& value )
	-{
	- AddRenderingEdgeRadiusParameters();
	- if ( IsValidEnumerationValue( value ) )
	- {
	- SetValue( value ) ;
	- }
	- else
	- {
	- SetValue( EDGE_RADIUS_CONSTANT );
	- }
	-}
	-
	-mitk::ConnectomicsRenderingEdgeRadiusParameterProperty::ConnectomicsRenderingEdgeRadiusParameterProperty( const std::string& value )
	-{
	- AddRenderingEdgeRadiusParameters();
	- if ( IsValidEnumerationValue( value ) )
	- {
	- SetValue( value );
	- }
	- else
	- {
	- SetValue( EDGE_RADIUS_CONSTANT );
	- }
	-}
	-
	-
	-
	-void mitk::ConnectomicsRenderingEdgeRadiusParameterProperty::AddRenderingEdgeRadiusParameters()
	-{
	- AddEnum( connectomicsRenderingEdgeParameterConstant , EDGE_RADIUS_CONSTANT );
	- AddEnum( connectomicsRenderingEdgeParameterWeight , EDGE_RADIUS_WEIGHT );
	- AddEnum( connectomicsRenderingEdgeParameterCentrality , EDGE_RADIUS_CENTRALITY );
	-}
	-
	-
	-bool mitk::ConnectomicsRenderingEdgeRadiusParameterProperty::AddEnum( const std::string& name, const IdType& id )
	-{
	- return Superclass::AddEnum( name, id );
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingEdgeRadiusParameterProperty.h b/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingEdgeRadiusParameterProperty.h
	deleted file mode 100644
	index df71aa5303..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingEdgeRadiusParameterProperty.h
	+++ /dev/null
	@@ -1,95 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_CONNECTOMICS_RENDERING_EDGE_RADIUS_PARAMETER_PROPERTY__H_
	-#define _MITK_CONNECTOMICS_RENDERING_EDGE_RADIUS_PARAMETER_PROPERTY__H_
	-
	-#include "mitkEnumerationProperty.h"
	-#include <MitkConnectomicsExports.h>
	-
	-namespace mitk
	-{
	-
	-#ifdef _MSC_VER
	-# pragma warning(push)
	-# pragma warning(disable: 4522)
	-#endif
	-
	-/**
	- * Encapsulates the enumeration of different rendering schemes for connectomics networks
	- */
	-class MITKCONNECTOMICS_EXPORT ConnectomicsRenderingEdgeRadiusParameterProperty : public EnumerationProperty
	-{
	-public:
	-
	- mitkClassMacro( ConnectomicsRenderingEdgeRadiusParameterProperty, EnumerationProperty );
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- mitkNewMacro1Param(ConnectomicsRenderingEdgeRadiusParameterProperty, const IdType&);
	-
	- mitkNewMacro1Param(ConnectomicsRenderingEdgeRadiusParameterProperty, const std::string&);
	-
	- using BaseProperty::operator=;
	-
	-protected:
	-
	- /**
	- * Constructor. Sets the representation to a default value of 0
	- */
	- ConnectomicsRenderingEdgeRadiusParameterProperty( );
	-
	- /**
	- * Constructor. Sets the parameter to the given value. If it is not
	- * valid, the value is set to 0
	- * @param value the integer representation of the parameter
	- */
	- ConnectomicsRenderingEdgeRadiusParameterProperty( const IdType& value );
	-
	- /**
	- * Constructor. Sets the parameter to the given value. If it is not
	- * valid, the value is set to 0
	- * @param value the string representation of the parameter
	- */
	- ConnectomicsRenderingEdgeRadiusParameterProperty( const std::string& value );
	-
	- /**
	- * this function is overridden as protected, so that the user may not add
	- * additional enumerations.
	- */
	- bool AddEnum( const std::string& name, const IdType& id ) override;
	-
	- /**
	- * Adds the enumeration types as defined by vtk to the list of known
	- * enumeration values.
	- */
	- virtual void AddRenderingEdgeRadiusParameters();
	-
	-private:
	-
	- // purposely not implemented
	- ConnectomicsRenderingEdgeRadiusParameterProperty(const ConnectomicsRenderingEdgeRadiusParameterProperty&);
	- ConnectomicsRenderingEdgeRadiusParameterProperty& operator=(const ConnectomicsRenderingEdgeRadiusParameterProperty&);
	-};
	-
	-#ifdef _MSC_VER
	-# pragma warning(pop)
	-#endif
	-
	-} // end of namespace mitk
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingEdgeThresholdParameterProperty.cpp b/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingEdgeThresholdParameterProperty.cpp
	deleted file mode 100644
	index 0241e2bb13..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingEdgeThresholdParameterProperty.cpp
	+++ /dev/null
	@@ -1,68 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkConnectomicsRenderingEdgeThresholdParameterProperty.h"
	-#include "mitkConnectomicsRenderingProperties.h"
	-
	-#define EDGE_THRESHOLD_WEIGHT 0
	-#define EDGE_THRESHOLD_CENTRALITY 1
	-
	-mitk::ConnectomicsRenderingEdgeThresholdParameterProperty::ConnectomicsRenderingEdgeThresholdParameterProperty( )
	-{
	- AddRenderingEdgeThresholdParameters();
	- SetValue( EDGE_THRESHOLD_WEIGHT );
	-}
	-
	-
	-mitk::ConnectomicsRenderingEdgeThresholdParameterProperty::ConnectomicsRenderingEdgeThresholdParameterProperty( const IdType& value )
	-{
	- AddRenderingEdgeThresholdParameters();
	- if ( IsValidEnumerationValue( value ) )
	- {
	- SetValue( value ) ;
	- }
	- else
	- {
	- SetValue( EDGE_THRESHOLD_WEIGHT );
	- }
	-}
	-
	-mitk::ConnectomicsRenderingEdgeThresholdParameterProperty::ConnectomicsRenderingEdgeThresholdParameterProperty( const std::string& value )
	-{
	- AddRenderingEdgeThresholdParameters();
	- if ( IsValidEnumerationValue( value ) )
	- {
	- SetValue( value );
	- }
	- else
	- {
	- SetValue( EDGE_THRESHOLD_WEIGHT );
	- }
	-}
	-
	-
	-
	-void mitk::ConnectomicsRenderingEdgeThresholdParameterProperty::AddRenderingEdgeThresholdParameters()
	-{
	- AddEnum( connectomicsRenderingEdgeParameterWeight , EDGE_THRESHOLD_WEIGHT );
	- AddEnum( connectomicsRenderingEdgeParameterCentrality , EDGE_THRESHOLD_CENTRALITY );
	-}
	-
	-
	-bool mitk::ConnectomicsRenderingEdgeThresholdParameterProperty::AddEnum( const std::string& name, const IdType& id )
	-{
	- return Superclass::AddEnum( name, id );
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingEdgeThresholdParameterProperty.h b/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingEdgeThresholdParameterProperty.h
	deleted file mode 100644
	index bb9c933c5e..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingEdgeThresholdParameterProperty.h
	+++ /dev/null
	@@ -1,95 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_CONNECTOMICS_RENDERING_EDGE_THRESHOLD_PARAMETER_PROPERTY__H_
	-#define _MITK_CONNECTOMICS_RENDERING_EDGE_THRESHOLD_PARAMETER_PROPERTY__H_
	-
	-#include "mitkEnumerationProperty.h"
	-#include <MitkConnectomicsExports.h>
	-
	-namespace mitk
	-{
	-
	-#ifdef _MSC_VER
	-# pragma warning(push)
	-# pragma warning(disable: 4522)
	-#endif
	-
	-/**
	- * Encapsulates the enumeration of different rendering schemes for connectomics networks
	- */
	-class MITKCONNECTOMICS_EXPORT ConnectomicsRenderingEdgeThresholdParameterProperty : public EnumerationProperty
	-{
	-public:
	-
	- mitkClassMacro( ConnectomicsRenderingEdgeThresholdParameterProperty, EnumerationProperty );
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- mitkNewMacro1Param(ConnectomicsRenderingEdgeThresholdParameterProperty, const IdType&);
	-
	- mitkNewMacro1Param(ConnectomicsRenderingEdgeThresholdParameterProperty, const std::string&);
	-
	- using BaseProperty::operator=;
	-
	-protected:
	-
	- /**
	- * Constructor. Sets the representation to a default value of 0
	- */
	- ConnectomicsRenderingEdgeThresholdParameterProperty( );
	-
	- /**
	- * Constructor. Sets the parameter to the given value. If it is not
	- * valid, the value is set to 0
	- * @param value the integer representation of the parameter
	- */
	- ConnectomicsRenderingEdgeThresholdParameterProperty( const IdType& value );
	-
	- /**
	- * Constructor. Sets the parameter to the given value. If it is not
	- * valid, the value is set to 0
	- * @param value the string representation of the parameter
	- */
	- ConnectomicsRenderingEdgeThresholdParameterProperty( const std::string& value );
	-
	- /**
	- * this function is overridden as protected, so that the user may not add
	- * additional enumerations.
	- */
	- bool AddEnum( const std::string& name, const IdType& id ) override;
	-
	- /**
	- * Adds the enumeration types as defined by vtk to the list of known
	- * enumeration values.
	- */
	- virtual void AddRenderingEdgeThresholdParameters();
	-
	-private:
	-
	- // purposely not implemented
	- ConnectomicsRenderingEdgeThresholdParameterProperty(const ConnectomicsRenderingEdgeThresholdParameterProperty&);
	- ConnectomicsRenderingEdgeThresholdParameterProperty& operator=(const ConnectomicsRenderingEdgeThresholdParameterProperty&);
	-};
	-
	-#ifdef _MSC_VER
	-# pragma warning(pop)
	-#endif
	-
	-} // end of namespace mitk
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingNodeColorParameterProperty.cpp b/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingNodeColorParameterProperty.cpp
	deleted file mode 100644
	index 849fced415..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingNodeColorParameterProperty.cpp
	+++ /dev/null
	@@ -1,71 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkConnectomicsRenderingNodeColorParameterProperty.h"
	-#include "mitkConnectomicsRenderingProperties.h"
	-
	-#define NODE_COLOR_CONSTANT 0
	-#define NODE_COLOR_DEGREE 1
	-#define NODE_COLOR_BETWEENNESS 2
	-#define NODE_COLOR_CLUSTERING 3
	-#define NODE_COLOR_SHORTEST_PATH 4
	-
	-mitk::ConnectomicsRenderingNodeColorParameterProperty::ConnectomicsRenderingNodeColorParameterProperty( )
	-{
	- AddRenderingNodeColorParameters();
	- SetValue( NODE_COLOR_CONSTANT );
	-}
	-
	-
	-mitk::ConnectomicsRenderingNodeColorParameterProperty::ConnectomicsRenderingNodeColorParameterProperty( const IdType& value )
	-{
	- AddRenderingNodeColorParameters();
	- if ( IsValidEnumerationValue( value ) )
	- {
	- SetValue( value ) ;
	- }
	- else
	- {
	- SetValue( NODE_COLOR_CONSTANT );
	- }
	-}
	-
	-mitk::ConnectomicsRenderingNodeColorParameterProperty::ConnectomicsRenderingNodeColorParameterProperty( const std::string& value )
	-{
	- AddRenderingNodeColorParameters();
	- if ( IsValidEnumerationValue( value ) )
	- {
	- SetValue( value );
	- }
	- else
	- {
	- SetValue( NODE_COLOR_CONSTANT );
	- }
	-}
	-
	-void mitk::ConnectomicsRenderingNodeColorParameterProperty::AddRenderingNodeColorParameters()
	-{
	- AddEnum( connectomicsRenderingNodeParameterConstant , NODE_COLOR_CONSTANT );
	- AddEnum( connectomicsRenderingNodeParameterDegree , NODE_COLOR_DEGREE );
	- AddEnum( connectomicsRenderingNodeParameterBetweenness , NODE_COLOR_BETWEENNESS );
	- AddEnum( connectomicsRenderingNodeParameterClustering , NODE_COLOR_CLUSTERING );
	- AddEnum( connectomicsRenderingNodeParameterColoringShortestPath , NODE_COLOR_SHORTEST_PATH );
	-}
	-
	-bool mitk::ConnectomicsRenderingNodeColorParameterProperty::AddEnum( const std::string& name, const IdType& id )
	-{
	- return Superclass::AddEnum( name, id );
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingNodeColorParameterProperty.h b/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingNodeColorParameterProperty.h
	deleted file mode 100644
	index 3ac12023b2..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingNodeColorParameterProperty.h
	+++ /dev/null
	@@ -1,95 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_CONNECTOMICS_RENDERING_NODE_COLOR_PARAMETER_PROPERTY__H_
	-#define _MITK_CONNECTOMICS_RENDERING_NODE_COLOR_PARAMETER_PROPERTY__H_
	-
	-#include "mitkEnumerationProperty.h"
	-#include <MitkConnectomicsExports.h>
	-
	-namespace mitk
	-{
	-
	-#ifdef _MSC_VER
	-# pragma warning(push)
	-# pragma warning(disable: 4522)
	-#endif
	-
	-/**
	- * Encapsulates the enumeration of different rendering schemes for connectomics networks
	- */
	-class MITKCONNECTOMICS_EXPORT ConnectomicsRenderingNodeColorParameterProperty : public EnumerationProperty
	-{
	-public:
	-
	- mitkClassMacro( ConnectomicsRenderingNodeColorParameterProperty, EnumerationProperty );
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- mitkNewMacro1Param(ConnectomicsRenderingNodeColorParameterProperty, const IdType&);
	-
	- mitkNewMacro1Param(ConnectomicsRenderingNodeColorParameterProperty, const std::string&);
	-
	- using BaseProperty::operator=;
	-
	-protected:
	-
	- /**
	- * Constructor. Sets the representation to a default value of 0
	- */
	- ConnectomicsRenderingNodeColorParameterProperty( );
	-
	- /**
	- * Constructor. Sets the parameter to the given value. If it is not
	- * valid, the value is set to 0
	- * @param value the integer representation of the parameter
	- */
	- ConnectomicsRenderingNodeColorParameterProperty( const IdType& value );
	-
	- /**
	- * Constructor. Sets the parameter to the given value. If it is not
	- * valid, the value is set to 0
	- * @param value the string representation of the parameter
	- */
	- ConnectomicsRenderingNodeColorParameterProperty( const std::string& value );
	-
	- /**
	- * this function is overridden as protected, so that the user may not add
	- * additional enumerations.
	- */
	- bool AddEnum( const std::string& name, const IdType& id ) override;
	-
	- /**
	- * Adds the enumeration types as defined by vtk to the list of known
	- * enumeration values.
	- */
	- virtual void AddRenderingNodeColorParameters();
	-
	-private:
	-
	- // purposely not implemented
	- ConnectomicsRenderingNodeColorParameterProperty(const ConnectomicsRenderingNodeColorParameterProperty&);
	- ConnectomicsRenderingNodeColorParameterProperty& operator=(const ConnectomicsRenderingNodeColorParameterProperty&);
	-};
	-
	-#ifdef _MSC_VER
	-# pragma warning(pop)
	-#endif
	-
	-} // end of namespace mitk
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingNodeFilteringProperty.cpp b/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingNodeFilteringProperty.cpp
	deleted file mode 100644
	index 265785f019..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingNodeFilteringProperty.cpp
	+++ /dev/null
	@@ -1,68 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkConnectomicsRenderingNodeFilteringProperty.h"
	-#include "mitkConnectomicsRenderingProperties.h"
	-
	-#define NO_FILTER 0
	-#define THRESHOLDING_FILTER 1
	-
	-mitk::ConnectomicsRenderingNodeFilteringProperty::ConnectomicsRenderingNodeFilteringProperty( )
	-{
	- AddRenderingFilter();
	- SetValue( NO_FILTER );
	-}
	-
	-
	-mitk::ConnectomicsRenderingNodeFilteringProperty::ConnectomicsRenderingNodeFilteringProperty( const IdType& value )
	-{
	- AddRenderingFilter();
	- if ( IsValidEnumerationValue( value ) )
	- {
	- SetValue( value ) ;
	- }
	- else
	- {
	- SetValue( NO_FILTER );
	- }
	-}
	-
	-mitk::ConnectomicsRenderingNodeFilteringProperty::ConnectomicsRenderingNodeFilteringProperty( const std::string& value )
	-{
	- AddRenderingFilter();
	- if ( IsValidEnumerationValue( value ) )
	- {
	- SetValue( value );
	- }
	- else
	- {
	- SetValue( NO_FILTER );
	- }
	-}
	-
	-
	-
	-void mitk::ConnectomicsRenderingNodeFilteringProperty::AddRenderingFilter()
	-{
	- AddEnum( connectomicsRenderingNodeNoFilter, NO_FILTER );
	- AddEnum( connectomicsRenderingNodeThresholdingFilter, THRESHOLDING_FILTER );
	-}
	-
	-
	-bool mitk::ConnectomicsRenderingNodeFilteringProperty::AddEnum( const std::string& name, const IdType& id )
	-{
	- return Superclass::AddEnum( name, id );
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingNodeFilteringProperty.h b/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingNodeFilteringProperty.h
	deleted file mode 100644
	index eeea251a86..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingNodeFilteringProperty.h
	+++ /dev/null
	@@ -1,95 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_CONNECTOMICS_RENDERING_NODE_FILTERING_PROPERTY__H_
	-#define _MITK_CONNECTOMICS_RENDERING_NODE_FILTERING_PROPERTY__H_
	-
	-#include "mitkEnumerationProperty.h"
	-#include <MitkConnectomicsExports.h>
	-
	-namespace mitk
	-{
	-
	-#ifdef _MSC_VER
	-# pragma warning(push)
	-# pragma warning(disable: 4522)
	-#endif
	-
	-/**
	- * Encapsulates the enumeration of different node filtering options for rendering connectomics networks
	- */
	-class MITKCONNECTOMICS_EXPORT ConnectomicsRenderingNodeFilteringProperty : public EnumerationProperty
	-{
	-public:
	-
	- mitkClassMacro( ConnectomicsRenderingNodeFilteringProperty, EnumerationProperty );
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- mitkNewMacro1Param(ConnectomicsRenderingNodeFilteringProperty, const IdType&);
	-
	- mitkNewMacro1Param(ConnectomicsRenderingNodeFilteringProperty, const std::string&);
	-
	- using BaseProperty::operator=;
	-
	-protected:
	-
	- /**
	- * Constructor. Sets the representation to a default value of 0
	- */
	- ConnectomicsRenderingNodeFilteringProperty( );
	-
	- /**
	- * Constructor. Sets the filter to the given value. If it is not
	- * valid, the value is set to 0
	- * @param value the integer representation of the filter
	- */
	- ConnectomicsRenderingNodeFilteringProperty( const IdType& value );
	-
	- /**
	- * Constructor. Sets the filter to the given value. If it is not
	- * valid, the value is set to 0
	- * @param value the string representation of the filter
	- */
	- ConnectomicsRenderingNodeFilteringProperty( const std::string& value );
	-
	- /**
	- * this function is overridden as protected, so that the user may not add
	- * additional enumerations.
	- */
	- bool AddEnum( const std::string& name, const IdType& id ) override;
	-
	- /**
	- * Adds the enumeration types as defined by vtk to the list of known
	- * enumeration values.
	- */
	- virtual void AddRenderingFilter();
	-
	-private:
	-
	- // purposely not implemented
	- ConnectomicsRenderingNodeFilteringProperty(const ConnectomicsRenderingNodeFilteringProperty&);
	- ConnectomicsRenderingNodeFilteringProperty& operator=(const ConnectomicsRenderingNodeFilteringProperty&);
	-};
	-
	-#ifdef _MSC_VER
	-# pragma warning(pop)
	-#endif
	-
	-} // end of namespace mitk
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingNodeRadiusParameterProperty.cpp b/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingNodeRadiusParameterProperty.cpp
	deleted file mode 100644
	index 08261cc4a1..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingNodeRadiusParameterProperty.cpp
	+++ /dev/null
	@@ -1,72 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkConnectomicsRenderingNodeRadiusParameterProperty.h"
	-#include "mitkConnectomicsRenderingProperties.h"
	-
	-#define NODE_RADIUS_CONSTANT 0
	-#define NODE_RADIUS_DEGREE 1
	-#define NODE_RADIUS_BETWEENNESS 2
	-#define NODE_RADIUS_CLUSTERING 3
	-
	-mitk::ConnectomicsRenderingNodeRadiusParameterProperty::ConnectomicsRenderingNodeRadiusParameterProperty( )
	-{
	- AddRenderingNodeRadiusParameters();
	- SetValue( NODE_RADIUS_CONSTANT );
	-}
	-
	-
	-mitk::ConnectomicsRenderingNodeRadiusParameterProperty::ConnectomicsRenderingNodeRadiusParameterProperty( const IdType& value )
	-{
	- AddRenderingNodeRadiusParameters();
	- if ( IsValidEnumerationValue( value ) )
	- {
	- SetValue( value ) ;
	- }
	- else
	- {
	- SetValue( NODE_RADIUS_CONSTANT );
	- }
	-}
	-
	-mitk::ConnectomicsRenderingNodeRadiusParameterProperty::ConnectomicsRenderingNodeRadiusParameterProperty( const std::string& value )
	-{
	- AddRenderingNodeRadiusParameters();
	- if ( IsValidEnumerationValue( value ) )
	- {
	- SetValue( value );
	- }
	- else
	- {
	- SetValue( NODE_RADIUS_CONSTANT );
	- }
	-}
	-
	-
	-
	-void mitk::ConnectomicsRenderingNodeRadiusParameterProperty::AddRenderingNodeRadiusParameters()
	-{
	- AddEnum( connectomicsRenderingNodeParameterConstant, NODE_RADIUS_CONSTANT );
	- AddEnum( connectomicsRenderingNodeParameterDegree , NODE_RADIUS_DEGREE );
	- AddEnum( connectomicsRenderingNodeParameterBetweenness , NODE_RADIUS_BETWEENNESS );
	- AddEnum( connectomicsRenderingNodeParameterClustering , NODE_RADIUS_CLUSTERING );
	-}
	-
	-
	-bool mitk::ConnectomicsRenderingNodeRadiusParameterProperty::AddEnum( const std::string& name, const IdType& id )
	-{
	- return Superclass::AddEnum( name, id );
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingNodeRadiusParameterProperty.h b/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingNodeRadiusParameterProperty.h
	deleted file mode 100644
	index 1d61ad475a..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingNodeRadiusParameterProperty.h
	+++ /dev/null
	@@ -1,95 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_CONNECTOMICS_RENDERING_NODE_RADIUS_PARAMETER_PROPERTY__H_
	-#define _MITK_CONNECTOMICS_RENDERING_NODE_RADIUS_PARAMETER_PROPERTY__H_
	-
	-#include "mitkEnumerationProperty.h"
	-#include <MitkConnectomicsExports.h>
	-
	-namespace mitk
	-{
	-
	-#ifdef _MSC_VER
	-# pragma warning(push)
	-# pragma warning(disable: 4522)
	-#endif
	-
	-/**
	- * Encapsulates the enumeration of different rendering schemes for connectomics networks
	- */
	-class MITKCONNECTOMICS_EXPORT ConnectomicsRenderingNodeRadiusParameterProperty : public EnumerationProperty
	-{
	-public:
	-
	- mitkClassMacro( ConnectomicsRenderingNodeRadiusParameterProperty, EnumerationProperty );
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- mitkNewMacro1Param(ConnectomicsRenderingNodeRadiusParameterProperty, const IdType&);
	-
	- mitkNewMacro1Param(ConnectomicsRenderingNodeRadiusParameterProperty, const std::string&);
	-
	- using BaseProperty::operator=;
	-
	-protected:
	-
	- /**
	- * Constructor. Sets the representation to a default value of 0
	- */
	- ConnectomicsRenderingNodeRadiusParameterProperty( );
	-
	- /**
	- * Constructor. Sets the parameter to the given value. If it is not
	- * valid, the value is set to 0
	- * @param value the integer representation of the parameter
	- */
	- ConnectomicsRenderingNodeRadiusParameterProperty( const IdType& value );
	-
	- /**
	- * Constructor. Sets the parameter to the given value. If it is not
	- * valid, the value is set to 0
	- * @param value the string representation of the parameter
	- */
	- ConnectomicsRenderingNodeRadiusParameterProperty( const std::string& value );
	-
	- /**
	- * this function is overridden as protected, so that the user may not add
	- * additional enumerations.
	- */
	- bool AddEnum( const std::string& name, const IdType& id ) override;
	-
	- /**
	- * Adds the enumeration types as defined by vtk to the list of known
	- * enumeration values.
	- */
	- virtual void AddRenderingNodeRadiusParameters();
	-
	-private:
	-
	- // purposely not implemented
	- ConnectomicsRenderingNodeRadiusParameterProperty(const ConnectomicsRenderingNodeRadiusParameterProperty&);
	- ConnectomicsRenderingNodeRadiusParameterProperty& operator=(const ConnectomicsRenderingNodeRadiusParameterProperty&);
	-};
	-
	-#ifdef _MSC_VER
	-# pragma warning(pop)
	-#endif
	-
	-} // end of namespace mitk
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingNodeThresholdParameterProperty.cpp b/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingNodeThresholdParameterProperty.cpp
	deleted file mode 100644
	index 0fbb89f439..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingNodeThresholdParameterProperty.cpp
	+++ /dev/null
	@@ -1,70 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkConnectomicsRenderingNodeThresholdParameterProperty.h"
	-#include "mitkConnectomicsRenderingProperties.h"
	-
	-#define NODE_THRESHOLD_DEGREE 0
	-#define NODE_THRESHOLD_BETWEENNESS 1
	-#define NODE_THRESHOLD_CLUSTERING 2
	-
	-mitk::ConnectomicsRenderingNodeThresholdParameterProperty::ConnectomicsRenderingNodeThresholdParameterProperty( )
	-{
	- AddRenderingNodeThresholdParameters();
	- SetValue( NODE_THRESHOLD_DEGREE );
	-}
	-
	-
	-mitk::ConnectomicsRenderingNodeThresholdParameterProperty::ConnectomicsRenderingNodeThresholdParameterProperty( const IdType& value )
	-{
	- AddRenderingNodeThresholdParameters();
	- if ( IsValidEnumerationValue( value ) )
	- {
	- SetValue( value ) ;
	- }
	- else
	- {
	- SetValue( NODE_THRESHOLD_DEGREE );
	- }
	-}
	-
	-mitk::ConnectomicsRenderingNodeThresholdParameterProperty::ConnectomicsRenderingNodeThresholdParameterProperty( const std::string& value )
	-{
	- AddRenderingNodeThresholdParameters();
	- if ( IsValidEnumerationValue( value ) )
	- {
	- SetValue( value );
	- }
	- else
	- {
	- SetValue( NODE_THRESHOLD_DEGREE );
	- }
	-}
	-
	-
	-
	-void mitk::ConnectomicsRenderingNodeThresholdParameterProperty::AddRenderingNodeThresholdParameters()
	-{
	- AddEnum( connectomicsRenderingNodeParameterDegree , NODE_THRESHOLD_DEGREE );
	- AddEnum( connectomicsRenderingNodeParameterBetweenness , NODE_THRESHOLD_BETWEENNESS );
	- AddEnum( connectomicsRenderingNodeParameterClustering , NODE_THRESHOLD_CLUSTERING );
	-}
	-
	-
	-bool mitk::ConnectomicsRenderingNodeThresholdParameterProperty::AddEnum( const std::string& name, const IdType& id )
	-{
	- return Superclass::AddEnum( name, id );
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingNodeThresholdParameterProperty.h b/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingNodeThresholdParameterProperty.h
	deleted file mode 100644
	index 680cf68993..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingNodeThresholdParameterProperty.h
	+++ /dev/null
	@@ -1,95 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_CONNECTOMICS_RENDERING_NODE_THRESHOLD_PARAMETER_PROPERTY__H_
	-#define _MITK_CONNECTOMICS_RENDERING_NODE_THRESHOLD_PARAMETER_PROPERTY__H_
	-
	-#include "mitkEnumerationProperty.h"
	-#include <MitkConnectomicsExports.h>
	-
	-namespace mitk
	-{
	-
	-#ifdef _MSC_VER
	-# pragma warning(push)
	-# pragma warning(disable: 4522)
	-#endif
	-
	-/**
	- * Encapsulates the enumeration of different rendering schemes for connectomics networks
	- */
	-class MITKCONNECTOMICS_EXPORT ConnectomicsRenderingNodeThresholdParameterProperty : public EnumerationProperty
	-{
	-public:
	-
	- mitkClassMacro( ConnectomicsRenderingNodeThresholdParameterProperty, EnumerationProperty );
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- mitkNewMacro1Param(ConnectomicsRenderingNodeThresholdParameterProperty, const IdType&);
	-
	- mitkNewMacro1Param(ConnectomicsRenderingNodeThresholdParameterProperty, const std::string&);
	-
	- using BaseProperty::operator=;
	-
	-protected:
	-
	- /**
	- * Constructor. Sets the representation to a default value of 0
	- */
	- ConnectomicsRenderingNodeThresholdParameterProperty( );
	-
	- /**
	- * Constructor. Sets the parameter to the given value. If it is not
	- * valid, the value is set to 0
	- * @param value the integer representation of the parameter
	- */
	- ConnectomicsRenderingNodeThresholdParameterProperty( const IdType& value );
	-
	- /**
	- * Constructor. Sets the parameter to the given value. If it is not
	- * valid, the value is set to 0
	- * @param value the string representation of the parameter
	- */
	- ConnectomicsRenderingNodeThresholdParameterProperty( const std::string& value );
	-
	- /**
	- * this function is overridden as protected, so that the user may not add
	- * additional enumerations.
	- */
	- bool AddEnum( const std::string& name, const IdType& id ) override;
	-
	- /**
	- * Adds the enumeration types as defined by vtk to the list of known
	- * enumeration values.
	- */
	- virtual void AddRenderingNodeThresholdParameters();
	-
	-private:
	-
	- // purposely not implemented
	- ConnectomicsRenderingNodeThresholdParameterProperty(const ConnectomicsRenderingNodeThresholdParameterProperty&);
	- ConnectomicsRenderingNodeThresholdParameterProperty& operator=(const ConnectomicsRenderingNodeThresholdParameterProperty&);
	-};
	-
	-#ifdef _MSC_VER
	-# pragma warning(pop)
	-#endif
	-
	-} // end of namespace mitk
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingProperties.h b/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingProperties.h
	deleted file mode 100644
	index ec6b56f716..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingProperties.h
	+++ /dev/null
	@@ -1,338 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef ConnectomicsRenderingProperties_H_HEADER_INCLUDED
	-#define ConnectomicsRenderingProperties_H_HEADER_INCLUDED
	-
	-#include <cstring>
	-#include "mitkProperties.h"
	-#include "mitkStringProperty.h"
	-#include "mitkEnumerationProperty.h"
	-#include "mitkColorProperty.h"
	-
	-namespace mitk {
	-
	- /** \file mitkConnectomicsRenderingProperties.h
	- * \brief This file defines the rendering properties available for connectomics networks in MITK.
	- *
	- * This file collects and explains the properties which can be used to modify the visualisation
	- * of connectomics networks.
	- */
	-
	- // Switching between rendering modes
	- /**
	- * \brief Define the rendering scheme to be used.
	- *
	- * Currently there are two possible rendering schemes in MITK.
	- * <ol>
	- * <li> The VTK Graph Layout
	- * <li> The MITK Connectomics Visualisation - Default
	- * </ol>
	- *
	- * The VTK Graph Layout is faster than the MITK Connectomics Visualisation, but provides less features
	- * and settings.
	- */
	- const std::string connectomicsRenderingSchemePropertyName = "Connectomics.Rendering.Scheme";
	-
	- /**
	- * \brief Much faster but less features.
	- */
	- const std::string connectomicsRenderingVTKScheme = "VTK Graph Layout";
	-
	- /**
	- * \brief Slower but with several visualisation options.
	- */
	- const std::string connectomicsRenderingMITKScheme = "MITK Connectomics Visualisation";
	-
	- // All options below are only for the MITK Connectomics Visualisation scheme
	-
	- ////////////////////////////////////////
	- // Filtering Options
	- ////////////////////////////////////////
	-
	- /** \brief Edge filter option
	- *
	- * This option controls the filtering of edges for visualization purposes. Edges filtered out will not be shown, but still included in calculations.
	- *
	- * Currently there these options:
	- * <ol>
	- * <li> No Edge Filtering - Default
	- * <li> Shortest Path to Node
	- * <li> Thresholding
	- * </ol>
	- *
	- */
	- const std::string connectomicsRenderingEdgeFilteringPropertyName = "Connectomics.Rendering.Edges.Filtering";
	-
	- /**
	- * \brief Do not filter edges
	- */
	- const std::string connectomicsRenderingEdgeNoFilter = "No Edge Filtering";
	-
	- /**
	- * \brief Only show edges which are part of a shortest path to the selected node from any other node
	- */
	- const std::string connectomicsRenderingEdgeShortestPathFilter = "Shortest Path to Node";
	-
	- /**
	- * \brief Show only edges above a certain parameter threshold
	- */
	- const std::string connectomicsRenderingEdgeThresholdFilter = "Thresholding";
	-
	- /**
	- * \brief Parameter to be thresholded
	- */
	- const std::string connectomicsRenderingEdgeThresholdFilterParameterName = "Connectomics.Rendering.Edges.Filtering.ThresholdParameter";
	-
	- /**
	- * \brief Threshold
	- */
	- const std::string connectomicsRenderingEdgeThresholdFilterThresholdName = "Connectomics.Rendering.Edges.Filtering.Threshold";
	-
	- /** \brief Node filter option
	- *
	- * This option controls the filtering of nodes for visualization purposes. Nodes filtered out will not be shown, but still included in calculations.
	- *
	- * Currently there these options:
	- * <ol>
	- * <li> No Node Filtering - Default
	- * <li> Thresholding
	- * </ol>
	- *
	- */
	- const std::string connectomicsRenderingNodeFilteringPropertyName = "Connectomics.Rendering.Nodes.Filtering";
	-
	- /**
	- * \brief Do not filter nodes
	- */
	- const std::string connectomicsRenderingNodeNoFilter = "No Node Filtering";
	-
	- /**
	- * \brief Only show nodes above a certain parameter threshold
	- */
	- const std::string connectomicsRenderingNodeThresholdingFilter = "Thresholding";
	-
	- /**
	- * \brief Parameter to be thresholded
	- */
	- const std::string connectomicsRenderingNodeThresholdFilterParameterName = "Connectomics.Rendering.Nodes.Filtering.ThresholdParameter";
	-
	- /**
	- * \brief Threshold
	- */
	- const std::string connectomicsRenderingNodeThresholdFilterThresholdName = "Connectomics.Rendering.Nodes.Filtering.Threshold";
	-
	- // Default values
	- const mitk::StringProperty::Pointer connectomicsRenderingEdgeThresholdFilterParameterDefault =
	- mitk::StringProperty::New( "" );
	- const mitk::FloatProperty::Pointer connectomicsRenderingEdgeThresholdFilterThresholdDefault =
	- mitk::FloatProperty::New( 1.0 );
	-
	- const mitk::StringProperty::Pointer connectomicsRenderingNodeThresholdFilterParameterDefault =
	- mitk::StringProperty::New( "" );
	- const mitk::FloatProperty::Pointer connectomicsRenderingNodeThresholdFilterThresholdDefault =
	- mitk::FloatProperty::New( 1.0 );
	-
	- ////////////////////////////////////////
	- // Node Options
	- ////////////////////////////////////////
	-
	- // Color gradient
	- /**
	- * \brief Start Color
	- *
	- * The start color that will be used for gradient creation
	- */
	- const std::string connectomicsRenderingNodeGradientStartColorName = "Connectomics.Rendering.Nodes.Gradient.StartColor";
	-
	- /**
	- * \brief End Color
	- *
	- * The end color that will be used for gradient creation
	- */
	- const std::string connectomicsRenderingNodeGradientEndColorName = "Connectomics.Rendering.Nodes.Gradient.EndColor";
	-
	- /**
	- * \brief Color parameter
	- *
	- * This parameter will be used to select the color of the node.
	- */
	- const std::string connectomicsRenderingNodeGradientColorParameterName = "Connectomics.Rendering.Nodes.Gradient.Parameter";
	-
	- /**
	- * \brief The chosen node label
	- *
	- * This node will be used for any visualisation requiring a specific node
	- */
	- const std::string connectomicsRenderingNodeChosenNodeName = "Connectomics.Rendering.Nodes.ChosenNode";
	-
	- // Radius
	- /**
	- * \brief Start Radius
	- *
	- * The start radius that will be used
	- */
	- const std::string connectomicsRenderingNodeRadiusStartName = "Connectomics.Rendering.Nodes.Radius.Start";
	-
	- /**
	- * \brief End Radius
	- *
	- * The end radius that will be used
	- */
	- const std::string connectomicsRenderingNodeRadiusEndName = "Connectomics.Rendering.Nodes.Radius.End";
	-
	- /**
	- * \brief Radius parameter
	- *
	- * This parameter will be used to select the radius of the node.
	- */
	- const std::string connectomicsRenderingNodeRadiusParameterName = "Connectomics.Rendering.Nodes.Radius.Parameter";
	-
	- // Possible parameters
	- /**
	- * \brief Using the node degree as parameter
	- */
	- const std::string connectomicsRenderingNodeParameterDegree = "Degree";
	-
	- /**
	- * \brief Using the node betweenness as parameter
	- */
	- const std::string connectomicsRenderingNodeParameterBetweenness = "Betweenness centrality";
	-
	- /**
	- * \brief Using the node clustering coefficient as parameter
	- */
	- const std::string connectomicsRenderingNodeParameterClustering = "Clustering coefficient";
	-
	- /**
	- * \brief Color nodes by shortest path length to a chosen node
	- */
	- const std::string connectomicsRenderingNodeParameterColoringShortestPath = "Shortest Path Steps";
	-
	- /**
	- * \brief Constant
	- *
	- * The node property will be constant.
	- */
	- const std::string connectomicsRenderingNodeParameterConstant = "Constant";
	-
	- // Default values
	- const mitk::StringProperty::Pointer connectomicsRenderingNodeChosenNodeDefault =
	- mitk::StringProperty::New("");
	-
	- const mitk::ColorProperty::Pointer connectomicsRenderingNodeGradientStartColorDefault =
	- mitk::ColorProperty::New(0.0f, 0.0f, 1.0f);
	- const mitk::ColorProperty::Pointer connectomicsRenderingNodeGradientEndColorDefault =
	- mitk::ColorProperty::New(0.0f, 1.0f, 0.0f);
	-
	- const mitk::FloatProperty::Pointer connectomicsRenderingNodeRadiusStartDefault =
	- mitk::FloatProperty::New( 1.0 );
	- const mitk::FloatProperty::Pointer connectomicsRenderingNodeRadiusEndDefault =
	- mitk::FloatProperty::New( 1.0 );
	-
	- ////////////////////////////////////////
	- // Edge Options
	- ////////////////////////////////////////
	-
	-
	- // Color gradient
	- /**
	- * \brief Start Color
	- *
	- * The start color that will be used for gradient creation
	- */
	- const std::string connectomicsRenderingEdgeGradientStartColorName = "Connectomics.Rendering.Edges.Gradient.StartColor";
	-
	- /**
	- * \brief End Color
	- *
	- * The end color that will be used for gradient creation
	- */
	- const std::string connectomicsRenderingEdgeGradientEndColorName = "Connectomics.Rendering.Edges.Gradient.EndColor";
	-
	- /**
	- * \brief Color parameter
	- *
	- * This parameter will be used to select the color of the edge.
	- */
	- const std::string connectomicsRenderingEdgeGradientColorParameterName = "Connectomics.Rendering.Edges.Gradient.Parameter";
	-
	- // Radius
	- /**
	- * \brief Start Radius
	- *
	- * The start radius that will be used
	- */
	- const std::string connectomicsRenderingEdgeRadiusStartName = "Connectomics.Rendering.Edges.Radius.Start";
	-
	- /**
	- * \brief End Radius
	- *
	- * The end radius that will be used
	- */
	- const std::string connectomicsRenderingEdgeRadiusEndName = "Connectomics.Rendering.Edges.Radius.End";
	-
	- /**
	- * \brief Radius parameter
	- *
	- * This parameter will be used to select the radius of the edge.
	- */
	- const std::string connectomicsRenderingEdgeRadiusParameterName = "Connectomics.Rendering.Edges.Radius.Parameter";
	-
	- // Possible parameters
	- /**
	- * \brief Using the weight as parameter
	- */
	- const std::string connectomicsRenderingEdgeParameterWeight = "Weight";
	-
	- /**
	- * \brief Using the edge centrality as parameter
	- */
	- const std::string connectomicsRenderingEdgeParameterCentrality = "Edge betweenness centrality";
	-
	- /**
	- * \brief Constant
	- *
	- * The edge property will be constant.
	- */
	- const std::string connectomicsRenderingEdgeParameterConstant = "Constant";
	-
	- // Default values
	- const mitk::ColorProperty::Pointer connectomicsRenderingEdgeGradientStartColorDefault =
	- mitk::ColorProperty::New(0.8f, 0.0f, 0.6f);
	- const mitk::ColorProperty::Pointer connectomicsRenderingEdgeGradientEndColorDefault =
	- mitk::ColorProperty::New(0.0f, 0.8f, 0.2f);
	-
	- const mitk::FloatProperty::Pointer connectomicsRenderingEdgeRadiusStartDefault =
	- mitk::FloatProperty::New( 0.1 );
	- const mitk::FloatProperty::Pointer connectomicsRenderingEdgeRadiusEndDefault =
	- mitk::FloatProperty::New( 0.4 );
	-
	- /**
	- * \brief Balloon controls and content
	- */
	- const std::string connectomicsRenderingBalloonTextName =
	- "Connectomics.Rendering.Balloon.Text";
	- const std::string connectomicsRenderingBalloonAllNodeLabelsName =
	- "Connectomics.Rendering.Balloon.AllNodeLabels";
	- const std::string connectomicsRenderingBalloonNodeStatsName =
	- "Connectomics.Rendering.Balloon.NodeStats";
	-
	-} // namespace mitk
	-
	-
	-#endif /* ConnectomicsRenderingProperties_H_HEADER_INCLUDED */
	diff --git a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingSchemeProperty.cpp b/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingSchemeProperty.cpp
	deleted file mode 100644
	index 988fb32bd1..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingSchemeProperty.cpp
	+++ /dev/null
	@@ -1,68 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkConnectomicsRenderingSchemeProperty.h"
	-#include "mitkConnectomicsRenderingProperties.h"
	-
	-#define MITK_SCHEME 0
	-#define VTK_SCHEME 1
	-
	-mitk::ConnectomicsRenderingSchemeProperty::ConnectomicsRenderingSchemeProperty( )
	-{
	- AddRenderingSchemes();
	- SetValue( MITK_SCHEME );
	-}
	-
	-
	-mitk::ConnectomicsRenderingSchemeProperty::ConnectomicsRenderingSchemeProperty( const IdType& value )
	-{
	- AddRenderingSchemes();
	- if ( IsValidEnumerationValue( value ) )
	- {
	- SetValue( value ) ;
	- }
	- else
	- {
	- SetValue( MITK_SCHEME );
	- }
	-}
	-
	-mitk::ConnectomicsRenderingSchemeProperty::ConnectomicsRenderingSchemeProperty( const std::string& value )
	-{
	- AddRenderingSchemes();
	- if ( IsValidEnumerationValue( value ) )
	- {
	- SetValue( value );
	- }
	- else
	- {
	- SetValue( MITK_SCHEME );
	- }
	-}
	-
	-
	-
	-void mitk::ConnectomicsRenderingSchemeProperty::AddRenderingSchemes()
	-{
	- AddEnum( connectomicsRenderingMITKScheme, MITK_SCHEME );
	- AddEnum( connectomicsRenderingVTKScheme, VTK_SCHEME );
	-}
	-
	-
	-bool mitk::ConnectomicsRenderingSchemeProperty::AddEnum( const std::string& name, const IdType& id )
	-{
	- return Superclass::AddEnum( name, id );
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingSchemeProperty.h b/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingSchemeProperty.h
	deleted file mode 100644
	index 723d879a50..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Rendering/mitkConnectomicsRenderingSchemeProperty.h
	+++ /dev/null
	@@ -1,95 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_CONNECTOMICS_RENDERING_SCHEME_PROPERTY__H_
	-#define _MITK_CONNECTOMICS_RENDERING_SCHEME_PROPERTY__H_
	-
	-#include "mitkEnumerationProperty.h"
	-#include <MitkConnectomicsExports.h>
	-
	-namespace mitk
	-{
	-
	-#ifdef _MSC_VER
	-# pragma warning(push)
	-# pragma warning(disable: 4522)
	-#endif
	-
	-/**
	- * Encapsulates the enumeration of different rendering schemes for connectomics networks
	- */
	-class MITKCONNECTOMICS_EXPORT ConnectomicsRenderingSchemeProperty : public EnumerationProperty
	-{
	-public:
	-
	- mitkClassMacro( ConnectomicsRenderingSchemeProperty, EnumerationProperty );
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- mitkNewMacro1Param(ConnectomicsRenderingSchemeProperty, const IdType&);
	-
	- mitkNewMacro1Param(ConnectomicsRenderingSchemeProperty, const std::string&);
	-
	- using BaseProperty::operator=;
	-
	-protected:
	-
	- /**
	- * Constructor. Sets the representation to a default value of 0
	- */
	- ConnectomicsRenderingSchemeProperty( );
	-
	- /**
	- * Constructor. Sets the scheme to the given value. If it is not
	- * valid, the value is set to 0
	- * @param value the integer representation of the scheme
	- */
	- ConnectomicsRenderingSchemeProperty( const IdType& value );
	-
	- /**
	- * Constructor. Sets the scheme to the given value. If it is not
	- * valid, the value is set to 0
	- * @param value the string representation of the scheme
	- */
	- ConnectomicsRenderingSchemeProperty( const std::string& value );
	-
	- /**
	- * this function is overridden as protected, so that the user may not add
	- * additional enumerations.
	- */
	- bool AddEnum( const std::string& name, const IdType& id ) override;
	-
	- /**
	- * Adds the enumeration types as defined by vtk to the list of known
	- * enumeration values.
	- */
	- virtual void AddRenderingSchemes();
	-
	-private:
	-
	- // purposely not implemented
	- ConnectomicsRenderingSchemeProperty(const ConnectomicsRenderingSchemeProperty&);
	- ConnectomicsRenderingSchemeProperty& operator=(const ConnectomicsRenderingSchemeProperty&);
	-};
	-
	-#ifdef _MSC_VER
	-# pragma warning(pop)
	-#endif
	-
	-} // end of namespace mitk
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/Connectomics/Testing/CMakeLists.txt b/Modules/DiffusionImaging/Connectomics/Testing/CMakeLists.txt
	deleted file mode 100644
	index 153cd81e2e..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Testing/CMakeLists.txt
	+++ /dev/null
	@@ -1 +0,0 @@
	-MITK_CREATE_MODULE_TESTS()
	diff --git a/Modules/DiffusionImaging/Connectomics/Testing/files.cmake b/Modules/DiffusionImaging/Connectomics/Testing/files.cmake
	deleted file mode 100644
	index 150b651c4b..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Testing/files.cmake
	+++ /dev/null
	@@ -1,9 +0,0 @@
	-set(MODULE_TESTS
	- mitkConnectomicsNetworkTest.cpp
	- mitkConnectomicsNetworkCreationTest.cpp
	- mitkConnectomicsStatisticsCalculatorTest.cpp
	- mitkCorrelationCalculatorTest.cpp
	-)
	-
	-SET(MODULE_CUSTOM_TESTS
	-)
	diff --git a/Modules/DiffusionImaging/Connectomics/Testing/mitkConnectomicsNetworkCreationTest.cpp b/Modules/DiffusionImaging/Connectomics/Testing/mitkConnectomicsNetworkCreationTest.cpp
	deleted file mode 100644
	index e07ba8b76b..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Testing/mitkConnectomicsNetworkCreationTest.cpp
	+++ /dev/null
	@@ -1,113 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-// Testing
	-#include "mitkTestingMacros.h"
	-#include "mitkTestFixture.h"
	-
	-// std includes
	-#include <string>
	-
	-// MITK includes
	-#include "mitkConnectomicsNetworkCreator.h"
	-#include "mitkIOUtil.h"
	-
	-// VTK includes
	-#include <vtkDebugLeaks.h>
	-
	-class mitkConnectomicsNetworkCreationTestSuite : public mitk::TestFixture
	-{
	- CPPUNIT_TEST_SUITE(mitkConnectomicsNetworkCreationTestSuite);
	-
	- /// \todo Fix VTK memory leaks. Bug 18097.
	- vtkDebugLeaks::SetExitError(0);
	-
	- MITK_TEST(CreateNetworkFromFibersAndParcellation);
	- CPPUNIT_TEST_SUITE_END();
	-
	-private:
	-
	- std::string m_ParcellationPath;
	- std::string m_FiberPath;
	- std::string m_ReferenceNetworkPath;
	-
	-public:
	-
	- /**
	- * @brief Setup Always call this method before each Test-case to ensure correct and new intialization of the used members for a new test case. (If the members are not used in a test, the method does not need to be called).
	- */
	- void setUp() override
	- {
	- m_ReferenceNetworkPath = GetTestDataFilePath("DiffusionImaging/Connectomics/reference.cnf");
	- m_ParcellationPath = GetTestDataFilePath("DiffusionImaging/Connectomics/parcellation.nrrd");
	- m_FiberPath = GetTestDataFilePath("DiffusionImaging/Connectomics/fiberBundle.fib");
	- }
	-
	- void tearDown() override
	- {
	- m_ReferenceNetworkPath = "";
	- m_ParcellationPath = "";
	- m_FiberPath = "";
	- }
	-
	- void CreateNetworkFromFibersAndParcellation()
	- {
	- // load fiber image
	- std::vector<mitk::BaseData::Pointer> fiberInfile = mitk::IOUtil::Load( m_FiberPath );
	- if( fiberInfile.empty() )
	- {
	- std::string errorMessage = "Fiber Image at " + m_FiberPath + " could not be read. Aborting.";
	- CPPUNIT_ASSERT_MESSAGE( errorMessage, false );
	- }
	- mitk::BaseData* fiberBaseData = fiberInfile.at(0);
	- mitk::FiberBundle* fiberBundle = dynamic_cast<mitk::FiberBundle*>( fiberBaseData );
	-
	- // load parcellation
	- std::vector<mitk::BaseData::Pointer> parcellationInFile = mitk::IOUtil::Load( m_ParcellationPath );
	- if( parcellationInFile.empty() )
	- {
	- std::string errorMessage = "Parcellation at " + m_ParcellationPath + " could not be read. Aborting.";
	- CPPUNIT_ASSERT_MESSAGE( errorMessage, false );
	- }
	- mitk::BaseData* parcellationBaseData = parcellationInFile.at(0);
	- mitk::Image* parcellationImage = dynamic_cast<mitk::Image*>( parcellationBaseData );
	-
	- // do creation
	- mitk::ConnectomicsNetworkCreator::Pointer connectomicsNetworkCreator = mitk::ConnectomicsNetworkCreator::New();
	- connectomicsNetworkCreator->SetSegmentation( parcellationImage );
	- connectomicsNetworkCreator->SetFiberBundle( fiberBundle );
	- connectomicsNetworkCreator->CalculateCenterOfMass();
	- connectomicsNetworkCreator->SetEndPointSearchRadius( 15 );
	- connectomicsNetworkCreator->CreateNetworkFromFibersAndSegmentation();
	-
	- // load network
	- std::vector<mitk::BaseData::Pointer> referenceFile = mitk::IOUtil::Load( m_ReferenceNetworkPath );
	- if( referenceFile.empty() )
	- {
	- std::string errorMessage = "Reference Network at " + m_ReferenceNetworkPath + " could not be read. Aborting.";
	- CPPUNIT_ASSERT_MESSAGE( errorMessage, false );
	- }
	- mitk::BaseData* referenceBaseData = referenceFile.at(0);
	- mitk::ConnectomicsNetwork* referenceNetwork = dynamic_cast<mitk::ConnectomicsNetwork*>( referenceBaseData );
	-
	- mitk::ConnectomicsNetwork::Pointer network = connectomicsNetworkCreator->GetNetwork();
	-
	- CPPUNIT_ASSERT_MESSAGE( "Comparing created and reference network.", mitk::Equal( network.GetPointer(), referenceNetwork, mitk::eps, true) );
	-
	- }
	-};
	-
	-MITK_TEST_SUITE_REGISTRATION(mitkConnectomicsNetworkCreation)
	diff --git a/Modules/DiffusionImaging/Connectomics/Testing/mitkConnectomicsNetworkTest.cpp b/Modules/DiffusionImaging/Connectomics/Testing/mitkConnectomicsNetworkTest.cpp
	deleted file mode 100644
	index 480635edc5..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Testing/mitkConnectomicsNetworkTest.cpp
	+++ /dev/null
	@@ -1,530 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkTestingMacros.h"
	-
	-#include "mitkConnectomicsNetwork.h"
	-#include "mitkConnectomicsSyntheticNetworkGenerator.h"
	-#include "mitkConnectomicsSimulatedAnnealingManager.h"
	-#include "mitkConnectomicsSimulatedAnnealingPermutationModularity.h"
	-#include "mitkConnectomicsSimulatedAnnealingCostFunctionModularity.h"
	-
	-#include <vtkDebugLeaks.h>
	-
	-#include <vector>
	-#include <string>
	-#include <utility>
	-
	-/**Documentation
	-* Test for synthetic connectomics generation and connectomics network functionality
	-*/
	-int mitkConnectomicsNetworkTest(int, char* [])
	-{
	- // Test begins
	- MITK_TEST_BEGIN("mitkConnectomicsNetworkTest");
	-
	- /// \todo Fix VTK memory leaks. Bug 18097.
	- vtkDebugLeaks::SetExitError(0);
	-
	- // Typedefs
	- typedef mitk::ConnectomicsNetwork::VertexDescriptorType VertexType;
	- typedef mitk::ConnectomicsNetwork::NetworkNode NodeType;
	-
	- // The test network
	-
	- std::vector< NodeType > inNodes;
	-
	- NodeType node;
	-
	- node.id = 0;
	- node.label = "1-1";
	- node.coordinates.clear();
	- node.coordinates.push_back( 0 );
	- node.coordinates.push_back( 0 );
	- node.coordinates.push_back( 0 );
	- inNodes.push_back(node);
	-
	- node.id = 1;
	- node.label = "2-1";
	- node.coordinates.clear();
	- node.coordinates.push_back( 10 );
	- node.coordinates.push_back( 0 );
	- node.coordinates.push_back( 0 );
	- inNodes.push_back(node);
	-
	- node.id = 2;
	- node.label = "3-1";
	- node.coordinates.clear();
	- node.coordinates.push_back( 20 );
	- node.coordinates.push_back( 10 );
	- node.coordinates.push_back( 0 );
	- inNodes.push_back(node);
	-
	- node.id = 3;
	- node.label = "4-1";
	- node.coordinates.clear();
	- node.coordinates.push_back( 30 );
	- node.coordinates.push_back( 20 );
	- node.coordinates.push_back( 0 );
	- inNodes.push_back(node);
	-
	- node.id = 4;
	- node.label = "5-1";
	- node.coordinates.clear();
	- node.coordinates.push_back( 40 );
	- node.coordinates.push_back( 50 );
	- node.coordinates.push_back( 0 );
	- inNodes.push_back(node);
	-
	- node.id = 5;
	- node.label = "6-2";
	- node.coordinates.clear();
	- node.coordinates.push_back( 0 );
	- node.coordinates.push_back( 0 );
	- node.coordinates.push_back( 10 );
	- inNodes.push_back(node);
	-
	- node.id = 6;
	- node.label = "7-2";
	- node.coordinates.clear();
	- node.coordinates.push_back( 0 );
	- node.coordinates.push_back( 10 );
	- node.coordinates.push_back( 20 );
	- inNodes.push_back(node);
	-
	- node.id = 7;
	- node.label = "8-2";
	- node.coordinates.clear();
	- node.coordinates.push_back( 0 );
	- node.coordinates.push_back( 20 );
	- node.coordinates.push_back( 30 );
	- inNodes.push_back(node);
	-
	- node.id = 8;
	- node.label = "9-2";
	- node.coordinates.clear();
	- node.coordinates.push_back( 0 );
	- node.coordinates.push_back( 30 );
	- node.coordinates.push_back( 40 );
	- inNodes.push_back(node);
	-
	- node.id = 9;
	- node.label = "10-3";
	- node.coordinates.clear();
	- node.coordinates.push_back( 20 );
	- node.coordinates.push_back( 0 );
	- node.coordinates.push_back( 10 );
	- inNodes.push_back(node);
	-
	- node.id = 10;
	- node.label = "11-3";
	- node.coordinates.clear();
	- node.coordinates.push_back( 30 );
	- node.coordinates.push_back( 0 );
	- node.coordinates.push_back( 20 );
	- inNodes.push_back(node);
	-
	- node.id = 11;
	- node.label = "12-3";
	- node.coordinates.clear();
	- node.coordinates.push_back( 40 );
	- node.coordinates.push_back( 0 );
	- node.coordinates.push_back( 30 );
	- inNodes.push_back(node);
	-
	- std::vector< mitk::ConnectomicsNetwork::NetworkEdge > inEdges;
	-
	- mitk::ConnectomicsNetwork::NetworkEdge edge;
	-
	- edge.sourceId = 0;
	- edge.targetId = 1;
	- edge.fiber_count = 2;
	- inEdges.push_back( edge );
	-
	- edge.sourceId = 0;
	- edge.targetId = 2;
	- edge.fiber_count = 2;
	- inEdges.push_back( edge );
	-
	- edge.sourceId = 0;
	- edge.targetId = 4;
	- edge.fiber_count = 2;
	- inEdges.push_back( edge );
	-
	- edge.sourceId = 1;
	- edge.targetId = 4;
	- edge.fiber_count = 2;
	- inEdges.push_back( edge );
	-
	- edge.sourceId = 1;
	- edge.targetId = 3;
	- edge.fiber_count = 2;
	- inEdges.push_back( edge );
	-
	- edge.sourceId = 2;
	- edge.targetId = 3;
	- edge.fiber_count = 2;
	- inEdges.push_back( edge );
	-
	- edge.sourceId = 3;
	- edge.targetId = 4;
	- edge.fiber_count = 2;
	- inEdges.push_back( edge );
	-
	- edge.sourceId = 4;
	- edge.targetId = 5;
	- edge.fiber_count = 2;
	- inEdges.push_back( edge );
	-
	- edge.sourceId = 5;
	- edge.targetId = 6;
	- edge.fiber_count = 2;
	- inEdges.push_back( edge );
	-
	- edge.sourceId = 5;
	- edge.targetId = 7;
	- edge.fiber_count = 2;
	- inEdges.push_back( edge );
	-
	- edge.sourceId = 5;
	- edge.targetId = 8;
	- edge.fiber_count = 2;
	- inEdges.push_back( edge );
	-
	- edge.sourceId = 7;
	- edge.targetId = 8;
	- edge.fiber_count = 2;
	- inEdges.push_back( edge );
	-
	- edge.sourceId = 6;
	- edge.targetId = 8;
	- edge.fiber_count = 2;
	- inEdges.push_back( edge );
	-
	- edge.sourceId = 6;
	- edge.targetId = 9;
	- edge.fiber_count = 2;
	- inEdges.push_back( edge );
	-
	- edge.sourceId = 3;
	- edge.targetId = 10;
	- edge.fiber_count = 2;
	- inEdges.push_back( edge );
	-
	- edge.sourceId = 9;
	- edge.targetId = 10;
	- edge.fiber_count = 2;
	- inEdges.push_back( edge );
	-
	- edge.sourceId = 10;
	- edge.targetId = 11;
	- edge.fiber_count = 2;
	- inEdges.push_back( edge );
	-
	- edge.sourceId = 9;
	- edge.targetId = 11;
	- edge.fiber_count = 2;
	- inEdges.push_back( edge );
	-
	- // further variables
	-
	- double eps(0.001);
	-
	- try
	- {
	- // Testing synthetic network generation
	- mitk::ConnectomicsSyntheticNetworkGenerator::Pointer generator = mitk::ConnectomicsSyntheticNetworkGenerator::New();
	- MITK_TEST_CONDITION_REQUIRED(generator.IsNotNull(),"Synthetic network generator has been instantiated")
	-
	- // first and second parameter
	- std::vector< std::pair<int, double> > parameterVector;
	- // name and isRandom
	- std::vector< std::pair<std::string, bool> > messageVector;
	- // order of results is # vertices, # edges, # self loops, average degree, connection density
	- // global clustering coefficient
	- std::vector< std::vector< double > > resultVector;
	-
	- int numberOfOptions = 3;
	-
	- parameterVector.resize(numberOfOptions);
	- messageVector.resize(numberOfOptions);
	- resultVector.resize(numberOfOptions);
	-
	- // Create regular lattice network in the form of a cube with sidelength 5 and distance 10 between nodes
	- parameterVector[0] = std::pair< int, double>(5, 10);
	- messageVector[0] = std::pair<std::string, bool>("Regular Lattice Network", false);
	- resultVector[0].push_back( 5 * 5 * 5 );
	- resultVector[0].push_back( 300 );
	- resultVector[0].push_back( 0 );
	- resultVector[0].push_back( 4.8 );
	- resultVector[0].push_back(0.0387);
	- resultVector[0].push_back(0);
	-
	- // Create a heterogeneous sphere network with 1 central node and 49 nodes on the surface and radius 10
	- parameterVector[1] = std::pair< int, double>(50, 10);
	- messageVector[1] = std::pair<std::string, bool>("Heterogeneous Sphere Network", false);
	- resultVector[1].push_back( 50 );
	- resultVector[1].push_back( 49 );
	- resultVector[1].push_back( 0 );
	- resultVector[1].push_back( 1.96 );
	- resultVector[1].push_back(0.0400);
	- resultVector[1].push_back(0);
	-
	- // Create random network with 50 nodes and edges between them generated with a 0.1 likelihood
	- parameterVector[2] = std::pair< int, double>(50, 0.1);
	- messageVector[2] = std::pair<std::string, bool>("Random Network", true);
	- resultVector[2].push_back( 50 );
	-
	- for(int loop(0); loop < numberOfOptions; loop++)
	- {
	- mitk::ConnectomicsNetwork::Pointer network =
	- generator->CreateSyntheticNetwork(loop, parameterVector[loop].first, parameterVector[loop].second);
	- bool generationWorked = generator->WasGenerationSuccessfull() && network.IsNotNull();
	-
	- std::string message = messageVector[loop].first + " has been instantiated";
	- MITK_TEST_CONDITION_REQUIRED(generationWorked,message)
	-
	- bool verticesCloseEnough( std::abs(resultVector[loop][0] - network->GetNumberOfVertices()) < eps);
	- MITK_TEST_CONDITION_REQUIRED( verticesCloseEnough, "Expected number of vertices")
	-
	- if(!messageVector[loop].second)
	- {
	- bool edgesCloseEnough( std::abs(resultVector[loop][1] - network->GetNumberOfEdges()) < eps);
	- MITK_TEST_CONDITION_REQUIRED( edgesCloseEnough, "Expected number of edges")
	-
	- bool selfLoopsCloseEnough( std::abs(resultVector[loop][2] - network->GetNumberOfSelfLoops()) < eps);
	- MITK_TEST_CONDITION_REQUIRED( selfLoopsCloseEnough, "Expected number of self loops")
	-
	- bool avDegCloseEnough( std::abs(resultVector[loop][3] - network->GetAverageDegree()) < eps);
	- MITK_TEST_CONDITION_REQUIRED( avDegCloseEnough, "Expected average degree")
	-
	- bool conDensCloseEnough( std::abs(resultVector[loop][4] - network->GetConnectionDensity()) < eps);
	- MITK_TEST_CONDITION_REQUIRED( conDensCloseEnough, "Expected connection density")
	-
	- bool clustCoeffCloseEnough( std::abs(resultVector[loop][5] - network->GetGlobalClusteringCoefficient()) < eps);
	- MITK_TEST_CONDITION_REQUIRED( clustCoeffCloseEnough, "Expected global clustering coefficient")
	- }
	- }
	- }
	- catch (...)
	- {
	- MITK_ERROR << "Unhandled exception caught while testing synthetic network generation [FAILED]" ;
	- return EXIT_FAILURE;
	- }
	-
	- try
	- {
	- // Testing network interface
	-
	- // Create network
	-
	- mitk::ConnectomicsNetwork::Pointer network = mitk::ConnectomicsNetwork::New();
	-
	- std::vector< VertexType > vertexVector;
	- vertexVector.resize( inNodes.size() );
	-
	- for(unsigned int loop(0); loop < inNodes.size(); loop++)
	- {
	- VertexType newVertex = network->AddVertex( inNodes[loop].id );
	- vertexVector[ inNodes[loop].id ] = newVertex;
	- network->SetLabel( newVertex, inNodes[loop].label );
	- network->SetCoordinates( newVertex, inNodes[loop].coordinates );
	- }
	-
	- for(unsigned int loop(0); loop < inEdges.size(); loop++)
	- {
	- int sourceId = inEdges[loop].sourceId;
	- int targetId = inEdges[loop].targetId;
	- VertexType sourceVertex = vertexVector[ sourceId ];
	- VertexType targetVertex = vertexVector[ targetId ];
	-
	- // there are two methods to add nodes
	- if( loop % 2 == 0 )
	- {
	- network->AddEdge(sourceVertex, targetVertex, 1);
	- for( int remaining( inEdges[loop].fiber_count ); remaining > 1; remaining-- )
	- {
	- network->IncreaseEdgeWeight( sourceVertex, targetVertex, 1 );
	- }
	- }
	- else
	- {
	- network->AddEdge(sourceVertex, targetVertex, sourceId, targetId, inEdges[loop].fiber_count );
	- }
	- }
	-
	- // Test whether network parameters are as expected
	- MITK_TEST_CONDITION_REQUIRED( inNodes.size() == (unsigned int)network->GetNumberOfVertices(), "Expected number of vertices")
	-
	- MITK_TEST_CONDITION_REQUIRED( inEdges.size() == (unsigned int)network->GetNumberOfEdges(), "Expected number of edges")
	-
	- MITK_TEST_CONDITION_REQUIRED( 0 == network->GetNumberOfSelfLoops(), "Expected number of self loops")
	-
	- bool avDegCloseEnough( std::abs(3 - network->GetAverageDegree()) < eps);
	- MITK_TEST_CONDITION_REQUIRED( avDegCloseEnough, "Expected average degree")
	-
	- bool conDensCloseEnough( std::abs(0.2727 - network->GetConnectionDensity()) < eps);
	- MITK_TEST_CONDITION_REQUIRED( conDensCloseEnough, "Expected connection density")
	-
	- bool clustCoeffCloseEnough( std::abs(0.4583 - network->GetGlobalClusteringCoefficient()) < eps);
	- MITK_TEST_CONDITION_REQUIRED( clustCoeffCloseEnough, "Expected global clustering coefficient")
	-
	- MITK_TEST_CONDITION_REQUIRED( network->GetMaximumWeight() == 2, "Expected maximum weight")
	-
	- MITK_TEST_CONDITION_REQUIRED( network->GetVectorOfAllVertexDescriptors().size() == vertexVector.size(), "Expected number of vertex descriptors")
	- }
	- catch (...)
	- {
	- MITK_ERROR << "Unhandled exception caught while testing network interface [FAILED]" ;
	- return EXIT_FAILURE;
	- }
	-
	- try
	- {
	- // Testing modularity calculation
	-
	- typedef std::map< VertexType, int > ToModuleMapType;
	-
	- // Create network
	-
	- mitk::ConnectomicsNetwork::Pointer network = mitk::ConnectomicsNetwork::New();
	-
	- std::vector< VertexType > vertexVector;
	- vertexVector.resize( inNodes.size() );
	-
	- for(unsigned int loop(0); loop < inNodes.size(); loop++)
	- {
	- VertexType newVertex = network->AddVertex( inNodes[loop].id );
	- vertexVector[ inNodes[loop].id ] = newVertex;
	- network->SetLabel( newVertex, inNodes[loop].label );
	- network->SetCoordinates( newVertex, inNodes[loop].coordinates );
	- }
	-
	- for(unsigned int loop(0); loop < inEdges.size(); loop++)
	- {
	- int sourceId = inEdges[loop].sourceId;
	- int targetId = inEdges[loop].targetId;
	- VertexType sourceVertex = vertexVector[ sourceId ];
	- VertexType targetVertex = vertexVector[ targetId ];
	-
	- // there are two methods to add nodes
	- if( loop % 2 == 0 )
	- {
	- network->AddEdge(sourceVertex, targetVertex, 1);
	- for( int remaining( inEdges[loop].fiber_count ); remaining > 1; remaining-- )
	- {
	- network->IncreaseEdgeWeight( sourceVertex, targetVertex, 1 );
	- }
	- }
	- else
	- {
	- network->AddEdge(sourceVertex, targetVertex, sourceId, targetId, inEdges[loop].fiber_count );
	- }
	- }
	-
	- // Simulated annealing classes
	- mitk::ConnectomicsSimulatedAnnealingManager::Pointer manager = mitk::ConnectomicsSimulatedAnnealingManager::New();
	- mitk::ConnectomicsSimulatedAnnealingPermutationModularity::Pointer permutation = mitk::ConnectomicsSimulatedAnnealingPermutationModularity::New();
	- mitk::ConnectomicsSimulatedAnnealingCostFunctionModularity::Pointer costFunction = mitk::ConnectomicsSimulatedAnnealingCostFunctionModularity::New();
	-
	- // Test whether modularity calculation behaves as expected
	-
	- ToModuleMapType threeModuleSolution;
	- std::vector< VertexType > vertexInVector = network->GetVectorOfAllVertexDescriptors();
	-
	- threeModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 0 ], 0 ) );
	- threeModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 1 ], 0 ) );
	- threeModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 2 ], 0 ) );
	- threeModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 3 ], 0 ) );
	- threeModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 4 ], 0 ) );
	- threeModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 5 ], 1 ) );
	- threeModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 6 ], 1 ) );
	- threeModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 7 ], 1 ) );
	- threeModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 8 ], 1 ) );
	- threeModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 9 ], 2 ) );
	- threeModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 10 ], 2 ) );
	- threeModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 11 ], 2 ) );
	-
	- bool threeModuleModularity( std::abs(0.4753 - costFunction->CalculateModularity( network, &threeModuleSolution )) < eps);
	- MITK_TEST_CONDITION_REQUIRED( threeModuleModularity, "Expected three module modularity")
	-
	- bool correctNumberOfModules( permutation->getNumberOfModules( &threeModuleSolution ) == 3 );
	- MITK_TEST_CONDITION_REQUIRED( correctNumberOfModules, "Expected number of modules")
	-
	- bool correctNumberOfVertices( permutation->getNumberOfVerticesInModule( &threeModuleSolution, 0 ) == 5
	- && permutation->getNumberOfVerticesInModule( &threeModuleSolution, 1 ) == 4
	- && permutation->getNumberOfVerticesInModule( &threeModuleSolution, 2 ) == 3 );
	- MITK_TEST_CONDITION_REQUIRED( correctNumberOfVertices, "Expected number of vertices per module")
	-
	- ToModuleMapType oneModuleSolution;
	- oneModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 0 ], 0 ) );
	- oneModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 1 ], 0 ) );
	- oneModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 2 ], 0 ) );
	- oneModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 3 ], 0 ) );
	- oneModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 4 ], 0 ) );
	- oneModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 5 ], 0 ) );
	- oneModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 6 ], 0 ) );
	- oneModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 7 ], 0 ) );
	- oneModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 8 ], 0 ) );
	- oneModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 9 ], 0 ) );
	- oneModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 10 ], 0 ) );
	- oneModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 11 ], 0 ) );
	-
	- bool oneModuleModularity( std::abs(0.0 - costFunction->CalculateModularity( network, &oneModuleSolution )) < eps);
	- MITK_TEST_CONDITION_REQUIRED( oneModuleModularity, "Expected one module modularity")
	-
	- ToModuleMapType badTwoModuleSolution;
	- badTwoModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 0 ], 0 ) );
	- badTwoModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 1 ], 0 ) );
	- badTwoModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 2 ], 0 ) );
	- badTwoModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 3 ], 0 ) );
	- badTwoModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 4 ], 0 ) );
	- badTwoModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 5 ], 1 ) );
	- badTwoModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 6 ], 1 ) );
	- badTwoModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 7 ], 1 ) );
	- badTwoModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 8 ], 0 ) );
	- badTwoModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 9 ], 1 ) );
	- badTwoModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 10 ], 1 ) );
	- badTwoModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 11 ], 0 ) );
	-
	- bool badTwoModuleModularity( std::abs(0.097222 - costFunction->CalculateModularity( network, &badTwoModuleSolution )) < eps);
	- MITK_TEST_CONDITION_REQUIRED( badTwoModuleModularity, "Expected bad two module modularity")
	-
	- ToModuleMapType noInternalLinksThreeModuleSolution;
	- noInternalLinksThreeModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 0 ], 0 ) );
	- noInternalLinksThreeModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 1 ], 2 ) );
	- noInternalLinksThreeModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 2 ], 1 ) );
	- noInternalLinksThreeModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 3 ], 0 ) );
	- noInternalLinksThreeModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 4 ], 1 ) );
	- noInternalLinksThreeModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 5 ], 2 ) );
	- noInternalLinksThreeModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 6 ], 0 ) );
	- noInternalLinksThreeModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 7 ], 0 ) );
	- noInternalLinksThreeModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 8 ], 1 ) );
	- noInternalLinksThreeModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 9 ], 2 ) );
	- noInternalLinksThreeModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 10 ], 1 ) );
	- noInternalLinksThreeModuleSolution.insert( std::pair<VertexType, int>( vertexInVector[ 11 ], 0 ) );
	-
	- bool noInternalThreeModuleModularity( std::abs(-0.3395 - costFunction->CalculateModularity( network, &noInternalLinksThreeModuleSolution )) < eps);
	- MITK_TEST_CONDITION_REQUIRED( noInternalThreeModuleModularity, "Expected three module modularity containing no internal links")
	- }
	- catch (...)
	- {
	- MITK_ERROR << "Unhandled exception caught while testing modularity calculation [FAILED]" ;
	- return EXIT_FAILURE;
	- }
	- // Test ends
	- MITK_TEST_END();
	-}
	diff --git a/Modules/DiffusionImaging/Connectomics/Testing/mitkConnectomicsStatisticsCalculatorTest.cpp b/Modules/DiffusionImaging/Connectomics/Testing/mitkConnectomicsStatisticsCalculatorTest.cpp
	deleted file mode 100644
	index 6518413a87..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Testing/mitkConnectomicsStatisticsCalculatorTest.cpp
	+++ /dev/null
	@@ -1,141 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-// Testing
	-#include "mitkTestingMacros.h"
	-#include "mitkTestFixture.h"
	-
	-// std includes
	-#include <string>
	-#include <sstream>
	-
	-// MITK includes
	-#include <mitkIOUtil.h>
	-#include <mitkConnectomicsStatisticsCalculator.h>
	-
	-// VTK includes
	-#include <vtkDebugLeaks.h>
	-
	-
	-class mitkConnectomicsStatisticsCalculatorTestSuite : public mitk::TestFixture
	-{
	- CPPUNIT_TEST_SUITE(mitkConnectomicsStatisticsCalculatorTestSuite);
	-
	- /// \todo Fix VTK memory leaks. Bug 18097.
	- vtkDebugLeaks::SetExitError(0);
	-
	- MITK_TEST(StatisticsCalculatorUpdate);
	- CPPUNIT_TEST_SUITE_END();
	-
	-private:
	-
	- mitk::ConnectomicsNetwork::Pointer m_Network;
	- std::string m_NetworkPath;
	-
	-public:
	-
	- /**
	- * @brief Setup Always call this method before each Test-case to ensure correct and new intialization of the used members for a new test case. (If the members are not used in a test, the method does not need to be called).
	- */
	- void setUp() override
	- {
	- //load network
	-
	- m_NetworkPath = GetTestDataFilePath("DiffusionImaging/Connectomics/reference.cnf");
	-
	- std::vector<mitk::BaseData::Pointer> networkFile = mitk::IOUtil::Load( m_NetworkPath );
	- if( networkFile.empty() )
	- {
	- std::string errorMessage = "File at " + m_NetworkPath + " could not be read. Aborting.";
	- CPPUNIT_ASSERT_MESSAGE( errorMessage, !networkFile.empty() );
	- return;
	- }
	- mitk::BaseData* networkBaseData = networkFile.at(0);
	- mitk::ConnectomicsNetwork* network = dynamic_cast<mitk::ConnectomicsNetwork*>( networkBaseData );
	-
	- if( !network )
	- {
	- std::string errorMessage = "Read file at " + m_NetworkPath + " could not be recognized as network. Aborting.";
	- CPPUNIT_ASSERT_MESSAGE( errorMessage, network);
	- return;
	- }
	-
	- m_Network = network;
	- }
	-
	- void tearDown() override
	- {
	- m_Network = nullptr;
	- m_NetworkPath = "";
	- }
	-
	- void StatisticsCalculatorUpdate()
	- {
	- mitk::ConnectomicsStatisticsCalculator::Pointer statisticsCalculator = mitk::ConnectomicsStatisticsCalculator::New();
	-
	- statisticsCalculator->SetNetwork( m_Network );
	- statisticsCalculator->Update();
	-
	- double eps( 0.0001 );
	-
	- CPPUNIT_ASSERT_MESSAGE( "GetNumberOfVertices", mitk::Equal( statisticsCalculator->GetNumberOfVertices( ), 4 , eps, true ) );
	- CPPUNIT_ASSERT_MESSAGE( "GetNumberOfEdges" , mitk::Equal( statisticsCalculator->GetNumberOfEdges( ), 5 , eps, true ) );
	- CPPUNIT_ASSERT_MESSAGE( "GetAverageDegree", mitk::Equal( statisticsCalculator->GetAverageDegree( ), 2.5 , eps, true ) );
	- CPPUNIT_ASSERT_MESSAGE( "GetConnectionDensity", mitk::Equal( statisticsCalculator->GetConnectionDensity( ), 0.833333 , eps, true ) );
	- CPPUNIT_ASSERT_MESSAGE( "GetNumberOfConnectedComponents", mitk::Equal( statisticsCalculator->GetNumberOfConnectedComponents( ), 1 , eps, true ) );
	- CPPUNIT_ASSERT_MESSAGE( "GetAverageComponentSize", mitk::Equal( statisticsCalculator->GetAverageComponentSize( ), 4 , eps, true ) );
	- CPPUNIT_ASSERT_MESSAGE( "GetLargestComponentSize", mitk::Equal( statisticsCalculator->GetLargestComponentSize( ), 4 , eps, true ) );
	- CPPUNIT_ASSERT_MESSAGE( "GetRatioOfNodesInLargestComponent", mitk::Equal( statisticsCalculator->GetRatioOfNodesInLargestComponent( ), 1 , eps, true ) );
	- CPPUNIT_ASSERT_MESSAGE( "GetHopPlotExponent", mitk::Equal( statisticsCalculator->GetHopPlotExponent( ), 0.192645 , eps, true ) );
	- CPPUNIT_ASSERT_MESSAGE( "GetEffectiveHopDiameter", mitk::Equal( statisticsCalculator->GetEffectiveHopDiameter( ), 1 , eps, true ) );
	- CPPUNIT_ASSERT_MESSAGE( "GetAverageClusteringCoefficientsC", mitk::Equal( statisticsCalculator->GetAverageClusteringCoefficientsC( ), 0.833333 , eps, true ) );
	- CPPUNIT_ASSERT_MESSAGE( "GetAverageClusteringCoefficientsD", mitk::Equal( statisticsCalculator->GetAverageClusteringCoefficientsD( ), 0.916667 , eps, true ) );
	- CPPUNIT_ASSERT_MESSAGE( "GetAverageClusteringCoefficientsE", mitk::Equal( statisticsCalculator->GetAverageClusteringCoefficientsE( ), 0.833333 , eps, true ) );
	- CPPUNIT_ASSERT_MESSAGE( "GetAverageVertexBetweennessCentrality", mitk::Equal( statisticsCalculator->GetAverageVertexBetweennessCentrality( ), 0.25 , eps, true ) );
	- CPPUNIT_ASSERT_MESSAGE( "GetAverageEdgeBetweennessCentrality", mitk::Equal( statisticsCalculator->GetAverageEdgeBetweennessCentrality( ), 1.4 , eps, true ) );
	- CPPUNIT_ASSERT_MESSAGE( "GetNumberOfIsolatedPoints" , mitk::Equal( statisticsCalculator->GetNumberOfIsolatedPoints( ), 0 , eps, true ) );
	- CPPUNIT_ASSERT_MESSAGE( "GetRatioOfIsolatedPoints", mitk::Equal( statisticsCalculator->GetRatioOfIsolatedPoints( ), 0 , eps, true ) );
	- CPPUNIT_ASSERT_MESSAGE( "GetNumberOfEndPoints", mitk::Equal( statisticsCalculator->GetNumberOfEndPoints( ), 0 , eps, true ) );
	- CPPUNIT_ASSERT_MESSAGE( "GetRatioOfEndPoints", mitk::Equal( statisticsCalculator->GetRatioOfEndPoints( ), 0 , eps, true ) );
	- CPPUNIT_ASSERT_MESSAGE( "GetDiameter", mitk::Equal( statisticsCalculator->GetDiameter( ), 2 , eps, true ) );
	- CPPUNIT_ASSERT_MESSAGE( "GetDiameter90", mitk::Equal( statisticsCalculator->GetDiameter90( ), 2 , eps, true ) );
	- CPPUNIT_ASSERT_MESSAGE( "GetRadius" , mitk::Equal( statisticsCalculator->GetRadius( ), 1 , eps, true ) );
	- CPPUNIT_ASSERT_MESSAGE( "GetRadius90", mitk::Equal( statisticsCalculator->GetRadius90( ), 1 , eps, true ) );
	- CPPUNIT_ASSERT_MESSAGE( "GetAverageEccentricity", mitk::Equal( statisticsCalculator->GetAverageEccentricity( ), 1.5 , eps, true ) );
	- CPPUNIT_ASSERT_MESSAGE( "GetAverageEccentricity90", mitk::Equal( statisticsCalculator->GetAverageEccentricity90( ), 1.5 , eps, true ) );
	- CPPUNIT_ASSERT_MESSAGE( "GetAveragePathLength" , mitk::Equal( statisticsCalculator->GetAveragePathLength( ), 1.16667 , eps, true ) );
	- CPPUNIT_ASSERT_MESSAGE( "GetNumberOfCentralPoints" , mitk::Equal( statisticsCalculator->GetNumberOfCentralPoints( ), 2 , eps, true ) );
	- CPPUNIT_ASSERT_MESSAGE( "GetRatioOfCentralPoints", mitk::Equal( statisticsCalculator->GetRatioOfCentralPoints( ), 0.5 , eps, true ) );
	- // CPPUNIT_ASSERT_MESSAGE( " ", mitk::Equal( statisticsCalculator->GetSpectralRadius( ), , eps, true ) );
	- // CPPUNIT_ASSERT_MESSAGE( " ", mitk::Equal( statisticsCalculator->GetSecondLargestEigenValue( ), , eps, true ) );
	- // CPPUNIT_ASSERT_MESSAGE( " ", mitk::Equal( statisticsCalculator->GetAdjacencyTrace( ), , eps, true ) );
	- // CPPUNIT_ASSERT_MESSAGE( " ", mitk::Equal( statisticsCalculator->GetAdjacencyEnergy( ), , eps, true ) );
	- // CPPUNIT_ASSERT_MESSAGE( " ", mitk::Equal( statisticsCalculator->GetLaplacianTrace( ), , eps, true ) );
	- // CPPUNIT_ASSERT_MESSAGE( " ", mitk::Equal( statisticsCalculator->GetLaplacianEnergy( ), , eps, true ) );
	- // CPPUNIT_ASSERT_MESSAGE( " ", mitk::Equal( statisticsCalculator->GetLaplacianSpectralGap( ), , eps, true ) );
	- // CPPUNIT_ASSERT_MESSAGE( " ", mitk::Equal( statisticsCalculator->GetNormalizedLaplacianTrace( ), , eps, true ) );
	- // CPPUNIT_ASSERT_MESSAGE( " ", mitk::Equal( statisticsCalculator->GetNormalizedLaplacianEnergy( ), , eps, true ) );
	- // CPPUNIT_ASSERT_MESSAGE( " ", mitk::Equal( statisticsCalculator->GetNormalizedLaplacianNumberOf2s( ), , eps, true ) );
	- // CPPUNIT_ASSERT_MESSAGE( " ", mitk::Equal( statisticsCalculator->GetNormalizedLaplacianNumberOf1s( ), , eps, true ) );
	- // CPPUNIT_ASSERT_MESSAGE( " ", mitk::Equal( statisticsCalculator->GetNormalizedLaplacianNumberOf0s( ), , eps, true ) );
	- // CPPUNIT_ASSERT_MESSAGE( " ", mitk::Equal( statisticsCalculator->GetNormalizedLaplacianLowerSlope( ), , eps, true ) );
	- // CPPUNIT_ASSERT_MESSAGE( " ", mitk::Equal( statisticsCalculator->GetNormalizedLaplacianUpperSlope( ), , eps, true ) );
	- CPPUNIT_ASSERT_MESSAGE( "GetSmallWorldness", mitk::Equal( statisticsCalculator->GetSmallWorldness( ), 1.72908 , eps, true ) );
	-
	- }
	-};
	-
	-MITK_TEST_SUITE_REGISTRATION(mitkConnectomicsStatisticsCalculator)
	diff --git a/Modules/DiffusionImaging/Connectomics/Testing/mitkCorrelationCalculatorTest.cpp b/Modules/DiffusionImaging/Connectomics/Testing/mitkCorrelationCalculatorTest.cpp
	deleted file mode 100644
	index 3d77bca95e..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/Testing/mitkCorrelationCalculatorTest.cpp
	+++ /dev/null
	@@ -1,294 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-// Testing
	-#include "mitkTestingMacros.h"
	-#include "mitkTestFixture.h"
	-
	-// std includes
	-#include <string>
	-
	-// MITK includes
	-#include "mitkCorrelationCalculator.h"
	-#include <mitkImage.h>
	-#include <mitkImagePixelWriteAccessor.h>
	-#include <mitkImageCast.h>
	-#include <mitkITKImageImport.h>
	-
	-// VTK includes
	-#include <vtkDebugLeaks.h>
	-
	-class mitkCorrelationCalculatorTestSuite : public mitk::TestFixture
	-{
	- CPPUNIT_TEST_SUITE(mitkCorrelationCalculatorTestSuite);
	-
	- /// \todo Fix VTK memory leaks. Bug 18097.
	- vtkDebugLeaks::SetExitError(0);
	-
	- MITK_TEST(CalculateWholeCorrelation);
	- MITK_TEST(CalculateParcelCorrelation);
	- CPPUNIT_TEST_SUITE_END();
	-
	-private:
	-
	- mitk::Image::Pointer m_ParcellationImage;
	- mitk::Image::Pointer m_TimeSeriesImage;
	-
	-public:
	-
	- /**
	- * @brief Setup Always call this method before each Test-case to ensure correct and new intialization of the used members for a new test case. (If the members are not used in a test, the method does not need to be called).
	- */
	- void setUp() override
	- {
	- // The setup is somewhat cumbersome, due to the fact, that the mitk-itk conversion
	- // functions do not play nicely with 4D images
	-
	- //create test images
	- itk::Image<int, 4>::Pointer timeSeriesTestImage = itk::Image<int, 4>::New();
	- itk::Image<int, 4>::RegionType timeSeriesTestRegion;
	- itk::Image<int, 4>::IndexType timeSeriesTestIndex;
	- itk::Image<int, 4>::SizeType timeSeriesTestSize;
	- timeSeriesTestIndex[0] = 0;
	- timeSeriesTestIndex[1] = 0;
	- timeSeriesTestIndex[2] = 0;
	- timeSeriesTestIndex[3] = 0;
	-
	- timeSeriesTestSize[0] = 3;
	- timeSeriesTestSize[1] = 3;
	- timeSeriesTestSize[2] = 3;
	- timeSeriesTestSize[3] = 10;
	-
	- timeSeriesTestRegion.SetIndex(timeSeriesTestIndex);
	- timeSeriesTestRegion.SetSize(timeSeriesTestSize);
	-
	- timeSeriesTestImage->SetRegions(timeSeriesTestRegion);
	- timeSeriesTestImage->Allocate();
	- timeSeriesTestImage->FillBuffer(0);
	- timeSeriesTestImage->Update();
	-
	- itk::Image<int, 3>::Pointer parcellationTestImage = itk::Image<int, 3>::New();
	- itk::Image<int, 3>::RegionType parcellationTestRegion;
	- itk::Image<int, 3>::IndexType parcellationTestIndex;
	- itk::Image<int, 3>::SizeType parcellationTestSize;
	- parcellationTestIndex[0] = 0;
	- parcellationTestIndex[1] = 0;
	- parcellationTestIndex[2] = 0;
	-
	- parcellationTestSize[0] = 3;
	- parcellationTestSize[1] = 3;
	- parcellationTestSize[2] = 3;
	-
	- parcellationTestRegion.SetIndex(parcellationTestIndex);
	- parcellationTestRegion.SetSize(parcellationTestSize);
	-
	- parcellationTestImage->SetRegions(parcellationTestRegion);
	- parcellationTestImage->Allocate();
	-
	- //Fill test images with values
	-
	- mitk::Image::Pointer tsTestImage = mitk::Image::New();
	- mitk::GrabItkImageMemory( timeSeriesTestImage, tsTestImage.GetPointer() );
	- mitk::Image::Pointer pTestImage = mitk::Image::New();
	- mitk::GrabItkImageMemory( parcellationTestImage, pTestImage.GetPointer());
	-
	- //divide parcellation image into 3 different parcels
	- for( int loop(0); loop < 27; ++loop)
	- {
	- itk::Image<int, 3>::IndexType parcellationIndex;
	- parcellationIndex[2] = (loop / 9);
	- parcellationIndex[1] = (loop / 3) % 3;
	- parcellationIndex[0] = loop % 3;
	- if(loop < 9)
	- {
	- parcellationTestImage->SetPixel(parcellationIndex, 1);
	- }
	- else if( loop < 15 \|\| (loop > 17 && loop < 21) )
	- {
	- parcellationTestImage->SetPixel(parcellationIndex, 2);
	- }
	- else
	- {
	- parcellationTestImage->SetPixel(parcellationIndex, 3);
	- }
	- }
	-
	- mitk::ImagePixelWriteAccessor<int,4> writeAccess( tsTestImage );
	-
	- //fill time series image with similar time series in each parcel
	- for( int loop(0); loop < 270; ++loop)
	- {
	- itk::Image<int, 4>::IndexType timeSeriesIndex;
	- timeSeriesIndex[3] = (loop / 27);
	- timeSeriesIndex[2] = (loop / 9) % 3;
	- timeSeriesIndex[1] = (loop / 3) % 3;
	- timeSeriesIndex[0] = loop % 3;
	-
	- itk::Image<int, 3>::IndexType parcellationIndex;
	- parcellationIndex[2] = (loop / 9) % 3;
	- parcellationIndex[1] = (loop / 3) % 3;
	- parcellationIndex[0] = loop % 3;
	-
	- if( mitk::Equal(parcellationTestImage->GetPixel(parcellationIndex), 1) )
	- {
	- writeAccess.SetPixelByIndex(timeSeriesIndex, 1 + loop);
	- }
	- else if( mitk::Equal(parcellationTestImage->GetPixel(parcellationIndex), 2) )
	- {
	- writeAccess.SetPixelByIndex(timeSeriesIndex, 1 + (loop % 13 - loop % 11) );
	- }
	- else
	- {
	- writeAccess.SetPixelByIndex(timeSeriesIndex, 1 + ( loop - loop % 2) );
	- }
	- }
	-
	- //end create test images
	-
	- m_ParcellationImage = pTestImage;
	- m_TimeSeriesImage = tsTestImage;
	- }
	-
	- void tearDown() override
	- {
	- m_ParcellationImage = nullptr;
	- m_TimeSeriesImage = nullptr;
	- }
	-
	- void CalculateWholeCorrelation()
	- {
	- mitk::CorrelationCalculator<int>::Pointer correlationCalculator = mitk::CorrelationCalculator<int>::New();
	- correlationCalculator->SetTimeSeriesImage( m_TimeSeriesImage );
	- correlationCalculator->DoWholeCorrelation();
	-
	- const vnl_matrix< double >* cM = correlationCalculator->GetCorrelationMatrix();
	-
	- bool equal(true);
	- // instead of checking the entire 27 x 27 matrix
	- // just check 3 values and assume if they are equal entire
	- // matrix is likely to be equal
	- if( std::abs((*cM)[0][0] - 1) > 0.00001 )
	- {
	- equal = false;
	- }
	- if( std::abs((*cM)[2][10] - 0.00828941) > 0.00001 )
	- {
	- equal = false;
	- }
	- if( std::abs((*cM)[14][8] - 0.636613) > 0.00001 )
	- {
	- equal = false;
	- }
	- CPPUNIT_ASSERT_MESSAGE( "Comparing created and reference correlation matrix sample points.", equal );
	- }
	-
	- void CalculateParcelCorrelation()
	- {
	- mitk::CorrelationCalculator<int>::Pointer correlationCalculator = mitk::CorrelationCalculator<int>::New();
	- correlationCalculator->SetTimeSeriesImage( m_TimeSeriesImage );
	- correlationCalculator->SetParcellationImage( m_ParcellationImage );
	- correlationCalculator->DoParcelCorrelation();
	-
	- const vnl_matrix< double >* cM = correlationCalculator->GetCorrelationMatrix();
	-
	- bool equal(true);
	- // diagonal should be 1
	- if( std::abs((*cM)[0][0] - 1) > 0.00001 )
	- {
	- equal = false;
	- }
	- if( std::abs((*cM)[1][1] - 1) > 0.00001 )
	- {
	- equal = false;
	- }
	- if( std::abs((*cM)[2][2] - 1) > 0.00001 )
	- {
	- equal = false;
	- }
	- // parcel 0 and parcel 1 should correlate with -0.431111
	- if( std::abs((*cM)[1][0] - -0.431111) > 0.00001 )
	- {
	- equal = false;
	- }
	- if( std::abs((*cM)[0][1] - -0.431111) > 0.00001 )
	- {
	- equal = false;
	- }
	- // parcel 0 and parcel 2 should correlate with 1
	- if( std::abs((*cM)[0][2] - 1) > 0.00001 )
	- {
	- equal = false;
	- }
	- if( std::abs((*cM)[2][0] - 1) > 0.00001 )
	- {
	- equal = false;
	- }
	- // parcel 1 and parcel 2 should correlate with -0.430522
	- if( std::abs((*cM)[1][2] - -0.430522) > 0.00001 )
	- {
	- equal = false;
	- }
	- if( std::abs((*cM)[2][1] - -0.430522) > 0.00001 )
	- {
	- equal = false;
	- }
	- CPPUNIT_ASSERT_MESSAGE( "Comparing created and reference correlation matrix.", equal );
	-
	- mitk::ConnectomicsNetwork::Pointer network = correlationCalculator->GetConnectomicsNetwork();
	-
	- mitk::ConnectomicsNetwork::Pointer refNetwork = mitk::ConnectomicsNetwork::New();
	- mitk::ConnectomicsNetwork::VertexDescriptorType x = refNetwork->AddVertex( 1 );
	- mitk::ConnectomicsNetwork::VertexDescriptorType y = refNetwork->AddVertex( 2 );
	- mitk::ConnectomicsNetwork::VertexDescriptorType z = refNetwork->AddVertex( 3 );
	- refNetwork->AddEdge(x,y,1);
	- refNetwork->AddEdge(x,z,1);
	- refNetwork->AddEdge(y,z,1);
	- CPPUNIT_ASSERT_MESSAGE( "Comparing created and reference network.", mitk::Equal( network.GetPointer(), refNetwork, mitk::eps, true) );
	-
	- // check sample parcels for other methods
	- correlationCalculator->DoParcelCorrelation( mitk::CorrelationCalculator<int>::UseAverageCorrelation );
	- cM = correlationCalculator->GetCorrelationMatrix();
	- // parcel 0 and parcel 1 should correlate with -0.0643023
	- equal = true;
	- if( std::abs((*cM)[1][0] - -0.0643023) > 0.00001 )
	- {
	- equal = false;
	- }
	- // parcel 0 and parcel 2 should correlate with 0.99998
	- if( std::abs((*cM)[2][0] - 0.99998) > 0.00001 )
	- {
	- equal = false;
	- }
	- CPPUNIT_ASSERT_MESSAGE( "Comparing sample parcel correlation for average correlation.", equal );
	-
	- correlationCalculator->DoParcelCorrelation( mitk::CorrelationCalculator<int>::UseMaximumCorrelation );
	- cM = correlationCalculator->GetCorrelationMatrix();
	- // parcel 0 and parcel 1 should correlate with 0.636613
	- equal = true;
	- if( std::abs((*cM)[1][0] - 0.636613) > 0.00001 )
	- {
	- equal = false;
	- }
	- // parcel 0 and parcel 2 should correlate with 0.99998
	- if( std::abs((*cM)[2][0] - 0.99998) > 0.00001 )
	- {
	- equal = false;
	- }
	- CPPUNIT_ASSERT_MESSAGE( "Comparing sample parcel correlation for maximum correlation.", equal );
	- }
	-};
	-
	-MITK_TEST_SUITE_REGISTRATION(mitkCorrelationCalculator)
	diff --git a/Modules/DiffusionImaging/Connectomics/files.cmake b/Modules/DiffusionImaging/Connectomics/files.cmake
	deleted file mode 100644
	index 03b16a4300..0000000000
	--- a/Modules/DiffusionImaging/Connectomics/files.cmake
	+++ /dev/null
	@@ -1,82 +0,0 @@
	-set(CPP_FILES
	-
	- # DataStructures Connectomics
	- IODataStructures/mitkConnectomicsNetwork.cpp
	- IODataStructures/mitkConnectomicsConstantsManager.cpp
	-
	- # Rendering Connectomics
	- Rendering/mitkConnectomicsNetworkMapper3D.cpp
	- Rendering/mitkConnectomicsRenderingSchemeProperty.cpp
	- Rendering/mitkConnectomicsRenderingEdgeFilteringProperty.cpp
	- Rendering/mitkConnectomicsRenderingNodeFilteringProperty.cpp
	- Rendering/mitkConnectomicsRenderingEdgeColorParameterProperty.cpp
	- Rendering/mitkConnectomicsRenderingEdgeRadiusParameterProperty.cpp
	- Rendering/mitkConnectomicsRenderingNodeColorParameterProperty.cpp
	- Rendering/mitkConnectomicsRenderingNodeRadiusParameterProperty.cpp
	- Rendering/mitkConnectomicsRenderingNodeThresholdParameterProperty.cpp
	- Rendering/mitkConnectomicsRenderingEdgeThresholdParameterProperty.cpp
	- Rendering/mitkConnectomicsEnumerationSubclassesSerializer.cpp
	-
	- # Algorithms Connectomics
	- Algorithms/mitkConnectomicsNetworkCreator.cpp
	- Algorithms/mitkConnectomicsHistogramBase.cpp
	- Algorithms/mitkConnectomicsDegreeHistogram.cpp
	- Algorithms/mitkConnectomicsShortestPathHistogram.cpp
	- Algorithms/mitkConnectomicsBetweennessHistogram.cpp
	- Algorithms/mitkConnectomicsHistogramCache.cpp
	- Algorithms/mitkConnectomicsSyntheticNetworkGenerator.cpp
	- Algorithms/mitkConnectomicsSimulatedAnnealingPermutationBase.cpp
	- Algorithms/mitkConnectomicsSimulatedAnnealingPermutationModularity.cpp
	- Algorithms/mitkConnectomicsSimulatedAnnealingManager.cpp
	- Algorithms/mitkConnectomicsSimulatedAnnealingCostFunctionBase.cpp
	- Algorithms/mitkConnectomicsSimulatedAnnealingCostFunctionModularity.cpp
	- Algorithms/mitkConnectomicsStatisticsCalculator.cpp
	- Algorithms/mitkConnectomicsNetworkConverter.cpp
	- Algorithms/mitkConnectomicsNetworkThresholder.cpp
	- Algorithms/mitkFreeSurferParcellationTranslator.cpp
	-)
	-
	-set(H_FILES
	- # Rendering Connectomics
	- Rendering/mitkConnectomicsNetworkMapper3D.h
	- Rendering/mitkConnectomicsRenderingProperties.h
	- Rendering/mitkConnectomicsRenderingSchemeProperty.h
	- Rendering/mitkConnectomicsRenderingEdgeFilteringProperty.h
	- Rendering/mitkConnectomicsRenderingNodeFilteringProperty.h
	- Rendering/mitkConnectomicsRenderingEdgeColorParameterProperty.h
	- Rendering/mitkConnectomicsRenderingEdgeRadiusParameterProperty.h
	- Rendering/mitkConnectomicsRenderingNodeColorParameterProperty.h
	- Rendering/mitkConnectomicsRenderingNodeRadiusParameterProperty.h
	- Rendering/mitkConnectomicsRenderingNodeThresholdParameterProperty.h
	- Rendering/mitkConnectomicsRenderingEdgeThresholdParameterProperty.h
	-
	-
	- # Datastructures Connectomics
	- IODataStructures/mitkConnectomicsConstantsManager.h
	- IODataStructures/mitkConnectomicsNetwork.h
	- IODataStructures/mitkConnectomicsNetworkProperties.h
	-
	- # Algorithms Connectomics
	- Algorithms/mitkConnectomicsNetworkCreator.h
	- Algorithms/mitkConnectomicsHistogramBase.h
	- Algorithms/mitkConnectomicsDegreeHistogram.h
	- Algorithms/mitkConnectomicsShortestPathHistogram.h
	- Algorithms/mitkConnectomicsBetweennessHistogram.h
	- Algorithms/mitkConnectomicsHistogramCache.h
	- Algorithms/mitkConnectomicsSyntheticNetworkGenerator.h
	- Algorithms/mitkConnectomicsSimulatedAnnealingPermutationBase.h
	- Algorithms/mitkConnectomicsSimulatedAnnealingPermutationModularity.h
	- Algorithms/mitkConnectomicsSimulatedAnnealingManager.h
	- Algorithms/mitkConnectomicsSimulatedAnnealingCostFunctionBase.h
	- Algorithms/mitkConnectomicsSimulatedAnnealingCostFunctionModularity.h
	- Algorithms/itkConnectomicsNetworkToConnectivityMatrixImageFilter.h
	- Algorithms/mitkConnectomicsStatisticsCalculator.h
	- Algorithms/mitkConnectomicsNetworkConverter.h
	- Algorithms/BrainParcellation/mitkCostFunctionBase.h
	- Algorithms/BrainParcellation/mitkRandomParcellationGenerator.h
	- Algorithms/BrainParcellation/mitkRegionVoxelCounter.h
	- Algorithms/mitkFreeSurferParcellationTranslator.h
	- Algorithms/mitkCorrelationCalculator.h
	-)
	-
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/CMakeLists.txt b/Modules/DiffusionImaging/DiffusionCmdApps/CMakeLists.txt
	deleted file mode 100644
	index ffbde72f1d..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/CMakeLists.txt
	+++ /dev/null
	@@ -1,20 +0,0 @@
	-MITK_CREATE_MODULE(
	- SUBPROJECTS MITK-DTI
	- # INCLUDE_DIRS Helpers
	- DEPENDS MitkDiffusionCore MitkDiffusionIO MitkFiberTracking MitkQuantification MitkConnectomics
	- PACKAGE_DEPENDS PUBLIC ITK
	-)
	-
	-if(MODULE_IS_ENABLED)
	- add_subdirectory(Connectomics)
	- add_subdirectory(Fiberfox)
	- add_subdirectory(FiberProcessing)
	- add_subdirectory(Tractography)
	- add_subdirectory(TractographyEvaluation)
	- add_subdirectory(Misc)
	- add_subdirectory(Quantification)
	-
	-if(MITK_USE_Python)
	- add_subdirectory(Python)
	-endif()
	-endif()
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Connectomics/CMakeLists.txt b/Modules/DiffusionImaging/DiffusionCmdApps/Connectomics/CMakeLists.txt
	deleted file mode 100755
	index bcfc777262..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Connectomics/CMakeLists.txt
	+++ /dev/null
	@@ -1,39 +0,0 @@
	-option(BUILD_DiffusionConnectomicsCmdApps "Build commandline tools for diffusion connectomics" OFF)
	-
	-if(BUILD_DiffusionConnectomicsCmdApps OR MITK_BUILD_ALL_APPS)
	-
	- # needed include directories
	- include_directories(
	- ${CMAKE_CURRENT_SOURCE_DIR}
	- ${CMAKE_CURRENT_BINARY_DIR}
	- )
	-
	- # list of DiffusionConnectomics cmdapps
	- # if an app requires additional dependencies
	- # they are added after a "^^" and separated by "_"
	- set( DiffusionConnectomicscmdapps
	- NetworkCreation^^
	- NetworkStatistics^^
	- )
	-
	- foreach(DiffusionConnectomicscmdapp ${DiffusionConnectomicscmdapps})
	- # extract cmd app name and dependencies
	- string(REPLACE "^^" "\\;" cmdapp_info ${DiffusionConnectomicscmdapp})
	- set(cmdapp_info_list ${cmdapp_info})
	- list(GET cmdapp_info_list 0 appname)
	- list(GET cmdapp_info_list 1 raw_dependencies)
	- string(REPLACE "_" "\\;" dependencies "${raw_dependencies}")
	- set(dependencies_list ${dependencies})
	-
	- mitkFunctionCreateCommandLineApp(
	- NAME ${appname}
	- DEPENDS MitkDiffusionCmdApps ${dependencies_list}
	- PACKAGE_DEPENDS
	- )
	- endforeach()
	-
	- if(EXECUTABLE_IS_ENABLED)
	- MITK_INSTALL_TARGETS(EXECUTABLES ${EXECUTABLE_TARGET})
	- endif()
	-
	- endif()
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Connectomics/NetworkCreation.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Connectomics/NetworkCreation.cpp
	deleted file mode 100644
	index d9646e0316..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Connectomics/NetworkCreation.cpp
	+++ /dev/null
	@@ -1,119 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-// std includes
	-#include <string>
	-
	-// CTK includes
	-#include "mitkCommandLineParser.h"
	-
	-// MITK includes
	-#include "mitkConnectomicsNetworkCreator.h"
	-#include <mitkCoreObjectFactory.h>
	-#include <mitkIOUtil.h>
	-
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Network Creation");
	- parser.setCategory("Connectomics");
	- parser.setDescription("");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "f", mitkCommandLineParser::String, "Input Tractogram", "input tractogram (.fib)", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "p", mitkCommandLineParser::String, "Parcellation", "parcellation image", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output network", "where to save the output (.cnf; .mat)", us::Any(), false);
	-
	- parser.addArgument("noCenterOfMass", "", mitkCommandLineParser::Bool, "No center of mass", "Do not use center of mass for node positions");
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- //default values
	- bool noCenterOfMass( false );
	-
	- // parse command line arguments
	- std::string fiberFilename = us::any_cast<std::string>(parsedArgs["f"]);
	- std::string parcellationFilename = us::any_cast<std::string>(parsedArgs["p"]);
	- std::string outputFilename = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- if (parsedArgs.count("noCenterOfMass"))
	- noCenterOfMass = us::any_cast<bool>(parsedArgs["noCenterOfMass"]);
	-
	- try
	- {
	- // load fiber image
	- std::vector<mitk::BaseData::Pointer> fiberInfile = mitk::IOUtil::Load( fiberFilename);
	-
	- if( fiberInfile.empty() )
	- {
	- std::string errorMessage = "Fiber Image at " + fiberFilename + " could not be read. Aborting.";
	- MITK_ERROR << errorMessage;
	- return EXIT_FAILURE;
	- }
	- mitk::BaseData* fiberBaseData = fiberInfile.at(0);
	- mitk::FiberBundle* fiberBundle = dynamic_cast<mitk::FiberBundle*>( fiberBaseData );
	-
	- // load parcellation
	- std::vector<mitk::BaseData::Pointer> parcellationInFile =
	- mitk::IOUtil::Load( parcellationFilename);
	- if( parcellationInFile.empty() )
	- {
	- std::string errorMessage = "Parcellation at " + parcellationFilename + " could not be read. Aborting.";
	- MITK_ERROR << errorMessage;
	- return EXIT_FAILURE;
	- }
	- mitk::BaseData* parcellationBaseData = parcellationInFile.at(0);
	- mitk::Image* parcellationImage = dynamic_cast<mitk::Image*>( parcellationBaseData );
	-
	- // do creation
	- mitk::ConnectomicsNetworkCreator::Pointer connectomicsNetworkCreator = mitk::ConnectomicsNetworkCreator::New();
	- connectomicsNetworkCreator->SetSegmentation( parcellationImage );
	- connectomicsNetworkCreator->SetFiberBundle( fiberBundle );
	- if( !noCenterOfMass )
	- {
	- connectomicsNetworkCreator->CalculateCenterOfMass();
	- }
	- connectomicsNetworkCreator->SetMappingStrategy(mitk::ConnectomicsNetworkCreator::MappingStrategy::EndElementPosition);
	- connectomicsNetworkCreator->CreateNetworkFromFibersAndSegmentation();
	-
	-
	- mitk::ConnectomicsNetwork::Pointer network = connectomicsNetworkCreator->GetNetwork();
	- mitk::IOUtil::Save(network.GetPointer(), outputFilename );
	-
	- return EXIT_SUCCESS;
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- std::cout << "DONE";
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Connectomics/NetworkStatistics.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Connectomics/NetworkStatistics.cpp
	deleted file mode 100644
	index 758babe74d..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Connectomics/NetworkStatistics.cpp
	+++ /dev/null
	@@ -1,570 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-// std includes
	-#include <string>
	-#include <sstream>
	-#include <fstream>
	-#include <vector>
	-#include <map>
	-#include <utility>
	-
	-// boost includes
	-#include <boost/algorithm/string.hpp>
	-
	-// ITK includes
	-#include <itkImageFileWriter.h>
	-
	-// CTK includes
	-#include "mitkCommandLineParser.h"
	-
	-// MITK includes
	-#include <mitkConnectomicsStatisticsCalculator.h>
	-#include <mitkConnectomicsNetworkThresholder.h>
	-#include <itkConnectomicsNetworkToConnectivityMatrixImageFilter.h>
	-#include <mitkIOUtil.h>
	-#include <mitkLocaleSwitch.h>
	-
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Network Creation");
	- parser.setCategory("Connectomics");
	- parser.setDescription("");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	-
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input network", "input connectomics network (.cnf)", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output file", "name of output file", us::Any(), false, false, false, mitkCommandLineParser::Output);
	-
	- parser.addArgument("noGlobalStatistics", "g", mitkCommandLineParser::Bool, "No global statistics", "Do not calculate global statistics");
	- parser.addArgument("createConnectivityMatriximage", "I", mitkCommandLineParser::Bool, "Write connectivity matrix image", "Write connectivity matrix image");
	- parser.addArgument("binaryConnectivity", "b", mitkCommandLineParser::Bool, "Binary connectivity", "Whether to create a binary connectivity matrix");
	- parser.addArgument("rescaleConnectivity", "r", mitkCommandLineParser::Bool, "Rescale connectivity", "Whether to rescale the connectivity matrix");
	- parser.addArgument("localStatistics", "L", mitkCommandLineParser::StringList, "Local statistics", "Provide a list of node labels for local statistics", us::Any());
	- parser.addArgument("regionList", "R", mitkCommandLineParser::StringList, "Region list", "A space separated list of regions. Each region has the format\n regionname;label1;label2;...;labelN", us::Any());
	- parser.addArgument("granularity", "gr", mitkCommandLineParser::Int, "Granularity", "How finely to test the density range and how many thresholds to consider",1);
	- parser.addArgument("startDensity", "d", mitkCommandLineParser::Float, "Start Density", "Largest density for the range",1.0);
	- parser.addArgument("thresholdStepSize", "t", mitkCommandLineParser::Int, "Step size threshold", "Distance of two adjacent thresholds",3);
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- //default values
	- bool noGlobalStatistics( false );
	- bool binaryConnectivity( false );
	- bool rescaleConnectivity( false );
	- bool createConnectivityMatriximage( false );
	- int granularity( 1 );
	- double startDensity( 1.0 );
	- int thresholdStepSize( 3 );
	-
	-
	- // parse command line arguments
	- std::string networkName = us::any_cast<std::string>(parsedArgs["i"]);
	- std::string outName = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- mitkCommandLineParser::StringContainerType localLabels;
	-
	- if(parsedArgs.count("localStatistics"))
	- {
	- localLabels = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["localStatistics"]);
	- }
	-
	- mitkCommandLineParser::StringContainerType unparsedRegions;
	- std::map< std::string, std::vector<std::string> > parsedRegions;
	- std::map< std::string, std::vector<std::string> >::iterator parsedRegionsIterator;
	-
	- if(parsedArgs.count("regionList"))
	- {
	- unparsedRegions = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["regionList"]);
	-
	- for(unsigned int index(0); index < unparsedRegions.size(); index++ )
	- {
	- std::vector< std::string > tempRegionVector;
	-
	- boost::split(tempRegionVector, unparsedRegions.at(index), boost::is_any_of(";"));
	-
	- std::vector< std::string >::const_iterator begin = tempRegionVector.begin();
	- std::vector< std::string >::const_iterator last = tempRegionVector.begin() + tempRegionVector.size();
	- std::vector< std::string > insertRegionVector(begin + 1, last);
	-
	- if( parsedRegions.count( tempRegionVector.at(0) ) == 0 )
	- {
	- parsedRegions.insert( std::pair< std::string, std::vector<std::string> >( tempRegionVector.at(0), insertRegionVector) );
	- }
	- else
	- {
	- MITK_ERROR << "Region already exists. Skipping second occurrence.";
	- }
	- }
	- }
	-
	- if (parsedArgs.count("noGlobalStatistics"))
	- noGlobalStatistics = us::any_cast<bool>(parsedArgs["noGlobalStatistics"]);
	- if (parsedArgs.count("binaryConnectivity"))
	- binaryConnectivity = us::any_cast<bool>(parsedArgs["binaryConnectivity"]);
	- if (parsedArgs.count("rescaleConnectivity"))
	- rescaleConnectivity = us::any_cast<bool>(parsedArgs["rescaleConnectivity"]);
	- if (parsedArgs.count("createConnectivityMatriximage"))
	- createConnectivityMatriximage = us::any_cast<bool>(parsedArgs["createConnectivityMatriximage"]);
	- if (parsedArgs.count("granularity"))
	- granularity = us::any_cast<int>(parsedArgs["granularity"]);
	- if (parsedArgs.count("startDensity"))
	- startDensity = us::any_cast<float>(parsedArgs["startDensity"]);
	- if (parsedArgs.count("thresholdStepSize"))
	- thresholdStepSize = us::any_cast<int>(parsedArgs["thresholdStepSize"]);
	-
	- try
	- {
	- // load network
	- std::vector<mitk::BaseData::Pointer> networkFile =
	- mitk::IOUtil::Load( networkName);
	- if( networkFile.empty() )
	- {
	- std::string errorMessage = "File at " + networkName + " could not be read. Aborting.";
	- MITK_ERROR << errorMessage;
	- return EXIT_FAILURE;
	- }
	- mitk::BaseData* networkBaseData = networkFile.at(0);
	- mitk::ConnectomicsNetwork* network = dynamic_cast<mitk::ConnectomicsNetwork*>( networkBaseData );
	-
	- if( !network )
	- {
	- std::string errorMessage = "Read file at " + networkName + " could not be recognized as network. Aborting.";
	- MITK_ERROR << errorMessage;
	- return EXIT_FAILURE;
	- }
	-
	- // streams
	- std::stringstream globalHeaderStream;
	- globalHeaderStream << "NumberOfVertices "
	- << "NumberOfEdges "
	- << "AverageDegree "
	- << "ConnectionDensity "
	- << "NumberOfConnectedComponents "
	- << "AverageComponentSize "
	- << "LargestComponentSize "
	- << "RatioOfNodesInLargestComponent "
	- << "HopPlotExponent "
	- << "EffectiveHopDiameter "
	- << "AverageClusteringCoefficientsC "
	- << "AverageClusteringCoefficientsD "
	- << "AverageClusteringCoefficientsE "
	- << "AverageVertexBetweennessCentrality "
	- << "AverageEdgeBetweennessCentrality "
	- << "NumberOfIsolatedPoints "
	- << "RatioOfIsolatedPoints "
	- << "NumberOfEndPoints "
	- << "RatioOfEndPoints "
	- << "Diameter "
	- << "Diameter90 "
	- << "Radius "
	- << "Radius90 "
	- << "AverageEccentricity "
	- << "AverageEccentricity90 "
	- << "AveragePathLength "
	- << "NumberOfCentralPoints "
	- << "RatioOfCentralPoints "
	- << "SpectralRadius "
	- << "SecondLargestEigenValue "
	- << "AdjacencyTrace "
	- << "AdjacencyEnergy "
	- << "LaplacianTrace "
	- << "LaplacianEnergy "
	- << "LaplacianSpectralGap "
	- << "NormalizedLaplacianTrace "
	- << "NormalizedLaplacianEnergy "
	- << "NormalizedLaplacianNumberOf2s "
	- << "NormalizedLaplacianNumberOf1s "
	- << "NormalizedLaplacianNumberOf0s "
	- << "NormalizedLaplacianLowerSlope "
	- << "NormalizedLaplacianUpperSlope "
	- << "SmallWorldness"
	- << std::endl;
	-
	- std::stringstream localHeaderStream;
	- std::stringstream regionalHeaderStream;
	-
	- std::stringstream globalDataStream;
	- std::stringstream localDataStream;
	- std::stringstream regionalDataStream;
	-
	- std::string globalOutName = outName + "_global.txt";
	- std::string localOutName = outName + "_local.txt";
	- std::string regionalOutName = outName + "_regional.txt";
	-
	- bool firstRun( true );
	- // iterate over all three possible methods
	- for(unsigned int method( 0 ); method < 3; method++)
	- {
	- // 0 - Random removal threshold
	- // 1 - Largest density below threshold
	- // 2 - Threshold based
	-
	- // iterate over possible targets
	- for( int step = 0; step < granularity; ++step )
	- {
	- double targetValue( 0.0 );
	-
	- switch ( method )
	- {
	- case mitk::ConnectomicsNetworkThresholder::RandomRemovalOfWeakest :
	- case mitk::ConnectomicsNetworkThresholder::LargestLowerThanDensity :
	- targetValue = startDensity * (1 - static_cast<double>( step ) / ( granularity + 0.5 ) );
	- break;
	- case mitk::ConnectomicsNetworkThresholder::ThresholdBased :
	- targetValue = static_cast<double>( thresholdStepSize * step );
	- break;
	- default:
	- MITK_ERROR << "Invalid thresholding method called, aborting.";
	- return EXIT_FAILURE;
	- break;
	- }
	-
	- mitk::ConnectomicsNetworkThresholder::Pointer thresholder = mitk::ConnectomicsNetworkThresholder::New();
	- thresholder->SetNetwork( network );
	- thresholder->SetTargetThreshold( targetValue );
	- thresholder->SetTargetDensity( targetValue );
	- thresholder->SetThresholdingScheme( static_cast<mitk::ConnectomicsNetworkThresholder::ThresholdingSchemes>(method) );
	- mitk::ConnectomicsNetwork::Pointer thresholdedNetwork = thresholder->GetThresholdedNetwork();
	-
	- mitk::ConnectomicsStatisticsCalculator::Pointer statisticsCalculator = mitk::ConnectomicsStatisticsCalculator::New();
	- statisticsCalculator->SetNetwork( thresholdedNetwork );
	- statisticsCalculator->Update();
	-
	- // global statistics
	- if( !noGlobalStatistics )
	- {
	- globalDataStream << statisticsCalculator->GetNumberOfVertices() << " "
	- << statisticsCalculator->GetNumberOfEdges() << " "
	- << statisticsCalculator->GetAverageDegree() << " "
	- << statisticsCalculator->GetConnectionDensity() << " "
	- << statisticsCalculator->GetNumberOfConnectedComponents() << " "
	- << statisticsCalculator->GetAverageComponentSize() << " "
	- << statisticsCalculator->GetLargestComponentSize() << " "
	- << statisticsCalculator->GetRatioOfNodesInLargestComponent() << " "
	- << statisticsCalculator->GetHopPlotExponent() << " "
	- << statisticsCalculator->GetEffectiveHopDiameter() << " "
	- << statisticsCalculator->GetAverageClusteringCoefficientsC() << " "
	- << statisticsCalculator->GetAverageClusteringCoefficientsD() << " "
	- << statisticsCalculator->GetAverageClusteringCoefficientsE() << " "
	- << statisticsCalculator->GetAverageVertexBetweennessCentrality() << " "
	- << statisticsCalculator->GetAverageEdgeBetweennessCentrality() << " "
	- << statisticsCalculator->GetNumberOfIsolatedPoints() << " "
	- << statisticsCalculator->GetRatioOfIsolatedPoints() << " "
	- << statisticsCalculator->GetNumberOfEndPoints() << " "
	- << statisticsCalculator->GetRatioOfEndPoints() << " "
	- << statisticsCalculator->GetDiameter() << " "
	- << statisticsCalculator->GetDiameter90() << " "
	- << statisticsCalculator->GetRadius() << " "
	- << statisticsCalculator->GetRadius90() << " "
	- << statisticsCalculator->GetAverageEccentricity() << " "
	- << statisticsCalculator->GetAverageEccentricity90() << " "
	- << statisticsCalculator->GetAveragePathLength() << " "
	- << statisticsCalculator->GetNumberOfCentralPoints() << " "
	- << statisticsCalculator->GetRatioOfCentralPoints() << " "
	- << statisticsCalculator->GetSpectralRadius() << " "
	- << statisticsCalculator->GetSecondLargestEigenValue() << " "
	- << statisticsCalculator->GetAdjacencyTrace() << " "
	- << statisticsCalculator->GetAdjacencyEnergy() << " "
	- << statisticsCalculator->GetLaplacianTrace() << " "
	- << statisticsCalculator->GetLaplacianEnergy() << " "
	- << statisticsCalculator->GetLaplacianSpectralGap() << " "
	- << statisticsCalculator->GetNormalizedLaplacianTrace() << " "
	- << statisticsCalculator->GetNormalizedLaplacianEnergy() << " "
	- << statisticsCalculator->GetNormalizedLaplacianNumberOf2s() << " "
	- << statisticsCalculator->GetNormalizedLaplacianNumberOf1s() << " "
	- << statisticsCalculator->GetNormalizedLaplacianNumberOf0s() << " "
	- << statisticsCalculator->GetNormalizedLaplacianLowerSlope() << " "
	- << statisticsCalculator->GetNormalizedLaplacianUpperSlope() << " "
	- << statisticsCalculator->GetSmallWorldness()
	- << std::endl;
	-
	- } // end global statistics
	-
	- //create connectivity matrix png
	- if( createConnectivityMatriximage )
	- {
	- std::string connectivity_png_postfix = "_connectivity";
	- if( binaryConnectivity )
	- {
	- connectivity_png_postfix += "_binary";
	- }
	- else if( rescaleConnectivity )
	- {
	- connectivity_png_postfix += "_rescaled";
	- }
	- connectivity_png_postfix += ".png";
	-
	- /* File format
	- * A png file depicting the binary connectivity matrix
	- */
	- itk::ConnectomicsNetworkToConnectivityMatrixImageFilter::Pointer filter = itk::ConnectomicsNetworkToConnectivityMatrixImageFilter::New();
	- filter->SetInputNetwork( network );
	- filter->SetBinaryConnectivity( binaryConnectivity );
	- filter->SetRescaleConnectivity( rescaleConnectivity );
	- filter->Update();
	-
	- typedef itk::ConnectomicsNetworkToConnectivityMatrixImageFilter::OutputImageType connectivityMatrixImageType;
	-
	- mitk::LocaleSwitch localeSwitch("C");
	- itk::ImageFileWriter< connectivityMatrixImageType >::Pointer connectivityWriter = itk::ImageFileWriter< connectivityMatrixImageType >::New();
	-
	- connectivityWriter->SetInput( filter->GetOutput() );
	- connectivityWriter->SetFileName( outName + connectivity_png_postfix);
	- connectivityWriter->Update();
	-
	- std::cout << "Connectivity matrix image written.";
	- } // end create connectivity matrix png
	-
	- /*
	- * We can either calculate local indices for specific nodes, or specific regions
	- */
	-
	- // Create LabelToIndex translation
	- std::map< std::string, int > labelToIdMap;
	- std::vector< mitk::ConnectomicsNetwork::NetworkNode > nodeVector = thresholdedNetwork->GetVectorOfAllNodes();
	- for(std::size_t loop(0); loop < nodeVector.size(); loop++)
	- {
	- labelToIdMap.insert( std::pair< std::string, int>(nodeVector.at(loop).label, nodeVector.at(loop).id) );
	- }
	-
	- std::vector< int > degreeVector = thresholdedNetwork->GetDegreeOfNodes();
	- std::vector< double > ccVector = thresholdedNetwork->GetLocalClusteringCoefficients( );
	- std::vector< double > bcVector = thresholdedNetwork->GetNodeBetweennessVector( );
	-
	-
	- // calculate local indices
	-
	- {
	- // only add to header for the first step of the first method
	- if( firstRun )
	- {
	- localHeaderStream << "Th_method " << "Th_target " << "density";
	- }
	-
	- double density = statisticsCalculator->GetConnectionDensity();
	-
	- localDataStream << "\n"
	- << method << " "
	- << targetValue << " "
	- << density;
	-
	- for(unsigned int loop(0); loop < localLabels.size(); loop++ )
	- {
	- if( network->CheckForLabel(localLabels.at( loop )) )
	- {
	- if( firstRun )
	- {
	- localHeaderStream << " "
	- << localLabels.at( loop ) << "_Degree "
	- << localLabels.at( loop ) << "_CC "
	- << localLabels.at( loop ) << "_BC";
	- }
	-
	- localDataStream << " " << degreeVector.at( labelToIdMap.find( localLabels.at( loop ) )->second )
	- << " " << ccVector.at( labelToIdMap.find( localLabels.at( loop ) )->second )
	- << " " << bcVector.at( labelToIdMap.find( localLabels.at( loop ) )->second );
	- }
	- else
	- {
	- MITK_ERROR << "Illegal label. Label: \"" << localLabels.at( loop ) << "\" not found.";
	- }
	- }
	- }
	-
	- // calculate regional indices
	-
	- {
	- // only add to header for the first step of the first method
	- if( firstRun )
	- {
	- regionalHeaderStream << "Th_method " << "Th_target " << "density";
	- }
	-
	- double density = statisticsCalculator->GetConnectionDensity();
	-
	- regionalDataStream << "\n"
	- << method << " "
	- << targetValue << " "
	- << density;
	-
	- for( parsedRegionsIterator = parsedRegions.begin(); parsedRegionsIterator != parsedRegions.end(); parsedRegionsIterator++ )
	- {
	- std::vector<std::string> regionLabelsVector = parsedRegionsIterator->second;
	- std::string regionName = parsedRegionsIterator->first;
	-
	- double sumDegree( 0 );
	- double sumCC( 0 );
	- double sumBC( 0 );
	- double count( 0 );
	-
	- for( std::size_t loop(0); loop < regionLabelsVector.size(); loop++ )
	- {
	- if( thresholdedNetwork->CheckForLabel(regionLabelsVector.at( loop )) )
	- {
	- sumDegree = sumDegree + degreeVector.at( labelToIdMap.find( regionLabelsVector.at( loop ) )->second );
	- sumCC = sumCC + ccVector.at( labelToIdMap.find( regionLabelsVector.at( loop ) )->second );
	- sumBC = sumBC + bcVector.at( labelToIdMap.find( regionLabelsVector.at( loop ) )->second );
	- count = count + 1;
	- }
	- else
	- {
	- MITK_ERROR << "Illegal label. Label: \"" << regionLabelsVector.at( loop ) << "\" not found.";
	- }
	- }
	-
	- // only add to header for the first step of the first method
	- if( firstRun )
	- {
	- regionalHeaderStream << " " << regionName << "_LocalAverageDegree "
	- << regionName << "_LocalAverageCC "
	- << regionName << "_LocalAverageBC "
	- << regionName << "_NumberOfNodes";
	- }
	-
	- regionalDataStream << " " << sumDegree / count
	- << " " << sumCC / count
	- << " " << sumBC / count
	- << " " << count;
	-
	- // count number of connections and fibers between regions
	- std::map< std::string, std::vector<std::string> >::iterator loopRegionsIterator;
	- for (loopRegionsIterator = parsedRegionsIterator; loopRegionsIterator != parsedRegions.end(); loopRegionsIterator++)
	- {
	- int numberConnections(0), possibleConnections(0);
	- double summedFiberCount(0.0);
	- std::vector<std::string> loopLabelsVector = loopRegionsIterator->second;
	- std::string loopName = loopRegionsIterator->first;
	-
	- for (std::size_t loop(0); loop < regionLabelsVector.size(); loop++)
	- {
	- if (thresholdedNetwork->CheckForLabel(regionLabelsVector.at(loop)))
	- {
	- for (std::size_t innerLoop(0); innerLoop < loopLabelsVector.size(); innerLoop++)
	- {
	- if (thresholdedNetwork->CheckForLabel(loopLabelsVector.at(loop)))
	- {
	- bool exists = thresholdedNetwork->EdgeExists(
	- labelToIdMap.find(regionLabelsVector.at(loop))->second,
	- labelToIdMap.find(loopLabelsVector.at(innerLoop))->second);
	- possibleConnections++;
	- if (exists)
	- {
	- numberConnections++;
	- summedFiberCount += thresholdedNetwork->GetEdge(
	- labelToIdMap.find(regionLabelsVector.at(loop))->second,
	- labelToIdMap.find(loopLabelsVector.at(innerLoop))->second).fiber_count;
	- }
	- }
	- else
	- {
	- MITK_ERROR << "Illegal label. Label: \"" << loopLabelsVector.at(loop) << "\" not found.";
	- }
	- }
	- }
	- else
	- {
	- MITK_ERROR << "Illegal label. Label: \"" << regionLabelsVector.at(loop) << "\" not found.";
	- }
	- }
	-
	- if (firstRun)
	- {
	- regionalHeaderStream << " " << regionName << "_" << loopName << "_Connections "
	- << " " << regionName << "_" << loopName << "_possibleConnections "
	- << " " << regionName << "_" << loopName << "_ConnectingFibers";
	- }
	-
	- regionalDataStream << " " << numberConnections
	- << " " << possibleConnections
	- << " " << summedFiberCount;
	-
	- }
	- }
	- }
	-
	- firstRun = false;
	- }
	-
	- }// end calculate local averages
	-
	- if( !noGlobalStatistics )
	- {
	- std::cout << "Writing to " << globalOutName;
	- std::ofstream glocalOutFile( globalOutName.c_str(), ios::out );
	- if( ! glocalOutFile.is_open() )
	- {
	- std::string errorMessage = "Could not open " + globalOutName + " for writing.";
	- MITK_ERROR << errorMessage;
	- return EXIT_FAILURE;
	- }
	- glocalOutFile << globalHeaderStream.str() << globalDataStream.str();
	- glocalOutFile.close();
	- }
	-
	- if( localLabels.size() > 0 )
	- {
	- std::cout << "Writing to " << localOutName;
	- std::ofstream localOutFile( localOutName.c_str(), ios::out );
	- if( ! localOutFile.is_open() )
	- {
	- std::string errorMessage = "Could not open " + localOutName + " for writing.";
	- MITK_ERROR << errorMessage;
	- return EXIT_FAILURE;
	- }
	- localOutFile << localHeaderStream.str() << localDataStream.str();
	- localOutFile.close();
	- }
	-
	- if( parsedRegions.size() > 0 )
	- {
	- std::cout << "Writing to " << regionalOutName;
	- std::ofstream regionalOutFile( regionalOutName.c_str(), ios::out );
	- if( ! regionalOutFile.is_open() )
	- {
	- std::string errorMessage = "Could not open " + regionalOutName + " for writing.";
	- MITK_ERROR << errorMessage;
	- return EXIT_FAILURE;
	- }
	- regionalOutFile << regionalHeaderStream.str() << regionalDataStream.str();
	- regionalOutFile.close();
	- }
	-
	- return EXIT_SUCCESS;
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- std::cout << "DONE";
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/CMakeLists.txt b/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/CMakeLists.txt
	deleted file mode 100755
	index fdf23fbbd0..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/CMakeLists.txt
	+++ /dev/null
	@@ -1,47 +0,0 @@
	-option(BUILD_DiffusionFiberProcessingCmdApps "Build commandline tools for diffusion fiber processing" OFF)
	-
	-if(BUILD_DiffusionFiberProcessingCmdApps OR MITK_BUILD_ALL_APPS)
	-
	- # needed include directories
	- include_directories(
	- ${CMAKE_CURRENT_SOURCE_DIR}
	- ${CMAKE_CURRENT_BINARY_DIR}
	- )
	-
	- # list of diffusion cmdapps
	- # if an app requires additional dependencies
	- # they are added after a "^^" and separated by "_"
	- set( diffusionFiberProcessingcmdapps
	- TractDensity^^
	- Sift2WeightCopy^^
	- FiberExtraction^^
	- FiberExtractionRoi^^
	- FiberProcessing^^
	- FitFibersToImage^^
	- FiberDirectionExtraction^^
	- FiberJoin^^
	- FiberClustering^^
	- TractDensityFilter^^
	- )
	-
	- foreach(diffusionFiberProcessingcmdapp ${diffusionFiberProcessingcmdapps})
	- # extract cmd app name and dependencies
	- string(REPLACE "^^" "\\;" cmdapp_info ${diffusionFiberProcessingcmdapp})
	- set(cmdapp_info_list ${cmdapp_info})
	- list(GET cmdapp_info_list 0 appname)
	- list(GET cmdapp_info_list 1 raw_dependencies)
	- string(REPLACE "_" "\\;" dependencies "${raw_dependencies}")
	- set(dependencies_list ${dependencies})
	-
	- mitkFunctionCreateCommandLineApp(
	- NAME ${appname}
	- DEPENDS MitkDiffusionCmdApps ${dependencies_list}
	- PACKAGE_DEPENDS
	- )
	- endforeach()
	-
	- if(EXECUTABLE_IS_ENABLED)
	- MITK_INSTALL_TARGETS(EXECUTABLES ${EXECUTABLE_TARGET})
	- endif()
	-
	- endif()
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberClustering.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberClustering.cpp
	deleted file mode 100644
	index 0ddcd5aff6..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberClustering.cpp
	+++ /dev/null
	@@ -1,273 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkFiberBundle.h>
	-#include <mitkCommandLineParser.h>
	-#include <mitkLexicalCast.h>
	-#include <mitkIOUtil.h>
	-#include <itkTractClusteringFilter.h>
	-#include <mitkClusteringMetricEuclideanMean.h>
	-#include <mitkClusteringMetricEuclideanMax.h>
	-#include <mitkClusteringMetricEuclideanStd.h>
	-#include <mitkClusteringMetricAnatomic.h>
	-#include <mitkClusteringMetricScalarMap.h>
	-#include <mitkClusteringMetricInnerAngles.h>
	-#include <mitkClusteringMetricLength.h>
	-#include <itksys/SystemTools.hxx>
	-
	-typedef itksys::SystemTools ist;
	-
	-mitk::FiberBundle::Pointer LoadFib(std::string filename)
	-{
	- std::vector<mitk::BaseData::Pointer> fibInfile = mitk::IOUtil::Load(filename);
	- if( fibInfile.empty() )
	- std::cout << "File " << filename << " could not be read!";
	- mitk::BaseData::Pointer baseData = fibInfile.at(0);
	- return dynamic_cast<mitk::FiberBundle*>(baseData.GetPointer());
	-}
	-
	-/*!
	-\brief Spatially cluster fibers
	-*/
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Fiber Clustering");
	- parser.setCategory("Fiber Processing");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input:", "input fiber bundle (.fib; .trk; .tck)", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "output root", us::Any(), false, false, false, mitkCommandLineParser::Output);
	-
	- parser.addArgument("cluster_size", "", mitkCommandLineParser::Int, "Cluster size:", "", 10);
	- parser.addArgument("fiber_points", "", mitkCommandLineParser::Int, "Fiber points:", "", 12);
	- parser.addArgument("min_fibers", "", mitkCommandLineParser::Int, "Min. fibers per cluster:", "", 1);
	- parser.addArgument("max_clusters", "", mitkCommandLineParser::Int, "Max. clusters:", "");
	- parser.addArgument("merge_clusters", "", mitkCommandLineParser::Float, "Merge clusters:", "Set to 0 to avoid merging and to -1 to use the original cluster size", -1.0);
	- parser.addArgument("output_centroids", "", mitkCommandLineParser::Bool, "Output centroids:", "");
	- parser.addArgument("only_centroids", "", mitkCommandLineParser::Bool, "Output only centroids:", "");
	- parser.addArgument("merge_centroids", "", mitkCommandLineParser::Bool, "Merge centroids:", "");
	- parser.addArgument("metrics", "", mitkCommandLineParser::StringList, "Metrics:", "EU_MEAN; EU_STD; EU_MAX; ANAT; MAP; LENGTH", std::string("EU_MEAN"));
	- parser.addArgument("metric_weights", "", mitkCommandLineParser::StringList, "Metric weights:", "add one float weight for each used metric");
	- parser.addArgument("input_centroids", "", mitkCommandLineParser::String, "Input centroids:", "", us::Any(), true, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("scalar_map", "", mitkCommandLineParser::String, "Scalar map:", "", us::Any(), true, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("parcellation", "", mitkCommandLineParser::String, "Parcellation:", "", us::Any(), true, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("file_ending", "", mitkCommandLineParser::String, "File ending:", "");
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- std::string inFileName = us::any_cast<std::string>(parsedArgs["i"]);
	- std::string out_root = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- bool only_centroids = false;
	- if (parsedArgs.count("only_centroids"))
	- only_centroids = us::any_cast<bool>(parsedArgs["only_centroids"]);
	-
	- bool merge_centroids = false;
	- if (parsedArgs.count("merge_centroids"))
	- merge_centroids = us::any_cast<bool>(parsedArgs["merge_centroids"]);
	-
	- int cluster_size = 10;
	- if (parsedArgs.count("cluster_size"))
	- cluster_size = us::any_cast<int>(parsedArgs["cluster_size"]);
	-
	- int fiber_points = 12;
	- if (parsedArgs.count("fiber_points"))
	- fiber_points = us::any_cast<int>(parsedArgs["fiber_points"]);
	-
	- int min_fibers = 1;
	- if (parsedArgs.count("min_fibers"))
	- min_fibers = us::any_cast<int>(parsedArgs["min_fibers"]);
	-
	- int max_clusters = 0;
	- if (parsedArgs.count("max_clusters"))
	- max_clusters = us::any_cast<int>(parsedArgs["max_clusters"]);
	-
	- float merge_clusters = -1.0;
	- if (parsedArgs.count("merge_clusters"))
	- merge_clusters = us::any_cast<float>(parsedArgs["merge_clusters"]);
	-
	- bool output_centroids = false;
	- if (parsedArgs.count("output_centroids"))
	- output_centroids = us::any_cast<bool>(parsedArgs["output_centroids"]);
	-
	- std::vector< std::string > metric_strings = {"EU_MEAN"};
	- if (parsedArgs.count("metrics"))
	- metric_strings = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["metrics"]);
	-
	- std::vector< std::string > metric_weights = {"1.0"};
	- if (parsedArgs.count("metric_weights"))
	- metric_weights = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["metric_weights"]);
	-
	- std::string input_centroids = "";
	- if (parsedArgs.count("input_centroids"))
	- input_centroids = us::any_cast<std::string>(parsedArgs["input_centroids"]);
	-
	- std::string scalar_map = "";
	- if (parsedArgs.count("scalar_map"))
	- scalar_map = us::any_cast<std::string>(parsedArgs["scalar_map"]);
	-
	- std::string parcellation = "";
	- if (parsedArgs.count("parcellation"))
	- parcellation = us::any_cast<std::string>(parsedArgs["parcellation"]);
	-
	- std::string file_ending = ".fib";
	- if (parsedArgs.count("file_ending"))
	- file_ending = us::any_cast<std::string>(parsedArgs["file_ending"]);
	-
	- if (metric_strings.size()!=metric_weights.size())
	- {
	- MITK_INFO << "Each metric needs an associated metric weight!";
	- return EXIT_FAILURE;
	- }
	-
	- try
	- {
	- typedef itk::Image< float, 3 > FloatImageType;
	- typedef itk::Image< short, 3 > ShortImageType;
	-
	- mitk::FiberBundle::Pointer fib = LoadFib(inFileName);
	-
	- float max_d = 0;
	- int i=1;
	- std::vector< float > distances;
	- while (max_d < fib->GetGeometry()->GetDiagonalLength()/2)
	- {
	- distances.push_back(cluster_size*i);
	- max_d = cluster_size*i;
	- ++i;
	- }
	-
	- itk::TractClusteringFilter::Pointer clusterer = itk::TractClusteringFilter::New();
	- clusterer->SetDistances(distances);
	- clusterer->SetTractogram(fib);
	-
	- if (input_centroids!="")
	- {
	-
	- mitk::FiberBundle::Pointer in_centroids = LoadFib(input_centroids);
	- clusterer->SetInCentroids(in_centroids);
	- }
	-
	- std::vector< mitk::ClusteringMetric* > metrics;
	-
	- int mc = 0;
	- for (auto m : metric_strings)
	- {
	- float w = boost::lexical_cast<float>(metric_weights.at(mc));
	- MITK_INFO << "Metric: " << m << " (w=" << w << ")";
	- if (m=="EU_MEAN")
	- metrics.push_back({new mitk::ClusteringMetricEuclideanMean()});
	- else if (m=="EU_STD")
	- metrics.push_back({new mitk::ClusteringMetricEuclideanStd()});
	- else if (m=="EU_MAX")
	- metrics.push_back({new mitk::ClusteringMetricEuclideanMax()});
	- else if (m=="ANGLES")
	- metrics.push_back({new mitk::ClusteringMetricInnerAngles()});
	- else if (m=="LENGTH")
	- metrics.push_back({new mitk::ClusteringMetricLength()});
	- else if (m=="MAP" && scalar_map!="")
	- {
	- mitk::Image::Pointer mitk_map = mitk::IOUtil::Load<mitk::Image>(scalar_map);
	- if (mitk_map->GetDimension()==3)
	- {
	- FloatImageType::Pointer itk_map = FloatImageType::New();
	- mitk::CastToItkImage(mitk_map, itk_map);
	-
	- mitk::ClusteringMetricScalarMap* metric = new mitk::ClusteringMetricScalarMap();
	- metric->SetImages({itk_map});
	- metric->SetScale(distances.at(0));
	- metrics.push_back(metric);
	- }
	- }
	- else if (m=="ANAT" && parcellation!="")
	- {
	- mitk::Image::Pointer mitk_map = mitk::IOUtil::Load<mitk::Image>(parcellation);
	- if (mitk_map->GetDimension()==3)
	- {
	- ShortImageType::Pointer itk_map = ShortImageType::New();
	- mitk::CastToItkImage(mitk_map, itk_map);
	-
	- mitk::ClusteringMetricAnatomic* metric = new mitk::ClusteringMetricAnatomic();
	- metric->SetParcellations({itk_map});
	- metrics.push_back(metric);
	- }
	- }
	- metrics.back()->SetScale(w);
	- mc++;
	- }
	-
	- if (metrics.empty())
	- {
	- MITK_INFO << "No metric selected!";
	- return EXIT_FAILURE;
	- }
	-
	- clusterer->SetMetrics(metrics);
	- clusterer->SetMergeDuplicateThreshold(merge_clusters);
	- clusterer->SetNumPoints(fiber_points);
	- clusterer->SetMaxClusters(max_clusters);
	- clusterer->SetMinClusterSize(min_fibers);
	- clusterer->Update();
	- std::vector<mitk::FiberBundle::Pointer> tracts = clusterer->GetOutTractograms();
	- std::vector<mitk::FiberBundle::Pointer> centroids = clusterer->GetOutCentroids();
	-
	- MITK_INFO << "Saving clusters";
	- std::streambuf *old = cout.rdbuf(); // <-- save
	- std::stringstream ss;
	- std::cout.rdbuf (ss.rdbuf()); // <-- redirect
	-
	- if (!only_centroids)
	- for (unsigned int i=0; i<tracts.size(); ++i)
	- mitk::IOUtil::Save(tracts.at(i), out_root + "Cluster_" + boost::lexical_cast<std::string>(i) + file_ending);
	-
	-
	- if (output_centroids && !merge_centroids)
	- {
	- for (unsigned int i=0; i<centroids.size(); ++i)
	- mitk::IOUtil::Save(centroids.at(i), out_root + "Centroid_" + boost::lexical_cast<std::string>(i) + file_ending);
	- }
	- else if (output_centroids)
	- {
	- mitk::FiberBundle::Pointer centroid = mitk::FiberBundle::New();
	- centroid = centroid->AddBundles(centroids);
	- mitk::IOUtil::Save(centroid, out_root + ist::GetFilenameWithoutExtension(inFileName) + "_Centroids" + file_ending);
	- }
	-
	- std::cout.rdbuf (old); // <-- restore
	-
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberDirectionExtraction.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberDirectionExtraction.cpp
	deleted file mode 100755
	index 4bb955b3af..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberDirectionExtraction.cpp
	+++ /dev/null
	@@ -1,183 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkBaseData.h>
	-#include <mitkImageCast.h>
	-#include <mitkImageToItk.h>
	-#include <metaCommand.h>
	-#include "mitkCommandLineParser.h"
	-#include <usAny.h>
	-#include <itkImageFileWriter.h>
	-#include <mitkIOUtil.h>
	-#include <mitkLexicalCast.h>
	-#include <itkEvaluateDirectionImagesFilter.h>
	-#include <itkTractsToVectorImageFilter.h>
	-#include <mitkCoreObjectFactory.h>
	-#include <mitkLocaleSwitch.h>
	-
	-/*!
	-\brief Extract principal fiber directions from a tractogram
	-*/
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Fiber Direction Extraction");
	- parser.setCategory("Fiber Tracking and Processing Methods");
	- parser.setDescription("Extract principal fiber directions from a tractogram");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input:", "input tractogram (.fib/.trk)", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "output root", us::Any(), false, false, false, mitkCommandLineParser::Output);
	- parser.addArgument("mask", "", mitkCommandLineParser::String, "Mask:", "mask image", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("athresh", "", mitkCommandLineParser::Float, "Angular threshold:", "angular threshold in degrees. closer fiber directions are regarded as one direction and clustered together.", 25, true);
	- parser.addArgument("peakthresh", "", mitkCommandLineParser::Float, "Peak size threshold:", "peak size threshold relative to largest peak in voxel", 0.2, true);
	- parser.addArgument("only_mask_geometry", "", mitkCommandLineParser::Bool, "Only mask geometry:", "don't use content of mask image, only use it's geometry", false);
	- parser.addArgument("verbose", "", mitkCommandLineParser::Bool, "Verbose:", "output optional and intermediate calculation results");
	- parser.addArgument("numdirs", "", mitkCommandLineParser::Int, "Max. num. directions:", "maximum number of fibers per voxel", 3, true);
	- parser.addArgument("normalization", "", mitkCommandLineParser::Int, "Normalization method:", "1=global maximum; 2=single vector; 3=voxel-wise maximum", 1);
	- parser.addArgument("file_ending", "", mitkCommandLineParser::String, "Image type:", ".nrrd; .nii; .nii.gz", std::string(".nii.gz"));
	-
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- std::string fibFile = us::any_cast<std::string>(parsedArgs["i"]);
	-
	- std::string maskImage("");
	- if (parsedArgs.count("mask"))
	- maskImage = us::any_cast<std::string>(parsedArgs["mask"]);
	-
	- float peakThreshold = 0.2;
	- if (parsedArgs.count("peakthresh"))
	- peakThreshold = us::any_cast<float>(parsedArgs["peakthresh"]);
	-
	- float angularThreshold = 25;
	- if (parsedArgs.count("athresh"))
	- angularThreshold = us::any_cast<float>(parsedArgs["athresh"]);
	-
	- std::string outRoot = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- bool verbose = false;
	- if (parsedArgs.count("verbose"))
	- verbose = us::any_cast<bool>(parsedArgs["verbose"]);
	-
	- bool only_mask_geometry = false;
	- if (parsedArgs.count("only_mask_geometry"))
	- only_mask_geometry = us::any_cast<bool>(parsedArgs["only_mask_geometry"]);
	-
	- int maxNumDirs = 3;
	- if (parsedArgs.count("numdirs"))
	- maxNumDirs = us::any_cast<int>(parsedArgs["numdirs"]);
	-
	- int normalization = 1;
	- if (parsedArgs.count("normalization"))
	- normalization = us::any_cast<int>(parsedArgs["normalization"]);
	-
	- std::string file_ending = ".nii.gz";
	- if (parsedArgs.count("file_ending"))
	- file_ending = us::any_cast<std::string>(parsedArgs["file_ending"]);
	-
	-
	- try
	- {
	- typedef itk::Image<unsigned char, 3> ItkUcharImgType;
	-
	- // load fiber bundle
	- mitk::FiberBundle::Pointer inputTractogram = mitk::IOUtil::Load<mitk::FiberBundle>(fibFile);
	-
	- // load/create mask image
	- ItkUcharImgType::Pointer itkMaskImage = nullptr;
	- if (maskImage.compare("")!=0)
	- {
	- std::cout << "Using mask image";
	- itkMaskImage = ItkUcharImgType::New();
	- mitk::Image::Pointer mitkMaskImage = mitk::IOUtil::Load<mitk::Image>(maskImage);
	- mitk::CastToItkImage(mitkMaskImage, itkMaskImage);
	- }
	-
	- // extract directions from fiber bundle
	- itk::TractsToVectorImageFilter<float>::Pointer fOdfFilter = itk::TractsToVectorImageFilter<float>::New();
	- fOdfFilter->SetFiberBundle(inputTractogram);
	- fOdfFilter->SetOnlyUseMaskGeometry(only_mask_geometry);
	- fOdfFilter->SetMaskImage(itkMaskImage);
	- fOdfFilter->SetAngularThreshold(cos(angularThreshold*itk::Math::pi/180));
	- switch (normalization)
	- {
	- case 1:
	- fOdfFilter->SetNormalizationMethod(itk::TractsToVectorImageFilter<float>::NormalizationMethods::GLOBAL_MAX);
	- break;
	- case 2:
	- fOdfFilter->SetNormalizationMethod(itk::TractsToVectorImageFilter<float>::NormalizationMethods::SINGLE_VEC_NORM);
	- break;
	- case 3:
	- fOdfFilter->SetNormalizationMethod(itk::TractsToVectorImageFilter<float>::NormalizationMethods::MAX_VEC_NORM);
	- break;
	- }
	- fOdfFilter->SetSizeThreshold(peakThreshold);
	- fOdfFilter->SetMaxNumDirections(maxNumDirs);
	- fOdfFilter->Update();
	-
	- mitk::LocaleSwitch localeSwitch("C");
	- {
	- itk::TractsToVectorImageFilter<float>::ItkDirectionImageType::Pointer itkImg = fOdfFilter->GetDirectionImage();
	- typedef itk::ImageFileWriter< itk::TractsToVectorImageFilter<float>::ItkDirectionImageType > WriterType;
	- WriterType::Pointer writer = WriterType::New();
	-
	- std::string outfilename = outRoot;
	- outfilename.append("_DIRECTIONS");
	- outfilename.append(file_ending);
	-
	- writer->SetFileName(outfilename.c_str());
	- writer->SetInput(itkImg);
	- writer->Update();
	- }
	-
	- if (verbose)
	- {
	- // write num direction image
	- ItkUcharImgType::Pointer numDirImage = fOdfFilter->GetNumDirectionsImage();
	- typedef itk::ImageFileWriter< ItkUcharImgType > WriterType;
	- WriterType::Pointer writer = WriterType::New();
	-
	- std::string outfilename = outRoot;
	- outfilename.append("_NUM_DIRECTIONS");
	- outfilename.append(file_ending);
	-
	- writer->SetFileName(outfilename.c_str());
	- writer->SetInput(numDirImage);
	- writer->Update();
	- }
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberExtraction.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberExtraction.cpp
	deleted file mode 100755
	index 9eb0dbeedc..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberExtraction.cpp
	+++ /dev/null
	@@ -1,151 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <metaCommand.h>
	-#include "mitkCommandLineParser.h"
	-#include <usAny.h>
	-#include <mitkIOUtil.h>
	-#include <mitkLexicalCast.h>
	-#include <mitkCoreObjectFactory.h>
	-#include <mitkPlanarFigure.h>
	-#include <mitkPlanarFigureComposite.h>
	-#include <mitkFiberBundle.h>
	-#include <mitkImageCast.h>
	-#include <mitkImageToItk.h>
	-#include <mitkStandaloneDataStorage.h>
	-
	-#define _USE_MATH_DEFINES
	-#include <math.h>
	-
	-/*!
	-\brief Extract fibers from a tractogram using planar figure ROIs
	-*/
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Fiber Extraction");
	- parser.setCategory("Fiber Tracking and Processing Methods");
	- parser.setContributor("MIC");
	- parser.setDescription("Extract fibers from a tractogram using planar figure ROIs");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input:", "input tractogram (.fib/.trk)", us::Any(), false);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "output tractogram", us::Any(), false);
	- parser.addArgument("planfirgure1", "pf1", mitkCommandLineParser::String, "Figure 1:", "first planar figure ROI", us::Any(), false);
	- parser.addArgument("planfirgure2", "pf2", mitkCommandLineParser::String, "Figure 2:", "second planar figure ROI", us::Any());
	- parser.addArgument("operation", "op", mitkCommandLineParser::String, "Operation:", "logical operation (AND; OR; NOT)", us::Any());
	-
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- std::string inFib = us::any_cast<std::string>(parsedArgs["i"]);
	- std::string outFib = us::any_cast<std::string>(parsedArgs["o"]);
	- std::string pf1_path = us::any_cast<std::string>(parsedArgs["planfirgure1"]);
	-
	- std::string operation("");
	- std::string pf2_path("");
	- if (parsedArgs.count("operation"))
	- {
	- operation = us::any_cast<std::string>(parsedArgs["operation"]);
	- if (parsedArgs.count("planfirgure2") && (operation=="AND" \|\| operation=="OR"))
	- pf2_path = us::any_cast<std::string>(parsedArgs["planfirgure2"]);
	- }
	-
	- try
	- {
	- // load fiber bundle
	- mitk::FiberBundle::Pointer inputTractogram = mitk::IOUtil::Load<mitk::FiberBundle>(inFib);
	- mitk::FiberBundle::Pointer result;
	-
	- mitk::StandaloneDataStorage::Pointer storage = mitk::StandaloneDataStorage::New();
	- auto data = mitk::IOUtil::Load(pf1_path)[0];
	- auto input1 = mitk::DataNode::New();
	- input1->SetData(data);
	-
	- if (input1.IsNotNull())
	- {
	- mitk::PlanarFigureComposite::Pointer pfc = mitk::PlanarFigureComposite::New();
	- mitk::DataNode::Pointer pfcNode = mitk::DataNode::New();
	- pfcNode->SetData(pfc);
	- mitk::DataStorage::SetOfObjects::Pointer set1 = mitk::DataStorage::SetOfObjects::New();
	- set1->push_back(pfcNode);
	- storage->Add(pfcNode);
	-
	- auto input2 = mitk::DataNode::New();
	- if (!pf2_path.empty())
	- {
	- data = mitk::IOUtil::Load(pf2_path)[0];
	- input2->SetData(data);
	- }
	-
	- if (operation.empty())
	- {
	- result = inputTractogram->ExtractFiberSubset(input1, nullptr);
	- }
	- else if (operation=="NOT")
	- {
	- pfc->setOperationType(mitk::PlanarFigureComposite::NOT);
	- storage->Add(input1, set1);
	- result = inputTractogram->ExtractFiberSubset(pfcNode, storage);
	- }
	- else if (operation=="AND" && input2.IsNotNull())
	- {
	- pfc->setOperationType(mitk::PlanarFigureComposite::AND);
	- storage->Add(input1, set1);
	- storage->Add(input2, set1);
	- result = inputTractogram->ExtractFiberSubset(pfcNode, storage);
	- }
	- else if (operation=="OR" && input2.IsNotNull())
	- {
	- pfc->setOperationType(mitk::PlanarFigureComposite::OR);
	- storage->Add(input1, set1);
	- storage->Add(input2, set1);
	- result = inputTractogram->ExtractFiberSubset(pfcNode, storage);
	- }
	- else
	- {
	- std::cout << "Could not process input:";
	- std::cout << pf1_path;
	- std::cout << pf2_path;
	- std::cout << operation;
	- }
	- }
	-
	- if (result.IsNotNull())
	- mitk::IOUtil::Save(result, outFib);
	- else
	- std::cout << "No valid fiber bundle extracted.";
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberExtractionRoi.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberExtractionRoi.cpp
	deleted file mode 100755
	index a464985d16..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberExtractionRoi.cpp
	+++ /dev/null
	@@ -1,276 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <metaCommand.h>
	-#include "mitkCommandLineParser.h"
	-#include <usAny.h>
	-#include <mitkIOUtil.h>
	-#include <mitkLexicalCast.h>
	-#include <mitkCoreObjectFactory.h>
	-#include <mitkPlanarFigure.h>
	-#include <mitkPlanarFigureComposite.h>
	-#include <mitkFiberBundle.h>
	-#include <mitkImageCast.h>
	-#include <mitkImageToItk.h>
	-#include <mitkStandaloneDataStorage.h>
	-#include <itksys/SystemTools.hxx>
	-#include <itkFiberExtractionFilter.h>
	-
	-#define _USE_MATH_DEFINES
	-#include <math.h>
	-
	-typedef itksys::SystemTools ist;
	-typedef itk::Image<float, 3> ItkFloatImgType;
	-
	-ItkFloatImgType::Pointer LoadItkImage(const std::string& filename)
	-{
	- mitk::Image::Pointer img = mitk::IOUtil::Load<mitk::Image>(filename);
	- ItkFloatImgType::Pointer itk_image = ItkFloatImgType::New();
	- mitk::CastToItkImage(img, itk_image);
	- return itk_image;
	-}
	-
	-/*!
	-\brief Extract fibers from a tractogram using binary image ROIs
	-*/
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Fiber Extraction With ROI Image");
	- parser.setCategory("Fiber Tracking and Processing Methods");
	- parser.setContributor("MIC");
	- parser.setDescription("Extract fibers from a tractogram using binary image ROIs");
	-
	- parser.setArgumentPrefix("--", "-");
	-
	- parser.beginGroup("1. Mandatory arguments:");
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input:", "input tractogram (.fib/.trk/.tck/.dcm)", us::Any(), false);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "output root", us::Any(), false);
	- parser.addArgument("rois", "", mitkCommandLineParser::StringList, "ROI images:", "ROI images", us::Any(), false);
	- parser.endGroup();
	-
	- parser.beginGroup("2. Label based extraction:");
	- parser.addArgument("split_labels", "", mitkCommandLineParser::Bool, "Split labels:", "output a separate tractogram for each label-->label tract", false);
	- parser.addArgument("skip_self_connections", "", mitkCommandLineParser::Bool, "Skip self connections:", "ignore streamlines between two identical labels", false);
	- parser.addArgument("all_labels", "", mitkCommandLineParser::Bool, "All labels:", "use all labels (0 is excluded)", false);
	- parser.addArgument("labels", "", mitkCommandLineParser::StringList, "Labels:", "positive means roi image value in labels vector", us::Any());
	- parser.addArgument("start_labels", "", mitkCommandLineParser::StringList, "Start Labels:", "use separate start and end labels instead of one mixed set", us::Any());
	- parser.addArgument("end_labels", "", mitkCommandLineParser::StringList, "End Labels:", "use separate start and end labels instead of one mixed set", us::Any());
	- parser.addArgument("paired", "", mitkCommandLineParser::Bool, "Paired:", "start and end label list are paired", false);
	- parser.endGroup();
	-
	- parser.beginGroup("3. Misc:");
	- parser.addArgument("both_ends", "", mitkCommandLineParser::Bool, "Both ends:", "Fibers are extracted if both endpoints are located in the ROI.", false);
	- parser.addArgument("overlap_fraction", "", mitkCommandLineParser::Float, "Overlap fraction:", "Extract by overlap, not by endpoints. Extract fibers that overlap to at least the provided factor (0-1) with the ROI.", -1);
	- parser.addArgument("invert", "", mitkCommandLineParser::Bool, "Invert:", "get streamlines not positive for any of the ROI images", false);
	- parser.addArgument("output_negatives", "", mitkCommandLineParser::Bool, "Negatives:", "output negatives", false);
	- parser.addArgument("interpolate", "", mitkCommandLineParser::Bool, "Interpolate:", "interpolate ROI images (only for endpoint based extraction)", false);
	- parser.addArgument("threshold", "", mitkCommandLineParser::Float, "Threshold:", "positive means ROI image value threshold", 0.5);
	- parser.addArgument("min_fibers", "", mitkCommandLineParser::Int, "Min. num. fibers:", "discard positive tracts with less fibers", 0);
	- parser.addArgument("split_rois", "", mitkCommandLineParser::Bool, "Split ROIs:", "output a separate tractogram for each ROI", false);
	- parser.endGroup();
	-
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- std::string inFib = us::any_cast<std::string>(parsedArgs["i"]);
	- std::string outFib = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- mitkCommandLineParser::StringContainerType roi_files = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["rois"]);
	-
	- bool both_ends = false;
	- if (parsedArgs.count("both_ends"))
	- both_ends = us::any_cast<bool>(parsedArgs["both_ends"]);
	-
	- bool invert = false;
	- if (parsedArgs.count("invert"))
	- invert = us::any_cast<bool>(parsedArgs["invert"]);
	-
	- unsigned int min_fibers = 0;
	- if (parsedArgs.count("min_fibers"))
	- min_fibers = us::any_cast<int>(parsedArgs["min_fibers"]);
	-
	- bool all_labels = false;
	- if (parsedArgs.count("all_labels"))
	- all_labels = us::any_cast<bool>(parsedArgs["all_labels"]);
	-
	- bool split_labels = false;
	- if (parsedArgs.count("split_labels"))
	- split_labels = us::any_cast<bool>(parsedArgs["split_labels"]);
	-
	- bool split_rois = false;
	- if (parsedArgs.count("split_rois"))
	- split_rois = us::any_cast<bool>(parsedArgs["split_rois"]);
	-
	- bool skip_self_connections = false;
	- if (parsedArgs.count("skip_self_connections"))
	- skip_self_connections = us::any_cast<bool>(parsedArgs["skip_self_connections"]);
	-
	- bool output_negatives = false;
	- if (parsedArgs.count("output_negatives"))
	- output_negatives = us::any_cast<bool>(parsedArgs["output_negatives"]);
	-
	- float overlap_fraction = -1;
	- if (parsedArgs.count("overlap_fraction"))
	- overlap_fraction = us::any_cast<float>(parsedArgs["overlap_fraction"]);
	-
	- bool any_point = false;
	- if (overlap_fraction>=0)
	- any_point = true;
	-
	- bool interpolate = false;
	- if (parsedArgs.count("interpolate"))
	- interpolate = us::any_cast<bool>(parsedArgs["interpolate"]);
	-
	- float threshold = 0.5;
	- if (parsedArgs.count("threshold"))
	- threshold = us::any_cast<float>(parsedArgs["threshold"]);
	-
	- mitkCommandLineParser::StringContainerType labels;
	- if (parsedArgs.count("labels"))
	- labels = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["labels"]);
	-
	- mitkCommandLineParser::StringContainerType start_labels;
	- if (parsedArgs.count("start_labels"))
	- start_labels = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["start_labels"]);
	-
	- mitkCommandLineParser::StringContainerType end_labels;
	- if (parsedArgs.count("end_labels"))
	- end_labels = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["end_labels"]);
	-
	- bool paired = false;
	- if (parsedArgs.count("paired"))
	- paired = us::any_cast<bool>(parsedArgs["paired"]);
	-
	- try
	- {
	- // load fiber bundle
	- mitk::FiberBundle::Pointer inputTractogram = mitk::IOUtil::Load<mitk::FiberBundle>(inFib);
	-
	- std::streambuf *old = cout.rdbuf(); // <-- save
	- std::stringstream ss;
	- std::cout.rdbuf (ss.rdbuf()); // <-- redirect
	- std::vector< ItkFloatImgType::Pointer > roi_images;
	- std::vector< std::string > roi_names;
	- for (std::size_t i=0; i<roi_files.size(); ++i)
	- {
	- roi_images.push_back( LoadItkImage(roi_files.at(i)) );
	- roi_names.push_back(itksys::SystemTools::GetFilenameWithoutExtension(roi_files.at(i)));
	- }
	- std::cout.rdbuf (old); // <-- restore
	- MITK_INFO << "Loaded " << roi_images.size() << " ROI images.";
	-
	- std::vector< ItkFloatImgType* > roi_images2;
	- for (auto roi : roi_images)
	- roi_images2.push_back(roi);
	-
	- std::vector< unsigned short > short_labels;
	- for (auto l : labels)
	- short_labels.push_back(boost::lexical_cast<unsigned short>(l));
	-
	- std::vector< unsigned short > short_start_labels;
	- for (auto l : start_labels)
	- short_start_labels.push_back(boost::lexical_cast<unsigned short>(l));
	-
	- std::vector< unsigned short > short_end_labels;
	- for (auto l : end_labels)
	- short_end_labels.push_back(boost::lexical_cast<unsigned short>(l));
	-
	- itk::FiberExtractionFilter<float>::Pointer extractor = itk::FiberExtractionFilter<float>::New();
	- extractor->SetInputFiberBundle(inputTractogram);
	- extractor->SetRoiImages(roi_images2);
	- extractor->SetRoiImageNames(roi_names);
	- extractor->SetOverlapFraction(overlap_fraction);
	- extractor->SetBothEnds(both_ends);
	- extractor->SetInterpolate(interpolate);
	- extractor->SetThreshold(threshold);
	- extractor->SetLabels(short_labels);
	- extractor->SetStartLabels(short_start_labels);
	- extractor->SetEndLabels(short_end_labels);
	- extractor->SetSplitLabels(split_labels);
	- extractor->SetSplitByRoi(split_rois);
	- extractor->SetMinFibersPerTract(min_fibers);
	- extractor->SetSkipSelfConnections(skip_self_connections);
	- extractor->SetPairedStartEndLabels(paired);
	- if (!any_point)
	- extractor->SetMode(itk::FiberExtractionFilter<float>::MODE::ENDPOINTS);
	- if (all_labels \|\| short_labels.size()>0 \|\| short_start_labels.size()>0 \|\| short_end_labels.size()>0)
	- extractor->SetInputType(itk::FiberExtractionFilter<float>::INPUT::LABEL_MAP);
	- extractor->Update();
	-
	- std::string ext = itksys::SystemTools::GetFilenameExtension(outFib);
	- if (ext.empty())
	- ext = ".trk";
	- outFib = itksys::SystemTools::GetFilenamePath(outFib) + '/' + itksys::SystemTools::GetFilenameWithoutExtension(outFib);
	- if (invert)
	- mitk::IOUtil::Save(extractor->GetNegatives().at(0), outFib + ext);
	- else
	- {
	- int c = 0;
	- std::vector< std::string > positive_labels = extractor->GetPositiveLabels();
	- for (auto fib : extractor->GetPositives())
	- {
	- std::string l = positive_labels.at(c);
	- if (l.size()>0)
	- mitk::IOUtil::Save(fib, outFib + "_" + l + ext);
	- else
	- mitk::IOUtil::Save(fib, outFib + ext);
	- ++c;
	- }
	- }
	-
	- if (output_negatives)
	- {
	- invert = !invert;
	- if (invert)
	- mitk::IOUtil::Save(extractor->GetNegatives().at(0), outFib + "_negatives" + ext);
	- else
	- {
	- int c = 0;
	- std::vector< std::string > positive_labels = extractor->GetPositiveLabels();
	- for (auto fib : extractor->GetPositives())
	- {
	- std::string l = positive_labels.at(c);
	-
	- if (l.size()>0)
	- mitk::IOUtil::Save(fib, outFib + "_" + l + "_negatives" + ext);
	- else
	- mitk::IOUtil::Save(fib, outFib + "_negatives" + ext);
	- ++c;
	- }
	- }
	- }
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberJoin.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberJoin.cpp
	deleted file mode 100755
	index fb9bcdd533..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberJoin.cpp
	+++ /dev/null
	@@ -1,100 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkIOUtil.h>
	-#include <metaCommand.h>
	-#include "mitkCommandLineParser.h"
	-#include <usAny.h>
	-#include <mitkIOUtil.h>
	-#include <mitkLexicalCast.h>
	-#include <mitkCoreObjectFactory.h>
	-#include <mitkPlanarFigure.h>
	-#include <mitkPlanarFigureComposite.h>
	-#include <mitkFiberBundle.h>
	-
	-#define _USE_MATH_DEFINES
	-#include <math.h>
	-
	-mitk::FiberBundle::Pointer LoadFib(std::string filename)
	-{
	- std::vector<mitk::BaseData::Pointer> fibInfile = mitk::IOUtil::Load(filename);
	- if( fibInfile.empty() )
	- std::cout << "File " << filename << " could not be read!";
	- mitk::BaseData::Pointer baseData = fibInfile.at(0);
	- return dynamic_cast<mitk::FiberBundle*>(baseData.GetPointer());
	-}
	-
	-/*!
	-\brief Join multiple tractograms
	-*/
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Fiber Join");
	- parser.setCategory("Fiber Tracking and Processing Methods");
	- parser.setContributor("MIC");
	- parser.setDescription("Join multiple tractograms");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i", mitkCommandLineParser::StringList, "Input:", "input tractograms", us::Any(), false);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "output tractogram", us::Any(), false);
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- mitkCommandLineParser::StringContainerType inFibs = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["i"]);
	- std::string outFib = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- if (inFibs.size()<=1)
	- {
	- std::cout << "More than one input tractogram required!";
	- return EXIT_FAILURE;
	- }
	-
	- try
	- {
	- std::vector< mitk::FiberBundle::Pointer > tractograms;
	- mitk::FiberBundle::Pointer result = LoadFib(inFibs.at(0));
	- for (std::size_t i=1; i<inFibs.size(); ++i)
	- {
	- try
	- {
	- tractograms.push_back(LoadFib(inFibs.at(i)));
	- }
	- catch(...){ std::cout << "could not load: " << inFibs.at(i); }
	- }
	- result = result->AddBundles(tractograms);
	- mitk::IOUtil::Save(result, outFib);
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberProcessing.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberProcessing.cpp
	deleted file mode 100644
	index 648fe2042e..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberProcessing.cpp
	+++ /dev/null
	@@ -1,301 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <vector>
	-#include <iostream>
	-#include <fstream>
	-#include <algorithm>
	-
	-#include <itkImageFileWriter.h>
	-#include <itkMetaDataObject.h>
	-#include <itkVectorImage.h>
	-
	-#include <mitkBaseData.h>
	-#include <mitkFiberBundle.h>
	-#include "mitkCommandLineParser.h"
	-#include <mitkLexicalCast.h>
	-#include <mitkCoreObjectFactory.h>
	-#include <mitkIOUtil.h>
	-#include <itkFiberCurvatureFilter.h>
	-#include <mitkDiffusionDataIOHelper.h>
	-#include <itkImage.h>
	-
	-
	-mitk::FiberBundle::Pointer LoadFib(std::string filename)
	-{
	- std::vector<mitk::BaseData::Pointer> fibInfile = mitk::IOUtil::Load(filename);
	- if( fibInfile.empty() )
	- std::cout << "File " << filename << " could not be read!";
	- mitk::BaseData::Pointer baseData = fibInfile.at(0);
	- return dynamic_cast<mitk::FiberBundle*>(baseData.GetPointer());
	-}
	-
	-/*!
	-\brief Modify input tractogram: fiber resampling, compression, pruning and transformation.
	-*/
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Fiber Processing");
	- parser.setCategory("Fiber Tracking and Processing Methods");
	- parser.setDescription("Modify input tractogram: fiber resampling, compression, pruning and transformation.");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	-
	- parser.beginGroup("1. Mandatory arguments:");
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input:", "Input fiber bundle (.fib, .trk, .tck)", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "Output fiber bundle (.fib, .trk)", us::Any(), false, false, false, mitkCommandLineParser::Output);
	- parser.endGroup();
	-
	- parser.beginGroup("2. Resampling:");
	- parser.addArgument("spline_resampling", "", mitkCommandLineParser::Float, "Spline resampling:", "Resample fiber using splines with the given point distance (in mm)");
	- parser.addArgument("linear_resampling", "", mitkCommandLineParser::Float, "Linear resampling:", "Resample fiber linearly with the given point distance (in mm)");
	- parser.addArgument("num_resampling", "", mitkCommandLineParser::Int, "Num. fiber points resampling:", "Resample all fibers to the given number of points");
	- parser.addArgument("compress", "", mitkCommandLineParser::Float, "Compress:", "Compress fiber using the given error threshold (in mm)");
	- parser.endGroup();
	-
	- parser.beginGroup("3. Filtering:");
	- parser.addArgument("min_length", "", mitkCommandLineParser::Float, "Minimum length:", "Minimum fiber length (in mm)");
	- parser.addArgument("max_length", "", mitkCommandLineParser::Float, "Maximum length:", "Maximum fiber length (in mm)");
	- parser.addArgument("max_angle", "", mitkCommandLineParser::Float, "Maximum angle:", "Maximum angular STDEV (in degree) over given distance");
	- parser.addArgument("max_angle_dist", "", mitkCommandLineParser::Float, "Distance:", "Distance in mm", 10);
	- parser.addArgument("remove", "", mitkCommandLineParser::Bool, "Remove fibers exceeding curvature threshold:", "If false, only the high curvature parts are removed");
	- parser.addArgument("subsample", "", mitkCommandLineParser::Float, "Randomly select fraction of streamlines:", "Randomly select the specified fraction of streamlines from the input tractogram");
	- parser.addArgument("random_subsample", "", mitkCommandLineParser::Bool, "Randomly seed subsampling:", "Randomly seed subsampling. Else, use seed 0.");
	- parser.endGroup();
	-
	- parser.beginGroup("4. Transformation:");
	- parser.addArgument("mirror", "", mitkCommandLineParser::Int, "Invert coordinates:", "Invert fiber coordinates XYZ (e.g. 010 to invert y-coordinate of each fiber point)");
	-
	- parser.addArgument("rotate_x", "", mitkCommandLineParser::Float, "Rotate x-axis:", "Rotate around x-axis (in deg)");
	- parser.addArgument("rotate_y", "", mitkCommandLineParser::Float, "Rotate y-axis:", "Rotate around y-axis (in deg)");
	- parser.addArgument("rotate_z", "", mitkCommandLineParser::Float, "Rotate z-axis:", "Rotate around z-axis (in deg)");
	-
	- parser.addArgument("scale_x", "", mitkCommandLineParser::Float, "Scale x-axis:", "Scale in direction of x-axis");
	- parser.addArgument("scale_y", "", mitkCommandLineParser::Float, "Scale y-axis:", "Scale in direction of y-axis");
	- parser.addArgument("scale_z", "", mitkCommandLineParser::Float, "Scale z-axis", "Scale in direction of z-axis");
	-
	- parser.addArgument("translate_x", "", mitkCommandLineParser::Float, "Translate x-axis:", "Translate in direction of x-axis (in mm)");
	- parser.addArgument("translate_y", "", mitkCommandLineParser::Float, "Translate y-axis:", "Translate in direction of y-axis (in mm)");
	- parser.addArgument("translate_z", "", mitkCommandLineParser::Float, "Translate z-axis:", "Translate in direction of z-axis (in mm)");
	-
	- parser.endGroup();
	-
	- parser.beginGroup("5. Remove fiber parts:");
	- parser.addArgument("remove_inside", "", mitkCommandLineParser::Bool, "Remove fibers inside mask:", "remove fibers inside mask");
	- parser.addArgument("remove_outside", "", mitkCommandLineParser::Bool, "Remove fibers outside mask:", "remove fibers outside mask");
	- parser.addArgument("mask", "", mitkCommandLineParser::String, "Mask image:", "mask image", us::Any(), true, false, false, mitkCommandLineParser::Input);
	- parser.endGroup();
	-
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- bool remove_outside = false;
	- if (parsedArgs.count("remove_outside"))
	- remove_outside = us::any_cast<bool>(parsedArgs["remove_outside"]);
	-
	- bool remove_inside = false;
	- if (!remove_outside && parsedArgs.count("remove_inside"))
	- remove_inside = us::any_cast<bool>(parsedArgs["remove_inside"]);
	-
	- typedef itk::Image< unsigned char, 3 > UcharImageType;
	- UcharImageType::Pointer mask = nullptr;
	- if (remove_inside \|\| remove_outside)
	- {
	- if (parsedArgs.count("mask"))
	- mask = mitk::DiffusionDataIOHelper::load_itk_image< UcharImageType >(us::any_cast<std::string>(parsedArgs["mask"]));
	- else {
	- MITK_INFO << "Mask needed to remove fibers inside or outside mask!";
	- return EXIT_FAILURE;
	- }
	- }
	-
	- bool remove = false;
	- if (parsedArgs.count("remove"))
	- remove = us::any_cast<bool>(parsedArgs["remove"]);
	-
	- bool random_subsample = false;
	- if (parsedArgs.count("random_subsample"))
	- random_subsample = us::any_cast<bool>(parsedArgs["random_subsample"]);
	-
	- float spline_resampling = -1;
	- if (parsedArgs.count("spline_resampling"))
	- spline_resampling = us::any_cast<float>(parsedArgs["spline_resampling"]);
	-
	- float linear_resampling = -1;
	- if (parsedArgs.count("linear_resampling"))
	- linear_resampling = us::any_cast<float>(parsedArgs["linear_resampling"]);
	-
	- int num_resampling = -1;
	- if (parsedArgs.count("num_resampling"))
	- num_resampling = us::any_cast<int>(parsedArgs["num_resampling"]);
	-
	- float subsample = -1;
	- if (parsedArgs.count("subsample"))
	- subsample = us::any_cast<float>(parsedArgs["subsample"]);
	-
	- float compress = -1;
	- if (parsedArgs.count("compress"))
	- compress = us::any_cast<float>(parsedArgs["compress"]);
	-
	- float minFiberLength = -1;
	- if (parsedArgs.count("min_length"))
	- minFiberLength = us::any_cast<float>(parsedArgs["min_length"]);
	-
	- float maxFiberLength = -1;
	- if (parsedArgs.count("max_length"))
	- maxFiberLength = us::any_cast<float>(parsedArgs["max_length"]);
	-
	- float max_angle_dist = 10;
	- if (parsedArgs.count("max_angle_dist"))
	- max_angle_dist = us::any_cast<float>(parsedArgs["max_angle_dist"]);
	-
	- float maxAngularDev = -1;
	- if (parsedArgs.count("max_angle"))
	- maxAngularDev = us::any_cast<float>(parsedArgs["max_angle"]);
	-
	- int axis = 0;
	- if (parsedArgs.count("mirror"))
	- axis = us::any_cast<int>(parsedArgs["mirror"]);
	-
	- float rotateX = 0;
	- if (parsedArgs.count("rotate_x"))
	- rotateX = us::any_cast<float>(parsedArgs["rotate_x"]);
	-
	- float rotateY = 0;
	- if (parsedArgs.count("rotate_y"))
	- rotateY = us::any_cast<float>(parsedArgs["rotate_y"]);
	-
	- float rotateZ = 0;
	- if (parsedArgs.count("rotate_z"))
	- rotateZ = us::any_cast<float>(parsedArgs["rotate_z"]);
	-
	- float scaleX = 0;
	- if (parsedArgs.count("scale_x"))
	- scaleX = us::any_cast<float>(parsedArgs["scale_x"]);
	-
	- float scaleY = 0;
	- if (parsedArgs.count("scale_y"))
	- scaleY = us::any_cast<float>(parsedArgs["scale_y"]);
	-
	- float scaleZ = 0;
	- if (parsedArgs.count("scale_z"))
	- scaleZ = us::any_cast<float>(parsedArgs["scale_z"]);
	-
	- float translateX = 0;
	- if (parsedArgs.count("translate_x"))
	- translateX = us::any_cast<float>(parsedArgs["translate_x"]);
	-
	- float translateY = 0;
	- if (parsedArgs.count("translate_y"))
	- translateY = us::any_cast<float>(parsedArgs["translate_y"]);
	-
	- float translateZ = 0;
	- if (parsedArgs.count("translate_z"))
	- translateZ = us::any_cast<float>(parsedArgs["translate_z"]);
	-
	-
	- std::string inFileName = us::any_cast<std::string>(parsedArgs["i"]);
	- std::string outFileName = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- try
	- {
	- mitk::FiberBundle::Pointer fib = LoadFib(inFileName);
	-
	- if (subsample>0)
	- fib = fib->SubsampleFibers(subsample, random_subsample);
	-
	- if (maxAngularDev>0)
	- {
	- auto filter = itk::FiberCurvatureFilter::New();
	- filter->SetInputFiberBundle(fib);
	- filter->SetAngularDeviation(maxAngularDev);
	- filter->SetDistance(max_angle_dist);
	- filter->SetRemoveFibers(remove);
	- filter->Update();
	- fib = filter->GetOutputFiberBundle();
	- }
	-
	- if (minFiberLength>0)
	- fib->RemoveShortFibers(minFiberLength);
	-
	- if (maxFiberLength>0)
	- fib->RemoveLongFibers(maxFiberLength);
	-
	- if (spline_resampling>0)
	- fib->ResampleSpline(spline_resampling);
	-
	- if (linear_resampling>0)
	- fib->ResampleLinear(linear_resampling);
	-
	- if (num_resampling>0)
	- fib->ResampleToNumPoints(num_resampling);
	-
	- if (compress>0)
	- fib->Compress(compress);
	-
	- if ( mask.IsNotNull() )
	- {
	- if (remove_outside)
	- fib = fib->RemoveFibersOutside(mask, false);
	- else if (remove_inside)
	- fib = fib->RemoveFibersOutside(mask, true);
	- }
	-
	- if (axis/100==1)
	- fib->MirrorFibers(0);
	-
	- if ((axis%100)/10==1)
	- fib->MirrorFibers(1);
	-
	- if (axis%10==1)
	- fib->MirrorFibers(2);
	-
	-
	- if (rotateX > 0 \|\| rotateY > 0 \|\| rotateZ > 0){
	- std::cout << "Rotate " << rotateX << " " << rotateY << " " << rotateZ;
	- fib->RotateAroundAxis(rotateX, rotateY, rotateZ);
	- }
	- if (translateX > 0 \|\| translateY > 0 \|\| translateZ > 0){
	- fib->TranslateFibers(translateX, translateY, translateZ);
	- }
	- if (scaleX > 0 \|\| scaleY > 0 \|\| scaleZ > 0)
	- fib->ScaleFibers(scaleX, scaleY, scaleZ);
	-
	- mitk::IOUtil::Save(fib.GetPointer(), outFileName );
	-
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FitFibersToImage.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FitFibersToImage.cpp
	deleted file mode 100755
	index bd9b319e7d..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FitFibersToImage.cpp
	+++ /dev/null
	@@ -1,321 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkBaseData.h>
	-#include <mitkImageCast.h>
	-#include <mitkImageToItk.h>
	-#include <metaCommand.h>
	-#include <mitkCommandLineParser.h>
	-#include <usAny.h>
	-#include <mitkIOUtil.h>
	-#include <mitkFiberBundle.h>
	-#include <mitkPreferenceListReaderOptionsFunctor.h>
	-#include <itkImageFileWriter.h>
	-#include <mitkPeakImage.h>
	-#include <itkFitFibersToImageFilter.h>
	-#include <mitkTensorModel.h>
	-#include <mitkITKImageImport.h>
	-#include <mitkDiffusionDataIOHelper.h>
	-
	-typedef itk::Point<float, 4> PointType4;
	-typedef itk::Image< float, 4 > PeakImgType;
	-
	-/*!
	-\brief Fits the tractogram to the input peak image by assigning a weight to each fiber (similar to https://doi.org/10.1016/j.neuroimage.2015.06.092).
	-*/
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Fit Fibers To Image");
	- parser.setCategory("Fiber Tracking and Processing Methods");
	- parser.setDescription("Assigns a weight to each fiber in order to optimally explain the input peak image");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i1", mitkCommandLineParser::StringList, "Input tractograms:", "input tractograms (files or folder)", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "i2", mitkCommandLineParser::String, "Input image:", "input image", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "output root", us::Any(), false, false, false, mitkCommandLineParser::Output);
	-
	- parser.addArgument("max_iter", "", mitkCommandLineParser::Int, "Max. iterations:", "maximum number of optimizer iterations", 20);
	- parser.addArgument("bundle_based", "", mitkCommandLineParser::Bool, "Bundle based fit:", "fit one weight per input tractogram/bundle, not for each fiber", false);
	- parser.addArgument("min_g", "", mitkCommandLineParser::Float, "Min. g:", "lower termination threshold for gradient magnitude", 1e-5);
	- parser.addArgument("lambda", "", mitkCommandLineParser::Float, "Lambda:", "modifier for regularization", 1.0);
	- parser.addArgument("save_res", "", mitkCommandLineParser::Bool, "Save Residuals:", "save residual images", false);
	- parser.addArgument("save_weights", "", mitkCommandLineParser::Bool, "Save Weights:", "save fiber weights in a separate text file", false);
	- parser.addArgument("filter_zero", "", mitkCommandLineParser::Bool, "Filter Zero Weights:", "filter fibers with zero weight", false);
	- parser.addArgument("filter_outliers", "", mitkCommandLineParser::Bool, "Filter outliers:", "perform second optimization run with an upper weight bound based on the first weight estimation (99% quantile)", false);
	- parser.addArgument("join_tracts", "", mitkCommandLineParser::Bool, "Join output tracts:", "outout tracts are merged into a single tractogram", false);
	- parser.addArgument("regu", "", mitkCommandLineParser::String, "Regularization:", "MSM; Variance; VoxelVariance; Lasso; GroupLasso; GroupVariance; NONE", std::string("VoxelVariance"));
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- mitkCommandLineParser::StringContainerType fib_files = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["i1"]);
	- std::string input_image_name = us::any_cast<std::string>(parsedArgs["i2"]);
	- std::string outRoot = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- bool single_fib = true;
	- if (parsedArgs.count("bundle_based"))
	- single_fib = !us::any_cast<bool>(parsedArgs["bundle_based"]);
	-
	- bool save_residuals = false;
	- if (parsedArgs.count("save_res"))
	- save_residuals = us::any_cast<bool>(parsedArgs["save_res"]);
	-
	- bool filter_zero = false;
	- if (parsedArgs.count("filter_zero"))
	- filter_zero = us::any_cast<bool>(parsedArgs["filter_zero"]);
	-
	- bool save_weights = false;
	- if (parsedArgs.count("save_weights"))
	- save_weights = us::any_cast<bool>(parsedArgs["save_weights"]);
	-
	- std::string regu = "VoxelVariance";
	- if (parsedArgs.count("regu"))
	- regu = us::any_cast<std::string>(parsedArgs["regu"]);
	-
	- bool join_tracts = false;
	- if (parsedArgs.count("join_tracts"))
	- join_tracts = us::any_cast<bool>(parsedArgs["join_tracts"]);
	-
	- int max_iter = 20;
	- if (parsedArgs.count("max_iter"))
	- max_iter = us::any_cast<int>(parsedArgs["max_iter"]);
	-
	- float g_tol = 1e-5;
	- if (parsedArgs.count("min_g"))
	- g_tol = us::any_cast<float>(parsedArgs["min_g"]);
	-
	- float lambda = 1.0;
	- if (parsedArgs.count("lambda"))
	- lambda = us::any_cast<float>(parsedArgs["lambda"]);
	-
	- bool filter_outliers = false;
	- if (parsedArgs.count("filter_outliers"))
	- filter_outliers = us::any_cast<bool>(parsedArgs["filter_outliers"]);
	-
	- try
	- {
	- MITK_INFO << "Loading data";
	-
	- mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Peak Image", "Fiberbundles"}, {});
	-
	- std::vector< std::string > fib_names;
	- auto input_tracts = mitk::DiffusionDataIOHelper::load_fibs(fib_files, &fib_names);
	-
	- itk::FitFibersToImageFilter::Pointer fitter = itk::FitFibersToImageFilter::New();
	-
	- mitk::BaseData::Pointer inputData = mitk::IOUtil::Load(input_image_name, &functor)[0].GetPointer();
	- mitk::Image::Pointer mitk_image = dynamic_cast<mitk::Image*>(inputData.GetPointer());
	- mitk::PeakImage::Pointer mitk_peak_image = dynamic_cast<mitk::PeakImage*>(inputData.GetPointer());
	- if (mitk_peak_image.IsNotNull())
	- {
	- typedef mitk::ImageToItk< mitk::PeakImage::ItkPeakImageType > CasterType;
	- CasterType::Pointer caster = CasterType::New();
	- caster->SetInput(mitk_peak_image);
	- caster->Update();
	- mitk::PeakImage::ItkPeakImageType::Pointer peak_image = caster->GetOutput();
	- fitter->SetPeakImage(peak_image);
	- }
	- else if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(mitk_image))
	- {
	- fitter->SetDiffImage(mitk::DiffusionPropertyHelper::GetItkVectorImage(mitk_image));
	- mitk::TensorModel<>* model = new mitk::TensorModel<>();
	- model->SetBvalue(1000);
	- model->SetDiffusivity1(0.0010);
	- model->SetDiffusivity2(0.00015);
	- model->SetDiffusivity3(0.00015);
	- model->SetGradientList(mitk::DiffusionPropertyHelper::GetGradientContainer(mitk_image));
	- fitter->SetSignalModel(model);
	- }
	- else if (mitk_image->GetDimension()==3)
	- {
	- itk::FitFibersToImageFilter::DoubleImgType::Pointer scalar_image = itk::FitFibersToImageFilter::DoubleImgType::New();
	- mitk::CastToItkImage(mitk_image, scalar_image);
	- fitter->SetScalarImage(scalar_image);
	- }
	- else
	- {
	- MITK_INFO << "Input image invalid. Valid options are peak image, 3D scalar image or raw diffusion-weighted image.";
	- return EXIT_FAILURE;
	- }
	-
	- fitter->SetTractograms(input_tracts);
	- fitter->SetFitIndividualFibers(single_fib);
	- fitter->SetMaxIterations(max_iter);
	- fitter->SetGradientTolerance(g_tol);
	- fitter->SetLambda(lambda);
	- fitter->SetFilterOutliers(filter_outliers);
	-
	- if (regu=="MSM")
	- fitter->SetRegularization(VnlCostFunction::REGU::MSM);
	- else if (regu=="Variance")
	- fitter->SetRegularization(VnlCostFunction::REGU::VARIANCE);
	- else if (regu=="Lasso")
	- fitter->SetRegularization(VnlCostFunction::REGU::LASSO);
	- else if (regu=="VoxelVariance")
	- fitter->SetRegularization(VnlCostFunction::REGU::VOXEL_VARIANCE);
	- else if (regu=="GroupLasso")
	- fitter->SetRegularization(VnlCostFunction::REGU::GROUP_LASSO);
	- else if (regu=="GroupVariance")
	- fitter->SetRegularization(VnlCostFunction::REGU::GROUP_VARIANCE);
	- else if (regu=="NONE")
	- fitter->SetRegularization(VnlCostFunction::REGU::NONE);
	-
	- fitter->Update();
	-
	- mitk::LocaleSwitch localeSwitch("C");
	- if (save_residuals && mitk_peak_image.IsNotNull())
	- {
	- itk::ImageFileWriter< PeakImgType >::Pointer writer = itk::ImageFileWriter< PeakImgType >::New();
	- writer->SetInput(fitter->GetFittedImage());
	- writer->SetFileName(outRoot + "_fitted.nii.gz");
	- writer->Update();
	-
	- writer->SetInput(fitter->GetResidualImage());
	- writer->SetFileName(outRoot + "_residual.nii.gz");
	- writer->Update();
	-
	- writer->SetInput(fitter->GetOverexplainedImage());
	- writer->SetFileName(outRoot + "_overexplained.nii.gz");
	- writer->Update();
	-
	- writer->SetInput(fitter->GetUnderexplainedImage());
	- writer->SetFileName(outRoot + "_underexplained.nii.gz");
	- writer->Update();
	- }
	- else if (save_residuals && mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(mitk_image))
	- {
	- {
	- mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetFittedImageDiff().GetPointer() );
	- mitk::DiffusionPropertyHelper::CopyProperties(mitk_image, outImage, true);
	- mitk::DiffusionPropertyHelper::InitializeImage( outImage );
	- mitk::IOUtil::Save(outImage, "application/vnd.mitk.nii.gz", outRoot + "_fitted_image.nii.gz");
	- }
	-
	- {
	- mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetResidualImageDiff().GetPointer() );
	- mitk::DiffusionPropertyHelper::CopyProperties(mitk_image, outImage, true);
	- mitk::DiffusionPropertyHelper::InitializeImage( outImage );
	- mitk::IOUtil::Save(outImage, "application/vnd.mitk.nii.gz", outRoot + "_residual_image.nii.gz");
	- }
	-
	- {
	- mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetOverexplainedImageDiff().GetPointer() );
	- mitk::DiffusionPropertyHelper::CopyProperties(mitk_image, outImage, true);
	- mitk::DiffusionPropertyHelper::InitializeImage( outImage );
	- mitk::IOUtil::Save(outImage, "application/vnd.mitk.nii.gz", outRoot + "_overexplained_image.nii.gz");
	- }
	-
	- {
	- mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetUnderexplainedImageDiff().GetPointer() );
	- mitk::DiffusionPropertyHelper::CopyProperties(mitk_image, outImage, true);
	- mitk::DiffusionPropertyHelper::InitializeImage( outImage );
	- mitk::IOUtil::Save(outImage, "application/vnd.mitk.nii.gz", outRoot + "_underexplained_image.nii.gz");
	- }
	- }
	- else if (save_residuals)
	- {
	- itk::ImageFileWriter< itk::FitFibersToImageFilter::DoubleImgType >::Pointer writer = itk::ImageFileWriter< itk::FitFibersToImageFilter::DoubleImgType >::New();
	- writer->SetInput(fitter->GetFittedImageScalar());
	- writer->SetFileName(outRoot + "_fitted_image.nii.gz");
	- writer->Update();
	-
	- writer->SetInput(fitter->GetResidualImageScalar());
	- writer->SetFileName(outRoot + "_residual_image.nii.gz");
	- writer->Update();
	-
	- writer->SetInput(fitter->GetOverexplainedImageScalar());
	- writer->SetFileName(outRoot + "_overexplained_image.nii.gz");
	- writer->Update();
	-
	- writer->SetInput(fitter->GetUnderexplainedImageScalar());
	- writer->SetFileName(outRoot + "_underexplained_image.nii.gz");
	- writer->Update();
	- }
	-
	- std::vector< mitk::FiberBundle::Pointer > output_tracts = fitter->GetTractograms();
	-
	- if (!join_tracts)
	- {
	- for (unsigned int bundle=0; bundle<output_tracts.size(); bundle++)
	- {
	- std::string name = fib_names.at(bundle);
	- name = ist::GetFilenameWithoutExtension(name);
	- auto fib = output_tracts.at(bundle);
	- if (filter_zero)
	- fib = fib->FilterByWeights(0.0);
	- if (fib->GetNumFibers()>0)
	- {
	- fib->ColorFibersByFiberWeights(false, true);
	- mitk::IOUtil::Save(fib, outRoot + name + "_fitted.fib");
	-
	- if (save_weights)
	- {
	- ofstream logfile;
	- logfile.open (outRoot + name + "_weights.txt");
	- for (unsigned int f=0; f<output_tracts.at(bundle)->GetNumFibers(); ++f)
	- logfile << output_tracts.at(bundle)->GetFiberWeight(f) << "\n";
	- logfile.close();
	- }
	- }
	- else
	- MITK_INFO << "Output contains no fibers!";
	- }
	- }
	- else
	- {
	- mitk::FiberBundle::Pointer out = mitk::FiberBundle::New();
	- out = out->AddBundles(output_tracts);
	- if (filter_zero)
	- out = out->FilterByWeights(0.0);
	- if (out->GetNumFibers()>0)
	- {
	- out->ColorFibersByFiberWeights(false, true);
	- mitk::IOUtil::Save(out, outRoot + "_fitted.fib");
	-
	- if (save_weights)
	- {
	- ofstream logfile;
	- logfile.open (outRoot + "_weights.txt");
	- for (unsigned int f=0; f<out->GetNumFibers(); ++f)
	- logfile << out->GetFiberWeight(f) << "\n";
	- logfile.close();
	- }
	- }
	- else
	- MITK_INFO << "Output contains no fibers!";
	- }
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/Sift2WeightCopy.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/Sift2WeightCopy.cpp
	deleted file mode 100644
	index e0cd36395c..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/Sift2WeightCopy.cpp
	+++ /dev/null
	@@ -1,107 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <vector>
	-#include <iostream>
	-#include <fstream>
	-#include <algorithm>
	-#include <string>
	-#include <istream>
	-
	-#include <itkMetaDataObject.h>
	-#include <itkVectorImage.h>
	-#include <mitkImageCast.h>
	-
	-#include <mitkBaseData.h>
	-#include <mitkFiberBundle.h>
	-#include "mitkCommandLineParser.h"
	-#include <mitkLexicalCast.h>
	-#include <mitkCoreObjectFactory.h>
	-#include <mitkIOUtil.h>
	-#include <itkTractDensityImageFilter.h>
	-#include <itkTractsToFiberEndingsImageFilter.h>
	-
	-
	-mitk::FiberBundle::Pointer LoadFib(std::string filename)
	-{
	- std::vector<mitk::BaseData::Pointer> fibInfile = mitk::IOUtil::Load(filename);
	- if( fibInfile.empty() )
	- std::cout << "File " << filename << " could not be read!";
	- mitk::BaseData::Pointer baseData = fibInfile.at(0);
	- return dynamic_cast<mitk::FiberBundle*>(baseData.GetPointer());
	-}
	-
	-/*!
	-\brief Import Sift2 Fiber Weights txt file.
	-*/
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("SIFT2 Fiber Weight Import");
	- parser.setCategory("Fiber Tracking and Processing Methods");
	- parser.setDescription("Import SIFT2 fiber weights.");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input:", "input fiber bundle", us::Any(), false);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "output fiber bundle (.fib)", us::Any(), false);
	- parser.addArgument("weights", "", mitkCommandLineParser::String, "Weights:", "input weights file (.txt)", us::Any(), false);
	-
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- std::string inFileName = us::any_cast<std::string>(parsedArgs["i"]);
	- std::string weightsFileName = us::any_cast<std::string>(parsedArgs["weights"]);
	- std::string outFileName = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- try
	- {
	- mitk::FiberBundle::Pointer fib = LoadFib(inFileName);
	-
	- std::ifstream fin;
	- fin.open(weightsFileName);
	- if (!fin.good())
	- return 1; // exit if file not found
	-
	- std::vector<float> weights;
	- for (float d; fin >> d; ) { weights.push_back(d); }
	-
	- for(std::size_t i = 0; i != weights.size(); i++) {
	- fib->SetFiberWeight(i, weights[i]);
	- }
	-
	- mitk::IOUtil::Save(fib.GetPointer(), outFileName );
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/TractDensity.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/TractDensity.cpp
	deleted file mode 100644
	index 0fdc8162da..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/TractDensity.cpp
	+++ /dev/null
	@@ -1,213 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <vector>
	-#include <iostream>
	-#include <fstream>
	-#include <algorithm>
	-#include <string>
	-
	-#include <itkImageFileWriter.h>
	-#include <itkMetaDataObject.h>
	-#include <itkVectorImage.h>
	-#include <mitkImageCast.h>
	-
	-#include <mitkBaseData.h>
	-#include <mitkFiberBundle.h>
	-#include "mitkCommandLineParser.h"
	-#include <mitkLexicalCast.h>
	-#include <mitkCoreObjectFactory.h>
	-#include <mitkIOUtil.h>
	-#include <itkTractDensityImageFilter.h>
	-#include <itkTractsToFiberEndingsImageFilter.h>
	-
	-
	-mitk::FiberBundle::Pointer LoadFib(std::string filename)
	-{
	- std::vector<mitk::BaseData::Pointer> fibInfile = mitk::IOUtil::Load(filename);
	- if( fibInfile.empty() )
	- std::cout << "File " << filename << " could not be read!";
	- mitk::BaseData::Pointer baseData = fibInfile.at(0);
	- return dynamic_cast<mitk::FiberBundle*>(baseData.GetPointer());
	-}
	-
	-/*!
	-\brief Modify input tractogram: fiber resampling, compression, pruning and transformation.
	-*/
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Tract Density");
	- parser.setCategory("Fiber Tracking and Processing Methods");
	- parser.setDescription("Generate tract density image, fiber envelope or fiber endpoints image.");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input:", "input fiber bundle", us::Any(), false);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "output image", us::Any(), false);
	- parser.addArgument("binary", "", mitkCommandLineParser::Bool, "Binary output:", "calculate binary tract envelope", us::Any());
	- parser.addArgument("normalize", "", mitkCommandLineParser::Bool, "Normalized output:", "normalize output to 0-1", us::Any());
	- parser.addArgument("endpoints", "", mitkCommandLineParser::Bool, "Output endpoints image:", "calculate image of fiber endpoints instead of mask", us::Any());
	- parser.addArgument("reference_image", "", mitkCommandLineParser::String, "Reference image:", "output image will have geometry of this reference image", us::Any());
	- parser.addArgument("upsampling", "", mitkCommandLineParser::Float, "Upsampling:", "upsampling", 1.0);
	-
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- bool binary = false;
	- if (parsedArgs.count("binary"))
	- binary = us::any_cast<bool>(parsedArgs["binary"]);
	-
	- bool endpoints = false;
	- if (parsedArgs.count("endpoints"))
	- endpoints = us::any_cast<bool>(parsedArgs["endpoints"]);
	-
	- bool normalize = false;
	- if (parsedArgs.count("normalize"))
	- normalize = us::any_cast<bool>(parsedArgs["normalize"]);
	-
	- float upsampling = 1.0;
	- if (parsedArgs.count("upsampling"))
	- upsampling = us::any_cast<float>(parsedArgs["upsampling"]);
	-
	- MITK_INFO << "Upsampling: " << upsampling;
	-
	- std::string reference_image = "";
	- if (parsedArgs.count("reference_image"))
	- reference_image = us::any_cast<std::string>(parsedArgs["reference_image"]);
	-
	- std::string inFileName = us::any_cast<std::string>(parsedArgs["i"]);
	- std::string outFileName = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- try
	- {
	- mitk::FiberBundle::Pointer fib = LoadFib(inFileName);
	-
	- mitk::Image::Pointer ref_img;
	- if (!reference_image.empty())
	- ref_img = mitk::IOUtil::Load<mitk::Image>(reference_image);
	-
	- if (endpoints)
	- {
	- typedef unsigned int OutPixType;
	- typedef itk::Image<OutPixType, 3> OutImageType;
	-
	- typedef itk::TractsToFiberEndingsImageFilter< OutImageType > ImageGeneratorType;
	- ImageGeneratorType::Pointer generator = ImageGeneratorType::New();
	- generator->SetFiberBundle(fib);
	- generator->SetUpsamplingFactor(upsampling);
	-
	- if (ref_img.IsNotNull())
	- {
	- OutImageType::Pointer itkImage = OutImageType::New();
	- CastToItkImage(ref_img, itkImage);
	- generator->SetInputImage(itkImage);
	- generator->SetUseImageGeometry(true);
	-
	- }
	- generator->Update();
	-
	- // get output image
	- typedef itk::Image<OutPixType,3> OutType;
	- OutType::Pointer outImg = generator->GetOutput();
	- mitk::Image::Pointer img = mitk::Image::New();
	- img->InitializeByItk(outImg.GetPointer());
	- img->SetVolume(outImg->GetBufferPointer());
	-
	- mitk::IOUtil::Save(img, outFileName );
	- }
	- else if (binary)
	- {
	- typedef unsigned char OutPixType;
	- typedef itk::Image<OutPixType, 3> OutImageType;
	-
	- itk::TractDensityImageFilter< OutImageType >::Pointer generator = itk::TractDensityImageFilter< OutImageType >::New();
	- generator->SetFiberBundle(fib);
	- generator->SetBinaryOutput(binary);
	- generator->SetOutputAbsoluteValues(!normalize);
	- generator->SetUpsamplingFactor(upsampling);
	-
	- if (ref_img.IsNotNull())
	- {
	- OutImageType::Pointer itkImage = OutImageType::New();
	- CastToItkImage(ref_img, itkImage);
	- generator->SetInputImage(itkImage);
	- generator->SetUseImageGeometry(true);
	-
	- }
	- generator->Update();
	-
	- // get output image
	- typedef itk::Image<OutPixType,3> OutType;
	- OutType::Pointer outImg = generator->GetOutput();
	- mitk::Image::Pointer img = mitk::Image::New();
	- img->InitializeByItk(outImg.GetPointer());
	- img->SetVolume(outImg->GetBufferPointer());
	-
	- mitk::IOUtil::Save(img, outFileName );
	- }
	- else
	- {
	- typedef float OutPixType;
	- typedef itk::Image<OutPixType, 3> OutImageType;
	-
	- itk::TractDensityImageFilter< OutImageType >::Pointer generator = itk::TractDensityImageFilter< OutImageType >::New();
	- generator->SetFiberBundle(fib);
	- generator->SetBinaryOutput(binary);
	- generator->SetOutputAbsoluteValues(!normalize);
	- generator->SetUpsamplingFactor(upsampling);
	-
	- if (ref_img.IsNotNull())
	- {
	- OutImageType::Pointer itkImage = OutImageType::New();
	- CastToItkImage(ref_img, itkImage);
	- generator->SetInputImage(itkImage);
	- generator->SetUseImageGeometry(true);
	-
	- }
	- generator->Update();
	-
	- // get output image
	- typedef itk::Image<OutPixType,3> OutType;
	- OutType::Pointer outImg = generator->GetOutput();
	- mitk::Image::Pointer img = mitk::Image::New();
	- img->InitializeByItk(outImg.GetPointer());
	- img->SetVolume(outImg->GetBufferPointer());
	-
	- mitk::IOUtil::Save(img, outFileName );
	- }
	-
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/TractDensityFilter.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/TractDensityFilter.cpp
	deleted file mode 100755
	index 125cf41a18..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/TractDensityFilter.cpp
	+++ /dev/null
	@@ -1,110 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <metaCommand.h>
	-#include "mitkCommandLineParser.h"
	-#include <usAny.h>
	-#include <mitkIOUtil.h>
	-#include <mitkLexicalCast.h>
	-#include <mitkFiberBundle.h>
	-#include <mitkImageCast.h>
	-#include <mitkImageToItk.h>
	-#include <itksys/SystemTools.hxx>
	-#include <itkFiberExtractionFilter.h>
	-#include <itkTractDensityImageFilter.h>
	-
	-#define _USE_MATH_DEFINES
	-#include <math.h>
	-
	-typedef itksys::SystemTools ist;
	-typedef itk::Image<float, 3> ItkFloatImgType;
	-
	-/*!
	-\brief Extract fibers from a tractogram using binary image ROIs
	-*/
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Filter Outliers by Tract Density");
	- parser.setCategory("Fiber Tracking and Processing Methods");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input:", "input tractogram (.fib/.trk/.tck/.dcm)", us::Any(), false);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "output tractogram", us::Any(), false);
	-
	- parser.addArgument("threshold", "", mitkCommandLineParser::Float, "Threshold:", "positive means ROI image value threshold", 0.05);
	- parser.addArgument("overlap", "", mitkCommandLineParser::Float, "Overlap:", "positive means ROI image value threshold", 0.5);
	- parser.addArgument("min_fibers", "", mitkCommandLineParser::Int, "Min. num. fibers:", "discard positive tracts with less fibers", 0);
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- std::string inFib = us::any_cast<std::string>(parsedArgs["i"]);
	- std::string outFib = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- int min_fibers = 0;
	- if (parsedArgs.count("min_fibers"))
	- min_fibers = us::any_cast<int>(parsedArgs["min_fibers"]);
	-
	- float overlap = 0.5;
	- if (parsedArgs.count("overlap"))
	- overlap = us::any_cast<float>(parsedArgs["overlap"]);
	-
	- float threshold = 0.05f;
	- if (parsedArgs.count("threshold"))
	- threshold = us::any_cast<float>(parsedArgs["threshold"]);
	-
	- try
	- {
	- mitk::FiberBundle::Pointer inputTractogram = mitk::IOUtil::Load<mitk::FiberBundle>(inFib);
	-
	- itk::TractDensityImageFilter< ItkFloatImgType >::Pointer generator = itk::TractDensityImageFilter< ItkFloatImgType >::New();
	- generator->SetFiberBundle(inputTractogram);
	- generator->SetBinaryOutput(false);
	- generator->SetOutputAbsoluteValues(false);
	- generator->Update();
	-
	- itk::FiberExtractionFilter<float>::Pointer extractor = itk::FiberExtractionFilter<float>::New();
	- extractor->SetRoiImages({generator->GetOutput()});
	- extractor->SetInputFiberBundle(inputTractogram);
	- extractor->SetOverlapFraction(overlap);
	- extractor->SetInterpolate(true);
	- extractor->SetThreshold(threshold);
	- extractor->SetNoNegatives(true);
	- extractor->Update();
	- if (extractor->GetPositives().at(0)->GetNumFibers() >= static_cast<unsigned int>(min_fibers))
	- mitk::IOUtil::Save(extractor->GetPositives().at(0), outFib);
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/CMakeLists.txt b/Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/CMakeLists.txt
	deleted file mode 100755
	index a2fe4c059d..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/CMakeLists.txt
	+++ /dev/null
	@@ -1,39 +0,0 @@
	-option(BUILD_DiffusionFiberfoxCmdApps "Build commandline tools for diffusion data simulation (Fiberfox)" OFF)
	-
	-if(BUILD_DiffusionFiberfoxCmdApps OR MITK_BUILD_ALL_APPS)
	-
	- # needed include directories
	- include_directories(
	- ${CMAKE_CURRENT_SOURCE_DIR}
	- ${CMAKE_CURRENT_BINARY_DIR}
	- )
	-
	- # list of diffusion cmdapps
	- # if an app requires additional dependencies
	- # they are added after a "^^" and separated by "_"
	- set( diffusionFiberfoxcmdapps
	- Fiberfox^^
	- RandomFiberPhantom^^
	- )
	-
	- foreach(diffusionFiberfoxcmdapp ${diffusionFiberfoxcmdapps})
	- # extract cmd app name and dependencies
	- string(REPLACE "^^" "\\;" cmdapp_info ${diffusionFiberfoxcmdapp})
	- set(cmdapp_info_list ${cmdapp_info})
	- list(GET cmdapp_info_list 0 appname)
	- list(GET cmdapp_info_list 1 raw_dependencies)
	- string(REPLACE "_" "\\;" dependencies "${raw_dependencies}")
	- set(dependencies_list ${dependencies})
	-
	- mitkFunctionCreateCommandLineApp(
	- NAME ${appname}
	- DEPENDS MitkDiffusionCmdApps ${dependencies_list}
	- PACKAGE_DEPENDS
	- )
	- endforeach()
	-
	- if(EXECUTABLE_IS_ENABLED)
	- MITK_INSTALL_TARGETS(EXECUTABLES ${EXECUTABLE_TARGET})
	- endif()
	-
	- endif()
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/Fiberfox.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/Fiberfox.cpp
	deleted file mode 100755
	index 534aef2528..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/Fiberfox.cpp
	+++ /dev/null
	@@ -1,288 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkImageCast.h>
	-#include <mitkITKImageImport.h>
	-#include <mitkProperties.h>
	-#include <mitkImage.h>
	-#include <mitkIOUtil.h>
	-#include <mitkFiberBundle.h>
	-#include <mitkFiberfoxParameters.h>
	-#include "mitkCommandLineParser.h"
	-
	-#include <itkTractsToDWIImageFilter.h>
	-#include <mitkLexicalCast.h>
	-#include <mitkPreferenceListReaderOptionsFunctor.h>
	-#include <itksys/SystemTools.hxx>
	-#include <mitkFiberfoxParameters.h>
	-
	-using namespace mitk;
	-
	-/*!
	-* \brief Command line interface to Fiberfox.
	-* Simulate a diffusion-weighted image from a tractogram using the specified parameter file.
	-*/
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	- parser.setTitle("Fiberfox");
	- parser.setCategory("Diffusion Simulation Tools");
	- parser.setContributor("MIC");
	- parser.setDescription("Command line interface to Fiberfox." " Simulate a diffusion-weighted image from a tractogram using the specified parameter file.");
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output root:", "output folder and file prefix", us::Any(), false, false, false, mitkCommandLineParser::Output);
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input:", "input tractogram or diffusion-weighted image", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("parameters", "p", mitkCommandLineParser::String, "Parameter file:", "fiberfox parameter file (.ffp)", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("template", "t", mitkCommandLineParser::String, "Template image:", "use parameters of the template image", us::Any(), true, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("verbose", "v", mitkCommandLineParser::Bool, "Output additional images:", "output volume fraction images etc.", us::Any());
	- parser.addArgument("dont_apply_direction_matrix", "", mitkCommandLineParser::Bool, "Don't apply direction matrix:", "don't rotate gradients by image direction matrix", us::Any());
	- parser.addArgument("fix_seed", "", mitkCommandLineParser::Bool, "Use fix random seed:", "always use same sequence of random numbers", us::Any());
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- {
	- return EXIT_FAILURE;
	- }
	- std::string outName = us::any_cast<std::string>(parsedArgs["o"]);
	- std::string paramName = us::any_cast<std::string>(parsedArgs["parameters"]);
	-
	- std::string input="";
	- if (parsedArgs.count("i"))
	- input = us::any_cast<std::string>(parsedArgs["i"]);
	-
	- bool fix_seed = false;
	- if (parsedArgs.count("fix_seed"))
	- fix_seed = us::any_cast<bool>(parsedArgs["fix_seed"]);
	-
	- bool verbose = false;
	- if (parsedArgs.count("verbose"))
	- verbose = us::any_cast<bool>(parsedArgs["verbose"]);
	-
	- bool apply_direction_matrix = true;
	- if (parsedArgs.count("dont_apply_direction_matrix"))
	- apply_direction_matrix = false;
	-
	- FiberfoxParameters parameters;
	- parameters.LoadParameters(paramName, fix_seed);
	-
	- // Test if /path/dir is an existing directory:
	- std::string file_extension = "";
	- if( itksys::SystemTools::FileIsDirectory( outName ) )
	- {
	- while( *(--(outName.cend())) == '/')
	- {
	- outName.pop_back();
	- }
	- outName = outName + '/';
	- parameters.m_Misc.m_OutputPath = outName;
	- outName = outName + parameters.m_Misc.m_OutputPrefix; // using default m_OutputPrefix as initialized.
	- }
	- else
	- {
	- // outName is NOT an existing directory, so we need to remove all trailing slashes:
	- while( *(--(outName.cend())) == '/')
	- {
	- outName.pop_back();
	- }
	-
	- // now split up the given outName into directory and (prefix of) filename:
	- if( ! itksys::SystemTools::GetFilenamePath( outName ).empty()
	- && itksys::SystemTools::FileIsDirectory(itksys::SystemTools::GetFilenamePath( outName ) ) )
	- {
	- parameters.m_Misc.m_OutputPath = itksys::SystemTools::GetFilenamePath( outName ) + '/';
	- }
	- else
	- {
	- parameters.m_Misc.m_OutputPath = itksys::SystemTools::GetCurrentWorkingDirectory() + '/';
	- }
	-
	- file_extension = itksys::SystemTools::GetFilenameExtension(outName);
	- if( ! itksys::SystemTools::GetFilenameWithoutExtension( outName ).empty() )
	- {
	- parameters.m_Misc.m_OutputPrefix = itksys::SystemTools::GetFilenameWithoutExtension( outName );
	- }
	- else
	- {
	- parameters.m_Misc.m_OutputPrefix = "fiberfox";
	- }
	-
	- outName = parameters.m_Misc.m_OutputPath + parameters.m_Misc.m_OutputPrefix;
	- }
	-
	- mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Diffusion Weighted Images", "Fiberbundles"}, {});
	- mitk::BaseData::Pointer inputData = mitk::IOUtil::Load(input, &functor)[0];
	-
	- itk::TractsToDWIImageFilter< short >::Pointer tractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New();
	-
	- if ( dynamic_cast<mitk::FiberBundle*>(inputData.GetPointer()) ) // simulate dataset from fibers
	- {
	- tractsToDwiFilter->SetFiberBundle(dynamic_cast<mitk::FiberBundle*>(inputData.GetPointer()));
	-
	- if (parsedArgs.count("template"))
	- {
	- MITK_INFO << "Loading template image";
	- typedef itk::VectorImage< short, 3 > ItkDwiType;
	- typedef itk::Image< short, 3 > ItkImageType;
	- mitk::BaseData::Pointer templateData = mitk::IOUtil::Load(us::any_cast<std::string>(parsedArgs["template"]), &functor)[0];
	- mitk::Image::Pointer template_image = dynamic_cast<mitk::Image*>(templateData.GetPointer());
	-
	- if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(template_image))
	- {
	- ItkDwiType::Pointer itkVectorImagePointer = mitk::DiffusionPropertyHelper::GetItkVectorImage(template_image);
	- parameters.m_SignalGen.m_ImageRegion = itkVectorImagePointer->GetLargestPossibleRegion();
	- parameters.m_SignalGen.m_ImageSpacing = itkVectorImagePointer->GetSpacing();
	- parameters.m_SignalGen.m_ImageOrigin = itkVectorImagePointer->GetOrigin();
	- parameters.m_SignalGen.m_ImageDirection = itkVectorImagePointer->GetDirection();
	- parameters.SetBvalue(mitk::DiffusionPropertyHelper::GetReferenceBValue(template_image));
	- parameters.SetGradienDirections(mitk::DiffusionPropertyHelper::GetOriginalGradientContainer(template_image));
	- }
	- else
	- {
	- ItkImageType::Pointer itkImagePointer = ItkImageType::New();
	- mitk::CastToItkImage(template_image, itkImagePointer);
	- parameters.m_SignalGen.m_ImageRegion = itkImagePointer->GetLargestPossibleRegion();
	- parameters.m_SignalGen.m_ImageSpacing = itkImagePointer->GetSpacing();
	- parameters.m_SignalGen.m_ImageOrigin = itkImagePointer->GetOrigin();
	- parameters.m_SignalGen.m_ImageDirection = itkImagePointer->GetDirection();
	- }
	- }
	- }
	- else if ( dynamic_cast<mitk::Image*>(inputData.GetPointer()) ) // add artifacts to existing image
	- {
	- typedef itk::VectorImage< short, 3 > ItkDwiType;
	- mitk::Image::Pointer diffImg = dynamic_cast<mitk::Image*>(inputData.GetPointer());
	- ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New();
	- mitk::CastToItkImage(diffImg, itkVectorImagePointer);
	-
	- parameters.m_SignalGen.m_SignalScale = 1;
	- parameters.m_SignalGen.m_ImageRegion = itkVectorImagePointer->GetLargestPossibleRegion();
	- parameters.m_SignalGen.m_ImageSpacing = itkVectorImagePointer->GetSpacing();
	- parameters.m_SignalGen.m_ImageOrigin = itkVectorImagePointer->GetOrigin();
	- parameters.m_SignalGen.m_ImageDirection = itkVectorImagePointer->GetDirection();
	- parameters.SetBvalue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg));
	- parameters.SetGradienDirections(mitk::DiffusionPropertyHelper::GetOriginalGradientContainer(diffImg));
	-
	- tractsToDwiFilter->SetInputImage(itkVectorImagePointer);
	- }
	-
	- if (verbose)
	- {
	- MITK_DEBUG << outName << ".ffp";
	- parameters.m_Misc.m_OutputAdditionalImages = true;
	- parameters.SaveParameters(outName+".ffp");
	- }
	- else
	- parameters.m_Misc.m_OutputAdditionalImages = false;
	-
	- if (apply_direction_matrix)
	- {
	- MITK_INFO << "Applying direction matrix to gradient directions.";
	- parameters.ApplyDirectionMatrix();
	- }
	- tractsToDwiFilter->SetParameters(parameters);
	- tractsToDwiFilter->SetUseConstantRandSeed(fix_seed);
	- tractsToDwiFilter->Update();
	-
	- mitk::Image::Pointer image = mitk::GrabItkImageMemory(tractsToDwiFilter->GetOutput());
	-
	- if (parameters.m_SignalGen.GetNumWeightedVolumes()>0)
	- {
	- if (apply_direction_matrix)
	- mitk::DiffusionPropertyHelper::SetGradientContainer(image, parameters.m_SignalGen.GetItkGradientContainer());
	- else
	- mitk::DiffusionPropertyHelper::SetOriginalGradientContainer(image, parameters.m_SignalGen.GetItkGradientContainer());
	- mitk::DiffusionPropertyHelper::SetReferenceBValue(image, parameters.m_SignalGen.GetBvalue());
	- mitk::DiffusionPropertyHelper::InitializeImage(image);
	-
	- if (file_extension=="")
	- mitk::IOUtil::Save(image, "DWI_NIFTI", outName+".nii.gz");
	- else if (file_extension==".nii" \|\| file_extension==".nii.gz")
	- mitk::IOUtil::Save(image, "DWI_NIFTI", outName+file_extension);
	- else
	- mitk::IOUtil::Save(image, outName+file_extension);
	- }
	- else
	- mitk::IOUtil::Save(image, outName+".nii.gz");
	-
	- if (verbose)
	- {
	- if (tractsToDwiFilter->GetTickImage().IsNotNull())
	- {
	- mitk::Image::Pointer mitkImage = mitk::Image::New();
	- itk::TractsToDWIImageFilter< short >::Float2DImageType::Pointer itkImage = tractsToDwiFilter->GetTickImage();
	- mitkImage = mitk::GrabItkImageMemory( itkImage.GetPointer() );
	- mitk::IOUtil::Save(mitkImage, outName+"_Ticks.nii.gz");
	- }
	-
	- if (tractsToDwiFilter->GetRfImage().IsNotNull())
	- {
	- mitk::Image::Pointer mitkImage = mitk::Image::New();
	- itk::TractsToDWIImageFilter< short >::Float2DImageType::Pointer itkImage = tractsToDwiFilter->GetRfImage();
	- mitkImage = mitk::GrabItkImageMemory( itkImage.GetPointer() );
	- mitk::IOUtil::Save(mitkImage, outName+"_TimeFromRf.nii.gz");
	- }
	-
	- std::vector< itk::TractsToDWIImageFilter< short >::ItkDoubleImgType::Pointer > volumeFractions = tractsToDwiFilter->GetVolumeFractions();
	- for (unsigned int k=0; k<volumeFractions.size(); k++)
	- {
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk(volumeFractions.at(k).GetPointer());
	- image->SetVolume(volumeFractions.at(k)->GetBufferPointer());
	- mitk::IOUtil::Save(image, outName+"_Compartment"+boost::lexical_cast<std::string>(k+1)+".nii.gz");
	- }
	-
	- if (tractsToDwiFilter->GetPhaseImage().IsNotNull())
	- {
	- mitk::Image::Pointer image = mitk::Image::New();
	- itk::TractsToDWIImageFilter< short >::DoubleDwiType::Pointer itkPhase = tractsToDwiFilter->GetPhaseImage();
	- image = mitk::GrabItkImageMemory( itkPhase.GetPointer() );
	- mitk::IOUtil::Save(image, outName+"_Phase.nii.gz");
	- }
	-
	- if (tractsToDwiFilter->GetKspaceImage().IsNotNull())
	- {
	- mitk::Image::Pointer image = mitk::Image::New();
	- itk::TractsToDWIImageFilter< short >::DoubleDwiType::Pointer itkImage = tractsToDwiFilter->GetKspaceImage();
	- image = mitk::GrabItkImageMemory( itkImage.GetPointer() );
	- mitk::IOUtil::Save(image, outName+"_kSpace.nii.gz");
	- }
	-
	- int c = 1;
	- std::vector< itk::TractsToDWIImageFilter< short >::DoubleDwiType::Pointer > output_real = tractsToDwiFilter->GetOutputImagesReal();
	- for (auto real : output_real)
	- {
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk(real.GetPointer());
	- image->SetVolume(real->GetBufferPointer());
	- mitk::IOUtil::Save(image, outName+"_Coil-"+boost::lexical_cast<std::string>(c)+"-real.nii.gz");
	- ++c;
	- }
	-
	- c = 1;
	- std::vector< itk::TractsToDWIImageFilter< short >::DoubleDwiType::Pointer > output_imag = tractsToDwiFilter->GetOutputImagesImag();
	- for (auto imag : output_imag)
	- {
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk(imag.GetPointer());
	- image->SetVolume(imag->GetBufferPointer());
	- mitk::IOUtil::Save(image, outName+"_Coil-"+boost::lexical_cast<std::string>(c)+"-imag.nii.gz");
	- ++c;
	- }
	- }
	-
	- return EXIT_SUCCESS;
	-}
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/RandomFiberPhantom.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/RandomFiberPhantom.cpp
	deleted file mode 100755
	index 12d4d29310..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/RandomFiberPhantom.cpp
	+++ /dev/null
	@@ -1,172 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <metaCommand.h>
	-#include "mitkCommandLineParser.h"
	-#include <usAny.h>
	-#include <mitkCoreObjectFactory.h>
	-#include <mitkFiberBundle.h>
	-#include <mitkDiffusionDataIOHelper.h>
	-#include <itkRandomPhantomFilter.h>
	-
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Random Fiber Phantom");
	- parser.setCategory("Diffusion Simulation Tools");
	- parser.setContributor("MIC");
	- parser.setDescription("Create Random Fiber Configurations");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("num_bundles", "", mitkCommandLineParser::Int, "", "", 50);
	- parser.addArgument("min_density", "", mitkCommandLineParser::Int, "", "", 50);
	- parser.addArgument("max_density", "", mitkCommandLineParser::Int, "", "", 200);
	- parser.addArgument("size_x", "", mitkCommandLineParser::Int, "", "", 250);
	- parser.addArgument("size_y", "", mitkCommandLineParser::Int, "", "", 250);
	- parser.addArgument("size_z", "", mitkCommandLineParser::Int, "", "", 250);
	- parser.addArgument("min_stepsize", "", mitkCommandLineParser::Int, "", "", 15);
	- parser.addArgument("max_stepsize", "", mitkCommandLineParser::Int, "", "", 30);
	- parser.addArgument("min_curve", "", mitkCommandLineParser::Int, "", "", 5);
	- parser.addArgument("max_curve", "", mitkCommandLineParser::Int, "", "", 45);
	- parser.addArgument("min_radius", "", mitkCommandLineParser::Int, "", "", 5);
	- parser.addArgument("max_radius", "", mitkCommandLineParser::Int, "", "", 25);
	- parser.addArgument("min_twist", "", mitkCommandLineParser::Int, "", "", 15);
	- parser.addArgument("max_twist", "", mitkCommandLineParser::Int, "", "", 30);
	- parser.addArgument("compress", "", mitkCommandLineParser::Float, "Compress:", "compress fiber using the given error threshold (in mm)", 0.1);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output folder:", "output folder", us::Any(), false, false, false, mitkCommandLineParser::Output);
	- parser.addArgument("fix_seed", "", mitkCommandLineParser::Int, "Fix random seed:", "if >= 0, produce same random values on each run using this seed.", -1);
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- std::string out_folder = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- float compress=0.1;
	- if (parsedArgs.count("compress"))
	- compress = us::any_cast<float>(parsedArgs["compress"]);
	-
	- int num_bundles=50;
	- if (parsedArgs.count("num_bundles"))
	- num_bundles = us::any_cast<int>(parsedArgs["num_bundles"]);
	-
	- int min_density=50;
	- if (parsedArgs.count("min_density"))
	- min_density = us::any_cast<int>(parsedArgs["min_density"]);
	-
	- int max_density=200;
	- if (parsedArgs.count("max_density"))
	- max_density = us::any_cast<int>(parsedArgs["max_density"]);
	-
	- int size_x=250;
	- if (parsedArgs.count("size_x"))
	- size_x = us::any_cast<int>(parsedArgs["size_x"]);
	-
	- int size_y=250;
	- if (parsedArgs.count("size_y"))
	- size_y = us::any_cast<int>(parsedArgs["size_y"]);
	-
	- int size_z=250;
	- if (parsedArgs.count("size_z"))
	- size_z = us::any_cast<int>(parsedArgs["size_z"]);
	-
	- int min_stepsize=15;
	- if (parsedArgs.count("min_stepsize"))
	- min_stepsize = us::any_cast<int>(parsedArgs["min_stepsize"]);
	-
	- int max_stepsize=30;
	- if (parsedArgs.count("max_stepsize"))
	- max_stepsize = us::any_cast<int>(parsedArgs["max_stepsize"]);
	-
	- int min_curve=5;
	- if (parsedArgs.count("min_curve"))
	- min_curve = us::any_cast<int>(parsedArgs["min_curve"]);
	-
	- int max_curve=45;
	- if (parsedArgs.count("max_curve"))
	- max_curve = us::any_cast<int>(parsedArgs["max_curve"]);
	-
	- int min_radius=5;
	- if (parsedArgs.count("min_radius"))
	- min_radius = us::any_cast<int>(parsedArgs["min_radius"]);
	-
	- int max_radius=25;
	- if (parsedArgs.count("max_radius"))
	- max_radius = us::any_cast<int>(parsedArgs["max_radius"]);
	-
	- int min_twist=15;
	- if (parsedArgs.count("min_twist"))
	- min_twist = us::any_cast<int>(parsedArgs["min_twist"]);
	-
	- int max_twist=30;
	- if (parsedArgs.count("max_twist"))
	- max_twist = us::any_cast<int>(parsedArgs["max_twist"]);
	-
	- int fix_seed = -1;
	- if (parsedArgs.count("fix_seed"))
	- fix_seed = us::any_cast<int>(parsedArgs["fix_seed"]);
	-
	- try
	- {
	- itk::RandomPhantomFilter::Pointer filter = itk::RandomPhantomFilter::New();
	- filter->SetNumTracts(static_cast<unsigned int>(num_bundles));
	- filter->SetMinStreamlineDensity(static_cast<unsigned int>(min_density));
	- filter->SetMaxStreamlineDensity(static_cast<unsigned int>(max_density));
	- mitk::Vector3D vol;
	- vol[0] = size_x;
	- vol[1] = size_y;
	- vol[2] = size_z;
	- filter->SetVolumeSize(vol);
	- filter->SetStepSizeMin(static_cast<unsigned int>(min_stepsize));
	- filter->SetStepSizeMax(static_cast<unsigned int>(max_stepsize));
	- filter->SetCurvynessMin(static_cast<unsigned int>(min_curve));
	- filter->SetCurvynessMax(static_cast<unsigned int>(max_curve));
	- filter->SetStartRadiusMin(static_cast<unsigned int>(min_radius));
	- filter->SetStartRadiusMax(static_cast<unsigned int>(max_radius));
	- filter->SetMinTwist(static_cast<unsigned int>(min_twist));
	- filter->SetMaxTwist(static_cast<unsigned int>(max_twist));
	- filter->SetFixSeed(fix_seed);
	- filter->Update();
	- auto fibs = filter->GetFiberBundles();
	-
	- std::vector< mitk::DataNode::Pointer > fiber_nodes;
	- int c = 1;
	- for (auto fib : fibs)
	- {
	- if (compress>0)
	- fib->Compress(compress);
	- mitk::IOUtil::Save(fib, out_folder + "Bundle_" + boost::lexical_cast<std::string>(c) + ".fib");
	- ++c;
	- }
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/CMakeLists.txt b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/CMakeLists.txt
	deleted file mode 100644
	index d4746a8381..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/CMakeLists.txt
	+++ /dev/null
	@@ -1,48 +0,0 @@
	-option(BUILD_DiffusionMiscCmdApps "Build miscellaneous commandline tools for diffusion" OFF)
	-
	-if(BUILD_DiffusionMiscCmdApps OR MITK_BUILD_ALL_APPS)
	-
	- # needed include directories
	- include_directories(
	- ${CMAKE_CURRENT_SOURCE_DIR}
	- ${CMAKE_CURRENT_BINARY_DIR}
	- )
	-
	- # list of diffusion cmdapps
	- # if an app requires additional dependencies
	- # they are added after a "^^" and separated by "_"
	- set( diffusionMisccmdapps
	- PeakExtraction^^
	- FileFormatConverter^^
	- FlipPeaks^^
	- ImageResampler^^
	- CopyGeometry^^
	- Registration^^
	- DiffusionDICOMLoader^^
	- ResampleGradients^^
	- ShToOdfImage^^
	- DImp^^
	- DReg^^
	- HeadMotionCorrection^^
	- DmriDenoising^^MitkImageDenoising
	- RoundBvalues^^
	- )
	-
	- foreach(diffusionMisccmdapp ${diffusionMisccmdapps})
	- # extract cmd app name and dependencies
	- string(REPLACE "^^" "\\;" cmdapp_info ${diffusionMisccmdapp})
	- set(cmdapp_info_list ${cmdapp_info})
	- list(GET cmdapp_info_list 0 appname)
	- list(GET cmdapp_info_list 1 raw_dependencies)
	- string(REPLACE "_" "\\;" dependencies "${raw_dependencies}")
	- set(dependencies_list ${dependencies})
	-
	- mitkFunctionCreateCommandLineApp(
	- NAME ${appname}
	- DEPENDS MitkDiffusionCmdApps ${dependencies_list}
	- PACKAGE_DEPENDS
	- )
	- endforeach()
	-
	-endif()
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/CopyGeometry.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/CopyGeometry.cpp
	deleted file mode 100644
	index 6ea85d3c7d..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/CopyGeometry.cpp
	+++ /dev/null
	@@ -1,114 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkImageCast.h>
	-#include <mitkImage.h>
	-#include <mitkIOUtil.h>
	-#include "mitkCommandLineParser.h"
	-
	-/*!
	-\brief Copies transformation matrix of one image to another
	-*/
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Copy Geometry");
	- parser.setCategory("Preprocessing Tools");
	- parser.setDescription("Copies transformation matrix of one image to another");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input:", "input image", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "output image", us::Any(), false, false, false, mitkCommandLineParser::Output);
	- parser.addArgument("ref", "r", mitkCommandLineParser::String, "Reference:", "reference image", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("alignCentroid", "a", mitkCommandLineParser::Bool, "align centroids", "align centroids", us::Any(), true);
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- // mandatory arguments
	- std::string imageName = us::any_cast<std::string>(parsedArgs["i"]);
	- std::string refImage = us::any_cast<std::string>(parsedArgs["ref"]);
	- std::string outImage = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- bool originOnly = false;
	-
	- // Show a help message
	- if ( parsedArgs.count("alignCentroid") \|\| parsedArgs.count("a"))
	- {
	- originOnly = true;
	- }
	-
	- try
	- {
	- mitk::Image::Pointer source = mitk::IOUtil::Load<mitk::Image>(refImage);
	- mitk::Image::Pointer target = mitk::IOUtil::Load<mitk::Image>(imageName);
	- if (originOnly)
	- {
	- // Calculate correction to align centroids
	- double c[3];
	- c[0] = source->GetGeometry()->GetOrigin()[0]
	- + source->GetGeometry()->GetExtent(0)/2.0
	- - target->GetGeometry()->GetOrigin()[0]
	- - target->GetGeometry()->GetExtent(0)/2.0;
	-
	- c[1] = source->GetGeometry()->GetOrigin()[1]
	- + source->GetGeometry()->GetExtent(1)/2.0
	- - target->GetGeometry()->GetOrigin()[1]
	- - target->GetGeometry()->GetExtent(1)/2.0;
	-
	-
	- c[2] = source->GetGeometry()->GetOrigin()[2]
	- + source->GetGeometry()->GetExtent(2)/2.0
	- - target->GetGeometry()->GetOrigin()[2]
	- - target->GetGeometry()->GetExtent(2)/2.0;
	-
	- double newOrigin[3];
	- newOrigin[0] = target->GetGeometry()->GetOrigin()[0] +c[0];
	- newOrigin[1] = target->GetGeometry()->GetOrigin()[1] +c[1];
	- newOrigin[2] = target->GetGeometry()->GetOrigin()[2] +c[2];
	-
	- target->GetGeometry()->SetOrigin(newOrigin);
	- }
	- else
	- {
	- mitk::BaseGeometry* s_geom = source->GetGeometry();
	- mitk::BaseGeometry* t_geom = target->GetGeometry();
	-
	- t_geom->SetIndexToWorldTransform(s_geom->GetIndexToWorldTransform());
	- target->SetGeometry(t_geom);
	- }
	- mitk::IOUtil::Save(target, outImage);
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/DICOMLoader.cmake b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/DICOMLoader.cmake
	deleted file mode 100644
	index 47ba810620..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/DICOMLoader.cmake
	+++ /dev/null
	@@ -1,4 +0,0 @@
	-set(CPP_FILES
	- mitkCommandLineParser.cpp
	- DICOMLoader.cpp
	-)
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/DImp.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/DImp.cpp
	deleted file mode 100644
	index a8b6a06238..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/DImp.cpp
	+++ /dev/null
	@@ -1,72 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkImageCast.h>
	-#include <mitkImage.h>
	-#include <mitkIOUtil.h>
	-#include "mitkCommandLineParser.h"
	-#include <itksys/SystemTools.hxx>
	-#include <mitkPreferenceListReaderOptionsFunctor.h>
	-
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("DIMP");
	- parser.setCategory("Preprocessing Tools");
	- parser.setDescription("TEMPORARY: Converts DICOM to other image types");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input:", "input image", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "output image", us::Any(), false, false, false, mitkCommandLineParser::Output);
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- // mandatory arguments
	- std::string imageName = us::any_cast<std::string>(parsedArgs["i"]);
	- std::string outImage = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- try
	- {
	- mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Diffusion Weighted Images"}, {});
	- mitk::Image::Pointer source = mitk::IOUtil::Load<mitk::Image>(imageName, &functor);
	-
	- std::string ext = itksys::SystemTools::GetFilenameExtension(outImage);
	- if (ext==".nii" \|\| ext==".nii.gz")
	- mitk::IOUtil::Save(source, "DWI_NIFTI", outImage);
	- else
	- mitk::IOUtil::Save(source, outImage);
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/DReg.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/DReg.cpp
	deleted file mode 100644
	index 96dc2ccabe..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/DReg.cpp
	+++ /dev/null
	@@ -1,222 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkImageCast.h>
	-#include <mitkImage.h>
	-#include <mitkIOUtil.h>
	-#include "mitkCommandLineParser.h"
	-#include <mitkMultiModalRigidDefaultRegistrationAlgorithm.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <mitkAlgorithmHelper.h>
	-#include <itkExtractDwiChannelFilter.h>
	-#include <mitkRegistrationHelper.h>
	-#include <mitkImageMappingHelper.h>
	-#include <itksys/SystemTools.hxx>
	-#include <mitkPreferenceListReaderOptionsFunctor.h>
	-#include <itkComposeImageFilter.h>
	-#include <mitkITKImageImport.h>
	-#include <mitkDiffusionImageCorrectionFilter.h>
	-#include <mitkDiffusionDataIOHelper.h>
	-
	-typedef mitk::DiffusionPropertyHelper DPH;
	-
	-
	-mitk::Image::Pointer apply_transform(mitk::Image::Pointer moving, mitk::Image::Pointer fixed_single, mitk::MAPRegistrationWrapper::Pointer reg, bool resample)
	-{
	- mitk::Image::Pointer registered_image;
	- if (!resample)
	- {
	- registered_image = mitk::ImageMappingHelper::refineGeometry(moving, reg, true);
	- }
	- else
	- {
	- if (!mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(moving))
	- {
	- registered_image = mitk::ImageMappingHelper::map(moving, reg, false, 0, fixed_single->GetGeometry(), false, 0, mitk::ImageMappingInterpolator::BSpline_3);
	- }
	- else
	- {
	- typedef itk::Image<mitk::DiffusionPropertyHelper::DiffusionPixelType, 3> ITKDiffusionVolumeType;
	- typedef itk::ComposeImageFilter < ITKDiffusionVolumeType > ComposeFilterType;
	- auto composer = ComposeFilterType::New();
	-
	- auto itkVectorImagePointer = mitk::DiffusionPropertyHelper::GetItkVectorImage(moving);
	- for (unsigned int i=0; i<itkVectorImagePointer->GetVectorLength(); ++i)
	- {
	- itk::ExtractDwiChannelFilter< short >::Pointer filter = itk::ExtractDwiChannelFilter< short >::New();
	- filter->SetInput( itkVectorImagePointer);
	- filter->SetChannelIndex(i);
	- filter->Update();
	-
	- mitk::Image::Pointer gradientVolume = mitk::Image::New();
	- gradientVolume->InitializeByItk( filter->GetOutput() );
	- gradientVolume->SetImportChannel( filter->GetOutput()->GetBufferPointer() );
	-
	- mitk::Image::Pointer registered_mitk_image = mitk::ImageMappingHelper::map(gradientVolume, reg, false, 0, fixed_single->GetGeometry(), false, 0, mitk::ImageMappingInterpolator::BSpline_3);
	-
	- auto registered_itk_image = ITKDiffusionVolumeType::New();
	- mitk::CastToItkImage(registered_mitk_image, registered_itk_image);
	- composer->SetInput(i, registered_itk_image);
	- }
	- composer->Update();
	-
	- registered_image = mitk::GrabItkImageMemory( composer->GetOutput() );
	- mitk::DiffusionPropertyHelper::CopyProperties(moving, registered_image, true);
	-
	- typedef mitk::DiffusionImageCorrectionFilter CorrectionFilterType;
	- CorrectionFilterType::Pointer corrector = CorrectionFilterType::New();
	- corrector->SetImage( registered_image );
	- corrector->CorrectDirections( mitk::MITKRegistrationHelper::getAffineMatrix(reg, false)->GetMatrix().GetVnlMatrix() );
	- }
	- }
	-
	- return registered_image;
	-}
	-
	-
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("DREG");
	- parser.setCategory("Preprocessing Tools");
	- parser.setDescription("TEMPORARY: Rigid registration of two images");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "f", mitkCommandLineParser::String, "Fixed:", "fixed image", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "m", mitkCommandLineParser::String, "Moving:", "moving image", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "output image", us::Any(), false, false, false, mitkCommandLineParser::Output);
	- parser.addArgument("resample", "", mitkCommandLineParser::Bool, "Resample:", "resample moving image", false);
	- parser.addArgument("coreg", "", mitkCommandLineParser::StringList, "", "additionally apply transform to these images", us::Any(), true, false, false, mitkCommandLineParser::Input);
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- // mandatory arguments
	- std::string f = us::any_cast<std::string>(parsedArgs["f"]);
	- std::string m = us::any_cast<std::string>(parsedArgs["m"]);
	- std::string o = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- bool resample = false;
	- if (parsedArgs.count("resample"))
	- resample = true;
	-
	- mitkCommandLineParser::StringContainerType coreg;
	- if (parsedArgs.count("coreg"))
	- coreg = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["coreg"]);
	-
	- try
	- {
	- typedef itk::Image< float, 3 > ItkFloatImageType;
	-
	- mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Diffusion Weighted Images"}, {});
	- mitk::Image::Pointer fixed = mitk::IOUtil::Load<mitk::Image>(f, &functor);
	- mitk::Image::Pointer moving = mitk::IOUtil::Load<mitk::Image>(m, &functor);
	-
	- mitk::Image::Pointer fixed_single = fixed;
	- mitk::Image::Pointer moving_single = moving;
	-
	- mitk::MultiModalRigidDefaultRegistrationAlgorithm< ItkFloatImageType >::Pointer algo = mitk::MultiModalRigidDefaultRegistrationAlgorithm< ItkFloatImageType >::New();
	- mitk::MITKAlgorithmHelper helper(algo);
	-
	- if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(fixed))
	- {
	- DPH::ImageType::Pointer itkVectorImagePointer = DPH::ImageType::New();
	- mitk::CastToItkImage(fixed, itkVectorImagePointer);
	-
	- itk::ExtractDwiChannelFilter< short >::Pointer filter = itk::ExtractDwiChannelFilter< short >::New();
	- filter->SetInput( itkVectorImagePointer);
	- filter->SetChannelIndex(0);
	- filter->Update();
	-
	- fixed_single = mitk::Image::New();
	- fixed_single->InitializeByItk( filter->GetOutput() );
	- fixed_single->SetImportChannel( filter->GetOutput()->GetBufferPointer() );
	- }
	-
	- if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(moving))
	- {
	- DPH::ImageType::Pointer itkVectorImagePointer = DPH::ImageType::New();
	- mitk::CastToItkImage(moving, itkVectorImagePointer);
	-
	- itk::ExtractDwiChannelFilter< short >::Pointer filter = itk::ExtractDwiChannelFilter< short >::New();
	- filter->SetInput( itkVectorImagePointer);
	- filter->SetChannelIndex(0);
	- filter->Update();
	-
	- moving_single = mitk::Image::New();
	- moving_single->InitializeByItk( filter->GetOutput() );
	- moving_single->SetImportChannel( filter->GetOutput()->GetBufferPointer() );
	- }
	-
	- helper.SetData(moving_single, fixed_single);
	- mitk::MAPRegistrationWrapper::Pointer reg = helper.GetMITKRegistrationWrapper();
	-
	- mitk::Image::Pointer registered_image = apply_transform(moving, fixed_single, reg, resample);
	- if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(registered_image))
	- {
	- mitk::DiffusionPropertyHelper::InitializeImage( registered_image );
	-
	- std::string file_extension = itksys::SystemTools::GetFilenameExtension(o);
	- if (file_extension==".nii" \|\| file_extension==".nii.gz")
	- mitk::IOUtil::Save(registered_image, "DWI_NIFTI", o);
	- else
	- mitk::IOUtil::Save(registered_image, o);
	- }
	- else
	- mitk::IOUtil::Save(registered_image, o);
	-
	- std::string path = ist::GetFilenamePath(o) + "/";
	- std::vector< std::string > file_names;
	- auto coreg_images = mitk::DiffusionDataIOHelper::load_mitk_images(coreg, &file_names);
	- for (unsigned int i=0; i<coreg_images.size(); ++i)
	- {
	- std::string ext = ist::GetFilenameExtension(file_names.at(i));
	- std::string out_name = path + ist::GetFilenameWithoutExtension(file_names.at(i)) + "_registered" + ext;
	-
	- registered_image = apply_transform(coreg_images.at(i), fixed_single, reg, resample);
	- if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(registered_image))
	- {
	- mitk::DiffusionPropertyHelper::InitializeImage( registered_image );
	-
	- if (ext==".nii" \|\| ext==".nii.gz")
	- mitk::IOUtil::Save(registered_image, "DWI_NIFTI", out_name);
	- else
	- mitk::IOUtil::Save(registered_image, out_name);
	- }
	- else
	- mitk::IOUtil::Save(registered_image, out_name);
	- }
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/DiffusionDICOMLoader.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/DiffusionDICOMLoader.cpp
	deleted file mode 100644
	index 0cff9056b8..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/DiffusionDICOMLoader.cpp
	+++ /dev/null
	@@ -1,315 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkImage.h"
	-#include "mitkBaseData.h"
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <mitkImageCast.h>
	-#include <mitkITKImageImport.h>
	-
	-#include "mitkCommandLineParser.h"
	-#include <itksys/SystemTools.hxx>
	-#include <itksys/Directory.hxx>
	-
	-#include "mitkDiffusionDICOMFileReader.h"
	-#include "mitkSortByImagePositionPatient.h"
	-#include "mitkDICOMTagBasedSorter.h"
	-#include "mitkDICOMSortByTag.h"
	-
	-#include "itkMergeDiffusionImagesFilter.h"
	-#include <mitkIOUtil.h>
	-
	-static mitk::StringList& GetInputFilenames()
	-{
	- static mitk::StringList inputs;
	- return inputs;
	-}
	-
	-// FIXME slash at the end
	-void SetInputFileNames( std::string input_directory )
	-{
	- // I. Get all files in directory
	- itksys::Directory input;
	- input.Load( input_directory.c_str() );
	-
	- // II. Push back files
	- mitk::StringList inputlist;//, mergedlist;
	- for( unsigned long idx=0; idx<input.GetNumberOfFiles(); idx++)
	- {
	- if( ! itksys::SystemTools::FileIsDirectory( input.GetFile(idx)) )
	- {
	- std::string fullpath = input_directory + "/" + std::string( input.GetFile(idx) );
	- //inputlist.push_back( itksys::SystemTools::ConvertToOutputPath( fullpath.c_str() ) );
	- inputlist.push_back( fullpath.c_str() );
	-
	- MITK_INFO("dicom.loader.inputdir.addfile") << input.GetFile(idx);
	- }
	- }
	-
	- /*mergedlist.reserve( GetInputFilenames().size() + inputlist.size() );
	-
	- mergedlist.insert( mergedlist.end(), GetInputFilenames().begin(), GetInputFilenames().end() );
	- mergedlist.insert( mergedlist.end(), inputlist.begin(), inputlist.end() );*/
	-
	- GetInputFilenames() = inputlist;//mergedlist;
	-
	- MITK_INFO("dicom.loader.setinputfiles.end") << "[]";
	-}
	-
	-
	-static mitk::Image::Pointer ReadInDICOMFiles( mitk::StringList& input_files, const std::string &)
	-{
	- mitk::DiffusionDICOMFileReader::Pointer gdcmReader = mitk::DiffusionDICOMFileReader::New();
	- //mitk::ClassicDICOMSeriesReader::Pointer gdcmReader = mitk::ClassicDICOMSeriesReader::New();
	- /* mitk::DICOMTagBasedSorter::Pointer tagSorter = mitk::DICOMTagBasedSorter::New();
	-
	- // Use tags as in Qmitk
	- // all the things that split by tag in DicomSeriesReader
	- tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0028, 0x0010) ); // Number of Rows
	- tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0028, 0x0011) ); // Number of Columns
	- tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0028, 0x0030) ); // Pixel Spacing
	- tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0018, 0x1164) ); // Imager Pixel Spacing
	- tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0020, 0x0037) ); // Image Orientation (Patient) // TODO add tolerance parameter (l. 1572 of original code)
	- // TODO handle as real vectors! cluster with configurable errors!
	- tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0020, 0x000e) ); // Series Instance UID
	- tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0018, 0x0050) ); // Slice Thickness
	- tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0028, 0x0008) ); // Number of Frames
	- //tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0020, 0x0052) ); // Frame of Reference UID
	-
	- // gdcmReader->AddSortingElement( tagSorter );
	- //mitk::DICOMFileReaderTestHelper::TestOutputsContainInputs( gdcmReader );
	-
	- mitk::DICOMSortCriterion::ConstPointer sorting =
	- mitk::SortByImagePositionPatient::New( // Image Position (Patient)
	- //mitk::DICOMSortByTag::New( mitk::DICOMTag(0x0020, 0x0013), // instance number
	- mitk::DICOMSortByTag::New( mitk::DICOMTag(0x0020, 0x0012), // aqcuisition number
	- mitk::DICOMSortByTag::New( mitk::DICOMTag(0x0008, 0x0032), // aqcuisition time
	- mitk::DICOMSortByTag::New( mitk::DICOMTag(0x0018, 0x1060), // trigger time
	- mitk::DICOMSortByTag::New( mitk::DICOMTag(0x0008, 0x0018) // SOP instance UID (last resort, not really meaningful but decides clearly)
	- ).GetPointer()
	- ).GetPointer()
	- ).GetPointer()
	- ).GetPointer()
	- // ).GetPointer()
	- ).GetPointer();
	- tagSorter->SetSortCriterion( sorting );
	-
	- // mosaic
	- //gdcmReader->SetResolveMosaic( this->m_Controls->m_SplitMosaicCheckBox->isChecked() );
	- gdcmReader->AddSortingElement( tagSorter );*/
	- gdcmReader->SetInputFiles( input_files );
	-
	- try
	- {
	- gdcmReader->AnalyzeInputFiles();
	- }
	- catch( const itk::ExceptionObject &e)
	- {
	- MITK_ERROR << "Failed to analyze data. " << e.what();
	- }
	- catch( const std::exception &se)
	- {
	- MITK_ERROR << "Std Exception " << se.what();
	- }
	-
	-
	- gdcmReader->LoadImages();
	-
	- mitk::Image::Pointer loaded_image = gdcmReader->GetOutput(0).GetMitkImage();
	-
	- return loaded_image;
	-}
	-
	-typedef short DiffusionPixelType;
	-typedef itk::VectorImage<DiffusionPixelType,3> DwiImageType;
	-typedef DwiImageType::PixelType DwiPixelType;
	-typedef DwiImageType::RegionType DwiRegionType;
	-typedef std::vector< DwiImageType::Pointer > DwiImageContainerType;
	-
	-typedef mitk::Image DiffusionImageType;
	-typedef mitk::DiffusionPropertyHelper::GradientDirectionsContainerType GradientContainerType;
	-typedef std::vector< GradientContainerType::Pointer > GradientListContainerType;
	-
	-void SearchForInputInSubdirs( std::string root_directory, std::string subdir_prefix , std::vector<DiffusionImageType::Pointer>& output_container)
	-{
	- // I. Get all dirs in directory
	- itksys::Directory rootdir;
	- rootdir.Load( root_directory.c_str() );
	-
	- MITK_INFO("dicom.loader.setinputdirs.start") << "Prefix = " << subdir_prefix;
	-
	- for( unsigned int idx=0; idx<rootdir.GetNumberOfFiles(); idx++)
	- {
	- std::string current_path = rootdir.GetFile(idx);
	-
	- std::string directory_path = std::string(rootdir.GetPath()) + current_path;
	-
	- MITK_INFO("dicom.loader.inputrootdir.test") << "ProbePath: " << current_path << "\n"
	- << "escaped to " << itksys::SystemTools::ConvertToOutputPath( directory_path.c_str() );
	-
	- MITK_INFO("dicom.loader.inputrootdir.test") << " IsDirectory: " << itksys::SystemTools::FileIsDirectory( directory_path.c_str() )
	- << " StartsWith: " << itksys::SystemTools::StringStartsWith( current_path.c_str(), subdir_prefix.c_str() );
	-
	- // test for prefix
	- if( itksys::SystemTools::FileIsDirectory( directory_path.c_str() )
	- && itksys::SystemTools::StringStartsWith( current_path.c_str(), subdir_prefix.c_str() )
	- )
	- {
	-
	- MITK_INFO("dicom.loader.inputrootdir.searchin") << directory_path;
	- SetInputFileNames( directory_path.c_str() );
	-
	- MITK_INFO("dicom.loader.inputrootdir.preload") << "[]" ;
	- DiffusionImageType::Pointer dwi = ReadInDICOMFiles( GetInputFilenames(), "" );
	-
	- output_container.push_back( dwi );
	-
	-
	- }
	- }
	-
	- MITK_INFO("dicom.loader.setinputdirs.end") << "[]";
	-}
	-
	-
	-
	-using namespace mitk;
	-/**
	- * Read DICOM Files through the new (refactored) Diffusion DICOM Loader. It serves also as a first test of the new functionality, it will replace the
	- * current loading mechanism after the necessary parts are merged into the master branch.
	- */
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	- parser.setArgumentPrefix("--", "-");
	-
	- parser.setTitle("Diffusion Dicom Loader");
	- parser.setCategory("Preprocessing Tools");
	- parser.setDescription("Loads Diffusion Dicom files.");
	- parser.setContributor("MIC");
	-
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input Directory" ,"input directory containing dicom files", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output File Name", "output file", us::Any(), false, false, false, mitkCommandLineParser::Output);
	- parser.addArgument("dwprefix", "p", mitkCommandLineParser::String, "Recursive Scan Prefix", "prefix for subfolders search rootdir is specified by the 'inputdir' argument value", us::Any(), true);
	- parser.addArgument("dryrun", "s", mitkCommandLineParser::Bool, "Dry run","do not read, only look for input files ", us::Any(), true );
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- {
	- return EXIT_FAILURE;
	- }
	-
	- std::string inputDirectory = us::any_cast<std::string>( parsedArgs["i"] );
	- MITK_INFO << "Loading data from directory: " << inputDirectory;
	-
	- // retrieve the prefix flag (if set)
	- bool search_for_subdirs = false;
	- std::string subdir_prefix;
	- if( parsedArgs.count("dwprefix"))
	- {
	- subdir_prefix = us::any_cast<std::string>( parsedArgs["dwprefix"] );
	- if (subdir_prefix != "")
	- {
	- MITK_INFO << "Prefix specified, will search for subdirs in the input directory!";
	- search_for_subdirs = true;
	- }
	- }
	-
	- // retrieve the output
	- std::string outputFile = us::any_cast< std::string >( parsedArgs["o"] );
	-
	- // if the executable is called with a single directory, just parse the given folder for files and read them into a diffusion image
	- if( !search_for_subdirs )
	- {
	- SetInputFileNames( inputDirectory );
	-
	- MITK_INFO << "Got " << GetInputFilenames().size() << " input files.";
	- mitk::Image::Pointer d_img = ReadInDICOMFiles( GetInputFilenames(), outputFile );
	-
	- try
	- {
	- mitk::IOUtil::Save(d_img, outputFile.c_str());
	- }
	- catch( const itk::ExceptionObject& e)
	- {
	- MITK_ERROR << "Failed to write out the output file. \n\t Reason : ITK Exception " << e.what();
	- }
	-
	- }
	- // if the --dwprefix flag is set, then we have to look for the directories, load each of them separately and afterwards merge the images
	- else
	- {
	- std::vector<mitk::Image::Pointer> output_container;
	-
	- SearchForInputInSubdirs( inputDirectory, subdir_prefix, output_container );
	-
	- // final output image
	- mitk::Image::Pointer image = mitk::Image::New();
	- if( output_container.size() > 1 )
	- {
	- DwiImageContainerType imageContainer;
	- GradientListContainerType gradientListContainer;
	- std::vector< double > bValueContainer;
	-
	- for ( std::vector< mitk::Image::Pointer >::iterator dwi = output_container.begin();
	- dwi != output_container.end(); ++dwi )
	- {
	- mitk::DiffusionPropertyHelper::ImageType::Pointer itkVectorImagePointer = mitk::DiffusionPropertyHelper::ImageType::New();
	- mitk::CastToItkImage(*dwi, itkVectorImagePointer);
	-
	- imageContainer.push_back(itkVectorImagePointer);
	- gradientListContainer.push_back( mitk::DiffusionPropertyHelper::GetGradientContainer(*dwi));
	- bValueContainer.push_back( mitk::DiffusionPropertyHelper::GetReferenceBValue(*dwi));
	- }
	-
	- typedef itk::MergeDiffusionImagesFilter<short> FilterType;
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetImageVolumes(imageContainer);
	- filter->SetGradientLists(gradientListContainer);
	- filter->SetBValues(bValueContainer);
	- filter->Update();
	-
	- vnl_matrix_fixed< double, 3, 3 > mf; mf.set_identity();
	-
	- image = mitk::GrabItkImageMemory( filter->GetOutput() );
	-
	- mitk::DiffusionPropertyHelper::SetGradientContainer(image, filter->GetOutputGradients());
	- mitk::DiffusionPropertyHelper::SetReferenceBValue(image, filter->GetB_Value());
	- mitk::DiffusionPropertyHelper::SetMeasurementFrame(image, mf);
	- mitk::DiffusionPropertyHelper::InitializeImage( image );
	- }
	- // just output the image if there was only one folder found
	- else
	- {
	- image = output_container.at(0);
	- }
	-
	- MITK_INFO("dicom.import.writeout") << " [OutputFile] " << outputFile.c_str();
	-
	- try
	- {
	- mitk::IOUtil::Save(image, outputFile.c_str());
	- }
	- catch( const itk::ExceptionObject& e)
	- {
	- MITK_ERROR << "Failed to write out the output file. \n\t Reason : ITK Exception " << e.what();
	- }
	-
	- }
	-
	- return 1;
	-}
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/DmriDenoising.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/DmriDenoising.cpp
	deleted file mode 100644
	index 054ce3fdfd..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/DmriDenoising.cpp
	+++ /dev/null
	@@ -1,234 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkImageCast.h>
	-#include <mitkImage.h>
	-#include <mitkIOUtil.h>
	-#include "mitkCommandLineParser.h"
	-#include <mitkPreferenceListReaderOptionsFunctor.h>
	-#include <itksys/SystemTools.hxx>
	-#include <itkTotalVariationDenoisingImageFilter.h>
	-#include <itkNonLocalMeansDenoisingFilter.h>
	-#include <itkDiscreteGaussianImageFilter.h>
	-#include <itkPatchBasedDenoisingImageFilter.h>
	-#include <itkVectorImageToImageFilter.h>
	-#include <itkComposeImageFilter.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <itkGaussianRandomSpatialNeighborSubsampler.h>
	-#include <mitkITKImageImport.h>
	-#include <mitkProperties.h>
	-
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("DmriDenoising");
	- parser.setCategory("Preprocessing Tools");
	- parser.setDescription("dMRI denoising tool");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	-
	- parser.beginGroup("1. Mandatory arguments:");
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input:", "input image", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "output image", us::Any(), false, false, false, mitkCommandLineParser::Output);
	- parser.addArgument("type", "", mitkCommandLineParser::Int, "Type:", "0 (TotalVariation), 1 (Gauss), 2 (NLM)", 0);
	- parser.endGroup();
	-
	- parser.beginGroup("2. Total variation parameters:");
	- parser.addArgument("tv_iterations", "", mitkCommandLineParser::Int, "Iterations:", "", 1);
	- parser.addArgument("lambda", "", mitkCommandLineParser::Float, "Lambda:", "", 0.1);
	- parser.endGroup();
	-
	- parser.beginGroup("3. Gauss parameters:");
	- parser.addArgument("variance", "", mitkCommandLineParser::Float, "Variance:", "", 1.0);
	- parser.endGroup();
	-
	- parser.beginGroup("4. NLM parameters:");
	- parser.addArgument("nlm_iterations", "", mitkCommandLineParser::Int, "Iterations:", "", 4);
	- parser.addArgument("sampling_radius", "", mitkCommandLineParser::Int, "Sampling radius:", "", 4);
	- parser.addArgument("patch_radius", "", mitkCommandLineParser::Int, "Patch radius:", "", 1);
	- parser.addArgument("num_patches", "", mitkCommandLineParser::Int, "Num. patches:", "", 10);
	- parser.endGroup();
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- // mandatory arguments
	- std::string imageName = us::any_cast<std::string>(parsedArgs["i"]);
	- std::string outImage = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- int type = 0;
	- if (parsedArgs.count("type"))
	- type = us::any_cast<int>(parsedArgs["type"]);
	-
	- int tv_iterations = 1;
	- if (parsedArgs.count("tv_iterations"))
	- tv_iterations = us::any_cast<int>(parsedArgs["tv_iterations"]);
	-
	- float lambda = 0.1;
	- if (parsedArgs.count("lambda"))
	- lambda = us::any_cast<float>(parsedArgs["lambda"]);
	-
	- float variance = 1.0;
	- if (parsedArgs.count("variance"))
	- variance = us::any_cast<float>(parsedArgs["variance"]);
	-
	- int nlm_iterations = 4;
	- if (parsedArgs.count("nlm_iterations"))
	- nlm_iterations = us::any_cast<int>(parsedArgs["nlm_iterations"]);
	-
	- int sampling_radius = 4;
	- if (parsedArgs.count("sampling_radius"))
	- sampling_radius = us::any_cast<int>(parsedArgs["sampling_radius"]);
	-
	- int patch_radius = 1;
	- if (parsedArgs.count("patch_radius"))
	- patch_radius = us::any_cast<int>(parsedArgs["patch_radius"]);
	-
	- int num_patches = 10;
	- if (parsedArgs.count("num_patches"))
	- num_patches = us::any_cast<int>(parsedArgs["num_patches"]);
	-
	- try
	- {
	- mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Diffusion Weighted Images"}, {});
	- mitk::Image::Pointer input_image = mitk::IOUtil::Load<mitk::Image>(imageName, &functor);
	-
	- typedef short DiffusionPixelType;
	- typedef itk::VectorImage<DiffusionPixelType, 3> DwiImageType;
	- typedef itk::Image<DiffusionPixelType, 3> DwiVolumeType;
	- typedef itk::DiscreteGaussianImageFilter < DwiVolumeType, DwiVolumeType > GaussianFilterType;
	- typedef itk::PatchBasedDenoisingImageFilter < DwiVolumeType, DwiVolumeType > NlmFilterType;
	- typedef itk::VectorImageToImageFilter < DiffusionPixelType > ExtractFilterType;
	- typedef itk::ComposeImageFilter < itk::Image<DiffusionPixelType, 3> > ComposeFilterType;
	-
	- if (!mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(input_image))
	- mitkThrow() << "Input is not a diffusion-weighted image!";
	-
	- DwiImageType::Pointer itkVectorImagePointer = mitk::DiffusionPropertyHelper::GetItkVectorImage(input_image);
	-
	- mitk::Image::Pointer denoised_image = nullptr;
	-
	- switch (type)
	- {
	- case 0:
	- {
	- ComposeFilterType::Pointer composer = ComposeFilterType::New();
	- for (unsigned int i=0; i<itkVectorImagePointer->GetVectorLength(); ++i)
	- {
	- ExtractFilterType::Pointer extractor = ExtractFilterType::New();
	- extractor->SetInput( itkVectorImagePointer );
	- extractor->SetIndex( i );
	- extractor->Update();
	- DwiVolumeType::Pointer gradient_volume = extractor->GetOutput();
	- itk::TotalVariationDenoisingImageFilter< DwiVolumeType, DwiVolumeType >::Pointer filter = itk::TotalVariationDenoisingImageFilter< DwiVolumeType, DwiVolumeType >::New();
	- filter->SetInput(gradient_volume);
	- filter->SetLambda(lambda);
	- filter->SetNumberIterations(tv_iterations);
	- filter->Update();
	- composer->SetInput(i, filter->GetOutput());
	- }
	- composer->Update();
	- denoised_image = mitk::GrabItkImageMemory(composer->GetOutput());
	- break;
	- }
	- case 1:
	- {
	- ExtractFilterType::Pointer extractor = ExtractFilterType::New();
	- extractor->SetInput( itkVectorImagePointer );
	- ComposeFilterType::Pointer composer = ComposeFilterType::New();
	- for (unsigned int i = 0; i < itkVectorImagePointer->GetVectorLength(); ++i)
	- {
	- extractor->SetIndex(i);
	- extractor->Update();
	- GaussianFilterType::Pointer filter = GaussianFilterType::New();
	- filter->SetVariance(variance);
	- filter->SetInput(extractor->GetOutput());
	- filter->Update();
	- composer->SetInput(i, filter->GetOutput());
	- }
	- composer->Update();
	- denoised_image = mitk::GrabItkImageMemory(composer->GetOutput());
	- break;
	- }
	- case 2:
	- {
	- typedef itk::Statistics::GaussianRandomSpatialNeighborSubsampler< NlmFilterType::PatchSampleType, DwiVolumeType::RegionType > SamplerType;
	- // sampling the image to find similar patches
	- SamplerType::Pointer sampler = SamplerType::New();
	- sampler->SetRadius( sampling_radius );
	- sampler->SetVariance( sampling_radius*sampling_radius );
	- sampler->SetNumberOfResultsRequested( num_patches );
	-
	- MITK_INFO << "Starting NLM denoising";
	- ExtractFilterType::Pointer extractor = ExtractFilterType::New();
	- extractor->SetInput( itkVectorImagePointer );
	- ComposeFilterType::Pointer composer = ComposeFilterType::New();
	- for (unsigned int i = 0; i < itkVectorImagePointer->GetVectorLength(); ++i)
	- {
	- extractor->SetIndex(i);
	- extractor->Update();
	- NlmFilterType::Pointer filter = NlmFilterType::New();
	- filter->SetInput(extractor->GetOutput());
	- filter->SetPatchRadius(patch_radius);
	- filter->SetNoiseModel(NlmFilterType::RICIAN);
	- filter->UseSmoothDiscPatchWeightsOn();
	- filter->UseFastTensorComputationsOn();
	-
	- filter->SetNumberOfIterations(nlm_iterations);
	- filter->SetSmoothingWeight( 1 );
	- filter->SetKernelBandwidthEstimation(true);
	-
	- filter->SetSampler( sampler );
	- filter->Update();
	- composer->SetInput(i, filter->GetOutput());
	- MITK_INFO << "Gradient " << i << " finished";
	- }
	- composer->Update();
	- denoised_image = mitk::GrabItkImageMemory(composer->GetOutput());
	- break;
	- }
	- }
	-
	- mitk::DiffusionPropertyHelper::SetGradientContainer(denoised_image, mitk::DiffusionPropertyHelper::GetGradientContainer(input_image));
	- mitk::DiffusionPropertyHelper::SetReferenceBValue(denoised_image, mitk::DiffusionPropertyHelper::GetReferenceBValue(input_image));
	- mitk::DiffusionPropertyHelper::InitializeImage( denoised_image );
	-
	- std::string ext = itksys::SystemTools::GetFilenameExtension(outImage);
	- if (ext==".nii" \|\| ext==".nii.gz")
	- mitk::IOUtil::Save(denoised_image, "DWI_NIFTI", outImage);
	- else
	- mitk::IOUtil::Save(denoised_image, outImage);
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/FileFormatConverter.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/FileFormatConverter.cpp
	deleted file mode 100644
	index 2e6eea39b0..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/FileFormatConverter.cpp
	+++ /dev/null
	@@ -1,80 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkImageCast.h>
	-#include <mitkImage.h>
	-#include <mitkIOUtil.h>
	-#include "mitkCommandLineParser.h"
	-#include <mitkPreferenceListReaderOptionsFunctor.h>
	-#include <mitkFiberBundle.h>
	-
	-/*!
	-\brief Load image and save as specified file type.
	-*/
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Format Converter");
	- parser.setCategory("Preprocessing Tools");
	- parser.setDescription("Load image and save as specified file type.");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input:", "input file", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "output file", us::Any(), false, false, false, mitkCommandLineParser::Output);
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- // mandatory arguments
	- std::string inName = us::any_cast<std::string>(parsedArgs["i"]);
	- std::string outName = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- try
	- {
	- mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Diffusion Weighted Images"}, {});
	- std::vector<mitk::BaseData::Pointer> baseData = mitk::IOUtil::Load(inName, &functor);
	-
	- if ( baseData.size()>0 && dynamic_cast<mitk::Image*>(baseData[0].GetPointer()) )
	- {
	- mitk::IOUtil::Save(dynamic_cast<mitk::Image*>(baseData[0].GetPointer()), outName.c_str());
	- }
	- else if ( baseData.size()>0 && dynamic_cast<mitk::FiberBundle*>(baseData[0].GetPointer()) )
	- {
	- mitk::IOUtil::Save(dynamic_cast<mitk::FiberBundle*>(baseData[0].GetPointer()) ,outName.c_str());
	- }
	- else
	- std::cout << "File type currently not supported!";
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/FlipPeaks.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/FlipPeaks.cpp
	deleted file mode 100644
	index 758265b0e9..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/FlipPeaks.cpp
	+++ /dev/null
	@@ -1,104 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkImageCast.h>
	-#include <mitkImage.h>
	-#include <mitkIOUtil.h>
	-#include "mitkCommandLineParser.h"
	-#include <mitkPeakImage.h>
	-#include <itkFlipPeaksFilter.h>
	-#include <mitkImageToItk.h>
	-#include <mitkPreferenceListReaderOptionsFunctor.h>
	-
	-/*!
	-\brief Copies transformation matrix of one image to another
	-*/
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Flip Peaks");
	- parser.setCategory("Preprocessing Tools");
	- parser.setDescription("Flips the peaks of the input peak image along the given dimensions.");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input", "input image", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output", "output image", us::Any(), false, false, false, mitkCommandLineParser::Output);
	- parser.addArgument("", "x", mitkCommandLineParser::Bool, "Flip x", "flip along x-axis");
	- parser.addArgument("", "y", mitkCommandLineParser::Bool, "Flip y", "flip along y-axis");
	- parser.addArgument("", "z", mitkCommandLineParser::Bool, "Flip z", "flip along z-axis");
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- std::string imageName = us::any_cast<std::string>(parsedArgs["i"]);
	- std::string outImage = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- bool x = false;
	- if (parsedArgs.count("x"))
	- x = us::any_cast<bool>(parsedArgs["x"]);
	-
	- bool y = false;
	- if (parsedArgs.count("y"))
	- y = us::any_cast<bool>(parsedArgs["y"]);
	-
	- bool z = false;
	- if (parsedArgs.count("z"))
	- z = us::any_cast<bool>(parsedArgs["z"]);
	-
	- try
	- {
	- mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Peak Image"}, {});
	- mitk::PeakImage::Pointer image = mitk::IOUtil::Load<mitk::PeakImage>(imageName, &functor);
	-
	- typedef mitk::ImageToItk< mitk::PeakImage::ItkPeakImageType > CasterType;
	- CasterType::Pointer caster = CasterType::New();
	- caster->SetInput(image);
	- caster->Update();
	- mitk::PeakImage::ItkPeakImageType::Pointer itkImg = caster->GetOutput();
	-
	- itk::FlipPeaksFilter< float >::Pointer flipper = itk::FlipPeaksFilter< float >::New();
	- flipper->SetInput(itkImg);
	- flipper->SetFlipX(x);
	- flipper->SetFlipY(y);
	- flipper->SetFlipZ(z);
	- flipper->Update();
	-
	- mitk::Image::Pointer resultImage = dynamic_cast<mitk::Image*>(mitk::PeakImage::New().GetPointer());
	- mitk::CastToMitkImage(flipper->GetOutput(), resultImage);
	- resultImage->SetVolume(flipper->GetOutput()->GetBufferPointer());
	-
	- mitk::IOUtil::Save(resultImage, outImage);
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/HeadMotionCorrection.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/HeadMotionCorrection.cpp
	deleted file mode 100644
	index 6633946b93..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/HeadMotionCorrection.cpp
	+++ /dev/null
	@@ -1,78 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkImageCast.h>
	-#include <mitkImage.h>
	-#include <mitkIOUtil.h>
	-#include "mitkCommandLineParser.h"
	-#include <mitkDWIHeadMotionCorrectionFilter.h>
	-#include <mitkPreferenceListReaderOptionsFunctor.h>
	-#include <itksys/SystemTools.hxx>
	-
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("HeadMotionCorrection");
	- parser.setCategory("Preprocessing Tools");
	- parser.setDescription("Simple affine head-motion correction tool");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input:", "input image", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "output image", us::Any(), false, false, false, mitkCommandLineParser::Output);
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- // mandatory arguments
	- std::string imageName = us::any_cast<std::string>(parsedArgs["i"]);
	- std::string outImage = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- try
	- {
	- mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Diffusion Weighted Images"}, {});
	- mitk::Image::Pointer in_image = mitk::IOUtil::Load<mitk::Image>(imageName, &functor);
	-
	- mitk::DWIHeadMotionCorrectionFilter::Pointer registerer = mitk::DWIHeadMotionCorrectionFilter::New();
	- registerer->SetInput(in_image);
	- registerer->Update();
	- mitk::Image::Pointer out_image = registerer->GetCorrectedImage();
	-
	- std::string ext = itksys::SystemTools::GetFilenameExtension(outImage);
	- if (ext==".nii" \|\| ext==".nii.gz")
	- mitk::IOUtil::Save(out_image, "DWI_NIFTI", outImage);
	- else
	- mitk::IOUtil::Save(out_image, outImage);
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/ImageResampler.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/ImageResampler.cpp
	deleted file mode 100644
	index ba2cfec567..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/ImageResampler.cpp
	+++ /dev/null
	@@ -1,420 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#include "mitkCommandLineParser.h"
	-
	-#include <mitkIOUtil.h>
	-#include <mitkRegistrationWrapper.h>
	-#include <mitkImage.h>
	-#include <mitkImageCast.h>
	-#include <mitkITKImageImport.h>
	-#include <mitkImageTimeSelector.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <mitkProperties.h>
	-
	-// ITK
	-#include <itksys/SystemTools.hxx>
	-#include <itkDirectory.h>
	-#include "itkLinearInterpolateImageFunction.h"
	-#include "itkWindowedSincInterpolateImageFunction.h"
	-#include "itkNearestNeighborInterpolateImageFunction.h"
	-#include "itkIdentityTransform.h"
	-#include "itkResampleImageFilter.h"
	-#include "itkResampleDwiImageFilter.h"
	-
	-typedef itk::Image<double, 3> InputImageType;
	-typedef itk::Image<unsigned char, 3> BinaryImageType;
	-
	-static mitk::Image::Pointer TransformToReference(mitk::Image reference, mitk::Image moving, bool sincInterpol = false, bool nn = false)
	-{
	- // Convert to itk Images
	-
	- // Identify Transform
	- typedef itk::IdentityTransform<double, 3> T_Transform;
	- T_Transform::Pointer _pTransform = T_Transform::New();
	- _pTransform->SetIdentity();
	-
	- typedef itk::WindowedSincInterpolateImageFunction< InputImageType, 3> WindowedSincInterpolatorType;
	- WindowedSincInterpolatorType::Pointer sinc_interpolator = WindowedSincInterpolatorType::New();
	-
	- typedef itk::LinearInterpolateImageFunction< InputImageType> LinearInterpolateImageFunctionType;
	- LinearInterpolateImageFunctionType::Pointer lin_interpolator = LinearInterpolateImageFunctionType::New();
	-
	- typedef itk::NearestNeighborInterpolateImageFunction< BinaryImageType> NearestNeighborInterpolateImageFunctionType;
	- NearestNeighborInterpolateImageFunctionType::Pointer nn_interpolator = NearestNeighborInterpolateImageFunctionType::New();
	-
	-
	- if (!nn)
	- {
	- InputImageType::Pointer itkReference = InputImageType::New();
	- InputImageType::Pointer itkMoving = InputImageType::New();
	- mitk::CastToItkImage(reference,itkReference);
	- mitk::CastToItkImage(moving,itkMoving);
	- typedef itk::ResampleImageFilter<InputImageType, InputImageType> ResampleFilterType;
	-
	-
	- ResampleFilterType::Pointer resampler = ResampleFilterType::New();
	- resampler->SetInput(itkMoving);
	- resampler->SetReferenceImage( itkReference );
	- resampler->UseReferenceImageOn();
	- resampler->SetTransform(_pTransform);
	- if ( sincInterpol)
	- resampler->SetInterpolator(sinc_interpolator);
	- else
	- resampler->SetInterpolator(lin_interpolator);
	-
	- resampler->Update();
	-
	- // Convert back to mitk
	- mitk::Image::Pointer result = mitk::Image::New();
	- result->InitializeByItk(resampler->GetOutput());
	- GrabItkImageMemory( resampler->GetOutput() , result );
	- return result;
	- }
	-
	-
	- BinaryImageType::Pointer itkReference = BinaryImageType::New();
	- BinaryImageType::Pointer itkMoving = BinaryImageType::New();
	- mitk::CastToItkImage(reference,itkReference);
	- mitk::CastToItkImage(moving,itkMoving);
	-
	-
	- typedef itk::ResampleImageFilter<BinaryImageType, BinaryImageType> ResampleFilterType;
	-
	-
	- ResampleFilterType::Pointer resampler = ResampleFilterType::New();
	- resampler->SetInput(itkMoving);
	- resampler->SetReferenceImage( itkReference );
	- resampler->UseReferenceImageOn();
	- resampler->SetTransform(_pTransform);
	- resampler->SetInterpolator(nn_interpolator);
	-
	- resampler->Update();
	- // Convert back to mitk
	- mitk::Image::Pointer result = mitk::Image::New();
	- result->InitializeByItk(resampler->GetOutput());
	- GrabItkImageMemory( resampler->GetOutput() , result );
	- return result;
	-
	-}
	-
	-
	-static std::vector<std::string> &split(const std::string &s, char delim, std::vector<std::string> &elems)
	-{
	- std::stringstream ss(s);
	- std::string item;
	- while (std::getline(ss, item, delim))
	- {
	- elems.push_back(item);
	- }
	- return elems;
	-}
	-
	-static std::vector<std::string> split(const std::string &s, char delim)
	-{
	- std::vector < std::string > elems;
	- return split(s, delim, elems);
	-}
	-
	-
	-static mitk::Image::Pointer ResampleBySpacing(mitk::Image input, float spacing, bool useLinInt = true, bool useNN = false)
	-{
	- if (!useNN)
	- {
	- InputImageType::Pointer itkImage = InputImageType::New();
	- CastToItkImage(input,itkImage);
	-
	- /**
	- * 1) Resampling
	- *
	- */
	- // Identity transform.
	- // We don't want any transform on our image except rescaling which is not
	- // specified by a transform but by the input/output spacing as we will see
	- // later.
	- // So no transform will be specified.
	- typedef itk::IdentityTransform<double, 3> T_Transform;
	-
	- // The resampler type itself.
	- typedef itk::ResampleImageFilter<InputImageType, InputImageType> T_ResampleFilter;
	-
	- // Prepare the resampler.
	- // Instantiate the transform and specify it should be the id transform.
	- T_Transform::Pointer _pTransform = T_Transform::New();
	- _pTransform->SetIdentity();
	-
	- // Instantiate the resampler. Wire in the transform and the interpolator.
	- T_ResampleFilter::Pointer _pResizeFilter = T_ResampleFilter::New();
	-
	- // Specify the input.
	- _pResizeFilter->SetInput(itkImage);
	-
	- _pResizeFilter->SetTransform(_pTransform);
	-
	- // Set the output origin.
	- _pResizeFilter->SetOutputOrigin(itkImage->GetOrigin());
	-
	- // Compute the size of the output.
	- // The size (# of pixels) in the output is recomputed using
	- // the ratio of the input and output sizes.
	- InputImageType::SpacingType inputSpacing = itkImage->GetSpacing();
	- InputImageType::SpacingType outputSpacing;
	- const InputImageType::RegionType& inputSize = itkImage->GetLargestPossibleRegion();
	-
	- InputImageType::SizeType outputSize;
	- typedef InputImageType::SizeType::SizeValueType SizeValueType;
	-
	- // Set the output spacing.
	- outputSpacing[0] = spacing[0];
	- outputSpacing[1] = spacing[1];
	- outputSpacing[2] = spacing[2];
	-
	- outputSize[0] = static_cast<SizeValueType>(inputSize.GetSize()[0] * inputSpacing[0] / outputSpacing[0] + .5);
	- outputSize[1] = static_cast<SizeValueType>(inputSize.GetSize()[1] * inputSpacing[1] / outputSpacing[1] + .5);
	- outputSize[2] = static_cast<SizeValueType>(inputSize.GetSize()[2] * inputSpacing[2] / outputSpacing[2] + .5);
	-
	- _pResizeFilter->SetOutputSpacing(outputSpacing);
	- _pResizeFilter->SetSize(outputSize);
	-
	- typedef itk::LinearInterpolateImageFunction< InputImageType > LinearInterpolatorType;
	- LinearInterpolatorType::Pointer lin_interpolator = LinearInterpolatorType::New();
	-
	-
	- typedef itk::WindowedSincInterpolateImageFunction< InputImageType, 4> WindowedSincInterpolatorType;
	- WindowedSincInterpolatorType::Pointer sinc_interpolator = WindowedSincInterpolatorType::New();
	-
	- if (useLinInt)
	- _pResizeFilter->SetInterpolator(lin_interpolator);
	- else
	- _pResizeFilter->SetInterpolator(sinc_interpolator);
	-
	- _pResizeFilter->Update();
	-
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk(_pResizeFilter->GetOutput());
	- mitk::GrabItkImageMemory( _pResizeFilter->GetOutput(), image);
	- return image;
	- }
	-
	- BinaryImageType::Pointer itkImage = BinaryImageType::New();
	- CastToItkImage(input,itkImage);
	-
	- /**
	- * 1) Resampling
	- *
	- */
	- // Identity transform.
	- // We don't want any transform on our image except rescaling which is not
	- // specified by a transform but by the input/output spacing as we will see
	- // later.
	- // So no transform will be specified.
	- typedef itk::IdentityTransform<double, 3> T_Transform;
	-
	- // The resampler type itself.
	- typedef itk::ResampleImageFilter<BinaryImageType, BinaryImageType> T_ResampleFilter;
	-
	- // Prepare the resampler.
	- // Instantiate the transform and specify it should be the id transform.
	- T_Transform::Pointer _pTransform = T_Transform::New();
	- _pTransform->SetIdentity();
	-
	- // Instantiate the resampler. Wire in the transform and the interpolator.
	- T_ResampleFilter::Pointer _pResizeFilter = T_ResampleFilter::New();
	-
	- // Specify the input.
	- _pResizeFilter->SetInput(itkImage);
	-
	- _pResizeFilter->SetTransform(_pTransform);
	-
	- // Set the output origin.
	- _pResizeFilter->SetOutputOrigin(itkImage->GetOrigin());
	-
	- // Compute the size of the output.
	- // The size (# of pixels) in the output is recomputed using
	- // the ratio of the input and output sizes.
	- BinaryImageType::SpacingType inputSpacing = itkImage->GetSpacing();
	- BinaryImageType::SpacingType outputSpacing;
	- const BinaryImageType::RegionType& inputSize = itkImage->GetLargestPossibleRegion();
	-
	- BinaryImageType::SizeType outputSize;
	- typedef BinaryImageType::SizeType::SizeValueType SizeValueType;
	-
	- // Set the output spacing.
	- outputSpacing[0] = spacing[0];
	- outputSpacing[1] = spacing[1];
	- outputSpacing[2] = spacing[2];
	-
	- outputSize[0] = static_cast<SizeValueType>(inputSize.GetSize()[0] * inputSpacing[0] / outputSpacing[0] + .5);
	- outputSize[1] = static_cast<SizeValueType>(inputSize.GetSize()[1] * inputSpacing[1] / outputSpacing[1] + .5);
	- outputSize[2] = static_cast<SizeValueType>(inputSize.GetSize()[2] * inputSpacing[2] / outputSpacing[2] + .5);
	-
	- _pResizeFilter->SetOutputSpacing(outputSpacing);
	- _pResizeFilter->SetSize(outputSize);
	-
	- typedef itk::NearestNeighborInterpolateImageFunction< BinaryImageType> NearestNeighborInterpolateImageType;
	- NearestNeighborInterpolateImageType::Pointer nn_interpolator = NearestNeighborInterpolateImageType::New();
	- _pResizeFilter->SetInterpolator(nn_interpolator);
	-
	- _pResizeFilter->Update();
	-
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk(_pResizeFilter->GetOutput());
	- mitk::GrabItkImageMemory( _pResizeFilter->GetOutput(), image);
	- return image;
	-}
	-
	-static mitk::Image::Pointer ResampleDWIbySpacing(mitk::Image::Pointer input, float* spacing)
	-{
	- itk::Vector<double, 3> spacingVector;
	- spacingVector[0] = spacing[0];
	- spacingVector[1] = spacing[1];
	- spacingVector[2] = spacing[2];
	-
	- typedef itk::ResampleDwiImageFilter<short> ResampleFilterType;
	-
	- mitk::DiffusionPropertyHelper::ImageType::Pointer itkVectorImagePointer = mitk::DiffusionPropertyHelper::ImageType::New();
	- mitk::CastToItkImage(input, itkVectorImagePointer);
	-
	- ResampleFilterType::Pointer resampler = ResampleFilterType::New();
	- resampler->SetInput( itkVectorImagePointer );
	- resampler->SetInterpolation(ResampleFilterType::Interpolate_Linear);
	- resampler->SetNewSpacing(spacingVector);
	- resampler->Update();
	-
	- mitk::Image::Pointer output = mitk::GrabItkImageMemory( resampler->GetOutput() );
	-
	- mitk::DiffusionPropertyHelper::SetGradientContainer(output, mitk::DiffusionPropertyHelper::GetGradientContainer(input));
	- mitk::DiffusionPropertyHelper::SetReferenceBValue(output, mitk::DiffusionPropertyHelper::GetReferenceBValue(input));
	- mitk::DiffusionPropertyHelper::InitializeImage( output );
	-
	- return output;
	-}
	-
	-int main( int argc, char* argv[] )
	-{
	- mitkCommandLineParser parser;
	- parser.setArgumentPrefix("--","-");
	-
	- parser.setTitle("Image Resampler");
	- parser.setCategory("Preprocessing Tools");
	- parser.setContributor("MIC");
	- parser.setDescription("Resample an image to eigther a specific spacing or to a reference image.");
	-
	- // Add command line argument names
	- parser.addArgument("help", "h",mitkCommandLineParser::Bool, "Show this help text");
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input:", "Input file",us::Any(),false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "Output file",us::Any(),false, false, false, mitkCommandLineParser::Output);
	- parser.addArgument("spacing", "s", mitkCommandLineParser::String, "Spacing:", "Resample provide x,y,z spacing in mm (e.g. -r 1,1,3), is not applied to tensor data",us::Any());
	- parser.addArgument("reference", "r", mitkCommandLineParser::String, "Reference:", "Resample using supplied reference image. Also cuts image to same dimensions",us::Any(), true, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("win-sinc", "w", mitkCommandLineParser::Bool, "Windowed-sinc interpolation:", "Use windowed-sinc interpolation (3) instead of linear interpolation ",us::Any());
	- parser.addArgument("nearest-neigh", "n", mitkCommandLineParser::Bool, "Nearest Neighbor:", "Use Nearest Neighbor interpolation instead of linear interpolation ",us::Any());
	-
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	-
	- // Handle special arguments
	- bool useSpacing = false;
	- bool useLinearInterpol = true;
	- bool useNN= false;
	- {
	- if (parsedArgs.size() == 0)
	- {
	- return EXIT_FAILURE;
	- }
	-
	- if (parsedArgs.count("sinc-int"))
	- useLinearInterpol = false;
	-
	- if (parsedArgs.count("nearest-neigh"))
	- useNN = true;
	-
	- // Show a help message
	- if ( parsedArgs.count("help") \|\| parsedArgs.count("h"))
	- {
	- std::cout << parser.helpText();
	- return EXIT_SUCCESS;
	- }
	- }
	-
	- std::string outputFile = us::any_cast<std::string>(parsedArgs["i"]);
	- std::string inputFile = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- std::vector<std::string> spacings;
	- float spacing[] = { 0.0f, 0.0f, 0.0f };
	- if (parsedArgs.count("spacing"))
	- {
	-
	- std::string arg = us::any_cast<std::string>(parsedArgs["spacing"]);
	- if (arg != "")
	- {
	- spacings = split(arg ,',');
	- spacing[0] = atoi(spacings.at(0).c_str());
	- spacing[1] = atoi(spacings.at(1).c_str());
	- spacing[2] = atoi(spacings.at(2).c_str());
	- useSpacing = true;
	- }
	- }
	-
	- std::string refImageFile = "";
	- if (parsedArgs.count("reference"))
	- {
	- refImageFile = us::any_cast<std::string>(parsedArgs["reference"]);
	- }
	-
	- if (refImageFile =="" && useSpacing == false)
	- {
	- MITK_ERROR << "No information how to resample is supplied. Use eigther --spacing or --reference !";
	- return EXIT_FAILURE;
	- }
	-
	-
	- mitk::Image::Pointer refImage;
	- if (!useSpacing)
	- refImage = mitk::IOUtil::Load<mitk::Image>(refImageFile);
	-
	- mitk::Image::Pointer inputDWI = mitk::IOUtil::Load<mitk::Image>(inputFile);
	- if ( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(inputDWI.GetPointer()))
	- {
	- mitk::Image::Pointer outputImage;
	-
	- if (useSpacing)
	- outputImage = ResampleDWIbySpacing(inputDWI, spacing);
	- else
	- {
	- MITK_WARN << "Not supported yet, to resample a DWI please set a new spacing.";
	- return EXIT_FAILURE;
	- }
	-
	- mitk::IOUtil::Save(outputImage, outputFile.c_str());
	-
	- return EXIT_SUCCESS;
	- }
	- mitk::Image::Pointer inputImage = mitk::IOUtil::Load<mitk::Image>(inputFile);
	-
	-
	- mitk::Image::Pointer resultImage;
	-
	- if (useSpacing)
	- resultImage = ResampleBySpacing(inputImage,spacing,useLinearInterpol,useNN);
	- else
	- resultImage = TransformToReference(refImage,inputImage,useLinearInterpol,useNN);
	-
	-
	- mitk::IOUtil::Save(resultImage, outputFile);
	-
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/PeakExtraction.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/PeakExtraction.cpp
	deleted file mode 100755
	index 5f6d486958..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/PeakExtraction.cpp
	+++ /dev/null
	@@ -1,294 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <itkImageFileWriter.h>
	-#include <itkResampleImageFilter.h>
	-#include <itkOdfMaximaExtractionFilter.h>
	-
	-#include <mitkImage.h>
	-#include <mitkOdfImage.h>
	-#include <mitkImageCast.h>
	-#include <mitkImageToItk.h>
	-#include <mitkTensorImage.h>
	-
	-#include <mitkCoreObjectFactory.h>
	-#include "mitkCommandLineParser.h"
	-#include <itkShCoefficientImageImporter.h>
	-#include <itkFlipImageFilter.h>
	-#include <mitkLexicalCast.h>
	-#include <boost/algorithm/string.hpp>
	-#include <mitkLocaleSwitch.h>
	-#include <mitkIOUtil.h>
	-
	-template<int shOrder>
	-int StartPeakExtraction(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input image", "sh coefficient image", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output directory", "output root", us::Any(), false, false, false, mitkCommandLineParser::Output);
	- parser.addArgument("mask", "", mitkCommandLineParser::String, "Mask", "mask image", us::Any(), true, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("normalization", "", mitkCommandLineParser::Int, "Normalization", "0=no norm, 1=max norm, 2=single vec norm", 1, true);
	- parser.addArgument("numpeaks", "", mitkCommandLineParser::Int, "Max. number of peaks", "maximum number of extracted peaks", 2, true);
	-
	- parser.addArgument("rel_peakthr", "", mitkCommandLineParser::Float, "Relative peak threshold", "peak threshold relative to largest peak", 0.4, true);
	- parser.addArgument("abs_peakthr", "", mitkCommandLineParser::Float, "Absolute peak threshold", "absolute peak magnitude threshold", 0.03, true);
	- parser.addArgument("angular_thr", "", mitkCommandLineParser::Float, "Angular threshold", "in degree", 15);
	-
	- parser.addArgument("shConvention", "", mitkCommandLineParser::String, "Use specified SH-basis", "use specified SH-basis (MRtrix, FSL)", std::string("MRtrix"), true);
	-
	- parser.addArgument("flipX", "", mitkCommandLineParser::Bool, "Flip X", "Flip peaks in x direction");
	- parser.addArgument("flipY", "", mitkCommandLineParser::Bool, "Flip Y", "Flip peaks in y direction");
	- parser.addArgument("flipZ", "", mitkCommandLineParser::Bool, "Flip Z", "Flip peaks in z direction");
	- parser.addArgument("scale_by_gfa", "", mitkCommandLineParser::Bool, "Scale by GFA", "Scale ODF values and peaks by GFA");
	-
	- parser.setCategory("Preprocessing Tools");
	- parser.setTitle("Peak Extraction");
	- parser.setDescription("");
	- parser.setContributor("MIC");
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- // mandatory arguments
	- std::string imageName = us::any_cast<std::string>(parsedArgs["i"]);
	- std::string outRoot = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- // optional arguments
	- std::string maskImageName("");
	- if (parsedArgs.count("mask"))
	- maskImageName = us::any_cast<std::string>(parsedArgs["mask"]);
	-
	- int normalization = 1;
	- if (parsedArgs.count("normalization"))
	- normalization = us::any_cast<int>(parsedArgs["normalization"]);
	-
	- int numPeaks = 2;
	- if (parsedArgs.count("numpeaks"))
	- numPeaks = us::any_cast<int>(parsedArgs["numpeaks"]);
	-
	- float rel_peakthr = 0.4;
	- if (parsedArgs.count("rel_peakthr"))
	- rel_peakthr = us::any_cast<float>(parsedArgs["rel_peakthr"]);
	-
	- float abs_peakthr = 0.03;
	- if (parsedArgs.count("abs_peakthr"))
	- abs_peakthr = us::any_cast<float>(parsedArgs["abs_peakthr"]);
	-
	- float angular_thr = 15;
	- if (parsedArgs.count("angular_thr"))
	- angular_thr = us::any_cast<float>(parsedArgs["angular_thr"]);
	- angular_thr = cos((float)angular_thr*itk::Math::pi / 180);
	-
	- bool scale_by_gfa = false;
	- if (parsedArgs.count("scale_by_gfa"))
	- scale_by_gfa = us::any_cast<bool>(parsedArgs["scale_by_gfa"]);
	-
	- bool flipX = false;
	- if (parsedArgs.count("flipX"))
	- flipX = us::any_cast<bool>(parsedArgs["flipX"]);
	-
	- bool flipY = false;
	- if (parsedArgs.count("flipY"))
	- flipY = us::any_cast<bool>(parsedArgs["flipY"]);
	-
	- bool flipZ = false;
	- if (parsedArgs.count("flipZ"))
	- flipZ = us::any_cast<bool>(parsedArgs["flipZ"]);
	-
	- std::cout << "image: " << imageName;
	- std::cout << "outroot: " << outRoot;
	- if (!maskImageName.empty())
	- std::cout << "mask: " << maskImageName;
	- else
	- std::cout << "no mask image selected";
	- std::cout << "numpeaks: " << numPeaks;
	- std::cout << "peakthres: " << rel_peakthr;
	- std::cout << "abspeakthres: " << abs_peakthr;
	- std::cout << "shOrder: " << shOrder;
	-
	- try
	- {
	- mitk::Image::Pointer image = mitk::IOUtil::Load<mitk::Image>(imageName);
	- mitk::Image::Pointer mask = mitk::IOUtil::Load<mitk::Image>(maskImageName);
	-
	- typedef itk::Image<unsigned char, 3> ItkUcharImgType;
	- typedef itk::OdfMaximaExtractionFilter< float, shOrder, 20242 > MaximaExtractionFilterType;
	- typename MaximaExtractionFilterType::Pointer peak_extraction_filter = MaximaExtractionFilterType::New();
	-
	-
	- ItkUcharImgType::Pointer itkMaskImage = nullptr;
	- if (mask.IsNotNull())
	- {
	- try{
	- itkMaskImage = ItkUcharImgType::New();
	- mitk::CastToItkImage(mask, itkMaskImage);
	- peak_extraction_filter->SetMaskImage(itkMaskImage);
	- }
	- catch(...)
	- {
	-
	- }
	- }
	-
	- if (parsedArgs.count("shConvention"))
	- {
	- std::string convention = us::any_cast<std::string>(parsedArgs["shConvention"]).c_str();
	- if ( convention=="FSL" )
	- peak_extraction_filter->SetToolkit(MaximaExtractionFilterType::FSL);
	- else
	- peak_extraction_filter->SetToolkit(MaximaExtractionFilterType::MRTRIX);
	- }
	- else
	- peak_extraction_filter->SetToolkit(MaximaExtractionFilterType::MRTRIX);
	-
	- try{
	- typedef mitk::ImageToItk< typename MaximaExtractionFilterType::CoefficientImageType > CasterType;
	- typename CasterType::Pointer caster = CasterType::New();
	- caster->SetInput(image);
	- caster->Update();
	- peak_extraction_filter->SetInput(caster->GetOutput());
	- }
	- catch(...)
	- {
	- std::cout << "wrong image type";
	- return EXIT_FAILURE;
	- }
	-
	- peak_extraction_filter->SetMaxNumPeaks(numPeaks);
	- peak_extraction_filter->SetRelativePeakThreshold(rel_peakthr);
	- peak_extraction_filter->SetAbsolutePeakThreshold(abs_peakthr);
	- peak_extraction_filter->SetAngularThreshold(angular_thr);
	- peak_extraction_filter->SetFlipX(flipX);
	- peak_extraction_filter->SetFlipY(flipY);
	- peak_extraction_filter->SetFlipZ(flipZ);
	- peak_extraction_filter->SetScaleByGfa(scale_by_gfa);
	-
	- switch (normalization)
	- {
	- case 0:
	- peak_extraction_filter->SetNormalizationMethod(MaximaExtractionFilterType::NO_NORM);
	- break;
	- case 1:
	- peak_extraction_filter->SetNormalizationMethod(MaximaExtractionFilterType::MAX_VEC_NORM);
	- break;
	- case 2:
	- peak_extraction_filter->SetNormalizationMethod(MaximaExtractionFilterType::SINGLE_VEC_NORM);
	- break;
	- }
	-
	- std::cout << "Starting extraction";
	- peak_extraction_filter->Update();
	-
	- mitk::LocaleSwitch localeSwitch("C");
	- // write direction image
	- {
	- typename MaximaExtractionFilterType::PeakImageType::Pointer itkImg = peak_extraction_filter->GetPeakImage();
	- std::string outfilename = outRoot;
	- outfilename.append("_PEAKS.nrrd");
	-
	- typedef itk::ImageFileWriter< typename MaximaExtractionFilterType::PeakImageType > WriterType;
	- typename WriterType::Pointer writer = WriterType::New();
	- writer->SetFileName(outfilename);
	- writer->SetInput(itkImg);
	- writer->Update();
	- }
	-
	- // write num directions image
	- {
	- ItkUcharImgType::Pointer numDirImage = peak_extraction_filter->GetNumDirectionsImage();
	-
	- if (itkMaskImage.IsNotNull())
	- {
	- numDirImage->SetDirection(itkMaskImage->GetDirection());
	- numDirImage->SetOrigin(itkMaskImage->GetOrigin());
	- }
	-
	- std::string outfilename = outRoot.c_str();
	- outfilename.append("_NUM_PEAKS.nrrd");
	- typedef itk::ImageFileWriter< ItkUcharImgType > WriterType;
	- WriterType::Pointer writer = WriterType::New();
	- writer->SetFileName(outfilename);
	- writer->SetInput(numDirImage);
	- writer->Update();
	- }
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	-
	-/*!
	-\brief Extract maxima in the input spherical harmonics image.
	-*/
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input image", "sh coefficient image", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output directory", "output root", us::Any(), false, false, false, mitkCommandLineParser::Output);
	- parser.addArgument("shOrder", "sh", mitkCommandLineParser::Int, "Spherical harmonics order", "spherical harmonics order");
	- parser.addArgument("mask", "m", mitkCommandLineParser::String, "Mask", "mask image", us::Any(), true, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("normalization", "n", mitkCommandLineParser::Int, "Normalization", "0=no norm, 1=max norm, 2=single vec norm", 1, true);
	- parser.addArgument("numpeaks", "p", mitkCommandLineParser::Int, "Max. number of peaks", "maximum number of extracted peaks", 2, true);
	- parser.addArgument("peakthres", "r", mitkCommandLineParser::Float, "Peak threshold", "peak threshold relative to largest peak", 0.4, true);
	- parser.addArgument("abspeakthres", "a", mitkCommandLineParser::Float, "Absolute peak threshold", "absolute peak threshold weighted with local GFA value", 0.06, true);
	- parser.addArgument("shConvention", "s", mitkCommandLineParser::String, "Use specified SH-basis", "use specified SH-basis (MITK, FSL, MRtrix)", std::string("MITK"), true);
	- parser.addArgument("noFlip", "f", mitkCommandLineParser::Bool, "No flip", "do not flip input image to match MITK coordinate convention");
	-
	- parser.setCategory("Preprocessing Tools");
	- parser.setTitle("Peak Extraction");
	- parser.setDescription("Extract maxima in the input spherical harmonics image.");
	- parser.setContributor("MIC");
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	-
	- int shOrder = -1;
	- if (parsedArgs.count("shOrder"))
	- shOrder = us::any_cast<int>(parsedArgs["shOrder"]);
	-
	- switch (shOrder)
	- {
	- case 4:
	- return StartPeakExtraction<4>(argc, argv);
	- case 6:
	- return StartPeakExtraction<6>(argc, argv);
	- case 8:
	- return StartPeakExtraction<8>(argc, argv);
	- case 10:
	- return StartPeakExtraction<10>(argc, argv);
	- case 12:
	- return StartPeakExtraction<12>(argc, argv);
	- }
	- return EXIT_FAILURE;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/Registration.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/Registration.cpp
	deleted file mode 100644
	index 947dcd8f44..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/Registration.cpp
	+++ /dev/null
	@@ -1,445 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-// CTK
	-#include "mitkCommandLineParser.h"
	-
	-#include <mitkIOUtil.h>
	-#include <mitkRegistrationWrapper.h>
	-#include <mitkImage.h>
	-#include <mitkImageCast.h>
	-#include <mitkImageReadAccessor.h>
	-#include <mitkITKImageImport.h>
	-#include <mitkImageTimeSelector.h>
	-// ITK
	-#include <itksys/SystemTools.hxx>
	-#include <itkDirectory.h>
	-#include "itkLinearInterpolateImageFunction.h"
	-#include "itkWindowedSincInterpolateImageFunction.h"
	-#include "itkIdentityTransform.h"
	-#include "itkResampleImageFilter.h"
	-#include "itkNrrdImageIO.h"
	-
	-typedef std::vector<std::string> FileListType;
	-typedef itk::Image<double, 3> InputImageType;
	-
	-static mitk::Image::Pointer ExtractFirstTS(mitk::Image* image, std::string fileType)
	-{
	- if (fileType == ".dwi")
	- return image;
	- mitk::ImageTimeSelector::Pointer selector = mitk::ImageTimeSelector::New();
	- selector->SetInput(image);
	- selector->SetTimeNr(0);
	- selector->UpdateLargestPossibleRegion();
	- mitk::Image::Pointer img =selector->GetOutput()->Clone();
	- return img;
	-}
	-
	-
	-static std::vector<std::string> &split(const std::string &s, char delim, std::vector<std::string> &elems)
	-{
	- std::stringstream ss(s);
	- std::string item;
	- while (std::getline(ss, item, delim))
	- {
	- elems.push_back(item);
	- }
	- return elems;
	-}
	-
	-static std::vector<std::string> split(const std::string &s, char delim)
	-{
	- std::vector < std::string > elems;
	- return split(s, delim, elems);
	-}
	-
	-/// Create list of all files in provided folder ending with same postfix
	-static FileListType CreateFileList(std::string folder , std::string postfix)
	-{
	- itk::Directory::Pointer dir = itk::Directory::New();
	- FileListType fileList;
	-
	- if( dir->Load(folder.c_str() ) )
	- {
	- int n = dir->GetNumberOfFiles();
	- for(int r=0;r<n;r++)
	- {
	- std::string filename = dir->GetFile( r );
	- if (filename == "." \|\| filename == "..")
	- continue;
	- filename = folder + filename;
	- if (!itksys::SystemTools::FileExists( filename.c_str()))
	- continue;
	- if (filename.length() <= postfix.length() )
	- continue;
	- if (filename.substr(filename.length() -postfix.length() ) == postfix)
	- fileList.push_back(filename);
	- }
	- }
	- return fileList;
	-}
	-
	-static std::string GetSavePath(std::string outputFolder, std::string fileName)
	-{
	- std::string fileType = itksys::SystemTools::GetFilenameExtension(fileName);
	- std::string fileStem = itksys::SystemTools::GetFilenameWithoutExtension(fileName);
	-
	- std::string savePathAndFileName = outputFolder +fileStem + fileType;
	-
	- return savePathAndFileName;
	-}
	-
	-
	-static mitk::Image::Pointer ResampleBySpacing(mitk::Image input, float spacing)
	-{
	- InputImageType::Pointer itkImage = InputImageType::New();
	- CastToItkImage(input,itkImage);
	-
	- /**
	- * 1) Resampling
	- *
	- */
	- // Identity transform.
	- // We don't want any transform on our image except rescaling which is not
	- // specified by a transform but by the input/output spacing as we will see
	- // later.
	- // So no transform will be specified.
	- typedef itk::IdentityTransform<double, 3> T_Transform;
	-
	- // The resampler type itself.
	- typedef itk::ResampleImageFilter<InputImageType, InputImageType> T_ResampleFilter;
	-
	- // Prepare the resampler.
	- // Instantiate the transform and specify it should be the id transform.
	- T_Transform::Pointer _pTransform = T_Transform::New();
	- _pTransform->SetIdentity();
	-
	- // Instantiate the resampler. Wire in the transform and the interpolator.
	- T_ResampleFilter::Pointer _pResizeFilter = T_ResampleFilter::New();
	- _pResizeFilter->SetTransform(_pTransform);
	-
	- // Set the output origin.
	- _pResizeFilter->SetOutputOrigin(itkImage->GetOrigin());
	-
	- // Compute the size of the output.
	- // The size (# of pixels) in the output is recomputed using
	- // the ratio of the input and output sizes.
	- InputImageType::SpacingType inputSpacing = itkImage->GetSpacing();
	- InputImageType::SpacingType outputSpacing;
	- const InputImageType::RegionType& inputSize = itkImage->GetLargestPossibleRegion();
	-
	- InputImageType::SizeType outputSize;
	- typedef InputImageType::SizeType::SizeValueType SizeValueType;
	-
	- // Set the output spacing.
	- outputSpacing[0] = spacing[0];
	- outputSpacing[1] = spacing[1];
	- outputSpacing[2] = spacing[2];
	-
	- outputSize[0] = static_cast<SizeValueType>(inputSize.GetSize()[0] * inputSpacing[0] / outputSpacing[0] + .5);
	- outputSize[1] = static_cast<SizeValueType>(inputSize.GetSize()[1] * inputSpacing[1] / outputSpacing[1] + .5);
	- outputSize[2] = static_cast<SizeValueType>(inputSize.GetSize()[2] * inputSpacing[2] / outputSpacing[2] + .5);
	-
	- _pResizeFilter->SetOutputSpacing(outputSpacing);
	- _pResizeFilter->SetSize(outputSize);
	-
	- typedef itk::Function::WelchWindowFunction<4> WelchWindowFunction;
	- typedef itk::WindowedSincInterpolateImageFunction< InputImageType, 4,WelchWindowFunction> WindowedSincInterpolatorType;
	- WindowedSincInterpolatorType::Pointer sinc_interpolator = WindowedSincInterpolatorType::New();
	-
	- _pResizeFilter->SetInterpolator(sinc_interpolator);
	-
	- // Specify the input.
	- _pResizeFilter->SetInput(itkImage);
	- _pResizeFilter->Update();
	-
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk(_pResizeFilter->GetOutput());
	- mitk::GrabItkImageMemory( _pResizeFilter->GetOutput(), image);
	-
	- return image;
	-}
	-
	-
	-
	-/// Build a derived file name from moving images e.g. xxx_T2.nrrd becomes xxx_GTV.nrrd
	-static FileListType CreateDerivedFileList(std::string baseFN, std::string baseSuffix, std::vector<std::string> derivedPatterns)
	-{
	- FileListType files;
	- for (unsigned int i=0; i < derivedPatterns.size(); i++)
	- {
	- std::string derResourceSuffix = derivedPatterns.at(i);
	- std::string derivedResourceFilename = baseFN.substr(0,baseFN.length() -baseSuffix.length()) + derResourceSuffix;
	- MITK_INFO <<" Looking for file: " << derivedResourceFilename;
	-
	- if (!itksys::SystemTools::FileExists(derivedResourceFilename.c_str()))
	- {
	- MITK_INFO << "CreateDerivedFileList: File does not exit. Skipping entry.";
	- continue;
	- }
	- files.push_back(derivedResourceFilename);
	- }
	- return files;
	-}
	-
	-/// Copy derived resources from first time step. Append _reg tag, but leave data untouched.
	-static void CopyResources(FileListType fileList, std::string outputPath)
	-{
	- for (unsigned int j=0; j < fileList.size(); j++)
	- {
	- std::string derivedResourceFilename = fileList.at(j);
	- std::string fileType = itksys::SystemTools::GetFilenameExtension(derivedResourceFilename);
	- std::string fileStem = itksys::SystemTools::GetFilenameWithoutExtension(derivedResourceFilename);
	- std::string savePathAndFileName = outputPath +fileStem + "." + fileType;
	- MITK_INFO << "Copy resource " << savePathAndFileName;
	- mitk::Image::Pointer resImage = ExtractFirstTS(mitk::IOUtil::Load<mitk::Image>(derivedResourceFilename), fileType);
	- mitk::IOUtil::Save(resImage, savePathAndFileName);
	- }
	-}
	-
	-int main( int argc, char* argv[] )
	-{
	- mitkCommandLineParser parser;
	- parser.setArgumentPrefix("--","-");
	-
	- parser.setTitle("Folder Registration");
	- parser.setCategory("Preprocessing Tools");
	- parser.setDescription("For detail description see http://docs.mitk.org/nightly/DiffusionMiniApps.html");
	- parser.setContributor("MIC");
	-
	- // Add command line argument names
	- parser.addArgument("help", "h",mitkCommandLineParser::Bool, "Help", "Show this help text");
	- //parser.addArgument("usemask", "u", QVariant::Bool, "Use segmentations (derived resources) to exclude areas from registration metrics");
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input:", "Input folder",us::Any(),false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "Output folder (ending with /)",us::Any(),false, false, false, mitkCommandLineParser::Output);
	- parser.addArgument("fixed", "f", mitkCommandLineParser::String, "Fixed images:", "Suffix for fixed image (if none is supplied first file matching moving pattern is chosen)",us::Any(),true);
	- parser.addArgument("moving", "m", mitkCommandLineParser::String, "Moving images:", "Suffix for moving images",us::Any(),false);
	- parser.addArgument("derived", "d", mitkCommandLineParser::String, "Derived resources:", "Derived resources suffixes (replaces suffix for moving images); comma separated",us::Any(),true);
	- parser.addArgument("silent", "s", mitkCommandLineParser::Bool, "Silent:", "No xml progress output.");
	- parser.addArgument("resample", "r", mitkCommandLineParser::String, "Resample (x,y,z)mm:", "Resample provide x,y,z spacing in mm (e.g. -r 1,1,3), is not applied to tensor data",us::Any());
	- parser.addArgument("binary", "b", mitkCommandLineParser::Bool, "Binary:", "Speficies that derived resource are binary (interpolation using nearest neighbor)",us::Any());
	- parser.addArgument("correct-origin", "c", mitkCommandLineParser::Bool, "Origin correction:", "Correct for large origin displacement. Use switch when you reveive: Joint PDF summed to zero ",us::Any());
	- parser.addArgument("sinc-int", "s", mitkCommandLineParser::Bool, "Windowed-sinc interpolation:", "Use windowed-sinc interpolation (3) instead of linear interpolation ",us::Any());
	-
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	-
	- // Handle special arguments
	- bool silent = false;
	- bool isBinary = false;
	- bool alignOrigin = false;
	-
	- {
	- if (parsedArgs.size() == 0)
	- {
	- return EXIT_FAILURE;
	- }
	-
	- if (parsedArgs.count("silent"))
	- silent = true;
	-
	- if (parsedArgs.count("binary"))
	- isBinary = true;
	-
	- if (parsedArgs.count("correct-origin"))
	- alignOrigin = true;
	-
	- // Show a help message
	- if ( parsedArgs.count("help") \|\| parsedArgs.count("h"))
	- {
	- std::cout << parser.helpText();
	- return EXIT_SUCCESS;
	- }
	- }
	- std::string refPattern = "";
	- bool useFirstMoving = false;
	- std::string movingImgPattern = us::any_cast<std::string>(parsedArgs["moving"]);
	-
	- if (parsedArgs.count("fixed"))
	- {
	- refPattern = us::any_cast<std::string>(parsedArgs["fixed"]);
	- }
	- else
	- {
	- useFirstMoving = true;
	- refPattern = movingImgPattern;
	- }
	-
	- std::string outputPath = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- std::string inputPath = us::any_cast<std::string>(parsedArgs["i"]);
	- //QString resampleReference = parsedArgs["resample"].toString();
	- //bool maskTumor = parsedArgs["usemask"].toBool();
	-
	- // if derived sources pattern is provided, populate QStringList with possible filename postfixes
	- std::vector<std::string> derPatterns;
	-
	- if (parsedArgs.count("derived") \|\| parsedArgs.count("d") )
	- {
	- std::string arg = us::any_cast<std::string>(parsedArgs["derived"]);
	- derPatterns = split(arg ,',');
	- }
	-
	-
	- std::vector<std::string> spacings;
	- float spacing[] = { 0.0f, 0.0f, 0.0f };
	- bool doResampling = false;
	- if (parsedArgs.count("resample") \|\| parsedArgs.count("d") )
	- {
	- std::string arg = us::any_cast<std::string>(parsedArgs["resample"]);
	- spacings = split(arg ,',');
	- spacing[0] = atoi(spacings.at(0).c_str());
	- spacing[1] = atoi(spacings.at(1).c_str());
	- spacing[2] = atoi(spacings.at(2).c_str());
	- doResampling = true;
	- }
	-
	- MITK_INFO << "Input Folder : " << inputPath;
	- MITK_INFO << "Looking for reference image ...";
	- FileListType referenceFileList = CreateFileList(inputPath,refPattern);
	-
	- if ((!useFirstMoving && referenceFileList.size() != 1) \|\| (useFirstMoving && referenceFileList.size() == 0))
	- {
	- MITK_ERROR << "None or more than one possible reference images (" << refPattern <<") found. Exiting." << referenceFileList.size();
	- MITK_INFO << "Choose a fixed arguement that is unique in the given folder!";
	- return EXIT_FAILURE;
	- }
	-
	- std::string referenceFileName = referenceFileList.at(0);
	-
	- MITK_INFO << "Loading Reference (fixed) image: " << referenceFileName;
	- std::string fileType = itksys::SystemTools::GetFilenameExtension(referenceFileName);
	- mitk::Image::Pointer refImage = ExtractFirstTS(mitk::IOUtil::Load<mitk::Image>(referenceFileName), fileType);
	- mitk::Image::Pointer resampleReference = nullptr;
	- if (doResampling)
	- {
	- refImage = ResampleBySpacing(refImage,spacing);
	- resampleReference = refImage;
	- }
	-
	- if (refImage.IsNull())
	- MITK_ERROR << "Loaded fixed image is nullptr";
	-
	- // Copy reference image to destination
	- std::string savePathAndFileName = GetSavePath(outputPath, referenceFileName);
	-
	- mitk::IOUtil::Save(refImage, savePathAndFileName);
	-
	- // Copy all derived resources also to output folder, adding _reg suffix
	- referenceFileList = CreateDerivedFileList(referenceFileName, movingImgPattern,derPatterns);
	- CopyResources(referenceFileList, outputPath);
	-
	- std::string derivedResourceFilename;
	- mitk::Image::Pointer referenceMask = nullptr; // union of all segmentations
	-
	- if (!silent)
	- {
	- // XML Output to report progress
	- std::cout << "<filter-start>";
	- std::cout << "<filter-name>Batched Registration</filter-name>";
	- std::cout << "<filter-comment>Starting registration ... </filter-comment>";
	- std::cout << "</filter-start>";
	- }
	-
	- // Now iterate over all files and register them to the reference image,
	- // also register derived resources based on file patterns
	- // ------------------------------------------------------------------------------
	-
	- // Create File list
	-
	- FileListType movingImagesList = CreateFileList(inputPath, movingImgPattern);
	-
	- for (unsigned int i =0; i < movingImagesList.size(); i++)
	- {
	- std::string fileMorphName = movingImagesList.at(i);
	- if (fileMorphName == referenceFileName)
	- {
	-
	- // do not process reference image again
	- continue;
	- }
	- MITK_INFO << "Processing image " << fileMorphName;
	-
	- // 1 Register morphological file to reference image
	-
	- if (!itksys::SystemTools::FileExists(fileMorphName.c_str()))
	- {
	- MITK_WARN << "File does not exit. Skipping entry.";
	- continue;
	- }
	- // Origin of images is cancelled
	- // TODO make this optional!!
	- double transf[6];
	- double offset[3];
	- {
	- std::string fileType = itksys::SystemTools::GetFilenameExtension(fileMorphName);
	- mitk::Image::Pointer movingImage = ExtractFirstTS(mitk::IOUtil::Load<mitk::Image>(fileMorphName), fileType);
	-
	- if (movingImage.IsNull())
	- MITK_ERROR << "Loaded moving image is nullptr";
	-
	- // Store transformation, apply it to morph file
	- MITK_INFO << "----------Registering moving image to reference----------";
	-
	- mitk::RegistrationWrapper::GetTransformation(refImage, movingImage, transf, offset, alignOrigin, referenceMask);
	- mitk::RegistrationWrapper::ApplyTransformationToImage(movingImage, transf,offset, resampleReference); // , resampleImage
	-
	- savePathAndFileName = GetSavePath(outputPath, fileMorphName);
	- if (fileType == ".dwi")
	- fileType = "dwi";
	-
	- {
	- mitk::ImageReadAccessor readAccess(movingImage);
	-
	- if (readAccess.GetData() == nullptr)
	- MITK_INFO <<"POST DATA is null";
	- }
	-
	- mitk::IOUtil::Save(movingImage, savePathAndFileName);
	- }
	-
	- if (!silent)
	- {
	- std::cout << "<filter-progress-text progress=\"" <<
	- (float)i / (float)movingImagesList.size()
	- << "\" >.</filter-progress-text>";
	- }
	-
	- // Now parse all derived resource and apply the above calculated transformation to them
	- // ------------------------------------------------------------------------------------
	-
	- FileListType fList = CreateDerivedFileList(fileMorphName, movingImgPattern,derPatterns);
	- if (fList.size() > 0)
	- MITK_INFO << "----------DERIVED RESOURCES ---------";
	- for (unsigned int j=0; j < fList.size(); j++)
	- {
	- derivedResourceFilename = fList.at(j);
	- MITK_INFO << "----Processing derived resorce " << derivedResourceFilename << " ...";
	- std::string fileType = itksys::SystemTools::GetFilenameExtension(derivedResourceFilename);
	- mitk::Image::Pointer derivedMovingResource = ExtractFirstTS(mitk::IOUtil::Load<mitk::Image>(derivedResourceFilename), fileType);
	- // Apply transformation to derived resource, treat derived resource as binary
	- mitk::RegistrationWrapper::ApplyTransformationToImage(derivedMovingResource, transf,offset, resampleReference,isBinary);
	-
	- savePathAndFileName = GetSavePath(outputPath, derivedResourceFilename);
	- mitk::IOUtil::Save(derivedMovingResource, savePathAndFileName);
	- }
	- }
	-
	- if (!silent)
	- std::cout << "<filter-end/>";
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/ResampleGradients.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/ResampleGradients.cpp
	deleted file mode 100644
	index 8d53507b0a..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/ResampleGradients.cpp
	+++ /dev/null
	@@ -1,230 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <vector>
	-#include <iostream>
	-#include <fstream>
	-#include <algorithm>
	-#include <string>
	-#include <istream>
	-#include <itkMetaDataObject.h>
	-#include <itkVectorImage.h>
	-#include <mitkImageCast.h>
	-#include <mitkBaseData.h>
	-#include "mitkCommandLineParser.h"
	-#include <mitkLexicalCast.h>
	-#include <mitkCoreObjectFactory.h>
	-#include <mitkIOUtil.h>
	-#include <mitkBValueMapProperty.h>
	-#include <mitkGradientDirectionsProperty.h>
	-#include <itkElectrostaticRepulsionDiffusionGradientReductionFilter.h>
	-#include <itkImage.h>
	-#include <mitkImage.h>
	-#include "itkDWIVoxelFunctor.h"
	-#include <mitkDiffusionPropertyHelper.h>
	-
	-typedef short DiffusionPixelType;
	-typedef itk::VectorImage< short, 3 > ItkDwiType;
	-
	-// itk includes
	-#include "itkTimeProbe.h"
	-#include "itkB0ImageExtractionImageFilter.h"
	-#include "itkB0ImageExtractionToSeparateImageFilter.h"
	-#include "itkBrainMaskExtractionImageFilter.h"
	-#include "itkCastImageFilter.h"
	-#include "itkVectorContainer.h"
	-#include <itkElectrostaticRepulsionDiffusionGradientReductionFilter.h>
	-#include <itkMergeDiffusionImagesFilter.h>
	-#include <itkDwiGradientLengthCorrectionFilter.h>
	-#include <itkDwiNormilzationFilter.h>
	-#include <mitkTensorImage.h>
	-#include <mitkOdfImage.h>
	-
	-// Multishell includes
	-#include <itkRadialMultishellToSingleshellImageFilter.h>
	-
	-// Multishell Functors
	-#include <itkADCAverageFunctor.h>
	-#include <itkKurtosisFitFunctor.h>
	-#include <itkBiExpFitFunctor.h>
	-#include <itkADCFitFunctor.h>
	-
	-// mitk includes
	-#include "mitkProgressBar.h"
	-#include "mitkStatusBar.h"
	-#include "mitkNodePredicateDataType.h"
	-#include "mitkProperties.h"
	-#include "mitkVtkResliceInterpolationProperty.h"
	-#include "mitkLookupTable.h"
	-#include "mitkLookupTableProperty.h"
	-#include "mitkTransferFunction.h"
	-#include "mitkTransferFunctionProperty.h"
	-//#include "mitkDataNodeObject.h"
	-#include "mitkOdfNormalizationMethodProperty.h"
	-#include "mitkOdfScaleByProperty.h"
	-#include <mitkPointSet.h>
	-#include <itkAdcImageFilter.h>
	-#include <itkBrainMaskExtractionImageFilter.h>
	-#include <mitkImageCast.h>
	-#include <mitkRotationOperation.h>
	-//#include <QTableWidgetItem>
	-//#include <QTableWidget>
	-#include <mitkInteractionConst.h>
	-#include <mitkImageAccessByItk.h>
	-#include <itkResampleDwiImageFilter.h>
	-#include <itkResampleImageFilter.h>
	-#include <itkImageDuplicator.h>
	-#include <itkMaskImageFilter.h>
	-#include <mitkNodePredicateProperty.h>
	-#include <mitkNodePredicateAnd.h>
	-#include <mitkNodePredicateNot.h>
	-#include <mitkNodePredicateOr.h>
	-#include <itkCropImageFilter.h>
	-#include <itkDiffusionTensor3DReconstructionImageFilter.h>
	-#include <itkRemoveDwiChannelFilter.h>
	-#include <itkExtractDwiChannelFilter.h>
	-#include <mitkITKImageImport.h>
	-#include <mitkBValueMapProperty.h>
	-#include <mitkGradientDirectionsProperty.h>
	-#include <mitkMeasurementFrameProperty.h>
	-#include <itkImageDuplicator.h>
	-#include <itkFlipImageFilter.h>
	-#include <mitkITKImageImport.h>
	-#include "mitkPreferenceListReaderOptionsFunctor.h"
	-
	-mitk::Image::Pointer DoReduceGradientDirections(mitk::Image::Pointer image, double BValue, unsigned int numOfGradientsToKeep, bool use_first_n)
	-{
	-
	- bool isDiffusionImage( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(image) );
	- if ( !isDiffusionImage ) {
	- std::cout << "Image is not a Diffusion Weighted Image" << std::endl;
	- //return;
	- }
	-
	- typedef itk::ElectrostaticRepulsionDiffusionGradientReductionFilter<DiffusionPixelType, DiffusionPixelType> FilterType;
	- typedef mitk::BValueMapProperty::BValueMap BValueMap;
	-
	- BValueMap shellSlectionMap;
	- BValueMap originalShellMap = mitk::DiffusionPropertyHelper::GetBValueMap(image);
	-
	- std::vector<unsigned int> newNumGradientDirections;
	-
	- //Keeps 1 b0 gradient
	- double B0Value = 0;
	- shellSlectionMap[B0Value] = originalShellMap[B0Value];
	- unsigned int num = 1;
	- newNumGradientDirections.push_back(num);
	-
	- //BValue = 1000;
	- shellSlectionMap[BValue] = originalShellMap[BValue];
	- //numOfGradientsToKeep = 32;
	- newNumGradientDirections.push_back(numOfGradientsToKeep);
	-
	-
	- if (newNumGradientDirections.empty()) {
	- std::cout << "newNumGradientDirections is empty" << std::endl;
	- //return;
	- }
	-
	- auto gradientContainer = mitk::DiffusionPropertyHelper::GetGradientContainer(image);
	-
	-
	- ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New();
	- mitk::CastToItkImage(image, itkVectorImagePointer);
	- std::cout << "1" << std::endl;
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetInput( itkVectorImagePointer );
	- filter->SetOriginalGradientDirections(gradientContainer);
	- filter->SetNumGradientDirections(newNumGradientDirections);
	- filter->SetOriginalBValueMap(originalShellMap);
	- filter->SetShellSelectionBValueMap(shellSlectionMap);
	- filter->SetUseFirstN(use_first_n);
	- filter->Update();
	- std::cout << "2" << std::endl;
	-
	- if( filter->GetOutput() == nullptr) {
	- std::cout << "filter get output is nullptr" << std::endl;
	- }
	-
	- mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( filter->GetOutput() );
	- mitk::DiffusionPropertyHelper::CopyProperties(image, newImage, true);
	- mitk::DiffusionPropertyHelper::SetGradientContainer(newImage, filter->GetGradientDirections());
	- mitk::DiffusionPropertyHelper::InitializeImage( newImage );
	-
	- return newImage;
	-}
	-
	-
	-
	-/*!
	-\brief Resample gradients of input DWI image.
	-*/
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Resample Gradients");
	- parser.setCategory("Preprocessing Tools");
	- parser.setDescription("Resample gradients of input DWI image. You can select one b-value shell and the number of gradients within this shell you want to have. It will also keep one b0 image.");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input:", "input image", us::Any(), false);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "output image", us::Any(), false);
	- parser.addArgument("b_value", "", mitkCommandLineParser::Float, "b-value:", "float", 1000, false);
	- parser.addArgument("num_gradients", "", mitkCommandLineParser::Int, "Nr of gradients:", "integer", 32, false);
	- parser.addArgument("use_first_n", "", mitkCommandLineParser::Bool, "Use first N:", "no optimization, simply use first n gradients", 0);
	-
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	-
	- std::string inFileName = us::any_cast<std::string>(parsedArgs["i"]);
	- std::string outFileName = us::any_cast<std::string>(parsedArgs["o"]);
	- double bValue = us::any_cast<float>(parsedArgs["b_value"]);
	- unsigned int nrOfGradients = us::any_cast<int>(parsedArgs["num_gradients"]);
	- bool use_first_n = false;
	- if (parsedArgs.count("use_first_n"))
	- use_first_n = true;
	-
	- try
	- {
	- mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({ "Diffusion Weighted Images" }, {});
	- mitk::Image::Pointer mitkImage = mitk::IOUtil::Load<mitk::Image>(inFileName, &functor);
	- mitk::Image::Pointer newImage = DoReduceGradientDirections(mitkImage, bValue, nrOfGradients, use_first_n);
	- //mitk::IOUtil::Save(newImage, outFileName); //save as dwi image
	- mitk::IOUtil::Save(newImage, "DWI_NIFTI", outFileName); //save as nifti image
	-
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/RoundBvalues.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/RoundBvalues.cpp
	deleted file mode 100644
	index c7170b97e8..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/RoundBvalues.cpp
	+++ /dev/null
	@@ -1,106 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkImageCast.h>
	-#include <mitkImage.h>
	-#include <mitkIOUtil.h>
	-#include "mitkCommandLineParser.h"
	-#include <mitkPreferenceListReaderOptionsFunctor.h>
	-#include <itksys/SystemTools.hxx>
	-#include <itkDwiGradientLengthCorrectionFilter.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("RoundBvalues");
	- parser.setCategory("Preprocessing Tools");
	- parser.setDescription("Round b-values");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input:", "input image", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "output image", us::Any(), false, false, false, mitkCommandLineParser::Output);
	- parser.addArgument("to_nearest", "", mitkCommandLineParser::Int, "To nearest:", "integer", 1000);
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- // mandatory arguments
	- std::string imageName = us::any_cast<std::string>(parsedArgs["i"]);
	- std::string outImage = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- int to_nearest = 1000;
	- if (parsedArgs.count("to_nearest"))
	- to_nearest = us::any_cast<int>(parsedArgs["to_nearest"]);
	-
	- try
	- {
	- typedef mitk::DiffusionPropertyHelper PropHelper;
	-
	- mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Diffusion Weighted Images"}, {});
	- mitk::Image::Pointer in_image = mitk::IOUtil::Load<mitk::Image>(imageName, &functor);
	-
	- if (!PropHelper::IsDiffusionWeightedImage(in_image))
	- {
	- mitkThrow() << "Input is not a diffusion weighted image: " << imageName;
	- }
	-
	- typedef itk::DwiGradientLengthCorrectionFilter FilterType;
	-
	- auto itkVectorImagePointer = PropHelper::GetItkVectorImage(in_image);
	-
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetRoundingValue(to_nearest);
	- filter->SetReferenceBValue(PropHelper::GetReferenceBValue(in_image));
	- filter->SetReferenceGradientDirectionContainer(PropHelper::GetGradientContainer(in_image));
	- filter->Update();
	-
	- mitk::Image::Pointer newImage = mitk::Image::New();
	- newImage->InitializeByItk( itkVectorImagePointer.GetPointer() );
	- newImage->SetImportVolume( itkVectorImagePointer->GetBufferPointer(), 0, 0, mitk::Image::CopyMemory);
	- itkVectorImagePointer->GetPixelContainer()->ContainerManageMemoryOff();
	-
	- PropHelper::CopyProperties(in_image, newImage, true);
	- PropHelper::SetReferenceBValue(newImage, filter->GetNewBValue());
	- PropHelper::SetGradientContainer(newImage, filter->GetOutputGradientDirectionContainer());
	- PropHelper::InitializeImage(newImage);
	-
	- std::string ext = itksys::SystemTools::GetFilenameExtension(outImage);
	- if (ext==".nii" \|\| ext==".nii.gz")
	- mitk::IOUtil::Save(newImage, "DWI_NIFTI", outImage);
	- else
	- mitk::IOUtil::Save(newImage, outImage);
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/ShToOdfImage.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/ShToOdfImage.cpp
	deleted file mode 100644
	index 55b2301be6..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Misc/ShToOdfImage.cpp
	+++ /dev/null
	@@ -1,72 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkImageCast.h>
	-#include <mitkImage.h>
	-#include <mitkIOUtil.h>
	-#include "mitkCommandLineParser.h"
	-#include <mitkPreferenceListReaderOptionsFunctor.h>
	-#include <itkShToOdfImageFilter.h>
	-#include <mitkShImage.h>
	-#include <mitkDiffusionFunctionCollection.h>
	-
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("ShToOdfImage");
	- parser.setCategory("Preprocessing Tools");
	- parser.setDescription("Calculate discrete ODF image from SH coefficient image");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input:", "input image", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "output image", us::Any(), false, false, false, mitkCommandLineParser::Output);
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- // mandatory arguments
	- std::string imageName = us::any_cast<std::string>(parsedArgs["i"]);
	- std::string outImage = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- try
	- {
	- mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"SH Image"}, {});
	- mitk::ShImage::Pointer source = mitk::IOUtil::Load<mitk::ShImage>(imageName, &functor);
	- mitk::Image::Pointer mitkImage = dynamic_cast<mitk::Image*>(source.GetPointer());
	- mitk::OdfImage::Pointer out_image = mitk::convert::GetOdfFromShImage(mitkImage);
	- if (out_image.IsNotNull())
	- mitk::IOUtil::Save(out_image, outImage);
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Python/BrainExtraction.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Python/BrainExtraction.cpp
	deleted file mode 100644
	index 093820c23a..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Python/BrainExtraction.cpp
	+++ /dev/null
	@@ -1,179 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkImageCast.h>
	-#include <mitkImage.h>
	-#include <mitkIOUtil.h>
	-#include "mitkCommandLineParser.h"
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <itksys/SystemTools.hxx>
	-#include <itkB0ImageExtractionToSeparateImageFilter.h>
	-#include <mitkIPythonService.h>
	-#include <mitkImageCast.h>
	-
	-#include <usGetModuleContext.h>
	-#include <usModuleContext.h>
	-#include <usModule.h>
	-#include <usModuleResource.h>
	-#include <usModuleResourceStream.h>
	-#include <BetData.h>
	-#include <mitkPreferenceListReaderOptionsFunctor.h>
	-#include <boost/algorithm/string.hpp>
	-
	-typedef mitk::DiffusionPropertyHelper DPH;
	-typedef itksys::SystemTools ist;
	-
	-std::string GetPythonFile(std::string filename, std::string exec_dir)
	-{
	- std::string out = "";
	- for (auto dir : mitk::bet::relative_search_dirs)
	- {
	- if ( ist::FileExists( exec_dir + dir + filename) )
	- {
	- out = exec_dir + dir + filename;
	- return out;
	- }
	- if ( ist::FileExists( ist::GetCurrentWorkingDirectory() + dir + filename) )
	- {
	- out = ist::GetCurrentWorkingDirectory() + dir + filename;
	- return out;
	- }
	- }
	- for (auto dir : mitk::bet::absolute_search_dirs)
	- {
	- if ( ist::FileExists( dir + filename) )
	- {
	- out = dir + filename;
	- return out;
	- }
	- }
	-
	- return out;
	-}
	-
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("BrainExtraction");
	- parser.setCategory("Preprocessing Tools");
	- parser.setDescription("Performs brain extraction using a deep learning model");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input:", "input image", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "output root", us::Any(), false, false, false, mitkCommandLineParser::Output);
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- // mandatory arguments
	- std::string i = us::any_cast<std::string>(parsedArgs["i"]);
	- std::string o = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- std::string exec_dir = ist::GetFilenamePath(argv[0]);
	- mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Diffusion Weighted Images"}, {});
	- mitk::Image::Pointer mitk_image = mitk::IOUtil::Load<mitk::Image>(i, &functor);
	-
	- bool missing_file = false;
	- std::string missing_file_string = "";
	- if ( GetPythonFile("run_mitk.py", exec_dir).empty() )
	- {
	- missing_file_string += "Brain extraction script file missing: run_mitk.py\n\n";
	- missing_file = true;
	- }
	-
	- if ( GetPythonFile("model_final.model", exec_dir).empty() )
	- {
	- missing_file_string += "Brain extraction model file missing: model_final.model\n\n";
	- missing_file = true;
	- }
	-
	- if ( GetPythonFile("basic_config_just_like_braintumor.py", exec_dir).empty() )
	- {
	- missing_file_string += "Config file missing: basic_config_just_like_braintumor.py\n\n";
	- missing_file = true;
	- }
	-
	- if (missing_file)
	- {
	- mitkThrow() << missing_file_string;
	- }
	-
	- us::ModuleContext* context = us::GetModuleContext();
	- us::ServiceReference<mitk::IPythonService> m_PythonServiceRef = context->GetServiceReference<mitk::IPythonService>();
	- mitk::IPythonService* m_PythonService = dynamic_cast<mitk::IPythonService*> ( context->GetService<mitk::IPythonService>(m_PythonServiceRef) );
	- mitk::IPythonService::ForceLoadModule();
	-
	- m_PythonService->AddAbsoluteSearchDirs(mitk::bet::absolute_search_dirs);
	- m_PythonService->AddRelativeSearchDirs(mitk::bet::relative_search_dirs);
	- m_PythonService->Execute("paths=[]");
	-
	- // set input files (model and config)
	- m_PythonService->Execute("model_file=\""+GetPythonFile("model_final.model", exec_dir)+"\"");
	- m_PythonService->Execute("config_file=\""+GetPythonFile("basic_config_just_like_braintumor.py", exec_dir)+"\"");
	-
	- // copy input image to python
	- m_PythonService->CopyToPythonAsSimpleItkImage( mitk_image, "in_image");
	-
	- // run segmentation script
	- m_PythonService->ExecuteScript( GetPythonFile("run_mitk.py", exec_dir) );
	-
	- // clean up after running script (better way than deleting individual variables?)
	- if(m_PythonService->DoesVariableExist("in_image"))
	- m_PythonService->Execute("del in_image");
	-
	- // check for errors
	- if(!m_PythonService->GetVariable("error_string").empty())
	- mitkThrow() << m_PythonService->GetVariable("error_string");
	-
	- // get output images and add to datastorage
	- std::string output_variables = m_PythonService->GetVariable("output_variables");
	- std::vector<std::string> outputs;
	- boost::split(outputs, output_variables, boost::is_any_of(","));
	-
	- std::string output_types = m_PythonService->GetVariable("output_types");
	- std::vector<std::string> types;
	- boost::split(types, output_types, boost::is_any_of(","));
	-
	- for (unsigned int i=0; i<outputs.size(); ++i)
	- {
	- if (m_PythonService->DoesVariableExist(outputs.at(i)))
	- {
	- mitk::Image::Pointer image = m_PythonService->CopySimpleItkImageFromPython(outputs.at(i));
	-
	- if(types.at(i)=="input" && mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(mitk_image))
	- {
	- mitk::DiffusionPropertyHelper::CopyProperties(mitk_image, image, true);
	- mitk::DiffusionPropertyHelper::InitializeImage(image);
	- }
	-
	- mitk::DataNode::Pointer corrected_node = mitk::DataNode::New();
	- corrected_node->SetData( image );
	- std::string name = o + "_";
	- name += outputs.at(i);
	-
	- if(types.at(i)=="input" && mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(mitk_image))
	- mitk::IOUtil::Save(image, "DWI_NIFTI", name+".nii.gz");
	- else
	- mitk::IOUtil::Save(image, name+".nii.gz");
	- }
	- }
	-
	- MITK_INFO << "Finished brain extraction";
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Python/CMakeLists.txt b/Modules/DiffusionImaging/DiffusionCmdApps/Python/CMakeLists.txt
	deleted file mode 100644
	index 8cfbef2cff..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Python/CMakeLists.txt
	+++ /dev/null
	@@ -1,34 +0,0 @@
	-option(BUILD_DiffusionPythonCmdApps "Build commandline tools for diffusion with python" OFF)
	-
	-if(BUILD_DiffusionPythonCmdApps OR MITK_BUILD_ALL_APPS)
	-
	- # needed include directories
	- include_directories(
	- ${CMAKE_CURRENT_SOURCE_DIR}
	- ${CMAKE_CURRENT_BINARY_DIR}
	- )
	-
	- # list of diffusion cmdapps
	- # if an app requires additional dependencies
	- # they are added after a "^^" and separated by "_"
	- set( diffusionpythoncmdapps
	- BrainExtraction^^
	- )
	-
	- foreach(diffusionpythoncmdapp ${diffusionpythoncmdapps})
	- # extract cmd app name and dependencies
	- string(REPLACE "^^" "\\;" cmdapp_info ${diffusionpythoncmdapp})
	- set(cmdapp_info_list ${cmdapp_info})
	- list(GET cmdapp_info_list 0 appname)
	- list(GET cmdapp_info_list 1 raw_dependencies)
	- string(REPLACE "_" "\\;" dependencies "${raw_dependencies}")
	- set(dependencies_list ${dependencies})
	-
	- mitkFunctionCreateCommandLineApp(
	- NAME ${appname}
	- DEPENDS CppMicroServices MitkDiffusionCmdApps MitkPython ${dependencies_list}
	- PACKAGE_DEPENDS
	- )
	- endforeach()
	-
	-endif()
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Quantification/CMakeLists.txt b/Modules/DiffusionImaging/DiffusionCmdApps/Quantification/CMakeLists.txt
	deleted file mode 100644
	index d0fac9521c..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Quantification/CMakeLists.txt
	+++ /dev/null
	@@ -1,38 +0,0 @@
	-option(BUILD_DiffusionQuantificationCmdApps "Build commandline tools for diffusion quantification (IVIM, ADC, ...)" OFF)
	-
	-if(BUILD_DiffusionQuantificationCmdApps OR MITK_BUILD_ALL_APPS)
	-
	- # needed include directories
	- include_directories(
	- ${CMAKE_CURRENT_SOURCE_DIR}
	- ${CMAKE_CURRENT_BINARY_DIR}
	- )
	-
	- # list of diffusion cmdapps
	- # if an app requires additional dependencies
	- # they are added after a "^^" and separated by "_"
	- set( diffusionQuantificationcmdapps
	- DiffusionIndices^^
	- QballReconstruction^^
	- TensorReconstruction^^
	- DiffusionKurtosisFit^^
	- MultishellMethods^^
	- )
	-
	- foreach(diffusionQuantificationcmdapp ${diffusionQuantificationcmdapps})
	- # extract cmd app name and dependencies
	- string(REPLACE "^^" "\\;" cmdapp_info ${diffusionQuantificationcmdapp})
	- set(cmdapp_info_list ${cmdapp_info})
	- list(GET cmdapp_info_list 0 appname)
	- list(GET cmdapp_info_list 1 raw_dependencies)
	- string(REPLACE "_" "\\;" dependencies "${raw_dependencies}")
	- set(dependencies_list ${dependencies})
	-
	- mitkFunctionCreateCommandLineApp(
	- NAME ${appname}
	- DEPENDS MitkDiffusionCmdApps ${dependencies_list}
	- PACKAGE_DEPENDS
	- )
	- endforeach()
	-
	-endif()
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Quantification/DiffusionIndices.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Quantification/DiffusionIndices.cpp
	deleted file mode 100644
	index 600874d58e..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Quantification/DiffusionIndices.cpp
	+++ /dev/null
	@@ -1,193 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkImageCast.h>
	-#include <itkExceptionObject.h>
	-#include <itkImageFileWriter.h>
	-#include <mitkOdfImage.h>
	-#include <itkTensorDerivedMeasurementsFilter.h>
	-#include <itkDiffusionOdfGeneralizedFaImageFilter.h>
	-#include <mitkTensorImage.h>
	-#include "mitkCommandLineParser.h"
	-#include <boost/algorithm/string.hpp>
	-#include <itksys/SystemTools.hxx>
	-#include <itkMultiThreader.h>
	-#include <mitkIOUtil.h>
	-#include <mitkPreferenceListReaderOptionsFunctor.h>
	-#include <mitkImage.h>
	-#include <mitkShImage.h>
	-#include <mitkOdfImage.h>
	-#include <mitkTensorImage.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <itkAdcImageFilter.h>
	-#include <mitkDiffusionFunctionCollection.h>
	-#include <mitkLocaleSwitch.h>
	-
	-/**
	- *
	- */
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Diffusion Indices");
	- parser.setCategory("Diffusion Related Measures");
	- parser.setDescription("Computes requested diffusion related measures");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input:", "input image (tensor, ODF or SH-coefficient image)", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "output image", us::Any(), false, false, false, mitkCommandLineParser::Output);
	- parser.addArgument("index", "idx", mitkCommandLineParser::String, "Index:", "index (fa, gfa, ra, ad, rd, ca, l2, l3, md, adc)", us::Any(), false);
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- std::string inFileName = us::any_cast<std::string>(parsedArgs["i"]);
	- std::string index = us::any_cast<std::string>(parsedArgs["index"]);
	- std::string outFileName = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- std::string ext = itksys::SystemTools::GetFilenameLastExtension(outFileName);
	- if (ext.empty())
	- outFileName += ".nii.gz";
	-
	- try
	- {
	- // load input image
	- mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Diffusion Weighted Images", "SH Image", "ODF Image", "Tensor Image"}, {});
	- auto input = mitk::IOUtil::Load<mitk::Image>(inFileName, &functor);
	-
	- bool is_odf = (dynamic_cast<mitk::ShImage>(input.GetPointer()) \|\| dynamic_cast<mitk::OdfImage>(input.GetPointer()));
	- bool is_dt = dynamic_cast<mitk::TensorImage*>(input.GetPointer());
	- bool is_dw = mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(input);
	-
	- if (is_odf)
	- MITK_INFO << "Input is ODF image";
	- else if (is_dt)
	- MITK_INFO << "Input is tensor image";
	- else if (is_dw)
	- MITK_INFO << "Input is dMRI";
	- else
	- {
	- MITK_WARN << "Input is no ODF, SH, tensor or raw dMRI.";
	- return EXIT_FAILURE;
	- }
	-
	- mitk::LocaleSwitch localeSwitch("C");
	- if( is_odf && index=="gfa" )
	- {
	- typedef itk::Vector<float,ODF_SAMPLING_SIZE> OdfVectorType;
	- typedef itk::Image<OdfVectorType,3> OdfVectorImgType;
	-
	- OdfVectorImgType::Pointer itkvol;
	- if (dynamic_cast<mitk::ShImage*>(input.GetPointer()))
	- itkvol = mitk::convert::GetItkOdfFromShImage(input);
	- else
	- itkvol = mitk::convert::GetItkOdfFromOdfImage(input);
	-
	- typedef itk::DiffusionOdfGeneralizedFaImageFilter<float,float,ODF_SAMPLING_SIZE> GfaFilterType;
	- GfaFilterType::Pointer gfaFilter = GfaFilterType::New();
	- gfaFilter->SetInput(itkvol);
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_STANDARD);
	- gfaFilter->Update();
	-
	- itk::ImageFileWriter< itk::Image<float,3> >::Pointer fileWriter = itk::ImageFileWriter< itk::Image<float,3> >::New();
	- fileWriter->SetInput(gfaFilter->GetOutput());
	- fileWriter->SetFileName(outFileName);
	- fileWriter->Update();
	- }
	- else if( is_dt )
	- {
	- typedef itk::Image< itk::DiffusionTensor3D<float>, 3 > ItkTensorImage;
	- mitk::TensorImage::Pointer mitkTensorImage = dynamic_cast<mitk::TensorImage*>(input.GetPointer());
	- ItkTensorImage::Pointer itk_dti = ItkTensorImage::New();
	- mitk::CastToItkImage(mitkTensorImage, itk_dti);
	-
	- typedef itk::TensorDerivedMeasurementsFilter<float> MeasurementsType;
	- MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New();
	- measurementsCalculator->SetInput(itk_dti.GetPointer() );
	-
	- if(index=="fa")
	- measurementsCalculator->SetMeasure(MeasurementsType::FA);
	- else if(index=="ra")
	- measurementsCalculator->SetMeasure(MeasurementsType::RA);
	- else if(index=="ad")
	- measurementsCalculator->SetMeasure(MeasurementsType::AD);
	- else if(index=="rd")
	- measurementsCalculator->SetMeasure(MeasurementsType::RD);
	- else if(index=="ca")
	- measurementsCalculator->SetMeasure(MeasurementsType::CA);
	- else if(index=="l2")
	- measurementsCalculator->SetMeasure(MeasurementsType::L2);
	- else if(index=="l3")
	- measurementsCalculator->SetMeasure(MeasurementsType::L3);
	- else if(index=="md")
	- measurementsCalculator->SetMeasure(MeasurementsType::MD);
	- else
	- {
	- MITK_WARN << "No valid diffusion index for input image (tensor image) defined";
	- return EXIT_FAILURE;
	- }
	-
	- measurementsCalculator->Update();
	-
	- itk::ImageFileWriter< itk::Image<float,3> >::Pointer fileWriter = itk::ImageFileWriter< itk::Image<float,3> >::New();
	- fileWriter->SetInput(measurementsCalculator->GetOutput());
	- fileWriter->SetFileName(outFileName);
	- fileWriter->Update();
	- }
	- else if(is_dw && (index=="adc" \|\| index=="md"))
	- {
	- typedef itk::AdcImageFilter< short, double > FilterType;
	-
	- auto itkVectorImagePointer = mitk::DiffusionPropertyHelper::GetItkVectorImage(input);
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetInput( itkVectorImagePointer );
	-
	- filter->SetGradientDirections( mitk::DiffusionPropertyHelper::GetGradientContainer(input) );
	- filter->SetB_value( static_cast<double>(mitk::DiffusionPropertyHelper::GetReferenceBValue(input)) );
	- if (index=="adc")
	- filter->SetFitSignal(true);
	- else
	- filter->SetFitSignal(false);
	- filter->Update();
	-
	- itk::ImageFileWriter< itk::Image<double,3> >::Pointer fileWriter = itk::ImageFileWriter< itk::Image<double,3> >::New();
	- fileWriter->SetInput(filter->GetOutput());
	- fileWriter->SetFileName(outFileName);
	- fileWriter->Update();
	- }
	- else
	- std::cout << "Diffusion index " << index << " not supported for supplied file type.";
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Quantification/DiffusionKurtosisFit.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Quantification/DiffusionKurtosisFit.cpp
	deleted file mode 100644
	index d2aa6cb5f5..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Quantification/DiffusionKurtosisFit.cpp
	+++ /dev/null
	@@ -1,254 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkCommandLineParser.h"
	-#include <mitkIOUtil.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-
	-#include <mitkImageCaster.h>
	-#include <itkDiffusionKurtosisReconstructionImageFilter.h>
	-
	-#include "mitkImage.h"
	-#include <iostream>
	-#include <usAny.h>
	-#include <fstream>
	-#include "mitkIOUtil.h"
	-
	-#include <itkFileTools.h>
	-#include <itksys/SystemTools.hxx>
	-
	-
	-//vnl_includes
	-#include "vnl/vnl_math.h"
	-#include "vnl/vnl_cost_function.h"
	-#include "vnl/vnl_least_squares_function.h"
	-#include "vnl/algo/vnl_lbfgsb.h"
	-#include "vnl/algo/vnl_lbfgs.h"
	-
	-#include "vnl/algo/vnl_levenberg_marquardt.h"
	-
	-typedef mitk::DiffusionPropertyHelper DPH;
	-
	-#include <itkGaussianBlurImageFunction.h>
	-#include <itkUnaryFunctorImageFilter.h>
	-
	-#include <itkImageFileWriter.h>
	-
	-#include <itkVectorIndexSelectionCastImageFilter.h>
	-#include <itkComposeImageFilter.h>
	-#include <itkDiscreteGaussianImageFilter.h>
	-#include <mitkPreferenceListReaderOptionsFunctor.h>
	-
	-
	-DPH::ImageType::Pointer GetBlurredVectorImage( DPH::ImageType::Pointer vectorImage, double sigma)
	-{
	- typedef itk::DiscreteGaussianImageFilter< itk::Image<DPH::DiffusionPixelType, 3 >, itk::Image<DPH::DiffusionPixelType, 3 > > GaussianFilterType;
	-
	- typedef itk::VectorIndexSelectionCastImageFilter< DPH::ImageType, itk::Image<DPH::DiffusionPixelType, 3 > > IndexSelectionType;
	- IndexSelectionType::Pointer indexSelectionFilter = IndexSelectionType::New();
	- indexSelectionFilter->SetInput( vectorImage );
	-
	- typedef itk::ComposeImageFilter< itk::Image<DPH::DiffusionPixelType, 3>, DPH::ImageType > ComposeFilterType;
	- ComposeFilterType::Pointer vec_composer = ComposeFilterType::New();
	-
	- for( unsigned int i=0; i<vectorImage->GetVectorLength(); ++i)
	- {
	- GaussianFilterType::Pointer gaussian_filter = GaussianFilterType::New();
	-
	- indexSelectionFilter->SetIndex( i );
	-
	- gaussian_filter->SetInput( indexSelectionFilter->GetOutput() );
	- gaussian_filter->SetVariance( sigma );
	-
	- vec_composer->SetInput(i, gaussian_filter->GetOutput() );
	-
	- gaussian_filter->Update();
	- }
	-
	- try
	- {
	- vec_composer->Update();
	- }
	- catch(const itk::ExceptionObject &e)
	- {
	- mitkThrow() << "[VectorImage.GaussianSmoothing] !! Failed with ITK Exception: " << e.what();
	- }
	-
	- DPH::ImageType::Pointer smoothed_vector = vec_composer->GetOutput();
	-
	- /*
	- itk::ImageFileWriter< DPH::ImageType >::Pointer writer =
	- itk::ImageFileWriter< DPH::ImageType >::New();
	-
	- writer->SetInput( smoothed_vector );
	- writer->SetFileName( "/tmp/itk_smoothed_vector.nrrd");
	- writer->Update();*/
	-
	- return smoothed_vector;
	-
	-
	-}
	-
	-void KurtosisMapComputation( mitk::Image::Pointer input,
	- std::string output_prefix ,
	- std::string output_type,
	- std::string maskPath,
	- bool omitBZero,
	- double lower,
	- double upper )
	-{
	- DPH::ImageType::Pointer vectorImage = DPH::ImageType::New();
	- mitk::CastToItkImage( input, vectorImage );
	-
	- typedef itk::DiffusionKurtosisReconstructionImageFilter< short, double > KurtosisFilterType;
	- KurtosisFilterType::Pointer kurtosis_filter = KurtosisFilterType::New();
	- kurtosis_filter->SetInput( GetBlurredVectorImage( vectorImage, 1.5 ) );
	- kurtosis_filter->SetReferenceBValue( DPH::GetReferenceBValue( input.GetPointer() ) );
	- kurtosis_filter->SetGradientDirections( DPH::GetGradientContainer( input.GetPointer() ) );
	-// kurtosis_filter->SetNumberOfThreads(1);
	- kurtosis_filter->SetOmitUnweightedValue(omitBZero);
	- kurtosis_filter->SetBoundariesForKurtosis(-lower,upper);
	-// kurtosis_filter->SetInitialSolution(const vnl_vector<double>& x0 );
	-
	-
	- if(maskPath != "")
	- {
	- mitk::Image::Pointer segmentation;
	- segmentation = mitk::IOUtil::Load<mitk::Image>(maskPath);
	- typedef itk::Image< short , 3> MaskImageType;
	- MaskImageType::Pointer vectorSeg = MaskImageType::New() ;
	- mitk::CastToItkImage( segmentation, vectorSeg );
	- kurtosis_filter->SetImageMask(vectorSeg) ;
	- }
	-
	- try
	- {
	- kurtosis_filter->Update();
	- }
	- catch( const itk::ExceptionObject& e)
	- {
	- mitkThrow() << "Kurtosis fit failed with an ITK Exception: " << e.what();
	- }
	-
	- mitk::Image::Pointer d_image = mitk::Image::New();
	- d_image->InitializeByItk( kurtosis_filter->GetOutput(0) );
	- d_image->SetVolume( kurtosis_filter->GetOutput(0)->GetBufferPointer() );
	-
	- mitk::Image::Pointer k_image = mitk::Image::New();
	- k_image->InitializeByItk( kurtosis_filter->GetOutput(1) );
	- k_image->SetVolume( kurtosis_filter->GetOutput(1)->GetBufferPointer() );
	-
	- std::string outputD_FileName = output_prefix + "_ADC_map." + output_type;
	- std::string outputK_FileName = output_prefix + "_AKC_map." + output_type;
	-
	- try
	- {
	- mitk::IOUtil::Save( d_image, outputD_FileName );
	- mitk::IOUtil::Save( k_image, outputK_FileName );
	- }
	- catch( const itk::ExceptionObject& e)
	- {
	- mitkThrow() << "Failed to save the KurtosisFit Results due to exception: " << e.what();
	- }
	-
	-}
	-
	-int main( int argc, char* argv[] )
	-{
	-
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Diffusion Kurtosis Fit");
	- parser.setCategory("Diffusion Related Measures");
	- parser.setContributor("MIC");
	- parser.setDescription("Fitting Kurtosis");
	- parser.setArgumentPrefix("--","-");
	-
	- // mandatory arguments
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input: ", "input image (DWI)", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output Preifx: ", "Prefix for the output images, will append _f, _K, _D accordingly ", us::Any(), false);
	- parser.addArgument("output_type", "", mitkCommandLineParser::String, "Output Type: ", "choose data type of output image, e.g. '.nii' or '.nrrd' ", us::Any(), false);
	-
	- // optional arguments
	- parser.addArgument("mask", "m", mitkCommandLineParser::String, "Masking Image: ", "ROI (segmentation)", us::Any(), true, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("help", "h", mitkCommandLineParser::Bool, "Help", "Show this help text");
	- parser.addArgument("omitbzero", "om", mitkCommandLineParser::Bool, "Omit b0:", "Omit b0 value during fit (default = false)", us::Any());
	- parser.addArgument("lowerkbound", "kl", mitkCommandLineParser::Float, "lower Kbound:", "Set (unsigned) lower boundary for Kurtosis parameter (default = -1000)", us::Any());
	- parser.addArgument("upperkbound", "ku", mitkCommandLineParser::Float, "upper Kbound:", "Set upper boundary for Kurtosis parameter (default = 1000)", us::Any());
	-
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	-
	- if (parsedArgs.size()==0 \|\| parsedArgs.count("help") \|\| parsedArgs.count("h")){
	- std::cout << parser.helpText();
	- return EXIT_SUCCESS;
	- }
	-
	- // mandatory arguments
	- std::string inFileName = us::any_cast<std::string>(parsedArgs["input"]);
	- std::string out_prefix = us::any_cast<std::string>(parsedArgs["output"]);
	- std::string maskPath = "";
	-
	- mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Diffusion Weighted Images"}, {});
	- mitk::Image::Pointer inputImage = mitk::IOUtil::Load<mitk::Image>(inFileName, &functor);
	-
	- bool omitBZero = false;
	- double lower = -1000;
	- double upper = 1000;
	- std::string out_type = "nrrd";
	-
	- if (parsedArgs.count("mask") \|\| parsedArgs.count("m"))
	- {
	- maskPath = us::any_cast<std::string>(parsedArgs["mask"]);
	- }
	-
	- if (parsedArgs.count("output_type") \|\| parsedArgs.count("ot"))
	- {
	- out_type = us::any_cast<std::string>(parsedArgs["output_type"]);
	- }
	-
	- if (parsedArgs.count("omitbzero") \|\| parsedArgs.count("om"))
	- {
	- omitBZero = us::any_cast<bool>(parsedArgs["omitbzero"]);
	- }
	-
	- if (parsedArgs.count("lowerkbound") \|\| parsedArgs.count("kl"))
	- {
	- lower = us::any_cast<float>(parsedArgs["lowerkbound"]);
	- }
	-
	- if (parsedArgs.count("upperkbound") \|\| parsedArgs.count("ku"))
	- {
	- upper = us::any_cast<float>(parsedArgs["upperkbound"]);
	- }
	-
	- if( !DPH::IsDiffusionWeightedImage( inputImage ) )
	- {
	- MITK_ERROR("DiffusionIVIMFit.Input") << "No valid diffusion-weighted image provided, failed to load " << inFileName << " as DW Image. Aborting...";
	- return EXIT_FAILURE;
	- }
	-
	-
	-
	-KurtosisMapComputation( inputImage,
	- out_prefix ,
	- out_type,
	- maskPath,
	- omitBZero,
	- lower,
	- upper);
	-
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Quantification/MultishellMethods.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Quantification/MultishellMethods.cpp
	deleted file mode 100644
	index 63eb7ec37e..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Quantification/MultishellMethods.cpp
	+++ /dev/null
	@@ -1,215 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#include <vector>
	-#include <iostream>
	-#include <fstream>
	-#include <algorithm>
	-
	-#include <itkImage.h>
	-#include <itkImageFileReader.h>
	-#include <itkExceptionObject.h>
	-#include <itkMetaDataObject.h>
	-#include <itkVectorImage.h>
	-#include <itkResampleImageFilter.h>
	-
	-#include <mitkImage.h>
	-#include <mitkOdfImage.h>
	-#include <mitkBaseData.h>
	-#include "mitkCommandLineParser.h"
	-#include <mitkLexicalCast.h>
	-
	-#include <itkRadialMultishellToSingleshellImageFilter.h>
	-#include <itkADCAverageFunctor.h>
	-#include <itkBiExpFitFunctor.h>
	-#include <itkKurtosisFitFunctor.h>
	-#include <itkDwiGradientLengthCorrectionFilter.h>
	-#include <mitkIOUtil.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <mitkProperties.h>
	-#include <mitkImageCast.h>
	-#include <mitkITKImageImport.h>
	-#include <mitkPreferenceListReaderOptionsFunctor.h>
	-
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Multishell Methods");
	- parser.setCategory("Preprocessing Tools");
	- parser.setDescription("");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input:", "input file", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "output file", us::Any(), false, false, false, mitkCommandLineParser::Output);
	- parser.addArgument("adc", "D", mitkCommandLineParser::Bool, "ADC:", "ADC Average", us::Any(), false);
	- parser.addArgument("akc", "K", mitkCommandLineParser::Bool, "Kurtosis fit:", "Kurtosis Fit", us::Any(), false);
	- parser.addArgument("biexp", "B", mitkCommandLineParser::Bool, "BiExp fit:", "BiExp fit", us::Any(), false);
	- parser.addArgument("targetbvalue", "b", mitkCommandLineParser::String, "b Value:", "target bValue (mean, min, max)", us::Any(), false);
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- // mandatory arguments
	- std::string inName = us::any_cast<std::string>(parsedArgs["i"]);
	- std::string outName = us::any_cast<std::string>(parsedArgs["o"]);
	- bool applyADC = us::any_cast<bool>(parsedArgs["adc"]);
	- bool applyAKC = us::any_cast<bool>(parsedArgs["akc"]);
	- bool applyBiExp = us::any_cast<bool>(parsedArgs["biexp"]);
	- std::string targetType = us::any_cast<std::string>(parsedArgs["targetbvalue"]);
	-
	- try
	- {
	- std::cout << "Loading " << inName;
	-
	- mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Diffusion Weighted Images"}, {});
	- mitk::Image::Pointer dwi = mitk::IOUtil::Load<mitk::Image>(inName, &functor);
	-
	- if ( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dwi ) )
	- {
	- typedef itk::RadialMultishellToSingleshellImageFilter<short, short> FilterType;
	-
	- typedef itk::DwiGradientLengthCorrectionFilter CorrectionFilterType;
	-
	- CorrectionFilterType::Pointer roundfilter = CorrectionFilterType::New();
	- roundfilter->SetRoundingValue( 1000 );
	- roundfilter->SetReferenceBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue( dwi ));
	- roundfilter->SetReferenceGradientDirectionContainer(mitk::DiffusionPropertyHelper::GetGradientContainer(dwi));
	- roundfilter->Update();
	-
	- mitk::DiffusionPropertyHelper::SetReferenceBValue(dwi, roundfilter->GetNewBValue());
	- mitk::DiffusionPropertyHelper::SetGradientContainer(dwi, roundfilter->GetOutputGradientDirectionContainer());
	-
	- // filter input parameter
	- const mitk::DiffusionPropertyHelper::BValueMapType
	- &originalShellMap = mitk::DiffusionPropertyHelper::GetBValueMap(dwi);
	-
	- mitk::DiffusionPropertyHelper::ImageType::Pointer vectorImage = mitk::DiffusionPropertyHelper::ImageType::New();
	- mitk::CastToItkImage(dwi, vectorImage);
	-
	- const mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer
	- gradientContainer = mitk::DiffusionPropertyHelper::GetGradientContainer(dwi);
	-
	- const unsigned int
	- &bValue = mitk::DiffusionPropertyHelper::GetReferenceBValue( dwi );
	-
	- // filter call
	-
	-
	- vnl_vector<double> bValueList(originalShellMap.size()-1);
	- double targetBValue = bValueList.mean();
	-
	- mitk::DiffusionPropertyHelper::BValueMapType::const_iterator it = originalShellMap.begin();
	- ++it; int i = 0 ;
	- for(; it != originalShellMap.end(); ++it)
	- bValueList.put(i++,it->first);
	-
	- if( targetType == "mean" )
	- targetBValue = bValueList.mean();
	- else if( targetType == "min" )
	- targetBValue = bValueList.min_value();
	- else if( targetType == "max" )
	- targetBValue = bValueList.max_value();
	-
	- if(applyADC)
	- {
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetInput(vectorImage);
	- filter->SetOriginalGradientDirections(gradientContainer);
	- filter->SetOriginalBValueMap(originalShellMap);
	- filter->SetOriginalBValue(bValue);
	-
	- itk::ADCAverageFunctor::Pointer functor = itk::ADCAverageFunctor::New();
	- functor->setListOfBValues(bValueList);
	- functor->setTargetBValue(targetBValue);
	-
	- filter->SetFunctor(functor);
	- filter->Update();
	- // create new DWI image
	- mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( filter->GetOutput() );
	-
	- mitk::DiffusionPropertyHelper::SetReferenceBValue(outImage, targetBValue);
	- mitk::DiffusionPropertyHelper::SetGradientContainer(outImage, filter->GetTargetGradientDirections());
	- mitk::DiffusionPropertyHelper::InitializeImage( outImage );
	-
	- mitk::IOUtil::Save(outImage, (outName + "_ADC.dwi").c_str());
	- }
	- if(applyAKC)
	- {
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetInput(vectorImage);
	- filter->SetOriginalGradientDirections(gradientContainer);
	- filter->SetOriginalBValueMap(originalShellMap);
	- filter->SetOriginalBValue(bValue);
	-
	- itk::KurtosisFitFunctor::Pointer functor = itk::KurtosisFitFunctor::New();
	- functor->setListOfBValues(bValueList);
	- functor->setTargetBValue(targetBValue);
	-
	- filter->SetFunctor(functor);
	- filter->Update();
	- // create new DWI image
	- mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( filter->GetOutput() );
	-
	- mitk::DiffusionPropertyHelper::SetReferenceBValue(outImage, targetBValue);
	- mitk::DiffusionPropertyHelper::SetGradientContainer(outImage, filter->GetTargetGradientDirections());
	- mitk::DiffusionPropertyHelper::InitializeImage( outImage );
	-
	- mitk::IOUtil::Save(outImage, (std::string(outName) + "_AKC.dwi").c_str());
	- }
	- if(applyBiExp)
	- {
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetInput(vectorImage);
	- filter->SetOriginalGradientDirections(gradientContainer);
	- filter->SetOriginalBValueMap(originalShellMap);
	- filter->SetOriginalBValue(bValue);
	-
	- itk::BiExpFitFunctor::Pointer functor = itk::BiExpFitFunctor::New();
	- functor->setListOfBValues(bValueList);
	- functor->setTargetBValue(targetBValue);
	-
	- filter->SetFunctor(functor);
	- filter->Update();
	- // create new DWI image
	- mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( filter->GetOutput() );
	-
	- mitk::DiffusionPropertyHelper::SetReferenceBValue(outImage, targetBValue);
	- mitk::DiffusionPropertyHelper::SetGradientContainer(outImage, filter->GetTargetGradientDirections());
	- mitk::DiffusionPropertyHelper::InitializeImage( outImage );
	-
	- mitk::IOUtil::Save(outImage, (std::string(outName) + "_BiExp.dwi").c_str());
	- }
	- }
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Quantification/QballReconstruction.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Quantification/QballReconstruction.cpp
	deleted file mode 100644
	index 6635eb7663..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Quantification/QballReconstruction.cpp
	+++ /dev/null
	@@ -1,266 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkCoreObjectFactory.h>
	-#include "mitkImage.h"
	-#include "itkAnalyticalDiffusionQballReconstructionImageFilter.h"
	-#include <mitkLexicalCast.h>
	-#include "mitkCommandLineParser.h"
	-#include <mitkIOUtil.h>
	-#include <itksys/SystemTools.hxx>
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <mitkITKImageImport.h>
	-#include <mitkImageCast.h>
	-#include <mitkProperties.h>
	-#include <mitkIOUtil.h>
	-#include <mitkPreferenceListReaderOptionsFunctor.h>
	-#include <itkDiffusionMultiShellQballReconstructionImageFilter.h>
	-#include <itkDwiGradientLengthCorrectionFilter.h>
	-
	-template<int L>
	-void TemplatedMultishellQBallReconstruction(float lambda, mitk::Image::Pointer dwi, bool output_sampled, int threshold, std::string outfilename)
	-{
	- typedef itk::DiffusionMultiShellQballReconstructionImageFilter<short,short,float,L,ODF_SAMPLING_SIZE> FilterType;
	- typename FilterType::Pointer filter = FilterType::New();
	-
	- auto bMap = mitk::DiffusionPropertyHelper::GetBValueMap(dwi);
	- auto it1 = bMap.rbegin();
	- auto it2 = bMap.rbegin();
	- ++it2;
	-
	- // Get average distance
	- int avdistance = 0;
	- for(; it2 != bMap.rend(); ++it1, ++it2)
	- avdistance += static_cast<int>(it1->first - it2->first);
	- avdistance /= bMap.size()-1;
	-
	- // Check if all shells are using the same averae distance
	- it1 = bMap.rbegin();
	- it2 = bMap.rbegin();
	- ++it2;
	- for(; it2 != bMap.rend(); ++it1,++it2)
	- {
	- if(avdistance != static_cast<int>(it1->first - it2->first))
	- {
	- mitkThrow() << "Shells are not equidistant.";
	- }
	- }
	-
	- auto itkVectorImagePointer = mitk::DiffusionPropertyHelper::GetItkVectorImage(dwi);
	- filter->SetBValueMap(bMap);
	- filter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(dwi), itkVectorImagePointer, mitk::DiffusionPropertyHelper::GetReferenceBValue(dwi));
	- filter->SetThreshold(static_cast<short>(threshold));
	- filter->SetLambda(static_cast<double>(lambda));
	- filter->Update();
	-
	- mitk::OdfImage::Pointer image = mitk::OdfImage::New();
	- mitk::Image::Pointer coeffsImage = dynamic_cast<mitk::Image*>(mitk::ShImage::New().GetPointer());
	- image->InitializeByItk( filter->GetOutput() );
	- image->SetVolume( filter->GetOutput()->GetBufferPointer() );
	- coeffsImage->InitializeByItk( filter->GetCoefficientImage().GetPointer() );
	- coeffsImage->SetVolume( filter->GetCoefficientImage()->GetBufferPointer() );
	-
	- std::string coeffout = outfilename;
	- coeffout += ".nii.gz";
	- mitk::IOUtil::Save(coeffsImage, "SH_IMAGE", coeffout);
	-
	- outfilename += ".odf";
	- if (output_sampled)
	- mitk::IOUtil::Save(image, outfilename);
	-}
	-
	-template<int L>
	-void TemplatedCsaQBallReconstruction(float lambda, mitk::Image::Pointer dwi, bool output_sampled, int threshold, std::string outfilename)
	-{
	- typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,4,ODF_SAMPLING_SIZE> FilterType;
	- auto itkVectorImagePointer = mitk::DiffusionPropertyHelper::GetItkVectorImage(dwi);
	-
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(dwi));
	- filter->SetGradientImage( mitk::DiffusionPropertyHelper::GetGradientContainer(dwi), itkVectorImagePointer );
	- filter->SetThreshold(static_cast<short>(threshold));
	- filter->SetLambda(static_cast<double>(lambda));
	-// filter->SetUseMrtrixBasis(mrTrix);
	- filter->SetNormalizationMethod(FilterType::QBAR_SOLID_ANGLE);
	- filter->Update();
	-
	- mitk::OdfImage::Pointer image = mitk::OdfImage::New();
	- mitk::Image::Pointer coeffsImage = dynamic_cast<mitk::Image*>(mitk::ShImage::New().GetPointer());
	- image->InitializeByItk( filter->GetOutput() );
	- image->SetVolume( filter->GetOutput()->GetBufferPointer() );
	- coeffsImage->InitializeByItk( filter->GetCoefficientImage().GetPointer() );
	- coeffsImage->SetVolume( filter->GetCoefficientImage()->GetBufferPointer() );
	-
	- std::string coeffout = outfilename;
	- coeffout += ".nii.gz";
	- mitk::IOUtil::Save(coeffsImage, "SH_IMAGE", coeffout);
	-
	- outfilename += ".odf";
	- if (output_sampled)
	- mitk::IOUtil::Save(image, outfilename);
	-}
	-
	-
	-/**
	- * Perform Q-ball reconstruction using a spherical harmonics basis
	- */
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input image", "input raw dwi (.dwi or .nii/.nii.gz)", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output image", "output image", us::Any(), false, false, false, mitkCommandLineParser::Output);
	- parser.addArgument("sh_order", "", mitkCommandLineParser::Int, "Spherical harmonics order", "spherical harmonics order", 4);
	- parser.addArgument("b0_threshold", "", mitkCommandLineParser::Int, "b0 threshold", "baseline image intensity threshold", 0);
	- parser.addArgument("round_bvalues", "", mitkCommandLineParser::Int, "Round b-values", "round to specified integer", 0);
	- parser.addArgument("lambda", "", mitkCommandLineParser::Float, "Lambda", "ragularization factor lambda", 0.006);
	- parser.addArgument("output_sampled", "", mitkCommandLineParser::Bool, "Output sampled ODFs", "output file containing the sampled ODFs");
	-
	- parser.setCategory("Signal Modelling");
	- parser.setTitle("Qball Reconstruction");
	- parser.setDescription("");
	- parser.setContributor("MIC");
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- std::string inFileName = us::any_cast<std::string>(parsedArgs["i"]);
	- std::string outfilename = us::any_cast<std::string>(parsedArgs["o"]);
	- if (itksys::SystemTools::GetFilenamePath(outfilename).size()>0)
	- outfilename = itksys::SystemTools::GetFilenamePath(outfilename)+"/"+itksys::SystemTools::GetFilenameWithoutExtension(outfilename);
	- else
	- outfilename = itksys::SystemTools::GetFilenameWithoutExtension(outfilename);
	-
	- int threshold = 0;
	- if (parsedArgs.count("b0_threshold"))
	- threshold = us::any_cast<int>(parsedArgs["b0_threshold"]);
	-
	- int round_bvalues = 0;
	- if (parsedArgs.count("round_bvalues"))
	- round_bvalues = us::any_cast<int>(parsedArgs["round_bvalues"]);
	-
	- int shOrder = 4;
	- if (parsedArgs.count("sh_order"))
	- shOrder = us::any_cast<int>(parsedArgs["sh_order"]);
	-
	- float lambda = 0.006f;
	- if (parsedArgs.count("lambda"))
	- lambda = us::any_cast<float>(parsedArgs["lambda"]);
	-
	- bool outCoeffs = false;
	- if (parsedArgs.count("output_coeffs"))
	- outCoeffs = us::any_cast<bool>(parsedArgs["output_coeffs"]);
	-
	-// bool mrTrix = false;
	-// if (parsedArgs.count("mrtrix"))
	-// mrTrix = us::any_cast<bool>(parsedArgs["mrtrix"]);
	-
	- try
	- {
	- mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Diffusion Weighted Images"}, {});
	- std::vector< mitk::BaseData::Pointer > infile = mitk::IOUtil::Load(inFileName, &functor);
	-
	- mitk::Image::Pointer dwi = dynamic_cast<mitk::Image*>(infile.at(0).GetPointer());
	-
	- if (round_bvalues>0)
	- {
	- MITK_INFO << "Rounding b-values";
	- typedef itk::DwiGradientLengthCorrectionFilter FilterType;
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetRoundingValue(round_bvalues);
	- filter->SetReferenceBValue(static_cast<double>(mitk::DiffusionPropertyHelper::GetReferenceBValue(dwi)));
	- filter->SetReferenceGradientDirectionContainer(mitk::DiffusionPropertyHelper::GetGradientContainer(dwi));
	- filter->Update();
	- mitk::DiffusionPropertyHelper::SetReferenceBValue(dwi, static_cast<float>(filter->GetNewBValue()));
	- mitk::DiffusionPropertyHelper::CopyProperties(dwi, dwi, true);
	- mitk::DiffusionPropertyHelper::SetGradientContainer(dwi, filter->GetOutputGradientDirectionContainer());
	- mitk::DiffusionPropertyHelper::InitializeImage(dwi);
	- }
	-
	- auto bMap = mitk::DiffusionPropertyHelper::GetBValueMap(dwi);
	- if(bMap.size()!=4 && bMap.size()!=2)
	- mitkThrow() << "Only three equidistant shells or a single shell are supported. Found " << bMap.size();
	-
	- MITK_INFO << "Averaging redundant gradients";
	- mitk::DiffusionPropertyHelper::AverageRedundantGradients(dwi, 0.001);
	-
	- MITK_INFO << "SH order: " << shOrder;
	- MITK_INFO << "lambda: " << lambda;
	- MITK_INFO << "B0 threshold: " << threshold;
	- MITK_INFO << "Round bvalues: " << round_bvalues;
	- switch ( shOrder )
	- {
	- case 4:
	- {
	- if(bMap.size()==2)
	- TemplatedCsaQBallReconstruction<4>(lambda, dwi, outCoeffs, threshold, outfilename);
	- else if(bMap.size()==4)
	- TemplatedMultishellQBallReconstruction<4>(lambda, dwi, outCoeffs, threshold, outfilename);
	- break;
	- }
	- case 6:
	- {
	- if(bMap.size()==2)
	- TemplatedCsaQBallReconstruction<6>(lambda, dwi, outCoeffs, threshold, outfilename);
	- else if(bMap.size()==4)
	- TemplatedMultishellQBallReconstruction<6>(lambda, dwi, outCoeffs, threshold, outfilename);
	- break;
	- }
	- case 8:
	- {
	- if(bMap.size()==2)
	- TemplatedCsaQBallReconstruction<8>(lambda, dwi, outCoeffs, threshold, outfilename);
	- else if(bMap.size()==4)
	- TemplatedMultishellQBallReconstruction<8>(lambda, dwi, outCoeffs, threshold, outfilename);
	- break;
	- }
	- case 10:
	- {
	- if(bMap.size()==2)
	- TemplatedCsaQBallReconstruction<10>(lambda, dwi, outCoeffs, threshold, outfilename);
	- else if(bMap.size()==4)
	- TemplatedMultishellQBallReconstruction<10>(lambda, dwi, outCoeffs, threshold, outfilename);
	- break;
	- }
	- case 12:
	- {
	- if(bMap.size()==2)
	- TemplatedCsaQBallReconstruction<12>(lambda, dwi, outCoeffs, threshold, outfilename);
	- else if(bMap.size()==4)
	- TemplatedMultishellQBallReconstruction<12>(lambda, dwi, outCoeffs, threshold, outfilename);
	- break;
	- }
	- default:
	- {
	- mitkThrow() << "SH order not supported";
	- }
	- }
	- }
	- catch ( itk::ExceptionObject &err)
	- {
	- std::cout << "Exception: " << err;
	- }
	- catch ( std::exception err)
	- {
	- std::cout << "Exception: " << err.what();
	- }
	- catch ( ... )
	- {
	- std::cout << "Exception!";
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Quantification/TensorReconstruction.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Quantification/TensorReconstruction.cpp
	deleted file mode 100644
	index 63b266804c..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Quantification/TensorReconstruction.cpp
	+++ /dev/null
	@@ -1,135 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkImage.h"
	-#include <mitkImageCast.h>
	-#include "mitkBaseData.h"
	-#include <mitkDiffusionPropertyHelper.h>
	-
	-#include <itkTensorReconstructionWithEigenvalueCorrectionFilter.h>
	-#include <itkDiffusionTensor3DReconstructionImageFilter.h>
	-#include <itkDiffusionTensor3D.h>
	-#include <itkImageFileWriter.h>
	-#include <itkNrrdImageIO.h>
	-#include "mitkCommandLineParser.h"
	-#include <itksys/SystemTools.hxx>
	-#include <mitkIOUtil.h>
	-#include <mitkLocaleSwitch.h>
	-
	-/**
	- * Convert files from one ending to the other
	- */
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input image", "input raw dwi", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output image", "output image", us::Any(), false, false, false, mitkCommandLineParser::Output);
	- parser.addArgument("b0_threshold", "", mitkCommandLineParser::Int, "b0 threshold", "baseline image intensity threshold", 0);
	- parser.addArgument("correct_negative_eigenv", "", mitkCommandLineParser::Bool, "Correct negative eigenvalues", "correct negative eigenvalues", us::Any(false));
	-
	- parser.setCategory("Signal Modelling");
	- parser.setTitle("Tensor Reconstruction");
	- parser.setDescription("");
	- parser.setContributor("MIC");
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- std::string inFileName = us::any_cast<std::string>(parsedArgs["i"]);
	- std::string outfilename = us::any_cast<std::string>(parsedArgs["o"]);
	- if (!itksys::SystemTools::GetFilenamePath(outfilename).empty())
	- outfilename = itksys::SystemTools::GetFilenamePath(outfilename)+"/"+itksys::SystemTools::GetFilenameWithoutExtension(outfilename);
	- else
	- outfilename = itksys::SystemTools::GetFilenameWithoutExtension(outfilename);
	- outfilename += ".dti";
	-
	- int threshold = 0;
	- if (parsedArgs.count("b0_threshold"))
	- threshold = us::any_cast<int>(parsedArgs["b0_threshold"]);
	-
	- bool correct_negative_eigenv = false;
	- if (parsedArgs.count("correct_negative_eigenv"))
	- correct_negative_eigenv = us::any_cast<bool>(parsedArgs["correct_negative_eigenv"]);
	-
	- try
	- {
	- mitk::Image::Pointer dwi = mitk::IOUtil::Load<mitk::Image>(inFileName);
	-
	- mitk::DiffusionPropertyHelper::ImageType::Pointer itkVectorImagePointer = mitk::DiffusionPropertyHelper::ImageType::New();
	- mitk::CastToItkImage(dwi, itkVectorImagePointer);
	-
	- if (correct_negative_eigenv)
	- {
	- typedef itk::TensorReconstructionWithEigenvalueCorrectionFilter< short, float > TensorReconstructionImageFilterType;
	- TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New();
	- filter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(dwi));
	- filter->SetGradientImage( mitk::DiffusionPropertyHelper::GetGradientContainer(dwi), itkVectorImagePointer);
	- filter->SetB0Threshold(threshold);
	- filter->Update();
	-
	- // Save tensor image
	- itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
	- io->SetFileType( itk::ImageIOBase::Binary );
	- io->UseCompressionOn();
	-
	- mitk::LocaleSwitch localeSwitch("C");
	- itk::ImageFileWriter< itk::Image< itk::DiffusionTensor3D< float >, 3 > >::Pointer writer = itk::ImageFileWriter< itk::Image< itk::DiffusionTensor3D< float >, 3 > >::New();
	- writer->SetInput(filter->GetOutput());
	- writer->SetFileName(outfilename);
	- writer->SetImageIO(io);
	- writer->UseCompressionOn();
	- writer->Update();
	- }
	- else {
	- typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, float > TensorReconstructionImageFilterType;
	- TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New();
	- filter->SetGradientImage( mitk::DiffusionPropertyHelper::GetGradientContainer(dwi), itkVectorImagePointer );
	- filter->SetBValue( mitk::DiffusionPropertyHelper::GetReferenceBValue( dwi ));
	- filter->SetThreshold(threshold);
	- filter->Update();
	-
	- // Save tensor image
	- itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
	- io->SetFileType( itk::ImageIOBase::Binary );
	- io->UseCompressionOn();
	-
	- mitk::LocaleSwitch localeSwitch("C");
	- itk::ImageFileWriter< itk::Image< itk::DiffusionTensor3D< float >, 3 > >::Pointer writer = itk::ImageFileWriter< itk::Image< itk::DiffusionTensor3D< float >, 3 > >::New();
	- writer->SetInput(filter->GetOutput());
	- writer->SetFileName(outfilename);
	- writer->SetImageIO(io);
	- writer->UseCompressionOn();
	- writer->Update();
	- }
	-
	- }
	- catch ( itk::ExceptionObject &err)
	- {
	- std::cout << "Exception: " << err;
	- }
	- catch ( std::exception err)
	- {
	- std::cout << "Exception: " << err.what();
	- }
	- catch ( ... )
	- {
	- std::cout << "Exception!";
	- }
	- return EXIT_SUCCESS;
	-
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Tractography/CMakeLists.txt b/Modules/DiffusionImaging/DiffusionCmdApps/Tractography/CMakeLists.txt
	deleted file mode 100755
	index a14ed6d992..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Tractography/CMakeLists.txt
	+++ /dev/null
	@@ -1,40 +0,0 @@
	-option(BUILD_DiffusionTractographyCmdApps "Build commandline tools for diffusion fiber tractography" OFF)
	-
	-if(BUILD_DiffusionTractographyCmdApps OR MITK_BUILD_ALL_APPS)
	-
	- # needed include directories
	- include_directories(
	- ${CMAKE_CURRENT_SOURCE_DIR}
	- ${CMAKE_CURRENT_BINARY_DIR}
	- )
	-
	- # list of diffusion cmdapps
	- # if an app requires additional dependencies
	- # they are added after a "^^" and separated by "_"
	- set( diffusiontractographycmdapps
	- StreamlineTractography^^
	- GlobalTractography^^
	- RfTraining^^
	- )
	-
	- foreach(diffusiontractographycmdapp ${diffusiontractographycmdapps})
	- # extract cmd app name and dependencies
	- string(REPLACE "^^" "\\;" cmdapp_info ${diffusiontractographycmdapp})
	- set(cmdapp_info_list ${cmdapp_info})
	- list(GET cmdapp_info_list 0 appname)
	- list(GET cmdapp_info_list 1 raw_dependencies)
	- string(REPLACE "_" "\\;" dependencies "${raw_dependencies}")
	- set(dependencies_list ${dependencies})
	-
	- mitkFunctionCreateCommandLineApp(
	- NAME ${appname}
	- DEPENDS MitkDiffusionCmdApps ${dependencies_list}
	- PACKAGE_DEPENDS
	- )
	- endforeach()
	-
	- if(EXECUTABLE_IS_ENABLED)
	- MITK_INSTALL_TARGETS(EXECUTABLES ${EXECUTABLE_TARGET})
	- endif()
	-
	- endif()
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Tractography/GlobalTractography.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Tractography/GlobalTractography.cpp
	deleted file mode 100755
	index 61973b7e12..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Tractography/GlobalTractography.cpp
	+++ /dev/null
	@@ -1,133 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkImageCast.h>
	-#include <mitkOdfImage.h>
	-#include <mitkTensorImage.h>
	-#include <mitkFiberBundle.h>
	-#include <itkGibbsTrackingFilter.h>
	-#include <itkDiffusionTensor3D.h>
	-#include <itkShCoefficientImageImporter.h>
	-#include <itkShToOdfImageFilter.h>
	-#include <mitkImageToItk.h>
	-#include <mitkIOUtil.h>
	-#include "mitkCommandLineParser.h"
	-#include <boost/algorithm/string.hpp>
	-#include <itkFlipImageFilter.h>
	-#include <mitkCoreObjectFactory.h>
	-#include <mitkPreferenceListReaderOptionsFunctor.h>
	-#include <mitkShImage.h>
	-#include <mitkDiffusionFunctionCollection.h>
	-
	-/*!
	-\brief Perform global fiber tractography (Gibbs tractography)
	-*/
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Gibbs Tracking");
	- parser.setCategory("Fiber Tracking and Processing Methods");
	- parser.setDescription("Perform global fiber tractography (Gibbs tractography)");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input:", "input image (tensor, ODF or SH-coefficient image)", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "output tractogram", us::Any(), false, false, false, mitkCommandLineParser::Output);
	- parser.addArgument("parameters", "", mitkCommandLineParser::String, "Parameters:", "parameter file (.gtp)", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("mask", "", mitkCommandLineParser::String, "Mask:", "binary mask image", us::Any(), false, false, false, mitkCommandLineParser::Input);
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- std::string inFileName = us::any_cast<std::string>(parsedArgs["i"]);
	- std::string paramFileName = us::any_cast<std::string>(parsedArgs["parameters"]);
	- std::string outFileName = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- try
	- {
	- // instantiate gibbs tracker
	- typedef itk::Vector<float, ODF_SAMPLING_SIZE> OdfVectorType;
	- typedef itk::Image<OdfVectorType,3> ItkOdfImageType;
	- typedef itk::GibbsTrackingFilter<ItkOdfImageType> GibbsTrackingFilterType;
	- GibbsTrackingFilterType::Pointer gibbsTracker = GibbsTrackingFilterType::New();
	-
	- // load input image
	- mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"SH Image"}, {});
	- mitk::Image::Pointer mitkImage = mitk::IOUtil::Load<mitk::Image>(inFileName, &functor);
	-
	- // try to cast to Odf image
	- if( dynamic_cast<mitk::OdfImage*>(mitkImage.GetPointer()) )
	- {
	- mitk::OdfImage::Pointer mitkOdfImage = dynamic_cast<mitk::OdfImage*>(mitkImage.GetPointer());
	- ItkOdfImageType::Pointer itk_odf = ItkOdfImageType::New();
	- mitk::CastToItkImage(mitkOdfImage, itk_odf);
	- gibbsTracker->SetOdfImage(itk_odf.GetPointer());
	- }
	- else if( dynamic_cast<mitk::TensorImage*>(mitkImage.GetPointer()) )
	- {
	- typedef itk::Image< itk::DiffusionTensor3D<float>, 3 > ItkTensorImage;
	- mitk::TensorImage::Pointer mitkTensorImage = dynamic_cast<mitk::TensorImage*>(mitkImage.GetPointer());
	- ItkTensorImage::Pointer itk_dti = ItkTensorImage::New();
	- mitk::CastToItkImage(mitkTensorImage, itk_dti);
	- gibbsTracker->SetTensorImage(itk_dti);
	- }
	- else if ( dynamic_cast<mitk::ShImage*>(mitkImage.GetPointer()) )
	- {
	- mitk::Image::Pointer shImage = dynamic_cast<mitk::Image*>(mitkImage.GetPointer());
	- gibbsTracker->SetOdfImage(mitk::convert::GetItkOdfFromShImage(shImage));
	- }
	- else
	- return EXIT_FAILURE;
	-
	- // global tracking
	- if (parsedArgs.count("mask"))
	- {
	- typedef itk::Image<float,3> MaskImgType;
	- mitk::Image::Pointer mitkMaskImage = mitk::IOUtil::Load<mitk::Image>(us::any_cast<std::string>(parsedArgs["mask"]));
	- MaskImgType::Pointer itk_mask = MaskImgType::New();
	- mitk::CastToItkImage(mitkMaskImage, itk_mask);
	- gibbsTracker->SetMaskImage(itk_mask);
	- }
	-
	- gibbsTracker->SetDuplicateImage(false);
	- gibbsTracker->SetLoadParameterFile( paramFileName );
	- // gibbsTracker->SetLutPath( "" );
	- gibbsTracker->Update();
	-
	- mitk::FiberBundle::Pointer mitkFiberBundle = mitk::FiberBundle::New(gibbsTracker->GetFiberBundle());
	- mitkFiberBundle->SetReferenceGeometry(mitkImage->GetGeometry());
	-
	- mitk::IOUtil::Save(mitkFiberBundle, outFileName );
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Tractography/RfTraining.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Tractography/RfTraining.cpp
	deleted file mode 100755
	index 138b1db3c7..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Tractography/RfTraining.cpp
	+++ /dev/null
	@@ -1,238 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkBaseData.h>
	-#include <mitkImageCast.h>
	-#include <mitkImageToItk.h>
	-#include <metaCommand.h>
	-#include "mitkCommandLineParser.h"
	-#include <usAny.h>
	-#include <mitkIOUtil.h>
	-#include <iostream>
	-#include <fstream>
	-#include <itksys/SystemTools.hxx>
	-#include <mitkCoreObjectFactory.h>
	-#include <mitkPreferenceListReaderOptionsFunctor.h>
	-#include <mitkFiberBundle.h>
	-#include <mitkTrackingHandlerRandomForest.h>
	-#include <mitkTractographyForest.h>
	-
	-#define _USE_MATH_DEFINES
	-#include <math.h>
	-
	-/*!
	-\brief Train random forest classifier for machine learning based streamline tractography
	-*/
	-int main(int argc, char* argv[])
	-{
	- MITK_INFO << "RfTraining";
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Trains Random Forests for Machine Learning Based Tractography");
	- parser.setCategory("Fiber Tracking and Processing Methods");
	- parser.setDescription("Train random forest classifier for machine learning based streamline tractography");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	-
	- parser.beginGroup("1. Mandatory arguments:");
	- parser.addArgument("", "i", mitkCommandLineParser::StringList, "DWIs:", "input diffusion-weighted images", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "t", mitkCommandLineParser::StringList, "Tractograms:", "input training tractograms", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Forest:", "output random forest (HDF5)", us::Any(), false, false, false, mitkCommandLineParser::Output);
	- parser.endGroup();
	-
	- parser.beginGroup("2. Additional input images:");
	- parser.addArgument("masks", "", mitkCommandLineParser::StringList, "Masks:", "restrict training using a binary mask image", us::Any(), true, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("wm_masks", "", mitkCommandLineParser::StringList, "WM-Masks:", "if no binary white matter mask is specified, the envelope of the input tractogram is used", us::Any(), true, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("volume_modification_images", "", mitkCommandLineParser::StringList, "Volume modification images:", "specify a list of float images that modify the fiber density", us::Any(), true, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("additional_feature_images", "", mitkCommandLineParser::StringList, "Additional feature images:", "specify a list of float images that hold additional features (float)", us::Any(), true, false, false, mitkCommandLineParser::Input);
	- parser.endGroup();
	-
	- parser.beginGroup("3. Forest parameters:");
	- parser.addArgument("num_trees", "", mitkCommandLineParser::Int, "Number of trees:", "number of trees", 30);
	- parser.addArgument("max_tree_depth", "", mitkCommandLineParser::Int, "Max. tree depth:", "maximum tree depth", 25);
	- parser.addArgument("sample_fraction", "", mitkCommandLineParser::Float, "Sample fraction:", "fraction of samples used per tree", 0.7);
	- parser.endGroup();
	-
	- parser.beginGroup("4. Feature parameters:");
	- parser.addArgument("use_sh_features", "", mitkCommandLineParser::Bool, "Use SH features:", "use SH features", false);
	- parser.addArgument("sampling_distance", "", mitkCommandLineParser::Float, "Sampling distance:", "resampling parameter for the input tractogram in mm (determines number of white-matter samples)", us::Any());
	- parser.addArgument("max_wm_samples", "", mitkCommandLineParser::Int, "Max. num. WM samples:", "upper limit for the number of WM samples");
	- parser.addArgument("num_gm_samples", "", mitkCommandLineParser::Int, "Number of gray matter samples per voxel:", "Number of gray matter samples per voxel", us::Any());
	- parser.endGroup();
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- bool shfeatures = false;
	- if (parsedArgs.count("use_sh_features"))
	- shfeatures = us::any_cast<bool>(parsedArgs["use_sh_features"]);
	-
	- mitkCommandLineParser::StringContainerType imageFiles = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["i"]);
	- mitkCommandLineParser::StringContainerType wmMaskFiles;
	- if (parsedArgs.count("wm_masks"))
	- wmMaskFiles = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["wm_masks"]);
	-
	- mitkCommandLineParser::StringContainerType volModFiles;
	- if (parsedArgs.count("volume_modification_images"))
	- volModFiles = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["volume_modification_images"]);
	-
	- mitkCommandLineParser::StringContainerType addFeatFiles;
	- if (parsedArgs.count("additional_feature_images"))
	- addFeatFiles = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["additional_feature_images"]);
	-
	- mitkCommandLineParser::StringContainerType maskFiles;
	- if (parsedArgs.count("masks"))
	- maskFiles = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["masks"]);
	-
	- std::string forestFile = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- mitkCommandLineParser::StringContainerType tractogramFiles;
	- if (parsedArgs.count("t"))
	- tractogramFiles = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["t"]);
	-
	- int num_trees = 30;
	- if (parsedArgs.count("num_trees"))
	- num_trees = us::any_cast<int>(parsedArgs["num_trees"]);
	-
	- int gm_samples = -1;
	- if (parsedArgs.count("num_gm_samples"))
	- gm_samples = us::any_cast<int>(parsedArgs["num_gm_samples"]);
	-
	- float sampling_distance = -1;
	- if (parsedArgs.count("sampling_distance"))
	- sampling_distance = us::any_cast<float>(parsedArgs["sampling_distance"]);
	-
	- int max_tree_depth = 25;
	- if (parsedArgs.count("max_tree_depth"))
	- max_tree_depth = us::any_cast<int>(parsedArgs["max_tree_depth"]);
	-
	- double sample_fraction = 0.7;
	- if (parsedArgs.count("sample_fraction"))
	- sample_fraction = us::any_cast<float>(parsedArgs["sample_fraction"]);
	-
	- int maxWmSamples = -1;
	- if (parsedArgs.count("max_wm_samples"))
	- maxWmSamples = us::any_cast<int>(parsedArgs["max_wm_samples"]);
	-
	-
	- MITK_INFO << "loading diffusion-weighted images";
	- std::vector< mitk::Image::Pointer > rawData;
	- mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Diffusion Weighted Images"}, {});
	- for (auto imgFile : imageFiles)
	- {
	- auto dwi = mitk::IOUtil::Load<mitk::Image>(imgFile, &functor);
	- rawData.push_back(dwi);
	- }
	-
	- typedef itk::Image<float, 3> ItkFloatImgType;
	- typedef itk::Image<unsigned char, 3> ItkUcharImgType;
	- MITK_INFO << "loading mask images";
	- std::vector< ItkUcharImgType::Pointer > maskImageVector;
	- for (auto maskFile : maskFiles)
	- {
	- mitk::Image::Pointer img = mitk::IOUtil::Load<mitk::Image>(maskFile);
	- ItkUcharImgType::Pointer mask = ItkUcharImgType::New();
	- mitk::CastToItkImage(img, mask);
	- maskImageVector.push_back(mask);
	- }
	-
	- MITK_INFO << "loading white matter mask images";
	- std::vector< ItkUcharImgType::Pointer > wmMaskImageVector;
	- for (auto wmFile : wmMaskFiles)
	- {
	- mitk::Image::Pointer img = mitk::IOUtil::Load<mitk::Image>(wmFile);
	- ItkUcharImgType::Pointer wmmask = ItkUcharImgType::New();
	- mitk::CastToItkImage(img, wmmask);
	- wmMaskImageVector.push_back(wmmask);
	- }
	-
	- MITK_INFO << "loading tractograms";
	- std::vector< mitk::FiberBundle::Pointer > tractograms;
	- for (auto tractFile : tractogramFiles)
	- {
	- mitk::FiberBundle::Pointer fib = mitk::IOUtil::Load<mitk::FiberBundle>(tractFile);
	- tractograms.push_back(fib);
	- }
	-
	- MITK_INFO << "loading white volume modification images";
	- std::vector< ItkFloatImgType::Pointer > volumeModImages;
	- for (auto file : volModFiles)
	- {
	- mitk::Image::Pointer img = mitk::IOUtil::Load<mitk::Image>(file);
	- ItkFloatImgType::Pointer itkimg = ItkFloatImgType::New();
	- mitk::CastToItkImage(img, itkimg);
	- volumeModImages.push_back(itkimg);
	- }
	-
	- MITK_INFO << "loading additional feature images";
	- std::vector< std::vector< ItkFloatImgType::Pointer > > addFeatImages;
	- for (std::size_t i=0; i<rawData.size(); ++i)
	- addFeatImages.push_back(std::vector< ItkFloatImgType::Pointer >());
	-
	- int c = 0;
	- for (auto file : addFeatFiles)
	- {
	- mitk::Image::Pointer img = mitk::IOUtil::Load<mitk::Image>(file);
	- ItkFloatImgType::Pointer itkimg = ItkFloatImgType::New();
	- mitk::CastToItkImage(img, itkimg);
	- addFeatImages.at(c%addFeatImages.size()).push_back(itkimg);
	- c++;
	- }
	-
	- mitk::TractographyForest::Pointer forest = nullptr;
	- if (shfeatures)
	- {
	- mitk::TrackingHandlerRandomForest<6,28> forestHandler;
	- forestHandler.SetDwis(rawData);
	- forestHandler.SetMaskImages(maskImageVector);
	- forestHandler.SetWhiteMatterImages(wmMaskImageVector);
	- forestHandler.SetFiberVolumeModImages(volumeModImages);
	- forestHandler.SetAdditionalFeatureImages(addFeatImages);
	- forestHandler.SetTractograms(tractograms);
	- forestHandler.SetNumTrees(num_trees);
	- forestHandler.SetMaxTreeDepth(max_tree_depth);
	- forestHandler.SetGrayMatterSamplesPerVoxel(gm_samples);
	- forestHandler.SetSampleFraction(sample_fraction);
	- forestHandler.SetFiberSamplingStep(sampling_distance);
	- forestHandler.SetMaxNumWmSamples(maxWmSamples);
	- forestHandler.StartTraining();
	- forest = forestHandler.GetForest();
	- }
	- else
	- {
	- mitk::TrackingHandlerRandomForest<6,100> forestHandler;
	- forestHandler.SetDwis(rawData);
	- forestHandler.SetMaskImages(maskImageVector);
	- forestHandler.SetWhiteMatterImages(wmMaskImageVector);
	- forestHandler.SetFiberVolumeModImages(volumeModImages);
	- forestHandler.SetAdditionalFeatureImages(addFeatImages);
	- forestHandler.SetTractograms(tractograms);
	- forestHandler.SetNumTrees(num_trees);
	- forestHandler.SetMaxTreeDepth(max_tree_depth);
	- forestHandler.SetGrayMatterSamplesPerVoxel(gm_samples);
	- forestHandler.SetSampleFraction(sample_fraction);
	- forestHandler.SetFiberSamplingStep(sampling_distance);
	- forestHandler.SetMaxNumWmSamples(maxWmSamples);
	- forestHandler.StartTraining();
	- forest = forestHandler.GetForest();
	- }
	-
	- mitk::IOUtil::Save(forest, forestFile);
	-
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Tractography/StreamlineTractography.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Tractography/StreamlineTractography.cpp
	deleted file mode 100755
	index e5f986b2f0..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/Tractography/StreamlineTractography.cpp
	+++ /dev/null
	@@ -1,566 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkBaseData.h>
	-#include <mitkImageCast.h>
	-#include <mitkImageToItk.h>
	-#include <metaCommand.h>
	-#include <mitkCommandLineParser.h>
	-#include <mitkLog.h>
	-#include <usAny.h>
	-#include <mitkIOUtil.h>
	-#include <iostream>
	-#include <fstream>
	-#include <itksys/SystemTools.hxx>
	-#include <mitkCoreObjectFactory.h>
	-#include <omp.h>
	-#include <itksys/SystemTools.hxx>
	-
	-#include <mitkFiberBundle.h>
	-#include <itkStreamlineTrackingFilter.h>
	-#include <Algorithms/TrackingHandlers/mitkTrackingDataHandler.h>
	-#include <Algorithms/TrackingHandlers/mitkTrackingHandlerRandomForest.h>
	-#include <Algorithms/TrackingHandlers/mitkTrackingHandlerPeaks.h>
	-#include <Algorithms/TrackingHandlers/mitkTrackingHandlerTensor.h>
	-#include <Algorithms/TrackingHandlers/mitkTrackingHandlerOdf.h>
	-#include <itkTensorImageToOdfImageFilter.h>
	-#include <mitkTractographyForest.h>
	-#include <mitkPreferenceListReaderOptionsFunctor.h>
	-#include <mitkStreamlineTractographyParameters.h>
	-
	-#define _USE_MATH_DEFINES
	-#include <math.h>
	-
	-const int numOdfSamples = 200;
	-typedef itk::Image< itk::Vector< float, numOdfSamples > , 3 > SampledShImageType;
	-
	-/*!
	-\brief
	-*/
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Streamline Tractography");
	- parser.setCategory("Fiber Tracking and Processing Methods");
	- parser.setDescription("Perform streamline tractography");
	- parser.setContributor("MIC");
	-
	- // parameters fo all methods
	- parser.setArgumentPrefix("--", "-");
	-
	- parser.beginGroup("1. Mandatory arguments:");
	- parser.addArgument("", "i", mitkCommandLineParser::StringList, "Input:", "input image (multiple possible for 'DetTensor' algorithm)", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "output fiberbundle/probability map", us::Any(), false, false, false, mitkCommandLineParser::Output);
	- parser.addArgument("type", "", mitkCommandLineParser::String, "Type:", "which tracker to use (Peaks; Tensor; ODF; RF)", us::Any(), false);
	- parser.addArgument("probabilistic", "", mitkCommandLineParser::Bool, "Probabilistic:", "Probabilistic tractography", us::Any(false));
	- parser.endGroup();
	-
	- parser.beginGroup("2. Seeding:");
	- parser.addArgument("seeds", "", mitkCommandLineParser::Int, "Seeds per voxel:", "number of seed points per voxel", 1);
	- parser.addArgument("seed_image", "", mitkCommandLineParser::String, "Seed image:", "mask image defining seed voxels", us::Any(), true, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("trials_per_seed", "", mitkCommandLineParser::Int, "Max. trials per seed:", "try each seed N times until a valid streamline is obtained (only for probabilistic tractography)", 10);
	- parser.addArgument("max_tracts", "", mitkCommandLineParser::Int, "Max. number of tracts:", "tractography is stopped if the reconstructed number of tracts is exceeded", -1);
	- parser.endGroup();
	-
	- parser.beginGroup("3. Tractography constraints:");
	- parser.addArgument("tracking_mask", "", mitkCommandLineParser::String, "Mask image:", "streamlines leaving the mask will stop immediately", us::Any(), true, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("stop_image", "", mitkCommandLineParser::String, "Stop ROI image:", "streamlines entering the mask will stop immediately", us::Any(), true, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("exclusion_image", "", mitkCommandLineParser::String, "Exclusion ROI image:", "streamlines entering the mask will be discarded", us::Any(), true, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("ep_constraint", "", mitkCommandLineParser::String, "Endpoint constraint:", "determines which fibers are accepted based on their endpoint location - options are NONE, EPS_IN_TARGET, EPS_IN_TARGET_LABELDIFF, EPS_IN_SEED_AND_TARGET, MIN_ONE_EP_IN_TARGET, ONE_EP_IN_TARGET and NO_EP_IN_TARGET", us::Any());
	- parser.addArgument("target_image", "", mitkCommandLineParser::String, "Target ROI image:", "effact depends on the chosen endpoint constraint (option ep_constraint)", us::Any(), true, false, false, mitkCommandLineParser::Input);
	- parser.endGroup();
	-
	- parser.beginGroup("4. Streamline integration parameters:");
	- parser.addArgument("sharpen_odfs", "", mitkCommandLineParser::Bool, "SHarpen ODFs:", "if you are using dODF images as input, it is advisable to sharpen the ODFs (min-max normalize and raise to the power of 4). this is not necessary for CSD fODFs, since they are narurally much sharper.");
	- parser.addArgument("cutoff", "", mitkCommandLineParser::Float, "Cutoff:", "set the FA, GFA or Peak amplitude cutoff for terminating tracks", 0.1);
	- parser.addArgument("odf_cutoff", "", mitkCommandLineParser::Float, "ODF Cutoff:", "threshold on the ODF magnitude. this is useful in case of CSD fODF tractography.", 0.0);
	- parser.addArgument("step_size", "", mitkCommandLineParser::Float, "Step size:", "step size (in voxels)", 0.5);
	- parser.addArgument("min_tract_length", "", mitkCommandLineParser::Float, "Min. tract length:", "minimum fiber length (in mm)", 20);
	- parser.addArgument("angular_threshold", "", mitkCommandLineParser::Float, "Angular threshold:", "angular threshold between two successive steps, (default: 90° * step_size, minimum 15°)");
	- parser.addArgument("loop_check", "", mitkCommandLineParser::Float, "Check for loops:", "threshold on angular stdev over the last 4 voxel lengths");
	- parser.addArgument("peak_jitter", "", mitkCommandLineParser::Float, "Peak jitter:", "important for probabilistic peak tractography and peak prior. actual jitter is drawn from a normal distribution with peak_jitter*fabs(direction_value) as standard deviation.", 0.01);
	- parser.endGroup();
	-
	- parser.beginGroup("5. Tractography prior:");
	- parser.addArgument("prior_image", "", mitkCommandLineParser::String, "Peak prior:", "tractography prior in thr for of a peak image", us::Any(), true, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("prior_weight", "", mitkCommandLineParser::Float, "Prior weight", "weighting factor between prior and data.", 0.5);
	- parser.addArgument("dont_restrict_to_prior", "", mitkCommandLineParser::Bool, "Don't restrict to prior:", "don't restrict tractography to regions where the prior is valid.", us::Any(false));
	- parser.addArgument("no_new_directions_from_prior", "", mitkCommandLineParser::Bool, "No new directios from prior:", "the prior cannot create directions where there are none in the data.", us::Any(false));
	- parser.addArgument("prior_flip_x", "", mitkCommandLineParser::Bool, "Prior Flip X:", "multiply x-coordinate of prior direction by -1");
	- parser.addArgument("prior_flip_y", "", mitkCommandLineParser::Bool, "Prior Flip Y:", "multiply y-coordinate of prior direction by -1");
	- parser.addArgument("prior_flip_z", "", mitkCommandLineParser::Bool, "Prior Flip Z:", "multiply z-coordinate of prior direction by -1");
	- parser.endGroup();
	-
	- parser.beginGroup("6. Neighborhood sampling:");
	- parser.addArgument("num_samples", "", mitkCommandLineParser::Int, "Num. neighborhood samples:", "number of neighborhood samples that are use to determine the next progression direction", 0);
	- parser.addArgument("sampling_distance", "", mitkCommandLineParser::Float, "Sampling distance:", "distance of neighborhood sampling points (in voxels)", 0.25);
	- parser.addArgument("use_stop_votes", "", mitkCommandLineParser::Bool, "Use stop votes:", "use stop votes");
	- parser.addArgument("use_only_forward_samples", "", mitkCommandLineParser::Bool, "Use only forward samples:", "use only forward samples");
	- parser.endGroup();
	-
	- parser.beginGroup("7. Tensor tractography specific:");
	- parser.addArgument("tend_f", "", mitkCommandLineParser::Float, "Weight f", "weighting factor between first eigenvector (f=1 equals FACT tracking) and input vector dependent direction (f=0).", 1.0);
	- parser.addArgument("tend_g", "", mitkCommandLineParser::Float, "Weight g", "weighting factor between input vector (g=0) and tensor deflection (g=1 equals TEND tracking)", 0.0);
	- parser.endGroup();
	-
	- parser.beginGroup("8. Random forest tractography specific:");
	- parser.addArgument("forest", "", mitkCommandLineParser::String, "Forest:", "input random forest (HDF5 file)", us::Any(), true, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("use_sh_features", "", mitkCommandLineParser::Bool, "Use SH features:", "use SH features");
	- parser.endGroup();
	-
	- parser.beginGroup("9. Additional input:");
	- parser.addArgument("additional_images", "", mitkCommandLineParser::StringList, "Additional images:", "specify a list of float images that hold additional information (FA, GFA, additional features for RF tractography)", us::Any(), true, false, false, mitkCommandLineParser::Input);
	- parser.endGroup();
	-
	- parser.beginGroup("10. Misc:");
	- parser.addArgument("flip_x", "", mitkCommandLineParser::Bool, "Flip X:", "multiply x-coordinate of direction proposal by -1");
	- parser.addArgument("flip_y", "", mitkCommandLineParser::Bool, "Flip Y:", "multiply y-coordinate of direction proposal by -1");
	- parser.addArgument("flip_z", "", mitkCommandLineParser::Bool, "Flip Z:", "multiply z-coordinate of direction proposal by -1");
	- parser.addArgument("no_data_interpolation", "", mitkCommandLineParser::Bool, "Don't interpolate input data:", "don't interpolate input image values");
	- parser.addArgument("no_mask_interpolation", "", mitkCommandLineParser::Bool, "Don't interpolate masks:", "don't interpolate mask image values");
	- parser.addArgument("compress", "", mitkCommandLineParser::Float, "Compress:", "compress output fibers using the given error threshold (in mm)");
	- parser.addArgument("fix_seed", "", mitkCommandLineParser::Bool, "Fix Random Seed:", "always use the same random numbers");
	- parser.addArgument("parameter_file", "", mitkCommandLineParser::String, "Parameter File:", "load parameters from json file (svae using MITK Diffusion GUI). the parameters loaded form this file are overwritten by the manually set parameters.", us::Any(), true, false, false, mitkCommandLineParser::Input);
	- parser.endGroup();
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- mitkCommandLineParser::StringContainerType input_files = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["i"]);
	- std::string outFile = us::any_cast<std::string>(parsedArgs["o"]);
	- std::string type = us::any_cast<std::string>(parsedArgs["type"]);
	-
	- std::shared_ptr< mitk::StreamlineTractographyParameters > params = std::make_shared<mitk::StreamlineTractographyParameters>();
	-
	- if (parsedArgs.count("parameter_file"))
	- {
	- auto parameter_file = us::any_cast<std::string>(parsedArgs["parameter_file"]);
	- params->LoadParameters(parameter_file);
	- }
	-
	- if (parsedArgs.count("probabilistic"))
	- params->m_Mode = mitk::StreamlineTractographyParameters::MODE::PROBABILISTIC;
	- else {
	- params->m_Mode = mitk::StreamlineTractographyParameters::MODE::DETERMINISTIC;
	- }
	-
	- std::string prior_image = "";
	- if (parsedArgs.count("prior_image"))
	- prior_image = us::any_cast<std::string>(parsedArgs["prior_image"]);
	-
	- if (parsedArgs.count("prior_weight"))
	- params->m_Weight = us::any_cast<float>(parsedArgs["prior_weight"]);
	-
	- if (parsedArgs.count("fix_seed"))
	- params->m_FixRandomSeed = us::any_cast<bool>(parsedArgs["fix_seed"]);
	-
	- params->m_RestrictToPrior = true;
	- if (parsedArgs.count("dont_restrict_to_prior"))
	- params->m_RestrictToPrior = !us::any_cast<bool>(parsedArgs["dont_restrict_to_prior"]);
	-
	- params->m_NewDirectionsFromPrior = true;
	- if (parsedArgs.count("no_new_directions_from_prior"))
	- params->m_NewDirectionsFromPrior = !us::any_cast<bool>(parsedArgs["no_new_directions_from_prior"]);
	-
	- params->m_SharpenOdfs = false;
	- if (parsedArgs.count("sharpen_odfs"))
	- params->m_SharpenOdfs = us::any_cast<bool>(parsedArgs["sharpen_odfs"]);
	-
	- params->m_InterpolateTractographyData = true;
	- if (parsedArgs.count("no_data_interpolation"))
	- params->m_InterpolateTractographyData = !us::any_cast<bool>(parsedArgs["no_data_interpolation"]);
	-
	- params->m_InterpolateRoiImages = true;
	- if (parsedArgs.count("no_mask_interpolation"))
	- params->m_InterpolateRoiImages = !us::any_cast<bool>(parsedArgs["no_mask_interpolation"]);
	-
	- bool use_sh_features = false;
	- if (parsedArgs.count("use_sh_features"))
	- use_sh_features = us::any_cast<bool>(parsedArgs["use_sh_features"]);
	-
	- params->m_StopVotes = false;
	- if (parsedArgs.count("use_stop_votes"))
	- params->m_StopVotes = us::any_cast<bool>(parsedArgs["use_stop_votes"]);
	-
	- params->m_OnlyForwardSamples = false;
	- if (parsedArgs.count("use_only_forward_samples"))
	- params->m_OnlyForwardSamples = us::any_cast<bool>(parsedArgs["use_only_forward_samples"]);
	-
	- params->m_FlipX = false;
	- if (parsedArgs.count("flip_x"))
	- params->m_FlipX = us::any_cast<bool>(parsedArgs["flip_x"]);
	- params->m_FlipY = false;
	- if (parsedArgs.count("flip_y"))
	- params->m_FlipY = us::any_cast<bool>(parsedArgs["flip_y"]);
	- params->m_FlipZ = false;
	- if (parsedArgs.count("flip_z"))
	- params->m_FlipZ = us::any_cast<bool>(parsedArgs["flip_z"]);
	-
	- bool prior_flip_x = false;
	- if (parsedArgs.count("prior_flip_x"))
	- prior_flip_x = us::any_cast<bool>(parsedArgs["prior_flip_x"]);
	- bool prior_flip_y = false;
	- if (parsedArgs.count("prior_flip_y"))
	- prior_flip_y = us::any_cast<bool>(parsedArgs["prior_flip_y"]);
	- bool prior_flip_z = false;
	- if (parsedArgs.count("prior_flip_z"))
	- prior_flip_z = us::any_cast<bool>(parsedArgs["prior_flip_z"]);
	-
	- params->m_ApplyDirectionMatrix = false;
	- if (parsedArgs.count("apply_image_rotation"))
	- params->m_ApplyDirectionMatrix = us::any_cast<bool>(parsedArgs["apply_image_rotation"]);
	-
	- float compress = -1;
	- if (parsedArgs.count("compress"))
	- compress = us::any_cast<float>(parsedArgs["compress"]);
	-
	- params->m_MinTractLengthMm = 20;
	- if (parsedArgs.count("min_tract_length"))
	- params->m_MinTractLengthMm = us::any_cast<float>(parsedArgs["min_tract_length"]);
	-
	- params->SetLoopCheckDeg(-1);
	- if (parsedArgs.count("loop_check"))
	- params->SetLoopCheckDeg(us::any_cast<float>(parsedArgs["loop_check"]));
	-
	- std::string forestFile;
	- if (parsedArgs.count("forest"))
	- forestFile = us::any_cast<std::string>(parsedArgs["forest"]);
	-
	- std::string maskFile = "";
	- if (parsedArgs.count("tracking_mask"))
	- maskFile = us::any_cast<std::string>(parsedArgs["tracking_mask"]);
	-
	- std::string seedFile = "";
	- if (parsedArgs.count("seed_image"))
	- seedFile = us::any_cast<std::string>(parsedArgs["seed_image"]);
	-
	- std::string targetFile = "";
	- if (parsedArgs.count("target_image"))
	- targetFile = us::any_cast<std::string>(parsedArgs["target_image"]);
	-
	- std::string exclusionFile = "";
	- if (parsedArgs.count("exclusion_image"))
	- exclusionFile = us::any_cast<std::string>(parsedArgs["exclusion_image"]);
	-
	- std::string stopFile = "";
	- if (parsedArgs.count("stop_image"))
	- stopFile = us::any_cast<std::string>(parsedArgs["stop_image"]);
	-
	- std::string ep_constraint = "NONE";
	- if (parsedArgs.count("ep_constraint"))
	- ep_constraint = us::any_cast<std::string>(parsedArgs["ep_constraint"]);
	-
	- params->m_Cutoff = 0.1f;
	- if (parsedArgs.count("cutoff"))
	- params->m_Cutoff = us::any_cast<float>(parsedArgs["cutoff"]);
	-
	- params->m_OdfCutoff = 0.0;
	- if (parsedArgs.count("odf_cutoff"))
	- params->m_OdfCutoff = us::any_cast<float>(parsedArgs["odf_cutoff"]);
	-
	- params->m_PeakJitter = 0.01;
	- if (parsedArgs.count("peak_jitter"))
	- params->m_PeakJitter = us::any_cast<float>(parsedArgs["peak_jitter"]);
	-
	- params->SetStepSizeVox(-1);
	- if (parsedArgs.count("step_size"))
	- params->SetStepSizeVox(us::any_cast<float>(parsedArgs["step_size"]));
	-
	- params->SetSamplingDistanceVox(-1);
	- if (parsedArgs.count("sampling_distance"))
	- params->SetSamplingDistanceVox(us::any_cast<float>(parsedArgs["sampling_distance"]));
	-
	- params->m_NumSamples = 0;
	- if (parsedArgs.count("num_samples"))
	- params->m_NumSamples = static_cast<unsigned int>(us::any_cast<int>(parsedArgs["num_samples"]));
	-
	- params->m_SeedsPerVoxel = 1;
	- if (parsedArgs.count("seeds"))
	- params->m_SeedsPerVoxel = us::any_cast<int>(parsedArgs["seeds"]);
	-
	- params->m_TrialsPerSeed = 10;
	- if (parsedArgs.count("trials_per_seed"))
	- params->m_TrialsPerSeed = static_cast<unsigned int>(us::any_cast<int>(parsedArgs["trials_per_seed"]));
	-
	- params->m_F = 1;
	- if (parsedArgs.count("tend_f"))
	- params->m_F = us::any_cast<float>(parsedArgs["tend_f"]);
	-
	- params->m_G = 0;
	- if (parsedArgs.count("tend_g"))
	- params->m_G = us::any_cast<float>(parsedArgs["tend_g"]);
	-
	- params->SetAngularThresholdDeg(-1);
	- if (parsedArgs.count("angular_threshold"))
	- params->SetAngularThresholdDeg(us::any_cast<float>(parsedArgs["angular_threshold"]));
	-
	- params->m_MaxNumFibers = -1;
	- if (parsedArgs.count("max_tracts"))
	- params->m_MaxNumFibers = us::any_cast<int>(parsedArgs["max_tracts"]);
	-
	-
	- std::string ext = itksys::SystemTools::GetFilenameExtension(outFile);
	- if (ext != ".fib" && ext != ".trk")
	- {
	- MITK_INFO << "Output file format not supported. Use one of .fib, .trk, .nii, .nii.gz, .nrrd";
	- return EXIT_FAILURE;
	- }
	-
	- // LOAD DATASETS
	- mitkCommandLineParser::StringContainerType addFiles;
	- if (parsedArgs.count("additional_images"))
	- addFiles = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["additional_images"]);
	-
	- typedef itk::Image<float, 3> ItkFloatImgType;
	-
	- ItkFloatImgType::Pointer mask = nullptr;
	- if (!maskFile.empty())
	- {
	- MITK_INFO << "loading mask image";
	- mitk::Image::Pointer img = mitk::IOUtil::Load<mitk::Image>(maskFile);
	- mask = ItkFloatImgType::New();
	- mitk::CastToItkImage(img, mask);
	- }
	-
	- ItkFloatImgType::Pointer seed = nullptr;
	- if (!seedFile.empty())
	- {
	- MITK_INFO << "loading seed ROI image";
	- mitk::Image::Pointer img = mitk::IOUtil::Load<mitk::Image>(seedFile);
	- seed = ItkFloatImgType::New();
	- mitk::CastToItkImage(img, seed);
	- }
	-
	- ItkFloatImgType::Pointer stop = nullptr;
	- if (!stopFile.empty())
	- {
	- MITK_INFO << "loading stop ROI image";
	- mitk::Image::Pointer img = mitk::IOUtil::Load<mitk::Image>(stopFile);
	- stop = ItkFloatImgType::New();
	- mitk::CastToItkImage(img, stop);
	- }
	-
	- ItkFloatImgType::Pointer target = nullptr;
	- if (!targetFile.empty())
	- {
	- MITK_INFO << "loading target ROI image";
	- mitk::Image::Pointer img = mitk::IOUtil::Load<mitk::Image>(targetFile);
	- target = ItkFloatImgType::New();
	- mitk::CastToItkImage(img, target);
	- }
	-
	- ItkFloatImgType::Pointer exclusion = nullptr;
	- if (!exclusionFile.empty())
	- {
	- MITK_INFO << "loading exclusion ROI image";
	- mitk::Image::Pointer img = mitk::IOUtil::Load<mitk::Image>(exclusionFile);
	- exclusion = ItkFloatImgType::New();
	- mitk::CastToItkImage(img, exclusion);
	- }
	-
	- MITK_INFO << "loading additional images";
	- std::vector< std::vector< ItkFloatImgType::Pointer > > addImages;
	- addImages.push_back(std::vector< ItkFloatImgType::Pointer >());
	- for (auto file : addFiles)
	- {
	- mitk::Image::Pointer img = mitk::IOUtil::Load<mitk::Image>(file);
	- ItkFloatImgType::Pointer itkimg = ItkFloatImgType::New();
	- mitk::CastToItkImage(img, itkimg);
	- addImages.at(0).push_back(itkimg);
	- }
	-
	- // //////////////////////////////////////////////////////////////////
	- // omp_set_num_threads(1);
	-
	- typedef itk::StreamlineTrackingFilter TrackerType;
	- TrackerType::Pointer tracker = TrackerType::New();
	-
	- if (!prior_image.empty())
	- {
	- mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Peak Image"}, {});
	- mitk::PeakImage::Pointer priorImage = mitk::IOUtil::Load<mitk::PeakImage>(prior_image, &functor);
	-
	- if (priorImage.IsNull())
	- {
	- MITK_INFO << "Only peak images are supported as prior at the moment!";
	- return EXIT_FAILURE;
	- }
	-
	- mitk::TrackingDataHandler* priorhandler = new mitk::TrackingHandlerPeaks();
	-
	- typedef mitk::ImageToItk< mitk::TrackingHandlerPeaks::PeakImgType > CasterType;
	- CasterType::Pointer caster = CasterType::New();
	- caster->SetInput(priorImage);
	- caster->Update();
	- mitk::TrackingHandlerPeaks::PeakImgType::Pointer itkImg = caster->GetOutput();
	-
	- std::shared_ptr< mitk::StreamlineTractographyParameters > prior_params = std::make_shared< mitk::StreamlineTractographyParameters >(*params);
	- prior_params->m_FlipX = prior_flip_x;
	- prior_params->m_FlipY = prior_flip_y;
	- prior_params->m_FlipZ = prior_flip_z;
	- prior_params->m_Cutoff = 0.0;
	- dynamic_cast<mitk::TrackingHandlerPeaks*>(priorhandler)->SetPeakImage(itkImg);
	- priorhandler->SetParameters(prior_params);
	- tracker->SetTrackingPriorHandler(priorhandler);
	- }
	-
	- mitk::TrackingDataHandler* handler;
	- if (type == "RF")
	- {
	- mitk::TractographyForest::Pointer forest = mitk::IOUtil::Load<mitk::TractographyForest>(forestFile);
	- if (forest.IsNull())
	- mitkThrow() << "Forest file " << forestFile << " could not be read.";
	-
	- mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Diffusion Weighted Images"}, {});
	- auto input = mitk::IOUtil::Load<mitk::Image>(input_files.at(0), &functor);
	-
	- if (use_sh_features)
	- {
	- handler = new mitk::TrackingHandlerRandomForest<6,28>();
	- dynamic_cast<mitk::TrackingHandlerRandomForest<6,28>*>(handler)->SetForest(forest);
	- dynamic_cast<mitk::TrackingHandlerRandomForest<6,28>*>(handler)->AddDwi(input);
	- dynamic_cast<mitk::TrackingHandlerRandomForest<6,28>*>(handler)->SetAdditionalFeatureImages(addImages);
	- }
	- else
	- {
	- handler = new mitk::TrackingHandlerRandomForest<6,100>();
	- dynamic_cast<mitk::TrackingHandlerRandomForest<6,100>*>(handler)->SetForest(forest);
	- dynamic_cast<mitk::TrackingHandlerRandomForest<6,100>*>(handler)->AddDwi(input);
	- dynamic_cast<mitk::TrackingHandlerRandomForest<6,100>*>(handler)->SetAdditionalFeatureImages(addImages);
	- }
	- }
	- else if (type == "Peaks")
	- {
	- handler = new mitk::TrackingHandlerPeaks();
	-
	- MITK_INFO << "loading input peak image";
	- mitk::Image::Pointer mitkImage = mitk::IOUtil::Load<mitk::Image>(input_files.at(0));
	- mitk::TrackingHandlerPeaks::PeakImgType::Pointer itkImg = mitk::convert::GetItkPeakFromPeakImage(mitkImage);
	- dynamic_cast<mitk::TrackingHandlerPeaks*>(handler)->SetPeakImage(itkImg);
	- }
	- else if (type == "Tensor" && params->m_Mode == mitk::StreamlineTractographyParameters::MODE::DETERMINISTIC)
	- {
	- handler = new mitk::TrackingHandlerTensor();
	-
	- MITK_INFO << "loading input tensor images";
	- std::vector< mitk::Image::Pointer > input_images;
	- for (unsigned int i=0; i<input_files.size(); i++)
	- {
	- mitk::Image::Pointer mitkImage = mitk::IOUtil::Load<mitk::Image>(input_files.at(i));
	- mitk::TensorImage::ItkTensorImageType::Pointer itkImg = mitk::convert::GetItkTensorFromTensorImage(mitkImage);
	- dynamic_cast<mitk::TrackingHandlerTensor*>(handler)->AddTensorImage(itkImg.GetPointer());
	- }
	-
	- if (addImages.at(0).size()>0)
	- dynamic_cast<mitk::TrackingHandlerTensor*>(handler)->SetFaImage(addImages.at(0).at(0));
	- }
	- else if (type == "ODF" \|\| (type == "Tensor" && params->m_Mode == mitk::StreamlineTractographyParameters::MODE::PROBABILISTIC))
	- {
	- handler = new mitk::TrackingHandlerOdf();
	-
	- mitk::OdfImage::ItkOdfImageType::Pointer itkImg = nullptr;
	-
	- if (type == "Tensor")
	- {
	- MITK_INFO << "Converting Tensor to ODF image";
	- auto input = mitk::IOUtil::Load<mitk::Image>(input_files.at(0));
	- itkImg = mitk::convert::GetItkOdfFromTensorImage(input);
	- dynamic_cast<mitk::TrackingHandlerOdf*>(handler)->SetIsOdfFromTensor(true);
	- }
	- else
	- {
	- mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"SH Image", "ODF Image"}, {});
	- auto input = mitk::IOUtil::Load(input_files.at(0), &functor)[0];
	- if (dynamic_cast<mitk::ShImage*>(input.GetPointer()))
	- {
	- MITK_INFO << "Converting SH to ODF image";
	- mitk::Image::Pointer mitkImg = dynamic_cast<mitk::Image*>(input.GetPointer());
	- itkImg = mitk::convert::GetItkOdfFromShImage(mitkImg);
	- }
	- else if (dynamic_cast<mitk::OdfImage*>(input.GetPointer()))
	- {
	- mitk::Image::Pointer mitkImg = dynamic_cast<mitk::Image*>(input.GetPointer());
	- itkImg = mitk::convert::GetItkOdfFromOdfImage(mitkImg);
	- }
	- else
	- mitkThrow() << "";
	- }
	-
	- dynamic_cast<mitk::TrackingHandlerOdf*>(handler)->SetOdfImage(itkImg);
	-
	- if (addImages.at(0).size()>0)
	- dynamic_cast<mitk::TrackingHandlerOdf*>(handler)->SetGfaImage(addImages.at(0).at(0));
	- }
	- else
	- {
	- MITK_INFO << "Unknown tractography algorithm (" + type+"). Known types are Peaks, DetTensor, ProbTensor, DetODF, ProbODF, DetRF, ProbRF.";
	- return EXIT_FAILURE;
	- }
	-
	- if (ep_constraint=="NONE")
	- params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::NONE;
	- else if (ep_constraint=="EPS_IN_TARGET")
	- params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_TARGET;
	- else if (ep_constraint=="EPS_IN_TARGET_LABELDIFF")
	- params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_TARGET_LABELDIFF;
	- else if (ep_constraint=="EPS_IN_SEED_AND_TARGET")
	- params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_SEED_AND_TARGET;
	- else if (ep_constraint=="MIN_ONE_EP_IN_TARGET")
	- params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::MIN_ONE_EP_IN_TARGET;
	- else if (ep_constraint=="ONE_EP_IN_TARGET")
	- params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::ONE_EP_IN_TARGET;
	- else if (ep_constraint=="NO_EP_IN_TARGET")
	- params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::NO_EP_IN_TARGET;
	-
	- MITK_INFO << "Tractography algorithm: " << type;
	- tracker->SetMaskImage(mask);
	- tracker->SetSeedImage(seed);
	- tracker->SetStoppingRegions(stop);
	- tracker->SetTargetRegions(target);
	- tracker->SetExclusionRegions(exclusion);
	- tracker->SetTrackingHandler(handler);
	- if (ext != ".fib" && ext != ".trk")
	- params->m_OutputProbMap = true;
	- tracker->SetParameters(params);
	- tracker->Update();
	-
	- if (ext == ".fib" \|\| ext == ".trk")
	- {
	- vtkSmartPointer< vtkPolyData > poly = tracker->GetFiberPolyData();
	- mitk::FiberBundle::Pointer outFib = mitk::FiberBundle::New(poly);
	- if (compress > 0)
	- outFib->Compress(compress);
	- mitk::IOUtil::Save(outFib, outFile);
	- }
	- else
	- {
	- TrackerType::ItkDoubleImgType::Pointer outImg = tracker->GetOutputProbabilityMap();
	- mitk::Image::Pointer img = mitk::Image::New();
	- img->InitializeByItk(outImg.GetPointer());
	- img->SetVolume(outImg->GetBufferPointer());
	-
	- if (ext != ".nii" && ext != ".nii.gz" && ext != ".nrrd")
	- outFile += ".nii.gz";
	-
	- mitk::IOUtil::Save(img, outFile);
	- }
	-
	- delete handler;
	-
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/AnchorConstrainedPlausibility.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/AnchorConstrainedPlausibility.cpp
	deleted file mode 100755
	index e8fa990b7e..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/AnchorConstrainedPlausibility.cpp
	+++ /dev/null
	@@ -1,447 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkBaseData.h>
	-#include <mitkImageCast.h>
	-#include <mitkImageToItk.h>
	-#include <metaCommand.h>
	-#include <mitkCommandLineParser.h>
	-#include <usAny.h>
	-#include <mitkIOUtil.h>
	-#include <itksys/SystemTools.hxx>
	-#include <itkDirectory.h>
	-#include <mitkFiberBundle.h>
	-#include <mitkPreferenceListReaderOptionsFunctor.h>
	-#include <itkImageFileWriter.h>
	-#include <mitkPeakImage.h>
	-#include <itkFitFibersToImageFilter.h>
	-#include <mitkLexicalCast.h>
	-#include <itkTractDensityImageFilter.h>
	-#include <itkFlipPeaksFilter.h>
	-#include <mitkDiffusionDataIOHelper.h>
	-
	-typedef itk::Point<float, 4> PointType4;
	-typedef mitk::PeakImage::ItkPeakImageType PeakImgType;
	-typedef itk::Image< unsigned char, 3 > ItkUcharImageType;
	-
	-/*!
	-\brief Score input candidate tracts using ACP analysis
	-*/
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Anchor Constrained Plausibility");
	- parser.setCategory("Fiber Tracking Evaluation");
	- parser.setDescription("Score input candidate tracts using ACP analysis");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "a", mitkCommandLineParser::String, "Anchor tractogram:", "anchor tracts in one tractogram file", us::Any(), true, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "p", mitkCommandLineParser::String, "Input peaks:", "input peak image", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "c", mitkCommandLineParser::StringList, "Candidates:", "Folder(s) or file list of candidate tracts", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output folder:", "output folder", us::Any(), false, false, false, mitkCommandLineParser::Output);
	-
	- parser.addArgument("reference_mask_folders", "", mitkCommandLineParser::StringList, "Reference Mask Folder(s):", "Folder(s) or file list containing reference tract masks for accuracy evaluation", true, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("reference_peaks_folders", "", mitkCommandLineParser::StringList, "Reference Peaks Folder(s):", "Folder(s) or file list containing reference peak images for accuracy evaluation", true, false, false, mitkCommandLineParser::Input);
	-
	- parser.addArgument("mask", "", mitkCommandLineParser::String, "Mask image:", "scoring is only performed inside the mask image", us::Any(), true, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("greedy_add", "", mitkCommandLineParser::Bool, "Greedy:", "if enabled, the candidate tracts are not jointly fitted to the residual image but one after the other employing a greedy scheme", false);
	- parser.addArgument("lambda", "", mitkCommandLineParser::Float, "Lambda:", "modifier for regularization", 0.1);
	- parser.addArgument("filter_outliers", "", mitkCommandLineParser::Bool, "Filter outliers:", "perform second optimization run with an upper weight bound based on the first weight estimation (99% quantile)", false);
	- parser.addArgument("regu", "", mitkCommandLineParser::String, "Regularization:", "MSM; Variance; VoxelVariance; Lasso; GroupLasso; GroupVariance; NONE", std::string("NONE"));
	- parser.addArgument("use_num_streamlines", "", mitkCommandLineParser::Bool, "Use number of streamlines as score:", "Don't fit candidates, simply use number of streamlines per candidate as score", false);
	- parser.addArgument("use_weights", "", mitkCommandLineParser::Bool, "Use input weights as score:", "Don't fit candidates, simply use first input streamline weight per candidate as score", false);
	- parser.addArgument("filter_zero_weights", "", mitkCommandLineParser::Bool, "Filter zero-weights", "Remove streamlines with weight 0 from candidates", false);
	- parser.addArgument("flipx", "", mitkCommandLineParser::Bool, "Flip x", "flip along x-axis", false);
	- parser.addArgument("flipy", "", mitkCommandLineParser::Bool, "Flip y", "flip along y-axis", false);
	- parser.addArgument("flipz", "", mitkCommandLineParser::Bool, "Flip z", "flip along z-axis", false);
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- std::string peak_file_name = us::any_cast<std::string>(parsedArgs["p"]);
	- std::string out_folder = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- mitkCommandLineParser::StringContainerType candidate_tract_folders = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["c"]);
	-
	- if (!out_folder.empty() && out_folder.back() != '/')
	- out_folder += "/";
	-
	- bool greedy_add = false;
	- if (parsedArgs.count("greedy_add"))
	- greedy_add = us::any_cast<bool>(parsedArgs["greedy_add"]);
	-
	- float lambda = 0.1f;
	- if (parsedArgs.count("lambda"))
	- lambda = us::any_cast<float>(parsedArgs["lambda"]);
	-
	- bool filter_outliers = false;
	- if (parsedArgs.count("filter_outliers"))
	- filter_outliers = us::any_cast<bool>(parsedArgs["filter_outliers"]);
	-
	- bool filter_zero_weights = false;
	- if (parsedArgs.count("filter_zero_weights"))
	- filter_zero_weights = us::any_cast<bool>(parsedArgs["filter_zero_weights"]);
	-
	- std::string mask_file = "";
	- if (parsedArgs.count("mask"))
	- mask_file = us::any_cast<std::string>(parsedArgs["mask"]);
	-
	- mitkCommandLineParser::StringContainerType reference_mask_files_folders;
	- if (parsedArgs.count("reference_mask_folders"))
	- reference_mask_files_folders = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["reference_mask_folders"]);
	-
	- mitkCommandLineParser::StringContainerType reference_peaks_files_folders;
	- if (parsedArgs.count("reference_peaks_folders"))
	- reference_peaks_files_folders = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["reference_peaks_folders"]);
	-
	- std::string regu = "NONE";
	- if (parsedArgs.count("regu"))
	- regu = us::any_cast<std::string>(parsedArgs["regu"]);
	-
	- bool use_weights = false;
	- if (parsedArgs.count("use_weights"))
	- use_weights = us::any_cast<bool>(parsedArgs["use_weights"]);
	-
	- bool use_num_streamlines = false;
	- if (parsedArgs.count("use_num_streamlines"))
	- use_num_streamlines = us::any_cast<bool>(parsedArgs["use_num_streamlines"]);
	-
	-
	- bool flipx = false;
	- if (parsedArgs.count("flipx"))
	- flipx = us::any_cast<bool>(parsedArgs["flipx"]);
	-
	- bool flipy = false;
	- if (parsedArgs.count("flipy"))
	- flipy = us::any_cast<bool>(parsedArgs["flipy"]);
	-
	- bool flipz = false;
	- if (parsedArgs.count("flipz"))
	- flipz = us::any_cast<bool>(parsedArgs["flipz"]);
	-
	- try
	- {
	- itk::TimeProbe clock;
	- clock.Start();
	-
	- if (!ist::PathExists(out_folder))
	- {
	- MITK_INFO << "Creating output directory";
	- ist::MakeDirectory(out_folder);
	- }
	-
	- MITK_INFO << "Loading data";
	-
	- // Load mask file. Fit is only performed inside the mask
	- MITK_INFO << "Loading mask image";
	- auto mask = mitk::DiffusionDataIOHelper::load_itk_image<itk::FitFibersToImageFilter::UcharImgType>(mask_file);
	-
	- // Load masks covering the true positives for evaluation purposes
	- MITK_INFO << "Loading reference peaks and masks";
	- std::vector< std::string > anchor_mask_files;
	- auto reference_masks = mitk::DiffusionDataIOHelper::load_itk_images<itk::FitFibersToImageFilter::UcharImgType>(reference_mask_files_folders, &anchor_mask_files);
	- auto reference_peaks = mitk::DiffusionDataIOHelper::load_itk_images<PeakImgType>(reference_peaks_files_folders);
	-
	- // Load peak image
	- MITK_INFO << "Loading peak image";
	- auto peak_image = mitk::DiffusionDataIOHelper::load_itk_image<PeakImgType>(peak_file_name);
	-
	- // Load all candidate tracts
	- MITK_INFO << "Loading candidate tracts";
	- std::vector< std::string > candidate_tract_files;
	- auto input_candidates = mitk::DiffusionDataIOHelper::load_fibs(candidate_tract_folders, &candidate_tract_files);
	-
	- if (flipx \|\| flipy \|\| flipz)
	- {
	- itk::FlipPeaksFilter< float >::Pointer flipper = itk::FlipPeaksFilter< float >::New();
	- flipper->SetInput(peak_image);
	- flipper->SetFlipX(flipx);
	- flipper->SetFlipY(flipy);
	- flipper->SetFlipZ(flipz);
	- flipper->Update();
	- peak_image = flipper->GetOutput();
	- }
	-
	- mitk::LocaleSwitch localeSwitch("C");
	- itk::ImageFileWriter< PeakImgType >::Pointer peak_image_writer = itk::ImageFileWriter< PeakImgType >::New();
	- ofstream logfile;
	- logfile.open (out_folder + "scores.txt");
	- double rmse = 0.0;
	- int iteration = 0;
	- std::string name = "NOANCHOR";
	-
	- if (parsedArgs.count("a"))
	- {
	- // Load reference tractogram consisting of all known tracts
	- std::string anchors_file = us::any_cast<std::string>(parsedArgs["a"]);
	- mitk::FiberBundle::Pointer anchor_tractogram = mitk::IOUtil::Load<mitk::FiberBundle>(anchors_file);
	- if ( !(anchor_tractogram.IsNull() \|\| anchor_tractogram->GetNumFibers()==0) )
	- {
	- // Fit known tracts to peak image to obtain underexplained image
	- MITK_INFO << "Fit anchor tracts";
	- itk::FitFibersToImageFilter::Pointer fitter = itk::FitFibersToImageFilter::New();
	- fitter->SetTractograms({anchor_tractogram});
	- fitter->SetLambda(static_cast<double>(lambda));
	- fitter->SetFilterOutliers(filter_outliers);
	- fitter->SetPeakImage(peak_image);
	- fitter->SetVerbose(true);
	- fitter->SetMaskImage(mask);
	- fitter->SetRegularization(VnlCostFunction::REGU::NONE);
	-
	- fitter->Update();
	- rmse = fitter->GetRMSE();
	- vnl_vector<double> rms_diff = fitter->GetRmsDiffPerBundle();
	-
	- name = ist::GetFilenameWithoutExtension(anchors_file);
	- mitk::FiberBundle::Pointer anchor_tracts = fitter->GetTractograms().at(0);
	- anchor_tracts->SetFiberColors(255,255,255);
	- mitk::IOUtil::Save(anchor_tracts, out_folder + boost::lexical_cast<std::string>(static_cast<int>(100000*rms_diff[0])) + "_" + name + ".fib");
	-
	- logfile << name << " " << setprecision(5) << rms_diff[0] << "\n";
	-
	- peak_image = fitter->GetUnderexplainedImage();
	- peak_image_writer->SetInput(peak_image);
	- peak_image_writer->SetFileName(out_folder + "Residual_" + name + ".nii.gz");
	- peak_image_writer->Update();
	- }
	- }
	-
	- if (use_weights \|\| use_num_streamlines)
	- {
	- MITK_INFO << "Using tract weights as scores";
	- unsigned int c = 0;
	- for (auto fib : input_candidates)
	- {
	- int mod = 1;
	- float score = 0;
	- if (use_weights)
	- {
	- score = fib->GetFiberWeight(0);
	- mod = 100000;
	- }
	- else if (use_num_streamlines)
	- score = fib->GetNumFibers();
	- fib->ColorFibersByOrientation();
	-
	- std::string bundle_name = ist::GetFilenameWithoutExtension(candidate_tract_files.at(c));
	-
	- std::streambuf *old = cout.rdbuf(); // <-- save
	- std::stringstream ss;
	- std::cout.rdbuf (ss.rdbuf()); // <-- redirect
	- mitk::IOUtil::Save(fib, out_folder + boost::lexical_cast<std::string>(static_cast<int>(mod*score)) + "_" + bundle_name + ".fib");
	-
	- unsigned int num_voxels = 0;
	- {
	- itk::TractDensityImageFilter< ItkUcharImageType >::Pointer masks_filter = itk::TractDensityImageFilter< ItkUcharImageType >::New();
	- masks_filter->SetInputImage(mask);
	- masks_filter->SetBinaryOutput(true);
	- masks_filter->SetFiberBundle(fib);
	- masks_filter->SetUseImageGeometry(true);
	- masks_filter->Update();
	- num_voxels = masks_filter->GetNumCoveredVoxels();
	- }
	-
	- float weight_sum = 0;
	- for (unsigned int i=0; i<fib->GetNumFibers(); i++)
	- weight_sum += fib->GetFiberWeight(i);
	-
	- std::cout.rdbuf (old); // <-- restore
	-
	- logfile << bundle_name << " " << setprecision(5) << score << " " << num_voxels << " " << fib->GetNumFibers() << " " << weight_sum << "\n";
	- ++c;
	- }
	- }
	- else if (!greedy_add)
	- {
	- MITK_INFO << "Fit candidate tracts";
	- itk::FitFibersToImageFilter::Pointer fitter = itk::FitFibersToImageFilter::New();
	- fitter->SetLambda(static_cast<double>(lambda));
	- fitter->SetFilterOutliers(filter_outliers);
	- fitter->SetVerbose(true);
	- fitter->SetPeakImage(peak_image);
	- fitter->SetMaskImage(mask);
	- fitter->SetTractograms(input_candidates);
	- fitter->SetFitIndividualFibers(true);
	-
	- if (regu=="MSM")
	- fitter->SetRegularization(VnlCostFunction::REGU::MSM);
	- else if (regu=="Variance")
	- fitter->SetRegularization(VnlCostFunction::REGU::VARIANCE);
	- else if (regu=="Lasso")
	- fitter->SetRegularization(VnlCostFunction::REGU::LASSO);
	- else if (regu=="VoxelVariance")
	- fitter->SetRegularization(VnlCostFunction::REGU::VOXEL_VARIANCE);
	- else if (regu=="GroupLasso")
	- fitter->SetRegularization(VnlCostFunction::REGU::GROUP_LASSO);
	- else if (regu=="GroupVariance")
	- fitter->SetRegularization(VnlCostFunction::REGU::GROUP_VARIANCE);
	- else if (regu=="NONE")
	- fitter->SetRegularization(VnlCostFunction::REGU::NONE);
	-
	- fitter->Update();
	- vnl_vector<double> rms_diff = fitter->GetRmsDiffPerBundle();
	-
	- unsigned int c = 0;
	- for (auto fib : input_candidates)
	- {
	- std::string bundle_name = ist::GetFilenameWithoutExtension(candidate_tract_files.at(c));
	-
	- std::streambuf *old = cout.rdbuf(); // <-- save
	- std::stringstream ss;
	- std::cout.rdbuf (ss.rdbuf()); // <-- redirect
	- if (filter_zero_weights)
	- fib = fib->FilterByWeights(0);
	- mitk::IOUtil::Save(fib, out_folder + boost::lexical_cast<std::string>((int)(100000*rms_diff[c])) + "_" + bundle_name + ".fib");
	-
	- unsigned int num_voxels = 0;
	- {
	- itk::TractDensityImageFilter< ItkUcharImageType >::Pointer masks_filter = itk::TractDensityImageFilter< ItkUcharImageType >::New();
	- masks_filter->SetInputImage(mask);
	- masks_filter->SetBinaryOutput(true);
	- masks_filter->SetFiberBundle(fib);
	- masks_filter->SetUseImageGeometry(true);
	- masks_filter->Update();
	- num_voxels = masks_filter->GetNumCoveredVoxels();
	- }
	-
	- float weight_sum = 0;
	- for (unsigned int i=0; i<fib->GetNumFibers(); i++)
	- weight_sum += fib->GetFiberWeight(i);
	-
	- std::cout.rdbuf (old); // <-- restore
	-
	- logfile << bundle_name << " " << setprecision(5) << rms_diff[c] << " " << num_voxels << " " << fib->GetNumFibers() << " " << weight_sum << "\n";
	- ++c;
	- }
	-
	- mitk::FiberBundle::Pointer out_fib = mitk::FiberBundle::New();
	- out_fib = out_fib->AddBundles(input_candidates);
	- out_fib->ColorFibersByFiberWeights(false, true);
	- mitk::IOUtil::Save(out_fib, out_folder + "AllCandidates.fib");
	-
	- peak_image = fitter->GetUnderexplainedImage();
	- peak_image_writer->SetInput(peak_image);
	- peak_image_writer->SetFileName(out_folder + "Residual_AllCandidates.nii.gz");
	- peak_image_writer->Update();
	- }
	- else
	- {
	- MITK_INFO << "RMSE: " << setprecision(5) << rmse;
	- // fitter->SetPeakImage(peak_image);
	-
	- // Iteratively add candidate bundles in a greedy manner
	- while (!input_candidates.empty())
	- {
	- double next_rmse = rmse;
	- mitk::FiberBundle::Pointer best_candidate = nullptr;
	- PeakImgType::Pointer best_candidate_peak_image = nullptr;
	-
	- for (unsigned int i=0; i<input_candidates.size(); ++i)
	- {
	- // WHY NECESSARY AGAIN??
	- itk::FitFibersToImageFilter::Pointer fitter = itk::FitFibersToImageFilter::New();
	- fitter->SetLambda(static_cast<double>(lambda));
	- fitter->SetFilterOutliers(filter_outliers);
	- fitter->SetVerbose(false);
	- fitter->SetPeakImage(peak_image);
	- fitter->SetMaskImage(mask);
	- // ******************************
	- fitter->SetTractograms({input_candidates.at(i)});
	-
	- std::streambuf *old = cout.rdbuf(); // <-- save
	- std::stringstream ss;
	- std::cout.rdbuf (ss.rdbuf()); // <-- redirect
	- fitter->Update();
	- std::cout.rdbuf (old); // <-- restore
	-
	- double candidate_rmse = fitter->GetRMSE();
	-
	- if (candidate_rmse<next_rmse)
	- {
	- next_rmse = candidate_rmse;
	- best_candidate = fitter->GetTractograms().at(0);
	- best_candidate_peak_image = fitter->GetUnderexplainedImage();
	- }
	- }
	-
	- if (best_candidate.IsNull())
	- break;
	-
	- // fitter->SetPeakImage(peak_image);
	- peak_image = best_candidate_peak_image;
	-
	- unsigned int i=0;
	- std::vector< mitk::FiberBundle::Pointer > remaining_candidates;
	- std::vector< std::string > remaining_candidate_files;
	- for (auto fib : input_candidates)
	- {
	- if (fib!=best_candidate)
	- {
	- remaining_candidates.push_back(fib);
	- remaining_candidate_files.push_back(candidate_tract_files.at(i));
	- }
	- else
	- name = ist::GetFilenameWithoutExtension(candidate_tract_files.at(i));
	- ++i;
	- }
	- input_candidates = remaining_candidates;
	- candidate_tract_files = remaining_candidate_files;
	-
	- iteration++;
	- std::streambuf *old = cout.rdbuf(); // <-- save
	- std::stringstream ss;
	- std::cout.rdbuf (ss.rdbuf()); // <-- redirect
	- // Save winning candidate
	- if (filter_zero_weights)
	- best_candidate = best_candidate->FilterByWeights(0);
	- mitk::IOUtil::Save(best_candidate, out_folder + boost::lexical_cast<std::string>(iteration) + "_" + name + ".fib");
	- peak_image_writer->SetInput(peak_image);
	- peak_image_writer->SetFileName(out_folder + boost::lexical_cast<std::string>(iteration) + "_" + name + ".nrrd");
	- peak_image_writer->Update();
	-
	- std::cout.rdbuf (old); // <-- restore
	-
	-// logfile << name << " " << setprecision(5) << score << " " << num_voxels << " " << fib->GetNumFibers() << " " << weight_sum << "\n";
	- }
	- }
	-
	- clock.Stop();
	- int h = static_cast<int>(clock.GetTotal()/3600);
	- int m = (static_cast<int>(clock.GetTotal())%3600)/60;
	- int s = static_cast<int>(clock.GetTotal())%60;
	- MITK_INFO << "Plausibility estimation took " << h << "h, " << m << "m and " << s << "s";
	- logfile.close();
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/CMakeLists.txt b/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/CMakeLists.txt
	deleted file mode 100755
	index 4328bcc7be..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/CMakeLists.txt
	+++ /dev/null
	@@ -1,46 +0,0 @@
	-option(BUILD_DiffusionTractographyEvaluationCmdApps "Build commandline tools for diffusion fiber tractography evaluation" OFF)
	-
	-if(BUILD_DiffusionTractographyEvaluationCmdApps OR MITK_BUILD_ALL_APPS)
	-
	- # needed include directories
	- include_directories(
	- ${CMAKE_CURRENT_SOURCE_DIR}
	- ${CMAKE_CURRENT_BINARY_DIR}
	- )
	-
	- # list of diffusion cmdapps
	- # if an app requires additional dependencies
	- # they are added after a "^^" and separated by "_"
	- set( diffusionTractographyEvaluationcmdapps
	- PeaksAngularError^^
	- MergeOverlappingTracts^^
	- GetOverlappingTracts^^
	- ExtractSimilarTracts^^
	- AnchorConstrainedPlausibility^^
	- CalculateOverlap^^
	- CheckEpsAndOverlap^^
	- ReferenceSimilarity^^
	- TractDistance^^
	- )
	-
	- foreach(diffusionTractographyEvaluationcmdapp ${diffusionTractographyEvaluationcmdapps})
	- # extract cmd app name and dependencies
	- string(REPLACE "^^" "\\;" cmdapp_info ${diffusionTractographyEvaluationcmdapp})
	- set(cmdapp_info_list ${cmdapp_info})
	- list(GET cmdapp_info_list 0 appname)
	- list(GET cmdapp_info_list 1 raw_dependencies)
	- string(REPLACE "_" "\\;" dependencies "${raw_dependencies}")
	- set(dependencies_list ${dependencies})
	-
	- mitkFunctionCreateCommandLineApp(
	- NAME ${appname}
	- DEPENDS MitkDiffusionCmdApps ${dependencies_list}
	- PACKAGE_DEPENDS
	- )
	- endforeach()
	-
	- if(EXECUTABLE_IS_ENABLED)
	- MITK_INSTALL_TARGETS(EXECUTABLES ${EXECUTABLE_TARGET})
	- endif()
	-
	- endif()
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/CalculateOverlap.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/CalculateOverlap.cpp
	deleted file mode 100755
	index 1c223ebadd..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/CalculateOverlap.cpp
	+++ /dev/null
	@@ -1,108 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkBaseData.h>
	-#include <mitkImageCast.h>
	-#include <mitkImageToItk.h>
	-#include <metaCommand.h>
	-#include <mitkCommandLineParser.h>
	-#include <usAny.h>
	-#include <mitkIOUtil.h>
	-#include <mitkLexicalCast.h>
	-#include <itksys/SystemTools.hxx>
	-#include <itkDirectory.h>
	-#include <mitkFiberBundle.h>
	-#include <vtkTransformPolyDataFilter.h>
	-#include <fstream>
	-#include <chrono>
	-#include <boost/progress.hpp>
	-#include <itkTractsToFiberEndingsImageFilter.h>
	-#include <itkTractDensityImageFilter.h>
	-#include <itkImageRegionConstIterator.h>
	-
	-typedef itksys::SystemTools ist;
	-typedef itk::Image<unsigned char, 3> ItkFloatImgType;
	-typedef itk::Image<unsigned int, 3> ItkUIntImgType;
	-
	-/*!
	-\brief
	-*/
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Calculate Overlap");
	- parser.setCategory("Fiber Tracking Evaluation");
	- parser.setDescription("");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("tractogram", "", mitkCommandLineParser::String, "", "", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("mask", "", mitkCommandLineParser::String, "", "", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("peaks", "", mitkCommandLineParser::String, "", "", us::Any(), true, false, false, mitkCommandLineParser::Input);
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- std::string input_tractogram = us::any_cast<std::string>(parsedArgs["tractogram"]);
	- std::string mask_file = us::any_cast<std::string>(parsedArgs["mask"]);
	-
	- try
	- {
	- mitk::FiberBundle::Pointer fib = mitk::IOUtil::Load<mitk::FiberBundle>(input_tractogram);
	- mitk::Image::Pointer mask = mitk::IOUtil::Load<mitk::Image>(mask_file);
	-
	- ItkFloatImgType::Pointer itk_mask;
	- mitk::CastToItkImage(mask, itk_mask);
	-
	- mitk::PeakImage::ItkPeakImageType::Pointer peaks = nullptr;
	- if (parsedArgs.count("peaks"))
	- {
	- mitk::Image::Pointer mitk_peaks = mitk::IOUtil::Load<mitk::Image>(us::any_cast<std::string>(parsedArgs["peaks"]));
	-
	- typedef mitk::ImageToItk< mitk::PeakImage::ItkPeakImageType > CasterType;
	- CasterType::Pointer caster = CasterType::New();
	- caster->SetInput(mitk_peaks);
	- caster->Update();
	- peaks = caster->GetOutput();
	-
	- float overlap = 0;
	- float directional_overlap = 0;
	- std::tie(directional_overlap, overlap) = fib->GetDirectionalOverlap(itk_mask, peaks);
	- MITK_INFO << "Overlap<<" << overlap;
	- MITK_INFO << "DirectionalOverlap<<" << directional_overlap;
	- }
	- else
	- MITK_INFO << "Overlap<<" << fib->GetOverlap(itk_mask);
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/CheckEpsAndOverlap.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/CheckEpsAndOverlap.cpp
	deleted file mode 100755
	index 8f0bb5d803..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/CheckEpsAndOverlap.cpp
	+++ /dev/null
	@@ -1,98 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkBaseData.h>
	-#include <mitkImageCast.h>
	-#include <mitkImageToItk.h>
	-#include <metaCommand.h>
	-#include <mitkCommandLineParser.h>
	-#include <usAny.h>
	-#include <mitkIOUtil.h>
	-#include <mitkLexicalCast.h>
	-#include <itksys/SystemTools.hxx>
	-#include <itkDirectory.h>
	-#include <mitkFiberBundle.h>
	-#include <vtkTransformPolyDataFilter.h>
	-#include <fstream>
	-#include <chrono>
	-#include <boost/progress.hpp>
	-#include <itkTractsToFiberEndingsImageFilter.h>
	-#include <itkTractDensityImageFilter.h>
	-#include <itkImageRegionConstIterator.h>
	-
	-typedef itksys::SystemTools ist;
	-typedef itk::Image<unsigned char, 3> ItkUcharImgType;
	-typedef itk::Image<unsigned int, 3> ItkUIntImgType;
	-
	-/*!
	-\brief
	-*/
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Calculate Overlap");
	- parser.setCategory("Fiber Tracking Evaluation");
	- parser.setDescription("");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("tractogram", "", mitkCommandLineParser::String, "", "file", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("overlap_image", "", mitkCommandLineParser::String, "", "file", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("ep_image", "", mitkCommandLineParser::String, "", "file", us::Any(), false, false, false, mitkCommandLineParser::Input);
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- std::string input_tractogram = us::any_cast<std::string>(parsedArgs["tractogram"]);
	- std::string mask_file = us::any_cast<std::string>(parsedArgs["overlap_image"]);
	- std::string mask_file2 = us::any_cast<std::string>(parsedArgs["ep_image"]);
	-
	- try
	- {
	- mitk::FiberBundle::Pointer fib = mitk::IOUtil::Load<mitk::FiberBundle>(input_tractogram);
	- mitk::Image::Pointer mask = mitk::IOUtil::Load<mitk::Image>(mask_file);
	- mitk::Image::Pointer mask2 = mitk::IOUtil::Load<mitk::Image>(mask_file2);
	-
	- ItkUcharImgType::Pointer itk_mask;
	- mitk::CastToItkImage(mask, itk_mask);
	-
	- ItkUcharImgType::Pointer itk_mask2;
	- mitk::CastToItkImage(mask2, itk_mask2);
	-
	- float ol = fib->GetOverlap(itk_mask);
	- float ep = fib->GetNumEpFractionInMask(itk_mask2, true);
	- MITK_INFO << "Overlap<<" << ol;
	- MITK_INFO << "EP-Fraction<<" << ep;
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/ExtractSimilarTracts.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/ExtractSimilarTracts.cpp
	deleted file mode 100644
	index d04dcb3773..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/ExtractSimilarTracts.cpp
	+++ /dev/null
	@@ -1,199 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkFiberBundle.h>
	-#include <mitkCommandLineParser.h>
	-#include <mitkLexicalCast.h>
	-#include <mitkIOUtil.h>
	-#include <itkTractClusteringFilter.h>
	-#include <mitkClusteringMetricEuclideanMean.h>
	-#include <mitkClusteringMetricEuclideanMax.h>
	-#include <mitkClusteringMetricEuclideanStd.h>
	-#include <mitkClusteringMetricAnatomic.h>
	-#include <mitkClusteringMetricScalarMap.h>
	-#include <mitkDiffusionDataIOHelper.h>
	-
	-typedef itk::Image<unsigned char, 3> ItkFloatImgType;
	-
	-/*!
	-\brief Spatially cluster fibers
	-*/
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Extract Similar Tracts");
	- parser.setCategory("Fiber Tracking Evaluation");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i", mitkCommandLineParser::String, "Input:", "input fiber bundle (.fib, .trk, .tck)", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("ref_tracts", "", mitkCommandLineParser::StringList, "Ref. Tracts:", "reference tracts (.fib, .trk, .tck)", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("ref_masks", "", mitkCommandLineParser::StringList, "Ref. Masks:", "reference bundle masks", us::Any(), true, false, false, mitkCommandLineParser::Input);
	-
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "output root", us::Any(), false, false, false, mitkCommandLineParser::Output);
	- parser.addArgument("distance", "", mitkCommandLineParser::Int, "Distance:", "", 10);
	- parser.addArgument("metric", "", mitkCommandLineParser::String, "Metric:", "EU_MEAN (default), EU_STD, EU_MAX");
	- parser.addArgument("subsample", "", mitkCommandLineParser::Float, "Subsampling factor:", "Only use specified fraction of input fibers", 1.0);
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- std::string in_fib = us::any_cast<std::string>(parsedArgs["i"]);
	- std::string out_root = us::any_cast<std::string>(parsedArgs["o"]);
	- mitkCommandLineParser::StringContainerType ref_bundle_files = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["ref_tracts"]);
	- mitkCommandLineParser::StringContainerType ref_mask_files;
	- if (parsedArgs.count("ref_masks"))
	- ref_mask_files = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["ref_masks"]);
	-
	- if (ref_mask_files.size()>0 && ref_mask_files.size()!=ref_bundle_files.size())
	- {
	- MITK_INFO << "If reference masks are used, there has to be one mask per reference tract.";
	- return EXIT_FAILURE;
	- }
	-
	- int distance = 10;
	- if (parsedArgs.count("distance"))
	- distance = us::any_cast<int>(parsedArgs["distance"]);
	-
	- std::string metric = "EU_MEAN";
	- if (parsedArgs.count("metric"))
	- metric = us::any_cast<std::string>(parsedArgs["metric"]);
	-
	- float subsample = 1.0;
	- if (parsedArgs.count("subsample"))
	- subsample = us::any_cast<float>(parsedArgs["subsample"]);
	-
	- try
	- {
	- mitk::FiberBundle::Pointer fib = mitk::IOUtil::Load<mitk::FiberBundle>(in_fib);
	-
	- std::srand(0);
	- if (subsample<1.0f)
	- fib = fib->SubsampleFibers(subsample, true);
	-
	- mitk::FiberBundle::Pointer resampled_fib = fib->GetDeepCopy();
	- resampled_fib->ResampleToNumPoints(12);
	-
	- auto ref_fibs = mitk::DiffusionDataIOHelper::load_fibs(ref_bundle_files);
	- auto ref_masks = mitk::DiffusionDataIOHelper::load_itk_images<ItkFloatImgType>(ref_mask_files);
	-
	- std::vector< float > distances;
	- distances.push_back(distance);
	-
	- mitk::FiberBundle::Pointer extracted = mitk::FiberBundle::New(nullptr);
	- unsigned int c = 0;
	- for (auto ref_fib : ref_fibs)
	- {
	- MITK_INFO << "Extracting " << ist::GetFilenameName(ref_bundle_files.at(c));
	-
	- std::streambuf *old = cout.rdbuf(); // <-- save
	- std::stringstream ss;
	- std::cout.rdbuf (ss.rdbuf()); // <-- redirect
	- try
	- {
	- itk::TractClusteringFilter::Pointer segmenter = itk::TractClusteringFilter::New();
	-
	- // calculate centroids from reference bundle
	- {
	- itk::TractClusteringFilter::Pointer clusterer = itk::TractClusteringFilter::New();
	- clusterer->SetDistances({10,20,30});
	- clusterer->SetTractogram(ref_fib);
	- clusterer->SetMetrics({new mitk::ClusteringMetricEuclideanStd()});
	- clusterer->SetMergeDuplicateThreshold(0.0);
	- clusterer->Update();
	- std::vector<mitk::FiberBundle::Pointer> tracts = clusterer->GetOutCentroids();
	- ref_fib = mitk::FiberBundle::New(nullptr);
	- ref_fib = ref_fib->AddBundles(tracts);
	- mitk::IOUtil::Save(ref_fib, out_root + "centroids_" + ist::GetFilenameName(ref_bundle_files.at(c)));
	- segmenter->SetInCentroids(ref_fib);
	- }
	-
	- // segment tract
	- if (c<ref_masks.size())
	- {
	- segmenter->SetFilterMask(ref_masks.at(c));
	- segmenter->SetOverlapThreshold(0.8f);
	- }
	- segmenter->SetDistances(distances);
	- segmenter->SetTractogram(resampled_fib);
	- segmenter->SetMergeDuplicateThreshold(0.0);
	- segmenter->SetDoResampling(false);
	- if (metric=="EU_MEAN")
	- segmenter->SetMetrics({new mitk::ClusteringMetricEuclideanMean()});
	- else if (metric=="EU_STD")
	- segmenter->SetMetrics({new mitk::ClusteringMetricEuclideanStd()});
	- else if (metric=="EU_MAX")
	- segmenter->SetMetrics({new mitk::ClusteringMetricEuclideanMax()});
	- segmenter->Update();
	-
	- std::vector< std::vector< unsigned int > > clusters = segmenter->GetOutFiberIndices();
	- if (clusters.size()>0)
	- {
	- vtkSmartPointer<vtkFloatArray> weights = vtkSmartPointer<vtkFloatArray>::New();
	-
	- mitk::FiberBundle::Pointer result = mitk::FiberBundle::New(nullptr);
	- std::vector< mitk::FiberBundle::Pointer > result_fibs;
	- for (unsigned int cluster_index=0; cluster_index<clusters.size()-1; ++cluster_index)
	- result_fibs.push_back(mitk::FiberBundle::New(fib->GeneratePolyDataByIds(clusters.at(cluster_index), weights)));
	- result = result->AddBundles(result_fibs);
	-
	- extracted = extracted->AddBundle(result);
	- mitk::IOUtil::Save(result, out_root + "extracted_" + ist::GetFilenameName(ref_bundle_files.at(c)));
	-
	- fib = mitk::FiberBundle::New(fib->GeneratePolyDataByIds(clusters.back(), weights));
	- resampled_fib = mitk::FiberBundle::New(resampled_fib->GeneratePolyDataByIds(clusters.back(), weights));
	- }
	- }
	- catch(itk::ExceptionObject& excpt)
	- {
	- MITK_INFO << "Exception while processing " << ist::GetFilenameName(ref_bundle_files.at(c));
	- MITK_INFO << excpt.GetDescription();
	- }
	- catch(std::exception& excpt)
	- {
	- MITK_INFO << "Exception while processing " << ist::GetFilenameName(ref_bundle_files.at(c));
	- MITK_INFO << excpt.what();
	- }
	- std::cout.rdbuf (old); // <-- restore
	- if (fib->GetNumFibers()==0)
	- break;
	- ++c;
	- }
	- MITK_INFO << "Extracted streamlines: " << extracted->GetNumFibers();
	- mitk::IOUtil::Save(extracted, out_root + "extracted_streamlines.trk");
	-
	- MITK_INFO << "Residual streamlines: " << fib->GetNumFibers();
	- mitk::IOUtil::Save(fib, out_root + "residual_streamlines.trk");
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/GetOverlappingTracts.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/GetOverlappingTracts.cpp
	deleted file mode 100755
	index 67bad8e9b2..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/GetOverlappingTracts.cpp
	+++ /dev/null
	@@ -1,167 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <metaCommand.h>
	-#include "mitkCommandLineParser.h"
	-#include <usAny.h>
	-#include <mitkIOUtil.h>
	-#include <mitkLexicalCast.h>
	-#include <mitkCoreObjectFactory.h>
	-#include <mitkFiberBundle.h>
	-#include <mitkImageCast.h>
	-#include <mitkImageToItk.h>
	-#include <itksys/SystemTools.hxx>
	-#include <itkTractDensityImageFilter.h>
	-#include <mitkDiffusionDataIOHelper.h>
	-
	-#define _USE_MATH_DEFINES
	-#include <math.h>
	-
	-typedef itksys::SystemTools ist;
	-typedef itk::Image<unsigned char, 3> ItkFloatImgType;
	-
	-/*!
	-\brief Extract fibers from a tractogram using binary image ROIs
	-*/
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Get Overlapping Tracts");
	- parser.setCategory("Fiber Tracking and Processing Methods");
	- parser.setContributor("MIC");
	- parser.setDescription("Find tracts that overlap with the reference masks or tracts");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i", mitkCommandLineParser::StringList, "Input:", "input tractograms (.fib/.trk/.tck/.dcm)", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output Folder:", "move input tracts that do/don't overlap here", us::Any(), false, false, false, mitkCommandLineParser::Output);
	- parser.addArgument("reference", "", mitkCommandLineParser::StringList, "Reference:", "reference tractograms or mask images", us::Any(), false, false, false, mitkCommandLineParser::Input);
	-
	- parser.addArgument("overlap_fraction", "", mitkCommandLineParser::Float, "Overlap fraction:", "", 0.9);
	- parser.addArgument("use_any_overlap", "", mitkCommandLineParser::Bool, "Use any overlap:", "Don't find maximum overlap but use first overlap larger threshold");
	- parser.addArgument("dont_save_tracts", "", mitkCommandLineParser::Bool, "Don't save tracts:", "if true, only text files documenting the overlaps are saved and no tract files are copied");
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- mitkCommandLineParser::StringContainerType input = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["i"]);
	- mitkCommandLineParser::StringContainerType reference = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["reference"]);
	-
	- std::string out_folder = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- bool use_any_overlap = false;
	- if (parsedArgs.count("use_any_overlap"))
	- use_any_overlap = us::any_cast<bool>(parsedArgs["use_any_overlap"]);
	-
	- bool dont_save_tracts = false;
	- if (parsedArgs.count("dont_save_tracts"))
	- dont_save_tracts = us::any_cast<bool>(parsedArgs["dont_save_tracts"]);
	-
	- float overlap_threshold = 0.9;
	- if (parsedArgs.count("overlap_fraction"))
	- overlap_threshold = us::any_cast<float>(parsedArgs["overlap_fraction"]);
	-
	- try
	- {
	- MITK_INFO << "Loading references";
	- std::vector< std::string > reference_names;
	- auto masks = mitk::DiffusionDataIOHelper::load_itk_images<ItkFloatImgType>(reference, &reference_names);
	- auto reference_fibs = mitk::DiffusionDataIOHelper::load_fibs(reference, &reference_names);
	-
	- std::streambuf *old = cout.rdbuf(); // <-- save
	- std::stringstream ss;
	- std::cout.rdbuf (ss.rdbuf()); // <-- redirect
	- itk::TractDensityImageFilter< ItkFloatImgType >::Pointer filter = itk::TractDensityImageFilter< ItkFloatImgType >::New();
	- filter->SetUpsamplingFactor(0.25);
	- filter->SetBinaryOutput(true);
	- for (auto fib : reference_fibs)
	- {
	- filter->SetFiberBundle(fib);
	- filter->Update();
	- masks.push_back(filter->GetOutput());
	- }
	- std::cout.rdbuf (old); // <-- restore
	-
	- MITK_INFO << "Loading input tractograms";
	- std::vector< std::string > input_names;
	- auto input_fibs = mitk::DiffusionDataIOHelper::load_fibs(input, &input_names);
	-
	- MITK_INFO << "Finding overlaps";
	- ofstream logfile;
	- logfile.open (out_folder + "Overlaps.txt");
	-
	- ofstream logfile2;
	- logfile2.open (out_folder + "AllOverlaps.txt");
	-
	- boost::progress_display disp(input.size());
	- unsigned int c = 0;
	- for (auto fib : input_fibs)
	- {
	- ++disp;
	- std::streambuf *old = cout.rdbuf(); // <-- save
	- std::stringstream ss;
	- std::cout.rdbuf (ss.rdbuf()); // <-- redirect
	- bool is_overlapping = false;
	- float overlap = 0;
	- float max_overlap = 0;
	- std::string max_ref = "-";
	- int i = 0;
	- std::string overlap_string = ist::GetFilenameWithoutExtension(input_names.at(c));
	- for (auto m : masks)
	- {
	- overlap = fib->GetOverlap(m);
	- if (overlap>max_overlap)
	- {
	- max_overlap = overlap;
	- max_ref = ist::GetFilenameWithoutExtension(reference_names.at(i));
	- }
	- if (use_any_overlap && overlap>=overlap_threshold)
	- break;
	- overlap_string += " " + ist::GetFilenameWithoutExtension(reference_names.at(i)) + " " + boost::lexical_cast<std::string>(overlap);
	- ++i;
	- }
	- if (overlap>=overlap_threshold)
	- is_overlapping = true;
	-
	- logfile << ist::GetFilenameWithoutExtension(input_names.at(c)) << " - " << max_ref << ": " << boost::lexical_cast<std::string>(max_overlap) << "\n";
	- logfile2 << overlap_string << "\n";
	-
	- if (!dont_save_tracts && is_overlapping)
	- ist::CopyAFile(input_names.at(c), out_folder + ist::GetFilenameName(input_names.at(c)));
	- std::cout.rdbuf (old); // <-- restore
	- ++c;
	- }
	- logfile.close();
	- logfile2.close();
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/MergeOverlappingTracts.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/MergeOverlappingTracts.cpp
	deleted file mode 100755
	index 93042bbdcc..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/MergeOverlappingTracts.cpp
	+++ /dev/null
	@@ -1,214 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkBaseData.h>
	-#include <mitkImageCast.h>
	-#include <mitkImageToItk.h>
	-#include <metaCommand.h>
	-#include <mitkCommandLineParser.h>
	-#include <usAny.h>
	-#include <mitkIOUtil.h>
	-#include <mitkLexicalCast.h>
	-#include <mitkFiberBundle.h>
	-#include <vtkTransformPolyDataFilter.h>
	-#include <fstream>
	-#include <chrono>
	-#include <boost/progress.hpp>
	-#include <itkTractsToFiberEndingsImageFilter.h>
	-#include <itkTractDensityImageFilter.h>
	-#include <itkImageRegionConstIterator.h>
	-#include <mitkDiffusionDataIOHelper.h>
	-
	-typedef itk::Image<unsigned char, 3> ItkFloatImgType;
	-typedef itk::Image<unsigned int, 3> ItkUIntImgType;
	-
	-
	-/*!
	-\brief
	-*/
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Merge Overlapping Tracts");
	- parser.setCategory("Fiber Tracking Evaluation");
	- parser.setDescription("");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i", mitkCommandLineParser::StringList, "Input:", "input tracts", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output Folder:", "output folder", us::Any(), false, false, false, mitkCommandLineParser::Output);
	- parser.addArgument("overlap", "", mitkCommandLineParser::Float, "Overlap threshold:", "Tracts with overlap larger than this threshold are merged", 0.8, false);
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- mitkCommandLineParser::StringContainerType input_folder = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["i"]);
	- std::string out_folder = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- float overlap = 0.8;
	- if (parsedArgs.count("overlap"))
	- overlap = us::any_cast<float>(parsedArgs["overlap"]);
	-
	- try
	- {
	- if (!ist::PathExists(out_folder))
	- ist::MakeDirectory(out_folder);
	-
	- std::vector< mitk::FiberBundle::Pointer > fibs = mitk::DiffusionDataIOHelper::load_fibs(input_folder);
	-
	-
	- std::streambuf *old = cout.rdbuf(); // <-- save
	- std::stringstream ss;
	- std::cout.rdbuf (ss.rdbuf()); // <-- redirect
	-
	- mitk::FiberBundle::Pointer combined = mitk::FiberBundle::New();
	- combined = combined->AddBundles(fibs);
	-
	- itk::TractsToFiberEndingsImageFilter< ItkFloatImgType >::Pointer endings = itk::TractsToFiberEndingsImageFilter< ItkFloatImgType >::New();
	- endings->SetFiberBundle(combined);
	- endings->SetUpsamplingFactor(0.25);
	- endings->Update();
	- ItkFloatImgType::Pointer ref_image = endings->GetOutput();
	-
	- std::cout.rdbuf (old); // <-- restore
	-
	- for (int its = 0; its<3; its++)
	- {
	- std::streambuf *old = cout.rdbuf(); // <-- save
	- std::stringstream ss;
	- std::cout.rdbuf (ss.rdbuf()); // <-- redirect
	-
	- std::vector< ItkFloatImgType::Pointer > mask_images;
	- for (auto fib : fibs)
	- {
	- itk::TractDensityImageFilter< ItkFloatImgType >::Pointer masks = itk::TractDensityImageFilter< ItkFloatImgType >::New();
	- masks->SetInputImage(ref_image);
	- masks->SetBinaryOutput(true);
	- masks->SetFiberBundle(fib);
	- masks->SetUseImageGeometry(true);
	- masks->Update();
	- mask_images.push_back(masks->GetOutput());
	- }
	-
	- int r=0;
	- vnl_matrix< int > mat; mat.set_size(mask_images.size(), mask_images.size()); mat.fill(0);
	- for (auto m1 : mask_images)
	- {
	- float max_overlap = overlap;
	- int c = 0;
	- for (auto m2 : mask_images)
	- {
	- if (c<=r)
	- {
	- ++c;
	- continue;
	- }
	-
	- itk::ImageRegionConstIterator<ItkFloatImgType> it1(m1, m1->GetLargestPossibleRegion());
	- itk::ImageRegionConstIterator<ItkFloatImgType> it2(m2, m2->GetLargestPossibleRegion());
	-
	- unsigned int c1 = 0;
	- unsigned int c2 = 0;
	- unsigned int intersect = 0;
	- while( !it1.IsAtEnd() )
	- {
	- if( it1.Get()>0 && it2.Get()>0)
	- ++intersect;
	- if(it1.Get()>0)
	- ++c1;
	- if(it2.Get()>0)
	- ++c2;
	- ++it1;
	- ++it2;
	- }
	-
	- if ( (float)intersect/c1>max_overlap )
	- {
	- max_overlap = (float)intersect/c1;
	- mat.put(r,c, 1);
	- }
	- if ( (float)intersect/c2>max_overlap )
	- {
	- max_overlap = (float)intersect/c2;
	- mat.put(r,c, 1);
	- }
	- ++c;
	- }
	-
	- ++r;
	- }
	-
	- std::vector< mitk::FiberBundle::Pointer > out_fibs;
	- std::vector< bool > used;
	- for (unsigned int i=0; i<fibs.size(); i++)
	- used.push_back(false);
	- for (unsigned int r=0; r<mask_images.size(); r++)
	- {
	- if (used.at(r))
	- continue;
	-
	- mitk::FiberBundle::Pointer fib = fibs.at(r);
	- for (unsigned int c=r+1; c<mask_images.size(); c++)
	- {
	- if (mat.get(r,c)>0)
	- {
	- fib = fib->AddBundle(fibs.at(c));
	- used[c] = true;
	- }
	- }
	-
	- out_fibs.push_back(fib);
	- }
	- std::cout.rdbuf (old); // <-- restore
	-
	- MITK_INFO << fibs.size() << " --> " << out_fibs.size();
	-
	- if (fibs.size()==out_fibs.size())
	- break;
	- fibs = out_fibs;
	- }
	-
	- int c = 0;
	- for (auto fib : fibs)
	- {
	- std::streambuf *old = cout.rdbuf(); // <-- save
	- std::stringstream ss;
	- std::cout.rdbuf (ss.rdbuf()); // <-- redirect
	- mitk::IOUtil::Save(fib, out_folder + "/bundle_" + boost::lexical_cast<std::string>(c) + ".trk");
	- std::cout.rdbuf (old); // <-- restore
	-
	- ++c;
	- }
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/PeaksAngularError.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/PeaksAngularError.cpp
	deleted file mode 100755
	index 57a3081893..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/PeaksAngularError.cpp
	+++ /dev/null
	@@ -1,190 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkBaseData.h>
	-#include <mitkImageCast.h>
	-#include <mitkImageToItk.h>
	-#include <itkEvaluateDirectionImagesFilter.h>
	-#include <metaCommand.h>
	-#include "mitkCommandLineParser.h"
	-#include <itkTractsToVectorImageFilter.h>
	-#include <usAny.h>
	-#include <itkImageFileWriter.h>
	-#include <mitkIOUtil.h>
	-#include <mitkLexicalCast.h>
	-#include <iostream>
	-#include <fstream>
	-#include <mitkPeakImage.h>
	-#include <mitkDiffusionDataIOHelper.h>
	-#include <mitkLocaleSwitch.h>
	-
	-typedef itk::Image< unsigned char, 3 > ItkUcharImageType;
	-
	-/*!
	-\brief Calculate angular error between two sets of directions stored in multiple 3D vector images where each pixel corresponds to a vector (itk::Image< itk::Vector< float, 3>, 3 >)
	-*/
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("test", "", mitkCommandLineParser::StringList, "Test images", "test direction images", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("reference", "", mitkCommandLineParser::StringList, "Reference images", "reference direction images", us::Any(), false, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output folder", "output folder", us::Any(), false, false, false, mitkCommandLineParser::Output);
	- parser.addArgument("masks", "", mitkCommandLineParser::StringList, "Mask(s)", "mask image(s)", us::Any(), true, false, false, mitkCommandLineParser::Input);
	- parser.addArgument("verbose", "", mitkCommandLineParser::Bool, "Verbose", "output error images");
	- parser.addArgument("ignore_test", "", mitkCommandLineParser::Bool, "Ignore missing test", "don't increase error if no test directions are found");
	- parser.addArgument("ignore_ref", "", mitkCommandLineParser::Bool, "Ignore ignore missing ref", "don't increase error if no ref directions are found");
	-
	- parser.setCategory("Fiber Tracking Evaluation");
	- parser.setTitle("Peaks Angular Error");
	- parser.setDescription("Calculate angular error between two sets of peak images (1-1 correspondence)");
	- parser.setContributor("MIC");
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- mitkCommandLineParser::StringContainerType testImages = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["test"]);
	- mitkCommandLineParser::StringContainerType referenceImages = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["reference"]);
	-
	- mitkCommandLineParser::StringContainerType maskImages;
	- if (parsedArgs.count("masks"))
	- maskImages = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["masks"]);
	-
	- std::string outRoot = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- bool verbose = false;
	- if (parsedArgs.count("verbose"))
	- verbose = us::any_cast<bool>(parsedArgs["verbose"]);
	-
	- bool ignore_test = false;
	- if (parsedArgs.count("ignore_test"))
	- ignore_test = us::any_cast<bool>(parsedArgs["ignore_test"]);
	-
	- bool ignore_ref = false;
	- if (parsedArgs.count("ignore_ref"))
	- ignore_ref = us::any_cast<bool>(parsedArgs["ignore_ref"]);
	-
	- try
	- {
	- typedef itk::ComparePeakImagesFilter< float > EvaluationFilterType;
	-
	- std::vector<std::string> test_names;
	- auto test_images = mitk::DiffusionDataIOHelper::load_itk_images<EvaluationFilterType::PeakImageType>(testImages, &test_names);
	-
	- // load reference directions
	- std::vector<std::string> ref_names;
	- auto ref_images = mitk::DiffusionDataIOHelper::load_itk_images<EvaluationFilterType::PeakImageType>(referenceImages, &ref_names);
	-
	- // load/create mask image
	- auto itkMaskImages = mitk::DiffusionDataIOHelper::load_itk_images<ItkUcharImageType>(maskImages);
	-
	- if (test_images.size()!=ref_images.size())
	- mitkThrow() << "Matching number of test and reference image required!";
	-
	- for (unsigned int i=0; i<test_images.size(); ++i)
	- {
	- // evaluate directions
	- EvaluationFilterType::Pointer evaluationFilter = EvaluationFilterType::New();
	- evaluationFilter->SetTestImage(test_images.at(i));
	- evaluationFilter->SetReferenceImage(ref_images.at(i));
	- if (i<maskImages.size())
	- evaluationFilter->SetMaskImage(itkMaskImages.at(i));
	- evaluationFilter->SetIgnoreMissingTestDirections(ignore_test);
	- evaluationFilter->SetIgnoreMissingRefDirections(ignore_ref);
	- evaluationFilter->Update();
	-
	- std::string ref_name = ist::GetFilenameWithoutExtension(ref_names.at(i));
	- std::string test_name = ist::GetFilenameWithoutExtension(test_names.at(i));
	-
	- if (verbose)
	- {
	- mitk::LocaleSwitch localeSwitch("C");
	- EvaluationFilterType::OutputImageType::Pointer angularErrorImage = evaluationFilter->GetOutput(0);
	- EvaluationFilterType::OutputImageType::Pointer lengthErrorImage = evaluationFilter->GetOutput(1);
	- typedef itk::ImageFileWriter< EvaluationFilterType::OutputImageType > WriterType;
	-
	- {
	- WriterType::Pointer writer = WriterType::New();
	- std::string outfilename = outRoot;
	- outfilename.append(ref_name + "_" + test_name + "_AngularError.nii.gz");
	- writer->SetFileName(outfilename.c_str());
	- writer->SetInput(angularErrorImage);
	- writer->Update();
	- }
	-
	- {
	- WriterType::Pointer writer = WriterType::New();
	- std::string outfilename = outRoot;
	- outfilename.append(ref_name + "_" + test_name + "_LengthError.nii.gz");
	- writer->SetFileName(outfilename.c_str());
	- writer->SetInput(lengthErrorImage);
	- writer->Update();
	- }
	- }
	-
	- std::string logFile = outRoot;
	- logFile.append("AngularErrors.csv");
	-
	- bool add_header = true;
	- if (ist::FileExists(logFile, true))
	- add_header = false;
	-
	- ofstream file;
	- file.open (logFile.c_str(), std::fstream::app);
	-
	- std::string sens;
	- if (add_header)
	- sens.append("Test,Reference,Mean,Median,Maximum,Minimum,Stdev\n");
	-
	- sens.append(test_name);
	- sens.append(",");
	- sens.append(ref_name);
	- sens.append(",");
	- sens.append(boost::lexical_cast<std::string>(evaluationFilter->GetMeanAngularError()));
	- sens.append(",");
	- sens.append(boost::lexical_cast<std::string>(evaluationFilter->GetMedianAngularError()));
	- sens.append(",");
	- sens.append(boost::lexical_cast<std::string>(evaluationFilter->GetMaxAngularError()));
	- sens.append(",");
	- sens.append(boost::lexical_cast<std::string>(evaluationFilter->GetMinAngularError()));
	- sens.append(",");
	- sens.append(boost::lexical_cast<std::string>(std::sqrt(evaluationFilter->GetVarAngularError())));
	- sens.append("\n");
	-
	- std::cout << sens;
	-
	- file << sens;
	- file.close();
	- }
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/ReferenceSimilarity.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/ReferenceSimilarity.cpp
	deleted file mode 100644
	index 37e07f888e..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/ReferenceSimilarity.cpp
	+++ /dev/null
	@@ -1,149 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkFiberBundle.h>
	-#include <mitkCommandLineParser.h>
	-#include <mitkDiffusionDataIOHelper.h>
	-#include <mitkLexicalCast.h>
	-#include <itkTractDistanceFilter.h>
	-#include <mitkClusteringMetricEuclideanMean.h>
	-#include <mitkClusteringMetricEuclideanMax.h>
	-#include <mitkClusteringMetricEuclideanStd.h>
	-#include <boost/progress.hpp>
	-
	-typedef itk::Image< unsigned char, 3 > ItkUcharImageType;
	-typedef itk::Image< float, 4 > ItkPeakImgType;
	-
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Reference Similarity");
	- parser.setCategory("Fiber Tracking Evaluation");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i", mitkCommandLineParser::StringList, "Input Tracts:", "input tracts folder", us::Any(), false);
	- parser.addArgument("reference_tracts", "", mitkCommandLineParser::StringList, "", "", us::Any(), false);
	- parser.addArgument("reference_masks", "", mitkCommandLineParser::StringList, "", "", us::Any(), false);
	- parser.addArgument("reference_peaks", "", mitkCommandLineParser::StringList, "", "", us::Any(), false);
	-
	- parser.addArgument("", "o", mitkCommandLineParser::String, "", "", us::Any(), false);
	-
	- parser.addArgument("fiber_points", "", mitkCommandLineParser::Int, "Fiber points:", "", 20);
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- std::string out_folder = us::any_cast<std::string>(parsedArgs["o"]);
	- mitkCommandLineParser::StringContainerType input_tract_files = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["i"]);
	- mitkCommandLineParser::StringContainerType reference_tract_files = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["reference_tracts"]);
	- mitkCommandLineParser::StringContainerType reference_mask_files = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["reference_masks"]);
	- mitkCommandLineParser::StringContainerType reference_peak_files = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["reference_peaks"]);
	-
	- int fiber_points = 20;
	- if (parsedArgs.count("fiber_points"))
	- fiber_points = us::any_cast<int>(parsedArgs["fiber_points"]);
	-
	- try
	- {
	- std::vector<std::string> input_tract_names;
	- std::vector<std::string> ref_tract_names;
	- std::vector< mitk::FiberBundle::Pointer > input_tracts = mitk::DiffusionDataIOHelper::load_fibs(input_tract_files, &input_tract_names);
	- std::vector< mitk::FiberBundle::Pointer > reference_tracts = mitk::DiffusionDataIOHelper::load_fibs(reference_tract_files, &ref_tract_names);
	- std::vector< ItkUcharImageType::Pointer > reference_masks = mitk::DiffusionDataIOHelper::load_itk_images<ItkUcharImageType>(reference_mask_files);
	- std::vector< ItkPeakImgType::Pointer > reference_peaks = mitk::DiffusionDataIOHelper::load_itk_images<ItkPeakImgType>(reference_peak_files);
	-
	- MITK_INFO << "Calculating distances";
	- itk::TractDistanceFilter::Pointer distance_calculator = itk::TractDistanceFilter::New();
	- distance_calculator->SetNumPoints(fiber_points);
	- distance_calculator->SetTracts1(input_tracts);
	- distance_calculator->SetTracts2(reference_tracts);
	- distance_calculator->SetMetrics({new mitk::ClusteringMetricEuclideanMean()});
	- distance_calculator->Update();
	- auto distances = distance_calculator->GetAllDistances();
	-
	- vnl_matrix<float> voxel_overlap; voxel_overlap.set_size(input_tracts.size(), reference_tracts.size());
	- vnl_matrix<float> dir_overlap; dir_overlap.set_size(input_tracts.size(), reference_tracts.size());
	-
	- MITK_INFO << "Calculating overlap";
	- boost::progress_display disp(input_tracts.size()*reference_tracts.size());
	- int r=0;
	- for (auto fib : input_tracts)
	- {
	- int c=0;
	- for (auto ref_mask : reference_masks)
	- {
	-// ++disp;
	-// std::streambuf *old = cout.rdbuf(); // <-- save
	-// std::stringstream ss;
	-// std::cout.rdbuf (ss.rdbuf()); // <-- redirect
	- float overlap = 0;
	- float directional_overlap = 0;
	- std::tie(directional_overlap, overlap) = fib->GetDirectionalOverlap(ref_mask, reference_peaks.at(c));
	- voxel_overlap[r][c] = overlap;
	- dir_overlap[r][c] = directional_overlap;
	-// std::cout.rdbuf (old); // <-- restore
	- ++c;
	- }
	- ++r;
	- }
	-
	- ofstream logfile;
	- logfile.open(out_folder + "ref_tract_names.txt");
	- for (unsigned int i=0; i<ref_tract_names.size(); ++i)
	- logfile << ist::GetFilenameWithoutExtension(ref_tract_names.at(i)) << std::endl;
	- logfile << "----------" << std::endl;
	- for (unsigned int i=0; i<input_tract_names.size(); ++i)
	- logfile << ist::GetFilenameWithoutExtension(input_tract_names.at(i)) << std::endl;
	- logfile.close();
	-
	- MITK_INFO << "Saving matrices";
	- {
	- std::ofstream OutputStream(out_folder + "ref_distances.txt");
	- OutputStream << distances;
	- OutputStream.close();
	- }
	- {
	- std::ofstream OutputStream(out_folder + "ref_voxel_overlap.txt");
	- OutputStream << voxel_overlap;
	- OutputStream.close();
	- }
	- {
	- std::ofstream OutputStream(out_folder + "ref_dir_overlap.txt");
	- OutputStream << dir_overlap;
	- OutputStream.close();
	- }
	-
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/TractDistance.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/TractDistance.cpp
	deleted file mode 100644
	index 468980fa3c..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/TractDistance.cpp
	+++ /dev/null
	@@ -1,139 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkFiberBundle.h>
	-#include <mitkCommandLineParser.h>
	-#include <mitkLexicalCast.h>
	-#include <mitkIOUtil.h>
	-#include <itkTractDistanceFilter.h>
	-#include <mitkClusteringMetricEuclideanMean.h>
	-#include <mitkClusteringMetricEuclideanMax.h>
	-#include <mitkClusteringMetricEuclideanStd.h>
	-#include <mitkDiffusionDataIOHelper.h>
	-
	-
	-int main(int argc, char* argv[])
	-{
	- mitkCommandLineParser parser;
	-
	- parser.setTitle("Tract Distance");
	- parser.setCategory("Fiber Processing");
	- parser.setContributor("MIC");
	-
	- parser.setArgumentPrefix("--", "-");
	- parser.addArgument("", "i1", mitkCommandLineParser::StringList, "Input tracts 1:", "input tracts 1", us::Any(), false);
	- parser.addArgument("", "i2", mitkCommandLineParser::StringList, "Input tracts 2:", "input tracts 2", us::Any(), false);
	- parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "output logfile", us::Any(), false);
	-
	- parser.addArgument("fiber_points", "", mitkCommandLineParser::Int, "Fiber points:", "", 12);
	- parser.addArgument("metrics", "", mitkCommandLineParser::StringList, "Metrics:", "EU_MEAN (default), EU_STD, EU_MAX");
	- parser.addArgument("metric_weights", "", mitkCommandLineParser::StringList, "Metric weights:", "add one float weight for each used metric");
	-
	- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
	- if (parsedArgs.size()==0)
	- return EXIT_FAILURE;
	-
	- mitkCommandLineParser::StringContainerType t1_folder = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["i1"]);
	- mitkCommandLineParser::StringContainerType t2_folder = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["i2"]);
	- std::string out_file = us::any_cast<std::string>(parsedArgs["o"]);
	-
	- int fiber_points = 12;
	- if (parsedArgs.count("fiber_points"))
	- fiber_points = us::any_cast<int>(parsedArgs["fiber_points"]);
	-
	- std::vector< std::string > metric_strings = {"EU_MEAN"};
	- if (parsedArgs.count("metrics"))
	- metric_strings = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["metrics"]);
	-
	- std::vector< std::string > metric_weights = {"1.0"};
	- if (parsedArgs.count("metric_weights"))
	- metric_weights = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["metric_weights"]);
	-
	- if (metric_strings.size()!=metric_weights.size())
	- {
	- MITK_INFO << "Each metric needs an associated metric weight!";
	- return EXIT_FAILURE;
	- }
	-
	- try
	- {
	- std::vector<std::string> t1_files;
	- std::vector< mitk::FiberBundle::Pointer > tractograms1 = mitk::DiffusionDataIOHelper::load_fibs(t1_folder, &t1_files);
	- std::vector<std::string> t2_files;
	- std::vector< mitk::FiberBundle::Pointer > tractograms2 = mitk::DiffusionDataIOHelper::load_fibs(t2_folder, &t2_files);
	-
	- MITK_INFO << "Loaded " << tractograms1.size() << " source tractograms.";
	- MITK_INFO << "Loaded " << tractograms2.size() << " target tractograms.";
	-
	- itk::TractDistanceFilter::Pointer distance_calculator = itk::TractDistanceFilter::New();
	- distance_calculator->SetNumPoints(fiber_points);
	- distance_calculator->SetTracts1(tractograms1);
	- distance_calculator->SetTracts2(tractograms2);
	-
	- std::vector< mitk::ClusteringMetric* > metrics;
	- int mc = 0;
	- for (auto m : metric_strings)
	- {
	- float w = boost::lexical_cast<float>(metric_weights.at(mc));
	- MITK_INFO << "Metric: " << m << " (w=" << w << ")";
	- if (m=="EU_MEAN")
	- metrics.push_back({new mitk::ClusteringMetricEuclideanMean()});
	- else if (m=="EU_STD")
	- metrics.push_back({new mitk::ClusteringMetricEuclideanStd()});
	- else if (m=="EU_MAX")
	- metrics.push_back({new mitk::ClusteringMetricEuclideanMax()});
	- metrics.back()->SetScale(w);
	- mc++;
	- }
	-
	- if (metrics.empty())
	- {
	- MITK_INFO << "No metric selected!";
	- return EXIT_FAILURE;
	- }
	-
	- distance_calculator->SetMetrics(metrics);
	- distance_calculator->Update();
	- MITK_INFO << "Distances:";
	- auto distances = distance_calculator->GetMinDistances();
	- auto indices = distance_calculator->GetMinIndices();
	-
	- ofstream logfile;
	- logfile.open (out_file);
	- for (unsigned int i=0; i<distances.size(); ++i)
	- {
	- std::cout << ist::GetFilenameWithoutExtension(t1_files.at(i)) << " << " << ist::GetFilenameWithoutExtension(t2_files.at(indices[i])) << ": " << distances[i] << std::endl;
	- logfile << ist::GetFilenameWithoutExtension(t1_files.at(i)) << " " << ist::GetFilenameWithoutExtension(t2_files.at(indices[i])) << " " << distances[i] << std::endl;
	- }
	- logfile.close();
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (std::exception e)
	- {
	- std::cout << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- std::cout << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/files.cmake b/Modules/DiffusionImaging/DiffusionCmdApps/files.cmake
	deleted file mode 100644
	index 4f4c7b86dd..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/files.cmake
	+++ /dev/null
	@@ -1,7 +0,0 @@
	-set(CPP_FILES
	- mitkDiffusionDataIOHelper.cpp
	-)
	-
	-set(H_FILES
	- mitkDiffusionDataIOHelper.h
	-)
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/mitkDiffusionDataIOHelper.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/mitkDiffusionDataIOHelper.cpp
	deleted file mode 100644
	index fea9ae9bbf..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/mitkDiffusionDataIOHelper.cpp
	+++ /dev/null
	@@ -1,127 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkDiffusionDataIOHelper.h"
	-
	-std::vector< std::string > mitk::DiffusionDataIOHelper::get_file_list(const std::string& path, const std::vector<std::string> extensions)
	-{
	- std::vector< std::string > file_list;
	- itk::Directory::Pointer dir = itk::Directory::New();
	-
	- if (dir->Load(path.c_str()))
	- {
	- int n = dir->GetNumberOfFiles();
	- for (int r = 0; r < n; r++)
	- {
	- const char *filename = dir->GetFile(r);
	- std::string ext = ist::GetFilenameExtension(filename);
	- for (auto e : extensions)
	- {
	- if (ext==e)
	- {
	- file_list.push_back(path + '/' + filename);
	- break;
	- }
	- }
	- }
	- }
	- std::sort(file_list.begin(), file_list.end());
	- return file_list;
	-}
	-
	-std::vector< mitk::Image::Pointer > mitk::DiffusionDataIOHelper::load_mitk_images(const std::vector<std::string> files, std::vector<std::string>* filenames)
	-{
	- mitk::LocaleSwitch localeSwitch("C");
	- std::streambuf *old = cout.rdbuf(); // <-- save
	- std::stringstream ss;
	- std::cout.rdbuf (ss.rdbuf()); // <-- redirect
	- std::vector< mitk::Image::Pointer > out;
	- for (auto f : files)
	- {
	- if (itksys::SystemTools::FileExists(f, true))
	- {
	- mitk::Image::Pointer image = mitk::IOUtil::Load<mitk::Image>(f);
	- if (image.IsNotNull())
	- {
	- out.push_back(image);
	- if (filenames!=nullptr)
	- filenames->push_back(f);
	- }
	- }
	- else if (itksys::SystemTools::PathExists(f))
	- {
	- if (!f.empty() && f.back() != '/')
	- f += "/";
	-
	- auto list = get_file_list(f, {".nrrd",".nii.gz",".nii"});
	- for (auto file : list)
	- {
	- mitk::Image::Pointer image = mitk::IOUtil::Load<mitk::Image>(file);
	- if (image.IsNotNull())
	- {
	- out.push_back(image);
	- if (filenames!=nullptr)
	- filenames->push_back(file);
	- }
	- }
	- }
	- }
	-
	- std::cout.rdbuf (old); // <-- restore
	- MITK_INFO << "Loaded " << out.size() << " images";
	- return out;
	-}
	-
	-std::vector< mitk::FiberBundle::Pointer > mitk::DiffusionDataIOHelper::load_fibs(const std::vector<std::string> files, std::vector<std::string>* filenames)
	-{
	- std::streambuf *old = cout.rdbuf(); // <-- save
	- std::stringstream ss;
	- std::cout.rdbuf (ss.rdbuf()); // <-- redirect
	- std::vector< mitk::FiberBundle::Pointer > out;
	- for (auto f : files)
	- {
	- if (itksys::SystemTools::FileExists(f, true))
	- {
	- mitk::FiberBundle::Pointer fib = mitk::IOUtil::Load<mitk::FiberBundle>(f);
	- if (fib.IsNotNull())
	- {
	- out.push_back(fib);
	- if (filenames!=nullptr)
	- filenames->push_back(f);
	- }
	- }
	- else if (itksys::SystemTools::PathExists(f))
	- {
	- if (!f.empty() && f.back() != '/')
	- f += "/";
	-
	- auto list = get_file_list(f, {".fib",".trk",".tck"});
	- for (auto file : list)
	- {
	- mitk::FiberBundle::Pointer fib = mitk::IOUtil::Load<mitk::FiberBundle>(file);
	- if (fib.IsNotNull())
	- {
	- out.push_back(fib);
	- if (filenames!=nullptr)
	- filenames->push_back(file);
	- }
	- }
	- }
	- }
	- std::cout.rdbuf (old); // <-- restore
	- MITK_INFO << "Loaded " << out.size() << " tractograms";
	- return out;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/mitkDiffusionDataIOHelper.h b/Modules/DiffusionImaging/DiffusionCmdApps/mitkDiffusionDataIOHelper.h
	deleted file mode 100644
	index ff1d046eef..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCmdApps/mitkDiffusionDataIOHelper.h
	+++ /dev/null
	@@ -1,134 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkDiffusionDataIOHelper_h_
	-#define __mitkDiffusionDataIOHelper_h_
	-
	-#include <MitkDiffusionCmdAppsExports.h>
	-#include <itkImage.h>
	-#include <mitkImage.h>
	-#include <mitkIOUtil.h>
	-#include <mitkFiberBundle.h>
	-#include <mitkImageToItk.h>
	-
	-#include <itksys/SystemTools.hxx>
	-#include <itkDirectory.h>
	-#include <mitkLocaleSwitch.h>
	-
	-typedef itksys::SystemTools ist;
	-
	-namespace mitk{
	-
	-class MITKDIFFUSIONCMDAPPS_EXPORT DiffusionDataIOHelper
	-{
	-public:
	-
	- static std::vector< std::string > get_file_list(const std::string& path, const std::vector< std::string > extensions={".fib", ".trk"});
	-
	- static std::vector< mitk::FiberBundle::Pointer > load_fibs(const std::vector<std::string> files, std::vector<std::string>* filenames=nullptr);
	-
	- static std::vector< mitk::Image::Pointer > load_mitk_images(const std::vector<std::string> files, std::vector<std::string>* filenames=nullptr);
	-
	- template< class TYPE >
	- static typename TYPE::Pointer load_itk_image(const std::string file)
	- {
	- mitk::LocaleSwitch localeSwitch("C");
	- std::streambuf *old = cout.rdbuf(); // <-- save
	- std::stringstream ss;
	- std::cout.rdbuf (ss.rdbuf()); // <-- redirect
	- std::vector< typename TYPE::Pointer > out;
	- if (file.compare("")!=0 && itksys::SystemTools::FileExists(file))
	- {
	- mitk::Image::Pointer image = mitk::IOUtil::Load<mitk::Image>(file);
	- if (image.IsNotNull())
	- {
	- typedef mitk::ImageToItk< TYPE > CasterType;
	- typename CasterType::Pointer caster = CasterType::New();
	- caster->SetInput(image);
	- caster->Update();
	- typename TYPE::Pointer itk_image = caster->GetOutput();
	- std::cout.rdbuf (old); // <-- restore
	- MITK_INFO << "Loaded 1 image";
	- return itk_image;
	- }
	- }
	- std::cout.rdbuf (old); // <-- restore // <-- restore
	- MITK_INFO << "Loaded 0 images";
	- return nullptr;
	- }
	-
	- template< class TYPE >
	- static std::vector< typename TYPE::Pointer > load_itk_images(const std::vector<std::string> files, std::vector<std::string>* filenames=nullptr)
	- {
	- mitk::LocaleSwitch localeSwitch("C");
	- std::streambuf *old = cout.rdbuf(); // <-- save
	- std::stringstream ss;
	- std::cout.rdbuf (ss.rdbuf()); // <-- redirect
	- std::vector< typename TYPE::Pointer > out;
	- for (auto f : files)
	- {
	- if (itksys::SystemTools::FileExists(f, true))
	- {
	- mitk::Image::Pointer image = mitk::IOUtil::Load<mitk::Image>(f);
	- if (image.IsNotNull())
	- {
	- typedef mitk::ImageToItk< TYPE > CasterType;
	- typename CasterType::Pointer caster = CasterType::New();
	- caster->SetInput(image);
	- caster->Update();
	- typename TYPE::Pointer itk_image = caster->GetOutput();
	-
	- out.push_back(itk_image);
	- if (filenames!=nullptr)
	- filenames->push_back(f);
	- }
	- }
	- else if (itksys::SystemTools::PathExists(f))
	- {
	- if (!f.empty() && f.back() != '/')
	- f += "/";
	-
	- auto list = get_file_list(f, {".nrrd",".nii.gz",".nii"});
	- for (auto file : list)
	- {
	- mitk::Image::Pointer image = mitk::IOUtil::Load<mitk::Image>(file);
	- if (image.IsNotNull())
	- {
	- typedef mitk::ImageToItk< TYPE > CasterType;
	- typename CasterType::Pointer caster = CasterType::New();
	- caster->SetInput(image);
	- caster->Update();
	- typename TYPE::Pointer itk_image = caster->GetOutput();
	-
	- out.push_back(itk_image);
	- if (filenames!=nullptr)
	- filenames->push_back(file);
	- }
	- }
	- }
	- }
	-
	- std::cout.rdbuf (old); // <-- restore
	- MITK_INFO << "Loaded " << out.size() << " images";
	- return out;
	- }
	-
	-};
	-
	-}
	-
	-#endif //__mitkDiffusionDataIOHelper_h_
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/CMakeLists.txt b/Modules/DiffusionImaging/DiffusionCore/CMakeLists.txt
	deleted file mode 100644
	index a3151db1ea..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/CMakeLists.txt
	+++ /dev/null
	@@ -1,24 +0,0 @@
	-# With apple gcc 4.2.1 the following waring leads to an build error if boost is enabled
	-if(APPLE)
	- mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=empty-body" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
	-endif()
	-
	-MITK_CREATE_MODULE(
	- SUBPROJECTS MITK-DTI
	- INCLUDE_DIRS include/ include/Algorithms include/Algorithms/Reconstruction include/Algorithms/Registration include/Algorithms/Reconstruction/MultishellProcessing include/Algorithms/Reconstruction/FittingFunctions include/DicomImport include/IODataStructures/DiffusionWeightedImages include/IODataStructures/Properties include/IODataStructures/OdfImages include/IODataStructures/TensorImages include/IODataStructures include/Rendering ${CMAKE_CURRENT_BINARY_DIR}
	- DEPENDS MitkMapperExt MitkPlanarFigure MitkImageExtraction MitkSceneSerializationBase MitkDICOMReader MitkMatchPointRegistration
	- PACKAGE_DEPENDS
	- PUBLIC ITK\|ITKTestKernel+ITKRegistrationCommon+ITKMetricsv4+ITKRegistrationMethodsv4+ITKDistanceMap+ITKLabelVoting+ITKVTK
	- PUBLIC VTK\|vtkFiltersProgrammable OpenMP\|OpenMP_CXX
	-)
	-
	-if(MSVC)
	- mitkFunctionCheckCAndCXXCompilerFlags("/wd4005" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
	-endif()
	-
	-add_subdirectory(Testing)
	-add_subdirectory(autoload/IO)
	-
	-if(MITK_USE_Python)
	-MITK_INSTALL(FILES PythonRequirements.txt)
	-endif()
	diff --git a/Modules/DiffusionImaging/DiffusionCore/DicomImport/test.txt b/Modules/DiffusionImaging/DiffusionCore/DicomImport/test.txt
	deleted file mode 100644
	index e69de29bb2..0000000000
	diff --git a/Modules/DiffusionImaging/DiffusionCore/PythonRequirements.txt b/Modules/DiffusionImaging/DiffusionCore/PythonRequirements.txt
	deleted file mode 100644
	index 034237bfe9..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/PythonRequirements.txt
	+++ /dev/null
	@@ -1,8 +0,0 @@
	-numpy
	-SimpleITK
	-dipy
	-sklearn
	-https://github.com/MIC-DKFZ/batchgenerators/archive/master.zip
	-https://github.com/MIC-DKFZ/TractSeg/archive/v1.9.zip
	-torch
	-torchvision
	diff --git a/Modules/DiffusionImaging/DiffusionCore/Testing/CMakeLists.txt b/Modules/DiffusionImaging/DiffusionCore/Testing/CMakeLists.txt
	deleted file mode 100644
	index c3fa88b681..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/Testing/CMakeLists.txt
	+++ /dev/null
	@@ -1,16 +0,0 @@
	-# The DiffusionCore tests need relaxed compiler flags...
	-# TODO fix tests to compile without these additional no-error flags
	-if(MSVC_VERSION)
	- # disable deprecated warnings (they would lead to errors)
	- mitkFunctionCheckCAndCXXCompilerFlags("/wd4996" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
	-else()
	- mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=deprecated" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
	- mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=deprecated-declarations" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
	-endif()
	-
	-MITK_CREATE_MODULE_TESTS()
	-if(TARGET ${TESTDRIVER})
	- mitk_use_modules(TARGET ${TESTDRIVER} PACKAGES ITK\|ITKIOTransformBase+ITKDiffusionTensorImage)
	-
	- mitkAddCustomModuleTest(mitkImageReconstructionTest mitkImageReconstructionTest ${MITK_DATA_DIR}/DiffusionImaging/ImageReconstruction/test.dwi ${MITK_DATA_DIR}/DiffusionImaging/ImageReconstruction/test_dti.dti ${MITK_DATA_DIR}/DiffusionImaging/ImageReconstruction/test_QN0.qbi ${MITK_DATA_DIR}/DiffusionImaging/ImageReconstruction/test_QA0.qbi ${MITK_DATA_DIR}/DiffusionImaging/ImageReconstruction/test_QA6.qbi ${MITK_DATA_DIR}/DiffusionImaging/ImageReconstruction/test_QA4.qbi ${MITK_DATA_DIR}/DiffusionImaging/ImageReconstruction/test_QA5.qbi)
	-endif()
	diff --git a/Modules/DiffusionImaging/DiffusionCore/Testing/files.cmake b/Modules/DiffusionImaging/DiffusionCore/Testing/files.cmake
	deleted file mode 100644
	index 9e87b8b605..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/Testing/files.cmake
	+++ /dev/null
	@@ -1,15 +0,0 @@
	-set(MODULE_TESTS
	- mitkNonLocalMeansDenoisingTest.cpp
	- mitkDiffusionPropertySerializerTest.cpp
	-)
	-
	-set(MODULE_CUSTOM_TESTS
	- mitkPyramidImageRegistrationMethodTest.cpp
	- mitkDWHeadMotionCorrectionTest.cpp
	- mitkImageReconstructionTest.cpp
	- mitkConvertDWITypeTest.cpp
	- mitkExtractSingleShellTest.cpp
	- mitkNonLocalMeansDenoisingTest.cpp
	- mitkDiffusionDICOMFileReaderTest.cpp
	-)
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/Testing/mitkB0ExtractionToSeparateImagesFilterTest.cpp b/Modules/DiffusionImaging/DiffusionCore/Testing/mitkB0ExtractionToSeparateImagesFilterTest.cpp
	deleted file mode 100644
	index ff443fc1a6..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/Testing/mitkB0ExtractionToSeparateImagesFilterTest.cpp
	+++ /dev/null
	@@ -1,109 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkTestingMacros.h"
	-#include "itkVectorImage.h"
	-#include "mitkBaseData.h"
	-#include "mitkBaseDataIOFactory.h"
	-
	-#include "mitkImageWriter.h"
	-#include "itkImageFileWriter.h"
	-
	-#include "itkB0ImageExtractionToSeparateImageFilter.h"
	-
	-#include "mitkDiffusionCoreObjectFactory.h"
	-
	-/** Documentation
	- * Test for factory registration
	- */
	-int mitkB0ExtractionToSeparateImagesFilterTest(int argc , char* argv[])
	-{
	- // always start with this!
	- MITK_TEST_BEGIN("mitkB0ExtractionToSeparateImagesFilterTest");
	-
	- MITK_TEST_CONDITION_REQUIRED(argc > 2, "Test image is specified. ");
	-
	- typedef short DiffusionPixelType;
	- typedef mitk::Image DiffusionImageType;
	- typedef mitk::NrrdDiffusionImageReader< DiffusionPixelType> DiffusionNrrdReaderType;
	-
	- RegisterDiffusionImagingObjectFactory();
	-
	- std::string inputFileName( argv[1] );
	-
	- std::vector<mitk::BaseData::Pointer> inputBaseDataVector = mitk::BaseDataIO::LoadBaseDataFromFile( inputFileName, "","",false);
	-
	- MITK_TEST_CONDITION_REQUIRED( inputBaseDataVector.size() > 0, "BaseDataIO returned non-empty vector.");
	-
	- mitk::BaseData::Pointer baseData = inputBaseDataVector.at(0);
	-
	- MITK_TEST_CONDITION_REQUIRED( baseData.IsNotNull(), "BaseData is not null")
	-
	- DiffusionImageType* vols = dynamic_cast< DiffusionImageType* >(baseData.GetPointer());
	-
	- MITK_TEST_CONDITION_REQUIRED( vols != nullptr, "Casting basedata to diffusion image successfull." );
	-
	- // filter
	- typedef itk::B0ImageExtractionToSeparateImageFilter< short, short> FilterType;
	- typename FilterType::Pointer filter = FilterType::New();
	-
	- MITK_TEST_CONDITION_REQUIRED(filter.IsNotNull(), "Filter instance created. ");
	-
	- filter->SetInput(vols->GetVectorImage());
	- filter->SetDirections(vols->GetDirections());
	- filter->Update();
	-
	- // output
	- mitk::Image::Pointer mitkImage = mitk::Image::New();
	-
	- MITK_TEST_CONDITION_REQUIRED( mitkImage.IsNotNull(), "mitkImage not null." );
	-
	- mitkImage->InitializeByItk( filter->GetOutput() );
	-
	- MITK_TEST_CONDITION_REQUIRED( mitkImage->GetDimension()==4, "Output image is a 4D image.");
	-
	- mitkImage->SetImportChannel( filter->GetOutput()->GetBufferPointer() );
	-
	- mitk::LocaleSwitch localeSwitch("C");
	- typedef itk::ImageFileWriter< FilterType::OutputImageType > itkImageWriterType;
	- typename itkImageWriterType::Pointer itkWriter = itkImageWriterType::New();
	-
	- itkWriter->SetFileName( argv[2] );
	- itkWriter->SetInput( filter->GetOutput() );
	-
	- try
	- {
	- itkWriter->Update();
	- }
	- catch(itk::ExceptionObject &e)
	- {
	- MITK_ERROR << "Catched exception from image writer. " << e.what();
	- }
	-
	- /*
	- // write output
	- mitk::ImageWriter::Pointer writer = mitk::ImageWriter::New();
	- MITK_TEST_CONDITION_REQUIRED( writer.IsNotNull(), "Writer instance created. ");
	-
	- writer->SetInput( mitkImage );
	- writer->SetExtension(".nrrd");
	- writer->SetFileName( "/localdata/hering/_Images/TestB0Extraction" );
	-
	- writer->Update();
	-*/
	- // always end with this!
	- MITK_TEST_END();
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/Testing/mitkConvertDWITypeTest.cpp b/Modules/DiffusionImaging/DiffusionCore/Testing/mitkConvertDWITypeTest.cpp
	deleted file mode 100644
	index 7594f39ce9..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/Testing/mitkConvertDWITypeTest.cpp
	+++ /dev/null
	@@ -1,46 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkTestingMacros.h"
	-#include "mitkIOUtil.h"
	-
	-#include "mitkDWIHeadMotionCorrectionFilter.h"
	-
	-/**
	- * @brief Custom test to provide CMD-line access to the mitk::DWIHeadMotionCorrectionFilter
	- *
	- * @param argv : Input and Output image full path
	- */
	-int mitkConvertDWITypeTest( int argc, char* argv[] )
	-{
	- MITK_TEST_BEGIN("mitkConvertDWITypeTest");
	-
	- MITK_TEST_CONDITION_REQUIRED( argc > 2, "Specify input and output.");
	-
	- mitk::Image::Pointer inputImage = mitk::IOUtil::Load<mitk::Image>( argv[1] );
	-
	- try
	- {
	- mitk::IOUtil::Save(inputImage, argv[2]);
	- }
	- catch( const itk::ExceptionObject& e)
	- {
	- MITK_ERROR << "Caught exception: " << e.what();
	- mitkThrow() << "Failed with exception from subprocess!";
	- }
	-
	- MITK_TEST_END();
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/Testing/mitkDWHeadMotionCorrectionTest.cpp b/Modules/DiffusionImaging/DiffusionCore/Testing/mitkDWHeadMotionCorrectionTest.cpp
	deleted file mode 100644
	index 7a6ec764e2..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/Testing/mitkDWHeadMotionCorrectionTest.cpp
	+++ /dev/null
	@@ -1,55 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkTestingMacros.h"
	-#include "mitkIOUtil.h"
	-
	-#include <mitkDWIHeadMotionCorrectionFilter.h>
	-
	-typedef short DiffusionPixelType;
	-typedef mitk::Image DiffusionImageType;
	-
	-/**
	- * @brief Custom test to provide CMD-line access to the mitk::DWIHeadMotionCorrectionFilter
	- *
	- * @param argv : Input and Output image full path
	- */
	-int mitkDWHeadMotionCorrectionTest( int argc, char* argv[] )
	-{
	- MITK_TEST_BEGIN("mitkDWHeadMotionCorrectionTest");
	-
	- MITK_TEST_CONDITION_REQUIRED( argc > 2, "Specify input and output.");
	-
	- mitk::Image::Pointer inputImage = mitk::IOUtil::Load<mitk::Image>( argv[1] );
	- DiffusionImageType* dwimage = static_cast<DiffusionImageType*>( inputImage.GetPointer() );
	-
	- mitk::DWIHeadMotionCorrectionFilter::Pointer corrfilter = mitk::DWIHeadMotionCorrectionFilter::New();
	-
	- corrfilter->SetInput( dwimage );
	- corrfilter->Update();
	-
	- try
	- {
	- mitk::IOUtil::Save(corrfilter->GetOutput(), argv[2]);
	- }
	- catch( const itk::ExceptionObject& e)
	- {
	- MITK_ERROR << "Catched exception: " << e.what();
	- mitkThrow() << "Failed with exception from subprocess!";
	- }
	-
	- MITK_TEST_END();
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/Testing/mitkDiffusionDICOMFileReaderTest.cpp b/Modules/DiffusionImaging/DiffusionCore/Testing/mitkDiffusionDICOMFileReaderTest.cpp
	deleted file mode 100644
	index bfdd73c944..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/Testing/mitkDiffusionDICOMFileReaderTest.cpp
	+++ /dev/null
	@@ -1,113 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkDiffusionDICOMFileReader.h"
	-#include "mitkDiffusionDICOMFileReaderTestHelper.h"
	-#include "mitkDICOMTagBasedSorter.h"
	-#include "mitkDICOMSortByTag.h"
	-
	-#include <mitkIOUtil.h>
	-
	-#include "mitkTestingMacros.h"
	-
	-using mitk::DICOMTag;
	-
	-int mitkDiffusionDICOMFileReaderTest(int argc, char* argv[])
	-{
	- MITK_TEST_BEGIN("mitkDiffusionDICOMFileReaderTest");
	-
	- mitk::DiffusionDICOMFileReader::Pointer gdcmReader = mitk::DiffusionDICOMFileReader::New();
	- MITK_TEST_CONDITION_REQUIRED(gdcmReader.IsNotNull(), "DICOMITKSeriesGDCMReader can be instantiated.");
	-
	- std::string output_filename = "/tmp/dicom_out.dwi";
	- if( argc > 3)
	- {
	- mitk::DICOMFileReaderTestHelper::SetTestInputFilenames( argc-1,argv );
	- output_filename = std::string( argv[argc-1] );
	- }
	- else
	- {
	- mitk::DICOMFileReaderTestHelper::SetTestInputFilenames( argc,argv );
	- }
	-
	- // check the Set/GetInput function
	- mitk::DICOMFileReaderTestHelper::TestInputFilenames( gdcmReader );
	- MITK_INFO << "Test input filenanems";
	-
	- // check that output is a good reproduction of input (no duplicates, no new elements)
	- mitk::DICOMFileReaderTestHelper::TestOutputsContainInputs( gdcmReader );
	- MITK_INFO << "Test output";
	-
	- // repeat test with some more realistic sorting
	- gdcmReader = mitk::DiffusionDICOMFileReader::New(); // this also tests destruction
	- mitk::DICOMTagBasedSorter::Pointer tagSorter = mitk::DICOMTagBasedSorter::New();
	-
	- // Use tags as in Qmitk
	- // all the things that split by tag in DicomSeriesReader
	- tagSorter->AddDistinguishingTag( DICOMTag(0x0028, 0x0010) ); // Number of Rows
	- tagSorter->AddDistinguishingTag( DICOMTag(0x0028, 0x0011) ); // Number of Columns
	- tagSorter->AddDistinguishingTag( DICOMTag(0x0028, 0x0030) ); // Pixel Spacing
	- tagSorter->AddDistinguishingTag( DICOMTag(0x0018, 0x1164) ); // Imager Pixel Spacing
	- tagSorter->AddDistinguishingTag( DICOMTag(0x0020, 0x0037) ); // Image Orientation (Patient) // TODO add tolerance parameter (l. 1572 of original code)
	- // TODO handle as real vectors! cluster with configurable errors!
	- //tagSorter->AddDistinguishingTag( DICOMTag(0x0020, 0x000e) ); // Series Instance UID
	- //tagSorter->AddDistinguishingTag( DICOMTag(0x0020, 0x0010) );
	- tagSorter->AddDistinguishingTag( DICOMTag(0x0018, 0x0050) ); // Slice Thickness
	- tagSorter->AddDistinguishingTag( DICOMTag(0x0028, 0x0008) ); // Number of Frames
	- tagSorter->AddDistinguishingTag( DICOMTag(0x0020, 0x0052) ); // Frame of Reference UID
	-
	- // gdcmReader->AddSortingElement( tagSorter );
	- //mitk::DICOMFileReaderTestHelper::TestOutputsContainInputs( gdcmReader );
	-
	- mitk::DICOMSortCriterion::ConstPointer sorting =
	- mitk::DICOMSortByTag::New( DICOMTag(0x0020, 0x0013), // instance number
	- mitk::DICOMSortByTag::New( DICOMTag(0x0020, 0x0012), // aqcuisition number
	- mitk::DICOMSortByTag::New( DICOMTag(0x0008, 0x0032), // aqcuisition time
	- mitk::DICOMSortByTag::New( DICOMTag(0x0018, 0x1060), // trigger time
	- mitk::DICOMSortByTag::New( DICOMTag(0x0008, 0x0018) // SOP instance UID (last resort, not really meaningful but decides clearly)
	- ).GetPointer()
	- ).GetPointer()
	- ).GetPointer()
	- ).GetPointer()
	- ).GetPointer();
	- tagSorter->SetSortCriterion( sorting );
	-
	- MITK_INFO << "Created sort";
	-
	- gdcmReader->AddSortingElement( tagSorter );
	- mitk::DICOMFileReaderTestHelper::TestOutputsContainInputs( gdcmReader );
	-
	- MITK_INFO << "Created sort";
	-
	- //gdcmReader->PrintOutputs(std::cout, true);
	-
	- // really load images
	- //mitk::DICOMFileReaderTestHelper::TestMitkImagesAreLoaded( gdcmReader );
	- gdcmReader->LoadImages();
	-
	- mitk::Image::Pointer loaded_image = gdcmReader->GetOutput(0).GetMitkImage();
	-
	- try
	- {
	- mitk::IOUtil::Save(loaded_image, output_filename.c_str());
	- }
	- catch( const itk::ExceptionObject& e)
	- {
	- MITK_TEST_FAILED_MSG( << "Writer failed : " << e.what() );
	- }
	-
	- MITK_TEST_END();
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/Testing/mitkDiffusionDICOMFileReaderTestHelper.h b/Modules/DiffusionImaging/DiffusionCore/Testing/mitkDiffusionDICOMFileReaderTestHelper.h
	deleted file mode 100644
	index 9453ba312d..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/Testing/mitkDiffusionDICOMFileReaderTestHelper.h
	+++ /dev/null
	@@ -1,153 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef mitkDiffusionDICOMFileReaderTestHelper_h
	-#define mitkDiffusionDICOMFileReaderTestHelper_h
	-
	-#include "mitkDICOMFileReader.h"
	-#include "mitkDICOMEnums.h"
	-
	-#include "mitkTestingMacros.h"
	-
	-namespace mitk
	-{
	-
	-class DICOMFileReaderTestHelper
	-{
	- public:
	-
	-static StringList& GetInputFilenames()
	-{
	- static StringList inputs;
	- return inputs;
	-}
	-
	-static void SetTestInputFilenames(int argc, char* argv[])
	-{
	- mitk::StringList inputFiles;
	-
	- for (int a = 1; a < argc; ++a)
	- {
	- inputFiles.push_back( argv[a] );
	- }
	-
	- GetInputFilenames() = inputFiles;
	-}
	-
	-
	-static void SetTestInputFilenames(const StringList& filenames)
	-{
	- GetInputFilenames() = filenames;
	-}
	-
	-static void TestInputFilenames(DICOMFileReader* reader)
	-{
	- StringList inputFiles = GetInputFilenames();
	- reader->SetInputFiles( inputFiles );
	-
	- const StringList& inputFilesReturned = reader->GetInputFiles();
	- MITK_TEST_CONDITION( inputFilesReturned.size() == inputFiles.size(), "Input file list is received")
	- MITK_TEST_CONDITION( reader->GetNumberOfOutputs() == 0, "No outputs without analysis")
	-
	- // TODO: check that strings are actually contained
	-}
	-
	-static void TestOutputsContainInputs(DICOMFileReader* reader)
	-{
	- StringList inputFiles = GetInputFilenames();
	- reader->SetInputFiles( inputFiles );
	-
	- reader->AnalyzeInputFiles();
	-
	- StringList allSortedInputsFiles;
	-
	- unsigned int numberOfOutputs = reader->GetNumberOfOutputs();
	- for (unsigned int o = 0; o < numberOfOutputs; ++o)
	- {
	- const DICOMImageBlockDescriptor block = reader->GetOutput(o);
	-
	- const DICOMImageFrameList& outputFiles = block.GetImageFrameList();
	- for(DICOMImageFrameList::const_iterator iter = outputFiles.begin();
	- iter != outputFiles.end();
	- ++iter)
	- {
	- // check that output is part of input
	- StringList::iterator inputPositionOfCurrentOutput = std::find( inputFiles.begin(), inputFiles.end(), (*iter)->Filename );
	- if (inputPositionOfCurrentOutput != inputFiles.end())
	- {
	- // check that output is only part of ONE output
	- StringList::iterator outputPositionOfCurrentOutput = std::find( allSortedInputsFiles.begin(), allSortedInputsFiles.end(), (*iter)->Filename );
	- if (outputPositionOfCurrentOutput == allSortedInputsFiles.end())
	- {
	- // was not in list before
	- allSortedInputsFiles.push_back( *inputPositionOfCurrentOutput );
	- }
	- else
	- {
	- reader->PrintOutputs(std::cout);
	- MITK_TEST_CONDITION_REQUIRED(false, "File '" << (*iter)->Filename << "' appears in TWO outputs. Readers are expected to use each frame only once." )
	- }
	- }
	- else
	- {
	- reader->PrintOutputs(std::cout);
	- MITK_TEST_CONDITION_REQUIRED(false, "File '" << (*iter)->Filename << "' appears in output, but it was never part of the input list." )
	- }
	- }
	- }
	-
	- MITK_TEST_CONDITION( allSortedInputsFiles.size() == inputFiles.size(), "Output list size (" << allSortedInputsFiles.size() << ") equals input list size (" << inputFiles.size() << ")" )
	-
	- try
	- {
	- const DICOMImageBlockDescriptor block = reader->GetOutput( inputFiles.size() );
	- MITK_TEST_CONDITION(false, "Invalid indices for GetOutput() should throw exception")
	- }
	- catch( std::invalid_argument& )
	- {
	- MITK_TEST_CONDITION(true, "Invalid indices for GetOutput() should throw exception")
	- }
	-}
	-
	-static void TestMitkImagesAreLoaded(DICOMFileReader* reader)
	-{
	- StringList inputFiles = GetInputFilenames();
	- reader->SetInputFiles( inputFiles );
	-
	- reader->AnalyzeInputFiles();
	- reader->LoadImages();
	-
	- unsigned int numberOfOutputs = reader->GetNumberOfOutputs();
	- for (unsigned int o = 0; o < numberOfOutputs; ++o)
	- {
	- const DICOMImageBlockDescriptor block = reader->GetOutput(o);
	-
	- const DICOMImageFrameList& outputFiles = block.GetImageFrameList();
	- mitk::Image::Pointer mitkImage = block.GetMitkImage();
	-
	- MITK_INFO << "-------------------------------------------";
	- MITK_INFO << "Output " << o << " at " << (void*) mitkImage.GetPointer();
	- MITK_INFO << " Number of files: " << outputFiles.size();
	- MITK_INFO << " Dimensions: " << mitkImage->GetDimension(0) << " " << mitkImage->GetDimension(1) << " " << mitkImage->GetDimension(2);
	- }
	-}
	-
	-
	-}; // end test class
	-
	-} // namespace
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/Testing/mitkDiffusionPropertySerializerTest.cpp b/Modules/DiffusionImaging/DiffusionCore/Testing/mitkDiffusionPropertySerializerTest.cpp
	deleted file mode 100644
	index c847a59745..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/Testing/mitkDiffusionPropertySerializerTest.cpp
	+++ /dev/null
	@@ -1,183 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkIOUtil.h"
	-#include "mitkTestingMacros.h"
	-#include "mitkTestFixture.h"
	-
	-#include <mitkBasePropertySerializer.h>
	-
	-#include <mitkBValueMapProperty.h>
	-
	-#include <mitkGradientDirectionsProperty.h>
	-#include <mitkMeasurementFrameProperty.h>
	-
	-#include <mitkDiffusionPropertyHelper.h>
	-
	-class mitkDiffusionPropertySerializerTestSuite : public mitk::TestFixture
	-{
	-
	- CPPUNIT_TEST_SUITE(mitkDiffusionPropertySerializerTestSuite);
	- MITK_TEST(Equal_SerializeandDeserialize_ReturnsTrue);
	-
	- //MITK_TEST(Equal_DifferentChannels_ReturnFalse);
	-
	-
	- CPPUNIT_TEST_SUITE_END();
	-
	-private:
	-
	- /** Members used inside the different (sub-)tests. All members are initialized via setUp().*/
	- mitk::PropertyList::Pointer propList; //represet image propertylist
	- mitk::BValueMapProperty::Pointer bvaluemap_prop;
	- mitk::GradientDirectionsProperty::Pointer gradientdirection_prop;
	- mitk::MeasurementFrameProperty::Pointer measurementframe_prop;
	-
	-public:
	-
	- /**
	-* @brief Setup Always call this method before each Test-case to ensure correct and new intialization of the used members for a new test case. (If the members are not used in a test, the method does not need to be called).
	-*/
	- void setUp() override
	- {
	-
	- propList = mitk::PropertyList::New();
	-
	- mitk::BValueMapProperty::BValueMap map;
	- std::vector<unsigned int> indices1;
	- indices1.push_back(1);
	- indices1.push_back(2);
	- indices1.push_back(3);
	- indices1.push_back(4);
	-
	- map[0] = indices1;
	- std::vector<unsigned int> indices2;
	- indices2.push_back(4);
	- indices2.push_back(3);
	- indices2.push_back(2);
	- indices2.push_back(1);
	-
	- map[1000] = indices2;
	- bvaluemap_prop = mitk::BValueMapProperty::New(map).GetPointer();
	- propList->SetProperty(mitk::DiffusionPropertyHelper::GetBvaluePropertyName().c_str(), bvaluemap_prop);
	-
	- mitk::GradientDirectionsProperty::GradientDirectionsContainerType::Pointer gdc;
	- gdc = mitk::GradientDirectionsProperty::GradientDirectionsContainerType::New();
	-
	- double a[3] = {3.0,4.0,1.4};
	- vnl_vector_fixed<double,3> vec1;
	- vec1.set(a);
	- gdc->push_back(vec1);
	-
	- double b[3] = {1.0,5.0,123.4};
	- vnl_vector_fixed<double,3> vec2;
	- vec2.set(b);
	- gdc->push_back(vec2);
	-
	- double c[3] = {13.0,84.02,13.4};
	- vnl_vector_fixed<double,3> vec3;
	- vec3.set(c);
	- gdc->push_back(vec3);
	-
	-
	- gradientdirection_prop = mitk::GradientDirectionsProperty::New(gdc.GetPointer()).GetPointer();
	- propList->ReplaceProperty(mitk::DiffusionPropertyHelper::GetGradientContainerPropertyName().c_str(), gradientdirection_prop);
	-
	- mitk::MeasurementFrameProperty::MeasurementFrameType mft;
	-
	- double row0[3] = {1,0,0};
	- double row1[3] = {0,1,0};
	- double row2[3] = {0,0,1};
	-
	- mft.set_row(0,row0);
	- mft.set_row(1,row1);
	- mft.set_row(2,row2);
	-
	- measurementframe_prop = mitk::MeasurementFrameProperty::New(mft).GetPointer();
	- propList->ReplaceProperty(mitk::DiffusionPropertyHelper::GetGradientContainerPropertyName().c_str(), measurementframe_prop);
	- }
	-
	- void tearDown() override
	- {
	-
	- }
	-
	- void Equal_SerializeandDeserialize_ReturnsTrue()
	- {
	-
	- assert(propList);
	-
	- /* try to serialize each property in the list, then deserialize again and check for equality */
	- for (mitk::PropertyList::PropertyMap::const_iterator it = propList->GetMap()->begin(); it != propList->GetMap()->end(); ++it)
	- {
	- const mitk::BaseProperty* prop = it->second;
	- // construct name of serializer class
	- std::string serializername = std::string(prop->GetNameOfClass()) + "Serializer";
	- std::list<itk::LightObject::Pointer> allSerializers = itk::ObjectFactoryBase::CreateAllInstance(serializername.c_str());
	- MITK_TEST_CONDITION(allSerializers.size() > 0, std::string("Creating serializers for ") + serializername);
	- if (allSerializers.size() == 0)
	- {
	- MITK_TEST_OUTPUT( << "serialization not possible, skipping " << prop->GetNameOfClass());
	- continue;
	- }
	- if (allSerializers.size() > 1)
	- {
	- MITK_TEST_OUTPUT (<< "Warning: " << allSerializers.size() << " serializers found for " << prop->GetNameOfClass() << "testing only the first one.");
	- }
	- mitk::BasePropertySerializer* serializer = dynamic_cast<mitk::BasePropertySerializer*>( allSerializers.begin()->GetPointer());
	- MITK_TEST_CONDITION(serializer != nullptr, serializername + std::string(" is valid"));
	- if (serializer != nullptr)
	- {
	- serializer->SetProperty(prop);
	- TiXmlElement* valueelement = nullptr;
	- try
	- {
	- valueelement = serializer->Serialize();
	-// TiXmlPrinter p;
	-// valueelement->Accept(&p);
	-// MITK_INFO << p.CStr();
	- }
	- catch (...)
	- {
	- }
	- MITK_TEST_CONDITION(valueelement != nullptr, std::string("Serialize property with ") + serializername);
	-
	- if (valueelement == nullptr)
	- {
	- MITK_TEST_OUTPUT( << "serialization failed, skipping deserialization");
	- continue;
	- }
	-
	- mitk::BaseProperty::Pointer deserializedProp = serializer->Deserialize( valueelement );
	- MITK_TEST_CONDITION(deserializedProp.IsNotNull(), "serializer created valid property");
	- if (deserializedProp.IsNotNull())
	- {
	- MITK_TEST_CONDITION((deserializedProp.GetPointer()) == prop, "deserialized property equals initial property for type " << prop->GetNameOfClass());
	- }
	-
	- }
	- else
	- {
	- MITK_TEST_OUTPUT( << "created serializer object is of class " << allSerializers.begin()->GetPointer()->GetNameOfClass())
	- }
	- } // for all properties
	-
	- }
	-
	-
	-};
	-
	-MITK_TEST_SUITE_REGISTRATION(mitkDiffusionPropertySerializer)
	diff --git a/Modules/DiffusionImaging/DiffusionCore/Testing/mitkExtractSingleShellTest.cpp b/Modules/DiffusionImaging/DiffusionCore/Testing/mitkExtractSingleShellTest.cpp
	deleted file mode 100644
	index acefe6811a..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/Testing/mitkExtractSingleShellTest.cpp
	+++ /dev/null
	@@ -1,97 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkTestingMacros.h"
	-#include "mitkIOUtil.h"
	-
	-#include <itkElectrostaticRepulsionDiffusionGradientReductionFilter.h>
	-
	-#include "mitkDWIHeadMotionCorrectionFilter.h"
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <mitkImageCast.h>
	-#include <mitkProperties.h>
	-
	-typedef short DiffusionPixelType;
	-
	-
	-int mitkExtractSingleShellTest( int argc, char* argv[] )
	-{
	- MITK_TEST_BEGIN("mitkExtractSingleShellTest");
	-
	- MITK_TEST_CONDITION_REQUIRED( argc > 3, "Specify input and output and the shell to be extracted");
	-
	- /*
	- 1. Get input data
	- */
	- mitk::Image::Pointer dwimage = mitk::IOUtil::Load<mitk::Image>( argv[1] );
	-
	- unsigned int extract_value = 0;
	- std::istringstream input(argv[3]);
	-
	- input >> extract_value;
	-
	- typedef itk::ElectrostaticRepulsionDiffusionGradientReductionFilter<DiffusionPixelType, DiffusionPixelType> FilterType;
	- typedef mitk::DiffusionPropertyHelper::BValueMapType BValueMap;
	-
	- // GetShellSelection from GUI
	- BValueMap shellSelectionMap;
	- BValueMap originalShellMap = mitk::DiffusionPropertyHelper::GetBValueMap(dwimage);
	- std::vector<unsigned int> newNumGradientDirections;
	-
	- shellSelectionMap[extract_value] = originalShellMap[extract_value];
	- newNumGradientDirections.push_back( originalShellMap[extract_value].size() ) ;
	-
	- itk::VectorImage< short, 3 >::Pointer itkVectorImagePointer = itk::VectorImage< short, 3 >::New();
	- mitk::CastToItkImage(dwimage, itkVectorImagePointer);
	- itk::VectorImage< short, 3 > *vectorImage = itkVectorImagePointer.GetPointer();
	-
	- mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer gradientContainer = mitk::DiffusionPropertyHelper::GetGradientContainer(dwimage);
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetInput(vectorImage);
	- filter->SetOriginalGradientDirections(gradientContainer);
	- filter->SetNumGradientDirections(newNumGradientDirections);
	- filter->SetOriginalBValueMap(originalShellMap);
	- filter->SetShellSelectionBValueMap(shellSelectionMap);
	-
	- try
	- {
	- filter->Update();
	- }
	- catch( const itk::ExceptionObject& e)
	- {
	- MITK_TEST_FAILED_MSG( << "Failed due to ITK exception: " << e.what() );
	- }
	-
	- mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( filter->GetOutput() );
	- mitk::DiffusionPropertyHelper::CopyProperties(dwimage, outImage, true);
	- mitk::DiffusionPropertyHelper::SetGradientContainer(outImage, filter->GetGradientDirections());
	- mitk::DiffusionPropertyHelper::InitializeImage( outImage );
	-
	- /*
	- * 3. Write output data
	- **/
	- try
	- {
	- mitk::IOUtil::Save(outImage, argv[2]);
	- }
	- catch( const itk::ExceptionObject& e)
	- {
	- MITK_ERROR << "Catched exception: " << e.what();
	- mitkThrow() << "Failed with exception from subprocess!";
	- }
	-
	- MITK_TEST_END();
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/Testing/mitkImageReconstructionTest.cpp b/Modules/DiffusionImaging/DiffusionCore/Testing/mitkImageReconstructionTest.cpp
	deleted file mode 100755
	index ca208846be..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/Testing/mitkImageReconstructionTest.cpp
	+++ /dev/null
	@@ -1,155 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkImageCast.h>
	-#include <mitkTensorImage.h>
	-#include <mitkOdfImage.h>
	-#include <mitkIOUtil.h>
	-#include <itkDiffusionTensor3D.h>
	-#include <mitkTestingMacros.h>
	-#include <itkDiffusionTensor3DReconstructionImageFilter.h>
	-#include <itkDiffusionTensor3D.h>
	-#include <itkDiffusionQballReconstructionImageFilter.h>
	-#include <itkAnalyticalDiffusionQballReconstructionImageFilter.h>
	-#include <mitkImage.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-
	-int mitkImageReconstructionTest(int argc, char* argv[])
	-{
	- MITK_TEST_BEGIN("mitkImageReconstructionTest");
	-
	- MITK_TEST_CONDITION_REQUIRED(argc>1,"check for input data")
	-
	- try
	- {
	- mitk::Image::Pointer dwi = mitk::IOUtil::Load<mitk::Image>(argv[1]);
	-
	- itk::VectorImage<short,3>::Pointer itkVectorImagePointer = itk::VectorImage<short,3>::New();
	- mitk::CastToItkImage(dwi, itkVectorImagePointer);
	-
	- float b_value = mitk::DiffusionPropertyHelper::GetReferenceBValue( dwi );
	- mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer gradients = mitk::DiffusionPropertyHelper::GetGradientContainer(dwi);
	- {
	- MITK_INFO << "Tensor reconstruction " << argv[2];
	- mitk::TensorImage::Pointer tensorImage = mitk::IOUtil::Load<mitk::TensorImage>(argv[2]);
	- typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, float > TensorReconstructionImageFilterType;
	- TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New();
	- filter->SetBValue( b_value );
	- filter->SetGradientImage( gradients, itkVectorImagePointer );
	- filter->Update();
	- mitk::TensorImage::Pointer testImage = mitk::TensorImage::New();
	- testImage->InitializeByItk( filter->GetOutput() );
	- testImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
	- MITK_TEST_CONDITION_REQUIRED(mitk::Equal(testImage, tensorImage, 0.0001, true), "tensor reconstruction test.");
	- }
	-
	- {
	- MITK_INFO << "Numerical Q-ball reconstruction " << argv[3];
	- mitk::OdfImage::Pointer odfImage = mitk::IOUtil::Load<mitk::OdfImage>(argv[3]);
	- typedef itk::DiffusionQballReconstructionImageFilter<short, short, float, ODF_SAMPLING_SIZE> QballReconstructionImageFilterType;
	- QballReconstructionImageFilterType::Pointer filter = QballReconstructionImageFilterType::New();
	- filter->SetBValue( b_value );
	- filter->SetGradientImage( gradients, itkVectorImagePointer );
	- filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_STANDARD);
	- filter->Update();
	- mitk::OdfImage::Pointer testImage = mitk::OdfImage::New();
	- testImage->InitializeByItk( filter->GetOutput() );
	- testImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
	- MITK_TEST_CONDITION_REQUIRED(mitk::Equal(testImage, odfImage, 0.0001, true), "Numerical Q-ball reconstruction test.");
	- }
	-
	- {
	- MITK_INFO << "Standard Q-ball reconstruction " << argv[4];
	- mitk::OdfImage::Pointer odfImage = mitk::IOUtil::Load<mitk::OdfImage>(argv[4]);
	- typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,4,ODF_SAMPLING_SIZE> FilterType;
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetBValue( b_value );
	- filter->SetGradientImage( gradients, itkVectorImagePointer );
	- filter->SetLambda(0.006);
	- filter->SetNormalizationMethod(FilterType::QBAR_STANDARD);
	- filter->Update();
	- mitk::OdfImage::Pointer testImage = mitk::OdfImage::New();
	- testImage->InitializeByItk( filter->GetOutput() );
	- testImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
	- MITK_TEST_CONDITION_REQUIRED(mitk::Equal(testImage, odfImage, 0.0001, true), "Standard Q-ball reconstruction test.");
	- }
	-
	- {
	- MITK_INFO << "CSA Q-ball reconstruction " << argv[5];
	- mitk::OdfImage::Pointer odfImage = mitk::IOUtil::Load<mitk::OdfImage>(argv[5]);
	- typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,4,ODF_SAMPLING_SIZE> FilterType;
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetBValue( b_value );
	- filter->SetGradientImage( gradients, itkVectorImagePointer );
	- filter->SetLambda(0.006);
	- filter->SetNormalizationMethod(FilterType::QBAR_SOLID_ANGLE);
	- filter->Update();
	- mitk::OdfImage::Pointer testImage = mitk::OdfImage::New();
	- testImage->InitializeByItk( filter->GetOutput() );
	- testImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
	- MITK_TEST_CONDITION_REQUIRED(mitk::Equal(testImage, odfImage, 0.0001, true), "CSA Q-ball reconstruction test.");
	- }
	-
	- {
	- MITK_INFO << "ADC profile reconstruction " << argv[6];
	- mitk::OdfImage::Pointer odfImage = mitk::IOUtil::Load<mitk::OdfImage>(argv[6]);
	- typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,4,ODF_SAMPLING_SIZE> FilterType;
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetBValue( b_value );
	- filter->SetGradientImage( gradients, itkVectorImagePointer );
	- filter->SetLambda(0.006);
	- filter->SetNormalizationMethod(FilterType::QBAR_ADC_ONLY);
	- filter->Update();
	- mitk::OdfImage::Pointer testImage = mitk::OdfImage::New();
	- testImage->InitializeByItk( filter->GetOutput() );
	- testImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
	- MITK_TEST_CONDITION_REQUIRED(mitk::Equal(testImage, odfImage, 0.0001, true), "ADC profile reconstruction test.");
	- }
	-
	- {
	- MITK_INFO << "Raw signal modeling " << argv[7];
	- mitk::OdfImage::Pointer odfImage = mitk::IOUtil::Load<mitk::OdfImage>(argv[7]);
	- typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,4,ODF_SAMPLING_SIZE> FilterType;
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetBValue( b_value );
	- filter->SetGradientImage( gradients, itkVectorImagePointer );
	- filter->SetLambda(0.006);
	- filter->SetNormalizationMethod(FilterType::QBAR_RAW_SIGNAL);
	- filter->Update();
	- mitk::OdfImage::Pointer testImage = mitk::OdfImage::New();
	- testImage->InitializeByItk( filter->GetOutput() );
	- testImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
	- MITK_TEST_CONDITION_REQUIRED(mitk::Equal(testImage, odfImage, 0.1, true), "Raw signal modeling test.");
	- }
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- MITK_INFO << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (const std::exception& e)
	- {
	- MITK_INFO << e.what();
	- return EXIT_FAILURE;
	- }
	- catch (...)
	- {
	- MITK_INFO << "ERROR!?!";
	- return EXIT_FAILURE;
	- }
	-
	- MITK_TEST_END();
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/Testing/mitkNonLocalMeansDenoisingTest.cpp b/Modules/DiffusionImaging/DiffusionCore/Testing/mitkNonLocalMeansDenoisingTest.cpp
	deleted file mode 100644
	index daa077efe1..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/Testing/mitkNonLocalMeansDenoisingTest.cpp
	+++ /dev/null
	@@ -1,169 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkIOUtil.h"
	-#include "mitkTestingMacros.h"
	-#include "mitkTestFixture.h"
	-#include "itkNonLocalMeansDenoisingFilter.h"
	-#include "mitkGradientDirectionsProperty.h"
	-#include "mitkITKImageImport.h"
	-#include <mitkImageCast.h>
	-
	-class mitkNonLocalMeansDenoisingTestSuite : public mitk::TestFixture
	-{
	-
	- CPPUNIT_TEST_SUITE(mitkNonLocalMeansDenoisingTestSuite);
	- MITK_TEST(Denoise_NLMg_shouldReturnTrue);
	- MITK_TEST(Denoise_NLMr_shouldReturnTrue);
	- MITK_TEST(Denoise_NLMv_shouldReturnTrue);
	- MITK_TEST(Denoise_NLMvr_shouldReturnTrue);
	- CPPUNIT_TEST_SUITE_END();
	-
	-private:
	-
	- typedef itk::VectorImage<short,3> VectorImagetType;
	-
	- /** Members used inside the different (sub-)tests. All members are initialized via setUp().*/
	- mitk::Image::Pointer m_Image;
	- mitk::Image::Pointer m_ReferenceImage;
	- mitk::Image::Pointer m_DenoisedImage;
	- itk::Image<short, 3>::Pointer m_ImageMask;
	- itk::NonLocalMeansDenoisingFilter<short>::Pointer m_DenoisingFilter;
	-
	-public:
	-
	- /**
	-* @brief Setup Always call this method before each Test-case to ensure correct and new intialization of the used members for a new test case. (If the members are not used in a test, the method does not need to be called).
	-*/
	- void setUp() override
	- {
	- //generate test images
	- std::string imagePath = GetTestDataFilePath("DiffusionImaging/Denoising/test_multi.dwi");
	-
	- m_Image = mitk::IOUtil::Load<mitk::Image>(imagePath);
	- m_ReferenceImage = nullptr;
	- m_DenoisedImage = mitk::Image::New();
	-
	- //initialise Filter
	- m_DenoisingFilter = itk::NonLocalMeansDenoisingFilter<short>::New();
	- VectorImagetType::Pointer vectorImage;
	- mitk::CastToItkImage(m_Image,vectorImage);
	- m_DenoisingFilter->SetInputImage(vectorImage);
	- m_DenoisingFilter->SetNumberOfThreads(1);
	- m_DenoisingFilter->SetComparisonRadius(1);
	- m_DenoisingFilter->SetSearchRadius(1);
	- m_DenoisingFilter->SetVariance(500);
	- }
	-
	- void tearDown() override
	- {
	- m_Image = nullptr;
	- m_ImageMask = nullptr;
	- m_ReferenceImage = nullptr;
	- m_DenoisingFilter = nullptr;
	- m_DenoisedImage = nullptr;
	- }
	-
	- void Denoise_NLMg_shouldReturnTrue()
	- {
	- std::string referenceImagePath = GetTestDataFilePath("DiffusionImaging/Denoising/test_multi_NLMg.dwi");
	- m_ReferenceImage = mitk::IOUtil::Load<mitk::Image>(referenceImagePath);
	-
	- m_DenoisingFilter->SetUseRicianAdaption(false);
	- m_DenoisingFilter->SetUseJointInformation(false);
	- try
	- {
	- m_DenoisingFilter->Update();
	- }
	- catch(std::exception& e)
	- {
	- MITK_ERROR << e.what();
	- }
	-
	- mitk::GrabItkImageMemory(m_DenoisingFilter->GetOutput(),m_DenoisedImage);
	- m_DenoisedImage->SetPropertyList(m_Image->GetPropertyList()->Clone());
	-
	- MITK_ASSERT_EQUAL( m_DenoisedImage, m_ReferenceImage, "NLMg should always return the same result.");
	- }
	-
	- void Denoise_NLMr_shouldReturnTrue()
	- {
	- std::string referenceImagePath = GetTestDataFilePath("DiffusionImaging/Denoising/test_multi_NLMr.dwi");
	- m_ReferenceImage = mitk::IOUtil::Load<mitk::Image>(referenceImagePath);
	-
	- m_DenoisingFilter->SetUseRicianAdaption(true);
	- m_DenoisingFilter->SetUseJointInformation(false);
	- try
	- {
	- m_DenoisingFilter->Update();
	- }
	- catch(std::exception& e)
	- {
	- MITK_ERROR << e.what();
	- }
	-
	- mitk::GrabItkImageMemory(m_DenoisingFilter->GetOutput(),m_DenoisedImage);
	- m_DenoisedImage->SetPropertyList(m_Image->GetPropertyList()->Clone());
	-
	- MITK_ASSERT_EQUAL( m_DenoisedImage, m_ReferenceImage, "NLMr should always return the same result.");
	- }
	-
	- void Denoise_NLMv_shouldReturnTrue()
	- {
	- std::string referenceImagePath = GetTestDataFilePath("DiffusionImaging/Denoising/test_multi_NLMv.dwi");
	- m_ReferenceImage = mitk::IOUtil::Load<mitk::Image>(referenceImagePath);
	- m_DenoisingFilter->SetUseRicianAdaption(false);
	- m_DenoisingFilter->SetUseJointInformation(true);
	- try
	- {
	- m_DenoisingFilter->Update();
	- }
	- catch(std::exception& e)
	- {
	- MITK_ERROR << e.what();
	- }
	-
	- mitk::GrabItkImageMemory(m_DenoisingFilter->GetOutput(),m_DenoisedImage);
	- m_DenoisedImage->SetPropertyList(m_Image->GetPropertyList()->Clone());
	-
	- MITK_ASSERT_EQUAL( m_DenoisedImage, m_ReferenceImage, "NLMv should always return the same result.");
	- }
	-
	- void Denoise_NLMvr_shouldReturnTrue()
	- {
	- std::string referenceImagePath = GetTestDataFilePath("DiffusionImaging/Denoising/test_multi_NLMvr.dwi");
	- m_ReferenceImage = mitk::IOUtil::Load<mitk::Image>(referenceImagePath);
	-
	- m_DenoisingFilter->SetUseRicianAdaption(true);
	- m_DenoisingFilter->SetUseJointInformation(true);
	- try
	- {
	- m_DenoisingFilter->Update();
	- }
	- catch(std::exception& e)
	- {
	- MITK_ERROR << e.what();
	- }
	-
	- mitk::GrabItkImageMemory(m_DenoisingFilter->GetOutput(),m_DenoisedImage);
	- m_DenoisedImage->SetPropertyList(m_Image->GetPropertyList()->Clone());
	-
	- MITK_ASSERT_EQUAL( m_DenoisedImage, m_ReferenceImage, "NLMvr should always return the same result.");
	- }
	-
	-};
	-
	-MITK_TEST_SUITE_REGISTRATION(mitkNonLocalMeansDenoising)
	diff --git a/Modules/DiffusionImaging/DiffusionCore/Testing/mitkPyramidImageRegistrationMethodTest.cpp b/Modules/DiffusionImaging/DiffusionCore/Testing/mitkPyramidImageRegistrationMethodTest.cpp
	deleted file mode 100644
	index 44a632e594..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/Testing/mitkPyramidImageRegistrationMethodTest.cpp
	+++ /dev/null
	@@ -1,156 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#include "mitkTestingMacros.h"
	-#include "mitkIOUtil.h"
	-
	-#include "Registration/mitkPyramidImageRegistrationMethod.h"
	-
	-#include <itkTransformFileWriter.h>
	-
	-
	-int mitkPyramidImageRegistrationMethodTest( int argc, char* argv[] )
	-{
	- if( argc < 4 )
	- {
	- MITK_ERROR << "Not enough input \n Usage: <TEST_NAME> fixed moving type [output_image [output_transform]]"
	- << "\n \t fixed : the path to the fixed image \n"
	- << " \t moving : path to the image to be registered"
	- << " \t type : Affine or Rigid defining the type of the transformation"
	- << " \t output_image : output file optional, (full) path, and optionally output_transform : also (full)path to file";
	- return EXIT_FAILURE;
	- }
	-
	- MITK_TEST_BEGIN("PyramidImageRegistrationMethodTest");
	-
	- mitk::Image::Pointer fixedImage = mitk::IOUtil::Load<mitk::Image>( argv[1] );
	- mitk::Image::Pointer movingImage = mitk::IOUtil::Load<mitk::Image>( argv[2] );
	-
	- std::string type_flag( argv[3] );
	-
	- mitk::PyramidImageRegistrationMethod::Pointer registrationMethod = mitk::PyramidImageRegistrationMethod::New();
	- registrationMethod->SetFixedImage( fixedImage );
	- registrationMethod->SetMovingImage( movingImage );
	-
	- if( type_flag == "Rigid" )
	- {
	- registrationMethod->SetTransformToRigid();
	- }
	- else if( type_flag == "Affine" )
	- {
	- registrationMethod->SetTransformToAffine();
	- }
	- else
	- {
	- MITK_WARN << " No type specified, using 'Affine' .";
	- }
	-
	- registrationMethod->Update();
	-
	- bool imageOutput = false;
	- bool transformOutput = false;
	-
	- std::string image_out_filename, transform_out_filename;
	-
	- std::string first_output( argv[4] );
	- // check for txt, otherwise suppose it is an image
	- if( first_output.find(".txt") != std::string::npos )
	- {
	- transformOutput = true;
	- transform_out_filename = first_output;
	- }
	- else
	- {
	- imageOutput = true;
	- image_out_filename = first_output;
	- }
	-
	- if( argc > 4 )
	- {
	- std::string second_output( argv[5] );
	- if( second_output.find(".txt") != std::string::npos )
	- {
	- transformOutput = true;
	- transform_out_filename = second_output;
	- }
	- }
	-
	- MITK_INFO << " Selected output: " << transform_out_filename << " " << image_out_filename;
	-
	- try{
	-
	- unsigned int paramCount = registrationMethod->GetNumberOfParameters();
	- double* params = new double[ paramCount ];
	- registrationMethod->GetParameters( &params[0] );
	-
	- std::cout << "Parameters: ";
	- for( unsigned int i=0; i< paramCount; i++)
	- {
	- std::cout << params[ i ] << " ";
	- }
	- std::cout << std::endl;
	-
	- if( imageOutput )
	- {
	- mitk::IOUtil::Save( registrationMethod->GetResampledMovingImage(), image_out_filename.c_str() );
	- }
	-
	-
	- if( transformOutput )
	- {
	-
	- itk::TransformFileWriter::Pointer writer = itk::TransformFileWriter::New();
	-
	- // Get transform parameter for resampling / saving
	- // Affine
	- if( paramCount == 12 )
	- {
	- typedef itk::AffineTransform< double > TransformType;
	- TransformType::Pointer transform = TransformType::New();
	-
	- TransformType::ParametersType affine_params( paramCount );
	- registrationMethod->GetParameters( &affine_params[0] );
	-
	- transform->SetParameters( affine_params );
	- writer->SetInput( transform );
	- }
	- // Rigid
	- else
	- {
	- typedef itk::Euler3DTransform< double > RigidTransformType;
	- RigidTransformType::Pointer rtransform = RigidTransformType::New();
	-
	- RigidTransformType::ParametersType rigid_params( paramCount );
	- registrationMethod->GetParameters( &rigid_params[0] );
	-
	- rtransform->SetParameters( rigid_params );
	- writer->SetInput( rtransform );
	- }
	-
	- writer->SetFileName( transform_out_filename );
	- writer->Update();
	- }
	-
	- }
	- catch( const std::exception &e)
	- {
	- MITK_ERROR << "Caught exception: " << e.what();
	- }
	-
	-
	- MITK_TEST_END();
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/CMakeLists.txt b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/CMakeLists.txt
	deleted file mode 100644
	index 81ada992e3..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/CMakeLists.txt
	+++ /dev/null
	@@ -1,9 +0,0 @@
	-MITK_CREATE_MODULE( DiffusionCoreIO
	- INCLUDE_DIRS
	- PRIVATE src/IO
	- DEPENDS PUBLIC MitkDiffusionCore MitkSceneSerialization
	- PACKAGE_DEPENDS
	- PRIVATE tinyxml
	- AUTOLOAD_WITH MitkCore
	- SUBPROJECTS MITK-DTI
	-)
	\ No newline at end of file
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/files.cmake b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/files.cmake
	deleted file mode 100644
	index a7f7003a49..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/files.cmake
	+++ /dev/null
	@@ -1,28 +0,0 @@
	-set(CPP_FILES
	- mitkDiffusionCoreIOActivator.cpp
	- mitkPeakImageReader.cpp
	- mitkNrrdTensorImageReader.cpp
	- mitkNrrdTensorImageWriter.cpp
	- mitkTensorImageSerializer.cpp
	- mitkTensorImageSource.cpp
	- mitkDiffusionCoreObjectFactory.cpp
	-
	- mitkDiffusionCoreIOMimeTypes.cpp
	-
	- mitkDiffusionImageDicomReaderService.cpp
	- mitkDiffusionImageNrrdReaderService.cpp
	- mitkDiffusionImageNrrdWriterService.cpp
	- mitkDiffusionImageNiftiReaderService.cpp
	- mitkDiffusionImageNiftiWriterService.cpp
	-
	- mitkNrrdOdfImageReader.cpp
	- mitkNrrdOdfImageWriter.cpp
	- mitkOdfImageSerializer.cpp
	- mitkPeakImageSerializer.cpp
	- mitkShImageReader.cpp
	- mitkShImageWriter.cpp
	- mitkShImageSerializer.cpp
	-
	- mitkCompositeMapper.cpp
	-)
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkCompositeMapper.cpp b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkCompositeMapper.cpp
	deleted file mode 100644
	index 402e56317d..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkCompositeMapper.cpp
	+++ /dev/null
	@@ -1,30 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-
	-#include "mitkCompositeMapper.h"
	-
	-
	-mitk::CompositeMapper::CompositeMapper()
	-{
	- m_OdfMapper = mitk::OdfVtkMapper2D<float,ODF_SAMPLING_SIZE>::New();
	- m_ImgMapper = mitk::CopyImageMapper2D::New();
	-}
	-
	-mitk::CompositeMapper::~CompositeMapper()
	-{
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkCompositeMapper.h b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkCompositeMapper.h
	deleted file mode 100644
	index a6c3b7fdcf..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkCompositeMapper.h
	+++ /dev/null
	@@ -1,162 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef COMPOSITEMAPPER_H_HEADER_INCLUDED
	-#define COMPOSITEMAPPER_H_HEADER_INCLUDED
	-
	-#include "mitkGLMapper.h"
	-#include "mitkVtkMapper.h"
	-#include "mitkOdfImage.h"
	-#include "mitkImageVtkMapper2D.h"
	-#include "mitkOdfVtkMapper2D.h"
	-#include "mitkLevelWindowProperty.h"
	-
	-namespace mitk {
	-
	- class CopyImageMapper2D : public ImageVtkMapper2D
	- {
	- public:
	- mitkClassMacro(CopyImageMapper2D,ImageVtkMapper2D);
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- friend class CompositeMapper;
	- };
	-
	- //##Documentation
	- //## @brief Composite pattern for combination of different mappers
	- //## @ingroup Mapper
	- class CompositeMapper : public VtkMapper
	- {
	- public:
	-
	- mitkClassMacro(CompositeMapper,VtkMapper);
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- void MitkRenderOverlay(BaseRenderer* renderer) override
	- {
	- m_ImgMapper->MitkRenderOverlay(renderer);
	- m_OdfMapper->MitkRenderOverlay(renderer);
	- }
	-
	- void MitkRenderOpaqueGeometry(BaseRenderer* renderer) override
	- {
	- m_ImgMapper->MitkRenderOpaqueGeometry(renderer);
	- m_OdfMapper->MitkRenderOpaqueGeometry(renderer);
	- if( mitk::RenderingManager::GetInstance()->GetNextLOD( renderer ) == 0 )
	- {
	- renderer->Modified();
	- }
	- }
	-
	- void MitkRenderTranslucentGeometry(BaseRenderer* renderer) override
	- {
	- m_ImgMapper->MitkRenderTranslucentGeometry(renderer);
	- m_OdfMapper->MitkRenderTranslucentGeometry(renderer);
	- }
	-
	- void MitkRenderVolumetricGeometry(BaseRenderer* renderer) override
	- {
	- m_ImgMapper->MitkRenderVolumetricGeometry(renderer);
	- m_OdfMapper->MitkRenderVolumetricGeometry(renderer);
	- }
	-
	- void SetDataNode(DataNode* node) override
	- {
	- m_DataNode = node;
	- m_ImgMapper->SetDataNode(node);
	- m_OdfMapper->SetDataNode(node);
	- }
	-
	- mitk::ImageVtkMapper2D::Pointer GetImageMapper()
	- {
	- ImageVtkMapper2D* retval = m_ImgMapper;
	- return retval;
	- }
	-
	- bool HasVtkProp( const vtkProp* prop, BaseRenderer* renderer ) override
	- {
	- return m_OdfMapper->HasVtkProp(prop, renderer);
	- }
	-
	- void ReleaseGraphicsResources(mitk::BaseRenderer* renderer) override
	- {
	- m_ImgMapper->ReleaseGraphicsResources(renderer);
	- m_OdfMapper->ReleaseGraphicsResources(renderer);
	- }
	-
	- static void SetDefaultProperties(DataNode* node, BaseRenderer* renderer = nullptr, bool overwrite = false )
	- {
	- mitk::OdfVtkMapper2D<float,ODF_SAMPLING_SIZE>::SetDefaultProperties(node, renderer, overwrite);
	- mitk::CopyImageMapper2D::SetDefaultProperties(node, renderer, overwrite);
	-
	- mitk::LevelWindow opaclevwin;
	- opaclevwin.SetRangeMinMax(0,255);
	- opaclevwin.SetWindowBounds(0,0);
	- mitk::LevelWindowProperty::Pointer prop = mitk::LevelWindowProperty::New(opaclevwin);
	- node->AddProperty( "opaclevelwindow", prop );
	- }
	-
	- bool IsLODEnabled( BaseRenderer * renderer ) const override
	- {
	- return m_ImgMapper->IsLODEnabled(renderer) \|\| m_OdfMapper->IsLODEnabled(renderer);
	- }
	-
	- vtkProp* GetVtkProp(mitk::BaseRenderer* renderer) override
	- {
	- m_PropAssembly = vtkSmartPointer<vtkPropAssembly>::New();
	- m_PropAssembly->AddPart( m_OdfMapper->GetVtkProp(renderer));
	- m_PropAssembly->AddPart( m_ImgMapper->GetVtkProp(renderer));
	- return m_PropAssembly;
	- }
	-
	- protected:
	-
	- void Update(mitk::BaseRenderer* renderer) override
	- {
	- m_OdfMapper->Update(renderer);
	- GenerateDataForRenderer(renderer);
	- }
	-
	- void GenerateDataForRenderer(mitk::BaseRenderer* renderer) override
	- {
	- m_ImgMapper->GenerateDataForRenderer(renderer);
	-// if( mitk::RenderingManager::GetInstance()->GetNextLOD( renderer ) > 0 )
	-// {
	-// m_OdfMapper->GenerateDataForRenderer(renderer);
	-// }
	- }
	-
	- CompositeMapper();
	-
	- ~CompositeMapper() override;
	-
	- private:
	-
	- mitk::OdfVtkMapper2D<float,ODF_SAMPLING_SIZE>::Pointer m_OdfMapper;
	- mitk::CopyImageMapper2D::Pointer m_ImgMapper;
	- vtkSmartPointer<vtkPropAssembly> m_PropAssembly;
	-
	- };
	-
	-} // namespace mitk
	-
	-
	-
	-#endif /* COMPOSITEMAPPER_H_HEADER_INCLUDED */
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionCoreIOActivator.cpp b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionCoreIOActivator.cpp
	deleted file mode 100644
	index 3bc408802c..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionCoreIOActivator.cpp
	+++ /dev/null
	@@ -1,128 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#include <usModuleActivator.h>
	-#include <usModuleContext.h>
	-
	-#include <mitkDiffusionImageNrrdReaderService.h>
	-#include <mitkDiffusionImageNiftiReaderService.h>
	-#include <mitkDiffusionImageDicomReaderService.h>
	-#include <mitkNrrdTensorImageReader.h>
	-#include <mitkNrrdOdfImageReader.h>
	-#include <mitkShImageReader.h>
	-#include <mitkPeakImageReader.h>
	-
	-#include <mitkDiffusionImageNrrdWriterService.h>
	-#include <mitkDiffusionImageNiftiWriterService.h>
	-#include <mitkNrrdTensorImageWriter.h>
	-#include <mitkNrrdOdfImageWriter.h>
	-#include <mitkShImageWriter.h>
	-
	-#include <mitkDiffusionPropertyHelper.h>
	-
	-#include <mitkCoreServices.h>
	-#include <mitkIPropertyDescriptions.h>
	-#include <mitkIPropertyPersistence.h>
	-
	-#include "mitkDiffusionCoreIOMimeTypes.h"
	-
	-namespace mitk
	-{
	- /**
	- \brief Registers services for segmentation module.
	- */
	- class DiffusionCoreIOActivator : public us::ModuleActivator
	- {
	- public:
	-
	- void Load(us::ModuleContext* context) override
	- {
	- m_MimeTypes = mitk::DiffusionCoreIOMimeTypes::Get();
	- for (std::vector<mitk::CustomMimeType*>::const_iterator mimeTypeIter = m_MimeTypes.begin(),
	- iterEnd = m_MimeTypes.end(); mimeTypeIter != iterEnd; ++mimeTypeIter)
	- {
	- us::ServiceProperties props;
	- mitk::CustomMimeType* mt = *mimeTypeIter;
	- if (mt->GetName()!=mitk::DiffusionCoreIOMimeTypes::PEAK_MIMETYPE_NAME() && mt->GetName()!=mitk::DiffusionCoreIOMimeTypes::SH_MIMETYPE_NAME())
	- props[ us::ServiceConstants::SERVICE_RANKING() ] = 10;
	-
	- context->RegisterService(*mimeTypeIter, props);
	- }
	-
	- m_DiffusionImageNrrdReaderService = new DiffusionImageNrrdReaderService();
	- m_DiffusionImageNiftiReaderService = new DiffusionImageNiftiReaderService( CustomMimeType( mitk::DiffusionCoreIOMimeTypes::DWI_NIFTI_MIMETYPE() ), mitk::DiffusionCoreIOMimeTypes::DWI_NIFTI_MIMETYPE_DESCRIPTION() );
	- m_DiffusionImageFslNiftiReaderService = new DiffusionImageNiftiReaderService( CustomMimeType( mitk::DiffusionCoreIOMimeTypes::DWI_FSL_MIMETYPE() ), mitk::DiffusionCoreIOMimeTypes::DWI_FSL_MIMETYPE_DESCRIPTION() );
	- m_DiffusionImageDicomReaderService = new DiffusionImageDicomReaderService();
	-
	- m_NrrdTensorImageReader = new NrrdTensorImageReader();
	- m_NrrdOdfImageReader = new NrrdOdfImageReader();
	- m_PeakImageReader = new PeakImageReader();
	- m_ShImageReader = new ShImageReader();
	-
	- m_DiffusionImageNrrdWriterService = new DiffusionImageNrrdWriterService();
	- m_DiffusionImageNiftiWriterService = new DiffusionImageNiftiWriterService();
	- m_NrrdTensorImageWriter = new NrrdTensorImageWriter();
	- m_NrrdOdfImageWriter = new NrrdOdfImageWriter();
	- m_ShImageWriter = new ShImageWriter();
	-
	- mitk::DiffusionPropertyHelper::SetupProperties();
	- }
	-
	- void Unload(us::ModuleContext*) override
	- {
	- for (unsigned int loop(0); loop < m_MimeTypes.size(); ++loop)
	- {
	- delete m_MimeTypes.at(loop);
	- }
	-
	- delete m_DiffusionImageNrrdReaderService;
	- delete m_DiffusionImageNiftiReaderService;
	- delete m_DiffusionImageFslNiftiReaderService;
	- delete m_DiffusionImageDicomReaderService;
	- delete m_NrrdTensorImageReader;
	- delete m_NrrdOdfImageReader;
	- delete m_PeakImageReader;
	- delete m_ShImageReader;
	-
	- delete m_DiffusionImageNrrdWriterService;
	- delete m_DiffusionImageNiftiWriterService;
	- delete m_NrrdTensorImageWriter;
	- delete m_NrrdOdfImageWriter;
	- delete m_ShImageWriter;
	- }
	-
	- private:
	-
	- DiffusionImageNrrdReaderService * m_DiffusionImageNrrdReaderService;
	- DiffusionImageNiftiReaderService * m_DiffusionImageNiftiReaderService;
	- DiffusionImageNiftiReaderService * m_DiffusionImageFslNiftiReaderService;
	- DiffusionImageDicomReaderService * m_DiffusionImageDicomReaderService;
	- NrrdTensorImageReader * m_NrrdTensorImageReader;
	- NrrdOdfImageReader * m_NrrdOdfImageReader;
	- PeakImageReader * m_PeakImageReader;
	- ShImageReader * m_ShImageReader;
	-
	- DiffusionImageNrrdWriterService * m_DiffusionImageNrrdWriterService;
	- DiffusionImageNiftiWriterService * m_DiffusionImageNiftiWriterService;
	- NrrdTensorImageWriter * m_NrrdTensorImageWriter;
	- NrrdOdfImageWriter * m_NrrdOdfImageWriter;
	- ShImageWriter * m_ShImageWriter;
	-
	- std::vector<mitk::CustomMimeType*> m_MimeTypes;
	-
	- };
	-}
	-
	-US_EXPORT_MODULE_ACTIVATOR(mitk::DiffusionCoreIOActivator)
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionCoreIOMimeTypes.cpp b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionCoreIOMimeTypes.cpp
	deleted file mode 100644
	index 1346a71759..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionCoreIOMimeTypes.cpp
	+++ /dev/null
	@@ -1,646 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkDiffusionCoreIOMimeTypes.h"
	-#include "mitkIOMimeTypes.h"
	-#include <itksys/SystemTools.hxx>
	-#include <itkNrrdImageIO.h>
	-#include <itkMetaDataDictionary.h>
	-#include <itkMetaDataObject.h>
	-#include <mitkLogMacros.h>
	-#include <mitkDICOMDCMTKTagScanner.h>
	-#include <mitkCustomMimeType.h>
	-#include <itkGDCMImageIO.h>
	-#include <itkNiftiImageIO.h>
	-
	-namespace mitk
	-{
	-
	-std::vector<CustomMimeType*> DiffusionCoreIOMimeTypes::Get()
	-{
	- std::vector<CustomMimeType*> mimeTypes;
	-
	- // order matters here (descending rank for mime types)
	-
	- mimeTypes.push_back(DWI_NRRD_MIMETYPE().Clone());
	- mimeTypes.push_back(DWI_NIFTI_MIMETYPE().Clone());
	- mimeTypes.push_back(DWI_FSL_MIMETYPE().Clone());
	- mimeTypes.push_back(DWI_DICOM_MIMETYPE().Clone());
	- mimeTypes.push_back(DTI_MIMETYPE().Clone());
	- mimeTypes.push_back(ODF_MIMETYPE().Clone());
	- mimeTypes.push_back(PEAK_MIMETYPE().Clone());
	- mimeTypes.push_back(SH_MIMETYPE().Clone());
	-
	- return mimeTypes;
	-}
	-
	-// Mime Types
	-
	-DiffusionCoreIOMimeTypes::DiffusionImageNrrdMimeType::DiffusionImageNrrdMimeType()
	- : CustomMimeType(DWI_NRRD_MIMETYPE_NAME())
	-{
	- std::string category = "Diffusion Weighted Images";
	- this->SetCategory(category);
	- this->SetComment("Diffusion Weighted Images");
	-
	- this->AddExtension("dwi");
	- //this->AddExtension("hdwi"); // saving with detached header does not work out of the box
	- this->AddExtension("nrrd");
	-}
	-
	-bool DiffusionCoreIOMimeTypes::DiffusionImageNrrdMimeType::AppliesTo(const std::string &path) const
	-{
	- bool canRead( CustomMimeType::AppliesTo(path) );
	-
	- // fix for bug 18572
	- // Currently this function is called for writing as well as reading, in that case
	- // the image information can of course not be read
	- // This is a bug, this function should only be called for reading.
	- if( ! itksys::SystemTools::FileExists( path.c_str() ) )
	- {
	- return canRead;
	- }
	- //end fix for bug 18572
	-
	- itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
	- // Simple NRRD files should only be considered for this mime type if they contain
	- // corresponding tags
	- if( io->CanReadFile(path.c_str()))
	- {
	- io->SetFileName(path);
	- try
	- {
	- io->ReadImageInformation();
	-
	- itk::MetaDataDictionary imgMetaDictionary = io->GetMetaDataDictionary();
	- std::vector<std::string> imgMetaKeys = imgMetaDictionary.GetKeys();
	- std::vector<std::string>::const_iterator itKey = imgMetaKeys.begin();
	- std::string metaString;
	-
	- for (; itKey != imgMetaKeys.end(); itKey ++)
	- {
	- itk::ExposeMetaData<std::string> (imgMetaDictionary, *itKey, metaString);
	- if (itKey->find("modality") != std::string::npos)
	- {
	- if (metaString.find("DWMRI") != std::string::npos)
	- {
	- return canRead;
	- }
	- }
	- }
	-
	- }
	- catch( const itk::ExceptionObject &e )
	- {
	- MITK_ERROR << "ITK Exception: " << e.what();
	- }
	- canRead = false;
	- }
	-
	- return canRead;
	-}
	-
	-DiffusionCoreIOMimeTypes::DiffusionImageNrrdMimeType* DiffusionCoreIOMimeTypes::DiffusionImageNrrdMimeType::Clone() const
	-{
	- return new DiffusionImageNrrdMimeType(*this);
	-}
	-
	-
	-DiffusionCoreIOMimeTypes::DiffusionImageNrrdMimeType DiffusionCoreIOMimeTypes::DWI_NRRD_MIMETYPE()
	-{
	- return DiffusionImageNrrdMimeType();
	-}
	-
	-DiffusionCoreIOMimeTypes::DiffusionImageNiftiMimeType::DiffusionImageNiftiMimeType()
	- : CustomMimeType(DWI_NIFTI_MIMETYPE_NAME())
	-{
	- std::string category = "Diffusion Weighted Images";
	- this->SetCategory(category);
	- this->SetComment("Diffusion Weighted Images");
	- this->AddExtension("nii.gz");
	- this->AddExtension("nii");
	-}
	-
	-bool DiffusionCoreIOMimeTypes::DiffusionImageNiftiMimeType::AppliesTo(const std::string &path) const
	-{
	- bool canRead(CustomMimeType::AppliesTo(path));
	-
	- // fix for bug 18572
	- // Currently this function is called for writing as well as reading, in that case
	- // the image information can of course not be read
	- // This is a bug, this function should only be called for reading.
	- if (!itksys::SystemTools::FileExists(path.c_str()))
	- {
	- return canRead;
	- }
	- //end fix for bug 18572
	-
	- std::string ext = this->GetExtension(path);
	- ext = itksys::SystemTools::LowerCase(ext);
	-
	- // Nifti files should only be considered for this mime type if they are
	- // accompanied by bvecs and bvals files defining the diffusion information
	- if (ext == ".nii" \|\| ext == ".nii.gz")
	- {
	- std::string base_path = itksys::SystemTools::GetFilenamePath(path);
	- std::string base = this->GetFilenameWithoutExtension(path);
	- std::string filename = base;
	- if (!base_path.empty())
	- {
	- base = base_path + "/" + base;
	- base_path += "/";
	- }
	-
	- if (itksys::SystemTools::FileExists(std::string(base + ".bvec").c_str())
	- && itksys::SystemTools::FileExists(std::string(base + ".bval").c_str())
	- )
	- {
	- return canRead;
	- }
	-
	- if (itksys::SystemTools::FileExists(std::string(base + ".bvecs").c_str())
	- && itksys::SystemTools::FileExists(std::string(base + ".bvals").c_str())
	- )
	- {
	- return canRead;
	- }
	-
	- // hack for HCP data
	- if ( filename=="data" && itksys::SystemTools::FileExists(std::string(base_path + "bvec").c_str()) && itksys::SystemTools::FileExists(std::string(base_path + "bval").c_str()) )
	- {
	- return canRead;
	- }
	-
	- if ( filename=="data" && itksys::SystemTools::FileExists(std::string(base_path + "bvecs").c_str()) && itksys::SystemTools::FileExists(std::string(base_path + "bvals").c_str()) )
	- {
	- return canRead;
	- }
	-
	- canRead = false;
	- }
	-
	- return canRead;
	-}
	-
	-DiffusionCoreIOMimeTypes::DiffusionImageNiftiMimeType* DiffusionCoreIOMimeTypes::DiffusionImageNiftiMimeType::Clone() const
	-{
	- return new DiffusionImageNiftiMimeType(*this);
	-}
	-
	-
	-DiffusionCoreIOMimeTypes::DiffusionImageNiftiMimeType DiffusionCoreIOMimeTypes::DWI_NIFTI_MIMETYPE()
	-{
	- return DiffusionImageNiftiMimeType();
	-}
	-
	-DiffusionCoreIOMimeTypes::DiffusionImageFslMimeType::DiffusionImageFslMimeType()
	- : CustomMimeType(DWI_FSL_MIMETYPE_NAME())
	-{
	- std::string category = "Diffusion Weighted Images";
	- this->SetCategory(category);
	- this->SetComment("Diffusion Weighted Images");
	- this->AddExtension("fslgz");
	- this->AddExtension("fsl");
	-}
	-
	-bool DiffusionCoreIOMimeTypes::DiffusionImageFslMimeType::AppliesTo(const std::string &path) const
	-{
	- bool canRead(CustomMimeType::AppliesTo(path));
	-
	- // fix for bug 18572
	- // Currently this function is called for writing as well as reading, in that case
	- // the image information can of course not be read
	- // This is a bug, this function should only be called for reading.
	- if (!itksys::SystemTools::FileExists(path.c_str()))
	- {
	- return canRead;
	- }
	- //end fix for bug 18572
	-
	- std::string ext = this->GetExtension(path);
	- ext = itksys::SystemTools::LowerCase(ext);
	-
	- // Nifti files should only be considered for this mime type if they are
	- // accompanied by bvecs and bvals files defining the diffusion information
	- if (ext == ".fsl" \|\| ext == ".fslgz")
	- {
	- std::string base_path = itksys::SystemTools::GetFilenamePath(path);
	- std::string base = this->GetFilenameWithoutExtension(path);
	- if (!base_path.empty())
	- base = base_path + "/" + base;
	-
	- if (itksys::SystemTools::FileExists(std::string(base + ".bvec").c_str())
	- && itksys::SystemTools::FileExists(std::string(base + ".bval").c_str())
	- )
	- {
	- return canRead;
	- }
	-
	- if (itksys::SystemTools::FileExists(std::string(base + ".bvecs").c_str())
	- && itksys::SystemTools::FileExists(std::string(base + ".bvals").c_str())
	- )
	- {
	- return canRead;
	- }
	-
	- if (itksys::SystemTools::FileExists(std::string(base + ext + ".bvec").c_str())
	- && itksys::SystemTools::FileExists(std::string(base + ext + ".bval").c_str())
	- )
	- {
	- return canRead;
	- }
	-
	- if (itksys::SystemTools::FileExists(std::string(base + ext + ".bvecs").c_str())
	- && itksys::SystemTools::FileExists(std::string(base + ext + ".bvals").c_str())
	- )
	- {
	- return canRead;
	- }
	-
	- canRead = false;
	- }
	-
	- return canRead;
	-}
	-
	-DiffusionCoreIOMimeTypes::DiffusionImageFslMimeType* DiffusionCoreIOMimeTypes::DiffusionImageFslMimeType::Clone() const
	-{
	- return new DiffusionImageFslMimeType(*this);
	-}
	-
	-
	-DiffusionCoreIOMimeTypes::DiffusionImageFslMimeType DiffusionCoreIOMimeTypes::DWI_FSL_MIMETYPE()
	-{
	- return DiffusionImageFslMimeType();
	-}
	-
	-
	-DiffusionCoreIOMimeTypes::DiffusionImageDicomMimeType::DiffusionImageDicomMimeType()
	- : CustomMimeType(DWI_DICOM_MIMETYPE_NAME())
	-{
	- std::string category = "Diffusion Weighted Images";
	- this->SetCategory(category);
	- this->SetComment("Diffusion Weighted Images");
	-
	- this->AddExtension("gdcm");
	- this->AddExtension("dcm");
	- this->AddExtension("DCM");
	- this->AddExtension("dc3");
	- this->AddExtension("DC3");
	- this->AddExtension("ima");
	- this->AddExtension("img");
	-}
	-
	-bool DiffusionCoreIOMimeTypes::DiffusionImageDicomMimeType::AppliesTo(const std::string &path) const
	-{
	- itk::GDCMImageIO::Pointer gdcmIO = itk::GDCMImageIO::New();
	- bool canRead = gdcmIO->CanReadFile(path.c_str());
	-
	- if (!canRead)
	- return canRead;
	-
	- mitk::DICOMDCMTKTagScanner::Pointer scanner = mitk::DICOMDCMTKTagScanner::New();
	- mitk::DICOMTag ImageTypeTag(0x0008, 0x0008);
	- mitk::DICOMTag SeriesDescriptionTag(0x0008, 0x103E);
	-
	- mitk::StringList relevantFiles;
	- relevantFiles.push_back(path);
	-
	- scanner->AddTag(ImageTypeTag);
	- scanner->AddTag(SeriesDescriptionTag);
	- scanner->SetInputFiles(relevantFiles);
	- scanner->Scan();
	- mitk::DICOMTagCache::Pointer tagCache = scanner->GetScanCache();
	-
	- mitk::DICOMImageFrameList imageFrameList = mitk::ConvertToDICOMImageFrameList(tagCache->GetFrameInfoList());
	- mitk::DICOMImageFrameInfo *firstFrame = imageFrameList.begin()->GetPointer();
	-
	- std::string byteString = tagCache->GetTagValue(firstFrame, ImageTypeTag).value;
	- if (byteString.empty())
	- return false;
	-
	- std::string byteString2 = tagCache->GetTagValue(firstFrame, SeriesDescriptionTag).value;
	- if (byteString2.empty())
	- return false;
	-
	- if (byteString.find("DIFFUSION")==std::string::npos && byteString2.find("diff")==std::string::npos)
	- return false;
	-// if (byteString.find("NONE")==std::string::npos)
	-// return false;
	-
	- return canRead;
	-}
	-
	-DiffusionCoreIOMimeTypes::DiffusionImageDicomMimeType* DiffusionCoreIOMimeTypes::DiffusionImageDicomMimeType::Clone() const
	-{
	- return new DiffusionImageDicomMimeType(*this);
	-}
	-
	-
	-DiffusionCoreIOMimeTypes::DiffusionImageDicomMimeType DiffusionCoreIOMimeTypes::DWI_DICOM_MIMETYPE()
	-{
	- return DiffusionImageDicomMimeType();
	-}
	-
	-
	-DiffusionCoreIOMimeTypes::PeakImageMimeType::PeakImageMimeType() : CustomMimeType(PEAK_MIMETYPE_NAME())
	-{
	- std::string category = "Peak Image";
	- this->SetCategory(category);
	- this->SetComment("Peak Image");
	-
	- this->AddExtension("nrrd");
	- this->AddExtension("nii");
	- this->AddExtension("nii.gz");
	- this->AddExtension("peak");
	-}
	-
	-bool DiffusionCoreIOMimeTypes::PeakImageMimeType::AppliesTo(const std::string &path) const
	-{
	- std::string ext = itksys::SystemTools::GetFilenameExtension(path);
	- if (ext==".peak")
	- return true;
	-
	- try
	- {
	- itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
	- if ( io->CanReadFile( path.c_str() ) )
	- {
	- io->SetFileName( path.c_str() );
	- io->ReadImageInformation();
	- if ( io->GetPixelType() == itk::ImageIOBase::SCALAR && io->GetNumberOfDimensions()==4 && io->GetDimensions(3)%3==0)
	- return true;
	- }
	- }
	- catch(...)
	- {}
	-
	- try
	- {
	- itk::NiftiImageIO::Pointer io = itk::NiftiImageIO::New();
	- if ( io->CanReadFile( path.c_str() ) )
	- {
	- io->SetFileName( path.c_str() );
	- io->ReadImageInformation();
	- if ( io->GetPixelType() == itk::ImageIOBase::SCALAR && io->GetNumberOfDimensions()==4 && io->GetDimensions(3)%3==0)
	- return true;
	- }
	- }
	- catch(...)
	- {}
	-
	- return false;
	-}
	-
	-DiffusionCoreIOMimeTypes::PeakImageMimeType* DiffusionCoreIOMimeTypes::PeakImageMimeType::Clone() const
	-{
	- return new PeakImageMimeType(*this);
	-}
	-
	-
	-DiffusionCoreIOMimeTypes::PeakImageMimeType DiffusionCoreIOMimeTypes::PEAK_MIMETYPE()
	-{
	- return PeakImageMimeType();
	-}
	-
	-
	-DiffusionCoreIOMimeTypes::SHImageMimeType::SHImageMimeType() : CustomMimeType(SH_MIMETYPE_NAME())
	-{
	- std::string category = "SH Image";
	- this->SetCategory(category);
	- this->SetComment("SH Image");
	-
	- this->AddExtension("nii.gz");
	- this->AddExtension("nii");
	- this->AddExtension("nrrd");
	- this->AddExtension("shi");
	-}
	-
	-bool DiffusionCoreIOMimeTypes::SHImageMimeType::AppliesTo(const std::string &path) const
	-{
	- std::string ext = itksys::SystemTools::GetFilenameExtension(path);
	- if (ext==".shi")
	- return true;
	-
	- {
	- try
	- {
	- itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
	- if (io->CanReadFile(path.c_str()))
	- {
	- io->SetFileName(path.c_str());
	- io->ReadImageInformation();
	- if (io->GetPixelType() == itk::ImageIOBase::SCALAR && io->GetNumberOfDimensions() == 4)
	- {
	- switch (io->GetDimensions(3))
	- {
	- case 6:
	- return true;
	- break;
	- case 15:
	- return true;
	- break;
	- case 28:
	- return true;
	- break;
	- case 45:
	- return true;
	- break;
	- case 66:
	- return true;
	- break;
	- case 91:
	- return true;
	- break;
	- default:
	- return false;
	- }
	- }
	- }
	- }
	- catch(...)
	- {}
	- }
	-
	- {
	- itk::NiftiImageIO::Pointer io = itk::NiftiImageIO::New();
	- if ( io->CanReadFile( path.c_str() ) )
	- {
	- io->SetFileName( path.c_str() );
	- io->ReadImageInformation();
	- if ( io->GetPixelType() == itk::ImageIOBase::SCALAR && io->GetNumberOfDimensions()==4)
	- {
	- switch (io->GetDimensions(3))
	- {
	- case 6:
	- return true;
	- break;
	- case 15:
	- return true;
	- break;
	- case 28:
	- return true;
	- break;
	- case 45:
	- return true;
	- break;
	- case 66:
	- return true;
	- break;
	- case 91:
	- return true;
	- break;
	- default :
	- return false;
	- }
	- }
	- }
	- }
	-
	- return false;
	-}
	-
	-DiffusionCoreIOMimeTypes::SHImageMimeType* DiffusionCoreIOMimeTypes::SHImageMimeType::Clone() const
	-{
	- return new SHImageMimeType(*this);
	-}
	-
	-
	-DiffusionCoreIOMimeTypes::SHImageMimeType DiffusionCoreIOMimeTypes::SH_MIMETYPE()
	-{
	- return SHImageMimeType();
	-}
	-
	-CustomMimeType DiffusionCoreIOMimeTypes::DTI_MIMETYPE()
	-{
	- CustomMimeType mimeType(DTI_MIMETYPE_NAME());
	- std::string category = "Tensor Image";
	- mimeType.SetComment("Diffusion Tensor Image");
	- mimeType.SetCategory(category);
	- mimeType.AddExtension("dti");
	- return mimeType;
	-}
	-
	-CustomMimeType DiffusionCoreIOMimeTypes::ODF_MIMETYPE()
	-{
	- CustomMimeType mimeType(ODF_MIMETYPE_NAME());
	- std::string category = "ODF Image";
	- mimeType.SetComment("Diffusion ODF Image");
	- mimeType.SetCategory(category);
	- mimeType.AddExtension("odf");
	- mimeType.AddExtension("qbi"); // legacy support
	- return mimeType;
	-}
	-
	-// Names
	-std::string DiffusionCoreIOMimeTypes::PEAK_MIMETYPE_NAME()
	-{
	- static std::string name ="ODF_PEAKS";
	- return name;
	-}
	-
	-std::string DiffusionCoreIOMimeTypes::DWI_NRRD_MIMETYPE_NAME()
	-{
	- static std::string name = "DWI_NRRD";
	- return name;
	-}
	-
	-std::string DiffusionCoreIOMimeTypes::DWI_NIFTI_MIMETYPE_NAME()
	-{
	- static std::string name = "DWI_NIFTI";
	- return name;
	-}
	-
	-std::string DiffusionCoreIOMimeTypes::DWI_FSL_MIMETYPE_NAME()
	-{
	- static std::string name = "DWI_FSL";
	- return name;
	-}
	-
	-std::string DiffusionCoreIOMimeTypes::DWI_DICOM_MIMETYPE_NAME()
	-{
	- static std::string name = "DWI_DICOM";
	- return name;
	-}
	-
	-std::string DiffusionCoreIOMimeTypes::DTI_MIMETYPE_NAME()
	-{
	- static std::string name = "DT_IMAGE";
	- return name;
	-}
	-
	-std::string DiffusionCoreIOMimeTypes::ODF_MIMETYPE_NAME()
	-{
	- static std::string name = "ODF_IMAGE";
	- return name;
	-}
	-
	-std::string DiffusionCoreIOMimeTypes::SH_MIMETYPE_NAME()
	-{
	- static std::string name = "SH_IMAGE";
	- return name;
	-}
	-
	-// Descriptions
	-std::string DiffusionCoreIOMimeTypes::PEAK_MIMETYPE_DESCRIPTION()
	-{
	- static std::string description = "Peak Image";
	- return description;
	-}
	-
	-std::string DiffusionCoreIOMimeTypes::DWI_NRRD_MIMETYPE_DESCRIPTION()
	-{
	- static std::string description = "Diffusion Weighted Images";
	- return description;
	-}
	-
	-std::string DiffusionCoreIOMimeTypes::DWI_NIFTI_MIMETYPE_DESCRIPTION()
	-{
	- static std::string description = "Diffusion Weighted Images";
	- return description;
	-}
	-
	-std::string DiffusionCoreIOMimeTypes::DWI_FSL_MIMETYPE_DESCRIPTION()
	-{
	- static std::string description = "Diffusion Weighted Images";
	- return description;
	-}
	-
	-std::string DiffusionCoreIOMimeTypes::DWI_DICOM_MIMETYPE_DESCRIPTION()
	-{
	- static std::string description = "Diffusion Weighted Images";
	- return description;
	-}
	-
	-std::string DiffusionCoreIOMimeTypes::DTI_MIMETYPE_DESCRIPTION()
	-{
	- static std::string description = "Diffusion Tensor Image";
	- return description;
	-}
	-
	-std::string DiffusionCoreIOMimeTypes::ODF_MIMETYPE_DESCRIPTION()
	-{
	- static std::string description = "ODF Image";
	- return description;
	-}
	-
	-std::string DiffusionCoreIOMimeTypes::SH_MIMETYPE_DESCRIPTION()
	-{
	- static std::string description = "SH Image";
	- return description;
	-}
	-
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionCoreIOMimeTypes.h b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionCoreIOMimeTypes.h
	deleted file mode 100644
	index 80441a180d..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionCoreIOMimeTypes.h
	+++ /dev/null
	@@ -1,118 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef MITKDiffusionCoreIOMimeTypes_H
	-#define MITKDiffusionCoreIOMimeTypes_H
	-
	-#include "mitkCustomMimeType.h"
	-#include <string>
	-
	-namespace mitk {
	-
	-class DiffusionCoreIOMimeTypes
	-{
	-public:
	-
	- class DiffusionImageNrrdMimeType : public CustomMimeType
	- {
	- public:
	- DiffusionImageNrrdMimeType();
	- bool AppliesTo(const std::string &path) const override;
	- DiffusionImageNrrdMimeType* Clone() const override;
	- };
	-
	- class DiffusionImageNiftiMimeType : public CustomMimeType
	- {
	- public:
	- DiffusionImageNiftiMimeType();
	- bool AppliesTo(const std::string &path) const override;
	- DiffusionImageNiftiMimeType* Clone() const override;
	- };
	-
	- class DiffusionImageFslMimeType : public CustomMimeType
	- {
	- public:
	- DiffusionImageFslMimeType();
	- bool AppliesTo(const std::string &path) const override;
	- DiffusionImageFslMimeType* Clone() const override;
	- };
	-
	- class DiffusionImageDicomMimeType : public CustomMimeType
	- {
	- public:
	- DiffusionImageDicomMimeType();
	- bool AppliesTo(const std::string &path) const override;
	- DiffusionImageDicomMimeType* Clone() const override;
	- };
	-
	- class PeakImageMimeType : public CustomMimeType
	- {
	- public:
	- PeakImageMimeType();
	- bool AppliesTo(const std::string &path) const override;
	- PeakImageMimeType* Clone() const override;
	- };
	-
	- class SHImageMimeType : public CustomMimeType
	- {
	- public:
	- SHImageMimeType();
	- bool AppliesTo(const std::string &path) const override;
	- SHImageMimeType* Clone() const override;
	- };
	-
	- // Get all Diffusion Mime Types
	- static std::vector<CustomMimeType*> Get();
	-
	- // ------------------------- Image formats (ITK based) --------------------------
	-
	- static DiffusionImageNrrdMimeType DWI_NRRD_MIMETYPE();
	- static DiffusionImageNiftiMimeType DWI_NIFTI_MIMETYPE();
	- static DiffusionImageFslMimeType DWI_FSL_MIMETYPE();
	- static DiffusionImageDicomMimeType DWI_DICOM_MIMETYPE();
	- static PeakImageMimeType PEAK_MIMETYPE();
	- static CustomMimeType DTI_MIMETYPE(); // dti
	- static CustomMimeType ODF_MIMETYPE(); // odf, qbi
	- static SHImageMimeType SH_MIMETYPE(); // spherical harmonics coefficients
	-
	- static std::string PEAK_MIMETYPE_NAME();
	- static std::string DWI_NRRD_MIMETYPE_NAME();
	- static std::string DWI_NIFTI_MIMETYPE_NAME();
	- static std::string DWI_FSL_MIMETYPE_NAME();
	- static std::string DWI_DICOM_MIMETYPE_NAME();
	- static std::string DTI_MIMETYPE_NAME();
	- static std::string ODF_MIMETYPE_NAME();
	- static std::string SH_MIMETYPE_NAME();
	-
	- static std::string PEAK_MIMETYPE_DESCRIPTION();
	- static std::string DWI_NRRD_MIMETYPE_DESCRIPTION();
	- static std::string DWI_NIFTI_MIMETYPE_DESCRIPTION();
	- static std::string DWI_FSL_MIMETYPE_DESCRIPTION();
	- static std::string DWI_DICOM_MIMETYPE_DESCRIPTION();
	- static std::string DTI_MIMETYPE_DESCRIPTION();
	- static std::string ODF_MIMETYPE_DESCRIPTION();
	- static std::string SH_MIMETYPE_DESCRIPTION();
	-
	-private:
	-
	- // purposely not implemented
	- DiffusionCoreIOMimeTypes();
	- DiffusionCoreIOMimeTypes(const DiffusionCoreIOMimeTypes&);
	-};
	-
	-}
	-
	-#endif // MITKDiffusionCoreIOMimeTypes_H
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionCoreObjectFactory.cpp b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionCoreObjectFactory.cpp
	deleted file mode 100644
	index 4c50855ab3..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionCoreObjectFactory.cpp
	+++ /dev/null
	@@ -1,175 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkDiffusionCoreObjectFactory.h"
	-
	-#include "mitkProperties.h"
	-#include "mitkBaseRenderer.h"
	-#include "mitkDataNode.h"
	-
	-#include "mitkCompositeMapper.h"
	-#include "mitkGPUVolumeMapper3D.h"
	-
	-
	-typedef short DiffusionPixelType;
	-
	-typedef std::multimap<std::string, std::string> MultimapType;
	-
	-mitk::DiffusionCoreObjectFactory::DiffusionCoreObjectFactory()
	- : CoreObjectFactoryBase()
	-{
	-
	- static bool alreadyDone = false;
	- if (!alreadyDone)
	- {
	- MITK_DEBUG << "DiffusionCoreObjectFactory c'tor" << std::endl;
	-
	- CreateFileExtensionsMap();
	-
	- alreadyDone = true;
	- }
	-
	-}
	-
	-mitk::DiffusionCoreObjectFactory::~DiffusionCoreObjectFactory()
	-{
	-
	-}
	-
	-mitk::Mapper::Pointer mitk::DiffusionCoreObjectFactory::CreateMapper(mitk::DataNode* node, MapperSlotId id)
	-{
	- mitk::Mapper::Pointer newMapper=nullptr;
	-
	- if ( id == mitk::BaseRenderer::Standard2D )
	- {
	- std::string classname("OdfImage");
	- if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0)
	- {
	- newMapper = mitk::CompositeMapper::New();
	- newMapper->SetDataNode(node);
	- node->SetMapper(3, static_cast<CompositeMapper*>(newMapper.GetPointer())->GetImageMapper());
	- }
	- classname = "TensorImage";
	- if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0)
	- {
	- newMapper = mitk::CompositeMapper::New();
	- newMapper->SetDataNode(node);
	- node->SetMapper(3, static_cast<CompositeMapper*>(newMapper.GetPointer())->GetImageMapper());
	- }
	- classname = "ShImage";
	- if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0)
	- {
	- newMapper = mitk::CompositeMapper::New();
	- newMapper->SetDataNode(node);
	- node->SetMapper(3, static_cast<CompositeMapper*>(newMapper.GetPointer())->GetImageMapper());
	- }
	-
	- }
	- else if ( id == mitk::BaseRenderer::Standard3D )
	- {
	- std::string classname("OdfImage");
	- if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0)
	- {
	- newMapper = mitk::GPUVolumeMapper3D::New();
	- newMapper->SetDataNode(node);
	- }
	- classname = "TensorImage";
	- if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0)
	- {
	- newMapper = mitk::GPUVolumeMapper3D::New();
	- newMapper->SetDataNode(node);
	- }
	- classname = "ShImage";
	- if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0)
	- {
	- newMapper = mitk::GPUVolumeMapper3D::New();
	- newMapper->SetDataNode(node);
	- }
	- }
	-
	- return newMapper;
	-}
	-
	-void mitk::DiffusionCoreObjectFactory::SetDefaultProperties(mitk::DataNode* node)
	-{
	- std::string classname = "OdfImage";
	- if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0)
	- {
	- mitk::CompositeMapper::SetDefaultProperties(node);
	- mitk::GPUVolumeMapper3D::SetDefaultProperties(node);
	- }
	-
	- classname = "TensorImage";
	- if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0)
	- {
	- mitk::CompositeMapper::SetDefaultProperties(node);
	- mitk::GPUVolumeMapper3D::SetDefaultProperties(node);
	- }
	-
	- classname = "ShImage";
	- if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0)
	- {
	- mitk::CompositeMapper::SetDefaultProperties(node);
	- mitk::GPUVolumeMapper3D::SetDefaultProperties(node);
	- }
	-}
	-
	-const char* mitk::DiffusionCoreObjectFactory::GetFileExtensions()
	-{
	- std::string fileExtension;
	- this->CreateFileExtensions(m_FileExtensionsMap, fileExtension);
	- return fileExtension.c_str();
	-}
	-
	-mitk::CoreObjectFactoryBase::MultimapType mitk::DiffusionCoreObjectFactory::GetFileExtensionsMap()
	-{
	- return m_FileExtensionsMap;
	-}
	-
	-const char* mitk::DiffusionCoreObjectFactory::GetSaveFileExtensions()
	-{
	- std::string fileExtension;
	- this->CreateFileExtensions(m_SaveFileExtensionsMap, fileExtension);
	- return fileExtension.c_str();
	-}
	-
	-mitk::CoreObjectFactoryBase::MultimapType mitk::DiffusionCoreObjectFactory::GetSaveFileExtensionsMap()
	-{
	- return m_SaveFileExtensionsMap;
	-}
	-
	-void mitk::DiffusionCoreObjectFactory::CreateFileExtensionsMap()
	-{
	-
	-}
	-
	-struct RegisterDiffusionCoreObjectFactory{
	- RegisterDiffusionCoreObjectFactory()
	- : m_Factory( mitk::DiffusionCoreObjectFactory::New() )
	- {
	- mitk::CoreObjectFactory::GetInstance()->RegisterExtraFactory( m_Factory );
	- }
	-
	- ~RegisterDiffusionCoreObjectFactory()
	- {
	- mitk::CoreObjectFactory::GetInstance()->UnRegisterExtraFactory( m_Factory );
	- }
	-
	- mitk::DiffusionCoreObjectFactory::Pointer m_Factory;
	-};
	-
	-static RegisterDiffusionCoreObjectFactory registerDiffusionCoreObjectFactory;
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionCoreObjectFactory.h b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionCoreObjectFactory.h
	deleted file mode 100644
	index cfb839a922..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionCoreObjectFactory.h
	+++ /dev/null
	@@ -1,66 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef DiffusionCoreObjectFactory_H_INCLUDED
	-#define DiffusionCoreObjectFactory_H_INCLUDED
	-
	-#include "mitkCoreObjectFactory.h"
	-
	-namespace mitk {
	-
	-class DiffusionCoreObjectFactory : public CoreObjectFactoryBase
	-{
	- public:
	- mitkClassMacro(DiffusionCoreObjectFactory,CoreObjectFactoryBase)
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- ~DiffusionCoreObjectFactory() override;
	-
	- Mapper::Pointer CreateMapper(mitk::DataNode* node, MapperSlotId slotId) override;
	-
	- void SetDefaultProperties(mitk::DataNode* node) override;
	-
	- const char* GetFileExtensions() override;
	-
	- mitk::CoreObjectFactoryBase::MultimapType GetFileExtensionsMap() override;
	-
	- const char* GetSaveFileExtensions() override;
	-
	- mitk::CoreObjectFactoryBase::MultimapType GetSaveFileExtensionsMap() override;
	-
	-protected:
	- DiffusionCoreObjectFactory();
	- void CreateFileExtensionsMap();
	- MultimapType m_FileExtensionsMap;
	- MultimapType m_SaveFileExtensionsMap;
	-private:
	-
	- std::string m_ExternalFileExtensions;
	- std::string m_InternalFileExtensions;
	- std::string m_SaveFileExtensions;
	-
	- itk::ObjectFactoryBase::Pointer m_NrrdDiffusionImageIOFactory;
	- itk::ObjectFactoryBase::Pointer m_NrrdOdfImageIOFactory;
	-
	- itk::ObjectFactoryBase::Pointer m_NrrdDiffusionImageWriterFactory;
	- itk::ObjectFactoryBase::Pointer m_NrrdOdfImageWriterFactory;
	-};
	-
	-}
	-
	-#endif
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageDicomReaderService.cpp b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageDicomReaderService.cpp
	deleted file mode 100644
	index a4e9350324..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageDicomReaderService.cpp
	+++ /dev/null
	@@ -1,327 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkDiffusionImageDicomReaderService_cpp
	-#define __mitkDiffusionImageDicomReaderService_cpp
	-
	-#include "mitkDiffusionImageDicomReaderService.h"
	-
	-#include <iostream>
	-#include <fstream>
	-
	-
	-// Diffusion properties
	-#include <mitkGradientDirectionsProperty.h>
	-#include <mitkBValueMapProperty.h>
	-#include <mitkMeasurementFrameProperty.h>
	-#include <mitkProperties.h>
	-
	-#include <itkImageRegionIterator.h>
	-#include <itkMetaDataObject.h>
	-#include "itksys/SystemTools.hxx"
	-#include "itkImageFileReader.h"
	-#include "itkMetaDataObject.h"
	-#include "itkNrrdImageIO.h"
	-
	-#include "mitkCustomMimeType.h"
	-#include "mitkDiffusionCoreIOMimeTypes.h"
	-#include <mitkDiffusionDICOMFileReader.h>
	-#include <mitkDICOMTagBasedSorter.h>
	-#include <mitkSortByImagePositionPatient.h>
	-#include <mitkDICOMSortByTag.h>
	-
	-#include <mitkITKImageImport.h>
	-#include <mitkImageWriteAccessor.h>
	-#include <mitkImageDataItem.h>
	-#include <mitkIOUtil.h>
	-#include <mitkLocaleSwitch.h>
	-#include <itksys/Directory.hxx>
	-#include <gdcmDirectory.h>
	-#include <mitkStringProperty.h>
	-
	-namespace mitk
	-{
	-
	-DiffusionImageDicomReaderService::
	-DiffusionImageDicomReaderService(const DiffusionImageDicomReaderService & other)
	- : AbstractFileReader(other)
	-{
	-}
	-
	-
	-DiffusionImageDicomReaderService* DiffusionImageDicomReaderService::Clone() const
	-{
	- return new DiffusionImageDicomReaderService(*this);
	-}
	-
	-
	-DiffusionImageDicomReaderService::
	-~DiffusionImageDicomReaderService()
	-{}
	-
	-DiffusionImageDicomReaderService::
	-DiffusionImageDicomReaderService()
	- : mitk::AbstractFileReader( CustomMimeType( mitk::DiffusionCoreIOMimeTypes::DWI_DICOM_MIMETYPE() ), mitk::DiffusionCoreIOMimeTypes::DWI_DICOM_MIMETYPE_DESCRIPTION() )
	-{
	- Options defaultOptions;
	- defaultOptions["Apply image rotation to gradients"] = true;
	- defaultOptions["Load recursive"] = false;
	- defaultOptions["Split mosaic"] = true;
	- this->SetDefaultOptions(defaultOptions);
	-
	- m_ServiceReg = this->RegisterService();
	-}
	-
	-std::vector<itk::SmartPointer<mitk::BaseData> >
	-DiffusionImageDicomReaderService::Read()
	-{
	- return InternalRead();
	-}
	-
	-
	-std::vector<itk::SmartPointer<mitk::BaseData> > DiffusionImageDicomReaderService::InternalRead()
	-{
	- std::vector<itk::SmartPointer<mitk::BaseData> > result_images;
	- OutputType::Pointer outputForCache = OutputType::New();
	- if ( this->GetInputLocation() == "")
	- {
	- throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, the filename to be read is empty!");
	- }
	- else
	- {
	- const std::string& locale = "C";
	- const std::string& currLocale = setlocale( LC_ALL, nullptr );
	-
	- if ( locale.compare(currLocale)!=0 )
	- {
	- try
	- {
	- setlocale(LC_ALL, locale.c_str());
	- }
	- catch(...)
	- {
	- MITK_INFO << "Could not set locale " << locale;
	- }
	- }
	-
	- try
	- {
	- Options options = this->GetOptions();
	- bool load_recursive = us::any_cast<bool>(options["Load recursive"]);
	- bool split_mosaic = us::any_cast<bool>(options["Split mosaic"]);
	-
	- gdcm::Directory::FilenamesType complete_list;
	- std::string folderName = itksys::SystemTools::GetFilenamePath( this->GetInputLocation() );
	-
	- if( load_recursive )
	- {
	- std::string subdir_prefix = "";
	-
	- itksys::Directory rootdir;
	- rootdir.Load( folderName.c_str() );
	-
	- for( unsigned int idx=0; idx<rootdir.GetNumberOfFiles(); idx++)
	- {
	- std::string current_path = rootdir.GetFile(idx);
	- std::string directory_path = std::string(rootdir.GetPath()) + std::string("/") + current_path;
	-
	- MITK_INFO("dicom.loader.inputrootdir.test") << "ProbePath: " << current_path;
	- MITK_INFO("dicom.loader.inputrootdir.test") << "IsDirectory: " << itksys::SystemTools::FileIsDirectory( itksys::SystemTools::ConvertToOutputPath( directory_path.c_str() ).c_str() )
	- << " StartsWith: " << itksys::SystemTools::StringStartsWith( current_path.c_str(), subdir_prefix.c_str() );
	-
	- // test for prefix
	- if( itksys::SystemTools::FileIsDirectory( itksys::SystemTools::ConvertToOutputPath( directory_path.c_str() ).c_str() )
	- && itksys::SystemTools::StringStartsWith( current_path.c_str(), subdir_prefix.c_str() ) )
	- {
	- gdcm::Directory d;
	- d.Load( itksys::SystemTools::ConvertToOutputPath( directory_path.c_str() ) , false);
	-
	- MITK_INFO("dicom.load.subdir.attempt") << "In directory " << itksys::SystemTools::ConvertToOutputPath( directory_path.c_str() );
	-
	- const gdcm::Directory::FilenamesType &l1 = d.GetFilenames();
	- const unsigned int ntotalfiles = l1.size();
	-
	- for( unsigned int i=0; i< ntotalfiles; i++)
	- {
	- complete_list.push_back( l1.at(i) );
	- m_ReadFiles.push_back( l1.at(i) );
	- }
	- }
	- }
	- }
	- else
	- {
	- gdcm::Directory d;
	- d.Load( folderName.c_str(), load_recursive ); // recursive !
	- const gdcm::Directory::FilenamesType &l1 = d.GetFilenames();
	- const unsigned int ntotalfiles = l1.size();
	-
	- for( unsigned int i=0; i< ntotalfiles; i++)
	- {
	- complete_list.push_back( l1.at(i) );
	- m_ReadFiles.push_back( l1.at(i) );
	- }
	- }
	-
	- mitk::DiffusionDICOMFileReader::Pointer gdcmReader = mitk::DiffusionDICOMFileReader::New();
	- mitk::DICOMTagBasedSorter::Pointer tagSorter = mitk::DICOMTagBasedSorter::New();
	-
	- // Use tags as in Qmitk
	- // all the things that split by tag in ClassicDicomSeriesReader
	- tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0028, 0x0010) ); // Number of Rows
	- tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0028, 0x0011) ); // Number of Columns
	- tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0028, 0x0030) ); // Pixel Spacing
	- tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0018, 0x1164) ); // Imager Pixel Spacing
	- tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0020, 0x0037) ); // Image Orientation (Patient) // TODO add tolerance parameter (l. 1572 of original code)
	- // TODO handle as real vectors! cluster with configurable errors!
	- tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0020, 0x000e) ); // Series Instance UID
	- tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0018, 0x0050) ); // Slice Thickness
	- tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0028, 0x0008) ); // Number of Frames
	- //tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0020, 0x0052) ); // Frame of Reference UID
	-
	- auto tag_sop_instance_uid = mitk::DICOMSortByTag::New( mitk::DICOMTag(0x0008, 0x0018), nullptr ); // SOP instance UID (last resort, not really meaningful but decides clearly)
	- auto tag_trigger_time = mitk::DICOMSortByTag::New( mitk::DICOMTag(0x0018, 0x1060), tag_sop_instance_uid.GetPointer() ); // trigger time
	- auto tag_aqcuisition_time = mitk::DICOMSortByTag::New( mitk::DICOMTag(0x0008, 0x0032), tag_trigger_time.GetPointer()); // aqcuisition time
	- auto tag_aqcuisition_number = mitk::DICOMSortByTag::New( mitk::DICOMTag(0x0020, 0x0012), tag_aqcuisition_time.GetPointer()); // aqcuisition number
	- mitk::DICOMSortCriterion::ConstPointer sorting = mitk::SortByImagePositionPatient::New(tag_aqcuisition_number.GetPointer()).GetPointer();
	- tagSorter->SetSortCriterion( sorting );
	-
	- // mosaic
	- gdcmReader->SetResolveMosaic( split_mosaic );
	- gdcmReader->AddSortingElement( tagSorter );
	- gdcmReader->SetInputFiles( complete_list );
	- gdcmReader->SetApplyRotationToGradients(us::any_cast<bool>(options["Apply image rotation to gradients"]));
	- try
	- {
	- gdcmReader->AnalyzeInputFiles();
	- }
	- catch( const itk::ExceptionObject &e)
	- {
	- MITK_ERROR << "Failed to analyze data. " << e.what();
	- }
	- catch( const std::exception &se)
	- {
	- MITK_ERROR << "Std Exception " << se.what();
	- }
	-
	- gdcmReader->LoadImages();
	-
	- for( unsigned int o = 0; o < gdcmReader->GetNumberOfOutputs(); o++ )
	- {
	- mitk::Image::Pointer loaded_image = gdcmReader->GetOutput(o).GetMitkImage();
	-
	- StringProperty::Pointer nameProp;
	- if (gdcmReader->GetSeriesName(o)!="-")
	- nameProp = StringProperty::New(gdcmReader->GetSeriesName(o));
	- else if (gdcmReader->GetStudyName(o)!="-")
	- nameProp = StringProperty::New(gdcmReader->GetStudyName(o));
	- else
	- nameProp = StringProperty::New(folderName);
	-
	- loaded_image->SetProperty("name", nameProp);
	-
	- std::string val = "-";
	-
	- if (gdcmReader->patient_ids().size()>o)
	- {
	- val = gdcmReader->patient_ids().at(o);
	- loaded_image->GetPropertyList()->SetStringProperty("DICOM.patient_id",val.c_str());
	- }
	-
	- if (gdcmReader->patient_names().size()>o)
	- {
	- val = gdcmReader->patient_names().at(o);
	- loaded_image->GetPropertyList()->SetStringProperty("DICOM.patient_name",val.c_str());
	- }
	-
	- if (gdcmReader->study_instance_uids().size()>o)
	- {
	- val = gdcmReader->study_instance_uids().at(o);
	- loaded_image->GetPropertyList()->SetStringProperty("DICOM.study_instance_uid",val.c_str());
	- }
	-
	- if (gdcmReader->series_instance_uids().size()>o)
	- {
	- val = gdcmReader->series_instance_uids().at(o);
	- loaded_image->GetPropertyList()->SetStringProperty("DICOM.series_instance_uid",val.c_str());
	- }
	-
	- if (gdcmReader->sop_instance_uids().size()>o)
	- {
	- val = gdcmReader->sop_instance_uids().at(o);
	- loaded_image->GetPropertyList()->SetStringProperty("DICOM.sop_instance_uid",val.c_str());
	- }
	-
	- if (gdcmReader->frame_of_reference_uids().size()>o)
	- {
	- val = gdcmReader->frame_of_reference_uids().at(o);
	- loaded_image->GetPropertyList()->SetStringProperty("DICOM.frame_of_reference_uid",val.c_str());
	- }
	- result_images.push_back(loaded_image.GetPointer());
	- }
	-
	-
	- // Since we have already read the tree, we can store it in a cache variable
	- // so that it can be assigned to the DataObject in GenerateData();
	- m_OutputCache = outputForCache;
	- m_CacheTime.Modified();
	-
	- try
	- {
	- setlocale(LC_ALL, currLocale.c_str());
	- }
	- catch(...)
	- {
	- MITK_INFO << "Could not reset locale " << currLocale;
	- }
	- }
	- catch(std::exception& e)
	- {
	- try
	- {
	- setlocale(LC_ALL, currLocale.c_str());
	- }
	- catch(...)
	- {
	- MITK_INFO << "Could not reset locale " << currLocale;
	- }
	-
	- MITK_INFO << "Std::Exception while reading file!!";
	- MITK_INFO << e.what();
	- throw itk::ImageFileReaderException(__FILE__, __LINE__, e.what());
	- }
	- catch(...)
	- {
	- try
	- {
	- setlocale(LC_ALL, currLocale.c_str());
	- }
	- catch(...)
	- {
	- MITK_INFO << "Could not reset locale " << currLocale;
	- }
	-
	- MITK_INFO << "Exception while reading file!!";
	- throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, an error occurred while reading the requested vessel tree file!");
	- }
	- }
	-
	- return result_images;
	-}
	-
	-} //namespace MITK
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageDicomReaderService.h b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageDicomReaderService.h
	deleted file mode 100644
	index e74fcfee71..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageDicomReaderService.h
	+++ /dev/null
	@@ -1,73 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkDiffusionImageDicomReaderService_h
	-#define __mitkDiffusionImageDicomReaderService_h
	-
	-#include "mitkCommon.h"
	-
	-// MITK includes
	-#include "mitkImageSource.h"
	-#include "mitkFileReader.h"
	-
	-#include <mitkDiffusionPropertyHelper.h>
	-
	-// ITK includes
	-#include "itkVectorImage.h"
	-#include "mitkAbstractFileReader.h"
	-
	-
	-
	-namespace mitk
	-{
	-
	- /** \brief
	- */
	-
	- class DiffusionImageDicomReaderService : public mitk::AbstractFileReader
	- {
	- public:
	-
	- DiffusionImageDicomReaderService(const DiffusionImageDicomReaderService & other);
	- DiffusionImageDicomReaderService();
	- ~DiffusionImageDicomReaderService() override;
	-
	- using AbstractFileReader::Read;
	- std::vector<itk::SmartPointer<BaseData> > Read() override;
	-
	- typedef short DiffusionPixelType;
	-
	- typedef mitk::Image OutputType;
	- typedef mitk::DiffusionPropertyHelper::ImageType VectorImageType;
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionType GradientDirectionType;
	- typedef mitk::DiffusionPropertyHelper::MeasurementFrameType MeasurementFrameType;
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionsContainerType GradientDirectionContainerType;
	-
	- protected:
	- OutputType::Pointer m_OutputCache;
	- itk::TimeStamp m_CacheTime;
	-
	- std::vector<itk::SmartPointer<BaseData> > InternalRead();
	-
	- private:
	-
	- DiffusionImageDicomReaderService* Clone() const override;
	- us::ServiceRegistration<mitk::IFileReader> m_ServiceReg;
	- };
	-
	-} //namespace MITK
	-
	-#endif // __mitkDiffusionImageDicomReaderService_h
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageNiftiReaderService.cpp b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageNiftiReaderService.cpp
	deleted file mode 100644
	index 7915778f27..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageNiftiReaderService.cpp
	+++ /dev/null
	@@ -1,425 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkDiffusionImageNiftiReaderService_cpp
	-#define __mitkDiffusionImageNiftiReaderService_cpp
	-
	-#include "mitkDiffusionImageNiftiReaderService.h"
	-
	-#include <iostream>
	-#include <fstream>
	-
	-
	-// Diffusion properties
	-#include <mitkGradientDirectionsProperty.h>
	-#include <mitkBValueMapProperty.h>
	-#include <mitkMeasurementFrameProperty.h>
	-#include <mitkProperties.h>
	-
	-// ITK includes
	-#include <itkImageRegionIterator.h>
	-#include <itkMetaDataObject.h>
	-#include "itksys/SystemTools.hxx"
	-#include "itkImageFileReader.h"
	-#include "itkMetaDataObject.h"
	-#include "itkNiftiImageIO.h"
	-
	-#include "mitkCustomMimeType.h"
	-#include "mitkDiffusionCoreIOMimeTypes.h"
	-
	-#include <mitkITKImageImport.h>
	-#include <mitkImageWriteAccessor.h>
	-#include <mitkImageDataItem.h>
	-#include <mitkLocaleSwitch.h>
	-#include "mitkIOUtil.h"
	-#include <mitkDiffusionFunctionCollection.h>
	-#include <vtkNIFTIImageReader.h>
	-#include <vtkNIFTIImageHeader.h>
	-#include <vtkImageIterator.h>
	-
	-namespace mitk
	-{
	-
	-DiffusionImageNiftiReaderService::
	-DiffusionImageNiftiReaderService(const DiffusionImageNiftiReaderService & other)
	- : AbstractFileReader(other)
	-{
	-}
	-
	-
	-DiffusionImageNiftiReaderService* DiffusionImageNiftiReaderService::Clone() const
	-{
	- return new DiffusionImageNiftiReaderService(*this);
	-}
	-
	-
	-DiffusionImageNiftiReaderService::
	-~DiffusionImageNiftiReaderService()
	-{}
	-
	-DiffusionImageNiftiReaderService::
	-DiffusionImageNiftiReaderService(CustomMimeType mime_type, std::string mime_type_description ) : mitk::AbstractFileReader( mime_type, mime_type_description )
	-{
	- Options defaultOptions;
	- defaultOptions["Apply image rotation to gradients"] = true;
	- this->SetDefaultOptions(defaultOptions);
	-
	- m_ServiceReg = this->RegisterService();
	-}
	-
	-//DiffusionImageNiftiReaderService::
	-//DiffusionImageNiftiReaderService() : mitk::AbstractFileReader( CustomMimeType( mitk::DiffusionCoreIOMimeTypes::DWI_NIFTI_MIMETYPE() ), mitk::DiffusionCoreIOMimeTypes::DWI_NIFTI_MIMETYPE_DESCRIPTION() )
	-//{
	-// m_ServiceReg = this->RegisterService();
	-//}
	-
	-std::vector<itk::SmartPointer<mitk::BaseData> >
	-DiffusionImageNiftiReaderService::
	-Read()
	-{
	- std::vector<itk::SmartPointer<mitk::BaseData> > result;
	-
	- // Since everything is completely read in GenerateOutputInformation() it is stored
	- // in a cache variable. A timestamp is associated.
	- // If the timestamp of the cache variable is newer than the MTime, we only need to
	- // assign the cache variable to the DataObject.
	- // Otherwise, the tree must be read again from the file and OuputInformation must
	- // be updated!
	-
	- if(m_OutputCache.IsNull()) InternalRead();
	-
	- result.push_back(m_OutputCache.GetPointer());
	- return result;
	-}
	-
	-
	-void DiffusionImageNiftiReaderService::InternalRead()
	-{
	- OutputType::Pointer outputForCache = OutputType::New();
	- if ( this->GetInputLocation() == "")
	- {
	- throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, the filename to be read is empty!");
	- }
	- else
	- {
	- try
	- {
	- mitk::LocaleSwitch localeSwitch("C");
	-
	- MITK_INFO << "DiffusionImageNiftiReaderService: reading image information";
	- VectorImageType::Pointer itkVectorImage;
	-
	- std::string ext = this->GetMimeType()->GetExtension( this->GetInputLocation() );
	- ext = itksys::SystemTools::LowerCase( ext );
	-
	- if(ext == ".fsl" \|\| ext == ".fslgz")
	- {
	- // create temporary file with correct ending for nifti-io
	- std::string fname3 = "temp_dwi";
	- fname3 += ext == ".fsl" ? ".nii" : ".nii.gz";
	- itksys::SystemTools::CopyAFile(this->GetInputLocation().c_str(), fname3.c_str());
	-
	- // create reader and read file
	- typedef itk::Image<DiffusionPixelType,4> ImageType4D;
	- itk::NiftiImageIO::Pointer io2 = itk::NiftiImageIO::New();
	- typedef itk::ImageFileReader<ImageType4D> FileReaderType;
	- FileReaderType::Pointer reader = FileReaderType::New();
	- reader->SetFileName(fname3);
	- reader->SetImageIO(io2);
	- reader->Update();
	- ImageType4D::Pointer img4 = reader->GetOutput();
	-
	- // delete temporary file
	- itksys::SystemTools::RemoveFile(fname3.c_str());
	-
	- // convert 4D file to vector image
	- itkVectorImage = VectorImageType::New();
	-
	- VectorImageType::SpacingType spacing;
	- ImageType4D::SpacingType spacing4 = img4->GetSpacing();
	- for(int i=0; i<3; i++)
	- spacing[i] = spacing4[i];
	- itkVectorImage->SetSpacing( spacing ); // Set the image spacing
	-
	- VectorImageType::PointType origin;
	- ImageType4D::PointType origin4 = img4->GetOrigin();
	- for(int i=0; i<3; i++)
	- origin[i] = origin4[i];
	- itkVectorImage->SetOrigin( origin ); // Set the image origin
	-
	- VectorImageType::DirectionType direction;
	- ImageType4D::DirectionType direction4 = img4->GetDirection();
	- for(int i=0; i<3; i++)
	- for(int j=0; j<3; j++)
	- direction[i][j] = direction4[i][j];
	- itkVectorImage->SetDirection( direction ); // Set the image direction
	-
	- VectorImageType::RegionType region;
	- ImageType4D::RegionType region4 = img4->GetLargestPossibleRegion();
	-
	- VectorImageType::RegionType::SizeType size;
	- ImageType4D::RegionType::SizeType size4 = region4.GetSize();
	-
	- for(int i=0; i<3; i++)
	- size[i] = size4[i];
	-
	- VectorImageType::RegionType::IndexType index;
	- ImageType4D::RegionType::IndexType index4 = region4.GetIndex();
	- for(int i=0; i<3; i++)
	- index[i] = index4[i];
	-
	- region.SetSize(size);
	- region.SetIndex(index);
	- itkVectorImage->SetRegions( region );
	-
	- itkVectorImage->SetVectorLength(size4[3]);
	- itkVectorImage->Allocate();
	-
	- itk::ImageRegionIterator<VectorImageType> it ( itkVectorImage, itkVectorImage->GetLargestPossibleRegion() );
	- typedef VectorImageType::PixelType VecPixType;
	- for (it.GoToBegin(); !it.IsAtEnd(); ++it)
	- {
	- VecPixType vec = it.Get();
	- VectorImageType::IndexType currentIndex = it.GetIndex();
	- for(int i=0; i<3; i++)
	- index4[i] = currentIndex[i];
	- for(unsigned int ind=0; ind<vec.Size(); ind++)
	- {
	- index4[3] = ind;
	- vec[ind] = img4->GetPixel(index4);
	- }
	- it.Set(vec);
	- }
	- }
	- else if(ext == ".nii" \|\| ext == ".nii.gz")
	- {
	- // create reader and read file
	- typedef itk::Image<DiffusionPixelType,4> ImageType4D;
	- itk::NiftiImageIO::Pointer io2 = itk::NiftiImageIO::New();
	-
	- ImageType4D::Pointer img4 = ImageType4D::New();
	- if (io2->CanReadFile(this->GetInputLocation().c_str()))
	- {
	- typedef itk::ImageFileReader<ImageType4D> FileReaderType;
	- FileReaderType::Pointer reader = FileReaderType::New();
	- reader->SetFileName( this->GetInputLocation() );
	- reader->SetImageIO(io2);
	- reader->Update();
	- img4 = reader->GetOutput();
	- }
	- else
	- {
	- vtkSmartPointer<vtkNIFTIImageReader> reader = vtkSmartPointer<vtkNIFTIImageReader>::New();
	- if (reader->CanReadFile(this->GetInputLocation().c_str()))
	- {
	- reader->SetFileName(this->GetInputLocation().c_str());
	- reader->SetTimeAsVector(true);
	- reader->Update();
	- auto vtk_image = reader->GetOutput();
	- auto header = reader->GetNIFTIHeader();
	- auto dim = header->GetDim(0);
	- auto matrix = reader->GetQFormMatrix();
	- if (matrix == nullptr)
	- matrix = reader->GetSFormMatrix();
	- itk::Matrix<double, 4, 4> direction; direction.SetIdentity();
	- itk::Matrix<double, 4, 4> ras_lps; ras_lps.SetIdentity();
	- ras_lps[0][0] = -1;
	- ras_lps[1][1] = -1;
	- if (matrix != nullptr)
	- {
	- for (int r=0; r<dim; r++)
	- for (int c=0; c<dim; c++)
	- direction[r][c] = matrix->GetElement(r, c);
	- }
	- direction = direction*ras_lps;
	-
	- itk::Vector< double, 4 > spacing; spacing.Fill(1.0);
	- vtk_image->GetSpacing(spacing.GetDataPointer());
	-
	- itk::Point< double, 4 > origin; origin.Fill(0.0);
	- vtk_image->GetOrigin(origin.GetDataPointer());
	-
	- itk::ImageRegion< 4 > region;
	- for (int i=0; i<4; ++i)
	- if (i<dim)
	- region.SetSize(i, header->GetDim(i+1));
	- else
	- region.SetSize(i, 1);
	-
	- img4->SetSpacing( spacing );
	- img4->SetOrigin( origin );
	- img4->SetDirection( direction );
	- img4->SetRegions( region );
	- img4->Allocate();
	- img4->FillBuffer(0);
	-
	- switch (header->GetDim(0)) {
	- case 4:
	- for (int g=0; g<header->GetDim(4); g++)
	- for (int z=0; z<header->GetDim(3); z++)
	- for (int y=0; y<header->GetDim(2); y++)
	- for (int x=0; x<header->GetDim(1); x++)
	- {
	- double val = vtk_image->GetScalarComponentAsDouble(x, y, z, g);
	-
	- ImageType4D::IndexType idx;
	- idx[0] = x;
	- idx[1] = y;
	- idx[2] = z;
	- idx[3] = g;
	- img4->SetPixel(idx, val);
	- }
	- break;
	- default:
	- mitkThrow() << "Image dimension " << header->GetDim(0) << " not supported!";
	- break;
	- }
	- }
	- }
	-
	- // convert 4D file to vector image
	- itkVectorImage = VectorImageType::New();
	-
	- VectorImageType::SpacingType spacing;
	- ImageType4D::SpacingType spacing4 = img4->GetSpacing();
	- for(int i=0; i<3; i++)
	- spacing[i] = spacing4[i];
	- itkVectorImage->SetSpacing( spacing ); // Set the image spacing
	-
	- VectorImageType::PointType origin;
	- ImageType4D::PointType origin4 = img4->GetOrigin();
	- for(int i=0; i<3; i++)
	- origin[i] = origin4[i];
	- itkVectorImage->SetOrigin( origin ); // Set the image origin
	-
	- VectorImageType::DirectionType direction;
	- ImageType4D::DirectionType direction4 = img4->GetDirection();
	- for(int i=0; i<3; i++)
	- for(int j=0; j<3; j++)
	- direction[i][j] = direction4[i][j];
	- itkVectorImage->SetDirection( direction ); // Set the image direction
	-
	- VectorImageType::RegionType region;
	- ImageType4D::RegionType region4 = img4->GetLargestPossibleRegion();
	-
	- VectorImageType::RegionType::SizeType size;
	- ImageType4D::RegionType::SizeType size4 = region4.GetSize();
	-
	- for(int i=0; i<3; i++)
	- size[i] = size4[i];
	-
	- VectorImageType::RegionType::IndexType index;
	- ImageType4D::RegionType::IndexType index4 = region4.GetIndex();
	- for(int i=0; i<3; i++)
	- index[i] = index4[i];
	-
	- region.SetSize(size);
	- region.SetIndex(index);
	- itkVectorImage->SetRegions( region );
	-
	- itkVectorImage->SetVectorLength(size4[3]);
	- itkVectorImage->Allocate();
	-
	- itk::ImageRegionIterator<VectorImageType> it ( itkVectorImage, itkVectorImage->GetLargestPossibleRegion() );
	- typedef VectorImageType::PixelType VecPixType;
	- for (it.GoToBegin(); !it.IsAtEnd(); ++it)
	- {
	- VecPixType vec = it.Get();
	- VectorImageType::IndexType currentIndex = it.GetIndex();
	- for(int i=0; i<3; i++)
	- index4[i] = currentIndex[i];
	- for(unsigned int ind=0; ind<vec.Size(); ind++)
	- {
	- index4[3] = ind;
	- vec[ind] = img4->GetPixel(index4);
	- }
	- it.Set(vec);
	- }
	- }
	-
	- // Diffusion Image information START
	- GradientDirectionContainerType::Pointer DiffusionVectors = GradientDirectionContainerType::New();
	- MeasurementFrameType MeasurementFrame;
	- double BValue = -1;
	- // Diffusion Image information END
	-
	- if(ext == ".fsl" \|\| ext == ".fslgz" \|\| ext == ".nii" \|\| ext == ".nii.gz")
	- {
	- std::string base_path = itksys::SystemTools::GetFilenamePath(this->GetInputLocation());
	- std::string base = this->GetMimeType()->GetFilenameWithoutExtension(this->GetInputLocation());
	- if (!base_path.empty())
	- {
	- base = base_path + "/" + base;
	- base_path += "/";
	- }
	-
	- // check for possible file names
	- std::string bvals_file, bvecs_file;
	- if (itksys::SystemTools::FileExists(base+".bvals"))
	- bvals_file = base+".bvals";
	- else if (itksys::SystemTools::FileExists(base+".bval"))
	- bvals_file = base+".bval";
	- else if (itksys::SystemTools::FileExists(base_path+"bvals"))
	- bvals_file = base_path + "bvals";
	- else if (itksys::SystemTools::FileExists(base_path+"bval"))
	- bvals_file = base_path + "bval";
	-
	- if (itksys::SystemTools::FileExists(std::string(base+".bvecs").c_str()))
	- bvecs_file = base+".bvecs";
	- else if (itksys::SystemTools::FileExists(base+".bvec"))
	- bvals_file = base+".bvec";
	- else if (itksys::SystemTools::FileExists(base_path+"bvecs"))
	- bvecs_file = base_path + "bvecs";
	- else if (itksys::SystemTools::FileExists(base_path+"bvec"))
	- bvecs_file = base_path + "bvec";
	-
	- DiffusionVectors = mitk::gradients::ReadBvalsBvecs(bvals_file, bvecs_file, BValue);
	- MeasurementFrame.set_identity();
	- }
	-
	- outputForCache = mitk::GrabItkImageMemory( itkVectorImage);
	-
	- // create BValueMap
	- mitk::BValueMapProperty::BValueMap BValueMap = mitk::BValueMapProperty::CreateBValueMap(DiffusionVectors,BValue);
	- mitk::DiffusionPropertyHelper::SetOriginalGradientContainer(outputForCache, DiffusionVectors);
	- mitk::DiffusionPropertyHelper::SetMeasurementFrame(outputForCache, MeasurementFrame);
	- mitk::DiffusionPropertyHelper::SetBValueMap(outputForCache, BValueMap);
	- mitk::DiffusionPropertyHelper::SetReferenceBValue(outputForCache, BValue);
	- mitk::DiffusionPropertyHelper::SetApplyMatrixToGradients(outputForCache, us::any_cast<bool>(this->GetOptions()["Apply image rotation to gradients"]));
	- mitk::DiffusionPropertyHelper::InitializeImage(outputForCache);
	-
	- // Since we have already read the tree, we can store it in a cache variable
	- // so that it can be assigned to the DataObject in GenerateData();
	- m_OutputCache = outputForCache;
	- m_CacheTime.Modified();
	- }
	- catch(std::exception& e)
	- {
	- MITK_INFO << "Std::Exception while reading file!!";
	- MITK_INFO << e.what();
	- throw itk::ImageFileReaderException(__FILE__, __LINE__, e.what());
	- }
	- catch(...)
	- {
	- MITK_INFO << "Exception while reading file!!";
	- throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, an error occurred while reading the requested vessel tree file!");
	- }
	- }
	-}
	-
	-} //namespace MITK
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageNiftiReaderService.h b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageNiftiReaderService.h
	deleted file mode 100644
	index c4a6b97c17..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageNiftiReaderService.h
	+++ /dev/null
	@@ -1,74 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkDiffusionImageNiftiReaderService_h
	-#define __mitkDiffusionImageNiftiReaderService_h
	-
	-#include "mitkCommon.h"
	-
	-// MITK includes
	-#include "mitkImageSource.h"
	-#include "mitkFileReader.h"
	-
	-#include <mitkDiffusionPropertyHelper.h>
	-
	-// ITK includes
	-#include "itkVectorImage.h"
	-#include "mitkAbstractFileReader.h"
	-
	-
	-
	-namespace mitk
	-{
	-
	- /** \brief
	- */
	-
	- class DiffusionImageNiftiReaderService : public mitk::AbstractFileReader
	- {
	- public:
	-
	- DiffusionImageNiftiReaderService(const DiffusionImageNiftiReaderService & other);
	- //DiffusionImageNiftiReaderService();
	- DiffusionImageNiftiReaderService(CustomMimeType mime_type, std::string mime_type_description );
	- ~DiffusionImageNiftiReaderService() override;
	-
	- using AbstractFileReader::Read;
	- std::vector<itk::SmartPointer<BaseData> > Read() override;
	-
	- typedef short DiffusionPixelType;
	-
	- typedef mitk::Image OutputType;
	- typedef mitk::DiffusionPropertyHelper::ImageType VectorImageType;
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionType GradientDirectionType;
	- typedef mitk::DiffusionPropertyHelper::MeasurementFrameType MeasurementFrameType;
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionsContainerType GradientDirectionContainerType;
	-
	- protected:
	- OutputType::Pointer m_OutputCache;
	- itk::TimeStamp m_CacheTime;
	-
	- void InternalRead();
	-
	- private:
	-
	- DiffusionImageNiftiReaderService* Clone() const override;
	- us::ServiceRegistration<mitk::IFileReader> m_ServiceReg;
	- };
	-
	-} //namespace MITK
	-
	-#endif // __mitkDiffusionImageNiftiReaderService_h
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageNiftiWriterService.cpp b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageNiftiWriterService.cpp
	deleted file mode 100644
	index 918773fd25..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageNiftiWriterService.cpp
	+++ /dev/null
	@@ -1,249 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkDiffusionImageNiftiWriterService__cpp
	-#define __mitkDiffusionImageNiftiWriterService__cpp
	-
	-#include "mitkDiffusionImageNiftiWriterService.h"
	-#include "itkMetaDataDictionary.h"
	-#include "itkMetaDataObject.h"
	-#include "itkNiftiImageIO.h"
	-#include "itkImageFileWriter.h"
	-#include "itksys/SystemTools.hxx"
	-#include "mitkDiffusionCoreIOMimeTypes.h"
	-#include "mitkImageCast.h"
	-#include <mitkLocaleSwitch.h>
	-
	-#include <iostream>
	-#include <fstream>
	-#include <mitkDiffusionFunctionCollection.h>
	-
	-mitk::DiffusionImageNiftiWriterService::DiffusionImageNiftiWriterService()
	- : AbstractFileWriter(mitk::Image::GetStaticNameOfClass(), CustomMimeType( mitk::DiffusionCoreIOMimeTypes::DWI_NIFTI_MIMETYPE() ), mitk::DiffusionCoreIOMimeTypes::DWI_NIFTI_MIMETYPE_DESCRIPTION())
	-{
	- RegisterService();
	-}
	-
	-mitk::DiffusionImageNiftiWriterService::DiffusionImageNiftiWriterService(const mitk::DiffusionImageNiftiWriterService& other)
	- : AbstractFileWriter(other)
	-{
	-}
	-
	-mitk::DiffusionImageNiftiWriterService::~DiffusionImageNiftiWriterService()
	-{}
	-
	-void mitk::DiffusionImageNiftiWriterService::Write()
	-{
	- mitk::Image::ConstPointer input = dynamic_cast<const mitk::Image *>(this->GetInput());
	-
	- VectorImageType::Pointer itkImg;
	- mitk::CastToItkImage(input,itkImg);
	-
	- if (input.IsNull())
	- {
	- MITK_ERROR <<"Sorry, input to DiffusionImageNiftiWriterService is nullptr!";
	- return;
	- }
	- if ( this->GetOutputLocation().empty() )
	- {
	- MITK_ERROR << "Sorry, filename has not been set!";
	- return ;
	- }
	- mitk::LocaleSwitch localeSwitch("C");
	-
	- char keybuffer[512];
	- char valbuffer[512];
	-
	- //itk::MetaDataDictionary dic = input->GetImage()->GetMetaDataDictionary();
	-
	- vnl_matrix_fixed<double,3,3> measurementFrame = mitk::DiffusionPropertyHelper::GetMeasurementFrame(input);
	- if (measurementFrame(0,0) \|\| measurementFrame(0,1) \|\| measurementFrame(0,2) \|\|
	- measurementFrame(1,0) \|\| measurementFrame(1,1) \|\| measurementFrame(1,2) \|\|
	- measurementFrame(2,0) \|\| measurementFrame(2,1) \|\| measurementFrame(2,2))
	- {
	- sprintf( valbuffer, " (%lf,%lf,%lf) (%lf,%lf,%lf) (%lf,%lf,%lf)", measurementFrame(0,0), measurementFrame(0,1), measurementFrame(0,2), measurementFrame(1,0), measurementFrame(1,1), measurementFrame(1,2), measurementFrame(2,0), measurementFrame(2,1), measurementFrame(2,2));
	- itk::EncapsulateMetaData<std::string>(itkImg->GetMetaDataDictionary(),std::string("measurement frame"),std::string(valbuffer));
	- }
	-
	- sprintf( valbuffer, "DWMRI");
	- itk::EncapsulateMetaData<std::string>(itkImg->GetMetaDataDictionary(),std::string("modality"),std::string(valbuffer));
	-
	- if(mitk::DiffusionPropertyHelper::GetGradientContainer(input)->Size())
	- {
	- sprintf( valbuffer, "%1f", mitk::DiffusionPropertyHelper::GetReferenceBValue(input) );
	- itk::EncapsulateMetaData<std::string>(itkImg->GetMetaDataDictionary(),std::string("DWMRI_b-value"),std::string(valbuffer));
	- }
	-
	- for(unsigned int i=0; i<mitk::DiffusionPropertyHelper::GetGradientContainer(input)->Size(); i++)
	- {
	- sprintf( keybuffer, "DWMRI_gradient_%04d", i );
	-
	- /*if(itk::ExposeMetaData<std::string>(input->GetMetaDataDictionary(),
	- std::string(keybuffer),tmp))
	- continue;*/
	-
	- sprintf( valbuffer, "%1f %1f %1f", mitk::DiffusionPropertyHelper::GetGradientContainer(input)->ElementAt(i).get(0),
	- mitk::DiffusionPropertyHelper::GetGradientContainer(input)->ElementAt(i).get(1), mitk::DiffusionPropertyHelper::GetGradientContainer(input)->ElementAt(i).get(2));
	-
	- itk::EncapsulateMetaData<std::string>(itkImg->GetMetaDataDictionary(),std::string(keybuffer),std::string(valbuffer));
	- }
	-
	- typedef itk::VectorImage<short,3> ImageType;
	-
	- std::string ext = this->GetMimeType()->GetExtension(this->GetOutputLocation());
	- ext = itksys::SystemTools::LowerCase(ext);
	-
	- // default extension is .nii.gz
	- if( ext == "")
	- {
	- ext = ".nii.gz";
	- this->SetOutputLocation(this->GetOutputLocation() + ext);
	- }
	- if (ext == ".nii" \|\| ext == ".nii.gz")
	- {
	- MITK_INFO << "Writing Nifti-Image";
	-
	- typedef itk::Image<short,4> ImageType4D;
	- ImageType4D::Pointer img4 = ImageType4D::New();
	-
	- ImageType::SpacingType spacing = itkImg->GetSpacing();
	- ImageType4D::SpacingType spacing4;
	- for(int i=0; i<3; i++)
	- spacing4[i] = spacing[i];
	- spacing4[3] = 1;
	- img4->SetSpacing( spacing4 ); // Set the image spacing
	-
	- ImageType::PointType origin = itkImg->GetOrigin();
	- ImageType4D::PointType origin4;
	- for(int i=0; i<3; i++)
	- origin4[i] = origin[i];
	- origin4[3] = 0;
	- img4->SetOrigin( origin4 ); // Set the image origin
	-
	- ImageType::DirectionType direction = itkImg->GetDirection();
	- ImageType4D::DirectionType direction4;
	- for(int i=0; i<3; i++)
	- for(int j=0; j<3; j++)
	- direction4[i][j] = direction[i][j];
	- for(int i=0; i<4; i++)
	- direction4[i][3] = 0;
	- for(int i=0; i<4; i++)
	- direction4[3][i] = 0;
	- direction4[3][3] = 1;
	- img4->SetDirection( direction4 ); // Set the image direction
	-
	- ImageType::RegionType region = itkImg->GetLargestPossibleRegion();
	- ImageType4D::RegionType region4;
	-
	- ImageType::RegionType::SizeType size = region.GetSize();
	- ImageType4D::RegionType::SizeType size4;
	-
	- for(int i=0; i<3; i++)
	- size4[i] = size[i];
	- size4[3] = itkImg->GetVectorLength();
	-
	- ImageType::RegionType::IndexType index = region.GetIndex();
	- ImageType4D::RegionType::IndexType index4;
	- for(int i=0; i<3; i++)
	- index4[i] = index[i];
	- index4[3] = 0;
	-
	- region4.SetSize(size4);
	- region4.SetIndex(index4);
	- img4->SetRegions( region4 );
	-
	- img4->Allocate();
	-
	- itk::ImageRegionIterator<ImageType> it (itkImg, itkImg->GetLargestPossibleRegion() );
	- typedef ImageType::PixelType VecPixType;
	-
	- for (it.GoToBegin(); !it.IsAtEnd(); ++it)
	- {
	- VecPixType vec = it.Get();
	- ImageType::IndexType currentIndex = it.GetIndex();
	- for(unsigned int ind=0; ind<vec.Size(); ind++)
	- {
	-
	- for(int i=0; i<3; i++)
	- index4[i] = currentIndex[i];
	- index4[3] = ind;
	- img4->SetPixel(index4, vec[ind]);
	- }
	- }
	-
	- itk::NiftiImageIO::Pointer io4 = itk::NiftiImageIO::New();
	-
	- typedef itk::ImageFileWriter<ImageType4D> WriterType4;
	- WriterType4::Pointer nrrdWriter4 = WriterType4::New();
	- nrrdWriter4->UseInputMetaDataDictionaryOn();
	- nrrdWriter4->SetInput( img4 );
	- nrrdWriter4->SetFileName(this->GetOutputLocation());
	- nrrdWriter4->UseCompressionOn();
	- nrrdWriter4->SetImageIO(io4);
	- try
	- {
	- nrrdWriter4->Update();
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.GetDescription() << std::endl;
	- throw;
	- }
	-
	-
	- std::string base_path = itksys::SystemTools::GetFilenamePath(this->GetOutputLocation());
	- std::string bvals_file = this->GetMimeType()->GetFilenameWithoutExtension(this->GetOutputLocation());
	- if (!base_path.empty())
	- bvals_file = base_path + "/" + bvals_file;
	- bvals_file += ".bvals";
	-
	- std::string bvecs_file = this->GetMimeType()->GetFilenameWithoutExtension(this->GetOutputLocation());
	- if (!base_path.empty())
	- bvecs_file = base_path + "/" + bvecs_file;
	- bvecs_file += ".bvecs";
	-
	- if(mitk::DiffusionPropertyHelper::GetOriginalGradientContainer(input)->Size())
	- {
	- MITK_INFO << "Saving original gradient directions";
	- mitk::gradients::WriteBvalsBvecs(bvals_file, bvecs_file, mitk::DiffusionPropertyHelper::GetOriginalGradientContainer(input), mitk::DiffusionPropertyHelper::GetReferenceBValue(input));
	- }
	- else if(mitk::DiffusionPropertyHelper::GetGradientContainer(input)->Size())
	- {
	- MITK_INFO << "Original gradient directions not found. Saving modified gradient directions";
	- mitk::gradients::WriteBvalsBvecs(bvals_file, bvecs_file, mitk::DiffusionPropertyHelper::GetGradientContainer(input), mitk::DiffusionPropertyHelper::GetReferenceBValue(input));
	- }
	- }
	-}
	-
	-mitk::DiffusionImageNiftiWriterService* mitk::DiffusionImageNiftiWriterService::Clone() const
	-{
	- return new DiffusionImageNiftiWriterService(*this);
	-}
	-
	-mitk::IFileWriter::ConfidenceLevel mitk::DiffusionImageNiftiWriterService::GetConfidenceLevel() const
	-{
	- mitk::Image::ConstPointer input = dynamic_cast<const mitk::Image*>(this->GetInput());
	- if (input.IsNull() \|\| !mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( input ) )
	- {
	- return Unsupported;
	- }
	- else
	- {
	- return Supported;
	- }
	-}
	-
	-#endif //__mitkDiffusionImageNiftiWriterService__cpp
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageNiftiWriterService.h b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageNiftiWriterService.h
	deleted file mode 100644
	index 4937d93def..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageNiftiWriterService.h
	+++ /dev/null
	@@ -1,58 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_DiffusionImageNiftiWriterService__H_
	-#define _MITK_DiffusionImageNiftiWriterService__H_
	-
	-#include <mitkAbstractFileWriter.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-
	-namespace mitk
	-{
	-
	-/**
	- * Writes diffusion volumes to a file
	- * @ingroup Process
	- */
	-class DiffusionImageNiftiWriterService : public mitk::AbstractFileWriter
	-{
	-public:
	-
	- DiffusionImageNiftiWriterService();
	- ~DiffusionImageNiftiWriterService() override;
	-
	- using AbstractFileWriter::Write;
	- void Write() override;
	-
	- ConfidenceLevel GetConfidenceLevel() const override;
	-
	- typedef mitk::DiffusionPropertyHelper::ImageType VectorImageType;
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionType GradientDirectionType;
	- typedef mitk::DiffusionPropertyHelper::MeasurementFrameType MeasurementFrameType;
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionsContainerType GradientDirectionContainerType;
	-
	- protected:
	-
	- DiffusionImageNiftiWriterService(const DiffusionImageNiftiWriterService& other);
	- mitk::DiffusionImageNiftiWriterService* Clone() const override;
	-
	-
	-};
	-
	-
	-} // end of namespace mitk
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageNrrdReaderService.cpp b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageNrrdReaderService.cpp
	deleted file mode 100644
	index 455463e020..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageNrrdReaderService.cpp
	+++ /dev/null
	@@ -1,249 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkDiffusionImageNrrdReaderService_cpp
	-#define __mitkDiffusionImageNrrdReaderService_cpp
	-
	-#include "mitkDiffusionImageNrrdReaderService.h"
	-
	-#include <iostream>
	-#include <fstream>
	-
	-
	-// Diffusion properties
	-#include <mitkGradientDirectionsProperty.h>
	-#include <mitkBValueMapProperty.h>
	-#include <mitkMeasurementFrameProperty.h>
	-#include <mitkProperties.h>
	-
	-// ITK includes
	-#include <itkImageRegionIterator.h>
	-#include <itkMetaDataObject.h>
	-#include "itksys/SystemTools.hxx"
	-#include "itkImageFileReader.h"
	-#include "itkMetaDataObject.h"
	-#include "itkNrrdImageIO.h"
	-
	-#include "mitkCustomMimeType.h"
	-#include "mitkDiffusionCoreIOMimeTypes.h"
	-
	-#include <mitkITKImageImport.h>
	-#include <mitkImageWriteAccessor.h>
	-#include <mitkImageDataItem.h>
	-#include "mitkIOUtil.h"
	-#include <mitkLocaleSwitch.h>
	-
	-namespace mitk
	-{
	-
	- DiffusionImageNrrdReaderService::
	- DiffusionImageNrrdReaderService(const DiffusionImageNrrdReaderService & other)
	- : AbstractFileReader(other)
	- {
	- }
	-
	-
	- DiffusionImageNrrdReaderService* DiffusionImageNrrdReaderService::Clone() const
	- {
	- return new DiffusionImageNrrdReaderService(*this);
	- }
	-
	-
	- DiffusionImageNrrdReaderService::
	- ~DiffusionImageNrrdReaderService()
	- {}
	-
	- DiffusionImageNrrdReaderService::
	- DiffusionImageNrrdReaderService()
	- : mitk::AbstractFileReader( CustomMimeType( mitk::DiffusionCoreIOMimeTypes::DWI_NRRD_MIMETYPE() ), mitk::DiffusionCoreIOMimeTypes::DWI_NRRD_MIMETYPE_DESCRIPTION() )
	- {
	- Options defaultOptions;
	- defaultOptions["Apply image rotation to gradients"] = true;
	- this->SetDefaultOptions(defaultOptions);
	- m_ServiceReg = this->RegisterService();
	- }
	-
	- std::vector<itk::SmartPointer<mitk::BaseData> >
	- DiffusionImageNrrdReaderService::
	- Read()
	- {
	- std::vector<itk::SmartPointer<mitk::BaseData> > result;
	-
	- // Since everything is completely read in GenerateOutputInformation() it is stored
	- // in a cache variable. A timestamp is associated.
	- // If the timestamp of the cache variable is newer than the MTime, we only need to
	- // assign the cache variable to the DataObject.
	- // Otherwise, the tree must be read again from the file and OuputInformation must
	- // be updated!
	-
	- if(m_OutputCache.IsNull()) InternalRead();
	-
	- result.push_back(m_OutputCache.GetPointer());
	- return result;
	- }
	-
	-
	- void DiffusionImageNrrdReaderService::InternalRead()
	- {
	- OutputType::Pointer outputForCache = OutputType::New();
	- if ( this->GetInputLocation() == "")
	- {
	- throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, the filename to be read is empty!");
	- }
	- else
	- {
	- try
	- {
	- mitk::LocaleSwitch localeSwitch("C");
	-
	- MITK_INFO << "DiffusionImageNrrdReaderService: reading image information";
	- VectorImageType::Pointer itkVectorImage;
	-
	- std::string ext = this->GetMimeType()->GetExtension( this->GetInputLocation() );
	- ext = itksys::SystemTools::LowerCase( ext );
	-
	- if (ext == ".hdwi" \|\| ext == ".dwi" \|\| ext == ".nrrd")
	- {
	- typedef itk::ImageFileReader<VectorImageType> FileReaderType;
	- FileReaderType::Pointer reader = FileReaderType::New();
	- reader->SetFileName(this->GetInputLocation());
	- itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
	- reader->SetImageIO(io);
	- reader->Update();
	- itkVectorImage = reader->GetOutput();
	- }
	-
	- // Diffusion Image information START
	- GradientDirectionContainerType::Pointer DiffusionVectors = GradientDirectionContainerType::New();
	- GradientDirectionContainerType::Pointer OriginalDiffusionVectors = GradientDirectionContainerType::New();
	- MeasurementFrameType MeasurementFrame;
	- float BValue = -1;
	- // Diffusion Image information END
	-
	- if (ext == ".hdwi" \|\| ext == ".dwi" \|\| ext == ".nrrd")
	- {
	-
	- itk::MetaDataDictionary imgMetaDictionary = itkVectorImage->GetMetaDataDictionary();
	- std::vector<std::string> imgMetaKeys = imgMetaDictionary.GetKeys();
	- std::vector<std::string>::const_iterator itKey = imgMetaKeys.begin();
	- std::string metaString;
	-
	- GradientDirectionType vect3d;
	-
	- int numberOfImages = 0;
	- int numberOfGradientImages = 0;
	- bool readb0 = false;
	- double xx, xy, xz, yx, yy, yz, zx, zy, zz;
	-
	- for (; itKey != imgMetaKeys.end(); itKey ++)
	- {
	- double x,y,z;
	-
	- itk::ExposeMetaData<std::string> (imgMetaDictionary, *itKey, metaString);
	- if (itKey->find("DWMRI_gradient") != std::string::npos)
	- {
	- sscanf(metaString.c_str(), "%lf %lf %lf\n", &x, &y, &z);
	- vect3d[0] = x; vect3d[1] = y; vect3d[2] = z;
	- DiffusionVectors->InsertElement( numberOfImages, vect3d );
	- ++numberOfImages;
	- // If the direction is 0.0, this is a reference image
	- if (vect3d[0] == 0.0 &&
	- vect3d[1] == 0.0 &&
	- vect3d[2] == 0.0)
	- {
	- continue;
	- }
	- ++numberOfGradientImages;;
	- }
	- else if (itKey->find("DWMRI_b-value") != std::string::npos)
	- {
	- readb0 = true;
	- BValue = atof(metaString.c_str());
	- }
	- else if (itKey->find("measurement frame") != std::string::npos)
	- {
	- sscanf(metaString.c_str(), " ( %lf , %lf , %lf ) ( %lf , %lf , %lf ) ( %lf , %lf , %lf ) \n", &xx, &xy, &xz, &yx, &yy, &yz, &zx, &zy, &zz);
	-
	- if (xx>10e-10 \|\| xy>10e-10 \|\| xz>10e-10 \|\|
	- yx>10e-10 \|\| yy>10e-10 \|\| yz>10e-10 \|\|
	- zx>10e-10 \|\| zy>10e-10 \|\| zz>10e-10 )
	- {
	- MeasurementFrame(0,0) = xx;
	- MeasurementFrame(0,1) = xy;
	- MeasurementFrame(0,2) = xz;
	- MeasurementFrame(1,0) = yx;
	- MeasurementFrame(1,1) = yy;
	- MeasurementFrame(1,2) = yz;
	- MeasurementFrame(2,0) = zx;
	- MeasurementFrame(2,1) = zy;
	- MeasurementFrame(2,2) = zz;
	- }
	- else
	- {
	- MeasurementFrame(0,0) = 1;
	- MeasurementFrame(0,1) = 0;
	- MeasurementFrame(0,2) = 0;
	- MeasurementFrame(1,0) = 0;
	- MeasurementFrame(1,1) = 1;
	- MeasurementFrame(1,2) = 0;
	- MeasurementFrame(2,0) = 0;
	- MeasurementFrame(2,1) = 0;
	- MeasurementFrame(2,2) = 1;
	- }
	- }
	- }
	-
	- if(!readb0)
	- {
	- MITK_INFO << "BValue not specified in header file";
	- }
	-
	- }
	-
	- outputForCache = mitk::GrabItkImageMemory( itkVectorImage);
	-
	- // create BValueMap
	- mitk::BValueMapProperty::BValueMap BValueMap = mitk::BValueMapProperty::CreateBValueMap(DiffusionVectors,BValue);
	- mitk::DiffusionPropertyHelper::SetOriginalGradientContainer(outputForCache, DiffusionVectors);
	- mitk::DiffusionPropertyHelper::SetMeasurementFrame(outputForCache, MeasurementFrame);
	- mitk::DiffusionPropertyHelper::SetBValueMap(outputForCache, BValueMap);
	- mitk::DiffusionPropertyHelper::SetReferenceBValue(outputForCache, BValue);
	- mitk::DiffusionPropertyHelper::SetApplyMatrixToGradients(outputForCache, us::any_cast<bool>(this->GetOptions()["Apply image rotation to gradients"]));
	- mitk::DiffusionPropertyHelper::InitializeImage(outputForCache);
	-
	- // Since we have already read the tree, we can store it in a cache variable
	- // so that it can be assigned to the DataObject in GenerateData();
	- m_OutputCache = outputForCache;
	- m_CacheTime.Modified();
	-
	- }
	- catch(std::exception& e)
	- {
	- MITK_INFO << "Std::Exception while reading file!!";
	- MITK_INFO << e.what();
	- throw itk::ImageFileReaderException(__FILE__, __LINE__, e.what());
	- }
	- catch(...)
	- {
	- MITK_INFO << "Exception while reading file!!";
	- throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, an error occurred while reading the requested vessel tree file!");
	- }
	- }
	- }
	-
	-} //namespace MITK
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageNrrdReaderService.h b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageNrrdReaderService.h
	deleted file mode 100644
	index 9faf34b74d..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageNrrdReaderService.h
	+++ /dev/null
	@@ -1,73 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkDiffusionImageNrrdReaderService_h
	-#define __mitkDiffusionImageNrrdReaderService_h
	-
	-#include "mitkCommon.h"
	-
	-// MITK includes
	-#include "mitkImageSource.h"
	-#include "mitkFileReader.h"
	-
	-#include <mitkDiffusionPropertyHelper.h>
	-
	-// ITK includes
	-#include "itkVectorImage.h"
	-#include "mitkAbstractFileReader.h"
	-
	-
	-
	-namespace mitk
	-{
	-
	- /** \brief
	- */
	-
	- class DiffusionImageNrrdReaderService : public mitk::AbstractFileReader
	- {
	- public:
	-
	- DiffusionImageNrrdReaderService(const DiffusionImageNrrdReaderService & other);
	- DiffusionImageNrrdReaderService();
	- ~DiffusionImageNrrdReaderService() override;
	-
	- using AbstractFileReader::Read;
	- std::vector<itk::SmartPointer<BaseData> > Read() override;
	-
	- typedef short DiffusionPixelType;
	-
	- typedef mitk::Image OutputType;
	- typedef mitk::DiffusionPropertyHelper::ImageType VectorImageType;
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionType GradientDirectionType;
	- typedef mitk::DiffusionPropertyHelper::MeasurementFrameType MeasurementFrameType;
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionsContainerType GradientDirectionContainerType;
	-
	- protected:
	- OutputType::Pointer m_OutputCache;
	- itk::TimeStamp m_CacheTime;
	-
	- void InternalRead();
	-
	- private:
	-
	- DiffusionImageNrrdReaderService* Clone() const override;
	- us::ServiceRegistration<mitk::IFileReader> m_ServiceReg;
	- };
	-
	-} //namespace MITK
	-
	-#endif // __mitkDiffusionImageNrrdReaderService_h
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageNrrdWriterService.cpp b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageNrrdWriterService.cpp
	deleted file mode 100644
	index 37e3479c66..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageNrrdWriterService.cpp
	+++ /dev/null
	@@ -1,173 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkDiffusionImageNrrdWriterService__cpp
	-#define __mitkDiffusionImageNrrdWriterService__cpp
	-
	-#include "mitkDiffusionImageNrrdWriterService.h"
	-#include "itkMetaDataDictionary.h"
	-#include "itkMetaDataObject.h"
	-#include "itkNrrdImageIO.h"
	-#include "itkImageFileWriter.h"
	-#include "itksys/SystemTools.hxx"
	-#include "mitkDiffusionCoreIOMimeTypes.h"
	-#include "mitkImageCast.h"
	-#include <mitkLocaleSwitch.h>
	-
	-#include <iostream>
	-#include <fstream>
	-
	-
	-mitk::DiffusionImageNrrdWriterService::DiffusionImageNrrdWriterService()
	- : AbstractFileWriter(mitk::Image::GetStaticNameOfClass(), CustomMimeType( mitk::DiffusionCoreIOMimeTypes::DWI_NRRD_MIMETYPE() ), mitk::DiffusionCoreIOMimeTypes::DWI_NRRD_MIMETYPE_DESCRIPTION())
	-{
	- RegisterService();
	-}
	-
	-mitk::DiffusionImageNrrdWriterService::DiffusionImageNrrdWriterService(const mitk::DiffusionImageNrrdWriterService& other)
	- : AbstractFileWriter(other)
	-{
	-}
	-
	-mitk::DiffusionImageNrrdWriterService::~DiffusionImageNrrdWriterService()
	-{}
	-
	-void mitk::DiffusionImageNrrdWriterService::Write()
	-{
	- mitk::Image::ConstPointer input = dynamic_cast<const mitk::Image *>(this->GetInput());
	-
	- VectorImageType::Pointer itkImg;
	- mitk::CastToItkImage(input,itkImg);
	-
	- if (input.IsNull())
	- {
	- MITK_ERROR <<"Sorry, input to DiffusionImageNrrdWriterService is nullptr!";
	- return;
	- }
	- if ( this->GetOutputLocation().empty() )
	- {
	- MITK_ERROR << "Sorry, filename has not been set!";
	- return ;
	- }
	- mitk::LocaleSwitch localeSwitch("C");
	-
	- char keybuffer[512];
	- char valbuffer[512];
	-
	- //itk::MetaDataDictionary dic = input->GetImage()->GetMetaDataDictionary();
	-
	- vnl_matrix_fixed<double,3,3> measurementFrame = mitk::DiffusionPropertyHelper::GetMeasurementFrame(input);
	- if (measurementFrame(0,0) \|\| measurementFrame(0,1) \|\| measurementFrame(0,2) \|\|
	- measurementFrame(1,0) \|\| measurementFrame(1,1) \|\| measurementFrame(1,2) \|\|
	- measurementFrame(2,0) \|\| measurementFrame(2,1) \|\| measurementFrame(2,2))
	- {
	- sprintf( valbuffer, " (%lf,%lf,%lf) (%lf,%lf,%lf) (%lf,%lf,%lf)", measurementFrame(0,0), measurementFrame(0,1), measurementFrame(0,2), measurementFrame(1,0), measurementFrame(1,1), measurementFrame(1,2), measurementFrame(2,0), measurementFrame(2,1), measurementFrame(2,2));
	- itk::EncapsulateMetaData<std::string>(itkImg->GetMetaDataDictionary(),std::string("measurement frame"),std::string(valbuffer));
	- }
	-
	- sprintf( valbuffer, "DWMRI");
	- itk::EncapsulateMetaData<std::string>(itkImg->GetMetaDataDictionary(),std::string("modality"),std::string(valbuffer));
	-
	- if (mitk::DiffusionPropertyHelper::GetOriginalGradientContainer(input)->Size())
	- {
	- MITK_INFO << "Saving original gradient directions";
	- sprintf( valbuffer, "%1f", mitk::DiffusionPropertyHelper::GetReferenceBValue(input) );
	- itk::EncapsulateMetaData<std::string>(itkImg->GetMetaDataDictionary(),std::string("DWMRI_b-value"),std::string(valbuffer));
	-
	- for(unsigned int i=0; i<mitk::DiffusionPropertyHelper::GetGradientContainer(input)->Size(); i++)
	- {
	- sprintf( keybuffer, "DWMRI_gradient_%04d", i );
	-
	- sprintf( valbuffer, "%1f %1f %1f", mitk::DiffusionPropertyHelper::GetOriginalGradientContainer(input)->ElementAt(i).get(0),
	- mitk::DiffusionPropertyHelper::GetOriginalGradientContainer(input)->ElementAt(i).get(1), mitk::DiffusionPropertyHelper::GetOriginalGradientContainer(input)->ElementAt(i).get(2));
	-
	- itk::EncapsulateMetaData<std::string>(itkImg->GetMetaDataDictionary(),std::string(keybuffer),std::string(valbuffer));
	- }
	- }
	- else if(mitk::DiffusionPropertyHelper::GetGradientContainer(input)->Size())
	- {
	- MITK_INFO << "Original gradient directions not found. Saving modified gradient directions";
	- sprintf( valbuffer, "%1f", mitk::DiffusionPropertyHelper::GetReferenceBValue(input) );
	- itk::EncapsulateMetaData<std::string>(itkImg->GetMetaDataDictionary(),std::string("DWMRI_b-value"),std::string(valbuffer));
	-
	- for(unsigned int i=0; i<mitk::DiffusionPropertyHelper::GetGradientContainer(input)->Size(); i++)
	- {
	- sprintf( keybuffer, "DWMRI_gradient_%04d", i );
	-
	- sprintf( valbuffer, "%1f %1f %1f", mitk::DiffusionPropertyHelper::GetGradientContainer(input)->ElementAt(i).get(0),
	- mitk::DiffusionPropertyHelper::GetGradientContainer(input)->ElementAt(i).get(1), mitk::DiffusionPropertyHelper::GetGradientContainer(input)->ElementAt(i).get(2));
	-
	- itk::EncapsulateMetaData<std::string>(itkImg->GetMetaDataDictionary(),std::string(keybuffer),std::string(valbuffer));
	- }
	- }
	-
	- typedef itk::VectorImage<short,3> ImageType;
	-
	- std::string ext = this->GetMimeType()->GetExtension(this->GetOutputLocation());
	- ext = itksys::SystemTools::LowerCase(ext);
	-
	- // default extension is .nrrd
	- if( ext == "")
	- {
	- ext = ".nrrd";
	- this->SetOutputLocation(this->GetOutputLocation() + ext);
	- }
	-
	- if (ext == ".hdwi" \|\| ext == ".nrrd" \|\| ext == ".dwi")
	- {
	- itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
	- io->SetFileType( itk::ImageIOBase::Binary );
	- io->UseCompressionOn();
	-
	- typedef itk::ImageFileWriter<ImageType> WriterType;
	- WriterType::Pointer nrrdWriter = WriterType::New();
	- nrrdWriter->UseInputMetaDataDictionaryOn();
	- nrrdWriter->SetInput( itkImg );
	- nrrdWriter->SetImageIO(io);
	- nrrdWriter->SetFileName(this->GetOutputLocation());
	- nrrdWriter->UseCompressionOn();
	- nrrdWriter->SetImageIO(io);
	- try
	- {
	- nrrdWriter->Update();
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.GetDescription() << std::endl;
	- throw;
	- }
	- }
	-}
	-
	-mitk::DiffusionImageNrrdWriterService* mitk::DiffusionImageNrrdWriterService::Clone() const
	-{
	- return new DiffusionImageNrrdWriterService(*this);
	-}
	-
	-mitk::IFileWriter::ConfidenceLevel mitk::DiffusionImageNrrdWriterService::GetConfidenceLevel() const
	-{
	- mitk::Image::ConstPointer input = dynamic_cast<const mitk::Image*>(this->GetInput());
	- if (input.IsNull() \|\| !mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( input ) )
	- {
	- return Unsupported;
	- }
	- else
	- {
	- return Supported;
	- }
	-}
	-
	-#endif //__mitkDiffusionImageNrrdWriterService__cpp
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageNrrdWriterService.h b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageNrrdWriterService.h
	deleted file mode 100644
	index f9d193a22a..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkDiffusionImageNrrdWriterService.h
	+++ /dev/null
	@@ -1,58 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_DiffusionImageNrrdWriterService__H_
	-#define _MITK_DiffusionImageNrrdWriterService__H_
	-
	-#include <mitkAbstractFileWriter.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-
	-namespace mitk
	-{
	-
	-/**
	- * Writes diffusion volumes to a file
	- * @ingroup Process
	- */
	-class DiffusionImageNrrdWriterService : public mitk::AbstractFileWriter
	-{
	-public:
	-
	- DiffusionImageNrrdWriterService();
	- ~DiffusionImageNrrdWriterService() override;
	-
	- using AbstractFileWriter::Write;
	- void Write() override;
	-
	- ConfidenceLevel GetConfidenceLevel() const override;
	-
	- typedef mitk::DiffusionPropertyHelper::ImageType VectorImageType;
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionType GradientDirectionType;
	- typedef mitk::DiffusionPropertyHelper::MeasurementFrameType MeasurementFrameType;
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionsContainerType GradientDirectionContainerType;
	-
	- protected:
	-
	- DiffusionImageNrrdWriterService(const DiffusionImageNrrdWriterService& other);
	- mitk::DiffusionImageNrrdWriterService* Clone() const override;
	-
	-
	-};
	-
	-
	-} // end of namespace mitk
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkNrrdOdfImageReader.cpp b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkNrrdOdfImageReader.cpp
	deleted file mode 100644
	index 8faf43b592..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkNrrdOdfImageReader.cpp
	+++ /dev/null
	@@ -1,118 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkNrrdOdfImageReader.h"
	-#include <mitkCustomMimeType.h>
	-#include "mitkDiffusionCoreIOMimeTypes.h"
	-
	-#include "itkImageFileReader.h"
	-#include "itkImageRegionIterator.h"
	-#include "itkMetaDataObject.h"
	-#include "itkNrrdImageIO.h"
	-#include "mitkITKImageImport.h"
	-#include "mitkImageDataItem.h"
	-#include <mitkLocaleSwitch.h>
	-
	-namespace mitk
	-{
	- NrrdOdfImageReader::NrrdOdfImageReader(const NrrdOdfImageReader& other)
	- : mitk::AbstractFileReader(other)
	- {
	- }
	-
	- NrrdOdfImageReader::NrrdOdfImageReader()
	- : mitk::AbstractFileReader( CustomMimeType( mitk::DiffusionCoreIOMimeTypes::ODF_MIMETYPE() ), mitk::DiffusionCoreIOMimeTypes::ODF_MIMETYPE_DESCRIPTION() )
	- {
	- m_ServiceReg = this->RegisterService();
	- }
	-
	- NrrdOdfImageReader::~NrrdOdfImageReader()
	- {
	- }
	-
	- std::vector<itk::SmartPointer<BaseData> > NrrdOdfImageReader::Read()
	- {
	- std::vector<itk::SmartPointer<mitk::BaseData> > result;
	- std::string location = GetInputLocation();
	-
	- if ( location == "")
	- {
	- throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, the filename of the ODF image to be read is empty!");
	- }
	- else
	- {
	- try
	- {
	- mitk::LocaleSwitch localeSwitch("C");
	-
	- typedef itk::VectorImage<float,3> ImageType;
	- itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
	- typedef itk::ImageFileReader<ImageType> FileReaderType;
	- FileReaderType::Pointer reader = FileReaderType::New();
	- reader->SetImageIO(io);
	- reader->SetFileName(location);
	- reader->Update();
	- ImageType::Pointer img = reader->GetOutput();
	-
	- typedef itk::Image<itk::Vector<float,ODF_SAMPLING_SIZE>,3> VecImgType;
	- VecImgType::Pointer vecImg = VecImgType::New();
	- vecImg->SetSpacing( img->GetSpacing() ); // Set the image spacing
	- vecImg->SetOrigin( img->GetOrigin() ); // Set the image origin
	- vecImg->SetDirection( img->GetDirection() ); // Set the image direction
	- vecImg->SetLargestPossibleRegion( img->GetLargestPossibleRegion());
	- vecImg->SetBufferedRegion( img->GetLargestPossibleRegion() );
	- vecImg->Allocate();
	-
	- itk::ImageRegionIterator<VecImgType> ot (vecImg, vecImg->GetLargestPossibleRegion() );
	- ot.GoToBegin();
	-
	- itk::ImageRegionIterator<ImageType> it (img, img->GetLargestPossibleRegion() );
	-
	- typedef ImageType::PixelType VarPixType;
	- typedef VecImgType::PixelType FixPixType;
	-
	- for (it.GoToBegin(); !it.IsAtEnd(); ++it)
	- {
	- VarPixType vec = it.Get();
	- FixPixType fixVec(vec.GetDataPointer());
	- ot.Set(fixVec);
	- ++ot;
	- }
	-
	- OutputType::Pointer resultImage = OutputType::New();
	- resultImage->InitializeByItk( vecImg.GetPointer() );
	- resultImage->SetVolume( vecImg->GetBufferPointer() );
	- result.push_back( resultImage.GetPointer() );
	-
	- }
	- catch(std::exception& e)
	- {
	- throw itk::ImageFileReaderException(__FILE__, __LINE__, e.what());
	- }
	- catch(...)
	- {
	- throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, an error occurred while reading the requested vessel tree file!");
	- }
	- }
	- return result;
	- }
	-
	-} //namespace MITK
	-
	-mitk::NrrdOdfImageReader* mitk::NrrdOdfImageReader::Clone() const
	-{
	- return new NrrdOdfImageReader(*this);
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkNrrdOdfImageReader.h b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkNrrdOdfImageReader.h
	deleted file mode 100644
	index d811780d71..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkNrrdOdfImageReader.h
	+++ /dev/null
	@@ -1,60 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkNrrdOdfImageReader_h
	-#define __mitkNrrdOdfImageReader_h
	-
	-#include "mitkCommon.h"
	-#include "itkVectorContainer.h"
	-#include "vnl/vnl_vector_fixed.h"
	-#include "mitkOdfImage.h"
	-#include "itkVectorImage.h"
	-#include <mitkAbstractFileReader.h>
	-#include <mitkBaseData.h>
	-#include <mitkMimeType.h>
	-
	-namespace mitk
	-{
	-
	- /** \brief
	- */
	-
	- class NrrdOdfImageReader : public mitk::AbstractFileReader
	- {
	- public:
	-
	- typedef mitk::OdfImage OutputType;
	-
	- NrrdOdfImageReader(const NrrdOdfImageReader& other);
	- NrrdOdfImageReader();
	- ~NrrdOdfImageReader() override;
	-
	- using AbstractFileReader::Read;
	- std::vector<itk::SmartPointer<BaseData> > Read() override;
	-
	- protected:
	-
	-
	- private:
	- private:
	- NrrdOdfImageReader* Clone() const override;
	-
	- us::ServiceRegistration<mitk::IFileReader> m_ServiceReg;
	- };
	-
	-} //namespace MITK
	-
	-#endif // __mitkNrrdOdfImageReader_h
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkNrrdOdfImageWriter.cpp b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkNrrdOdfImageWriter.cpp
	deleted file mode 100644
	index 9483f5946b..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkNrrdOdfImageWriter.cpp
	+++ /dev/null
	@@ -1,129 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkNrrdOdfImageWriter.h"
	-#include "itkMetaDataDictionary.h"
	-#include "itkMetaDataObject.h"
	-#include "itkNrrdImageIO.h"
	-#include "itkImageFileWriter.h"
	-#include "mitkImageCast.h"
	-#include "mitkIOMimeTypes.h"
	-#include "mitkDiffusionCoreIOMimeTypes.h"
	-#include <mitkLocaleSwitch.h>
	-
	-
	-mitk::NrrdOdfImageWriter::NrrdOdfImageWriter()
	- : AbstractFileWriter(mitk::OdfImage::GetStaticNameOfClass(), CustomMimeType( mitk::DiffusionCoreIOMimeTypes::ODF_MIMETYPE() ), mitk::DiffusionCoreIOMimeTypes::ODF_MIMETYPE_DESCRIPTION())
	-{
	- RegisterService();
	-}
	-
	-mitk::NrrdOdfImageWriter::NrrdOdfImageWriter(const mitk::NrrdOdfImageWriter& other)
	- : AbstractFileWriter(other)
	-{
	-}
	-
	-mitk::NrrdOdfImageWriter::~NrrdOdfImageWriter()
	-{}
	-
	-
	-void mitk::NrrdOdfImageWriter::Write()
	-{
	- InputType::ConstPointer input = dynamic_cast<const InputType*>(this->GetInput());
	- if (input.IsNull())
	- {
	- MITK_ERROR <<"Sorry, input to NrrdOdfImageWriter is nullptr!";
	- return;
	- }
	- if ( this->GetOutputLocation().empty() )
	- {
	- MITK_ERROR << "Sorry, filename has not been set!";
	- return ;
	- }
	-
	- mitk::LocaleSwitch localeSwitch("C");
	-
	- itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
	- io->SetFileType( itk::ImageIOBase::Binary );
	- io->UseCompressionOn();
	-
	- typedef itk::VectorImage<float, 3> VecImgType;
	-
	- typedef itk::Image<itk::Vector<float,ODF_SAMPLING_SIZE>,3> ImageType;
	- typedef itk::ImageFileWriter<VecImgType> WriterType;
	- WriterType::Pointer nrrdWriter = WriterType::New();
	-
	- ImageType::Pointer outimage = ImageType::New();
	- CastToItkImage(input, outimage);
	-
	- VecImgType::Pointer vecImg = VecImgType::New();
	- vecImg->SetSpacing( outimage->GetSpacing() ); // Set the image spacing
	- vecImg->SetOrigin( outimage->GetOrigin() ); // Set the image origin
	- vecImg->SetDirection( outimage->GetDirection() ); // Set the image direction
	- vecImg->SetLargestPossibleRegion( outimage->GetLargestPossibleRegion());
	- vecImg->SetBufferedRegion( outimage->GetLargestPossibleRegion() );
	- vecImg->SetVectorLength(ODF_SAMPLING_SIZE);
	- vecImg->Allocate();
	-
	- itk::ImageRegionIterator<VecImgType> ot (vecImg, vecImg->GetLargestPossibleRegion() );
	- ot.GoToBegin();
	-
	- itk::ImageRegionIterator<ImageType> it (outimage, outimage->GetLargestPossibleRegion() );
	-
	- typedef ImageType::PixelType VecPixType;
	- typedef VecImgType::PixelType VarVecType;
	-
	- for (it.GoToBegin(); !it.IsAtEnd(); ++it)
	- {
	- VecPixType vec = it.Get();
	- VarVecType varVec(vec.GetVnlVector().data_block(), ODF_SAMPLING_SIZE);
	- ot.Set(varVec);
	- ++ot;
	- }
	-
	- nrrdWriter->SetInput( vecImg );
	- nrrdWriter->SetImageIO(io);
	- nrrdWriter->SetFileName(this->GetOutputLocation().c_str());
	- nrrdWriter->UseCompressionOn();
	-
	-
	- try
	- {
	- nrrdWriter->Update();
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- MITK_INFO << e.what();
	- }
	-}
	-
	-mitk::NrrdOdfImageWriter* mitk::NrrdOdfImageWriter::Clone() const
	-{
	- return new NrrdOdfImageWriter(*this);
	-}
	-
	-mitk::IFileWriter::ConfidenceLevel mitk::NrrdOdfImageWriter::GetConfidenceLevel() const
	-{
	- InputType::ConstPointer input = dynamic_cast<const InputType*>(this->GetInput());
	- if (input.IsNull() )
	- {
	- return Unsupported;
	- }
	- else
	- {
	- return Supported;
	- }
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkNrrdOdfImageWriter.h b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkNrrdOdfImageWriter.h
	deleted file mode 100644
	index 3c17029edc..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkNrrdOdfImageWriter.h
	+++ /dev/null
	@@ -1,54 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_NRRDODF_WRITER__H_
	-#define _MITK_NRRDODF_WRITER__H_
	-
	-#include <mitkAbstractFileWriter.h>
	-#include <mitkOdfImage.h>
	-
	-
	-namespace mitk
	-{
	-
	-/**
	- * Writes diffusion volumes to a file
	- * @ingroup Process
	- */
	- class NrrdOdfImageWriter : public mitk::AbstractFileWriter
	- {
	- public:
	-
	- typedef mitk::OdfImage InputType;
	-
	- NrrdOdfImageWriter();
	- ~NrrdOdfImageWriter() override;
	-
	- using AbstractFileWriter::Write;
	- void Write() override;
	-
	- ConfidenceLevel GetConfidenceLevel() const override;
	-
	- protected:
	-
	- NrrdOdfImageWriter(const NrrdOdfImageWriter& other);
	- mitk::NrrdOdfImageWriter* Clone() const override;
	- };
	-
	-
	-} // end of namespace mitk
	-
	-#endif //_MITK_NRRDODF_WRITER__H_
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkNrrdTensorImageReader.cpp b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkNrrdTensorImageReader.cpp
	deleted file mode 100644
	index c6449ec8c0..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkNrrdTensorImageReader.cpp
	+++ /dev/null
	@@ -1,428 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkNrrdTensorImageReader.h"
	-#include <mitkCustomMimeType.h>
	-#include "mitkDiffusionCoreIOMimeTypes.h"
	-
	-#include "itkImageFileReader.h"
	-#include "itkImageRegionIterator.h"
	-#include "itkMetaDataObject.h"
	-#include "itkNrrdImageIO.h"
	-#include <itkNiftiImageIO.h>
	-
	-#include "mitkITKImageImport.h"
	-#include "mitkImageDataItem.h"
	-#include <mitkLocaleSwitch.h>
	-#include <mitkIOUtil.h>
	-#include <mitkLexicalCast.h>
	-
	-namespace mitk
	-{
	-
	- NrrdTensorImageReader::NrrdTensorImageReader(const NrrdTensorImageReader& other)
	- : mitk::AbstractFileReader(other)
	- {
	- }
	-
	- NrrdTensorImageReader::NrrdTensorImageReader()
	- : mitk::AbstractFileReader( CustomMimeType( mitk::DiffusionCoreIOMimeTypes::DTI_MIMETYPE() ), mitk::DiffusionCoreIOMimeTypes::DTI_MIMETYPE_DESCRIPTION() )
	- {
	- m_ServiceReg = this->RegisterService();
	- }
	-
	- NrrdTensorImageReader::~NrrdTensorImageReader()
	- {
	- }
	-
	- std::vector<itk::SmartPointer<BaseData> > NrrdTensorImageReader::Read()
	- {
	- std::vector<itk::SmartPointer<mitk::BaseData> > result;
	- std::string location = GetInputLocation();
	-
	- if ( location == "")
	- {
	- throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, the filename is empty!");
	- }
	- else
	- {
	- try
	- {
	- mitk::LocaleSwitch localeSwitch("C");
	-
	- try
	- {
	- std::string fname3 = mitk::IOUtil::GetTempPath()+"/temp_dti.nii.gz";
	-
	- int c = 0;
	- while( itksys::SystemTools::FileExists(fname3) )
	- {
	- fname3 = mitk::IOUtil::GetTempPath()+"/temp_dti_" + boost::lexical_cast<std::string>(c) + ".nii.gz";
	- ++c;
	- }
	-
	- itksys::SystemTools::CopyAFile(location.c_str(), fname3.c_str());
	-
	- typedef itk::VectorImage<float,3> ImageType;
	- itk::NiftiImageIO::Pointer io = itk::NiftiImageIO::New();
	- typedef itk::ImageFileReader<ImageType> FileReaderType;
	- FileReaderType::Pointer reader = FileReaderType::New();
	- reader->SetImageIO(io);
	- reader->SetFileName(fname3);
	- reader->Update();
	- ImageType::Pointer img = reader->GetOutput();
	-
	- TensorImage::ItkTensorImageType::Pointer vecImg = TensorImage::ItkTensorImageType::New();
	- vecImg->SetSpacing( img->GetSpacing() ); // Set the image spacing
	- vecImg->SetOrigin( img->GetOrigin() ); // Set the image origin
	- vecImg->SetDirection( img->GetDirection() ); // Set the image direction
	- vecImg->SetRegions( img->GetLargestPossibleRegion());
	- vecImg->Allocate();
	-
	- itk::ImageRegionIterator<TensorImage::ItkTensorImageType> ot (vecImg, vecImg->GetLargestPossibleRegion() );
	- ot.GoToBegin();
	-
	- itk::ImageRegionIterator<ImageType> it (img, img->GetLargestPossibleRegion() );
	- it.GoToBegin();
	-
	- typedef ImageType::PixelType VarPixType;
	- typedef TensorImage::PixelType FixPixType;
	- int numComponents = img->GetNumberOfComponentsPerPixel();
	-
	- if (numComponents==6)
	- {
	- MITK_INFO << "Trying to load dti as 6-comp nifti ...";
	- while (!it.IsAtEnd())
	- {
	- VarPixType vec = it.Get();
	- FixPixType fixVec(vec.GetDataPointer());
	-
	- TensorImage::PixelType tensor;
	- tensor.SetElement(0, vec.GetElement(0));
	- tensor.SetElement(1, vec.GetElement(1));
	- tensor.SetElement(2, vec.GetElement(2));
	- tensor.SetElement(3, vec.GetElement(3));
	- tensor.SetElement(4, vec.GetElement(4));
	- tensor.SetElement(5, vec.GetElement(5));
	-
	- fixVec = tensor;
	-
	- ot.Set(fixVec);
	- ++ot;
	- ++it;
	- }
	- }
	- else if(numComponents==9)
	- {
	- MITK_INFO << "Trying to load dti as 9-comp nifti ...";
	- while (!it.IsAtEnd())
	- {
	- VarPixType vec = it.Get();
	- TensorImage::PixelType tensor;
	- tensor.SetElement(0, vec.GetElement(0));
	- tensor.SetElement(1, vec.GetElement(1));
	- tensor.SetElement(2, vec.GetElement(2));
	- tensor.SetElement(3, vec.GetElement(4));
	- tensor.SetElement(4, vec.GetElement(5));
	- tensor.SetElement(5, vec.GetElement(8));
	-
	- FixPixType fixVec(tensor);
	- ot.Set(fixVec);
	- ++ot;
	- ++it;
	- }
	- }
	- else if (numComponents==1)
	- {
	- MITK_INFO << "Trying to load dti as 4D nifti ...";
	- typedef itk::Image<float,4> ImageType;
	- typedef itk::ImageFileReader<ImageType> FileReaderType;
	- FileReaderType::Pointer reader = FileReaderType::New();
	- reader->SetImageIO(io);
	- reader->SetFileName(fname3);
	- reader->Update();
	- ImageType::Pointer img = reader->GetOutput();
	-
	- itk::Size<4> size = img->GetLargestPossibleRegion().GetSize();
	-
	- while (!ot.IsAtEnd())
	- {
	- TensorImage::PixelType tensor;
	- ImageType::IndexType idx;
	- idx[0] = ot.GetIndex()[0]; idx[1] = ot.GetIndex()[1]; idx[2] = ot.GetIndex()[2];
	-
	- if (size[3]==6)
	- {
	- for (unsigned int te=0; te<size[3]; te++)
	- {
	- idx[3] = te;
	- tensor.SetElement(te, img->GetPixel(idx));
	- }
	- }
	- else if (size[3]==9)
	- {
	- idx[3] = 0;
	- tensor.SetElement(0, img->GetPixel(idx));
	- idx[3] = 1;
	- tensor.SetElement(1, img->GetPixel(idx));
	- idx[3] = 2;
	- tensor.SetElement(2, img->GetPixel(idx));
	- idx[3] = 4;
	- tensor.SetElement(3, img->GetPixel(idx));
	- idx[3] = 5;
	- tensor.SetElement(4, img->GetPixel(idx));
	- idx[3] = 8;
	- tensor.SetElement(5, img->GetPixel(idx));
	- }
	- else
	- throw itk::ImageFileReaderException(__FILE__, __LINE__, "Unknown number of components for DTI file. Should be 6 or 9!");
	-
	- FixPixType fixVec(tensor);
	- ot.Set(fixVec);
	- ++ot;
	- }
	- }
	- OutputType::Pointer resultImage = OutputType::New();
	- resultImage->InitializeByItk( vecImg.GetPointer() );
	- resultImage->SetVolume( vecImg->GetBufferPointer() );
	- result.push_back( resultImage.GetPointer() );
	- }
	- catch(...)
	- {
	- MITK_INFO << "Trying to load dti as nrrd ...";
	-
	- typedef itk::VectorImage<float,3> ImageType;
	- itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
	- typedef itk::ImageFileReader<ImageType> FileReaderType;
	- FileReaderType::Pointer reader = FileReaderType::New();
	- reader->SetImageIO(io);
	- reader->SetFileName(location);
	- reader->Update();
	- ImageType::Pointer img = reader->GetOutput();
	-
	- TensorImage::ItkTensorImageType::Pointer vecImg = TensorImage::ItkTensorImageType::New();
	- vecImg->SetSpacing( img->GetSpacing() ); // Set the image spacing
	- vecImg->SetOrigin( img->GetOrigin() ); // Set the image origin
	- vecImg->SetDirection( img->GetDirection() ); // Set the image direction
	- vecImg->SetRegions( img->GetLargestPossibleRegion());
	- vecImg->Allocate();
	-
	- itk::ImageRegionIterator<TensorImage::ItkTensorImageType> ot (vecImg, vecImg->GetLargestPossibleRegion() );
	- ot.GoToBegin();
	-
	- itk::ImageRegionIterator<ImageType> it (img, img->GetLargestPossibleRegion() );
	- it.GoToBegin();
	-
	- typedef ImageType::PixelType VarPixType;
	- typedef TensorImage::PixelType FixPixType;
	- int numComponents = img->GetNumberOfComponentsPerPixel();
	-
	- itk::MetaDataDictionary imgMetaDictionary = img->GetMetaDataDictionary();
	- std::vector<std::string> imgMetaKeys = imgMetaDictionary.GetKeys();
	- std::vector<std::string>::const_iterator itKey = imgMetaKeys.begin();
	- std::string metaString;
	-
	- bool readFrame = false;
	- double xx, xy, xz, yx, yy, yz, zx, zy, zz;
	- MeasurementFrameType measFrame;
	- measFrame.SetIdentity();
	- MeasurementFrameType measFrameTransp;
	- measFrameTransp.SetIdentity();
	-
	- for (; itKey != imgMetaKeys.end(); itKey ++)
	- {
	- itk::ExposeMetaData<std::string> (imgMetaDictionary, *itKey, metaString);
	- if (itKey->find("measurement frame") != std::string::npos)
	- {
	- sscanf(metaString.c_str(), " ( %lf , %lf , %lf ) ( %lf , %lf , %lf ) ( %lf , %lf , %lf ) \n", &xx, &xy, &xz, &yx, &yy, &yz, &zx, &zy, &zz);
	-
	- if (xx>10e-10 \|\| xy>10e-10 \|\| xz>10e-10 \|\|
	- yx>10e-10 \|\| yy>10e-10 \|\| yz>10e-10 \|\|
	- zx>10e-10 \|\| zy>10e-10 \|\| zz>10e-10 )
	- {
	- readFrame = true;
	-
	- measFrame(0,0) = xx;
	- measFrame(0,1) = xy;
	- measFrame(0,2) = xz;
	- measFrame(1,0) = yx;
	- measFrame(1,1) = yy;
	- measFrame(1,2) = yz;
	- measFrame(2,0) = zx;
	- measFrame(2,1) = zy;
	- measFrame(2,2) = zz;
	-
	- measFrameTransp = measFrame.GetTranspose();
	- }
	- }
	- }
	-
	- if (numComponents==6)
	- {
	- while (!it.IsAtEnd())
	- {
	- // T'=RTR'
	- VarPixType vec = it.Get();
	- FixPixType fixVec(vec.GetDataPointer());
	-
	- if(readFrame)
	- {
	- TensorImage::PixelType tensor;
	- tensor.SetElement(0, vec.GetElement(0));
	- tensor.SetElement(1, vec.GetElement(1));
	- tensor.SetElement(2, vec.GetElement(2));
	- tensor.SetElement(3, vec.GetElement(3));
	- tensor.SetElement(4, vec.GetElement(4));
	- tensor.SetElement(5, vec.GetElement(5));
	-
	- tensor = ConvertMatrixTypeToFixedArrayType(tensor.PreMultiply(measFrame));
	- tensor = ConvertMatrixTypeToFixedArrayType(tensor.PostMultiply(measFrameTransp));
	- fixVec = tensor;
	- }
	-
	- ot.Set(fixVec);
	- ++ot;
	- ++it;
	- }
	- }
	- else if(numComponents==9)
	- {
	- while (!it.IsAtEnd())
	- {
	- VarPixType vec = it.Get();
	- TensorImage::PixelType tensor;
	- tensor.SetElement(0, vec.GetElement(0));
	- tensor.SetElement(1, vec.GetElement(1));
	- tensor.SetElement(2, vec.GetElement(2));
	- tensor.SetElement(3, vec.GetElement(4));
	- tensor.SetElement(4, vec.GetElement(5));
	- tensor.SetElement(5, vec.GetElement(8));
	-
	- if(readFrame)
	- {
	- tensor = ConvertMatrixTypeToFixedArrayType(tensor.PreMultiply(measFrame));
	- tensor = ConvertMatrixTypeToFixedArrayType(tensor.PostMultiply(measFrameTransp));
	- }
	-
	- FixPixType fixVec(tensor);
	- ot.Set(fixVec);
	- ++ot;
	- ++it;
	- }
	- }
	- else if (numComponents==1)
	- {
	- typedef itk::Image<float,4> ImageType;
	- itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
	- typedef itk::ImageFileReader<ImageType> FileReaderType;
	- FileReaderType::Pointer reader = FileReaderType::New();
	- reader->SetImageIO(io);
	- reader->SetFileName(location);
	- reader->Update();
	- ImageType::Pointer img = reader->GetOutput();
	-
	- itk::Size<4> size = img->GetLargestPossibleRegion().GetSize();
	-
	- while (!ot.IsAtEnd())
	- {
	- TensorImage::PixelType tensor;
	- ImageType::IndexType idx;
	- idx[0] = ot.GetIndex()[0]; idx[1] = ot.GetIndex()[1]; idx[2] = ot.GetIndex()[2];
	-
	- if (size[3]==6)
	- {
	- for (unsigned int te=0; te<size[3]; te++)
	- {
	- idx[3] = te;
	- tensor.SetElement(te, img->GetPixel(idx));
	- }
	- }
	- else if (size[3]==9)
	- {
	- idx[3] = 0;
	- tensor.SetElement(0, img->GetPixel(idx));
	- idx[3] = 1;
	- tensor.SetElement(1, img->GetPixel(idx));
	- idx[3] = 2;
	- tensor.SetElement(2, img->GetPixel(idx));
	- idx[3] = 4;
	- tensor.SetElement(3, img->GetPixel(idx));
	- idx[3] = 5;
	- tensor.SetElement(4, img->GetPixel(idx));
	- idx[3] = 8;
	- tensor.SetElement(5, img->GetPixel(idx));
	- }
	- else
	- throw itk::ImageFileReaderException(__FILE__, __LINE__, "Unknown number of komponents for DTI file. Should be 6 or 9!");
	-
	- if(readFrame)
	- {
	- tensor = ConvertMatrixTypeToFixedArrayType(tensor.PreMultiply(measFrame));
	- tensor = ConvertMatrixTypeToFixedArrayType(tensor.PostMultiply(measFrameTransp));
	- }
	- FixPixType fixVec(tensor);
	- ot.Set(fixVec);
	- ++ot;
	- }
	- }
	- else
	- {
	- throw itk::ImageFileReaderException(__FILE__, __LINE__, "Image has wrong number of pixel components!");
	- }
	-
	- OutputType::Pointer resultImage = OutputType::New();
	- resultImage->InitializeByItk( vecImg.GetPointer() );
	- resultImage->SetVolume( vecImg->GetBufferPointer() );
	- result.push_back( resultImage.GetPointer() );
	- }
	-
	- }
	- catch(std::exception& e)
	- {
	- throw itk::ImageFileReaderException(__FILE__, __LINE__, e.what());
	- }
	- catch(...)
	- {
	- throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, an error occurred while reading the requested DTI file!");
	- }
	- }
	-
	- return result;
	- }
	-
	-TensorImage::PixelType NrrdTensorImageReader
	-::ConvertMatrixTypeToFixedArrayType(const TensorImage::PixelType::Superclass::MatrixType & matrix)
	-{
	- /* \| 0 1 2 \|
	- * \| X 3 4 \|
	- * \| X X 5 \|
	- */
	- TensorImage::PixelType arr;
	- arr.SetElement(0,matrix(0,0));
	- arr.SetElement(1,matrix(0,1));
	- arr.SetElement(2,matrix(0,2));
	- arr.SetElement(3,matrix(1,3));
	- arr.SetElement(4,matrix(1,4));
	- arr.SetElement(5,matrix(2,5));
	- return arr;
	-}
	-
	-} //namespace MITK
	-
	-mitk::NrrdTensorImageReader* mitk::NrrdTensorImageReader::Clone() const
	-{
	- return new NrrdTensorImageReader(*this);
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkNrrdTensorImageReader.h b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkNrrdTensorImageReader.h
	deleted file mode 100644
	index 3794c73415..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkNrrdTensorImageReader.h
	+++ /dev/null
	@@ -1,63 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkNrrdTensorImageReader_h
	-#define __mitkNrrdTensorImageReader_h
	-
	-#include "mitkCommon.h"
	-#include "itkVectorContainer.h"
	-#include "vnl/vnl_vector_fixed.h"
	-#include "mitkTensorImage.h"
	-#include "itkVectorImage.h"
	-#include "itkDiffusionTensor3D.h"
	-#include <mitkAbstractFileReader.h>
	-#include <mitkBaseData.h>
	-#include <mitkMimeType.h>
	-
	-namespace mitk
	-{
	-
	- /** \brief
	- */
	-
	- class NrrdTensorImageReader : public mitk::AbstractFileReader
	- {
	- public:
	-
	- typedef mitk::TensorImage OutputType;
	- typedef itk::Matrix< float, 3, 3 > MeasurementFrameType;
	-
	- NrrdTensorImageReader(const NrrdTensorImageReader& other);
	- NrrdTensorImageReader();
	- ~NrrdTensorImageReader() override;
	-
	- using AbstractFileReader::Read;
	- std::vector<itk::SmartPointer<BaseData> > Read() override;
	-
	- protected:
	-
	-
	- private:
	- NrrdTensorImageReader* Clone() const override;
	-
	- us::ServiceRegistration<mitk::IFileReader> m_ServiceReg;
	-
	- TensorImage::PixelType ConvertMatrixTypeToFixedArrayType(const TensorImage::PixelType::Superclass::MatrixType & matrix);
	- };
	-
	-} //namespace MITK
	-
	-#endif // __mitkNrrdTensorImageReader_h
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkNrrdTensorImageWriter.cpp b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkNrrdTensorImageWriter.cpp
	deleted file mode 100644
	index 3b30f62bed..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkNrrdTensorImageWriter.cpp
	+++ /dev/null
	@@ -1,100 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkNrrdTensorImageWriter.h"
	-#include "itkMetaDataDictionary.h"
	-#include "itkMetaDataObject.h"
	-#include "itkNrrdImageIO.h"
	-#include "itkImageFileWriter.h"
	-#include "itkDiffusionTensor3D.h"
	-#include "mitkImageCast.h"
	-#include "mitkDiffusionCoreIOMimeTypes.h"
	-#include <mitkLocaleSwitch.h>
	-
	-
	-mitk::NrrdTensorImageWriter::NrrdTensorImageWriter()
	- : AbstractFileWriter(mitk::TensorImage::GetStaticNameOfClass(), CustomMimeType( mitk::DiffusionCoreIOMimeTypes::DTI_MIMETYPE() ), mitk::DiffusionCoreIOMimeTypes::DTI_MIMETYPE_DESCRIPTION() )
	-{
	- RegisterService();
	-}
	-
	-mitk::NrrdTensorImageWriter::NrrdTensorImageWriter(const mitk::NrrdTensorImageWriter& other)
	- : AbstractFileWriter(other)
	-{
	-}
	-
	-
	-mitk::NrrdTensorImageWriter::~NrrdTensorImageWriter()
	-{}
	-
	-
	-void mitk::NrrdTensorImageWriter::Write()
	-{
	- InputType::ConstPointer input = dynamic_cast<const InputType*>(this->GetInput());
	- if (input.IsNull() )
	- {
	- MITK_ERROR <<"Sorry, input to NrrdTensorImageWriter is nullptr!";
	- return;
	- }
	- if ( this->GetOutputLocation().empty() )
	- {
	- MITK_ERROR << "Sorry, filename has not been set!" ;
	- return ;
	- }
	- mitk::LocaleSwitch localeSwitch("C");
	-
	- itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
	- io->SetFileType( itk::ImageIOBase::Binary );
	- io->UseCompressionOn();
	-
	- typedef itk::ImageFileWriter<TensorImage::ItkTensorImageType> WriterType;
	- WriterType::Pointer nrrdWriter = WriterType::New();
	-
	- TensorImage::ItkTensorImageType::Pointer outimage = TensorImage::ItkTensorImageType::New();
	- CastToItkImage(input, outimage);
	-
	- nrrdWriter->SetInput( outimage );
	- nrrdWriter->SetImageIO(io);
	- nrrdWriter->SetFileName(this->GetOutputLocation().c_str());
	- nrrdWriter->UseCompressionOn();
	-
	- try
	- {
	- nrrdWriter->Update();
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.GetDescription() << std::endl;
	- }
	-}
	-
	-mitk::NrrdTensorImageWriter* mitk::NrrdTensorImageWriter::Clone() const
	-{
	- return new NrrdTensorImageWriter(*this);
	-}
	-
	-mitk::IFileWriter::ConfidenceLevel mitk::NrrdTensorImageWriter::GetConfidenceLevel() const
	-{
	- InputType::ConstPointer input = dynamic_cast<const InputType*>(this->GetInput());
	- if (input.IsNull() )
	- {
	- return Unsupported;
	- }
	- else
	- {
	- return Supported;
	- }
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkNrrdTensorImageWriter.h b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkNrrdTensorImageWriter.h
	deleted file mode 100644
	index f5b2f4ea52..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkNrrdTensorImageWriter.h
	+++ /dev/null
	@@ -1,54 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_NRRDDTI_WRITER__H_
	-#define _MITK_NRRDDTI_WRITER__H_
	-
	-#include <mitkAbstractFileWriter.h>
	-#include <mitkTensorImage.h>
	-
	-
	-namespace mitk
	-{
	-
	-/**
	- * Writes diffusion volumes to a file
	- * @ingroup Process
	- */
	-class NrrdTensorImageWriter : public mitk::AbstractFileWriter
	-{
	-public:
	-
	- typedef mitk::TensorImage InputType;
	-
	- NrrdTensorImageWriter();
	- ~NrrdTensorImageWriter() override;
	-
	- using AbstractFileWriter::Write;
	- void Write() override;
	-
	- ConfidenceLevel GetConfidenceLevel() const override;
	-
	-protected:
	-
	- NrrdTensorImageWriter(const NrrdTensorImageWriter& other);
	- mitk::NrrdTensorImageWriter* Clone() const override;
	-};
	-
	-
	-} // end of namespace mitk
	-
	-#endif //_MITK_NRRDDTI_WRITER__H_
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkOdfImageSerializer.cpp b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkOdfImageSerializer.cpp
	deleted file mode 100644
	index ca6a94f95d..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkOdfImageSerializer.cpp
	+++ /dev/null
	@@ -1,74 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkOdfImageSerializer.h"
	-#include "mitkOdfImage.h"
	-#include "mitkNrrdOdfImageWriter.h"
	-
	-#include <itksys/SystemTools.hxx>
	-
	-
	-MITK_REGISTER_SERIALIZER(OdfImageSerializer)
	-
	-
	-mitk::OdfImageSerializer::OdfImageSerializer()
	-{
	-}
	-
	-
	-mitk::OdfImageSerializer::~OdfImageSerializer()
	-{
	-}
	-
	-
	-std::string mitk::OdfImageSerializer::Serialize()
	-{
	- const OdfImage* image = dynamic_cast<const OdfImage*>( m_Data.GetPointer() );
	- if (image == nullptr)
	- {
	- MITK_ERROR << " Object at " << (const void*) this->m_Data
	- << " is not an mitk::NrrdOdfImage. Cannot serialize as NrrdOdfImage.";
	- return "";
	- }
	-
	- std::string filename( this->GetUniqueFilenameInWorkingDirectory() );
	- filename += "_";
	- filename += m_FilenameHint;
	- filename += ".odf";
	-
	- std::string fullname(m_WorkingDirectory);
	- fullname += "/";
	- fullname += itksys::SystemTools::ConvertToOutputPath(filename.c_str());
	-
	- try
	- {
	- NrrdOdfImageWriter writer;
	- writer.SetOutputLocation(fullname);
	- writer.SetInput(image);
	- writer.Write();
	- }
	- catch (std::exception& e)
	- {
	- MITK_ERROR << " Error serializing object at " << (const void*) this->m_Data
	- << " to "
	- << fullname
	- << ": "
	- << e.what();
	- return "";
	- }
	- return filename;
	-}
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkOdfImageSerializer.h b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkOdfImageSerializer.h
	deleted file mode 100644
	index 7c25809d01..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkOdfImageSerializer.h
	+++ /dev/null
	@@ -1,39 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef mitkOdfImageSerializer_h_included
	-#define mitkOdfImageSerializer_h_included
	-
	-#include "mitkBaseDataSerializer.h"
	-
	-namespace mitk
	-{
	-/**
	- \brief Serializes mitk::Surface for mitk::SceneIO
	-*/
	-class OdfImageSerializer : public BaseDataSerializer
	-{
	- public:
	- mitkClassMacro( OdfImageSerializer, BaseDataSerializer );
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- std::string Serialize() override;
	- protected:
	- OdfImageSerializer();
	- ~OdfImageSerializer() override;
	-};
	-} // namespace
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkPeakImageReader.cpp b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkPeakImageReader.cpp
	deleted file mode 100644
	index 52bc764ad4..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkPeakImageReader.cpp
	+++ /dev/null
	@@ -1,85 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkPeakImageReader.h"
	-#include <mitkCustomMimeType.h>
	-#include <mitkDiffusionCoreIOMimeTypes.h>
	-#include <mitkPeakImage.h>
	-#include <mitkIOUtil.h>
	-#include <mitkPreferenceListReaderOptionsFunctor.h>
	-#include <itkImageFileReader.h>
	-#include <itksys/SystemTools.hxx>
	-#include <itkNiftiImageIO.h>
	-#include <itkNrrdImageIO.h>
	-#include <mitkITKImageImport.h>
	-#include <mitkImageCast.h>
	-#include <mitkLocaleSwitch.h>
	-
	-namespace mitk
	-{
	-
	- PeakImageReader::PeakImageReader(const PeakImageReader& other)
	- : mitk::AbstractFileReader(other)
	- {
	- }
	-
	- PeakImageReader::PeakImageReader()
	- : mitk::AbstractFileReader( CustomMimeType( mitk::DiffusionCoreIOMimeTypes::PEAK_MIMETYPE() ), mitk::DiffusionCoreIOMimeTypes::PEAK_MIMETYPE_DESCRIPTION() )
	- {
	- m_ServiceReg = this->RegisterService();
	- }
	-
	- PeakImageReader::~PeakImageReader()
	- {
	- }
	-
	- std::vector<itk::SmartPointer<BaseData> > PeakImageReader::Read()
	- {
	- mitk::LocaleSwitch localeSwitch("C");
	- std::vector<itk::SmartPointer<mitk::BaseData> > result;
	- std::string location = GetInputLocation();
	- std::string ext = itksys::SystemTools::GetFilenameExtension(location);
	- MITK_INFO << "Reading " << location;
	-
	- typedef itk::ImageFileReader<PeakImage::ItkPeakImageType> FileReaderType;
	- FileReaderType::Pointer reader = FileReaderType::New();
	- reader->SetFileName(location);
	- if (ext==".peak")
	- {
	- itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
	- reader->SetImageIO(io);
	- }
	- reader->Update();
	- Image::Pointer resultImage = dynamic_cast<Image*>(PeakImage::New().GetPointer());
	- mitk::CastToMitkImage(reader->GetOutput(), resultImage);
	- resultImage->SetVolume(reader->GetOutput()->GetBufferPointer());
	-
	- StringProperty::Pointer nameProp;
	- nameProp = StringProperty::New(itksys::SystemTools::GetFilenameWithoutExtension(GetInputLocation()));
	- resultImage->SetProperty("name", nameProp);
	- dynamic_cast<PeakImage*>(resultImage.GetPointer())->ConstructPolydata();
	-
	- result.push_back( resultImage.GetPointer() );
	-
	- return result;
	- }
	-
	-} //namespace MITK
	-
	-mitk::PeakImageReader* mitk::PeakImageReader::Clone() const
	-{
	- return new PeakImageReader(*this);
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkPeakImageReader.h b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkPeakImageReader.h
	deleted file mode 100644
	index 15c2f1650f..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkPeakImageReader.h
	+++ /dev/null
	@@ -1,53 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkPeakImageReader_h
	-#define __mitkPeakImageReader_h
	-
	-#include "mitkCommon.h"
	-#include <mitkAbstractFileReader.h>
	-#include <mitkBaseData.h>
	-#include <mitkMimeType.h>
	-
	-namespace mitk
	-{
	-
	- /** \brief
	- */
	-
	- class PeakImageReader : public mitk::AbstractFileReader
	- {
	- public:
	-
	- PeakImageReader(const PeakImageReader& other);
	- PeakImageReader();
	- ~PeakImageReader() override;
	-
	- using AbstractFileReader::Read;
	- std::vector<itk::SmartPointer<BaseData> > Read() override;
	-
	- protected:
	-
	-
	- private:
	- PeakImageReader* Clone() const override;
	-
	- us::ServiceRegistration<mitk::IFileReader> m_ServiceReg;
	- };
	-
	-} //namespace MITK
	-
	-#endif // __mitkPeakImageReader_h
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkPeakImageSerializer.cpp b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkPeakImageSerializer.cpp
	deleted file mode 100644
	index 7fdf7b0ea3..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkPeakImageSerializer.cpp
	+++ /dev/null
	@@ -1,86 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkPeakImageSerializer.h"
	-#include "mitkPeakImage.h"
	-#include "itkImageFileWriter.h"
	-#include <mitkImageToItk.h>
	-#include <itksys/SystemTools.hxx>
	-#include <itkNrrdImageIO.h>
	-#include <mitkLocaleSwitch.h>
	-
	-MITK_REGISTER_SERIALIZER(PeakImageSerializer)
	-
	-
	-mitk::PeakImageSerializer::PeakImageSerializer()
	-{
	-}
	-
	-
	-mitk::PeakImageSerializer::~PeakImageSerializer()
	-{
	-}
	-
	-
	-std::string mitk::PeakImageSerializer::Serialize()
	-{
	- mitk::LocaleSwitch localeSwitch("C");
	- const PeakImage* image = dynamic_cast<const PeakImage*>( m_Data.GetPointer() );
	- if (image == nullptr)
	- {
	- MITK_ERROR << " Object at " << (const void*) this->m_Data
	- << " is not an mitk::PeakImage. Cannot serialize as Nrrd.";
	- return "";
	- }
	-
	- std::string filename( this->GetUniqueFilenameInWorkingDirectory() );
	- filename += "_";
	- filename += m_FilenameHint;
	- filename += ".peak";
	-
	- std::string fullname(m_WorkingDirectory);
	- fullname += "/";
	- fullname += itksys::SystemTools::ConvertToOutputPath(filename.c_str());
	-
	- try
	- {
	- typedef mitk::ImageToItk< PeakImage::ItkPeakImageType > CasterType;
	- CasterType::Pointer caster = CasterType::New();
	- caster->SetInput(image);
	- caster->Update();
	- mitk::PeakImage::ItkPeakImageType::Pointer itk_image = caster->GetOutput();
	-
	- itk::ImageFileWriter< PeakImage::ItkPeakImageType >::Pointer writer = itk::ImageFileWriter< PeakImage::ItkPeakImageType >::New();
	- writer->SetInput(itk_image);
	- writer->SetFileName(fullname);
	- itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
	- io->SetFileType( itk::ImageIOBase::Binary );
	- io->UseCompressionOn();
	- writer->SetImageIO(io);
	- writer->Update();
	- }
	- catch (std::exception& e)
	- {
	- MITK_ERROR << " Error serializing object at " << (const void*) this->m_Data
	- << " to "
	- << fullname
	- << ": "
	- << e.what();
	- return "";
	- }
	- return filename;
	-}
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkPeakImageSerializer.h b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkPeakImageSerializer.h
	deleted file mode 100644
	index 6b37341b6b..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkPeakImageSerializer.h
	+++ /dev/null
	@@ -1,39 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef mitkPeakImageSerializer_h_included
	-#define mitkPeakImageSerializer_h_included
	-
	-#include "mitkBaseDataSerializer.h"
	-
	-namespace mitk
	-{
	-/**
	- \brief Serializes mitk::Surface for mitk::SceneIO
	-*/
	-class PeakImageSerializer : public BaseDataSerializer
	-{
	- public:
	- mitkClassMacro( PeakImageSerializer, BaseDataSerializer );
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- std::string Serialize() override;
	- protected:
	- PeakImageSerializer();
	- ~PeakImageSerializer() override;
	-};
	-} // namespace
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkShImageReader.cpp b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkShImageReader.cpp
	deleted file mode 100644
	index 3ea81d197c..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkShImageReader.cpp
	+++ /dev/null
	@@ -1,131 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkShImageReader.h"
	-#include <mitkCustomMimeType.h>
	-#include "mitkDiffusionCoreIOMimeTypes.h"
	-
	-#include "itkImageFileReader.h"
	-#include "itkImageRegionIterator.h"
	-#include "itkMetaDataObject.h"
	-#include "itkNrrdImageIO.h"
	-#include "itkNiftiImageIO.h"
	-#include "mitkITKImageImport.h"
	-#include "mitkImageDataItem.h"
	-#include <mitkLocaleSwitch.h>
	-#include <itkShCoefficientImageImporter.h>
	-#include <mitkImageCast.h>
	-
	-namespace mitk
	-{
	- ShImageReader::ShImageReader(const ShImageReader& other)
	- : mitk::AbstractFileReader(other)
	- {
	- }
	-
	- ShImageReader::ShImageReader()
	- : mitk::AbstractFileReader( CustomMimeType( mitk::DiffusionCoreIOMimeTypes::SH_MIMETYPE() ), mitk::DiffusionCoreIOMimeTypes::SH_MIMETYPE_DESCRIPTION() )
	- {
	- m_ServiceReg = this->RegisterService();
	- }
	-
	- ShImageReader::~ShImageReader()
	- {
	- }
	-
	- template <int shOrder>
	- mitk::Image::Pointer ShImageReader::ConvertShImage(ShImage::ShOnDiskType::Pointer img)
	- {
	- typedef itk::ShCoefficientImageImporter< float, shOrder > ImporterType;
	- typename ImporterType::Pointer importer = ImporterType::New();
	- importer->SetInputImage(img);
	- importer->GenerateData();
	-
	- mitk::ShImage::Pointer shImage = mitk::ShImage::New();
	- mitk::Image::Pointer resultImage = dynamic_cast<mitk::Image*>(shImage.GetPointer());
	- mitk::CastToMitkImage(importer->GetCoefficientImage(), resultImage);
	- resultImage->SetVolume(importer->GetCoefficientImage()->GetBufferPointer());
	- return resultImage;
	- }
	-
	- std::vector<itk::SmartPointer<BaseData> > ShImageReader::Read()
	- {
	- mitk::LocaleSwitch localeSwitch("C");
	- std::vector<itk::SmartPointer<mitk::BaseData> > result;
	- std::string location = GetInputLocation();
	-
	- if ( location == "")
	- {
	- throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, the filename is empty!");
	- }
	- else
	- {
	- try
	- {
	- std::string ext = itksys::SystemTools::GetFilenameExtension(location);
	- typedef itk::ImageFileReader< ShImage::ShOnDiskType > FileReaderType;
	- FileReaderType::Pointer reader = FileReaderType::New();
	- reader->SetFileName(location);
	- if (ext==".shi")
	- {
	- itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
	- reader->SetImageIO(io);
	- }
	- reader->Update();
	- ShImage::ShOnDiskType::Pointer img = reader->GetOutput();
	-
	- switch (img->GetLargestPossibleRegion().GetSize()[3])
	- {
	- case 6:
	- result.push_back( ConvertShImage<2>(img).GetPointer() );
	- break;
	- case 15:
	- result.push_back( ConvertShImage<4>(img).GetPointer() );
	- break;
	- case 28:
	- result.push_back( ConvertShImage<6>(img).GetPointer() );
	- break;
	- case 45:
	- result.push_back( ConvertShImage<8>(img).GetPointer() );
	- break;
	- case 66:
	- result.push_back( ConvertShImage<10>(img).GetPointer() );
	- break;
	- case 91:
	- result.push_back( ConvertShImage<12>(img).GetPointer() );
	- break;
	- default :
	- mitkThrow() << "SH order larger 12 not supported";
	- }
	- }
	- catch(std::exception& e)
	- {
	- throw itk::ImageFileReaderException(__FILE__, __LINE__, e.what());
	- }
	- catch(...)
	- {
	- throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, an error occurred while reading the requested vessel tree file!");
	- }
	- }
	- return result;
	- }
	-
	-} //namespace MITK
	-
	-mitk::ShImageReader* mitk::ShImageReader::Clone() const
	-{
	- return new ShImageReader(*this);
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkShImageReader.h b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkShImageReader.h
	deleted file mode 100644
	index 52138993a2..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkShImageReader.h
	+++ /dev/null
	@@ -1,63 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkNrrdShImageReader_h
	-#define __mitkNrrdShImageReader_h
	-
	-#include "mitkCommon.h"
	-#include "itkVectorContainer.h"
	-#include "vnl/vnl_vector_fixed.h"
	-#include "mitkShImage.h"
	-#include "itkVectorImage.h"
	-#include <mitkAbstractFileReader.h>
	-#include <mitkBaseData.h>
	-#include <mitkMimeType.h>
	-
	-namespace mitk
	-{
	-
	- /** \brief
	- */
	-
	- class ShImageReader : public mitk::AbstractFileReader
	- {
	- public:
	-
	- typedef mitk::ShImage OutputType;
	- typedef itk::VectorImage<float,3> VectorImageType;
	-
	- ShImageReader(const ShImageReader& other);
	- ShImageReader();
	- ~ShImageReader() override;
	-
	- using AbstractFileReader::Read;
	- std::vector<itk::SmartPointer<BaseData> > Read() override;
	-
	- protected:
	-
	-
	- private:
	- ShImageReader* Clone() const override;
	-
	- template <int sh_order>
	- mitk::Image::Pointer ConvertShImage(ShImage::ShOnDiskType::Pointer img);
	-
	- us::ServiceRegistration<mitk::IFileReader> m_ServiceReg;
	- };
	-
	-} //namespace MITK
	-
	-#endif // __mitkNrrdShImageReader_h
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkShImageSerializer.cpp b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkShImageSerializer.cpp
	deleted file mode 100644
	index 2a47d38bfb..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkShImageSerializer.cpp
	+++ /dev/null
	@@ -1,74 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkShImageSerializer.h"
	-#include "mitkShImage.h"
	-#include "mitkShImageWriter.h"
	-
	-#include <itksys/SystemTools.hxx>
	-
	-
	-MITK_REGISTER_SERIALIZER(ShImageSerializer)
	-
	-
	-mitk::ShImageSerializer::ShImageSerializer()
	-{
	-}
	-
	-
	-mitk::ShImageSerializer::~ShImageSerializer()
	-{
	-}
	-
	-
	-std::string mitk::ShImageSerializer::Serialize()
	-{
	- const ShImage* image = dynamic_cast<const ShImage*>( m_Data.GetPointer() );
	- if (image == nullptr)
	- {
	- MITK_ERROR << " Object at " << (const void*) this->m_Data
	- << " is not an mitk::NrrdShImage. Cannot serialize as NrrdShImage.";
	- return "";
	- }
	-
	- std::string filename( this->GetUniqueFilenameInWorkingDirectory() );
	- filename += "_";
	- filename += m_FilenameHint;
	- filename += ".shi";
	-
	- std::string fullname(m_WorkingDirectory);
	- fullname += "/";
	- fullname += itksys::SystemTools::ConvertToOutputPath(filename.c_str());
	-
	- try
	- {
	- mitk::ShImageWriter writer;
	- writer.SetOutputLocation(fullname);
	- writer.SetInput(image);
	- writer.Write();
	- }
	- catch (std::exception& e)
	- {
	- MITK_ERROR << " Error serializing object at " << (const void*) this->m_Data
	- << " to "
	- << fullname
	- << ": "
	- << e.what();
	- return "";
	- }
	- return filename;
	-}
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkShImageSerializer.h b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkShImageSerializer.h
	deleted file mode 100644
	index 71582abd8b..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkShImageSerializer.h
	+++ /dev/null
	@@ -1,39 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef mitkShImageSerializer_h_included
	-#define mitkShImageSerializer_h_included
	-
	-#include "mitkBaseDataSerializer.h"
	-
	-namespace mitk
	-{
	-/**
	- \brief Serializes mitk::Surface for mitk::SceneIO
	-*/
	-class ShImageSerializer : public BaseDataSerializer
	-{
	- public:
	- mitkClassMacro( ShImageSerializer, BaseDataSerializer );
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- std::string Serialize() override;
	- protected:
	- ShImageSerializer();
	- ~ShImageSerializer() override;
	-};
	-} // namespace
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkShImageWriter.cpp b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkShImageWriter.cpp
	deleted file mode 100644
	index 6e2ea52c96..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkShImageWriter.cpp
	+++ /dev/null
	@@ -1,138 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkShImageWriter.h"
	-#include "itkMetaDataDictionary.h"
	-#include "itkMetaDataObject.h"
	-#include "itkImageFileWriter.h"
	-#include "mitkImageCast.h"
	-#include "mitkIOMimeTypes.h"
	-#include "mitkDiffusionCoreIOMimeTypes.h"
	-#include <mitkLocaleSwitch.h>
	-#include <itkShCoefficientImageExporter.h>
	-#include <itksys/SystemTools.hxx>
	-#include <itkNrrdImageIO.h>
	-
	-mitk::ShImageWriter::ShImageWriter()
	- : AbstractFileWriter(mitk::ShImage::GetStaticNameOfClass(), CustomMimeType( mitk::DiffusionCoreIOMimeTypes::SH_MIMETYPE() ), mitk::DiffusionCoreIOMimeTypes::SH_MIMETYPE_DESCRIPTION())
	-{
	- RegisterService();
	-}
	-
	-mitk::ShImageWriter::ShImageWriter(const mitk::ShImageWriter& other)
	- : AbstractFileWriter(other)
	-{
	-}
	-
	-mitk::ShImageWriter::~ShImageWriter()
	-{}
	-
	-template <int shOrder>
	-void mitk::ShImageWriter::WriteShImage(InputType::ConstPointer input)
	-{
	- mitk::LocaleSwitch localeSwitch("C");
	- typename itk::ShCoefficientImageExporter< float, shOrder >::InputImageType::Pointer itk_image = itk::ShCoefficientImageExporter< float, shOrder >::InputImageType::New();
	- CastToItkImage(input, itk_image);
	-
	- typedef itk::ShCoefficientImageExporter< float, shOrder > ExporterType;
	- typename ExporterType::Pointer exporter = ExporterType::New();
	- exporter->SetInputImage(itk_image);
	- exporter->GenerateData();
	-
	- std::string ext = itksys::SystemTools::GetFilenameExtension(this->GetOutputLocation());
	-
	- typedef itk::ImageFileWriter<ShImage::ShOnDiskType> WriterType;
	- WriterType::Pointer writer = WriterType::New();
	- ShImage::ShOnDiskType::Pointer image = exporter->GetOutputImage();
	- writer->SetInput( image );
	-
	- if (ext==".shi")
	- {
	- itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
	- io->SetFileType( itk::ImageIOBase::Binary );
	- io->UseCompressionOn();
	- writer->SetImageIO(io);
	- }
	-
	- writer->SetFileName(this->GetOutputLocation().c_str());
	- writer->SetUseCompression(true);
	-
	- try
	- {
	- writer->Update();
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- MITK_INFO << e.what();
	- }
	-}
	-
	-void mitk::ShImageWriter::Write()
	-{
	- InputType::ConstPointer input = dynamic_cast<const InputType*>(this->GetInput());
	- if (input.IsNull())
	- {
	- MITK_ERROR <<"Sorry, input to ShImageWriter is nullptr!";
	- return;
	- }
	- if ( this->GetOutputLocation().empty() )
	- {
	- MITK_ERROR << "Sorry, filename has not been set!";
	- return ;
	- }
	-
	- switch (input->GetImageDescriptor()->GetChannelTypeById(0).GetNumberOfComponents())
	- {
	- case 6:
	- WriteShImage<2>(input);
	- break;
	- case 15:
	- WriteShImage<4>(input);
	- break;
	- case 28:
	- WriteShImage<6>(input);
	- break;
	- case 45:
	- WriteShImage<8>(input);
	- break;
	- case 66:
	- WriteShImage<10>(input);
	- break;
	- case 91:
	- WriteShImage<12>(input);
	- break;
	- default :
	- mitkThrow() << "SH order larger 12 not supported";
	- }
	-}
	-
	-mitk::ShImageWriter* mitk::ShImageWriter::Clone() const
	-{
	- return new ShImageWriter(*this);
	-}
	-
	-mitk::IFileWriter::ConfidenceLevel mitk::ShImageWriter::GetConfidenceLevel() const
	-{
	- InputType::ConstPointer input = dynamic_cast<const InputType*>(this->GetInput());
	- if (input.IsNull() )
	- {
	- return Unsupported;
	- }
	- else
	- {
	- return Supported;
	- }
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkShImageWriter.h b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkShImageWriter.h
	deleted file mode 100644
	index 060049159e..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkShImageWriter.h
	+++ /dev/null
	@@ -1,58 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_SH_WRITER__H_
	-#define _MITK_SH_WRITER__H_
	-
	-#include <mitkAbstractFileWriter.h>
	-#include <mitkShImage.h>
	-
	-
	-namespace mitk
	-{
	-
	-/**
	- * Writes diffusion volumes to a file
	- * @ingroup Process
	- */
	- class ShImageWriter : public mitk::AbstractFileWriter
	- {
	- public:
	-
	- typedef itk::VectorImage<float, 3> VecImgType;
	- typedef mitk::ShImage InputType;
	-
	- ShImageWriter();
	- ~ShImageWriter() override;
	-
	- using AbstractFileWriter::Write;
	- void Write() override;
	-
	- ConfidenceLevel GetConfidenceLevel() const override;
	-
	- protected:
	-
	- ShImageWriter(const ShImageWriter& other);
	- mitk::ShImageWriter* Clone() const override;
	-
	- template <int shOrder>
	- void WriteShImage(InputType::ConstPointer input);
	- };
	-
	-
	-} // end of namespace mitk
	-
	-#endif //_MITK_NRRDODF_WRITER__H_
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkTensorImageSerializer.cpp b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkTensorImageSerializer.cpp
	deleted file mode 100644
	index 0f396e3c0d..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkTensorImageSerializer.cpp
	+++ /dev/null
	@@ -1,74 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkTensorImageSerializer.h"
	-#include "mitkTensorImage.h"
	-#include "mitkNrrdTensorImageWriter.h"
	-
	-#include <itksys/SystemTools.hxx>
	-
	-
	-MITK_REGISTER_SERIALIZER(TensorImageSerializer)
	-
	-
	-mitk::TensorImageSerializer::TensorImageSerializer()
	-{
	-}
	-
	-
	-mitk::TensorImageSerializer::~TensorImageSerializer()
	-{
	-}
	-
	-
	-std::string mitk::TensorImageSerializer::Serialize()
	-{
	- const TensorImage* image = dynamic_cast<const TensorImage*>( m_Data.GetPointer() );
	- if (image == nullptr)
	- {
	- MITK_ERROR << " Object at " << (const void*) this->m_Data
	- << " is not an mitk::NrrdTensorImage. Cannot serialize as NrrdTensorImage.";
	- return "";
	- }
	-
	- std::string filename( this->GetUniqueFilenameInWorkingDirectory() );
	- filename += "_";
	- filename += m_FilenameHint;
	- filename += ".dti";
	-
	- std::string fullname(m_WorkingDirectory);
	- fullname += "/";
	- fullname += itksys::SystemTools::ConvertToOutputPath(filename.c_str());
	-
	- try
	- {
	- NrrdTensorImageWriter writer;
	- writer.SetOutputLocation(fullname);
	- writer.SetInput(image);
	- writer.Write();
	- }
	- catch (std::exception& e)
	- {
	- MITK_ERROR << " Error serializing object at " << (const void*) this->m_Data
	- << " to "
	- << fullname
	- << ": "
	- << e.what();
	- return "";
	- }
	- return filename;
	-}
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkTensorImageSerializer.h b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkTensorImageSerializer.h
	deleted file mode 100644
	index af52bcf3d9..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkTensorImageSerializer.h
	+++ /dev/null
	@@ -1,39 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef mitkTensorImageSerializer_h_included
	-#define mitkTensorImageSerializer_h_included
	-
	-#include "mitkBaseDataSerializer.h"
	-
	-namespace mitk
	-{
	-/**
	- \brief Serializes mitk::Surface for mitk::SceneIO
	-*/
	-class TensorImageSerializer : public BaseDataSerializer
	-{
	- public:
	- mitkClassMacro( TensorImageSerializer, BaseDataSerializer );
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- std::string Serialize() override;
	- protected:
	- TensorImageSerializer();
	- ~TensorImageSerializer() override;
	-};
	-} // namespace
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkTensorImageSource.cpp b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkTensorImageSource.cpp
	deleted file mode 100644
	index 79d0ea5a42..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkTensorImageSource.cpp
	+++ /dev/null
	@@ -1,45 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#include "mitkTensorImageSource.h"
	-
	-
	-mitk::TensorImageSource::TensorImageSource()
	-{
	- // Create the output. We use static_cast<> here because we know the default
	- // output must be of type TOutputImage
	- OutputImageType::Pointer output
	- = static_cast<OutputImageType*>(this->MakeOutput(0).GetPointer());
	- Superclass::SetNumberOfRequiredOutputs(1);
	- Superclass::SetNthOutput(0, output.GetPointer());
	-}
	-
	-itk::DataObject::Pointer mitk::TensorImageSource::MakeOutput ( DataObjectPointerArraySizeType /idx/ )
	-{
	- return OutputImageType::New().GetPointer();
	-}
	-
	-
	-itk::DataObject::Pointer mitk::TensorImageSource::MakeOutput( const DataObjectIdentifierType & name )
	-{
	- itkDebugMacro("MakeOutput(" << name << ")");
	- if( this->IsIndexedOutputName(name) )
	- {
	- return this->MakeOutput( this->MakeIndexFromOutputName(name) );
	- }
	- return static_cast<itk::DataObject *>(OutputImageType::New().GetPointer());
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkTensorImageSource.h b/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkTensorImageSource.h
	deleted file mode 100644
	index e2443d65d7..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/autoload/IO/mitkTensorImageSource.h
	+++ /dev/null
	@@ -1,63 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef TensorImageSource_H_HEADER_INCLUDED_C1E7D6EC
	-#define TensorImageSource_H_HEADER_INCLUDED_C1E7D6EC
	-
	-#include "mitkImageSource.h"
	-#include "mitkTensorImage.h"
	-
	-namespace mitk {
	-
	-class TensorImageSource : public ImageSource
	-{
	-public:
	-
	- typedef mitk::TensorImage OutputImageType;
	- typedef OutputImageType::Pointer OutputImagePointer;
	- typedef SlicedData::RegionType OutputImageRegionType;
	- typedef itk::DataObject::Pointer DataObjectPointer;
	-
	- mitkClassMacro(TensorImageSource,ImageSource);
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /**
	- * Allocates a new output object and returns it. Currently the
	- * index idx is not evaluated.
	- * @param idx the index of the output for which an object should be created
	- * @returns the new object
	- */
	- itk::DataObject::Pointer MakeOutput ( DataObjectPointerArraySizeType idx ) override;
	-
	- /**
	- * This is a default implementation to make sure we have something.
	- * Once all the subclasses of ProcessObject provide an appopriate
	- * MakeOutput(), then ProcessObject::MakeOutput() can be made pure
	- * virtual.
	- */
	- itk::DataObject::Pointer MakeOutput(const DataObjectIdentifierType &name) override;
	-
	-protected:
	- TensorImageSource();
	- ~TensorImageSource() override {}
	-
	-};
	-
	-} // namespace mitk
	-
	-#endif /* TensorImageSource_H_HEADER_INCLUDED_C1E7D6EC */
	diff --git a/Modules/DiffusionImaging/DiffusionCore/files.cmake b/Modules/DiffusionImaging/DiffusionCore/files.cmake
	deleted file mode 100644
	index b8972e792d..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/files.cmake
	+++ /dev/null
	@@ -1,162 +0,0 @@
	-set(CPP_FILES
	-
	- # DicomImport
	- # DicomImport/mitkGroupDiffusionHeadersFilter.cpp
	- DicomImport/mitkDicomDiffusionImageHeaderReader.cpp
	- DicomImport/mitkGEDicomDiffusionImageHeaderReader.cpp
	- DicomImport/mitkPhilipsDicomDiffusionImageHeaderReader.cpp
	- DicomImport/mitkSiemensDicomDiffusionImageHeaderReader.cpp
	- DicomImport/mitkSiemensMosaicDicomDiffusionImageHeaderReader.cpp
	-
	- DicomImport/mitkDiffusionDICOMFileReader.cpp
	- DicomImport/mitkDiffusionHeaderDICOMFileReader.cpp
	- DicomImport/mitkDiffusionHeaderSiemensDICOMFileReader.cpp
	- DicomImport/mitkDiffusionHeaderSiemensDICOMFileHelper.cpp
	- DicomImport/mitkDiffusionHeaderSiemensMosaicDICOMFileReader.cpp
	- DicomImport/mitkDiffusionHeaderGEDICOMFileReader.cpp
	- DicomImport/mitkDiffusionHeaderPhilipsDICOMFileReader.cpp
	-
	- # DataStructures -> DWI
	- IODataStructures/DiffusionWeightedImages/mitkDiffusionImageHeaderInformation.cpp
	- IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCorrectionFilter.cpp
	- IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCreationFilter.cpp
	-
	- # Properties
	- IODataStructures/Properties/mitkBValueMapProperty.cpp
	- IODataStructures/Properties/mitkGradientDirectionsProperty.cpp
	- IODataStructures/Properties/mitkMeasurementFrameProperty.cpp
	- IODataStructures/Properties/mitkDiffusionPropertyHelper.cpp
	- IODataStructures/Properties/mitkNodePredicateIsDWI.cpp
	-
	- # Serializer
	- IODataStructures/Properties/mitkBValueMapPropertySerializer.cpp
	- IODataStructures/Properties/mitkGradientDirectionsPropertySerializer.cpp
	- IODataStructures/Properties/mitkMeasurementFramePropertySerializer.cpp
	-
	- # DataStructures -> Odf
	- IODataStructures/OdfImages/mitkOdfImageSource.cpp
	- IODataStructures/OdfImages/mitkOdfImage.cpp
	- IODataStructures/mitkShImage.cpp
	- IODataStructures/mitkShImageSource.cpp
	-
	- # DataStructures -> Tensor
	- IODataStructures/TensorImages/mitkTensorImage.cpp
	-
	- # DataStructures -> Peaks
	- IODataStructures/mitkPeakImage.cpp
	-
	- Rendering/vtkMaskedProgrammableGlyphFilter.cpp
	- Rendering/mitkVectorImageVtkGlyphMapper3D.cpp
	- Rendering/vtkOdfSource.cxx
	- Rendering/vtkThickPlane.cxx
	- Rendering/mitkOdfNormalizationMethodProperty.cpp
	- Rendering/mitkOdfScaleByProperty.cpp
	-
	- # Algorithms
	- Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.cpp
	- Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.cpp
	- Algorithms/itkDwiGradientLengthCorrectionFilter.cpp
	-
	- # Registration Algorithms & Co.
	- Algorithms/Registration/mitkRegistrationWrapper.cpp
	- Algorithms/Registration/mitkPyramidImageRegistrationMethod.cpp
	- # Algorithms/Registration/mitkRegistrationMethodITK4.cpp
	- Algorithms/Registration/mitkDWIHeadMotionCorrectionFilter.cpp
	-
	-
	- # MultishellProcessing
	- Algorithms/Reconstruction/MultishellProcessing/itkADCAverageFunctor.cpp
	- Algorithms/Reconstruction/MultishellProcessing/itkADCFitFunctor.cpp
	- Algorithms/Reconstruction/MultishellProcessing/itkKurtosisFitFunctor.cpp
	- Algorithms/Reconstruction/MultishellProcessing/itkBiExpFitFunctor.cpp
	-
	- # Function Collection
	- mitkDiffusionFunctionCollection.cpp
	-)
	-
	-set(H_FILES
	- # function Collection
	- include/mitkDiffusionFunctionCollection.h
	-
	- # Rendering
	- include/Rendering/mitkOdfVtkMapper2D.h
	-
	- # Reconstruction
	- include/Algorithms/Reconstruction/itkDiffusionQballReconstructionImageFilter.h
	- include/Algorithms/Reconstruction/mitkTeemDiffusionTensor3DReconstructionImageFilter.h
	- include/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.h
	- include/Algorithms/Reconstruction/itkDiffusionMultiShellQballReconstructionImageFilter.h
	- include/Algorithms/Reconstruction/itkPointShell.h
	- include/Algorithms/Reconstruction/itkOrientationDistributionFunction.h
	- include/Algorithms/Reconstruction/itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.h
	- include/Algorithms/Reconstruction/itkDiffusionKurtosisReconstructionImageFilter.h
	- include/Algorithms/Reconstruction/itkBallAndSticksImageFilter.h
	- include/Algorithms/Reconstruction/itkMultiTensorImageFilter.h
	-
	- # Fitting functions
	- include/Algorithms/Reconstruction/FittingFunctions/mitkAbstractFitter.h
	- include/Algorithms/Reconstruction/FittingFunctions/mitkMultiTensorFitter.h
	- include/Algorithms/Reconstruction/FittingFunctions/mitkBallStickFitter.h
	-
	-
	- # MultishellProcessing
	- include/Algorithms/Reconstruction/MultishellProcessing/itkRadialMultishellToSingleshellImageFilter.h
	- include/Algorithms/Reconstruction/MultishellProcessing/itkDWIVoxelFunctor.h
	- include/Algorithms/Reconstruction/MultishellProcessing/itkADCAverageFunctor.h
	- include/Algorithms/Reconstruction/MultishellProcessing/itkKurtosisFitFunctor.h
	- include/Algorithms/Reconstruction/MultishellProcessing/itkBiExpFitFunctor.h
	- include/Algorithms/Reconstruction/MultishellProcessing/itkADCFitFunctor.h
	-
	- # Properties
	- include/IODataStructures/Properties/mitkBValueMapProperty.h
	- include/IODataStructures/Properties/mitkGradientDirectionsProperty.h
	- include/IODataStructures/Properties/mitkMeasurementFrameProperty.h
	- include/IODataStructures/Properties/mitkDiffusionPropertyHelper.h
	-
	- include/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageTransformedCreationFilter.h
	-
	- # Algorithms
	- include/Algorithms/itkDiffusionOdfGeneralizedFaImageFilter.h
	- include/Algorithms/itkDiffusionOdfPrepareVisualizationImageFilter.h
	- include/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.h
	- include/Algorithms/itkTensorDerivedMeasurementsFilter.h
	- include/Algorithms/itkBrainMaskExtractionImageFilter.h
	- include/Algorithms/itkB0ImageExtractionImageFilter.h
	- include/Algorithms/itkB0ImageExtractionToSeparateImageFilter.h
	- include/Algorithms/itkTensorImageToDiffusionImageFilter.h
	- include/Algorithms/itkTensorToL2NormImageFilter.h
	- include/Algorithms/itkGaussianInterpolateImageFunction.h
	- include/Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.h
	- include/Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.h
	- include/Algorithms/itkDiffusionTensorPrincipalDirectionImageFilter.h
	- include/Algorithms/itkCartesianToPolarVectorImageFilter.h
	- include/Algorithms/itkPolarToCartesianVectorImageFilter.h
	- include/Algorithms/itkDistanceMapFilter.h
	- include/Algorithms/itkProjectionFilter.h
	- include/Algorithms/itkResidualImageFilter.h
	- include/Algorithms/itkExtractChannelFromRgbaImageFilter.h
	- include/Algorithms/itkTensorReconstructionWithEigenvalueCorrectionFilter.h
	- include/Algorithms/itkMergeDiffusionImagesFilter.h
	- include/Algorithms/itkShCoefficientImageImporter.h
	- include/Algorithms/itkShCoefficientImageExporter.h
	- include/Algorithms/itkOdfMaximaExtractionFilter.h
	- include/Algorithms/itkResampleDwiImageFilter.h
	- include/Algorithms/itkDwiGradientLengthCorrectionFilter.h
	- include/Algorithms/itkAdcImageFilter.h
	- include/Algorithms/itkDwiNormilzationFilter.h
	- include/Algorithms/itkSplitDWImageFilter.h
	- include/Algorithms/itkRemoveDwiChannelFilter.h
	- include/Algorithms/itkExtractDwiChannelFilter.h
	- include/Algorithms/itkFlipPeaksFilter.h
	- include/Algorithms/itkShToOdfImageFilter.h
	- include/Algorithms/itkFourDToVectorImageFilter.h
	- include/Algorithms/itkVectorImageToFourDImageFilter.h
	- include/Algorithms/Registration/mitkDWIHeadMotionCorrectionFilter.h
	- include/Algorithms/itkNonLocalMeansDenoisingFilter.h
	- include/Algorithms/itkVectorImageToImageFilter.h
	- include/Algorithms/itkSplitVectorImageFilter.h
	-)
	-
	-set( TOOL_FILES
	-)
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/FittingFunctions/mitkAbstractFitter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/FittingFunctions/mitkAbstractFitter.h
	deleted file mode 100644
	index 2d090a6309..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/FittingFunctions/mitkAbstractFitter.h
	+++ /dev/null
	@@ -1,125 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_AbstractFitter_H
	-#define _MITK_AbstractFitter_H
	-
	-#include <vnl/vnl_least_squares_function.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <itkVectorImage.h>
	-#include <mitkTensorImage.h>
	-
	-namespace mitk {
	-
	-class AbstractFitter: public vnl_least_squares_function
	-{
	-
	-public:
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionType GradientDirectionType;
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionsContainerType GradientContainerType;
	- typedef itk::VectorImage< unsigned short, 3 > DiffusionImageType;
	- typedef TensorImage::PixelType TensorType;
	-
	- AbstractFitter(unsigned int number_of_parameters, unsigned int number_of_measurements) :
	- vnl_least_squares_function(number_of_parameters, number_of_measurements, no_gradient)
	- {
	-
	- }
	-
	- GradientContainerType::Pointer gradientDirections;
	- DiffusionImageType::PixelType measurements;
	- std::vector<double> bValues;
	- double S0;
	- std::vector<int> weightedIndices;
	-
	- void set_S0(double val)
	- {
	- S0 = val;
	- }
	-
	- void set_measurements(const DiffusionImageType::PixelType& m)
	- {
	- measurements = m;
	- }
	-
	- void set_bvalues(std::vector<double>& x)
	- {
	- bValues = x;
	- }
	-
	- void set_weightedIndices(std::vector<int>& x)
	- {
	- weightedIndices = x;
	- }
	-
	- void set_gradient_directions(const GradientContainerType::Pointer& directions)
	- {
	- gradientDirections = directions;
	- }
	-
	- static void Sph2Cart(vnl_vector_fixed<double,3>& dir, const double &theta, const double &phi)
	- {
	- dir[0] = std::sin(theta)*std::cos(phi);
	- dir[1] = std::sin(theta)*std::sin(phi);
	- dir[2] = std::cos(theta);
	- }
	-
	- static void Cart2Sph(const vnl_vector_fixed<double,3>& dir, double &theta, double &phi)
	- {
	- theta = std::acos( dir[2] );
	-
	- // phi goes from 0.0 (+x axis) and wraps at 2 * PI
	- // theta goes from 0.0 (+z axis) and wraps at PI
	-
	- // if x and y are 0.0 or very close, return phi == 0
	- if (fabs(dir[0]) + fabs(dir[1]) < 1E-9)
	- {
	- phi = 0.0;
	- }
	- else {
	- // ie, if ( x == 0 && y == 0 ) == false
	- if (dir[1] == 0.0)
	- {
	- if (dir[0] > 0.0)
	- phi = 0.0;
	- else
	- phi = itk::Math::pi;
	- }
	- else if (dir[0] == 0.0)
	- {
	- // avoid div by zero
	- if (dir[1] > 0) {
	- phi = itk::Math::pi / 2.0;
	- }
	- else {
	- phi = 1.5 * itk::Math::pi;
	- }
	- }
	- else if (dir[0] > 0.0 && dir[1] > 0.0) // first quadrant
	- phi = atan(dir[1] / dir[0]);
	- else if (dir[0] < 0.0 && dir[1] > 0.0) // second quadrant
	- phi = itk::Math::pi + atan(dir[1] / dir[0]);
	- else if (dir[0] < 0.0 && dir[1] < 0.0) // third quadrant
	- phi = itk::Math::pi + atan(dir[1] / dir[0]);
	- else // fourth quadrant
	- phi = 2.0 * itk::Math::pi + atan(dir[1] / dir[0]);
	- }
	- }
	-
	-};
	-}
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/FittingFunctions/mitkBallStickFitter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/FittingFunctions/mitkBallStickFitter.h
	deleted file mode 100644
	index 7e9acd51a6..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/FittingFunctions/mitkBallStickFitter.h
	+++ /dev/null
	@@ -1,72 +0,0 @@
	-#include <mitkAbstractFitter.h>
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_BallStickFitter_H
	-#define _MITK_BallStickFitter_H
	-
	-#include <mitkAbstractFitter.h>
	-
	-namespace mitk {
	-
	-struct BallStickFitter: public AbstractFitter
	-{
	-public :
	-
	- BallStickFitter(unsigned int number_of_parameters, unsigned int number_of_measurements) :
	- AbstractFitter(number_of_parameters, number_of_measurements)
	- {
	-
	- }
	-
	- double penalty(const vnl_vector<double>& x)
	- {
	- double p = 0;
	-
	- if (x[0]<0 \|\| x[0]>1)
	- p += 10e6;
	- if (x[1]<0)
	- p += 10e6;
	-
	- return p;
	- }
	-
	- void f(const vnl_vector<double>& x, vnl_vector<double>& fx) override
	- {
	- const double & f = x[0];
	- const double & d = x[1];
	- const double & theta = x[2];
	- const double & phi = x[3];
	- vnl_vector_fixed<double,3> dir;
	- Sph2Cart(dir, theta, phi);
	-
	- for(auto s : weightedIndices)
	- {
	- double s_iso = S0 * std::exp(-bValues[s] * d);
	- GradientDirectionType g = gradientDirections->GetElement(s);
	- g.normalize();
	- double dot = dot_product(g, dir);
	- double s_aniso = S0 * std::exp(-bValues[s] * d * dot*dot );
	- double approx = (1-f)s_iso + fs_aniso;
	- const double factor = measurements[s] - approx;
	- fx[s] = factor*factor + penalty(x);
	- }
	- }
	-};
	-
	-}
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/FittingFunctions/mitkMultiTensorFitter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/FittingFunctions/mitkMultiTensorFitter.h
	deleted file mode 100644
	index 7018e02f20..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/FittingFunctions/mitkMultiTensorFitter.h
	+++ /dev/null
	@@ -1,117 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_MultiTensorFitter_H
	-#define _MITK_MultiTensorFitter_H
	-
	-#include <mitkAbstractFitter.h>
	-
	-namespace mitk {
	-
	-class MultiTensorFitter: public AbstractFitter
	-{
	-public:
	-
	- MultiTensorFitter(unsigned int number_of_tensors=2, unsigned int number_of_measurements=1) :
	- AbstractFitter(check(number_of_tensors), number_of_measurements)
	- {
	- num_tensors = number_of_tensors;
	- }
	-
	- int num_tensors;
	-
	- int check(int n)
	- {
	- if (n==1)
	- return 6;
	- return n*7;
	- }
	-
	- vnl_vector_fixed<double,3> GetLargestEv(TensorType& tensor)
	- {
	- TensorType::EigenValuesArrayType eigenvalues;
	- TensorType::EigenVectorsMatrixType eigenvectors;
	- tensor.ComputeEigenAnalysis(eigenvalues, eigenvectors);
	- vnl_vector_fixed<double,3> ev;
	- ev[0] = eigenvectors(2, 0);
	- ev[1] = eigenvectors(2, 1);
	- ev[2] = eigenvectors(2, 2);
	- if (ev.magnitude()>mitk::eps)
	- ev.normalize();
	- else
	- ev.fill(0.0);
	-
	- return ev;
	- }
	-
	- double penalty(const vnl_vector<double>& x)
	- {
	- double p = 0;
	-
	- if (num_tensors>1)
	- {
	- double f = 0;
	- for (int i=0; i<num_tensors; i++)
	- {
	- if (x[6+i*7]<0)
	- p += 10e6;
	- f += x[6+i*7];
	- }
	- p += 10e7*fabs(1-f);
	- }
	-
	- return p;
	- }
	-
	- void f(const vnl_vector<double>& x, vnl_vector<double>& fx) override
	- {
	- int elements = 7;
	- for(auto s : weightedIndices)
	- {
	- GradientDirectionType g = gradientDirections->GetElement(s);
	- g.normalize();
	-
	- itk::DiffusionTensor3D< double > S;
	- S[0] = g[0]*g[0];
	- S[1] = g[1]*g[0];
	- S[2] = g[2]*g[0];
	- S[3] = g[1]*g[1];
	- S[4] = g[2]*g[1];
	- S[5] = g[2]*g[2];
	-
	- double approx = 0;
	- for (int i=0; i<num_tensors; i++)
	- {
	- double D = x[0+ielements]S[0] + x[1+ielements]S[1] + x[2+ielements]S[2] +
	- x[1+ielements]S[1] + x[3+ielements]S[3] + x[4+ielements]S[4] +
	- x[2+ielements]S[2] + x[4+ielements]S[4] + x[5+ielements]S[5];
	- double signal = S0 * std::exp ( -bValues[s] * D );
	- if (num_tensors>1 && x.size()>6)
	- signal = x[elements-1+ielements];
	- approx += signal;
	- }
	-
	- const double factor = measurements[s] - approx;
	-
	- fx[s] = factor*factor + penalty(x);
	- }
	- }
	-
	-};
	-
	-}
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkADCAverageFunctor.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkADCAverageFunctor.h
	deleted file mode 100644
	index 21c1d83f9d..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkADCAverageFunctor.h
	+++ /dev/null
	@@ -1,56 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _itk_ADCAverageFunctor_h_
	-#define _itk_ADCAverageFunctor_h_
	-
	-#include "itkDWIVoxelFunctor.h"
	-#include <cmath>
	-
	-
	-namespace itk
	-{
	-
	-class MITKDIFFUSIONCORE_EXPORT ADCAverageFunctor : public DWIVoxelFunctor
	-{
	-public:
	- ADCAverageFunctor(){}
	- ~ADCAverageFunctor() override{}
	-
	- typedef ADCAverageFunctor Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef DWIVoxelFunctor Superclass;
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- /** Runtime information support. */
	- itkTypeMacro(ADCAverageFunctor, DWIVoxelFunctor)
	-
	- void operator()(vnl_matrix<double> & newSignal, const vnl_matrix<double> & SignalMatrix, const double & S0) override;
	-
	- void setTargetBValue(const double & targetBValue){m_TargetBvalue = targetBValue;}
	- void setListOfBValues(const vnl_vector<double> & BValueList){m_BValueList = BValueList;}
	-
	-protected:
	- double m_TargetBvalue;
	- vnl_vector<double> m_BValueList;
	-
	-};
	-
	-}
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkADCFitFunctor.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkADCFitFunctor.h
	deleted file mode 100644
	index 49e5e89b92..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkADCFitFunctor.h
	+++ /dev/null
	@@ -1,102 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _itk_ADCFitFunctor_h_
	-#define _itk_ADCFitFunctor_h_
	-
	-#include "itkDWIVoxelFunctor.h"
	-#include "vnl/vnl_least_squares_function.h"
	-#include "vnl/vnl_math.h"
	-namespace itk
	-{
	-
	-class MITKDIFFUSIONCORE_EXPORT ADCFitFunctor : public DWIVoxelFunctor
	-{
	-public:
	- ADCFitFunctor(){}
	- ~ADCFitFunctor() override{}
	-
	- typedef ADCFitFunctor Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef DWIVoxelFunctor Superclass;
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- /** Runtime information support. */
	- itkTypeMacro(ADCFitFunctor, DWIVoxelFunctor)
	-
	- void operator()(vnl_matrix<double> & newSignal, const vnl_matrix<double> & SignalMatrix, const double & S0) override;
	-
	- void setTargetBValue(const double & targetBValue){m_TargetBvalue = targetBValue;}
	- void setListOfBValues(const vnl_vector<double> & BValueList){m_BValueList = BValueList;}
	-
	-protected:
	- double m_TargetBvalue;
	- vnl_vector<double> m_BValueList;
	-
	- /**
	- * \brief The lestSquaresFunction struct for Non-Linear-Least-Squres fit of monoexponential model
	- */
	- struct lestSquaresFunction: public vnl_least_squares_function
	- {
	-
	- void set_measurements(const vnl_vector<double>& x)
	- {
	- measurements.set_size(x.size());
	- measurements.copy_in(x.data_block());
	- }
	-
	- void set_bvalues(const vnl_vector<double>& x)
	- {
	- bValueVector.set_size(x.size());
	- bValueVector.copy_in(x.data_block());
	- }
	-
	- void set_reference_measurement(const double & x)
	- {
	- S0 = x;
	- }
	-
	- vnl_vector<double> measurements;
	- vnl_vector<double> bValueVector;
	- double S0;
	- int N;
	-
	- lestSquaresFunction(unsigned int number_of_measurements) :
	- vnl_least_squares_function(1 /number of unknowns [ ADC ]/, number_of_measurements, no_gradient)
	- {
	- N = get_number_of_residuals();
	- }
	-
	- void f(const vnl_vector<double>& x, vnl_vector<double>& fx) override {
	-
	- const double & ADC = x[0];
	-
	- const vnl_vector<double> & b = bValueVector;
	-
	- for(int s=0; s<N; s++)
	- {
	- double approx = S0 * std::exp(-b[s] * ADC);
	- fx[s] = vnl_math_abs( measurements[s] - approx );
	- }
	-
	- }
	- };
	-};
	-}
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkBiExpFitFunctor.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkBiExpFitFunctor.h
	deleted file mode 100644
	index 820e7170e4..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkBiExpFitFunctor.h
	+++ /dev/null
	@@ -1,111 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _itk_BiExpFitFunctor_h_
	-#define _itk_BiExpFitFunctor_h_
	-
	-#include "itkDWIVoxelFunctor.h"
	-#include <cmath>
	-
	-// vnl include
	-#include "vnl/vnl_least_squares_function.h"
	-#include "vnl/algo/vnl_levenberg_marquardt.h"
	-#include "vnl/vnl_math.h"
	-
	-namespace itk
	-{
	-
	-class MITKDIFFUSIONCORE_EXPORT BiExpFitFunctor : public DWIVoxelFunctor
	-{
	-public:
	- BiExpFitFunctor(){}
	- ~BiExpFitFunctor() override{}
	-
	- typedef BiExpFitFunctor Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef DWIVoxelFunctor Superclass;
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- /** Runtime information support. */
	- itkTypeMacro(BiExpFitFunctor, DWIVoxelFunctor)
	-
	- void operator()(vnl_matrix<double> & newSignal,const vnl_matrix<double> & SignalMatrix, const double & S0) override;
	-
	- void setTargetBValue(const double & targetBValue){m_TargetBvalue = targetBValue;}
	- void setListOfBValues(const vnl_vector<double> & BValueList){m_BValueList = BValueList;}
	-
	-protected:
	- double m_TargetBvalue;
	- vnl_vector<double> m_BValueList;
	-
	- /**
	- * \brief The lestSquaresFunction struct for Non-Linear-Least-Squres fit of Biexponential model
	- */
	- struct lestSquaresFunction: public vnl_least_squares_function
	- {
	-
	- void set_measurements(const vnl_vector<double>& x)
	- {
	- measurements.set_size(x.size());
	- measurements.copy_in(x.data_block());
	- }
	-
	- void set_bvalues(const vnl_vector<double>& x)
	- {
	- bValueVector.set_size(x.size());
	- bValueVector.copy_in(x.data_block());
	- }
	-
	- void set_reference_measurement(const double & x)
	- {
	- S0 = x;
	- }
	-
	- vnl_vector<double> measurements;
	- vnl_vector<double> bValueVector;
	- double S0;
	- int N;
	-
	- lestSquaresFunction(unsigned int number_of_measurements) :
	- vnl_least_squares_function(3 /number of unknowns [ ADC_slow ADC_fast lambda]/, number_of_measurements, no_gradient)
	- {
	- N = get_number_of_residuals();
	- }
	-
	- void f(const vnl_vector<double>& x, vnl_vector<double>& fx) override {
	-
	- const double & ADC_slow = x[0];
	- const double & ADC_fast = x[1];
	- const double & lambda = x[2];
	-
	- const vnl_vector<double> & b = bValueVector;
	-
	- for(int s=0; s<N; s++)
	- {
	- double approx = lambda * std::exp(-b[s] * ADC_slow) + (1-lambda) * std::exp(-b[s] * ADC_fast);
	- fx[s] = vnl_math_abs( measurements[s] - approx*S0 );
	- }
	-
	- }
	- };
	-
	-};
	-
	-}
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkDWIVoxelFunctor.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkDWIVoxelFunctor.h
	deleted file mode 100644
	index f5ceb4e803..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkDWIVoxelFunctor.h
	+++ /dev/null
	@@ -1,64 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _itk_DWIVoxelFunctor_h_
	-#define _itk_DWIVoxelFunctor_h_
	-
	-#include <MitkDiffusionCoreExports.h>
	-#include "vnl/vnl_vector.h"
	-#include "vnl/vnl_matrix.h"
	-#include <itkObject.h>
	-#include <itkObjectFactory.h>
	-
	-namespace itk
	-{
	-
	-/**
	- * \brief The DWIVoxelFunctor class
	- * Abstract basisclass for voxelprocessing of Diffusion Weighted Images
	- */
	-class MITKDIFFUSIONCORE_EXPORT DWIVoxelFunctor: public Object
	-{
	-protected:
	- DWIVoxelFunctor(){}
	- ~DWIVoxelFunctor() override{}
	-
	-public:
	- typedef DWIVoxelFunctor Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef itk::Object Superclass;
	-
	- /** Runtime information support. */
	- itkTypeMacro(DWIVoxelFunctor, Object)
	- /** Method for creation through the object factory. */
	- //itkFactorylessNewMacro(Self)
	- //itkCloneMacro(Self)
	-
	- /**
	- * \brief operator ()
	- * \param SignalMatrix is a NxM matrix (N = Number of gradients; M = Number of Shells)
	- * \param S0 is the reference signal (b=0)
	- * \return NxP Signal vector containing the new signal (e.g. [S_1 S_2 S_3 ... S_N] -> only diffusion weighted signal).
	- *The first column of the matrix is reserved for the new calculated signal (other columns can hold e.g. the RMS-error)
	- */
	- virtual void operator()(vnl_matrix<double> & /newSignal/,const vnl_matrix<double> & /SignalMatrix/, const double & /S0/)=0;
	-
	-};
	-
	-}
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkKurtosisFitFunctor.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkKurtosisFitFunctor.h
	deleted file mode 100644
	index f029cf4da5..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkKurtosisFitFunctor.h
	+++ /dev/null
	@@ -1,109 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _itk_KurtosisFitFunctor_h_
	-#define _itk_KurtosisFitFunctor_h_
	-
	-#include "itkDWIVoxelFunctor.h"
	-#include <cmath>
	-
	-// vnl include
	-#include "vnl/vnl_least_squares_function.h"
	-#include "vnl/algo/vnl_levenberg_marquardt.h"
	-#include "vnl/vnl_math.h"
	-
	-namespace itk
	-{
	-
	-class MITKDIFFUSIONCORE_EXPORT KurtosisFitFunctor : public DWIVoxelFunctor
	-{
	-public:
	- KurtosisFitFunctor(){}
	- ~KurtosisFitFunctor() override{}
	-
	- typedef KurtosisFitFunctor Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef DWIVoxelFunctor Superclass;
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- /** Runtime information support. */
	- itkTypeMacro(KurtosisFitFunctor, DWIVoxelFunctor)
	-
	- void operator()(vnl_matrix<double> & newSignal,const vnl_matrix<double> & SignalMatrix, const double & S0) override;
	-
	- void setTargetBValue(const double & targetBValue){m_TargetBvalue = targetBValue;}
	- void setListOfBValues(const vnl_vector<double> & BValueList){m_BValueList = BValueList;}
	-
	-protected:
	- double m_TargetBvalue;
	- vnl_vector<double> m_BValueList;
	-
	- /**
	- * \brief The lestSquaresFunction struct for Non-Linear-Least-Squres fit of Kurtosis
	- */
	- struct lestSquaresFunction: public vnl_least_squares_function
	- {
	-
	- void set_measurements(const vnl_vector<double>& x)
	- {
	- measurements.set_size(x.size());
	- measurements.copy_in(x.data_block());
	- }
	-
	- void set_bvalues(const vnl_vector<double>& x)
	- {
	- bValueVector.set_size(x.size());
	- bValueVector.copy_in(x.data_block());
	- }
	-
	- void set_reference_measurement(const double & x)
	- {
	- S0 = x;
	- }
	-
	- vnl_vector<double> measurements;
	- vnl_vector<double> bValueVector;
	- double S0;
	- int N;
	-
	- lestSquaresFunction(unsigned int number_of_measurements) :
	- vnl_least_squares_function(2 /number of unknowns [ADC AKC]/, number_of_measurements, no_gradient)
	- {
	- N = get_number_of_residuals();
	- }
	-
	- void f(const vnl_vector<double>& x, vnl_vector<double>& fx) override {
	-
	- const double & D = x[0];
	- const double & K = x[1];
	- const vnl_vector<double> & b = bValueVector;
	-
	- for(int s=0; s<N; s++)
	- {
	- double approx = S0 * std::exp(- b[s] * D + 1./6. b[s] b[s] D D * K);
	- fx[s] = vnl_math_abs( measurements[s] - approx );
	- }
	-
	- }
	- };
	-
	-};
	-
	-}
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkRadialMultishellToSingleshellImageFilter.cpp b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkRadialMultishellToSingleshellImageFilter.cpp
	deleted file mode 100644
	index 64ae9fdf70..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkRadialMultishellToSingleshellImageFilter.cpp
	+++ /dev/null
	@@ -1,237 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-/*=========================================================================
	-
	-Program: Tensor ToolKit - TTK
	-Module: $URL: svn://scm.gforge.inria.fr/svn/ttk/trunk/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.txx $
	-Language: C++
	-Date: $Date: 2010-06-07 13:39:13 +0200 (Mo, 07 Jun 2010) $
	-Version: $Revision: 68 $
	-
	-Copyright (c) INRIA 2010. All rights reserved.
	-See LICENSE.txt for details.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without even
	-the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
	-PURPOSE. See the above copyright notices for more information.
	-
	-=========================================================================*/
	-#ifndef _itk_RadialMultishellToSingleshellImageFilter_cpp_
	-#define _itk_RadialMultishellToSingleshellImageFilter_cpp_
	-#endif
	-
	-#define _USE_MATH_DEFINES
	-
	-#include "itkRadialMultishellToSingleshellImageFilter.h"
	-#include "mitkDiffusionFunctionCollection.h"
	-
	-
	-namespace itk
	-{
	-
	-
	-template <class TInputScalarType, class TOutputScalarType>
	-RadialMultishellToSingleshellImageFilter<TInputScalarType, TOutputScalarType>
	-::RadialMultishellToSingleshellImageFilter()
	-{
	- this->SetNumberOfRequiredInputs( 1 );
	- //this->SetNumberOfThreads(1);
	-}
	-
	-template <class TInputScalarType, class TOutputScalarType>
	-void RadialMultishellToSingleshellImageFilter<TInputScalarType, TOutputScalarType>
	-::BeforeThreadedGenerateData()
	-{
	- // test whether BvalueMap contains all necessary information
	- if(m_BValueMap.size() == 0)
	- {
	- itkWarningMacro(<< "No BValueMap given: create one using GradientDirectionContainer");
	-
	- GradientDirectionContainerType::ConstIterator gdcit;
	- for( gdcit = m_OriginalGradientDirections->Begin(); gdcit != m_OriginalGradientDirections->End(); ++gdcit)
	- {
	- double bValueKey = int(((m_OriginalBValue * gdcit.Value().two_norm() * gdcit.Value().two_norm())+7.5)/10)*10;
	- m_BValueMap[bValueKey].push_back(gdcit.Index());
	- }
	- }
	-
	- //# BValueMap contains no bZero --> itkException
	- if(m_BValueMap.find(0.0) == m_BValueMap.end())
	- {
	- MITK_INFO << "No ReferenceSignal (BZeroImages) found!";
	- itkExceptionMacro(<< "No ReferenceSignal (BZeroImages) found!");
	- }
	-
	- // [allDirectionsContainer] Gradient DirectionContainer containing all unique directions
	- m_TargetDirectionsIndicies = mitk::gradients::GetAllUniqueDirections(m_BValueMap, m_OriginalGradientDirections);
	- // [sizeAllDirections] size of GradientContainer cointaining all unique directions
	- m_NumberTargetDirections = m_TargetDirectionsIndicies.size();
	- m_TargetGradientDirections = mitk::gradients::CreateNormalizedUniqueGradientDirectionContainer(m_BValueMap,m_OriginalGradientDirections);
	-
	- m_ShellInterpolationMatrixVector.reserve(m_BValueMap.size()-1);
	-
	- // for each shell
	- BValueMap::const_iterator it = m_BValueMap.begin();
	- it++; //skip bZeroIndices
	-
	- unsigned int shellIndex = 0;
	- for(;it != m_BValueMap.end();++it)
	- {
	- //- calculate maxShOrder
	- const IndicesVector currentShell = it->second;
	- unsigned int SHMaxOrder = 12;
	- while( ((SHMaxOrder+1)(SHMaxOrder+2)/2) > currentShell.size() && ((SHMaxOrder+1)(SHMaxOrder+2)/2) >= 4 )
	- SHMaxOrder -= 2 ;
	-
	- //- get TragetSHBasis using allDirectionsContainer
	- vnl_matrix<double> sphericalCoordinates;
	- sphericalCoordinates = mitk::gradients::ComputeSphericalFromCartesian(m_TargetDirectionsIndicies, m_OriginalGradientDirections);
	- vnl_matrix<double> TargetSHBasis = mitk::gradients::ComputeSphericalHarmonicsBasis(sphericalCoordinates, SHMaxOrder);
	- //- get ShellSHBasis using currentShellDirections
	- sphericalCoordinates = mitk::gradients::ComputeSphericalFromCartesian(currentShell, m_OriginalGradientDirections);
	- vnl_matrix<double> ShellSHBasis = mitk::gradients::ComputeSphericalHarmonicsBasis(sphericalCoordinates, SHMaxOrder);
	- //- calculate interpolationSHBasis [TargetSHBasis * ShellSHBasis^-1]
	- vnl_matrix_inverse<double> invShellSHBasis(ShellSHBasis);
	- vnl_matrix<double> shellInterpolationMatrix = TargetSHBasis * invShellSHBasis.pinverse();
	- //- save interpolationSHBasis
	- m_ShellInterpolationMatrixVector.push_back(shellInterpolationMatrix);
	-
	- ++shellIndex;
	- }
	-
	- // initialize output image
	- typename OutputImageType::Pointer outImage = static_cast<OutputImageType * >(ProcessObject::GetOutput(0));
	- outImage->SetSpacing( this->GetInput()->GetSpacing() );
	- outImage->SetOrigin( this->GetInput()->GetOrigin() );
	- outImage->SetDirection( this->GetInput()->GetDirection() ); // Set the image direction using bZeroDirection+AllDirectionsContainer
	- outImage->SetLargestPossibleRegion( this->GetInput()->GetLargestPossibleRegion());
	- outImage->SetBufferedRegion( this->GetInput()->GetLargestPossibleRegion() );
	- outImage->SetRequestedRegion( this->GetInput()->GetLargestPossibleRegion() );
	- outImage->SetVectorLength( 1+m_NumberTargetDirections ); // size of 1(bzeroValue) + AllDirectionsContainer
	- outImage->Allocate();
	-
	- m_ErrorImage = ErrorImageType::New();
	- m_ErrorImage->SetSpacing( this->GetInput()->GetSpacing() );
	- m_ErrorImage->SetOrigin( this->GetInput()->GetOrigin() );
	- m_ErrorImage->SetDirection( this->GetInput()->GetDirection() ); // Set the image direction using bZeroDirection+AllDirectionsContainer
	- m_ErrorImage->SetLargestPossibleRegion( this->GetInput()->GetLargestPossibleRegion());
	- m_ErrorImage->SetBufferedRegion( this->GetInput()->GetLargestPossibleRegion() );
	- m_ErrorImage->SetRequestedRegion( this->GetInput()->GetLargestPossibleRegion() );
	- m_ErrorImage->Allocate();
	-
	- MITK_INFO << "Input:" << std::endl << std::endl
	- << " GradientDirections: " << m_OriginalGradientDirections->Size() << std::endl
	- << " Shells: " << (m_BValueMap.size() - 1) << std::endl
	- << " ReferenceImages: " << m_BValueMap[0.0].size() << std::endl;
	-
	- MITK_INFO << "Output:" << std::endl << std::endl
	- << " OutImageVectorLength: " << outImage->GetVectorLength() << std::endl
	- << " TargetDirections: " << m_NumberTargetDirections << std::endl
	- << std::endl;
	-
	-}
	-
	-template <class TInputScalarType, class TOutputScalarType>
	-void
	-RadialMultishellToSingleshellImageFilter<TInputScalarType, TOutputScalarType>
	-::ThreadedGenerateData(const OutputImageRegionType &outputRegionForThread, ThreadIdType /threadId/)
	-{
	- // Get input gradient image pointer
	- typename InputImageType::Pointer inputImage = static_cast< InputImageType * >(ProcessObject::GetInput(0));
	- // ImageRegionIterator for the input image
	- ImageRegionIterator< InputImageType > iit(inputImage, outputRegionForThread);
	- iit.GoToBegin();
	-
	- // Get output gradient image pointer
	- typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(ProcessObject::GetOutput(0));
	- // ImageRegionIterator for the output image
	- ImageRegionIterator< OutputImageType > oit(outputImage, outputRegionForThread);
	- oit.GoToBegin();
	-
	- // ImageRegionIterator for the output image
	- ImageRegionIterator< ErrorImageType > eit(m_ErrorImage, outputRegionForThread);
	- eit.GoToBegin();
	-
	- // calculate target bZero-Value [b0_t]
	- const IndicesVector IndicesS0 = m_BValueMap[0.0];
	- double AverageS0 = 0.0;
	-
	- unsigned int numberOfShells = m_BValueMap.size()-1;
	-
	- // create empty nxm SignalMatrix containing n->signals/directions (in case of interpolation ~ sizeAllDirections otherwise the size of any shell) for m->shells
	- vnl_matrix<double> SignalMatrix(m_NumberTargetDirections, numberOfShells);
	- // create nx1 targetSignalVector
	-
	- vnl_vector<double> SignalVector(m_NumberTargetDirections);
	- OutputPixelType out;
	- InputPixelType b;
	- BValueMap::const_iterator shellIterator;
	- vnl_matrix<double> NewSignalMatrix (m_NumberTargetDirections, 2);
	- vnl_vector<double> InterpVector;
	- unsigned int shellIndex = 0;
	- // ** walking over each Voxel
	- while(!iit.IsAtEnd())
	- {
	- b = iit.Get();
	- AverageS0=0.0;
	- for(unsigned int i = 0 ; i < IndicesS0.size(); i++){
	- AverageS0 += b[IndicesS0[i]];
	- }
	- AverageS0 /= (double)IndicesS0.size();
	- out = oit.Get();
	- out.SetElement(0,AverageS0);
	-
	- shellIterator = m_BValueMap.begin();
	- shellIterator++; //skip bZeroImages
	-
	- shellIndex = 0;
	- // for each shell
	- while(shellIterator != m_BValueMap.end())
	- {
	- const IndicesVector & currentShell = shellIterator->second;
	- InterpVector.set_size(currentShell.size());
	-
	- // get the raw signal for currente shell (signal for eacht direction)
	- for(unsigned int i = 0 ; i < currentShell.size(); i++)
	- InterpVector.put(i,b[currentShell[i]]);
	-
	- // interpolate the signal using corresponding interpolationSHBasis
	- SignalVector = m_ShellInterpolationMatrixVector.at(shellIndex) * InterpVector;
	-
	- // save interpolated signal column
	- SignalMatrix.set_column(shellIndex, SignalVector);
	-
	- shellIterator++;
	- shellIndex++;
	- }
	-
	- // apply voxel wise signal manipulation functor
	- (m_Functor)(NewSignalMatrix, /const &/SignalMatrix,/const &*/ AverageS0);
	- SignalVector = NewSignalMatrix.get_column(0);
	-
	- for(unsigned int i = 1 ; i < out.Size(); i ++)
	- out.SetElement(i,SignalVector.get(i-1));
	-
	- eit.Set(NewSignalMatrix.get_column(1).mean());
	-
	- oit.Set(out);
	- ++eit;
	- ++oit;
	- ++iit;
	- }
	-}
	-
	-} // end of namespace
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkRadialMultishellToSingleshellImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkRadialMultishellToSingleshellImageFilter.h
	deleted file mode 100644
	index 79a997ff7b..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/MultishellProcessing/itkRadialMultishellToSingleshellImageFilter.h
	+++ /dev/null
	@@ -1,111 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _itk_RadialMultishellToSingleshellImageFilterr_h_
	-#define _itk_RadialMultishellToSingleshellImageFilterr_h_
	-
	-#include <itkImageToImageFilter.h>
	-#include <itkVectorImage.h>
	-#include "itkDWIVoxelFunctor.h"
	-
	-
	-namespace itk
	-{
	-
	- template <class TInputScalarType, class TOutputScalarType>
	- class RadialMultishellToSingleshellImageFilter
	- : public ImageToImageFilter<itk::VectorImage<TInputScalarType,3>, itk::VectorImage<TOutputScalarType,3> >
	- {
	-
	- public:
	-
	- typedef RadialMultishellToSingleshellImageFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageToImageFilter< itk::VectorImage<TInputScalarType,3>, itk::VectorImage<TOutputScalarType,3> > Superclass;
	- typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(RadialMultishellToSingleshellImageFilter, ImageToImageFilter)
	-
	- typedef TInputScalarType InputScalarType;
	- typedef itk::VectorImage<InputScalarType,3> InputImageType;
	- typedef typename InputImageType::PixelType InputPixelType;
	-
	- typedef TOutputScalarType OutputScalarType;
	- typedef itk::VectorImage<OutputScalarType,3> OutputImageType;
	- typedef typename OutputImageType::PixelType OutputPixelType;
	-
	- typedef OutputScalarType BaselineScalarType;
	- typedef BaselineScalarType BaselinePixelType;
	- typedef typename itk::Image<BaselinePixelType,3> BaselineImageType;
	-
	- typedef float ErrorScalarType;
	- typedef ErrorScalarType ErrorPixelType;
	- typedef typename itk::Image<ErrorPixelType,3> ErrorImageType;
	-
	- typedef vnl_vector_fixed< double, 3 > GradientDirectionType;
	- typedef itk::VectorContainer< unsigned int, GradientDirectionType > GradientDirectionContainerType;
	-
	- typedef std::vector<unsigned int> IndicesVector;
	- typedef std::map<unsigned int, IndicesVector> BValueMap;
	-
	- void SetOriginalGradientDirections(GradientDirectionContainerType::Pointer ptr){m_OriginalGradientDirections = ptr;}
	- void SetOriginalBValue(const double & val){m_OriginalBValue = val;}
	- void SetOriginalBValueMap(const BValueMap & inp){m_BValueMap = inp;}
	- void SetFunctor(DWIVoxelFunctor * functor){m_Functor = functor;}
	- GradientDirectionContainerType::Pointer GetTargetGradientDirections(){return m_TargetGradientDirections;}
	- ErrorImageType::Pointer GetErrorImage(){return m_ErrorImage;}
	-
	-
	- protected:
	- RadialMultishellToSingleshellImageFilter();
	- ~RadialMultishellToSingleshellImageFilter() {}
	-
	- void BeforeThreadedGenerateData();
	- void ThreadedGenerateData( const OutputImageRegionType &, ThreadIdType);
	-
	- GradientDirectionContainerType::Pointer m_TargetGradientDirections; ///< container for the subsampled output gradient directions
	- GradientDirectionContainerType::Pointer m_OriginalGradientDirections; ///< input gradient directions
	-
	- BValueMap m_BValueMap;
	- double m_OriginalBValue;
	-
	- std::vector<vnl_matrix< double > > m_ShellInterpolationMatrixVector;
	-
	- IndicesVector m_TargetDirectionsIndicies;
	- unsigned int m_NumberTargetDirections;
	-
	- DWIVoxelFunctor * m_Functor;
	-
	- ErrorImageType::Pointer m_ErrorImage;
	-
	- };
	-
	-
	-} // end of namespace
	-
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkRadialMultishellToSingleshellImageFilter.cpp"
	-#endif
	-
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.cpp b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.cpp
	deleted file mode 100644
	index 5efbcdb46a..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.cpp
	+++ /dev/null
	@@ -1,655 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef __itkAnalyticalDiffusionQballReconstructionImageFilter_cpp
	-#define __itkAnalyticalDiffusionQballReconstructionImageFilter_cpp
	-
	-#include <itkAnalyticalDiffusionQballReconstructionImageFilter.h>
	-#include <itkImageRegionConstIterator.h>
	-#include <itkImageRegionConstIteratorWithIndex.h>
	-#include <itkImageRegionIterator.h>
	-#include <itkArray.h>
	-#include <vnl/vnl_vector.h>
	-#include <mitkDiffusionFunctionCollection.h>
	-
	-#include <cstdio>
	-#include <locale>
	-#include <fstream>
	-#include "itkPointShell.h"
	-
	-namespace itk {
	-
	-template< class T, class TG, class TO, int ShOrder, int NrOdfDirections>
	-AnalyticalDiffusionQballReconstructionImageFilter<T,TG,TO,ShOrder,NrOdfDirections>::AnalyticalDiffusionQballReconstructionImageFilter() :
	- m_GradientDirectionContainer(nullptr),
	- m_NumberOfGradientDirections(0),
	- m_NumberOfBaselineImages(1),
	- m_Threshold(NumericTraits< ReferencePixelType >::NonpositiveMin()),
	- m_BValue(-1),
	- m_Lambda(0.0),
	- m_DirectionsDuplicated(false),
	- m_Delta1(0.001),
	- m_Delta2(0.001),
	- m_UseMrtrixBasis(false)
	-{
	- // At least 1 inputs is necessary for a vector image.
	- // For images added one at a time we need at least six
	- this->SetNumberOfRequiredInputs( 1 );
	-}
	-
	-
	-template<
	- class TReferenceImagePixelType,
	- class TGradientImagePixelType,
	- class TOdfPixelType,
	- int ShOrder,
	- int NrOdfDirections>
	-typename itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType,TGradientImagePixelType,TOdfPixelType, ShOrder,NrOdfDirections>::OdfPixelType
	-itk::AnalyticalDiffusionQballReconstructionImageFilter<TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, ShOrder, NrOdfDirections>::Normalize( OdfPixelType odf, typename NumericTraits<ReferencePixelType>::AccumulateType b0 )
	-{
	- switch( m_NormalizationMethod )
	- {
	- case QBAR_STANDARD:
	- {
	- TOdfPixelType sum = 0;
	-
	- for(int i=0; i<NrOdfDirections; i++)
	- {
	- sum += odf[i];
	- }
	- if(sum>0)
	- odf /= sum;
	-
	- return odf;
	- break;
	- }
	- case QBAR_B_ZERO_B_VALUE:
	- {
	- for(int i=0; i<NrOdfDirections; i++)
	- {
	- odf[i] = ((TOdfPixelType)log((TOdfPixelType)b0)-odf[i])/m_BValue;
	- }
	- return odf;
	- break;
	- }
	- case QBAR_B_ZERO:
	- {
	- odf *= 1.0/b0;
	- return odf;
	- break;
	- }
	- case QBAR_NONE:
	- {
	- return odf;
	- break;
	- }
	- case QBAR_ADC_ONLY:
	- {
	- for(int i=0; i<NrOdfDirections; i++)
	- {
	- odf[i] = ((TOdfPixelType)log((TOdfPixelType)b0)-odf[i])/m_BValue;
	- }
	- return odf;
	- break;
	- }
	- case QBAR_RAW_SIGNAL:
	- {
	- return odf;
	- break;
	- }
	- case QBAR_SOLID_ANGLE:
	- {
	- for(int i=0; i<NrOdfDirections; i++)
	- odf[i] = itk::Math::pi4/NrOdfDirections;
	-
	- break;
	- }
	- case QBAR_NONNEG_SOLID_ANGLE:
	- {
	- break;
	- }
	- }
	-
	- return odf;
	-}
	-
	-
	-template<
	- class TReferenceImagePixelType,
	- class TGradientImagePixelType,
	- class TOdfPixelType,
	- int ShOrder,
	- int NrOdfDirections>
	-vnl_vector<TOdfPixelType> itk::AnalyticalDiffusionQballReconstructionImageFilter<TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, ShOrder, NrOdfDirections>::PreNormalize( vnl_vector<TOdfPixelType> vec, typename NumericTraits<ReferencePixelType>::AccumulateType b0 )
	-{
	- switch( m_NormalizationMethod )
	- {
	- case QBAR_STANDARD:
	- {
	- int n = vec.size();
	- double b0f = (double)b0;
	- for(int i=0; i<n; i++)
	- {
	- vec[i] = vec[i]/b0f;
	- }
	- return vec;
	- break;
	- }
	- case QBAR_B_ZERO_B_VALUE:
	- {
	- int n = vec.size();
	- for(int i=0; i<n; i++)
	- {
	- if (vec[i]<=0)
	- vec[i] = 0.001;
	-
	- vec[i] = log(vec[i]);
	- }
	- return vec;
	- break;
	- }
	- case QBAR_B_ZERO:
	- {
	- return vec;
	- break;
	- }
	- case QBAR_NONE:
	- {
	- return vec;
	- break;
	- }
	- case QBAR_ADC_ONLY:
	- {
	- int n = vec.size();
	- for(int i=0; i<n; i++)
	- {
	- if (vec[i]<=0)
	- vec[i] = 0.001;
	-
	- vec[i] = log(vec[i]);
	- }
	- return vec;
	- break;
	- }
	- case QBAR_RAW_SIGNAL:
	- {
	- return vec;
	- break;
	- }
	- case QBAR_SOLID_ANGLE:
	- case QBAR_NONNEG_SOLID_ANGLE:
	- {
	- int n = vec.size();
	- double b0f = (double)b0;
	- for(int i=0; i<n; i++)
	- {
	- vec[i] = vec[i]/b0f;
	-
	- if (vec[i]<0)
	- vec[i] = m_Delta1;
	- else if (vec[i]<m_Delta1)
	- vec[i] = m_Delta1/2 + vec[i]vec[i]/(2m_Delta1);
	- else if (vec[i]>=1)
	- vec[i] = 1-m_Delta2/2;
	- else if (vec[i]>=1-m_Delta2)
	- vec[i] = 1-m_Delta2/2-(1-vec[i])(1-vec[i])/(2m_Delta2);
	-
	- vec[i] = log(-log(vec[i]));
	- }
	- return vec;
	- break;
	- }
	- }
	-
	- return vec;
	-}
	-
	-template< class T, class TG, class TO, int ShOrder, int NrOdfDirections>
	-void AnalyticalDiffusionQballReconstructionImageFilter<T,TG,TO,ShOrder,NrOdfDirections>::BeforeThreadedGenerateData()
	-{
	- // If we have more than 2 inputs, then each input, except the first is a
	- // gradient image. The number of gradient images must match the number of
	- // gradient directions.
	- //const unsigned int numberOfInputs = this->GetNumberOfInputs();
	-
	- // There need to be at least 6 gradient directions to be able to compute the
	- // tensor basis
	- if( m_NumberOfGradientDirections < (ShOrder*ShOrder + ShOrder + 2)/2 + ShOrder )
	- {
	- itkExceptionMacro( << "Not enough gradient directions supplied (" << m_NumberOfGradientDirections << "). At least " << (ShOrder*ShOrder + ShOrder + 2)/2 + ShOrder << " needed for SH-order " << ShOrder);
	- }
	-
	- // Input must be an itk::VectorImage.
	- std::string gradientImageClassName(
	- this->ProcessObject::GetInput(0)->GetNameOfClass());
	- if ( strcmp(gradientImageClassName.c_str(),"VectorImage") != 0 )
	- {
	- itkExceptionMacro( << "There is only one Gradient image. I expect that to be a VectorImage. " << "But its of type: " << gradientImageClassName );
	- }
	-
	- this->ComputeReconstructionMatrix();
	-
	- typename GradientImagesType::Pointer img = static_cast< GradientImagesType * >( this->ProcessObject::GetInput(0) );
	-
	- m_BZeroImage = BZeroImageType::New();
	- m_BZeroImage->SetSpacing( img->GetSpacing() ); // Set the image spacing
	- m_BZeroImage->SetOrigin( img->GetOrigin() ); // Set the image origin
	- m_BZeroImage->SetDirection( img->GetDirection() ); // Set the image direction
	- m_BZeroImage->SetLargestPossibleRegion( img->GetLargestPossibleRegion());
	- m_BZeroImage->SetBufferedRegion( img->GetLargestPossibleRegion() );
	- m_BZeroImage->Allocate();
	-
	- m_ODFSumImage = BZeroImageType::New();
	- m_ODFSumImage->SetSpacing( img->GetSpacing() ); // Set the image spacing
	- m_ODFSumImage->SetOrigin( img->GetOrigin() ); // Set the image origin
	- m_ODFSumImage->SetDirection( img->GetDirection() ); // Set the image direction
	- m_ODFSumImage->SetLargestPossibleRegion( img->GetLargestPossibleRegion());
	- m_ODFSumImage->SetBufferedRegion( img->GetLargestPossibleRegion() );
	- m_ODFSumImage->Allocate();
	-
	- m_CoefficientImage = CoefficientImageType::New();
	- m_CoefficientImage->SetSpacing( img->GetSpacing() ); // Set the image spacing
	- m_CoefficientImage->SetOrigin( img->GetOrigin() ); // Set the image origin
	- m_CoefficientImage->SetDirection( img->GetDirection() ); // Set the image direction
	- m_CoefficientImage->SetLargestPossibleRegion( img->GetLargestPossibleRegion());
	- m_CoefficientImage->SetBufferedRegion( img->GetLargestPossibleRegion() );
	- m_CoefficientImage->Allocate();
	-
	- if(m_NormalizationMethod == QBAR_SOLID_ANGLE \|\| m_NormalizationMethod == QBAR_NONNEG_SOLID_ANGLE)
	- m_Lambda = 0.0;
	-}
	-
	-template< class T, class TG, class TO, int ShOrder, int NrOdfDirections>
	-void AnalyticalDiffusionQballReconstructionImageFilter<T,TG,TO,ShOrder,NrOdfDirections>
	-::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, ThreadIdType )
	-{
	- typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetPrimaryOutput());
	-
	- ImageRegionIterator< OutputImageType > oit(outputImage, outputRegionForThread);
	- oit.GoToBegin();
	-
	- ImageRegionIterator< BZeroImageType > oit2(m_BZeroImage, outputRegionForThread);
	- oit2.GoToBegin();
	-
	- ImageRegionIterator< FloatImageType > oit3(m_ODFSumImage, outputRegionForThread);
	- oit3.GoToBegin();
	-
	- ImageRegionIterator< CoefficientImageType > oit4(m_CoefficientImage, outputRegionForThread);
	- oit4.GoToBegin();
	-
	- typedef ImageRegionConstIterator< GradientImagesType > GradientIteratorType;
	- typedef typename GradientImagesType::PixelType GradientVectorType;
	- typename GradientImagesType::Pointer gradientImagePointer = nullptr;
	-
	- // Would have liked a dynamic_cast here, but seems SGI doesn't like it
	- // The enum will ensure that an inappropriate cast is not done
	- gradientImagePointer = static_cast< GradientImagesType * >(
	- this->ProcessObject::GetInput(0) );
	-
	- GradientIteratorType git(gradientImagePointer, outputRegionForThread );
	- git.GoToBegin();
	-
	- // Compute the indicies of the baseline images and gradient images
	- std::vector<unsigned int> baselineind; // contains the indicies of
	- // the baseline images
	- std::vector<unsigned int> gradientind; // contains the indicies of
	- // the gradient images
	-
	- for(GradientDirectionContainerType::ConstIterator gdcit = this->m_GradientDirectionContainer->Begin();
	- gdcit != this->m_GradientDirectionContainer->End(); ++gdcit)
	- {
	- float bval = gdcit.Value().two_norm();
	- bval = bvalbvalm_BValue;
	- if(bval < 100)
	- baselineind.push_back(gdcit.Index());
	- else
	- gradientind.push_back(gdcit.Index());
	- }
	-
	- if( m_DirectionsDuplicated )
	- {
	- int gradIndSize = gradientind.size();
	- for(int i=0; i<gradIndSize; i++)
	- gradientind.push_back(gradientind[i]);
	- }
	-
	- while( !git.IsAtEnd() )
	- {
	- GradientVectorType b = git.Get();
	-
	- typename NumericTraits<ReferencePixelType>::AccumulateType b0 = NumericTraits<ReferencePixelType>::Zero;
	-
	- // Average the baseline image pixels
	- for(unsigned int i = 0; i < baselineind.size(); ++i)
	- {
	- b0 += b[baselineind[i]];
	- }
	- b0 /= this->m_NumberOfBaselineImages;
	-
	- OdfPixelType odf(0.0);
	-
	- typename CoefficientImageType::PixelType coeffPixel(0.0);
	- vnl_vector<TO> B(m_NumberOfGradientDirections);
	-
	- if( (b0 != 0) && (b0 >= m_Threshold) )
	- {
	- for( unsigned int i = 0; i< m_NumberOfGradientDirections; i++ )
	- {
	- B[i] = static_cast<TO>(b[gradientind[i]]);
	- }
	-
	- B = PreNormalize(B, b0);
	- if(m_NormalizationMethod == QBAR_SOLID_ANGLE)
	- {
	- vnl_vector<TO> coeffs(m_NumberCoefficients);
	- coeffs = ( m_CoeffReconstructionMatrix * B );
	- coeffs[0] += 1.0/(2.0*sqrt(itk::Math::pi));
	- odf = ( m_SphericalHarmonicBasisMatrix * coeffs ).data_block();
	- coeffPixel = coeffs.data_block();
	- }
	- else if(m_NormalizationMethod == QBAR_NONNEG_SOLID_ANGLE)
	- {
	- /** this would be the place to implement a non-negative
	- * solver for quadratic programming problem:
	- * min .5\|\| Bc-s \|\|^2 subject to -CLPc <= 4pi*ones
	- * (refer to MICCAI 2009 Goh et al. "Estimating ODFs with PDF constraints")
	- * .5\|\| Bc-s \|\|^2 == .5c'B'Bc - x'B's + .5*s's
	- */
	-
	- itkExceptionMacro( << "Nonnegative Solid Angle not yet implemented");
	- }
	- else
	- {
	- vnl_vector<TO> coeffs(m_NumberCoefficients);
	- coeffs = ( m_CoeffReconstructionMatrix * B );
	- coeffs[0] += 1.0/(2.0*sqrt(itk::Math::pi));
	- coeffPixel = coeffs.data_block();
	- odf = ( m_ReconstructionMatrix * B ).data_block();
	- }
	- odf = Normalize(odf, b0);
	- }
	-
	- oit.Set( odf );
	- oit2.Set( b0 );
	- float sum = 0;
	- for (unsigned int k=0; k<odf.Size(); k++)
	- sum += (float) odf[k];
	- oit3.Set( sum-1 );
	- oit4.Set(coeffPixel);
	- ++oit; // odf image iterator
	- ++oit3; // odf sum image iterator
	- ++oit2; // b0 image iterator
	- ++oit4; // coefficient image iterator
	- ++git; // Gradient image iterator
	- }
	-
	- std::cout << "One Thread finished reconstruction" << std::endl;
	-}
	-
	-template< class T, class TG, class TO, int ShOrder, int NrOdfDirections>
	-void AnalyticalDiffusionQballReconstructionImageFilter<T,TG,TO,ShOrder,NrOdfDirections>
	-::tofile2(vnl_matrix<float> *pA, std::string fname)
	-{
	- vnl_matrix<float> A = (*pA);
	- std::ofstream myfile;
	- std::locale C("C");
	- std::locale originalLocale = myfile.getloc();
	- myfile.imbue(C);
	-
	- myfile.open (fname.c_str());
	- myfile << "A1=[";
	- for(unsigned int i=0; i<A.rows(); i++)
	- {
	- for(unsigned int j=0; j<A.columns(); j++)
	- {
	- myfile << A(i,j) << " ";
	- if(j==A.columns()-1 && i!=A.rows()-1)
	- myfile << ";";
	- }
	- }
	- myfile << "];";
	- myfile.close();
	-
	- myfile.imbue( originalLocale );
	-}
	-
	-template< class T, class TG, class TO, int ShOrder, int NrOdfDirections>
	-void AnalyticalDiffusionQballReconstructionImageFilter<T,TG,TO,ShOrder,NrOdfDirections>::ComputeReconstructionMatrix()
	-{
	- m_NumberCoefficients = (ShOrder*ShOrder + ShOrder + 2)/2 + ShOrder;
	- if( m_NumberOfGradientDirections < m_NumberCoefficients )
	- {
	- itkExceptionMacro( << "Not enough gradient directions supplied (" << m_NumberOfGradientDirections << "). At least " << (ShOrder*ShOrder + ShOrder + 2)/2 + ShOrder << " needed for SH-order " << ShOrder);
	- }
	-
	- // Gradient preprocessing
	- {
	- // check for duplicate diffusion gradients
	- bool warning = false;
	- for(GradientDirectionContainerType::ConstIterator gdcit1 = this->m_GradientDirectionContainer->Begin();
	- gdcit1 != this->m_GradientDirectionContainer->End(); ++gdcit1)
	- {
	- for(GradientDirectionContainerType::ConstIterator gdcit2 = this->m_GradientDirectionContainer->Begin();
	- gdcit2 != this->m_GradientDirectionContainer->End(); ++gdcit2)
	- {
	- if(gdcit1.Value() == gdcit2.Value() && gdcit1.Index() != gdcit2.Index())
	- {
	- itkWarningMacro( << "Some of the Diffusion Gradients equal each other. Corresponding image data should be averaged before calling this filter." );
	- warning = true;
	- break;
	- }
	- }
	- if (warning)
	- break;
	- }
	-
	- // handle acquisition schemes where only half of the spherical
	- // shell is sampled by the gradient directions. In this case,
	- // each gradient direction is duplicated in negative direction.
	- vnl_vector<double> centerMass(3);
	- centerMass.fill(0.0);
	- int count = 0;
	- for(GradientDirectionContainerType::ConstIterator gdcit1 = this->m_GradientDirectionContainer->Begin();
	- gdcit1 != this->m_GradientDirectionContainer->End(); ++gdcit1)
	- {
	- float bval = gdcit1.Value().two_norm();
	- bval = bvalbvalm_BValue;
	- if(bval > 100)
	- {
	- centerMass += gdcit1.Value();
	- count ++;
	- }
	- }
	- centerMass /= count;
	- if(centerMass.two_norm() > 0.1)
	- {
	- m_DirectionsDuplicated = true;
	- m_NumberOfGradientDirections *= 2;
	- }
	- }
	-
	- // Create 3xM matrix Q that contains the gradient vectors in polar coordinates
	- vnl_matrix<float> Q(3, m_NumberOfGradientDirections);
	- {
	- int i = 0;
	- for(GradientDirectionContainerType::ConstIterator gdcit = this->m_GradientDirectionContainer->Begin(); gdcit != this->m_GradientDirectionContainer->End(); ++gdcit)
	- {
	- float bval = gdcit.Value().two_norm();
	- bval = bvalbvalm_BValue;
	- if(bval > 100)
	- {
	- double x = gdcit.Value().get(0);
	- double y = gdcit.Value().get(1);
	- double z = gdcit.Value().get(2);
	- double cart[3];
	- mitk::sh::Cart2Sph(x,y,z,cart);
	- Q(0,i) = cart[0];
	- Q(1,i) = cart[1];
	- Q(2,i++) = cart[2];
	- }
	- }
	- if(m_DirectionsDuplicated)
	- {
	- for(GradientDirectionContainerType::ConstIterator gdcit = this->m_GradientDirectionContainer->Begin(); gdcit != this->m_GradientDirectionContainer->End(); ++gdcit)
	- {
	- float bval = gdcit.Value().two_norm();
	- bval = bvalbvalm_BValue;
	- if(bval > 100)
	- {
	- double x = gdcit.Value().get(0);
	- double y = gdcit.Value().get(1);
	- double z = gdcit.Value().get(2);
	- double cart[3];
	- mitk::sh::Cart2Sph(x,y,z,cart);
	- Q(0,i) = cart[0];
	- Q(1,i) = cart[1];
	- Q(2,i++) = cart[2];
	- }
	- }
	- }
	- }
	-
	- // Calcualte SH basis B
	- vnl_matrix<float> L(m_NumberCoefficients,m_NumberCoefficients, 0);
	- vnl_vector<int> lj(m_NumberCoefficients);
	- vnl_matrix<float> B(m_NumberOfGradientDirections,m_NumberCoefficients);
	- for(unsigned int i=0; i<m_NumberOfGradientDirections; i++)
	- {
	- for(int k=0; k<=ShOrder; k+=2)
	- {
	- for(int m=-k; m<=k; m++)
	- {
	- int j = (k*k + k + 2)/2 + m - 1;
	- L(j,j) = -k*(k+1);
	- lj[j] = k;
	- B(i,j) = mitk::sh::Yj(m, k, Q(1,i), Q(0,i));
	- }
	- }
	- }
	-
	- vnl_matrix<float> P(m_NumberCoefficients,m_NumberCoefficients, 0);
	- for(unsigned int i=0; i<m_NumberCoefficients; i++)
	- P(i,i) = mitk::sh::legendre0(lj[i]);
	-
	- vnl_matrix<float> B_transpose(B.transpose());
	- vnl_matrix_inverse<float>* pseudoInverse = new vnl_matrix_inverse<float>( B_transpose * B + LLm_Lambda );
	- m_CoeffReconstructionMatrix = pseudoInverse->pinverse() * B_transpose;
	-
	- switch(m_NormalizationMethod)
	- {
	- case QBAR_ADC_ONLY:
	- case QBAR_RAW_SIGNAL:
	- break;
	- case QBAR_STANDARD:
	- case QBAR_B_ZERO_B_VALUE:
	- case QBAR_B_ZERO:
	- case QBAR_NONE:
	- {
	- m_CoeffReconstructionMatrix = P * m_CoeffReconstructionMatrix;
	- break;
	- }
	- case QBAR_SOLID_ANGLE:
	- {
	- m_CoeffReconstructionMatrix = (float)(1.0/(8.0itk::Math::pi)) P * L * m_CoeffReconstructionMatrix;
	- break;
	- }
	- case QBAR_NONNEG_SOLID_ANGLE:
	- break;
	- }
	-
	- // needed to calculate the ODF values from the SH coefficients
	- vnl_matrix_fixed<double, 3, NrOdfDirections>* U = itk::PointShell<NrOdfDirections, vnl_matrix_fixed<double, 3, NrOdfDirections> >::DistributePointShell();
	-
	- m_SphericalHarmonicBasisMatrix = mitk::sh::CalcShBasisForDirections(ShOrder, U->as_matrix());
	- m_ReconstructionMatrix = m_SphericalHarmonicBasisMatrix * m_CoeffReconstructionMatrix;
	-}
	-
	-template< class T, class TG, class TO, int ShOrder, int NrOdfDirections>
	-void AnalyticalDiffusionQballReconstructionImageFilter<T,TG,TO,ShOrder,NrOdfDirections>
	-::SetGradientImage(const GradientDirectionContainerType *gradientDirection,
	- const GradientImagesType *gradientImage )
	-{
	- // Copy Gradient Direction Container
	- this->m_GradientDirectionContainer = GradientDirectionContainerType::New();
	- for(GradientDirectionContainerType::ConstIterator it = gradientDirection->Begin();
	- it != gradientDirection->End(); it++)
	- {
	- this->m_GradientDirectionContainer->push_back(it.Value());
	- }
	-
	- if (m_BValue<0)
	- mitkThrow() << "B-value needs to be set before gradient image! " << m_BValue;
	-
	- unsigned int numImages = gradientDirection->Size();
	- this->m_NumberOfBaselineImages = 0;
	- for(GradientDirectionContainerType::Iterator it = this->m_GradientDirectionContainer->Begin();
	- it != this->m_GradientDirectionContainer->End(); it++)
	- {
	- float bval = it.Value().two_norm();
	- bval = bvalbvalm_BValue;
	- if(bval < 100)
	- {
	- this->m_NumberOfBaselineImages++;
	- }
	- else // Normalize non-zero gradient directions
	- {
	- it.Value() = it.Value() / it.Value().two_norm();
	- }
	- }
	-
	- if (this->m_NumberOfBaselineImages==0)
	- itkExceptionMacro("No baseline image detected (no b-zero image)");
	-
	- this->m_NumberOfGradientDirections = numImages - this->m_NumberOfBaselineImages;
	-
	- // ensure that the gradient image we received has as many components as
	- // the number of gradient directions
	- if( gradientImage->GetVectorLength() != this->m_NumberOfBaselineImages + m_NumberOfGradientDirections )
	- {
	- itkExceptionMacro( << m_NumberOfGradientDirections << " gradients + " << this->m_NumberOfBaselineImages
	- << "baselines = " << m_NumberOfGradientDirections + this->m_NumberOfBaselineImages
	- << " directions specified but image has " << gradientImage->GetVectorLength()
	- << " components.");
	- }
	-
	- this->ProcessObject::SetNthInput( 0, const_cast< GradientImagesType* >(gradientImage) );
	-}
	-
	-template< class T, class TG, class TO, int ShOrder, int NrOdfDirections>
	-void AnalyticalDiffusionQballReconstructionImageFilter<T,TG,TO,ShOrder,NrOdfDirections>
	-::PrintSelf(std::ostream& os, Indent indent) const
	-{
	- std::locale C("C");
	- std::locale originalLocale = os.getloc();
	- os.imbue(C);
	-
	- Superclass::PrintSelf(os,indent);
	-
	- os << indent << "OdfReconstructionMatrix: " << m_ReconstructionMatrix << std::endl;
	- if ( m_GradientDirectionContainer )
	- os << indent << "GradientDirectionContainer: " << m_GradientDirectionContainer << std::endl;
	- else
	- os << indent << "GradientDirectionContainer: (Gradient directions not set)" << std::endl;
	-
	- os << indent << "NumberOfGradientDirections: " << m_NumberOfGradientDirections << std::endl;
	- os << indent << "NumberOfBaselineImages: " << m_NumberOfBaselineImages << std::endl;
	- os << indent << "Threshold for reference B0 image: " << m_Threshold << std::endl;
	- os << indent << "BValue: " << m_BValue << std::endl;
	- os.imbue( originalLocale );
	-}
	-
	-}
	-
	-#endif // __itkAnalyticalDiffusionQballReconstructionImageFilter_cpp
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.h
	deleted file mode 100644
	index d72320609f..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.h
	+++ /dev/null
	@@ -1,265 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkAnalyticalDiffusionQballReconstructionImageFilter_h_
	-#define __itkAnalyticalDiffusionQballReconstructionImageFilter_h_
	-
	-#include "itkImageToImageFilter.h"
	-#include "vnl/vnl_vector_fixed.h"
	-#include "vnl/vnl_matrix.h"
	-#include "vnl/algo/vnl_svd.h"
	-#include "itkVectorContainer.h"
	-#include "itkVectorImage.h"
	-
	-
	-namespace itk{
	-/** \class AnalyticalDiffusionQballReconstructionImageFilter
	- * \brief This class takes as input one or more reference image (acquired in the
	- * absence of diffusion sensitizing gradients) and 'n' diffusion
	- * weighted images and their gradient directions and computes an image of
	- * orientation distribution function coefficients in a spherical harmonic basis.
	- *
	- * \par Inputs and Usage
	- * \par
	- * When you have the 'n' gradient and one or more reference images in a single
	- * multi-component image (VectorImage), you can specify the images as
	- * \code
	- * filter->SetGradientImage( directionsContainer, vectorImage );
	- * \endcode
	- * Note that this method is used to specify both the reference and gradient images.
	- * This is convenient when the DWI images are read in using the
	- * <a href="http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format">NRRD</a>
	- * format. Like the Nrrd format, the reference images are those components of the
	- * vectorImage whose gradient direction is (0,0,0). If more than one reference image
	- * is present, they are averaged prior to the reconstruction.
	- *
	- * \par Outputs
	- * The output image is an image of vectors that must be understood as ODFs:
	- * \code
	- * Image< Vector< TPixelType, OdfNrDirections >, 3 >
	- * \endcode
	- *
	- * \par Parameters
	- * \li Threshold - Threshold on the reference image data. The output ODF will
	- * be a null pdf for pixels in the reference image that have a value less
	- * than this.
	- * \li BValue - See the documentation of SetBValue().
	- * \li At least 6 gradient images must be specified for the filter to be able
	- * to run. If the input gradient directions g_i are majorly sampled on one half
	- * of the sqhere, then each input image I_i will be duplicated and assign -g_i
	- * in order to guarantee stability of the algorithm.
	- * \li OdfDirections - directions of resulting orientation distribution function
	- * \li EquatorNrSamplingPoints - number of sampling points on equator when
	- * performing Funk Radeon Transform (FRT)
	- * \li BasisFunctionCenters - the centers of the basis functions are used for
	- * the sRBF (spherical radial basis functions interpolation). If not set, they
	- * will be defaulted to equal m_EquatorNrSamplingPoints
	- *
	- * \par Template parameters
	- * The class is templated over
	- * \li the pixel type of the reference and gradient images
	- * (expected to be scalar data types)
	- * \li the internal representation of the ODF pixels (double, float etc).
	- * \li the number of OdfDirections
	- * \li the number of basis function centers for the sRBF
	- *
	- * \par References:
	- * \li<a href="http://www3.interscience.wiley.com/cgi-bin/fulltext/109800293/PDFSTART">[1]</a>
	- * <em>Tuch DS,
	- * "Q-ball imaging", Magn Reson Med. 2004 Dec;52(6):1358-72.</em>
	- *
	- */
	-
	-template< class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int ShOrder, int NrOdfDirections>
	-class AnalyticalDiffusionQballReconstructionImageFilter : public ImageToImageFilter< Image< TReferenceImagePixelType, 3 >, Image< Vector< TOdfPixelType, NrOdfDirections >, 3 > >
	-{
	-
	-public:
	-
	- enum Normalization {
	- QBAR_STANDARD,
	- QBAR_B_ZERO_B_VALUE,
	- QBAR_B_ZERO,
	- QBAR_NONE,
	- QBAR_ADC_ONLY,
	- QBAR_RAW_SIGNAL,
	- QBAR_SOLID_ANGLE,
	- QBAR_NONNEG_SOLID_ANGLE
	- };
	-
	- typedef AnalyticalDiffusionQballReconstructionImageFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageToImageFilter< Image< TReferenceImagePixelType, 3>,
	- Image< Vector< TOdfPixelType, NrOdfDirections >, 3 > > Superclass;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(AnalyticalDiffusionQballReconstructionImageFilter, ImageToImageFilter)
	-
	- typedef TReferenceImagePixelType ReferencePixelType;
	-
	- typedef TGradientImagePixelType GradientPixelType;
	-
	- typedef Vector< TOdfPixelType, NrOdfDirections > OdfPixelType;
	-
	- typedef TOdfPixelType BZeroPixelType;
	-
	- /** Reference image data, This image is aquired in the absence
	- * of a diffusion sensitizing field gradient */
	- typedef typename Superclass::InputImageType ReferenceImageType;
	-
	- typedef Image< OdfPixelType, 3 > OdfImageType;
	-
	- typedef OdfImageType OutputImageType;
	-
	- typedef Image< Vector< TOdfPixelType, (ShOrder*ShOrder + ShOrder + 2)/2 + ShOrder >, 3 > CoefficientImageType;
	-
	- typedef Image< BZeroPixelType, 3 > BZeroImageType;
	-
	- typedef typename Superclass::OutputImageRegionType
	- OutputImageRegionType;
	-
	- /** Typedef defining one (of the many) gradient images. */
	- typedef Image< GradientPixelType, 3 > GradientImageType;
	-
	- /** An alternative typedef defining one (of the many) gradient images.
	- * It will be assumed that the vectorImage has the same dimension as the
	- * Reference image and a vector length parameter of \c n (number of
	- * gradient directions)*/
	- typedef VectorImage< GradientPixelType, 3 > GradientImagesType;
	-
	- /** Holds each magnetic field gradient used to acquire one DWImage */
	- typedef vnl_vector_fixed< double, 3 > GradientDirectionType;
	-
	- /** Container to hold gradient directions of the 'n' DW measurements */
	- typedef VectorContainer< unsigned int,
	- GradientDirectionType > GradientDirectionContainerType;
	-
	- /** set method to add gradient directions and its corresponding
	- * image. The image here is a VectorImage. The user is expected to pass the
	- * gradient directions in a container. The ith element of the container
	- * corresponds to the gradient direction of the ith component image the
	- * VectorImage. For the baseline image, a vector of all zeros
	- * should be set.*/
	- void SetGradientImage( const GradientDirectionContainerType *,
	- const GradientImagesType *image);
	-
	- /** Get reference image */
	- virtual ReferenceImageType * GetReferenceImage()
	- { return ( static_cast< ReferenceImageType *>(this->ProcessObject::GetInput(0)) ); }
	-
	- /** Return the gradient direction. idx is 0 based */
	- virtual GradientDirectionType GetGradientDirection( unsigned int idx) const
	- {
	- if( idx >= m_NumberOfGradientDirections )
	- itkExceptionMacro( << "Gradient direction " << idx << "does not exist" );
	- return m_GradientDirectionContainer->ElementAt( idx+1 );
	- }
	-
	- static void tofile2(vnl_matrix<float> *A, std::string fname);
	-
	- OdfPixelType Normalize(OdfPixelType odf, typename NumericTraits<ReferencePixelType>::AccumulateType b0 );
	- vnl_vector<TOdfPixelType> PreNormalize( vnl_vector<TOdfPixelType> vec, typename NumericTraits<ReferencePixelType>::AccumulateType b0 );
	-
	- /** Threshold on the reference image data. The output ODF will be a null
	- * pdf for pixels in the reference image that have a value less than this
	- * threshold. */
	- itkSetMacro( Threshold, ReferencePixelType )
	- itkGetMacro( Threshold, ReferencePixelType )
	-
	- itkSetMacro( NormalizationMethod, Normalization)
	- itkGetMacro( NormalizationMethod, Normalization )
	-
	- typedef Image<float, 3> FloatImageType;
	- itkGetMacro( BZeroImage, typename BZeroImageType::Pointer)
	- itkGetMacro( ODFSumImage, typename FloatImageType::Pointer)
	- itkGetMacro( CoefficientImage, typename CoefficientImageType::Pointer)
	-
	- itkSetMacro( BValue, float)
	- itkSetMacro( Lambda, double )
	- itkGetMacro( Lambda, double )
	-
	- itkSetMacro( UseMrtrixBasis, bool )
	-
	-#ifdef ITK_USE_CONCEPT_CHECKING
	- /** Begin concept checking */
	- itkConceptMacro(ReferenceEqualityComparableCheck,
	- (Concept::EqualityComparable<ReferencePixelType>));
	- itkConceptMacro(TensorEqualityComparableCheck,
	- (Concept::EqualityComparable<OdfPixelType>));
	- itkConceptMacro(GradientConvertibleToDoubleCheck,
	- (Concept::Convertible<GradientPixelType, double>));
	- itkConceptMacro(DoubleConvertibleToTensorCheck,
	- (Concept::Convertible<double, OdfPixelType>));
	- itkConceptMacro(GradientReferenceAdditiveOperatorsCheck,
	- (Concept::AdditiveOperators<GradientPixelType, GradientPixelType,
	- ReferencePixelType>));
	- itkConceptMacro(ReferenceOStreamWritableCheck,
	- (Concept::OStreamWritable<ReferencePixelType>));
	- itkConceptMacro(TensorOStreamWritableCheck,
	- (Concept::OStreamWritable<OdfPixelType>));
	- /** End concept checking */
	-#endif
	-
	-protected:
	- AnalyticalDiffusionQballReconstructionImageFilter();
	- ~AnalyticalDiffusionQballReconstructionImageFilter() override {};
	- void PrintSelf(std::ostream& os, Indent indent) const override;
	-
	- void ComputeReconstructionMatrix();
	- void BeforeThreadedGenerateData() override;
	- void ThreadedGenerateData( const
	- OutputImageRegionType &outputRegionForThread, ThreadIdType) override;
	-
	-private:
	-
	- vnl_matrix< float > m_ReconstructionMatrix;
	- vnl_matrix< float > m_CoeffReconstructionMatrix;
	- vnl_matrix< float > m_SphericalHarmonicBasisMatrix;
	- /** container to hold gradient directions */
	- GradientDirectionContainerType::Pointer m_GradientDirectionContainer;
	- /** Number of gradient measurements */
	- unsigned int m_NumberOfGradientDirections;
	- /** Number of baseline images */
	- unsigned int m_NumberOfBaselineImages;
	- /** Threshold on the reference image data */
	- ReferencePixelType m_Threshold;
	- /** LeBihan's b-value for normalizing tensors */
	- float m_BValue;
	- typename BZeroImageType::Pointer m_BZeroImage;
	- double m_Lambda;
	- bool m_DirectionsDuplicated;
	- Normalization m_NormalizationMethod;
	- unsigned int m_NumberCoefficients;
	- FloatImageType::Pointer m_ODFSumImage;
	- typename CoefficientImageType::Pointer m_CoefficientImage;
	- TOdfPixelType m_Delta1;
	- TOdfPixelType m_Delta2;
	- bool m_UseMrtrixBasis;
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkAnalyticalDiffusionQballReconstructionImageFilter.cpp"
	-#endif
	-
	-#endif //__itkAnalyticalDiffusionQballReconstructionImageFilter_h_
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkBallAndSticksImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkBallAndSticksImageFilter.h
	deleted file mode 100644
	index a60936bc66..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkBallAndSticksImageFilter.h
	+++ /dev/null
	@@ -1,104 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkBallAndSticksImageFilter_h_
	-#define __itkBallAndSticksImageFilter_h_
	-
	-#include "itkImageToImageFilter.h"
	-#include "itkVectorImage.h"
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <vnl/algo/vnl_levenberg_marquardt.h>
	-#include <mitkOdfImage.h>
	-#include <itkDiffusionTensor3D.h>
	-#include <itkDiffusionTensor3DReconstructionImageFilter.h>
	-#include <cmath>
	-#include <mitkTensorImage.h>
	-
	-#define NUM_TENSORS 2
	-
	-namespace itk{
	-/** \class BallAndSticksImageFilter
	- */
	-
	-template< class TInPixelType, class TOutPixelType >
	-class BallAndSticksImageFilter :
	- public ImageToImageFilter< VectorImage< TInPixelType, 3 >, Image< TOutPixelType, 3 > >
	-{
	-
	-public:
	-
	- typedef BallAndSticksImageFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageToImageFilter< VectorImage< TInPixelType, 3 >, Image< TOutPixelType, 3 > > Superclass;
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionType GradientDirectionType;
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionsContainerType GradientContainerType;
	- typedef itk::Image< unsigned char, 3> ItkUcharImageType;
	- typedef itk::Image< float, 4 > PeakImageType;
	-
	- typedef itk::DiffusionTensor3DReconstructionImageFilter< TInPixelType, TInPixelType, float > TensorRecFilterType;
	- typedef mitk::TensorImage::PixelType TensorType;
	- typedef mitk::TensorImage::ItkTensorImageType TensorImageType;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(BallAndSticksImageFilter, ImageToImageFilter)
	-
	- typedef typename Superclass::InputImageType InputImageType;
	- typedef typename Superclass::OutputImageType OutputImageType;
	- typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
	-
	- itkSetMacro( MaskImage, ItkUcharImageType::Pointer )
	- itkSetMacro( B_value, double )
	- itkSetMacro( GradientDirections, GradientContainerType::Pointer )
	- itkGetMacro( PeakImage, PeakImageType::Pointer )
	- itkGetMacro( OutDwi, typename InputImageType::Pointer )
	-
	- protected:
	- BallAndSticksImageFilter();
	- ~BallAndSticksImageFilter() {}
	- void PrintSelf(std::ostream& os, Indent indent) const override;
	-
	- void BeforeThreadedGenerateData() override;
	- void ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, ThreadIdType) override;
	-
	-
	- double m_B_value;
	- std::vector<double> m_B_values;
	- std::vector<int> m_WeightedIndices;
	- std::vector<int> m_UnWeightedIndices;
	- GradientContainerType::Pointer m_GradientDirections;
	-
	- ItkUcharImageType::Pointer m_MaskImage;
	- PeakImageType::Pointer m_PeakImage;
	- TensorImageType::Pointer m_TensorImage;
	- typename InputImageType::Pointer m_OutDwi;
	-
	- vnl_vector<double> FitSingleVoxel( const typename InputImageType::PixelType &input, const typename InputImageType::IndexType &idx);
	-
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkBallAndSticksImageFilter.txx"
	-#endif
	-
	-#endif //__itkBallAndSticksImageFilter_h_
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkBallAndSticksImageFilter.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkBallAndSticksImageFilter.txx
	deleted file mode 100644
	index c708ae2170..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkBallAndSticksImageFilter.txx
	+++ /dev/null
	@@ -1,252 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkBallAndSticksImageFilter_txx
	-#define __itkBallAndSticksImageFilter_txx
	-
	-#include <time.h>
	-#include <stdio.h>
	-#include <stdlib.h>
	-
	-#define _USE_MATH_DEFINES
	-#include <math.h>
	-
	-#include "itkImageRegionConstIterator.h"
	-#include "itkImageRegionConstIteratorWithIndex.h"
	-#include "itkImageRegionIterator.h"
	-#include <mitkBallStickFitter.h>
	-
	-
	-namespace itk {
	-
	-
	-template< class TInPixelType, class TOutPixelType >
	-BallAndSticksImageFilter< TInPixelType, TOutPixelType>
	-::BallAndSticksImageFilter()
	- : m_B_value(0)
	-{
	- this->SetNumberOfRequiredInputs( 1 );
	-}
	-
	-template< class TInPixelType, class TOutPixelType >
	-void
	-BallAndSticksImageFilter< TInPixelType, TOutPixelType>
	-::BeforeThreadedGenerateData()
	-{
	- typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0));
	- outputImage->FillBuffer(0.0);
	-
	- m_UnWeightedIndices.clear();
	- m_WeightedIndices.clear();
	- m_B_values.clear();
	-
	- for (unsigned int i=0; i<m_GradientDirections->Size(); i++)
	- {
	- GradientDirectionType g = m_GradientDirections->GetElement(i);
	- double twonorm = g.two_norm();
	- double b = m_B_valuetwonormtwonorm;
	- m_B_values.push_back(b);
	-
	- if (b>100)
	- m_WeightedIndices.push_back(i);
	- else
	- m_UnWeightedIndices.push_back(i);
	- }
	-
	- if (m_UnWeightedIndices.empty())
	- mitkThrow() << "Unweighted (b=0 s/mm²) image volume missing!";
	-
	-
	- itk::Vector<double, 3> spacing3 = outputImage->GetSpacing();
	- itk::Point<float, 3> origin3 = outputImage->GetOrigin();
	- itk::Matrix<double, 3, 3> direction3 = outputImage->GetDirection();
	- itk::ImageRegion<3> imageRegion3 = outputImage->GetLargestPossibleRegion();
	-
	- itk::Vector<double, 4> spacing4;
	- itk::Point<float, 4> origin4;
	- itk::Matrix<double, 4, 4> direction4;
	- itk::ImageRegion<4> imageRegion4;
	-
	- spacing4[0] = spacing3[0]; spacing4[1] = spacing3[1]; spacing4[2] = spacing3[2]; spacing4[3] = 1;
	- origin4[0] = origin3[0]; origin4[1] = origin3[1]; origin4[2] = origin3[2]; origin4[3] = 0;
	- for (int r=0; r<3; r++)
	- for (int c=0; c<3; c++)
	- direction4[r][c] = direction3[r][c];
	- direction4[3][3] = 1;
	- imageRegion4.SetSize(0, imageRegion3.GetSize()[0]);
	- imageRegion4.SetSize(1, imageRegion3.GetSize()[1]);
	- imageRegion4.SetSize(2, imageRegion3.GetSize()[2]);
	- imageRegion4.SetSize(3, 3);
	-
	- m_PeakImage = PeakImageType::New();
	- m_PeakImage->SetSpacing( spacing4 );
	- m_PeakImage->SetOrigin( origin4 );
	- m_PeakImage->SetDirection( direction4 );
	- m_PeakImage->SetRegions( imageRegion4 );
	- m_PeakImage->Allocate();
	- m_PeakImage->FillBuffer(0.0);
	-
	- m_OutDwi = InputImageType::New();
	- m_OutDwi->SetSpacing( spacing3 );
	- m_OutDwi->SetOrigin( origin3 );
	- m_OutDwi->SetDirection( direction3 );
	- m_OutDwi->SetRegions( imageRegion3 );
	- m_OutDwi->SetVectorLength(m_GradientDirections->Size());
	- m_OutDwi->Allocate();
	-
	- MITK_INFO << "Initial tensor fit";
	- typename InputImageType::Pointer inputImagePointer = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) );
	- typename TensorRecFilterType::Pointer tensorReconstructionFilter = TensorRecFilterType::New();
	- tensorReconstructionFilter->SetBValue( m_B_value );
	- tensorReconstructionFilter->SetGradientImage( m_GradientDirections, inputImagePointer );
	- tensorReconstructionFilter->Update();
	- m_TensorImage = tensorReconstructionFilter->GetOutput();
	-}
	-
	-template< class TInPixelType, class TOutPixelType >
	-vnl_vector<double>
	-BallAndSticksImageFilter< TInPixelType, TOutPixelType>::FitSingleVoxel( const typename InputImageType::PixelType &input, const typename InputImageType::IndexType &idx)
	-{
	- double S0 = 0;
	- for (auto i : m_UnWeightedIndices)
	- S0 += input[i];
	- S0 /= m_UnWeightedIndices.size();
	-
	- // Linear tensor fit
	- double md = 0.001;
	- double f = 0.5;
	- double theta = 0;
	- double phi = 0;
	- {
	- TensorType tensor = m_TensorImage->GetPixel(idx);
	- TensorType::EigenValuesArrayType eigenvalues;
	- TensorType::EigenVectorsMatrixType eigenvectors;
	- tensor.ComputeEigenAnalysis(eigenvalues, eigenvectors);
	- vnl_vector_fixed<double,3> ev;
	- ev[0] = eigenvectors(2, 0);
	- ev[1] = eigenvectors(2, 1);
	- ev[2] = eigenvectors(2, 2);
	- if (ev.magnitude()>mitk::eps)
	- ev.normalize();
	- else
	- ev.fill(0.0);
	-
	- md = fabs(eigenvalues[0]+eigenvalues[1]+eigenvalues[2])/3;
	- f = tensor.GetFractionalAnisotropy();
	- if (f<0.1)
	- f = 0.1;
	- else if (f>0.9)
	- f = 0.9;
	-
	- mitk::AbstractFitter::Cart2Sph(ev, theta, phi);
	- }
	-
	- int num_params = 4; // f, d, phi, theta
	-
	- vnl_vector<double> x; x.set_size(num_params); x.fill(0.0);
	- x[0] = f; // f (volume fraction)
	- x[1] = md; // d
	- x[2] = theta;
	- x[3] = phi;
	-
	- mitk::BallStickFitter bs_fit(num_params, m_GradientDirections->size());
	- bs_fit.set_S0(S0);
	- bs_fit.set_weightedIndices(m_WeightedIndices);
	- bs_fit.set_bvalues(m_B_values);
	- bs_fit.set_gradient_directions(m_GradientDirections);
	- bs_fit.set_measurements(input);
	-
	- vnl_levenberg_marquardt lm(bs_fit);
	- lm.minimize(x);
	- return x;
	-}
	-
	-template< class TInPixelType, class TOutPixelType >
	-void
	-BallAndSticksImageFilter< TInPixelType, TOutPixelType>
	-::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, ThreadIdType )
	-{
	- typename OutputImageType::Pointer outputImage =
	- static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0));
	-
	- ImageRegionIterator< OutputImageType > oit(outputImage, outputRegionForThread);
	- oit.GoToBegin();
	-
	- typedef ImageRegionConstIterator< InputImageType > InputIteratorType;
	- typename InputImageType::Pointer inputImagePointer = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) );
	-
	- InputIteratorType git( inputImagePointer, outputRegionForThread );
	- git.GoToBegin();
	- while( !git.IsAtEnd() )
	- {
	- typename InputImageType::PixelType pix = git.Get();
	- vnl_vector<double> x = FitSingleVoxel(pix, git.GetIndex());
	-
	- /// PEAKS
	- PeakImageType::IndexType idx4;
	- idx4[0] = oit.GetIndex()[0];
	- idx4[1] = oit.GetIndex()[1];
	- idx4[2] = oit.GetIndex()[2];
	-
	- oit.Set( x[0] );
	- vnl_vector_fixed<double,3> dir;
	- mitk::AbstractFitter::Sph2Cart(dir, x[2], x[3]);
	-
	- idx4[3] = 0;
	- m_PeakImage->SetPixel(idx4, dir[0]);
	- idx4[3] = 1;
	- m_PeakImage->SetPixel(idx4, dir[1]);
	- idx4[3] = 2;
	- m_PeakImage->SetPixel(idx4, dir[2]);
	-
	- /// DWI from ball-stick
	- typename InputImageType::PixelType dPix; dPix.SetSize(m_GradientDirections->Size()); dPix.Fill(0.0);
	- for (unsigned int i=0; i<m_GradientDirections->Size(); i++)
	- {
	- GradientDirectionType g = m_GradientDirections->GetElement(i);
	- double twonorm = g.two_norm();
	- double b = m_B_valuetwonormtwonorm;
	- g.normalize();
	-
	- double s_iso = 1000 * std::exp(-b * x[1]);
	-
	- double dot = dot_product(g, dir);
	- double s_aniso = 1000 * std::exp(-b * x[1] * dot*dot );
	-
	- double approx = (1-x[0])s_iso + x[0]s_aniso;
	-
	- dPix[i] = approx;
	- }
	- m_OutDwi->SetPixel(oit.GetIndex(), dPix);
	-
	- ++oit;
	- ++git;
	- }
	-
	- std::cout << "One Thread finished calculation" << std::endl;
	-}
	-
	-template< class TInPixelType, class TOutPixelType >
	-void
	-BallAndSticksImageFilter< TInPixelType, TOutPixelType>
	-::PrintSelf(std::ostream& os, Indent indent) const
	-{
	- Superclass::PrintSelf(os,indent);
	-}
	-
	-}
	-
	-#endif // __itkBallAndSticksImageFilter_txx
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.cpp b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.cpp
	deleted file mode 100644
	index 5dde370903..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.cpp
	+++ /dev/null
	@@ -1,781 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef __itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter_cpp
	-#define __itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter_cpp
	-
	-#include "itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.h"
	-#include "itkImageRegionConstIterator.h"
	-#include "itkImageRegionConstIteratorWithIndex.h"
	-#include "itkImageRegionIterator.h"
	-
	-#include "vnl/vnl_matrix.h"
	-#include "vnl/algo/vnl_symmetric_eigensystem.h"
	-
	-#include "itkRegularizedIVIMReconstructionFilter.h"
	-
	-#include <mitkLogMacros.h>
	-
	-#define IVIM_FOO -100000
	-
	-namespace itk {
	-
	-
	-template< class TIn, class TOut>
	-DiffusionIntravoxelIncoherentMotionReconstructionImageFilter<TIn, TOut>
	-::DiffusionIntravoxelIncoherentMotionReconstructionImageFilter() :
	- m_GradientDirectionContainer(nullptr),
	- m_Method(IVIM_DSTAR_FIX),
	- m_FitDStar(true),
	- m_Verbose(false)
	-{
	- this->SetNumberOfRequiredInputs( 1 );
	-
	- this->SetNumberOfRequiredOutputs( 3 );
	- typename OutputImageType::Pointer outputPtr1 = OutputImageType::New();
	- this->SetNthOutput(0, outputPtr1.GetPointer());
	- typename OutputImageType::Pointer outputPtr2 = OutputImageType::New();
	- this->SetNthOutput(1, outputPtr2.GetPointer());
	- typename OutputImageType::Pointer outputPtr3 = OutputImageType::New();
	- this->SetNthOutput(2, outputPtr3.GetPointer());
	-}
	-
	-
	-
	-template< class TIn, class TOut>
	-void DiffusionIntravoxelIncoherentMotionReconstructionImageFilter<TIn, TOut>
	-::BeforeThreadedGenerateData()
	-{
	-
	- // Input must be an itk::VectorImage.
	- std::string gradientImageClassName(
	- this->ProcessObject::GetInput(0)->GetNameOfClass());
	- if ( strcmp(gradientImageClassName.c_str(),"VectorImage") != 0 )
	- {
	- itkExceptionMacro( <<
	- "There is only one Gradient image. I expect that to be a VectorImage. "
	- << "But its of type: " << gradientImageClassName );
	- }
	-
	- // Compute the indicies of the baseline images and gradient images
	- // If no b=0 mm/s² gradients ar found, the next lowest b-value is used.
	- GradientDirectionContainerType::ConstIterator gdcit = this->m_GradientDirectionContainer->Begin();
	- double minNorm = itk::NumericTraits<double>::max();
	- while( gdcit != this->m_GradientDirectionContainer->End() )
	- {
	- double norm = gdcit.Value().one_norm();
	- if (norm<minNorm)
	- minNorm = norm;
	- ++gdcit;
	- }
	- minNorm += 0.001;
	- gdcit = this->m_GradientDirectionContainer->Begin();
	- while( gdcit != this->m_GradientDirectionContainer->End() )
	- {
	- if(gdcit.Value().one_norm() <= minNorm)
	- {
	- m_Snap.baselineind.push_back(gdcit.Index());
	- }
	- else
	- {
	- m_Snap.gradientind.push_back(gdcit.Index());
	- double twonorm = gdcit.Value().two_norm();
	- m_Snap.bvals.push_back( m_BValuetwonormtwonorm );
	- }
	- ++gdcit;
	- }
	- if (m_Snap.gradientind.size()==0)
	- itkExceptionMacro("Only one b-value supplied. At least two needed for IVIM fit.");
	-
	- // check sind die grad und base gleichlang? alle grad gerade und base ungerade? dann iterierende aufnahme!!
	- m_Snap.iterated_sequence = false;
	- if(m_Snap.baselineind.size() == m_Snap.gradientind.size())
	- {
	- int size = m_Snap.baselineind.size();
	- int sum_b = 0, sum_g = 0;
	- for(int i=0; i<size; i++)
	- {
	- sum_b += m_Snap.baselineind.at(i) % 2;
	- sum_g += m_Snap.gradientind.at(i) % 2;
	- }
	- if( (sum_b == size \|\| sum_b == 0)
	- && (sum_g == size \|\| sum_g == 0) )
	- {
	- m_Snap.iterated_sequence = true;
	- if(m_Verbose)
	- {
	- MITK_INFO << "Iterating b0 and diffusion weighted aquisition detected. Weighting each weighted measurement with its own b0.";
	- }
	- }
	- }
	-
	- // number of measurements
	- m_Snap.N = m_Snap.gradientind.size();
	-
	- // bvalue array
	- m_Snap.bvalues.set_size(m_Snap.N);
	- for(int i=0; i<m_Snap.N; i++)
	- {
	- m_Snap.bvalues[i] = m_Snap.bvals.at(i);
	- }
	-
	- if(m_Verbose)
	- {
	- std::cout << "ref bval: " << m_BValue << "; b-values: ";
	- for(int i=0; i<m_Snap.N; i++)
	- {
	- std::cout << m_Snap.bvalues[i] << "; ";
	- }
	- std::cout << std::endl;
	- }
	-
	- // extract bvals higher than threshold
	- if(m_Method == IVIM_D_THEN_DSTAR \|\| m_Method == IVIM_LINEAR_D_THEN_F \|\| m_Method == IVIM_REGULARIZED)
	- {
	- for(int i=0; i<m_Snap.N; i++)
	- {
	- if(m_Snap.bvalues[i]>m_BThres)
	- {
	- m_Snap.high_indices.push_back(i);
	- }
	- }
	- }
	- m_Snap.Nhigh = m_Snap.high_indices.size();
	- m_Snap.high_bvalues.set_size(m_Snap.Nhigh);
	- m_Snap.high_meas.set_size(m_Snap.Nhigh);
	- for(int i=0; i<m_Snap.Nhigh; i++)
	- {
	- m_Snap.high_bvalues[i] = m_Snap.bvalues[m_Snap.high_indices.at(i)];
	- }
	-
	-}
	-
	-template< class TIn, class TOut>
	-MeasAndBvals DiffusionIntravoxelIncoherentMotionReconstructionImageFilter<TIn, TOut>
	-::ApplyS0Threshold(vnl_vector<double> &meas, vnl_vector<double> &bvals)
	-{
	- std::vector<double> newmeas;
	- std::vector<double> newbvals;
	-
	- int N = meas.size();
	- for(int i=0; i<N; i++)
	- {
	- if( meas[i] != IVIM_FOO )
	- {
	- newmeas.push_back(meas[i]);
	- newbvals.push_back(bvals[i]);
	- }
	- }
	-
	- MeasAndBvals retval;
	-
	- retval.N = newmeas.size();
	-
	- retval.meas.set_size(retval.N);
	- for(size_t i=0; i<newmeas.size(); i++)
	- {
	- retval.meas[i] = newmeas[i];
	- }
	-
	- retval.bvals.set_size(retval.N);
	- for(size_t i=0; i<newbvals.size(); i++)
	- {
	- retval.bvals[i] = newbvals[i];
	- }
	-
	- return retval;
	-}
	-
	-template< class TIn, class TOut>
	-void DiffusionIntravoxelIncoherentMotionReconstructionImageFilter<TIn, TOut>
	-::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread,
	- ThreadIdType )
	-{
	-
	- typename OutputImageType::Pointer outputImage =
	- static_cast< OutputImageType * >(this->ProcessObject::GetPrimaryOutput());
	- ImageRegionIterator< OutputImageType > oit(outputImage, outputRegionForThread);
	- oit.GoToBegin();
	-
	- typename OutputImageType::Pointer dImage =
	- static_cast< OutputImageType * >(this->ProcessObject::GetOutput(1));
	- ImageRegionIterator< OutputImageType > oit1(dImage, outputRegionForThread);
	- oit1.GoToBegin();
	-
	- typename OutputImageType::Pointer dstarImage =
	- static_cast< OutputImageType * >(this->ProcessObject::GetOutput(2));
	- ImageRegionIterator< OutputImageType > oit2(dstarImage, outputRegionForThread);
	- oit2.GoToBegin();
	-
	- typedef ImageRegionConstIterator< InputImageType > InputIteratorType;
	- typedef typename InputImageType::PixelType InputVectorType;
	- typename InputImageType::Pointer inputImagePointer = nullptr;
	-
	- // Would have liked a dynamic_cast here, but seems SGI doesn't like it
	- // The enum will DiffusionIntravoxelIncoherentMotionReconstructionImageFilterensure that an inappropriate cast is not done
	- inputImagePointer = static_cast< InputImageType * >(
	- this->ProcessObject::GetInput(0) );
	-
	- InputIteratorType iit(inputImagePointer, outputRegionForThread );
	- iit.GoToBegin();
	-
	- // init internal vector image for regularized fit
	- m_InternalVectorImage = VectorImageType::New();
	- m_InternalVectorImage->SetSpacing( inputImagePointer->GetSpacing() ); // Set the image spacing
	- m_InternalVectorImage->SetOrigin( inputImagePointer->GetOrigin() ); // Set the image origin
	- m_InternalVectorImage->SetDirection( inputImagePointer->GetDirection() ); // Set the image direction
	- m_InternalVectorImage->SetRegions( inputImagePointer->GetLargestPossibleRegion() );
	-
	- m_InitialFitImage = InitialFitImageType::New();
	- m_InitialFitImage->SetSpacing( inputImagePointer->GetSpacing() ); // Set the image spacing
	- m_InitialFitImage->SetOrigin( inputImagePointer->GetOrigin() ); // Set the image origin
	- m_InitialFitImage->SetDirection( inputImagePointer->GetDirection() ); // Set the image direction
	- m_InitialFitImage->SetRegions( inputImagePointer->GetLargestPossibleRegion() );
	-
	- if(m_Method == IVIM_REGULARIZED)
	- {
	- m_InternalVectorImage->SetVectorLength(m_Snap.Nhigh);
	- m_InternalVectorImage->Allocate();
	- VectorImageType::PixelType varvec(m_Snap.Nhigh);
	- for(int i=0; i<m_Snap.Nhigh; i++) varvec[i] = IVIM_FOO;
	- m_InternalVectorImage->FillBuffer(varvec);
	-
	- m_InitialFitImage->Allocate();
	- InitialFitImageType::PixelType vec;
	- vec[0] = 0.5; vec[1] = 0.01; vec[2]=0.001;
	- m_InitialFitImage->FillBuffer(vec);
	- }
	-
	- typedef itk::ImageRegionIterator<VectorImageType> VectorIteratorType;
	- VectorIteratorType vecit(m_InternalVectorImage, outputRegionForThread );
	- vecit.GoToBegin();
	-
	- typedef itk::ImageRegionIterator<InitialFitImageType> InitIteratorType;
	- InitIteratorType initit(m_InitialFitImage, outputRegionForThread );
	- initit.GoToBegin();
	-
	- while( !iit.IsAtEnd() )
	- {
	- InputVectorType measvec = iit.Get();
	-
	- typename NumericTraits<InputPixelType>::AccumulateType b0 = NumericTraits<InputPixelType>::Zero;
	-
	- m_Snap.meas.set_size(m_Snap.N);
	- m_Snap.allmeas.set_size(m_Snap.N);
	- if(!m_Snap.iterated_sequence)
	- {
	- // Average the baseline image pixels
	- for(unsigned int i = 0; i < m_Snap.baselineind.size(); ++i)
	- {
	- b0 += measvec[m_Snap.baselineind[i]];
	- }
	- if(m_Snap.baselineind.size())
	- b0 /= m_Snap.baselineind.size();
	-
	- // measurement vector
	- for(int i = 0; i < m_Snap.N; ++i)
	- {
	- m_Snap.allmeas[i] = measvec[m_Snap.gradientind[i]] / (b0+.0001);
	-
	- if(measvec[m_Snap.gradientind[i]] > m_S0Thres)
	- {
	- m_Snap.meas[i] = measvec[m_Snap.gradientind[i]] / (b0+.0001);
	- }
	- else
	- {
	- m_Snap.meas[i] = IVIM_FOO;
	- }
	- }
	- }
	- else
	- {
	- // measurement vector
	- for(int i = 0; i < m_Snap.N; ++i)
	- {
	- b0 = measvec[m_Snap.baselineind[i]];
	-
	- m_Snap.allmeas[i] = measvec[m_Snap.gradientind[i]] / (b0+.0001);
	-
	- if(measvec[m_Snap.gradientind[i]] > m_S0Thres)
	- {
	- m_Snap.meas[i] = measvec[m_Snap.gradientind[i]] / (b0+.0001);
	- }
	- else
	- {
	- m_Snap.meas[i] = IVIM_FOO;
	- }
	- }
	- }
	-
	- m_Snap.currentF = 0;
	- m_Snap.currentD = 0;
	- m_Snap.currentDStar = 0;
	-
	- switch(m_Method)
	- {
	-
	- case IVIM_D_THEN_DSTAR:
	- {
	-
	- for(int i=0; i<m_Snap.Nhigh; i++)
	- {
	- m_Snap.high_meas[i] = m_Snap.meas[m_Snap.high_indices.at(i)];
	- }
	-
	- MeasAndBvals input = ApplyS0Threshold(m_Snap.high_meas, m_Snap.high_bvalues);
	- m_Snap.bvals1 = input.bvals;
	- m_Snap.meas1 = input.meas;
	-
	- if (input.N < 2)
	- {
	- if (input.N == 1)
	- {
	- m_Snap.currentD = - log(input.meas[0]) / input.bvals[0];
	- m_Snap.currentF = 0;
	- m_Snap.currentDStar = 0;
	- }
	- break;
	- }
	-
	- IVIM_d_and_f f_donly(input.N);
	- f_donly.set_bvalues(input.bvals);
	- f_donly.set_measurements(input.meas);
	-
	- vnl_vector< double > x_donly(2);
	- x_donly[0] = 0.001;
	- x_donly[1] = 0.1;
	- // f 0.1 Dstar 0.01 D 0.001
	-
	- vnl_levenberg_marquardt lm_donly(f_donly);
	- lm_donly.set_f_tolerance(0.0001);
	- lm_donly.minimize(x_donly);
	- m_Snap.currentD = x_donly[0];
	- m_Snap.currentF = x_donly[1];
	-
	-
	- if(m_FitDStar)
	- {
	- MeasAndBvals input2 = ApplyS0Threshold(m_Snap.meas, m_Snap.bvalues);
	- m_Snap.bvals2 = input2.bvals;
	- m_Snap.meas2 = input2.meas;
	- if (input2.N < 2) break;
	-
	- IVIM_dstar_only f_dstar_only(input2.N,m_Snap.currentD,m_Snap.currentF);
	- f_dstar_only.set_bvalues(input2.bvals);
	- f_dstar_only.set_measurements(input2.meas);
	-
	- vnl_vector< double > x_dstar_only(1);
	- vnl_vector< double > fx_dstar_only(input2.N);
	-
	- double opt = 1111111111111111.0;
	- int opt_idx = -1;
	- int num_its = 100;
	- double min_val = .001;
	- double max_val = .15;
	- for(int i=0; i<num_its; i++)
	- {
	- x_dstar_only[0] = min_val + i * ((max_val-min_val) / num_its);
	- f_dstar_only.f(x_dstar_only, fx_dstar_only);
	- double err = fx_dstar_only.two_norm();
	- if(err<opt)
	- {
	- opt = err;
	- opt_idx = i;
	- }
	- }
	-
	- m_Snap.currentDStar = min_val + opt_idx * ((max_val-min_val) / num_its);
	- // IVIM_fixd f_fixd(input2.N,m_Snap.currentD);
	- // f_fixd.set_bvalues(input2.bvals);
	- // f_fixd.set_measurements(input2.meas);
	-
	- // vnl_vector< double > x_fixd(2);
	- // x_fixd[0] = 0.1;
	- // x_fixd[1] = 0.01;
	- // // f 0.1 Dstar 0.01 D 0.001
	-
	- // vnl_levenberg_marquardt lm_fixd(f_fixd);
	- // lm_fixd.set_f_tolerance(0.0001);
	- // lm_fixd.minimize(x_fixd);
	-
	- // m_Snap.currentF = x_fixd[0];
	- // m_Snap.currentDStar = x_fixd[1];
	- }
	-
	- break;
	- }
	-
	- case IVIM_DSTAR_FIX:
	- {
	- MeasAndBvals input = ApplyS0Threshold(m_Snap.meas, m_Snap.bvalues);
	- m_Snap.bvals1 = input.bvals;
	- m_Snap.meas1 = input.meas;
	- if (input.N < 2) break;
	-
	- IVIM_fixdstar f_fixdstar(input.N,m_DStar);
	- f_fixdstar.set_bvalues(input.bvals);
	- f_fixdstar.set_measurements(input.meas);
	-
	- vnl_vector< double > x(2);
	- x[0] = 0.1;
	- x[1] = 0.001;
	- // f 0.1 Dstar 0.01 D 0.001
	-
	- vnl_levenberg_marquardt lm(f_fixdstar);
	- lm.set_f_tolerance(0.0001);
	- lm.minimize(x);
	-
	- m_Snap.currentF = x[0];
	- m_Snap.currentD = x[1];
	- m_Snap.currentDStar = m_DStar;
	-
	- break;
	- }
	-
	- case IVIM_FIT_ALL:
	- {
	-
	- MeasAndBvals input = ApplyS0Threshold(m_Snap.meas, m_Snap.bvalues);
	- m_Snap.bvals1 = input.bvals;
	- m_Snap.meas1 = input.meas;
	- if (input.N < 3) break;
	-
	- IVIM_3param f_3param(input.N);
	- f_3param.set_bvalues(input.bvals);
	- f_3param.set_measurements(input.meas);
	-
	- vnl_vector< double > x(3);
	- x[0] = 0.1;
	- x[1] = 0.001;
	- x[2] = 0.01;
	- // f 0.1 Dstar 0.01 D 0.001
	-
	- vnl_levenberg_marquardt lm(f_3param);
	- lm.set_f_tolerance(0.0001);
	- lm.minimize(x);
	-
	- m_Snap.currentF = x[0];
	- m_Snap.currentD = x[1];
	- m_Snap.currentDStar = x[2];
	-
	- break;
	- }
	-
	- case IVIM_LINEAR_D_THEN_F:
	- {
	-
	- // // neglect zero-measurements
	- // bool zero = false;
	- // for(int i=0; i<Nhigh; i++)
	- // {
	- // if( meas[high_indices.at(i)] == 0 )
	- // {
	- // f=0;
	- // zero = true;
	- // break;
	- // }
	- // }
	- // if(zero) break;
	-
	- for(int i=0; i<m_Snap.Nhigh; i++)
	- {
	- m_Snap.high_meas[i] = m_Snap.meas[m_Snap.high_indices.at(i)];
	- }
	-
	- MeasAndBvals input = ApplyS0Threshold(m_Snap.high_meas, m_Snap.high_bvalues);
	- m_Snap.bvals1 = input.bvals;
	- m_Snap.meas1 = input.meas;
	-
	- if (input.N < 2)
	- {
	- if (input.N == 1)
	- {
	- m_Snap.currentD = - log(input.meas[0]) / input.bvals[0];
	- m_Snap.currentF = 0;
	- m_Snap.currentDStar = 0;
	- }
	- break;
	- }
	-
	- for(int i=0; i<input.N; i++)
	- {
	- input.meas[i] = log(input.meas[i]);
	- }
	-
	- double bval_m = 0;
	- double meas_m = 0;
	- for(int i=0; i<input.N; i++)
	- {
	- bval_m += input.bvals[i];
	- meas_m += input.meas[i];
	- }
	- bval_m /= input.N;
	- meas_m /= input.N;
	-
	- vnl_matrix<double> X(input.N,2);
	- for(int i=0; i<input.N; i++)
	- {
	- X(i,0) = input.bvals[i] - bval_m;
	- X(i,1) = input.meas[i] - meas_m;
	- }
	-
	- vnl_matrix<double> XX = X.transpose() * X;
	- vnl_symmetric_eigensystem<double> eigs(XX);
	-
	- vnl_vector<double> eig;
	- if(eigs.get_eigenvalue(0) > eigs.get_eigenvalue(1))
	- eig = eigs.get_eigenvector(0);
	- else
	- eig = eigs.get_eigenvector(1);
	-
	- m_Snap.currentF = 1 - exp( meas_m - bval_m*(eig(1)/eig(0)) );
	- m_Snap.currentD = -eig(1)/eig(0);
	-
	- if(m_FitDStar)
	- {
	- MeasAndBvals input2 = ApplyS0Threshold(m_Snap.meas, m_Snap.bvalues);
	- m_Snap.bvals2 = input2.bvals;
	- m_Snap.meas2 = input2.meas;
	- if (input2.N < 2) break;
	-
	- IVIM_dstar_only f_dstar_only(input2.N,m_Snap.currentD,m_Snap.currentF);
	- f_dstar_only.set_bvalues(input2.bvals);
	- f_dstar_only.set_measurements(input2.meas);
	-
	- vnl_vector< double > x_dstar_only(1);
	- vnl_vector< double > fx_dstar_only(input2.N);
	-
	- double opt = 1111111111111111.0;
	- int opt_idx = -1;
	- int num_its = 100;
	- double min_val = .001;
	- double max_val = .15;
	- for(int i=0; i<num_its; i++)
	- {
	- x_dstar_only[0] = min_val + i * ((max_val-min_val) / num_its);
	- f_dstar_only.f(x_dstar_only, fx_dstar_only);
	- double err = fx_dstar_only.two_norm();
	- if(err<opt)
	- {
	- opt = err;
	- opt_idx = i;
	- }
	- }
	-
	- m_Snap.currentDStar = min_val + opt_idx * ((max_val-min_val) / num_its);
	- }
	- // MITK_INFO << "choosing " << opt_idx << " => " << DStar;
	- // x_dstar_only[0] = 0.01;
	- // // f 0.1 Dstar 0.01 D 0.001
	-
	- // vnl_levenberg_marquardt lm_dstar_only(f_dstar_only);
	- // lm_dstar_only.set_f_tolerance(0.0001);
	- // lm_dstar_only.minimize(x_dstar_only);
	-
	- // DStar = x_dstar_only[0];
	-
	- break;
	- }
	-
	- case IVIM_REGULARIZED:
	- {
	- //m_Snap.high_meas, m_Snap.high_bvalues;
	- for(int i=0; i<m_Snap.Nhigh; i++)
	- {
	- m_Snap.high_meas[i] = m_Snap.meas[m_Snap.high_indices.at(i)];
	- }
	-
	- MeasAndBvals input = ApplyS0Threshold(m_Snap.high_meas, m_Snap.high_bvalues);
	-
	- vnl_vector< double > x_donly(2);
	- x_donly[0] = 0.001;
	- x_donly[1] = 0.1;
	-
	- if(input.N >= 2)
	- {
	- IVIM_d_and_f f_donly(input.N);
	- f_donly.set_bvalues(input.bvals);
	- f_donly.set_measurements(input.meas);
	- //MITK_INFO << "initial fit N=" << input.N << ", min-b = " << input.bvals[0] << ", max-b = " << input.bvals[input.N-1];
	- vnl_levenberg_marquardt lm_donly(f_donly);
	- lm_donly.set_f_tolerance(0.0001);
	- lm_donly.minimize(x_donly);
	- }
	-
	- typename InitialFitImageType::PixelType initvec;
	- initvec[0] = x_donly[1];
	- initvec[1] = x_donly[0];
	- initit.Set(initvec);
	- //MITK_INFO << "Init vox " << initit.GetIndex() << " with " << initvec[0] << "; " << initvec[1];
	- ++initit;
	-
	- int N = m_Snap.high_meas.size();
	- typename VectorImageType::PixelType vec(N);
	- for(int i=0; i<N; i++)
	- {
	- vec[i] = m_Snap.high_meas[i];
	- //MITK_INFO << "vec" << i << " = " << m_Snap.high_meas[i];
	- }
	-
	- vecit.Set(vec);
	- ++vecit;
	-
	- if(!m_Verbose)
	- {
	- // report the middle voxel
	- if( vecit.GetIndex()[0] == m_CrossPosition[0]
	- && vecit.GetIndex()[0] == m_CrossPosition[1]
	- && vecit.GetIndex()[0] == m_CrossPosition[2] )
	- {
	- MeasAndBvals input = ApplyS0Threshold(m_Snap.high_meas, m_Snap.high_bvalues);
	- m_Snap.bvals1 = input.bvals;
	- m_Snap.meas1 = input.meas;
	-
	- MeasAndBvals input2 = ApplyS0Threshold(m_Snap.meas, m_Snap.bvalues);
	- m_Snap.bvals2 = input2.bvals;
	- m_Snap.meas2 = input2.meas;
	-
	- m_tmp_allmeas = m_Snap.allmeas;
	- }
	- }
	-
	- break;
	- }
	- }
	- m_Snap.currentFunceiled = m_Snap.currentF;
	- IVIM_CEIL( m_Snap.currentF, 0.0, 1.0 );
	-
	- oit.Set( m_Snap.currentF );
	- oit1.Set( m_Snap.currentD );
	- oit2.Set( m_Snap.currentDStar );
	-
	- // std::cout << "\tf=" << x[0] << "\tD=" << x[1] << " ; "<<std::endl;
	-
	- ++oit;
	- ++oit1;
	- ++oit2;
	- ++iit;
	- }
	-
	- if(m_Verbose)
	- {
	- std::cout << "One Thread finished reconstruction" << std::endl;
	- }
	-}
	-
	-template< class TIn, class TOut>
	-void DiffusionIntravoxelIncoherentMotionReconstructionImageFilter<TIn, TOut>
	-::AfterThreadedGenerateData()
	-{
	- if(m_Method == IVIM_REGULARIZED)
	- {
	- typename OutputImageType::Pointer outputImage =
	- static_cast< OutputImageType * >(this->ProcessObject::GetPrimaryOutput());
	- ImageRegionIterator< OutputImageType > oit0(outputImage, outputImage->GetLargestPossibleRegion());
	- oit0.GoToBegin();
	-
	- typename OutputImageType::Pointer dImage =
	- static_cast< OutputImageType * >(this->ProcessObject::GetOutput(1));
	- ImageRegionIterator< OutputImageType > oit1(dImage, dImage->GetLargestPossibleRegion());
	- oit1.GoToBegin();
	-
	- typename OutputImageType::Pointer dstarImage =
	- static_cast< OutputImageType * >(this->ProcessObject::GetOutput(2));
	- ImageRegionIterator< OutputImageType > oit2(dstarImage, dstarImage->GetLargestPossibleRegion());
	- oit2.GoToBegin();
	-
	- typedef itk::RegularizedIVIMReconstructionFilter
	- <double,double,float> RegFitType;
	- RegFitType::Pointer filter = RegFitType::New();
	- filter->SetInput(m_InitialFitImage);
	- filter->SetReferenceImage(m_InternalVectorImage);
	- filter->SetBValues(m_Snap.high_bvalues);
	- filter->SetNumberIterations(m_NumberIterations);
	- filter->SetNumberOfThreads(1);
	- filter->SetLambda(m_Lambda);
	- filter->Update();
	- typename RegFitType::OutputImageType::Pointer outimg = filter->GetOutput();
	-
	- ImageRegionConstIterator< RegFitType::OutputImageType > iit(outimg, outimg->GetLargestPossibleRegion());
	- iit.GoToBegin();
	-
	- while( !iit.IsAtEnd() )
	- {
	- double f = iit.Get()[0];
	- IVIM_CEIL( f, 0.0, 1.0 );
	-
	- oit0.Set( myround(f * 100.0) );
	- oit1.Set( myround(iit.Get()[1] * 10000.0) );
	- oit2.Set( myround(iit.Get()[2] * 1000.0) );
	-
	- if(!m_Verbose)
	- {
	- // report the middle voxel
	- if( iit.GetIndex()[0] == m_CrossPosition[0]
	- && iit.GetIndex()[1] == m_CrossPosition[1]
	- && iit.GetIndex()[2] == m_CrossPosition[2] )
	- {
	- m_Snap.currentF = f;
	- m_Snap.currentD = iit.Get()[1];
	- m_Snap.currentDStar = iit.Get()[2];
	- m_Snap.allmeas = m_tmp_allmeas;
	- MITK_INFO << "setting " << f << ";" << iit.Get()[1] << ";" << iit.Get()[2];
	- }
	- }
	-
	- ++oit0;
	- ++oit1;
	- ++oit2;
	- ++iit;
	- }
	- }
	-}
	-
	-template< class TIn, class TOut>
	-double DiffusionIntravoxelIncoherentMotionReconstructionImageFilter<TIn, TOut>
	-::myround(double number)
	-{
	- return number < 0.0 ? ceil(number - 0.5) : floor(number + 0.5);
	-}
	-
	-template< class TIn, class TOut>
	-void DiffusionIntravoxelIncoherentMotionReconstructionImageFilter<TIn, TOut>
	-::SetGradientDirections( GradientDirectionContainerType *gradientDirection )
	-{
	- this->m_GradientDirectionContainer = gradientDirection;
	- this->m_NumberOfGradientDirections = gradientDirection->Size();
	-}
	-
	-template< class TIn, class TOut>
	-void DiffusionIntravoxelIncoherentMotionReconstructionImageFilter<TIn, TOut>
	-::PrintSelf(std::ostream& os, Indent indent) const
	-{
	- Superclass::PrintSelf(os,indent);
	-
	- if ( m_GradientDirectionContainer )
	- {
	- os << indent << "GradientDirectionContainer: "
	- << m_GradientDirectionContainer << std::endl;
	- }
	- else
	- {
	- os << indent <<
	- "GradientDirectionContainer: (Gradient directions not set)" << std::endl;
	- }
	-}
	-
	-}
	-
	-#endif // __itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter_cpp
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.h
	deleted file mode 100644
	index 0bb6ae176a..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.h
	+++ /dev/null
	@@ -1,381 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef __itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter_h
	-#define __itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter_h
	-
	-#include "itkImageToImageFilter.h"
	-//#include "vnl/vnl_matrix.h"
	-#include "vnl/vnl_vector_fixed.h"
	-#include "vnl/vnl_matrix.h"
	-#include "vnl/algo/vnl_svd.h"
	-#include "itkVectorContainer.h"
	-#include "itkVectorImage.h"
	-//#include "QuadProg.h"
	-#include "itkVectorImage.h"
	-
	-#include "vnl/vnl_least_squares_function.h"
	-#include "vnl/algo/vnl_levenberg_marquardt.h"
	-#include "vnl/vnl_math.h"
	-
	-#define IVIM_CEIL(val,u,o) (val) = \
	- ( (val) < (u) ) ? ( (u) ) : ( ( (val)>(o) ) ? ( (o) ) : ( (val) ) );
	-
	-namespace itk{
	-
	- /** baseclass for IVIM fitting algorithms */
	- struct IVIM_base
	- {
	-
	- void set_measurements(const vnl_vector<double>& x)
	- {
	- measurements.set_size(x.size());
	- measurements.copy_in(x.data_block());
	- }
	-
	- void set_bvalues(const vnl_vector<double>& x)
	- {
	- bvalues.set_size(x.size());
	- bvalues.copy_in(x.data_block());
	- }
	-
	- vnl_vector<double> measurements;
	- vnl_vector<double> bvalues;
	-
	- int N;
	-
	- };
	-
	- /** Fitt all three parameters */
	- struct IVIM_3param : public IVIM_base, vnl_least_squares_function
	- {
	-
	- IVIM_3param(unsigned int number_of_measurements) :
	- vnl_least_squares_function(3, number_of_measurements, no_gradient)
	- {
	- N = get_number_of_residuals();
	- }
	-
	- void f(const vnl_vector<double>& x, vnl_vector<double>& fx) override {
	-
	- double ef = x[0];
	- double D = x[1];
	- double Dstar = x[2];
	-
	- for(int s=0; s<N; s++)
	- {
	- double approx = (1-ef)exp(-bvalues[s]D)+efexp(-bvalues[s](D+Dstar));
	- fx[s] = vnl_math_abs( measurements[s] - approx );
	- }
	-
	- }
	- };
	-
	- /** fit by setting DStar to a fix value */
	- struct IVIM_fixdstar : public IVIM_base, vnl_least_squares_function
	- {
	-
	- IVIM_fixdstar(unsigned int number_of_measurements, double DStar) :
	- vnl_least_squares_function(2, number_of_measurements, no_gradient)
	- {
	- N = get_number_of_residuals();
	- fixDStar = DStar;
	- }
	-
	- void f(const vnl_vector<double>& x, vnl_vector<double>& fx) override {
	-
	- double ef = x[0];
	- double D = x[1];
	-
	- for(int s=0; s<N; s++)
	- {
	- double approx = (1-ef)exp(-bvalues[s]D)+efexp(-bvalues[s](D+fixDStar));
	- fx[s] = vnl_math_abs( measurements[s] - approx );
	- }
	-
	- }
	-
	- double fixDStar;
	-
	- };
	-
	- /** fit a monoexponential curve only estimating D */
	- struct IVIM_d_and_f : public IVIM_base, vnl_least_squares_function
	- {
	-
	- IVIM_d_and_f(unsigned int number_of_measurements) :
	- vnl_least_squares_function(2, number_of_measurements, no_gradient)
	- {
	- N = get_number_of_residuals();
	- }
	-
	- void f(const vnl_vector<double>& x, vnl_vector<double>& fx) override {
	-
	- double D = x[0];
	- double f = x[1];
	-
	- for(int s=0; s<N; s++)
	- {
	- double approx = (1-f) * exp(-bvalues[s]*D);
	- fx[s] = vnl_math_abs( measurements[s] - approx );
	- }
	-
	- }
	- };
	-
	- /** fiting DStar and f with fix value of D */
	- struct IVIM_fixd : public IVIM_base, vnl_least_squares_function
	- {
	-
	- IVIM_fixd(unsigned int number_of_measurements, double D) :
	- vnl_least_squares_function(2, number_of_measurements, no_gradient)
	- {
	- N = get_number_of_residuals();
	- fixD = D;
	- }
	-
	- void f(const vnl_vector<double>& x, vnl_vector<double>& fx) override {
	-
	- double ef = x[0];
	- double Dstar = x[1];
	-
	- for(int s=0; s<N; s++)
	- {
	- double approx = (1-ef)exp(-bvalues[s]fixD)+efexp(-bvalues[s](fixD+Dstar));
	- fx[s] = vnl_math_abs( measurements[s] - approx );
	- }
	-
	- }
	-
	- double fixD;
	- };
	-
	- /** fiting DStar with given f and D */
	- struct IVIM_dstar_only : public IVIM_base, vnl_least_squares_function
	- {
	-
	- IVIM_dstar_only(unsigned int number_of_measurements, double D, double f) :
	- vnl_least_squares_function(1, number_of_measurements, no_gradient)
	- {
	- N = get_number_of_residuals();
	- fixD = D;
	- fixF = f;
	- }
	-
	- void f(const vnl_vector<double>& x, vnl_vector<double>& fx) override {
	-
	- double Dstar = x[0];
	-
	- for(int s=0; s<N; s++)
	- {
	- double approx = (1-fixF)exp(-bvalues[s]fixD)+fixFexp(-bvalues[s](fixD+Dstar));
	- fx[s] = vnl_math_abs( measurements[s] - approx );
	- }
	-
	- }
	-
	- double fixD;
	- double fixF;
	- };
	-
	- struct MeasAndBvals
	- {
	- vnl_vector<double> meas;
	- vnl_vector<double> bvals;
	- int N;
	- };
	-
	- /** \class DiffusionIntravoxelIncoherentMotionReconstructionImageFilter */
	- template< class TInputPixelType,
	- class TOutputPixelType>
	- class DiffusionIntravoxelIncoherentMotionReconstructionImageFilter :
	- public ImageToImageFilter< VectorImage< TInputPixelType, 3 >,
	- Image< TOutputPixelType, 3 > >
	- {
	-
	- public:
	-
	- struct IVIMSnapshot
	- {
	- double currentF;
	- double currentFunceiled;
	- double currentD;
	- double currentDStar;
	-
	- bool iterated_sequence; // wether each measurement has its own b0-acqu.
	- std::vector<unsigned int> baselineind; // baseline image indicies
	-
	- int N; // total number of measurements
	- std::vector<unsigned int> gradientind; // gradient image indicies
	- std::vector<double> bvals; // b-values != 0
	- vnl_vector<double> bvalues; // copy of bvalues != 0
	- vnl_vector<double> meas; // all measurements, thresholded blanked out
	- vnl_vector<double> allmeas; // all measurements
	-
	- int Nhigh; // number of used measurements
	- std::vector<int> high_indices; // indices of used measurements
	- vnl_vector<double> high_bvalues; // bvals of used measurements
	- vnl_vector<double> high_meas; // used measurements
	-
	- vnl_vector<double> meas1;
	- vnl_vector<double> bvals1;
	-
	- vnl_vector<double> meas2;
	- vnl_vector<double> bvals2;
	-
	- };
	-
	- enum IVIM_Method
	- {
	- IVIM_FIT_ALL,
	- IVIM_DSTAR_FIX,
	- IVIM_D_THEN_DSTAR,
	- IVIM_LINEAR_D_THEN_F,
	- IVIM_REGULARIZED
	- };
	-
	- typedef DiffusionIntravoxelIncoherentMotionReconstructionImageFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageToImageFilter< VectorImage< TInputPixelType, 3>,
	- Image< TOutputPixelType,3 > > Superclass;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(DiffusionIntravoxelIncoherentMotionReconstructionImageFilter,
	- ImageToImageFilter);
	-
	- typedef TOutputPixelType OutputPixelType;
	-
	- typedef TInputPixelType InputPixelType;
	-
	- /** Reference image data, This image is aquired in the absence
	- * of a diffusion sensitizing field gradient */
	- typedef typename Superclass::InputImageType InputImageType;
	-
	- typedef Image< OutputPixelType, 3 > OutputImageType;
	-
	- typedef typename Superclass::OutputImageRegionType
	- OutputImageRegionType;
	-
	- /** Holds each magnetic field gradient used to acquire one DWImage */
	- typedef vnl_vector_fixed< double, 3 > GradientDirectionType;
	-
	- /** Container to hold gradient directions of the 'n' DW measurements */
	- typedef VectorContainer< unsigned int,
	- GradientDirectionType > GradientDirectionContainerType;
	-
	- // vector image typedefs for regularized fit
	- typedef itk::VectorImage<float,3> VectorImageType;
	- typedef itk::Image<itk::Vector<double, 3>, 3> InitialFitImageType;
	-
	- /** set method to add gradient directions and its corresponding
	- * image. The image here is a VectorImage. The user is expected to pass the
	- * gradient directions in a container. The ith element of the container
	- * corresponds to the gradient direction of the ith component image the
	- * VectorImage. For the baseline image, a vector of all zeros
	- * should be set.*/
	- void SetGradientDirections( GradientDirectionContainerType * );
	-
	- void SetBValue(double bval){m_BValue = bval;}
	- void SetBThres(double bval){m_BThres = bval;}
	- void SetS0Thres(double val){m_S0Thres = val;}
	- void SetDStar(double dstar){m_DStar = dstar;}
	- void SetFitDStar(bool fit){m_FitDStar = fit;}
	- void SetVerbose(bool verbose){m_Verbose = verbose;}
	- void SetNumberIterations(int num){m_NumberIterations = num;}
	- void SetLambda(double lambda){m_Lambda = lambda;}
	- void SetCrossPosition(typename InputImageType::IndexType crosspos){this->m_CrossPosition = crosspos;}
	- void SetMethod(IVIM_Method method){m_Method = method;}
	-
	- IVIMSnapshot GetSnapshot(){return m_Snap;}
	-
	- /** Return the gradient direction. idx is 0 based */
	- virtual GradientDirectionType GetGradientDirection( unsigned int idx) const
	- {
	- if( idx >= m_NumberOfGradientDirections )
	- {
	- itkExceptionMacro( << "Gradient direction " << idx << "does not exist" );
	- }
	- return m_GradientDirectionContainer->ElementAt( idx+1 );
	- }
	-
	- protected:
	- DiffusionIntravoxelIncoherentMotionReconstructionImageFilter();
	- ~DiffusionIntravoxelIncoherentMotionReconstructionImageFilter() {};
	- void PrintSelf(std::ostream& os, Indent indent) const;
	-
	- void BeforeThreadedGenerateData();
	- void ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread,
	- ThreadIdType);
	- void AfterThreadedGenerateData();
	-
	- MeasAndBvals ApplyS0Threshold(vnl_vector<double> &meas, vnl_vector<double> &bvals);
	-
	- private:
	-
	- double myround(double number);
	-
	- /** container to hold gradient directions */
	- GradientDirectionContainerType::Pointer m_GradientDirectionContainer;
	-
	- /** Number of gradient measurements */
	- unsigned int m_NumberOfGradientDirections;
	-
	- double m_BValue;
	-
	- double m_BThres;
	-
	- double m_S0Thres;
	-
	- double m_DStar;
	-
	- IVIM_Method m_Method;
	-
	- typename OutputImageType::Pointer m_DMap;
	-
	- typename OutputImageType::Pointer m_DStarMap;
	-
	- bool m_FitDStar;
	-
	- IVIMSnapshot m_Snap;
	-
	- bool m_Verbose;
	-
	- typename VectorImageType::Pointer m_InternalVectorImage;
	-
	- typename InitialFitImageType::Pointer m_InitialFitImage;
	-
	- int m_NumberIterations; // for total variation
	-
	- vnl_vector<double> m_tmp_allmeas;
	-
	- double m_Lambda;
	-
	- typename InputImageType::IndexType m_CrossPosition;
	-
	- };
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.cpp"
	-#endif
	-
	-#endif //__itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter_h
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionKurtosisReconstructionImageFilter.cxx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionKurtosisReconstructionImageFilter.cxx
	deleted file mode 100644
	index cb988e355c..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionKurtosisReconstructionImageFilter.cxx
	+++ /dev/null
	@@ -1,484 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef DIFFUSIONKURTOSISRECONSTRUCTIONIMAGEFILTER_CXX
	-#define DIFFUSIONKURTOSISRECONSTRUCTIONIMAGEFILTER_CXX
	-
	-#include "itkDiffusionKurtosisReconstructionImageFilter.h"
	-
	-#include <itkImageRegionConstIterator.h>
	-#include <itkImageRegionConstIteratorWithIndex.h>
	-#include <itkImageRegionIteratorWithIndex.h>
	-#include <itkImageRegionIterator.h>
	-
	-#include <itkVectorIndexSelectionCastImageFilter.h>
	-#include <itkComposeImageFilter.h>
	-#include <itkDiscreteGaussianImageFilter.h>
	-
	-template< class TInputPixelType>
	-static void FitSingleVoxel( const itk::VariableLengthVector< TInputPixelType > &input,
	- const vnl_vector<double>& bvalues,
	- vnl_vector<double>& result,
	- itk::KurtosisFitConfiguration kf_config)
	-{
	- // check for length
	- assert( input.Size() == bvalues.size() );
	-
	- // assembly data vectors for fitting
	- auto bvalueIter = bvalues.begin();
	- unsigned int unused_values = 0;
	- while( bvalueIter != bvalues.end() )
	- {
	- if( *bvalueIter < vnl_math::eps && kf_config.omit_bzero )
	- {
	- ++unused_values;
	- }
	- ++bvalueIter;
	- }
	-
	- // initialize data vectors with the estimated size (after filtering)
	- vnl_vector<double> fit_measurements( input.Size() - unused_values, 0 );
	- vnl_vector<double> fit_bvalues( input.Size() - unused_values, 0 );
	-
	- bvalueIter = bvalues.begin();
	- unsigned int running_index = 0;
	- unsigned int skip_count = 0;
	- while( bvalueIter != bvalues.end() )
	- {
	- // skip b=0 if the corresponding flag is set
	- if( ( kf_config.omit_bzero && *bvalueIter < vnl_math::eps )
	- // skip bvalues higher than the limit provided, if the flag is activated
	- \|\| ( kf_config.exclude_high_b && *bvalueIter > kf_config.b_upper_threshold ) )
	- {
	- ++skip_count;
	- }
	- else
	- {
	- fit_measurements[ running_index - skip_count ] = input.GetElement(running_index);
	- fit_bvalues[ running_index - skip_count] = *bvalueIter;
	- }
	-
	- ++running_index;
	- ++bvalueIter;
	- }
	-
	-
	- MITK_DEBUG("KurtosisFilter.FitSingleVoxel.Meas") << fit_measurements;
	- MITK_DEBUG("KurtosisFilter.FitSingleVoxel.Bval") << fit_bvalues;
	-
	- // perform fit on data vectors
	- if( kf_config.omit_bzero )
	- {
	- itk::kurtosis_fit_omit_unweighted kurtosis_cost_fn( fit_measurements.size() );
	- // configuration
	- kurtosis_cost_fn.set_fit_logscale( static_cast<bool>(kf_config.fit_scale) );
	- kurtosis_cost_fn.initialize( fit_measurements, fit_bvalues );
	-
	- if( kf_config.use_K_limits)
	- {
	- kurtosis_cost_fn.set_K_bounds( kf_config.K_limits );
	- }
	-
	- vnl_levenberg_marquardt nonlinear_fit( kurtosis_cost_fn );
	- nonlinear_fit.minimize( result );
	- }
	- else
	- {
	- itk::kurtosis_fit_lsq_function kurtosis_cost_fn( fit_measurements.size() );
	- // configuration
	- kurtosis_cost_fn.set_fit_logscale( static_cast<bool>(kf_config.fit_scale) );
	- kurtosis_cost_fn.initialize( fit_measurements, fit_bvalues );
	-
	- if( kf_config.use_K_limits)
	- {
	- kurtosis_cost_fn.set_K_bounds( kf_config.K_limits );
	- }
	-
	-
	- vnl_levenberg_marquardt nonlinear_fit( kurtosis_cost_fn );
	- nonlinear_fit.minimize(result);
	- }
	-
	- MITK_DEBUG("KurtosisFilter.FitSingleVoxel.Rslt") << result;
	-}
	-
	-
	-
	-template< class TInputPixelType, class TOutputPixelType>
	-itk::DiffusionKurtosisReconstructionImageFilter<TInputPixelType, TOutputPixelType>
	-::DiffusionKurtosisReconstructionImageFilter()
	- : m_ReferenceBValue(-1),
	- m_OmitBZero(false),
	- m_ApplyPriorSmoothing(false),
	- m_SmoothingSigma(1.5),
	- m_UseKBounds( false ),
	- m_MaxFitBValue( 3000 ),
	- m_ScaleForFitting( STRAIGHT )
	-{
	- this->m_InitialPosition = vnl_vector<double>(3, 0);
	- this->m_InitialPosition[2] = 1000.0; // S_0
	- this->m_InitialPosition[0] = 0.001; // D
	- this->m_InitialPosition[1] = 1; // K
	-
	- this->m_KurtosisBounds.fill(0);
	-
	- // single input image
	- this->SetNumberOfRequiredInputs(1);
	-
	- // two output images (D, K)
	- this->SetNumberOfRequiredOutputs(2);
	- typename OutputImageType::Pointer outputPtr1 = OutputImageType::New();
	- typename OutputImageType::Pointer outputPtr2 = OutputImageType::New();
	-
	- this->SetNthOutput(0, outputPtr1.GetPointer() );
	- this->SetNthOutput(1, outputPtr2.GetPointer() );
	-
	-}
	-
	-template< class TInputPixelType, class TOutputPixelType>
	-void itk::DiffusionKurtosisReconstructionImageFilter<TInputPixelType, TOutputPixelType>
	-::GenerateOutputInformation()
	-{
	- // first call superclass
	- Superclass::GenerateOutputInformation();
	-}
	-
	-template< class TInputPixelType, class TOutputPixelType>
	-void itk::DiffusionKurtosisReconstructionImageFilter<TInputPixelType, TOutputPixelType>
	-::SetImageMask(MaskImageType::Pointer mask)
	-{
	- this->m_MaskImage = mask;
	-}
	-
	-template< class TInputPixelType, class TOutputPixelType>
	-void itk::DiffusionKurtosisReconstructionImageFilter<TInputPixelType, TOutputPixelType>
	-::BeforeThreadedGenerateData()
	-{
	- // if we have a region set, convert it to a mask image, which is to be used as default for telling
	- // we need to set the image anyway, so by default the mask is overall 1
	- if( m_MaskImage.IsNull() )
	- {
	- m_MaskImage = MaskImageType::New();
	- m_MaskImage->SetRegions( this->GetInput()->GetLargestPossibleRegion() );
	- m_MaskImage->CopyInformation( this->GetInput() );
	- m_MaskImage->Allocate();
	-
	- if( this->m_MapOutputRegion.GetNumberOfPixels() > 0 )
	- {
	-
	- m_MaskImage->FillBuffer(0);
	-
	- typedef itk::ImageRegionIteratorWithIndex< MaskImageType > MaskIteratorType;
	- MaskIteratorType maskIter( this->m_MaskImage, this->m_MapOutputRegion );
	- maskIter.GoToBegin();
	-
	- while( !maskIter.IsAtEnd() )
	- {
	- maskIter.Set( 1 );
	- ++maskIter;
	- }
	-
	- }
	- else
	- {
	- m_MaskImage->FillBuffer(1);
	- }
	-
	-
	- }
	-
	-
	- // apply smoothing to the input image
	- if( this->m_ApplyPriorSmoothing )
	- {
	- // filter typedefs
	- typedef itk::DiscreteGaussianImageFilter< itk::Image<TInputPixelType, 3 >, itk::Image<TInputPixelType, 3 > > GaussianFilterType;
	- typedef itk::VectorIndexSelectionCastImageFilter< InputImageType, itk::Image<TInputPixelType, 3 > > IndexSelectionType;
	- typedef itk::ComposeImageFilter< itk::Image<TInputPixelType, 3>, InputImageType > ComposeFilterType;
	-
	-
	- auto vectorImage = this->GetInput();
	- typename IndexSelectionType::Pointer indexSelectionFilter = IndexSelectionType::New();
	- indexSelectionFilter->SetInput( vectorImage );
	-
	- typename ComposeFilterType::Pointer vec_composer = ComposeFilterType::New();
	-
	- for( unsigned int i=0; i<vectorImage->GetVectorLength(); ++i)
	- {
	- typename GaussianFilterType::Pointer gaussian_filter = GaussianFilterType::New();
	-
	- indexSelectionFilter->SetIndex( i );
	-
	- gaussian_filter->SetInput( indexSelectionFilter->GetOutput() );
	- gaussian_filter->SetVariance( m_SmoothingSigma );
	-
	- vec_composer->SetInput(i, gaussian_filter->GetOutput() );
	-
	- gaussian_filter->Update();
	- }
	-
	- try
	- {
	- vec_composer->Update();
	- }
	- catch(const itk::ExceptionObject &e)
	- {
	- mitkThrow() << "[VectorImage.GaussianSmoothing] !! Failed with ITK Exception: " << e.what();
	- }
	-
	- this->m_ProcessedInputImage = vec_composer->GetOutput();
	- }
	- else
	- {
	- this->m_ProcessedInputImage = const_cast<InputImageType*>( this->GetInput() );
	- }
	-}
	-
	-template< class TInputPixelType, class TOutputPixelType>
	-void itk::DiffusionKurtosisReconstructionImageFilter<TInputPixelType, TOutputPixelType>
	-::AfterThreadedGenerateData()
	-{
	- /* // initialize buffer to zero overall, but don't forget the requested region pointer
	- for( unsigned int i=0; i<this->GetNumberOfOutputs(); ++i)
	- {
	- typename OutputImageType::Pointer output = this->GetOutput(i);
	-
	- // after generating, set the buffered region to max, we have taken care about filling it with valid data in
	- // UpdateOutputInformation, if not set, a writer (or any filter using the LargestPossibleRegion() during update may
	- // complain about not getting the requested region
	- output->SetBufferedRegion( output->GetLargestPossibleRegion() );
	-
	- std::cout << "[DiffusionKurtosisReconstructionImageFilter.After]" << output->GetLargestPossibleRegion() << std::endl;
	- }*/
	-
	-}
	-
	-template< class TInputPixelType, class TOutputPixelType>
	-typename itk::DiffusionKurtosisReconstructionImageFilter<TInputPixelType, TOutputPixelType>::KurtosisSnapshot
	-itk::DiffusionKurtosisReconstructionImageFilter<TInputPixelType, TOutputPixelType>
	-::GetSnapshot(const itk::VariableLengthVector<TInputPixelType> &input, GradientDirectionContainerType::Pointer gradients, float bvalue, KurtosisFitConfiguration kf_conf)
	-{
	- // initialize bvalues from reference value and the gradients provided on input
	- this->SetReferenceBValue(bvalue);
	- this->SetGradientDirections( gradients );
	-
	- // call the other method
	- return this->GetSnapshot( input, this->m_BValues, kf_conf );
	-}
	-
	-
	-template< class TInputPixelType, class TOutputPixelType>
	-typename itk::DiffusionKurtosisReconstructionImageFilter<TInputPixelType, TOutputPixelType>::KurtosisSnapshot
	-itk::DiffusionKurtosisReconstructionImageFilter<TInputPixelType, TOutputPixelType>
	-::GetSnapshot(const itk::VariableLengthVector<TInputPixelType> &input, vnl_vector<double> bvalues, KurtosisFitConfiguration kf_conf)
	-{
	- // initialize
	- vnl_vector<double> initial_position;
	- bool omit_bzero = kf_conf.omit_bzero;
	-
	- if( !omit_bzero )
	- {
	- initial_position.set_size(2);
	- initial_position[0] = this->m_InitialPosition[0];
	- initial_position[1] = this->m_InitialPosition[1];
	- }
	- else
	- {
	- initial_position.set_size(3);
	- initial_position = this->m_InitialPosition;
	- }
	-
	- // fit
	- FitSingleVoxel( input, bvalues, initial_position, kf_conf );
	-
	- // assembly result snapshot
	- KurtosisSnapshot result;
	- result.m_D = initial_position[0];
	- result.m_K = initial_position[1];
	-
	- if( omit_bzero )
	- {
	- result.m_f = 1 - initial_position[2] / std::fmax(0.01, input.GetElement(0));
	- result.m_BzeroFit = initial_position[2];
	- }
	- else
	- result.m_f = 1;
	-
	- // assembly data vectors for fitting
	- auto bvalueIter = bvalues.begin();
	- unsigned int unused_values = 0;
	- while( bvalueIter != bvalues.end() )
	- {
	- if( *bvalueIter < vnl_math::eps && omit_bzero )
	- {
	- ++unused_values;
	- }
	- ++bvalueIter;
	- }
	-
	- // initialize data vectors with the estimated size (after filtering)
	- vnl_vector<double> fit_measurements( input.Size() - unused_values, 0 );
	- vnl_vector<double> fit_bvalues( input.Size() - unused_values, 0 );
	-
	- // original data
	- vnl_vector<double> orig_measurements( input.Size(), 0 );
	-
	- bvalueIter = bvalues.begin();
	- unsigned int running_index = 0;
	- unsigned int skip_count = 0;
	- while( bvalueIter != bvalues.end() )
	- {
	- if( *bvalueIter < vnl_math::eps && omit_bzero )
	- {
	- ++skip_count;
	- }
	- else
	- {
	- fit_measurements[ running_index - skip_count ] = input.GetElement(running_index);
	- fit_bvalues[ running_index - skip_count ] = *bvalueIter;
	- }
	-
	- orig_measurements[ running_index ] = input.GetElement(running_index);
	-
	- ++running_index;
	- ++bvalueIter;
	- }
	-
	- result.fit_bvalues = fit_bvalues;
	- result.fit_measurements = fit_measurements;
	-
	- result.bvalues = bvalues;
	- result.measurements = orig_measurements;
	-
	- result.m_fittedBZero = omit_bzero;
	-
	- return result;
	-}
	-
	-template< class TInputPixelType, class TOutputPixelType>
	-void itk::DiffusionKurtosisReconstructionImageFilter<TInputPixelType, TOutputPixelType>
	-::SetGradientDirections(GradientDirectionContainerType::Pointer gradients)
	-{
	- if( this->m_ReferenceBValue < 0)
	- {
	- itkExceptionMacro( << "Specify reference b-value prior to setting the gradient directions." );
	- }
	-
	- if( gradients->Size() == 0 )
	- {
	- itkExceptionMacro( << "Empty gradient directions container retrieved" );
	- }
	-
	- vnl_vector<double> vnl_bvalues( gradients->Size(), 0 );
	-
	- // initialize the b-values
	- auto grIter = gradients->Begin();
	- unsigned int index = 0;
	- while( grIter != gradients->End() )
	- {
	- const double twonorm = grIter.Value().two_norm();
	- vnl_bvalues( index++ ) = this->m_ReferenceBValue * twonorm * twonorm;
	-
	- ++grIter;
	- }
	-
	- this->m_BValues = vnl_bvalues;
	-
	-
	-}
	-
	-template< class TInputPixelType, class TOutputPixelType>
	-void itk::DiffusionKurtosisReconstructionImageFilter<TInputPixelType, TOutputPixelType>
	-::SetInitialSolution(const vnl_vector<double>& x0 )
	-{
	- assert( x0.size() == (2 + static_cast<int>( this->m_OmitBZero )) );
	-
	- this->m_InitialPosition = x0;
	-}
	-
	-template< class TInputPixelType, class TOutputPixelType>
	-void itk::DiffusionKurtosisReconstructionImageFilter<TInputPixelType, TOutputPixelType>
	-::ThreadedGenerateData(const OutputImageRegionType &outputRegionForThread, ThreadIdType /threadId/)
	-{
	- typename OutputImageType::Pointer dImage = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0));
	- itk::ImageRegionIteratorWithIndex< OutputImageType > dImageIt(dImage, outputRegionForThread);
	- dImageIt.GoToBegin();
	-
	- typename OutputImageType::Pointer kImage = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(1));
	- itk::ImageRegionIteratorWithIndex< OutputImageType > kImageIt(kImage, outputRegionForThread);
	- kImageIt.GoToBegin();
	-
	- typedef itk::ImageRegionConstIteratorWithIndex< InputImageType > InputIteratorType;
	- InputIteratorType inputIter( m_ProcessedInputImage, outputRegionForThread );
	- inputIter.GoToBegin();
	-
	- typedef itk::ImageRegionConstIteratorWithIndex< MaskImageType > MaskIteratorType;
	- MaskIteratorType maskIter( this->m_MaskImage, outputRegionForThread );
	- maskIter.GoToBegin();
	-
	- KurtosisFitConfiguration fit_config;
	- fit_config.omit_bzero = this->m_OmitBZero;
	- fit_config.fit_scale = this->m_ScaleForFitting;
	-
	- fit_config.use_K_limits = this->m_UseKBounds;
	- fit_config.K_limits = this->m_KurtosisBounds;
	-
	- vnl_vector<double> initial_position;
	- if( !this->m_OmitBZero )
	- {
	- initial_position.set_size(2);
	- initial_position[0] = this->m_InitialPosition[0];
	- initial_position[1] = this->m_InitialPosition[1];
	-
	- }
	- else
	- {
	- initial_position.set_size(3);
	- initial_position = this->m_InitialPosition;
	- }
	-
	- while( !inputIter.IsAtEnd() )
	- {
	- // set (reset) each iteration
	- vnl_vector<double> result = initial_position;
	-
	- // fit single voxel (if inside mask )
	- if( maskIter.Get() > 0 )
	- {
	- FitSingleVoxel( inputIter.Get(), this->m_BValues, result, fit_config );
	- }
	- else
	- {
	- result.fill(0);
	- }
	-
	- // regardless the fit type, the parameters are always in the first two position
	- // of the results vector
	- dImageIt.Set( result[0] );
	- kImageIt.Set( result[1] );
	-
	- //std::cout << "[Kurtosis.Fit]" << inputIter.GetIndex() << " --> " << dImageIt.GetIndex() << " result: " << result << std::endl;
	-
	- ++maskIter;
	- ++inputIter;
	- ++dImageIt;
	- ++kImageIt;
	- }
	-
	-}
	-
	-#endif // guards
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionKurtosisReconstructionImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionKurtosisReconstructionImageFilter.h
	deleted file mode 100644
	index 138b27f8c4..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionKurtosisReconstructionImageFilter.h
	+++ /dev/null
	@@ -1,442 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef DIFFUSIONKURTOSISRECONSTRUCTIONIMAGEFILTER_H
	-#define DIFFUSIONKURTOSISRECONSTRUCTIONIMAGEFILTER_H
	-
	-#include "itkImageToImageFilter.h"
	-#include "itkVectorImage.h"
	-
	-#include "mitkDiffusionPropertyHelper.h"
	-
	-// vnl includes
	-#include <vnl/algo/vnl_levenberg_marquardt.h>
	-#include <vnl/vnl_least_squares_function.h>
	-
	-namespace itk
	-{
	-
	- // Fitting routines
	-
	- /** @struct Kurtosis_fit_lsq_function
	- @brief A base least-squares function for the diffusion kurtosis fit (non-IVIM)
	-
	- The basic function fits the signal to S_0 = S * exp [ -b * D + -b^2 * D^2 * K^2 ]
	- */
	- struct kurtosis_fit_lsq_function :
	- public vnl_least_squares_function
	- {
	- public:
	- /** full lsq_function constructor */
	- kurtosis_fit_lsq_function( unsigned int num_params, unsigned int num_measurements, UseGradient g=no_gradient)
	- : vnl_least_squares_function( num_params, num_measurements, g),
	- m_use_bounds(false),
	- m_use_logscale(false),
	- m_skip_fit(false)
	- {}
	-
	- /** simplified constructor for the 2-parameters fit */
	- kurtosis_fit_lsq_function( unsigned int number_measurements)
	- : kurtosis_fit_lsq_function( 2, number_measurements, no_gradient )
	- {}
	-
	-
	- /** Initialize the function by setting measurements and the corresponding b-values */
	- void initialize( vnl_vector< double > const& _meas, vnl_vector< double> const& _bvals )
	- {
	- meas = _meas;
	- if( m_use_logscale )
	- {
	- for( unsigned int i=0; i< meas.size(); ++i)
	- {
	- // would produce NaN values, skip the fit
	- // using the virtual function from the superclass (sets a boolean flag)
	- if( meas[i] < vnl_math::eps )
	- {
	- m_skip_fit = true;
	- throw_failure();
	-
	- continue;
	- }
	-
	- meas[i] = log( meas[i] );
	-
	- }
	- }
	-
	- bvalues = _bvals;
	- }
	-
	-
	- /** use penalty terms on fitting to force the parameters stay within the default bounds */
	- void use_bounds()
	- {
	- m_use_bounds = true;
	-
	- // initialize bounds
	- double upper_bounds[2] = {4e-3, 4 };
	- kurtosis_upper_bounds = vnl_vector<double>(2, 2, upper_bounds);
	- kurtosis_lower_bounds = vnl_vector<double>(2, 0);
	- }
	-
	- void set_fit_logscale( bool flag )
	- {
	- this->m_use_logscale = flag;
	- }
	-
	- void set_K_bounds( const vnl_vector_fixed<double, 2> k_bounds )
	- {
	- // init
	- this->use_bounds();
	-
	- // override K bounds
	- kurtosis_lower_bounds[1] = k_bounds[0];
	- kurtosis_upper_bounds[1] = k_bounds[1];
	- }
	-
	- virtual void f(const vnl_vector<double> &x, vnl_vector<double> &fx)
	- {
	- for ( unsigned int s=0; s < fx.size(); s++ )
	- {
	- const double factor = ( meas[s] - M(x, s) );
	- fx[s] = factor * factor + penalty_term(x);
	- }
	-
	- MITK_DEBUG("Fit.x_and_f") << x << " \| " << fx;
	- }
	-
	- protected:
	-
	- /** Formula for diffusion term, use for internal computations */
	- double Diff( double x1, double x2, double b)
	- {
	- const double quotient = -1. * b * x1 + bb x1 * x1 * x2 / 6;
	-
	- if( m_use_logscale )
	- return quotient;
	- else
	- return exp(quotient);
	- }
	-
	- /** The fitting measurement function, has to be reimplemented in the classes */
	- virtual double M( vnl_vector<double> const& x, unsigned int idx )
	- {
	- const double bvalue = bvalues[idx];
	-
	- double result = Diff( x[0], x[1], bvalue);
	-
	- if( m_use_logscale )
	- return meas[0] + result;
	- else
	- return meas[0] * result ;
	- }
	-
	- /** Penalty term on D and K during fitting, make sure the vector that is passed in contains (D, K) in this ordering */
	- virtual double penalty_term( vnl_vector<double> const& x)
	- {
	- double penalty = 0;
	-
	- // skip when turned off
	- if( !m_use_bounds )
	- return penalty;
	-
	- // we have bounds for D and K only (the first two params )
	- for( unsigned int i=0; i< 2; i++)
	- {
	- // 5% penalty boundary
	- // use exponential function to scale the penalty (max when x[i] == bounds )
	- double penalty_boundary = 0.02 * (kurtosis_upper_bounds[i] - kurtosis_lower_bounds[i]);
	-
	- if( x[i] < kurtosis_lower_bounds[i] + penalty_boundary )
	- {
	- penalty += 1e6 * exp( -1 * ( x[i] - kurtosis_lower_bounds[i]) / penalty_boundary );
	- }
	- else if ( x[i] > kurtosis_upper_bounds[i] - penalty_boundary )
	- {
	- penalty += 1e6 * exp( -1 * ( kurtosis_upper_bounds[i] - x[i]) / penalty_boundary );
	- }
	- }
	-
	- MITK_DEBUG("Fit.Orig.Penalty") << x << " \|\| penalty: " << penalty;
	-
	- return penalty;
	- }
	-
	- bool m_use_bounds;
	-
	- bool m_use_logscale;
	-
	- bool m_skip_fit;
	-
	- vnl_vector<double> kurtosis_upper_bounds;
	- vnl_vector<double> kurtosis_lower_bounds;
	-
	- vnl_vector<double> meas;
	- vnl_vector<double> bvalues;
	-
	- };
	-
	- /** @struct kurtosis_fit_omit_unweighted
	- @brief A fitting function handling the unweighted signal b_0 as a fitted parameter */
	- struct kurtosis_fit_omit_unweighted
	- : public kurtosis_fit_lsq_function
	- {
	- public:
	- /** simplified constructor for the 3-parameters fit */
	- kurtosis_fit_omit_unweighted( unsigned int number_measurements)
	- : kurtosis_fit_lsq_function( 3, number_measurements, no_gradient )
	- {}
	-
	- protected:
	- virtual double M(const vnl_vector<double> &x, unsigned int idx) override
	- {
	- const double bvalue = bvalues[idx];
	-
	- double result = Diff( x[0], x[1], bvalue);
	-
	- if( m_use_logscale )
	- return log( x[2] ) + result;
	- else
	- return x[2] * result ;
	- }
	- };
	-
	- enum FitScale
	- {
	- STRAIGHT = 0,
	- LOGARITHMIC
	- };
	-
	- struct KurtosisFitConfiguration
	- {
	- KurtosisFitConfiguration()
	- : omit_bzero(false)
	- , use_K_limits(false)
	- , exclude_high_b(false)
	- , b_upper_threshold(10e9)
	- {}
	-
	- bool omit_bzero;
	- FitScale fit_scale;
	-
	- bool use_K_limits;
	- vnl_vector_fixed<double, 2> K_limits;
	-
	- bool exclude_high_b;
	- double b_upper_threshold;
	- };
	-
	-/**
	- @class DiffusionKurtosisReconstructionImageFilter
	- @brief This filter provides the fit of the kurtosis (non-IVIM) signal to the data
	-
	- It has two main modes of operation, either as an image filter to compute the D and K maps, i.e. fitting the values to each voxel or a computation on a single voxel
	- or a voxel group (with mask) can be triggered by @sa GetSnapshot, GetCurrentSnapshot methods.
	- */
	-template< class TInputPixelType, class TOutputPixelType >
	-class DiffusionKurtosisReconstructionImageFilter :
	- public ImageToImageFilter< VectorImage< TInputPixelType, 3>, Image<TOutputPixelType, 3> >
	-{
	-public:
	-
	- /**
	- @struct KurtosisSnapshot
	-
	- @brief Struct describing a result (and the data) of a Kurtosis model fit
	- */
	- struct KurtosisSnapshot
	- {
	- KurtosisSnapshot()
	- : m_f(1), m_BzeroFit(1), m_D(0.001), m_K(0) {}
	-
	- // input data structures
	- //vnl_vector<double> filtered_measurements;
	- vnl_vector<double> bvalues;
	- vnl_vector<double> measurements;
	-
	- vnl_vector<double> fit_bvalues;
	- vnl_vector<double> fit_measurements;
	- vnl_vector<unsigned int> weighted_image_indices;
	-
	- bool m_fittedBZero;
	-
	- // variables holding the fitted values
	- double m_f;
	- double m_BzeroFit;
	- double m_D;
	- double m_K;
	- };
	-
	- //-- class typedefs
	- typedef DiffusionKurtosisReconstructionImageFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageToImageFilter< VectorImage< TInputPixelType, 3>,
	- Image< TOutputPixelType,3 > > Superclass;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(DiffusionKurtosisReconstructionImageFilter, ImageToImageFilter)
	-
	- typedef TOutputPixelType OutputPixelType;
	- typedef TInputPixelType InputPixelType;
	-
	- typedef typename Superclass::InputImageType InputImageType;
	- typedef Image< OutputPixelType, 3 > OutputImageType;
	-
	- typedef itk::Image< short , 3> MaskImageType;
	-
	- typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
	-
	-
	- /** Holds each magnetic field gradient used to acquire one DWImage */
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionsContainerType
	- GradientDirectionContainerType;
	-
	- // vector image typedefs for regularized fit
	- typedef itk::VectorImage<float,3> VectorImageType;
	- typedef itk::Image<itk::Vector<double, 3>, 3> InitialFitImageType;
	-
	- //-- input (Set) methods
	- /** Set the initial solution for fitting, make sure the length and the values correspond to the parameters
	- * x0 = ( S_0, ADC_0, AKC_0 ) when also the S_0 is estimated
	- * x0 = ( ADC_0, AKC_0 ) when the S_0 is used in fitting
	- */
	- void SetInitialSolution(const vnl_vector<double>& x0 );
	-
	- /** Set whether the S_0 value is fitted or used in fitting */
	- void SetOmitUnweightedValue( bool flag)
	- { this->m_OmitBZero = flag; }
	-
	- /**
	- Trigger a single computation of the Kurtosis values from the given input vector and the bvalues and returns the result as a KurtosisSnapshot object */
	- KurtosisSnapshot GetSnapshot( const itk::VariableLengthVector< TInputPixelType > &input, vnl_vector<double> bvalues, KurtosisFitConfiguration kf_conf);
	-
	- /**
	- Trigger a single computation of the kurtosis values, first the bvalues vector is computed internally but then also stored into the returend snapshot */
	- KurtosisSnapshot GetSnapshot( const itk::VariableLengthVector< TInputPixelType > &input, GradientDirectionContainerType::Pointer, float bvalue, KurtosisFitConfiguration kf_conf);
	-
	- /**
	- * Returns the value of the current data presented to the filter.
	-
	- If a mask is set, the voxels are first averaged before passed to the fitting procedure
	- */
	- KurtosisSnapshot GetCurrentSnapshot(bool omit_bzero);
	-
	- /** Set the reference bvalue of the input DW image */
	- void SetReferenceBValue( double bvalue )
	- { this->m_ReferenceBValue = bvalue; }
	-
	- /** Set the gradient directions */
	- void SetGradientDirections( GradientDirectionContainerType::Pointer gradients );
	-
	- /** Restrict map generation to an image region */
	- void SetMapOutputRegion( OutputImageRegionType region )
	- {
	- m_MapOutputRegion = region;
	- this->m_ApplyPriorSmoothing = true;
	- }
	-
	- void SetImageMask( MaskImageType::Pointer mask );
	-
	- /** Set smoothing sigma (default = 1.5 ), automatically enables smoothing prior to fitting */
	- void SetSmoothingSigma( double sigma )
	- {
	- this->m_SmoothingSigma = sigma;
	- this->m_ApplyPriorSmoothing = true;
	- }
	-
	- /** Activate/Deactivate the gaussian smoothing applied to the input prior to fitting ( default = off ) */
	- void SetUseSmoothingPriorToFitting( bool flag)
	- {
	- this->m_ApplyPriorSmoothing = flag;
	- }
	-
	- /** Set boundaries enforced by penalty terms in the fitting procedure */
	- void SetBoundariesForKurtosis( double lower, double upper )
	- {
	- m_UseKBounds = true;
	-
	- m_KurtosisBounds[0] = lower; m_KurtosisBounds[1] = upper;
	- }
	-
	- /** Exclude measurements associated with b-values higher than max_bvalue from fitting */
	- void SetMaximalBValueUsedForFitting( double max_bvalue )
	- {
	- m_MaxFitBValue = max_bvalue;
	- }
	-
	- /** Select the method used in fitting of the data
	-
	- STRAIHT - fit the exponential signal equation S / S_0 = exp [ ... ]
	- LOGARITHMIC - fit the logarithmic signal equation ln( S / S_0 ) = []
	- */
	- void SetFittingScale( FitScale scale )
	- {
	- m_ScaleForFitting = scale;
	- }
	-
	-protected:
	- DiffusionKurtosisReconstructionImageFilter();
	- virtual ~DiffusionKurtosisReconstructionImageFilter() {}
	-
	- void GenerateOutputInformation() override;
	-
	- void AfterThreadedGenerateData() override;
	-
	- void BeforeThreadedGenerateData() override;
	-
	- void ThreadedGenerateData(const OutputImageRegionType &outputRegionForThread, ThreadIdType threadId) override;
	-
	- double m_ReferenceBValue;
	-
	- vnl_vector<double> m_BValues;
	-
	- vnl_vector<double> m_InitialPosition;
	-
	- bool m_OmitBZero;
	-
	- OutputImageRegionType m_MapOutputRegion;
	-
	- MaskImageType::Pointer m_MaskImage;
	-
	- typename InputImageType::Pointer m_ProcessedInputImage;
	-
	- bool m_ApplyPriorSmoothing;
	- double m_SmoothingSigma;
	-
	- bool m_UseKBounds;
	- vnl_vector_fixed<double, 2> m_KurtosisBounds;
	- double m_MaxFitBValue;
	-
	- FitScale m_ScaleForFitting;
	-
	-private:
	-
	-
	-};
	-
	-} //end namespace itk
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkDiffusionKurtosisReconstructionImageFilter.cxx"
	-#endif
	-
	-
	-#endif // DIFFUSIONKURTOSISRECONSTRUCTIONIMAGEFILTER_H
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionMultiShellQballReconstructionImageFilter.cpp b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionMultiShellQballReconstructionImageFilter.cpp
	deleted file mode 100644
	index 31b1c63b35..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionMultiShellQballReconstructionImageFilter.cpp
	+++ /dev/null
	@@ -1,1261 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef __itkDiffusionMultiShellQballReconstructionImageFilter_cpp
	-#define __itkDiffusionMultiShellQballReconstructionImageFilter_cpp
	-
	-#include <itkDiffusionMultiShellQballReconstructionImageFilter.h>
	-
	-#include <itkTimeProbe.h>
	-#include <itkPointShell.h>
	-#include <mitkDiffusionFunctionCollection.h>
	-
	-namespace itk {
	-
	-template< class T, class TG, class TO, int L, int NODF>
	-DiffusionMultiShellQballReconstructionImageFilter<T,TG,TO,L,NODF>
	-::DiffusionMultiShellQballReconstructionImageFilter() :
	- m_ReconstructionType(Mode_Standard1Shell),
	- m_Interpolation_Flag(false),
	- m_Interpolation_SHT1_inv(nullptr),
	- m_Interpolation_SHT2_inv(nullptr),
	- m_Interpolation_SHT3_inv(nullptr),
	- m_TARGET_SH_shell1(nullptr),
	- m_TARGET_SH_shell2(nullptr),
	- m_TARGET_SH_shell3(nullptr),
	- m_MaxDirections(0),
	- m_CoeffReconstructionMatrix(nullptr),
	- m_ODFSphericalHarmonicBasisMatrix(nullptr),
	- m_GradientDirectionContainer(nullptr),
	- m_NumberOfGradientDirections(0),
	- m_NumberOfBaselineImages(0),
	- m_Threshold(0),
	- m_BZeroImage(nullptr),
	- m_CoefficientImage(nullptr),
	- m_BValue(1.0),
	- m_Lambda(0.0),
	- m_IsHemisphericalArrangementOfGradientDirections(false),
	- m_IsArithmeticProgession(false)
	-{
	- // At least 1 inputs is necessary for a vector image.
	- // For images added one at a time we need at least six
	- this->SetNumberOfRequiredInputs( 1 );
	-}
	-
	-
	-template< class T, class TG, class TO, int L, int NODF>
	-void DiffusionMultiShellQballReconstructionImageFilter<T,TG,TO,L,NODF>
	-::SetGradientImage(const GradientDirectionContainerType *gradientDirection
	- , const GradientImagesType *gradientImage
	- , float bvalue)
	-{
	- m_BValue = bvalue;
	- m_NumberOfBaselineImages = 0;
	-
	- this->m_GradientDirectionContainer = GradientDirectionContainerType::New();
	- for(GradientDirectionContainerType::ConstIterator it = gradientDirection->Begin();
	- it != gradientDirection->End(); it++)
	- {
	- this->m_GradientDirectionContainer->push_back(it.Value());
	- }
	-
	-
	- if(m_BValueMap.size() == 0){
	- itkWarningMacro(<< "DiffusionMultiShellQballReconstructionImageFilter.cpp : no GradientIndexMapAvalible");
	-
	- GradientDirectionContainerType::ConstIterator gdcit;
	- for( gdcit = m_GradientDirectionContainer->Begin(); gdcit != m_GradientDirectionContainer->End(); ++gdcit)
	- {
	- double bValueKey = int(((m_BValue * gdcit.Value().two_norm() * gdcit.Value().two_norm())+7.5)/10)*10;
	- MITK_INFO << bValueKey;
	- m_BValueMap[bValueKey].push_back(gdcit.Index());
	- }
	-
	- }
	- if(m_BValueMap.find(0) == m_BValueMap.end())
	- {
	- itkExceptionMacro(<< "DiffusionMultiShellQballReconstructionImageFilter.cpp : GradientIndxMap with no b-Zero indecies found: check input BValueMap");
	- }
	-
	-
	- m_NumberOfBaselineImages = m_BValueMap[0].size();
	- m_NumberOfGradientDirections = gradientDirection->Size() - m_NumberOfBaselineImages;
	- // ensure that the gradient image we received has as many components as
	- // the number of gradient directions
	- if( gradientImage->GetVectorLength() != m_NumberOfBaselineImages + m_NumberOfGradientDirections )
	- {
	- itkExceptionMacro( << m_NumberOfGradientDirections << " gradients + " << m_NumberOfBaselineImages
	- << "baselines = " << m_NumberOfGradientDirections + m_NumberOfBaselineImages
	- << " directions specified but image has " << gradientImage->GetVectorLength()
	- << " components.");
	- }
	-
	-
	- ProcessObject::SetNthInput( 0, const_cast< GradientImagesType* >(gradientImage) );
	-
	- std::string gradientImageClassName(ProcessObject::GetInput(0)->GetNameOfClass());
	- if ( strcmp(gradientImageClassName.c_str(),"VectorImage") != 0 )
	- itkExceptionMacro( << "There is only one Gradient image. I expect that to be a VectorImage. But its of type: " << gradientImageClassName );
	-
	-
	- m_BZeroImage = BZeroImageType::New();
	- typename GradientImagesType::Pointer img = static_cast< GradientImagesType * >( ProcessObject::GetInput(0) );
	- m_BZeroImage->SetSpacing( img->GetSpacing() ); // Set the image spacing
	- m_BZeroImage->SetOrigin( img->GetOrigin() ); // Set the image origin
	- m_BZeroImage->SetDirection( img->GetDirection() ); // Set the image direction
	- m_BZeroImage->SetLargestPossibleRegion( img->GetLargestPossibleRegion());
	- m_BZeroImage->SetBufferedRegion( img->GetLargestPossibleRegion() );
	- m_BZeroImage->Allocate();
	-
	- m_CoefficientImage = CoefficientImageType::New();
	- m_CoefficientImage->SetSpacing( img->GetSpacing() ); // Set the image spacing
	- m_CoefficientImage->SetOrigin( img->GetOrigin() ); // Set the image origin
	- m_CoefficientImage->SetDirection( img->GetDirection() ); // Set the image direction
	- m_CoefficientImage->SetLargestPossibleRegion( img->GetLargestPossibleRegion());
	- m_CoefficientImage->SetBufferedRegion( img->GetLargestPossibleRegion() );
	- m_CoefficientImage->Allocate();
	-
	-}
	-
	-template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
	-void DiffusionMultiShellQballReconstructionImageFilter<TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType,NOrderL, NrOdfDirections>
	-::Normalize( OdfPixelType & out)
	-{
	- for(int i=0; i<NrOdfDirections; i++)
	- {
	- out[i] = out[i] < 0 ? 0 : out[i];
	- out[i] = itk::Math::pi 4 / NrOdfDirections;
	- }
	-}
	-
	-template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
	-void DiffusionMultiShellQballReconstructionImageFilter<TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType,NOrderL, NrOdfDirections>
	-::Projection1(vnl_vector<double> & vec, double delta)
	-{
	- if (delta==0){ //Clip attenuation values. If att<0 => att=0, if att>1 => att=1
	- for (unsigned int i=0; i<vec.size(); i++)
	- vec[i]=(vec[i]>=0 && vec[i]<=1)*vec[i]+(vec[i]>1);
	- }
	- else{ //Use function from Aganj et al, MRM, 2010
	- for (unsigned int i=0; i< vec.size(); i++)
	- vec[i]=CalculateThreashold(vec[i], delta);
	- }
	-}
	-
	-template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
	-double DiffusionMultiShellQballReconstructionImageFilter<TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType,NOrderL, NrOdfDirections>
	-::CalculateThreashold(const double value, const double delta)
	-{
	- return (value<0)(0.5delta) + (value>=0 && value<delta)(0.5delta+0.5(valuevalue)/delta)
	- + (value>=delta && value<1-delta)value+(value>=1-delta && value<1)(1-0.5delta-0.5((1-value)*(1-value))/delta)
	- + (value>=1)(1-0.5delta);
	-}
	-
	-template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
	-void DiffusionMultiShellQballReconstructionImageFilter<TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType,NOrderL, NrOdfDirections>
	-::Projection2( vnl_vector<double> & E1,vnl_vector<double> & E2, vnl_vector<double> & E3, double delta )
	-{
	-
	- const double sF = sqrt(5.0);
	-
	- vnl_vector<double> vOnes(m_MaxDirections);
	- vOnes.fill(1.0);
	-
	- vnl_matrix<double> T0(m_MaxDirections, 3);
	- vnl_matrix<unsigned char> C(m_MaxDirections, 7);
	- vnl_matrix<double> A(m_MaxDirections, 7);
	- vnl_matrix<double> B(m_MaxDirections, 7);
	-
	- vnl_vector<double> s0(m_MaxDirections);
	- vnl_vector<double> a0(m_MaxDirections);
	- vnl_vector<double> b0(m_MaxDirections);
	- vnl_vector<double> ta(m_MaxDirections);
	- vnl_vector<double> tb(m_MaxDirections);
	- vnl_vector<double> e(m_MaxDirections);
	- vnl_vector<double> m(m_MaxDirections);
	- vnl_vector<double> a(m_MaxDirections);
	- vnl_vector<double> b(m_MaxDirections);
	-
	-
	- // logarithmierung aller werte in E
	- for(unsigned int i = 0 ; i < m_MaxDirections; i++)
	- {
	- T0(i,0) = -log(E1(i));
	- T0(i,1) = -log(E2(i));
	- T0(i,2) = -log(E3(i));
	- }
	-
	- //T0 = -T0.apply(std::log);
	-
	-
	- // Summeiere Zeilenweise über alle Shells sum = E1+E2+E3
	- for(unsigned int i = 0 ; i < m_MaxDirections; i++)
	- {
	- s0[i] = T0(i,0) + T0(i,1) + T0(i,2);
	- }
	-
	- for(unsigned int i = 0; i < m_MaxDirections; i ++)
	- {
	- // Alle Signal-Werte auf der Ersten shell E(N,0) normiert auf s0
	- a0[i] = T0(i,0) / s0[i];
	- // Alle Signal-Werte auf der Zweiten shell E(N,1) normiert auf s0
	- b0[i] = T0(i,1) / s0[i];
	- }
	-
	- ta = a0 * 3.0;
	- tb = b0 * 3.0;
	- e = tb - (ta * 2.0);
	- m = (tb * 2.0 ) + ta;
	-
	- for(unsigned int i = 0; i <m_MaxDirections; i++)
	- {
	- C(i,0) = (tb[i] < 1+3delta && 0.5+1.5(sF+1)delta < ta[i] && ta[i] < 1-3 (sF+2) *delta);
	- C(i,1) = (e[i] <= -1+3(2sF+5)delta) && (ta[i]>=1-3(sF+2)*delta);
	- C(i,2) = (m[i] > 3-3sFdelta) && (-1+3(2sF+5)delta<e[i]) && (e[i]<-3sF*delta);
	- C(i,3) = (m[i] >= 3-3sFdelta && e[i] >= -3 sF delta);
	- C(i,4) = (2.5 + 1.5(5+sF)delta < m[i] && m[i] < 3-3sFdelta && e[i] > -3sFdelta);
	- C(i,5) = (ta[i] <= 0.5+1.5 (sF+1)delta && m[i] <= 2.5 + 1.5 (5+sF) delta);
	- C(i,6) = !((bool) C(i,0) \|\|(bool) C(i,1) \|\|(bool) C(i,2) \|\|(bool) C(i,3) \|\|(bool) C(i,4) \|\|(bool) C(i,5) ); // ~ANY(C(i,[0-5] ),2)
	-
	- A(i,0)=(bool)C(i,0) * a0(i);
	- A(i,1)=(bool)C(i,1) * (1.0/3.0-(sF+2)*delta);
	- A(i,2)=(bool)C(i,2) * (0.2+0.8a0(i)-0.4b0(i)-delta/sF);
	- A(i,3)=(bool)C(i,3) * (0.2+delta/sF);
	- A(i,4)=(bool)C(i,4) * (0.2a0(i)+0.4b0(i)+2*delta/sF);
	- A(i,5)=(bool)C(i,5) * (1.0/6.0+0.5(sF+1)delta);
	- A(i,6)=(bool)C(i,6) * a0(i);
	-
	- B(i,0)=(bool)C(i,0) * (1.0/3.0+delta);
	- B(i,1)=(bool)C(i,1) * (1.0/3.0+delta);
	- B(i,2)=(bool)C(i,2) * (0.4-0.4a0(i)+0.2b0(i)-2*delta/sF);
	- B(i,3)=(bool)C(i,3) * (0.4-3*delta/sF);
	- B(i,4)=(bool)C(i,4) * (0.4a0(i)+0.8b0(i)-delta/sF);
	- B(i,5)=(bool)C(i,5) * (1.0/3.0+delta);
	- B(i,6)=(bool)C(i,6) * b0(i);
	- }
	-
	- for(unsigned int i = 0 ; i < m_MaxDirections; i++)
	- {
	- double sumA = 0;
	- double sumB = 0;
	- for(int j = 0 ; j < 7; j++)
	- {
	- sumA += A(i,j);
	- sumB += B(i,j);
	- }
	- a[i] = sumA;
	- b[i] = sumB;
	- }
	-
	- for(unsigned int i = 0; i < m_MaxDirections; i++)
	- {
	- E1(i) = exp(-(a[i]*s0[i]));
	- E2(i) = exp(-(b[i]*s0[i]));
	- E3(i) = exp(-((1-a[i]-b[i])*s0[i]));
	- }
	-
	-}
	-
	-template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
	-void DiffusionMultiShellQballReconstructionImageFilter<TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType,NOrderL, NrOdfDirections>
	-::Projection3( vnl_vector<double> & A, vnl_vector<double> & a, vnl_vector<double> & b, double delta0)
	-{
	-
	- const double s6 = sqrt(6.0);
	- const double s15 = s6/2.0;
	-
	- vnl_vector<double> delta(a.size());
	- delta.fill(delta0);
	-
	- vnl_matrix<double> AM(a.size(), 15);
	- vnl_matrix<double> aM(a.size(), 15);
	- vnl_matrix<double> bM(a.size(), 15);
	- vnl_matrix<unsigned char> B(a.size(), 15);
	-
	- AM.set_column(0, A);
	- AM.set_column(1, A);
	- AM.set_column(2, A);
	- AM.set_column(3, delta);
	- AM.set_column(4, (A+a-b - (delta*s6))/3.0);
	- AM.set_column(5, delta);
	- AM.set_column(6, delta);
	- AM.set_column(7, delta);
	- AM.set_column(8, A);
	- AM.set_column(9, 0.2(a2+A-2(s6+1)delta));
	- AM.set_column(10,0.2(b(-2)+A+2-2(s6+1)delta));
	- AM.set_column(11, delta);
	- AM.set_column(12, delta);
	- AM.set_column(13, delta);
	- AM.set_column(14, 0.5-(1+s15)*delta);
	-
	-
	- aM.set_column(0, a);
	- aM.set_column(1, a);
	- aM.set_column(2, -delta + 1);
	- aM.set_column(3, a);
	- aM.set_column(4, (A2+a5+b+s6*delta)/6.0);
	- aM.set_column(5, a);
	- aM.set_column(6, -delta + 1);
	- aM.set_column(7, 0.5(a+b)+(1+s15)delta);
	- aM.set_column(8, -delta + 1);
	- aM.set_column(9, 0.2(a4+A2+(s6+1)delta));
	- aM.set_column(10, -delta + 1);
	- aM.set_column(11, (s6+3)*delta);
	- aM.set_column(12, -delta + 1);
	- aM.set_column(13, -delta + 1);
	- aM.set_column(14, -delta + 1);
	-
	- bM.set_column(0, b);
	- bM.set_column(1, delta);
	- bM.set_column(2, b);
	- bM.set_column(3, b);
	- bM.set_column(4, (A(-2)+a+b5-s6*delta)/6.0);
	- bM.set_column(5, delta);
	- bM.set_column(6, b);
	- bM.set_column(7, 0.5(a+b)-(1+s15)delta);
	- bM.set_column(8, delta);
	- bM.set_column(9, delta);
	- bM.set_column(10, 0.2(b4-A2+1-(s6+1)delta));
	- bM.set_column(11, delta);
	- bM.set_column(12, delta);
	- bM.set_column(13, -delta*(s6+3) + 1);
	- bM.set_column(14, delta);
	-
	- delta0 *= 0.99;
	-
	- vnl_matrix<double> R2(a.size(), 15);
	- std::vector<unsigned int> I(a.size());
	-
	- for (unsigned int i=0; i<AM.rows(); i++){
	- for (unsigned int j=0; j<AM.cols(); j++){
	- if (delta0 < AM(i,j) && 2(AM(i,j)+delta0s15)<aM(i,j)-bM(i,j) && bM(i,j)>delta0 && aM(i,j)<1-delta0)
	- R2(i,j) = (AM(i,j)-A(i))(AM(i,j)-A(i))+ (aM(i,j)-a(i))(aM(i,j)-a(i))+(bM(i,j)-b(i))*(bM(i,j)-b(i));
	- else
	- R2(i,j) = 1e20;
	- }
	- unsigned int index = 0;
	- double minvalue = 999;
	- for(int j = 0 ; j < 15 ; j++)
	- {
	- if(R2(i,j) < minvalue){
	- minvalue = R2(i,j);
	- index = j;
	- }
	- }
	- I[i] = index;
	- }
	-
	- for (unsigned int i=0; i < A.size(); i++){
	- A(i) = AM(i,(int)I[i]);
	- a(i) = aM(i,(int)I[i]);
	- b(i) = bM(i,(int)I[i]);
	- }
	-
	-}
	-
	-template<class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
	-void DiffusionMultiShellQballReconstructionImageFilter<TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType,NOrderL, NrOdfDirections>
	-::S_S0Normalization( vnl_vector<double> & vec, double S0 )
	-{
	- for(unsigned int i = 0; i < vec.size(); i++)
	- {
	- if (S0==0)
	- S0 = 0.01;
	- vec[i] /= S0;
	- }
	-
	-}
	-
	-template< class T, class TG, class TO, int L, int NODF>
	-void DiffusionMultiShellQballReconstructionImageFilter<T,TG,TO,L,NODF>
	-::DoubleLogarithm(vnl_vector<double> & vec)
	-{
	- for(unsigned int i = 0; i < vec.size(); i++)
	- {
	- vec[i] = log(-log(vec[i]));
	- }
	-}
	-
	-template< class T, class TG, class TO, int L, int NODF>
	-void DiffusionMultiShellQballReconstructionImageFilter<T,TG,TO,L,NODF>
	-::AfterThreadedGenerateData()
	-{
	- MITK_INFO << "Finished reconstruction";
	-}
	-
	-template< class T, class TG, class TO, int L, int NODF>
	-void DiffusionMultiShellQballReconstructionImageFilter<T,TG,TO,L,NODF>
	-::BeforeThreadedGenerateData()
	-{
	- m_ReconstructionType = Mode_Standard1Shell;
	-
	- if(m_BValueMap.size() == 4 ){
	-
	- BValueMapIteraotr it = m_BValueMap.begin();
	- it++; // skip b0 entry
	- const unsigned int bValue_shell1 = it->first;
	- const unsigned int size_shell1 = it->second.size();
	- IndiciesVector shell1 = it->second;
	- it++;
	- const unsigned int bValue_shell2 = it->first;
	- const unsigned int size_shell2 = it->second.size();
	- IndiciesVector shell2 = it->second;
	- it++;
	- const unsigned int bValue_shell3 = it->first;
	- const unsigned int size_shell3 = it->second.size();
	- IndiciesVector shell3 = it->second;
	-
	- // arithmetic progrssion
	- if(bValue_shell2 - bValue_shell1 == bValue_shell1 && bValue_shell3 - bValue_shell2 == bValue_shell1 )
	- {
	- // check if Interpolation is needed
	- // if shells with different numbers of directions exist
	- m_Interpolation_Flag = false;
	- if(size_shell1 != size_shell2 \|\| size_shell2 != size_shell3 \|\| size_shell1 != size_shell3)
	- {
	- m_Interpolation_Flag = true;
	- MITK_INFO << "Shell interpolation: shells with different numbers of directions";
	- }
	- else
	- {
	- // else if each shell holds same numbers of directions, but the gradient direction differ more than one 1 degree
	- m_Interpolation_Flag = CheckForDifferingShellDirections();
	- if(m_Interpolation_Flag) MITK_INFO << "Shell interpolation: gradient direction differ more than one 1 degree";
	- }
	-
	- m_ReconstructionType = Mode_Analytical3Shells;
	-
	- if(m_Interpolation_Flag)
	- {
	- unsigned int interp_SHOrder_shell1 = 12;
	- while( ((interp_SHOrder_shell1+1)*(interp_SHOrder_shell1+2)/2) > size_shell1 && interp_SHOrder_shell1 > L )
	- interp_SHOrder_shell1 -= 2 ;
	-
	- const int number_coeffs_shell1 = (int)(interp_SHOrder_shell1*interp_SHOrder_shell1 + interp_SHOrder_shell1 + 2.0)/2.0 + interp_SHOrder_shell1;
	-
	- unsigned int interp_SHOrder_shell2 = 12;
	- while( ((interp_SHOrder_shell2+1)*(interp_SHOrder_shell2+2)/2) > size_shell2 && interp_SHOrder_shell2 > L )
	- interp_SHOrder_shell2 -= 2 ;
	-
	- const int number_coeffs_shell2 = (int)(interp_SHOrder_shell2*interp_SHOrder_shell2 + interp_SHOrder_shell2 + 2.0)/2.0 + interp_SHOrder_shell2;
	-
	- unsigned int interp_SHOrder_shell3 = 12;
	- while( ((interp_SHOrder_shell3+1)*(interp_SHOrder_shell3+2)/2) > size_shell3 && interp_SHOrder_shell3 > L )
	- interp_SHOrder_shell3 -= 2 ;
	-
	- const int number_coeffs_shell3 = (int)(interp_SHOrder_shell3*interp_SHOrder_shell3 + interp_SHOrder_shell3 + 2.0)/2.0 + interp_SHOrder_shell3;
	-
	- // Create direction container for all directions (no duplicates, different directions from all shells)
	- IndiciesVector all_directions_container = GetAllDirections();
	- m_MaxDirections = all_directions_container.size();
	-
	- // create target SH-Basis
	- // initialize empty target matrix and set the wanted directions
	- vnl_matrix<double> * Q = new vnl_matrix<double>(3, m_MaxDirections);
	- ComputeSphericalFromCartesian(Q, all_directions_container);
	- // initialize a SH Basis, neede to interpolate from oldDirs -> newDirs
	- m_TARGET_SH_shell1 = new vnl_matrix<double>(m_MaxDirections, number_coeffs_shell1);
	- ComputeSphericalHarmonicsBasis(Q, m_TARGET_SH_shell1, interp_SHOrder_shell1);
	- delete Q;
	-
	- Q = new vnl_matrix<double>(3, m_MaxDirections);
	- ComputeSphericalFromCartesian(Q, all_directions_container);
	- m_TARGET_SH_shell2 = new vnl_matrix<double>(m_MaxDirections, number_coeffs_shell2);
	- ComputeSphericalHarmonicsBasis(Q, m_TARGET_SH_shell2, interp_SHOrder_shell2);
	- delete Q;
	-
	- Q = new vnl_matrix<double>(3, m_MaxDirections);
	- ComputeSphericalFromCartesian(Q, all_directions_container);
	- m_TARGET_SH_shell3 = new vnl_matrix<double>(m_MaxDirections, number_coeffs_shell3);
	- ComputeSphericalHarmonicsBasis(Q, m_TARGET_SH_shell3, interp_SHOrder_shell3);
	- delete Q;
	- // end creat target SH-Basis
	-
	-
	- // create measured-SHBasis
	- // Shell 1
	- vnl_matrix<double> * tempSHBasis;
	- vnl_matrix_inverse<double> * temp;
	-
	- // initialize empty matrix and set the measured directions of shell1
	- Q = new vnl_matrix<double>(3, shell1.size());
	- ComputeSphericalFromCartesian(Q, shell1);
	- // initialize a SH Basis, need to get the coeffs from measuredShell
	- tempSHBasis = new vnl_matrix<double>(shell1.size(), number_coeffs_shell1);
	- ComputeSphericalHarmonicsBasis(Q, tempSHBasis, interp_SHOrder_shell1);
	- // inversion of the SH=Basis
	- // c_s1 = B^-1 * shell1
	- // interp_Values = targetSHBasis * c_s1
	-
	- // Values = m_TARGET_SH_shell1 * Interpolation_SHT1_inv * DataShell1;
	- temp = new vnl_matrix_inverse<double>((*tempSHBasis));
	- m_Interpolation_SHT1_inv = new vnl_matrix<double>(temp->inverse());
	-
	- delete Q;
	- delete temp;
	- delete tempSHBasis;
	-
	- // Shell 2
	- Q = new vnl_matrix<double>(3, shell2.size());
	- ComputeSphericalFromCartesian(Q, shell2);
	-
	- tempSHBasis = new vnl_matrix<double>(shell2.size(), number_coeffs_shell2);
	- ComputeSphericalHarmonicsBasis(Q, tempSHBasis, interp_SHOrder_shell2);
	-
	- temp = new vnl_matrix_inverse<double>((*tempSHBasis));
	-
	- m_Interpolation_SHT2_inv = new vnl_matrix<double>(temp->inverse());
	-
	- delete Q;
	- delete temp;
	- delete tempSHBasis;
	-
	- // Shell 3
	- Q = new vnl_matrix<double>(3, shell3.size());
	- ComputeSphericalFromCartesian(Q, shell3);
	-
	- tempSHBasis = new vnl_matrix<double>(shell3.size(), number_coeffs_shell3);
	- ComputeSphericalHarmonicsBasis(Q, tempSHBasis, interp_SHOrder_shell3);
	-
	- temp = new vnl_matrix_inverse<double>((*tempSHBasis));
	-
	- m_Interpolation_SHT3_inv = new vnl_matrix<double>(temp->inverse());
	-
	- delete Q;
	- delete temp;
	- delete tempSHBasis;
	-
	- ComputeReconstructionMatrix(all_directions_container);
	-
	- MITK_INFO << "Reconstruction information: Multishell Reconstruction filter - Interpolation";
	- MITK_INFO << "Shell 1";
	- MITK_INFO << " SHOrder: " << interp_SHOrder_shell1;
	- MITK_INFO << " Number of Coeffs: " << number_coeffs_shell1;
	- MITK_INFO << " Number of Gradientdirections: " << size_shell1;
	-
	-
	- MITK_INFO << "Shell 2";
	- MITK_INFO << " SHOrder: " << interp_SHOrder_shell2;
	- MITK_INFO << " Number of Coeffs: " << number_coeffs_shell2;
	- MITK_INFO << " Number of Gradientdirections: " << size_shell2;
	-
	-
	- MITK_INFO << "Shell 3";
	- MITK_INFO << " SHOrder: " << interp_SHOrder_shell3;
	- MITK_INFO << " Number of Coeffs: " << number_coeffs_shell3;
	- MITK_INFO << " Number of Gradientdirections: " << size_shell3;
	-
	-
	- MITK_INFO << "Overall";
	- MITK_INFO << " SHOrder: " << L;
	- MITK_INFO << " Number of Coeffs: " << (L+1)(L+2)0.5;
	- MITK_INFO << " Number of Gradientdirections: " << m_MaxDirections;
	-
	- return;
	- }else
	- {
	- ComputeReconstructionMatrix(shell1);
	- }
	- }
	- }
	-
	- if(m_BValueMap.size() > 2 && m_ReconstructionType != Mode_Analytical3Shells)
	- {
	- m_ReconstructionType = Mode_NumericalNShells;
	- }
	- if(m_BValueMap.size() == 2){
	- BValueMapIteraotr it = m_BValueMap.begin();
	- it++; // skip b0 entry
	- IndiciesVector shell = it->second;
	- ComputeReconstructionMatrix(shell);
	- }
	-
	-}
	-
	-
	-template< class T, class TG, class TO, int L, int NODF>
	-void DiffusionMultiShellQballReconstructionImageFilter<T,TG,TO,L,NODF>
	-::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, ThreadIdType /NumberOfThreads/)
	-{
	-
	- itk::TimeProbe clock;
	- clock.Start();
	- switch(m_ReconstructionType)
	- {
	- case Mode_Standard1Shell:
	- StandardOneShellReconstruction(outputRegionForThread);
	- break;
	- case Mode_Analytical3Shells:
	- AnalyticalThreeShellReconstruction(outputRegionForThread);
	- break;
	- case Mode_NumericalNShells:
	- break;
	- }
	- clock.Stop();
	-}
	-
	-
	-template< class T, class TG, class TO, int L, int NODF>
	-void DiffusionMultiShellQballReconstructionImageFilter<T,TG,TO,L,NODF>
	-::StandardOneShellReconstruction(const OutputImageRegionType& outputRegionForThread)
	-{
	- // Get output image pointer
	- typename OdfImageType::Pointer outputImage = static_cast< OdfImageType * >(ProcessObject::GetPrimaryOutput());
	- // Get input gradient image pointer
	- typename GradientImagesType::Pointer gradientImagePointer = static_cast< GradientImagesType * >( ProcessObject::GetInput(0) );
	-
	- // ImageRegionIterator for the output image
	- ImageRegionIterator< OdfImageType > oit(outputImage, outputRegionForThread);
	- oit.GoToBegin();
	-
	- // ImageRegionIterator for the BZero (output) image
	- ImageRegionIterator< BZeroImageType > bzeroIterator(m_BZeroImage, outputRegionForThread);
	- bzeroIterator.GoToBegin();
	-
	- // Const ImageRegionIterator for input gradient image
	- typedef ImageRegionConstIterator< GradientImagesType > GradientIteratorType;
	- GradientIteratorType git(gradientImagePointer, outputRegionForThread );
	- git.GoToBegin();
	-
	- BValueMapIteraotr it = m_BValueMap.begin();
	- it++; // skip b0 entry
	- IndiciesVector SignalIndicies = it->second;
	- IndiciesVector BZeroIndicies = m_BValueMap[0];
	-
	- unsigned int NumbersOfGradientIndicies = SignalIndicies.size();
	-
	- typedef typename GradientImagesType::PixelType GradientVectorType;
	-
	- // iterate overall voxels of the gradient image region
	- while( ! git.IsAtEnd() )
	- {
	- GradientVectorType b = git.Get();
	- // ODF Vector
	- OdfPixelType odf(0.0);
	-
	- double b0average = 0;
	- const unsigned int b0size = BZeroIndicies.size();
	- for(unsigned int i = 0; i < b0size ; ++i)
	- {
	- b0average += b[BZeroIndicies[i]];
	- }
	- b0average /= b0size;
	- bzeroIterator.Set(b0average);
	- ++bzeroIterator;
	-
	- // Create the Signal Vector
	- vnl_vector<double> SignalVector(NumbersOfGradientIndicies);
	- if( (b0average != 0) && (b0average >= m_Threshold) )
	- {
	-
	- for( unsigned int i = 0; i< SignalIndicies.size(); i++ )
	- {
	- SignalVector[i] = static_cast<double>(b[SignalIndicies[i]]);
	- }
	-
	- // apply threashold an generate ln(-ln(E)) signal
	- // Replace SignalVector with PreNormalized SignalVector
	- S_S0Normalization(SignalVector, b0average);
	- Projection1(SignalVector);
	-
	- DoubleLogarithm(SignalVector);
	-
	- // approximate ODF coeffs
	- vnl_vector<double> coeffs = ( (m_CoeffReconstructionMatrix) SignalVector );
	- coeffs[0] = 1.0/(2.0*sqrt(itk::Math::pi));
	-
	- odf = element_cast<double, TO>(( (m_ODFSphericalHarmonicBasisMatrix) coeffs )).data_block();
	- odf = (itk::Math::pi4/NODF);
	- }
	- // set ODF to ODF-Image
	- oit.Set( odf );
	- ++oit;
	- ++git;
	-
	- }
	-}
	-
	-//#include "itkLevenbergMarquardtOptimizer.h"
	-
	-template< class T, class TG, class TO, int L, int NODF>
	-void DiffusionMultiShellQballReconstructionImageFilter<T,TG,TO,L,NODF>
	-::NumericalNShellReconstruction(const OutputImageRegionType& /outputRegionForThread/)
	-{
	-
	- /* itk::LevenbergMarquardtOptimizer::Pointer optimizer = itk::LevenbergMarquardtOptimizer::New();
	- optimizer->SetUseCostFunctionGradient(false);
	-
	- // Scale the translation components of the Transform in the Optimizer
	- itk::LevenbergMarquardtOptimizer::ScalesType scales(transform->GetNumberOfParameters());
	- scales.Fill(0.01);
	- unsigned long numberOfIterations = 80000;
	- double gradientTolerance = 1e-10; // convergence criterion
	- double valueTolerance = 1e-10; // convergence criterion
	- double epsilonFunction = 1e-10; // convergence criterion
	- optimizer->SetScales( scales );
	- optimizer->SetNumberOfIterations( numberOfIterations );
	- optimizer->SetValueTolerance( valueTolerance );
	- optimizer->SetGradientTolerance( gradientTolerance );
	- optimizer->SetEpsilonFunction( epsilonFunction );*/
	-
	-
	-}
	-
	-
	-template< class T, class TG, class TO, int L, int NODF>
	-void DiffusionMultiShellQballReconstructionImageFilter<T,TG,TO,L,NODF>
	-::AnalyticalThreeShellReconstruction(const OutputImageRegionType& outputRegionForThread)
	-{
	- // Input Gradient Image and Output ODF Image
	- typedef typename GradientImagesType::PixelType GradientVectorType;
	- typename OdfImageType::Pointer outputImage = static_cast< OdfImageType * >(ProcessObject::GetPrimaryOutput());
	- typename GradientImagesType::Pointer gradientImagePointer = static_cast< GradientImagesType * >( ProcessObject::GetInput(0) );
	-
	- // Define Image iterators
	- ImageRegionIterator< OdfImageType > odfOutputImageIterator(outputImage, outputRegionForThread);
	- ImageRegionConstIterator< GradientImagesType > gradientInputImageIterator(gradientImagePointer, outputRegionForThread );
	- ImageRegionIterator< BZeroImageType > bzeroIterator(m_BZeroImage, outputRegionForThread);
	- ImageRegionIterator< CoefficientImageType > coefficientImageIterator(m_CoefficientImage, outputRegionForThread);
	-
	- // All iterators seht to Begin of the specific OutputRegion
	- coefficientImageIterator.GoToBegin();
	- bzeroIterator.GoToBegin();
	- odfOutputImageIterator.GoToBegin();
	- gradientInputImageIterator.GoToBegin();
	-
	- // Get Shell Indicies for all non-BZero Gradients
	- // it MUST be a arithmetic progression eg.: 1000, 2000, 3000
	- BValueMapIteraotr it = m_BValueMap.begin();
	- it++;
	- // it = b-value = 1000
	- IndiciesVector Shell1Indiecies = it->second;
	- it++;
	- // it = b-value = 2000
	- IndiciesVector Shell2Indiecies = it->second;
	- it++;
	- // it = b-value = 3000
	- IndiciesVector Shell3Indiecies = it->second;
	- IndiciesVector BZeroIndicies = m_BValueMap[0];
	-
	- if(!m_Interpolation_Flag)
	- {
	- m_MaxDirections = Shell1Indiecies.size();
	- }// else: m_MaxDirection is set in BeforeThreadedGenerateData
	-
	- // Nx3 Signal Matrix with E(0) = Shell 1, E(1) = Shell 2, E(2) = Shell 3
	- vnl_vector< double > E1(m_MaxDirections);
	- vnl_vector< double > E2(m_MaxDirections);
	- vnl_vector< double > E3(m_MaxDirections);
	-
	- vnl_vector<double> AlphaValues(m_MaxDirections);
	- vnl_vector<double> BetaValues(m_MaxDirections);
	- vnl_vector<double> LAValues(m_MaxDirections);
	- vnl_vector<double> PValues(m_MaxDirections);
	-
	- vnl_vector<double> DataShell1(Shell1Indiecies.size());
	- vnl_vector<double> DataShell2(Shell2Indiecies.size());
	- vnl_vector<double> DataShell3(Shell3Indiecies.size());
	-
	- vnl_matrix<double> tempInterpolationMatrixShell1,tempInterpolationMatrixShell2,tempInterpolationMatrixShell3;
	-
	- if(m_Interpolation_Flag)
	- {
	- tempInterpolationMatrixShell1 = (m_TARGET_SH_shell1) (*m_Interpolation_SHT1_inv);
	- tempInterpolationMatrixShell2 = (m_TARGET_SH_shell2) (*m_Interpolation_SHT2_inv);
	- tempInterpolationMatrixShell3 = (m_TARGET_SH_shell3) (*m_Interpolation_SHT3_inv);
	- }
	-
	- OdfPixelType odf(0.0);
	- typename CoefficientImageType::PixelType coeffPixel(0.0);
	-
	- double P2,A,B2,B,P,alpha,beta,lambda, ER1, ER2;
	-
	-
	-
	- // iterate overall voxels of the gradient image region
	- while( ! gradientInputImageIterator.IsAtEnd() )
	- {
	-
	- odf = 0.0;
	- coeffPixel = 0.0;
	-
	- GradientVectorType b = gradientInputImageIterator.Get();
	-
	- // calculate for each shell the corresponding b0-averages
	- double shell1b0Norm =0;
	- double shell2b0Norm =0;
	- double shell3b0Norm =0;
	- double b0average = 0;
	- const unsigned int b0size = BZeroIndicies.size();
	-
	- if(b0size == 1)
	- {
	- shell1b0Norm = b[BZeroIndicies[0]];
	- shell2b0Norm = b[BZeroIndicies[0]];
	- shell3b0Norm = b[BZeroIndicies[0]];
	- b0average = b[BZeroIndicies[0]];
	- }else if(b0size % 3 ==0)
	- {
	- for(unsigned int i = 0; i < b0size ; ++i)
	- {
	- if(i < b0size / 3) shell1b0Norm += b[BZeroIndicies[i]];
	- if(i >= b0size / 3 && i < (b0size / 3)*2) shell2b0Norm += b[BZeroIndicies[i]];
	- if(i >= (b0size / 3) * 2) shell3b0Norm += b[BZeroIndicies[i]];
	- }
	- shell1b0Norm /= (b0size/3);
	- shell2b0Norm /= (b0size/3);
	- shell3b0Norm /= (b0size/3);
	- b0average = (shell1b0Norm + shell2b0Norm+ shell3b0Norm)/3;
	- }else
	- {
	- for(unsigned int i = 0; i <b0size ; ++i)
	- {
	- shell1b0Norm += b[BZeroIndicies[i]];
	- }
	- shell1b0Norm /= b0size;
	- shell2b0Norm = shell1b0Norm;
	- shell3b0Norm = shell1b0Norm;
	- b0average = shell1b0Norm;
	- }
	-
	- bzeroIterator.Set(b0average);
	- ++bzeroIterator;
	-
	- if( (b0average != 0) && ( b0average >= m_Threshold) )
	- {
	- // Get the Signal-Value for each Shell at each direction (specified in the ShellIndicies Vector .. this direction corresponse to this shell...)
	-
	- /*//fsl fix ---------------------------------------------------
	- for(int i = 0 ; i < Shell1Indiecies.size(); i++)
	- DataShell1[i] = static_cast<double>(b[Shell1Indiecies[i]]);
	- for(int i = 0 ; i < Shell2Indiecies.size(); i++)
	- DataShell2[i] = static_cast<double>(b[Shell2Indiecies[i]]);
	- for(int i = 0 ; i < Shell3Indiecies.size(); i++)
	- DataShell3[i] = static_cast<double>(b[Shell2Indiecies[i]]);
	-
	- // Normalize the Signal: Si/S0
	- S_S0Normalization(DataShell1, shell1b0Norm);
	- S_S0Normalization(DataShell2, shell2b0Norm);
	- S_S0Normalization(DataShell3, shell2b0Norm);
	- *///fsl fix -------------------------------------------ende--
	-
	- ///correct version
	- for(unsigned int i = 0 ; i < Shell1Indiecies.size(); i++)
	- DataShell1[i] = static_cast<double>(b[Shell1Indiecies[i]]);
	- for(unsigned int i = 0 ; i < Shell2Indiecies.size(); i++)
	- DataShell2[i] = static_cast<double>(b[Shell2Indiecies[i]]);
	- for(unsigned int i = 0 ; i < Shell3Indiecies.size(); i++)
	- DataShell3[i] = static_cast<double>(b[Shell3Indiecies[i]]);
	-
	-
	-
	- // Normalize the Signal: Si/S0
	- S_S0Normalization(DataShell1, shell1b0Norm);
	- S_S0Normalization(DataShell2, shell2b0Norm);
	- S_S0Normalization(DataShell3, shell3b0Norm);
	-
	-
	- if(m_Interpolation_Flag)
	- {
	- E1 = tempInterpolationMatrixShell1 * DataShell1;
	- E2 = tempInterpolationMatrixShell2 * DataShell2;
	- E3 = tempInterpolationMatrixShell3 * DataShell3;
	- }else{
	- E1 = (DataShell1);
	- E2 = (DataShell2);
	- E3 = (DataShell3);
	- }
	-
	- //Implements Eq. [19] and Fig. 4.
	- Projection1(E1);
	- Projection1(E2);
	- Projection1(E3);
	- //inqualities [31]. Taking the lograithm of th first tree inqualities
	- //convert the quadratic inqualities to linear ones.
	- Projection2(E1,E2,E3);
	-
	- for( unsigned int i = 0; i< m_MaxDirections; i++ )
	- {
	- double e1 = E1.get(i);
	- double e2 = E2.get(i);
	- double e3 = E3.get(i);
	-
	- P2 = e2-e1*e1;
	- A = (e3 -e1e2) / ( 2 P2);
	- B2 = A * A -(e1 * e3 - e2 * e2) /P2;
	- B = 0;
	- if(B2 > 0) B = sqrt(B2);
	- P = 0;
	- if(P2 > 0) P = sqrt(P2);
	-
	- alpha = A + B;
	- beta = A - B;
	-
	- PValues.put(i, P);
	- AlphaValues.put(i, alpha);
	- BetaValues.put(i, beta);
	-
	- }
	-
	- Projection3(PValues, AlphaValues, BetaValues);
	-
	- for(unsigned int i = 0 ; i < m_MaxDirections; i++)
	- {
	- const double fac = (PValues[i] * 2 ) / (AlphaValues[i] - BetaValues[i]);
	- lambda = 0.5 + 0.5 * std::sqrt(1 - fac * fac);;
	- ER1 = std::fabs(lambda * (AlphaValues[i] - BetaValues[i]) + (BetaValues[i] - E1.get(i) ))
	- + std::fabs(lambda * (AlphaValues[i] * AlphaValues[i] - BetaValues[i] * BetaValues[i]) + (BetaValues[i] * BetaValues[i] - E2.get(i) ))
	- + std::fabs(lambda * (AlphaValues[i] * AlphaValues[i] * AlphaValues[i] - BetaValues[i] * BetaValues[i] * BetaValues[i]) + (BetaValues[i] * BetaValues[i] * BetaValues[i] - E3.get(i) ));
	- ER2 = std::fabs((1-lambda) * (AlphaValues[i] - BetaValues[i]) + (BetaValues[i] - E1.get(i) ))
	- + std::fabs((1-lambda) * (AlphaValues[i] * AlphaValues[i] - BetaValues[i] * BetaValues[i]) + (BetaValues[i] * BetaValues[i] - E2.get(i) ))
	- + std::fabs((1-lambda) * (AlphaValues[i] * AlphaValues[i] * AlphaValues[i] - BetaValues[i] * BetaValues[i] * BetaValues[i]) + (BetaValues[i] * BetaValues[i] * BetaValues[i] - E3.get(i)));
	- if(ER1 < ER2)
	- LAValues.put(i, lambda);
	- else
	- LAValues.put(i, 1-lambda);
	-
	- }
	-
	- DoubleLogarithm(AlphaValues);
	- DoubleLogarithm(BetaValues);
	-
	- vnl_vector<double> SignalVector(element_product((LAValues) , (AlphaValues)-(BetaValues)) + (BetaValues));
	-
	- vnl_vector<double> coeffs((m_CoeffReconstructionMatrix) SignalVector );
	-
	- // the first coeff is a fix value
	- coeffs[0] = 1.0/(2.0*sqrt(itk::Math::pi));
	- coeffPixel = element_cast<double, TO>(coeffs).data_block();
	-
	- // Cast the Signal-Type from double to float for the ODF-Image
	- odf = element_cast<double, TO>( (m_ODFSphericalHarmonicBasisMatrix) coeffs ).data_block();
	- odf = ((itk::Math::pi4)/NODF);
	- }
	-
	- // set ODF to ODF-Image
	- coefficientImageIterator.Set(coeffPixel);
	- odfOutputImageIterator.Set( odf );
	- ++odfOutputImageIterator;
	- ++coefficientImageIterator;
	- ++gradientInputImageIterator;
	- }
	-
	-}
	-
	-
	-
	-template< class T, class TG, class TO, int L, int NODF>
	-void DiffusionMultiShellQballReconstructionImageFilter<T, TG, TO, L, NODF>::
	-ComputeSphericalHarmonicsBasis(vnl_matrix<double> * QBallReference, vnl_matrix<double> SHBasisOutput, int LOrder , vnl_matrix<double> LaplaciaBaltramiOutput, vnl_vector<int>* SHOrderAssociation, vnl_matrix<double>* SHEigenvalues)
	-{
	- for(unsigned int i=0; i< (*SHBasisOutput).rows(); i++)
	- {
	- for(int k = 0; k <= LOrder; k += 2)
	- {
	- for(int m =- k; m <= k; m++)
	- {
	- int j = ( k * k + k + 2 ) / 2 + m - 1;
	-
	- // Compute SHBasisFunctions
	- if(QBallReference){
	- double phi = (*QBallReference)(0,i);
	- double th = (*QBallReference)(1,i);
	- (*SHBasisOutput)(i,j) = mitk::sh::Yj(m,k,th,phi);
	- }
	-
	- // Laplacian Baltrami Order Association
	- if(LaplaciaBaltramiOutput)
	- (LaplaciaBaltramiOutput)(j,j) = kk(k + 1)(k+1);
	-
	- // SHEigenvalues with order Accosiation kj
	- if(SHEigenvalues)
	- (SHEigenvalues)(j,j) = -k (k+1);
	-
	- // Order Association
	- if(SHOrderAssociation)
	- (*SHOrderAssociation)[j] = k;
	-
	- }
	- }
	- }
	-}
	-
	-template< class T, class TG, class TO, int L, int NOdfDirections>
	-void DiffusionMultiShellQballReconstructionImageFilter<T,TG,TO,L,NOdfDirections>
	-::ComputeReconstructionMatrix(IndiciesVector const & refVector)
	-{
	-
	- typedef std::unique_ptr< vnl_matrix< double> > MatrixDoublePtr;
	- typedef std::unique_ptr< vnl_vector< int > > VectorIntPtr;
	- typedef std::unique_ptr< vnl_matrix_inverse< double > > InverseMatrixDoublePtr;
	-
	- int numberOfGradientDirections = refVector.size();
	-
	- if( numberOfGradientDirections <= (((L+1)*(L+2))/2) \|\| numberOfGradientDirections < 6 )
	- {
	- itkExceptionMacro( << "At least (L+1)(L+2)/2 gradient directions for each shell are required; current : " << numberOfGradientDirections );
	- }
	-
	- CheckDuplicateDiffusionGradients();
	-
	- const int LOrder = L;
	- int NumberOfCoeffs = (int)(LOrder*LOrder + LOrder + 2.0)/2.0 + LOrder;
	- MatrixDoublePtr SHBasisMatrix(new vnl_matrix<double>(numberOfGradientDirections,NumberOfCoeffs));
	- SHBasisMatrix->fill(0.0);
	- VectorIntPtr SHOrderAssociation(new vnl_vector<int>(NumberOfCoeffs));
	- SHOrderAssociation->fill(0.0);
	- MatrixDoublePtr LaplacianBaltrami(new vnl_matrix<double>(NumberOfCoeffs,NumberOfCoeffs));
	- LaplacianBaltrami->fill(0.0);
	- MatrixDoublePtr FRTMatrix(new vnl_matrix<double>(NumberOfCoeffs,NumberOfCoeffs));
	- FRTMatrix->fill(0.0);
	- MatrixDoublePtr SHEigenvalues(new vnl_matrix<double>(NumberOfCoeffs,NumberOfCoeffs));
	- SHEigenvalues->fill(0.0);
	-
	- MatrixDoublePtr Q(new vnl_matrix<double>(3, numberOfGradientDirections));
	-
	- // Convert Cartesian to Spherical Coordinates refVector -> Q
	- ComputeSphericalFromCartesian(Q.get(), refVector);
	-
	- // SHBasis-Matrix + LaplacianBaltrami-Matrix + SHOrderAssociationVector
	- ComputeSphericalHarmonicsBasis(Q.get() ,SHBasisMatrix.get() , LOrder , LaplacianBaltrami.get(), SHOrderAssociation.get(), SHEigenvalues.get());
	-
	- // Compute FunkRadon Transformation Matrix Associated to SHBasis Order lj
	- for(int i=0; i<NumberOfCoeffs; i++)
	- {
	- (FRTMatrix)(i,i) = 2.0 itk::Math::pi * mitk::sh::legendre0((*SHOrderAssociation)[i]);
	- }
	-
	- MatrixDoublePtr temp(new vnl_matrix<double>(((SHBasisMatrix->transpose()) * (SHBasisMatrix)) + (m_Lambda (*LaplacianBaltrami))));
	-
	- InverseMatrixDoublePtr pseudo_inv(new vnl_matrix_inverse<double>((*temp)));
	- MatrixDoublePtr inverse(new vnl_matrix<double>(NumberOfCoeffs,NumberOfCoeffs));
	- (*inverse) = pseudo_inv->inverse();
	-
	- const double factor = (1.0/(16.0itk::Math::piitk::Math::pi));
	- MatrixDoublePtr SignalReonstructionMatrix (new vnl_matrix<double>((inverse) (SHBasisMatrix->transpose())));
	- m_CoeffReconstructionMatrix = new vnl_matrix<double>(( factor * ((FRTMatrix) ((SHEigenvalues) (*SignalReonstructionMatrix))) ));
	-
	-
	- // SH Basis for ODF-reconstruction
	- vnl_matrix_fixed<double, 3, NOdfDirections>* U = PointShell<NOdfDirections, vnl_matrix_fixed<double, 3, NOdfDirections> >::DistributePointShell();
	- for(int i=0; i<NOdfDirections; i++)
	- {
	- double x = (*U)(0,i);
	- double y = (*U)(1,i);
	- double z = (*U)(2,i);
	- double cart[3];
	- mitk::sh::Cart2Sph(x,y,z,cart);
	- (*U)(0,i) = cart[0];
	- (*U)(1,i) = cart[1];
	- (*U)(2,i) = cart[2];
	- }
	-
	- MatrixDoublePtr tempPtr (new vnl_matrix<double>( U->as_matrix() ));
	- m_ODFSphericalHarmonicBasisMatrix = new vnl_matrix<double>(NOdfDirections,NumberOfCoeffs);
	- ComputeSphericalHarmonicsBasis(tempPtr.get(), m_ODFSphericalHarmonicBasisMatrix, LOrder);
	-}
	-
	-template< class T, class TG, class TO, int L, int NOdfDirections>
	-void DiffusionMultiShellQballReconstructionImageFilter<T,TG,TO,L,NOdfDirections>
	-::ComputeSphericalFromCartesian(vnl_matrix<double> * Q, IndiciesVector const & refShell)
	-{
	- for(unsigned int i = 0; i < refShell.size(); i++)
	- {
	- double x = m_GradientDirectionContainer->ElementAt(refShell[i]).normalize().get(0);
	- double y = m_GradientDirectionContainer->ElementAt(refShell[i]).normalize().get(1);
	- double z = m_GradientDirectionContainer->ElementAt(refShell[i]).normalize().get(2);
	- double cart[3];
	- mitk::sh::Cart2Sph(x,y,z,cart);
	- (*Q)(0,i) = cart[0];
	- (*Q)(1,i) = cart[1];
	- (*Q)(2,i) = cart[2];
	- }
	-}
	-
	-
	-template< class T, class TG, class TO, int L, int NODF>
	-bool DiffusionMultiShellQballReconstructionImageFilter<T,TG,TO,L,NODF>
	-::CheckDuplicateDiffusionGradients()
	-{
	- bool value = false;
	-
	- BValueMapIteraotr mapIterator = m_BValueMap.begin();
	- mapIterator++;
	- while(mapIterator != m_BValueMap.end())
	- {
	- std::vector<unsigned int>::const_iterator it1 = mapIterator->second.begin();
	- std::vector<unsigned int>::const_iterator it2 = mapIterator->second.begin();
	-
	- for(; it1 != mapIterator->second.end(); ++it1)
	- {
	- for(; it2 != mapIterator->second.end(); ++it2)
	- {
	- if(m_GradientDirectionContainer->ElementAt(it1) == m_GradientDirectionContainer->ElementAt(it2) && it1 != it2)
	- {
	- itkWarningMacro( << "Some of the Diffusion Gradients equal each other. Corresponding image data should be averaged before calling this filter." );
	- value = true;
	- }
	- }
	- }
	- ++mapIterator;
	- }
	- return value;
	-}
	-
	-template< class T, class TG, class TO, int L, int NODF>
	-std::vector<unsigned int> DiffusionMultiShellQballReconstructionImageFilter<T,TG,TO,L,NODF>
	-::GetAllDirections()
	-{
	- IndiciesVector directioncontainer;
	-
	- BValueMapIteraotr mapIterator = m_BValueMap.begin();
	- mapIterator++;
	- IndiciesVector shell1 = mapIterator->second;
	- mapIterator++;
	- IndiciesVector shell2 = mapIterator->second;
	- mapIterator++;
	- IndiciesVector shell3 = mapIterator->second;
	-
	- while(shell1.size()>0)
	- {
	- unsigned int wntIndex = shell1.back();
	- shell1.pop_back();
	-
	- IndiciesVector::iterator containerIt = directioncontainer.begin();
	- bool directionExist = false;
	- while(containerIt != directioncontainer.end())
	- {
	- if (fabs(dot(m_GradientDirectionContainer->ElementAt(*containerIt), m_GradientDirectionContainer->ElementAt(wntIndex))) > 0.9998)
	- {
	- directionExist = true;
	- break;
	- }
	- containerIt++;
	- }
	- if(!directionExist)
	- {
	- directioncontainer.push_back(wntIndex);
	- }
	- }
	-
	- while(shell2.size()>0)
	- {
	- unsigned int wntIndex = shell2.back();
	- shell2.pop_back();
	-
	- IndiciesVector::iterator containerIt = directioncontainer.begin();
	- bool directionExist = false;
	- while(containerIt != directioncontainer.end())
	- {
	- if (fabs(dot(m_GradientDirectionContainer->ElementAt(*containerIt), m_GradientDirectionContainer->ElementAt(wntIndex))) > 0.9998)
	- {
	- directionExist = true;
	- break;
	- }
	- containerIt++;
	- }
	- if(!directionExist)
	- {
	- directioncontainer.push_back(wntIndex);
	- }
	- }
	-
	- while(shell3.size()>0)
	- {
	- unsigned int wntIndex = shell3.back();
	- shell3.pop_back();
	-
	- IndiciesVector::iterator containerIt = directioncontainer.begin();
	- bool directionExist = false;
	- while(containerIt != directioncontainer.end())
	- {
	- if (fabs(dot(m_GradientDirectionContainer->ElementAt(*containerIt), m_GradientDirectionContainer->ElementAt(wntIndex))) > 0.9998)
	- {
	- directionExist = true;
	- break;
	- }
	- containerIt++;
	- }
	- if(!directionExist)
	- {
	- directioncontainer.push_back(wntIndex);
	- }
	- }
	-
	- return directioncontainer;
	-}
	-
	-// corresponding directions between shells (e.g. dir1_shell1 vs dir1_shell2) differ more than 1 degree.
	-template< class T, class TG, class TO, int L, int NODF>
	-bool DiffusionMultiShellQballReconstructionImageFilter<T,TG,TO,L,NODF>
	-::CheckForDifferingShellDirections()
	-{
	- bool interp_flag = false;
	-
	- BValueMapIteraotr mapIterator = m_BValueMap.begin();
	- mapIterator++;
	- IndiciesVector shell1 = mapIterator->second;
	- mapIterator++;
	- IndiciesVector shell2 = mapIterator->second;
	- mapIterator++;
	- IndiciesVector shell3 = mapIterator->second;
	-
	- for (unsigned int i=0; i< shell1.size(); i++)
	- if (fabs(dot(m_GradientDirectionContainer->ElementAt(shell1[i]), m_GradientDirectionContainer->ElementAt(shell2[i]))) <= 0.9998) {interp_flag=true; break;}
	- for (unsigned int i=0; i< shell1.size(); i++)
	- if (fabs(dot(m_GradientDirectionContainer->ElementAt(shell1[i]), m_GradientDirectionContainer->ElementAt(shell3[i]))) <= 0.9998) {interp_flag=true; break;}
	- for (unsigned int i=0; i< shell1.size(); i++)
	- if (fabs(dot(m_GradientDirectionContainer->ElementAt(shell2[i]), m_GradientDirectionContainer->ElementAt(shell3[i]))) <= 0.9998) {interp_flag=true; break;}
	- return interp_flag;
	-}
	-
	-
	-template< class T, class TG, class TO, int L, int NODF>
	-void DiffusionMultiShellQballReconstructionImageFilter<T,TG,TO,L,NODF>
	-::PrintSelf(std::ostream& os, Indent indent) const
	-{
	- std::locale C("C");
	- std::locale originalLocale = os.getloc();
	- os.imbue(C);
	-
	- Superclass::PrintSelf(os,indent);
	-
	- //os << indent << "OdfReconstructionMatrix: " << m_ReconstructionMatrix << std::endl;
	- if ( m_GradientDirectionContainer )
	- {
	- os << indent << "GradientDirectionContainer: "
	- << m_GradientDirectionContainer << std::endl;
	- }
	- else
	- {
	- os << indent <<
	- "GradientDirectionContainer: (Gradient directions not set)" << std::endl;
	- }
	- os << indent << "NumberOfGradientDirections: " <<
	- m_NumberOfGradientDirections << std::endl;
	- os << indent << "NumberOfBaselineImages: " <<
	- m_NumberOfBaselineImages << std::endl;
	- os << indent << "Threshold for reference B0 image: " << m_Threshold << std::endl;
	- os << indent << "BValue: " << m_BValue << std::endl;
	-
	- os.imbue( originalLocale );
	-}
	-
	-
	-
	-
	-}
	-
	-#endif // __itkDiffusionMultiShellQballReconstructionImageFilter_cpp
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionMultiShellQballReconstructionImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionMultiShellQballReconstructionImageFilter.h
	deleted file mode 100644
	index ca788873e5..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionMultiShellQballReconstructionImageFilter.h
	+++ /dev/null
	@@ -1,221 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkDiffusionMultiShellQballReconstructionImageFilter_h_
	-#define __itkDiffusionMultiShellQballReconstructionImageFilter_h_
	-
	-#include <itkImageToImageFilter.h>
	-
	-namespace itk{
	-/** \class DiffusionMultiShellQballReconstructionImageFilter
	- I. Aganj, C. Lenglet, G. Sapiro, E. Yacoub, K. Ugurbil, and N. Harel, “Reconstruction of the orientation distribution function in single and multiple shell q-ball imaging within constant solid angle,” Magnetic Resonance in Medicine, vol. 64, no. 2, pp. 554–566, 2010.
	- */
	-
	-template< class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections>
	-class DiffusionMultiShellQballReconstructionImageFilter : public ImageToImageFilter< Image< TReferenceImagePixelType, 3 >, Image< Vector< TOdfPixelType, NrOdfDirections >, 3 > >
	-{
	-
	-public:
	-
	- typedef DiffusionMultiShellQballReconstructionImageFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageToImageFilter< Image< TReferenceImagePixelType, 3>, Image< Vector< TOdfPixelType, NrOdfDirections >, 3 > > Superclass;
	- typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
	-
	- typedef TReferenceImagePixelType ReferencePixelType;
	-
	- /** GradientImageType
	- * (e.g. type short)*/
	- typedef TGradientImagePixelType GradientPixelType;
	-
	- /** GradientImageType
	- * 3D VectorImage containing GradientPixelTypes */
	-
	- typedef VectorImage< GradientPixelType, 3 > GradientImagesType;
	-
	- /** ODF PixelType */
	- typedef Vector< TOdfPixelType, NrOdfDirections > OdfPixelType;
	- /** ODF ImageType */
	- typedef Image< OdfPixelType, 3 > OdfImageType;
	- /** BzeroImageType */
	- typedef Image< TOdfPixelType, 3 > BZeroImageType;
	-
	-
	- /** Container to hold gradient directions of the 'n' DW measurements */
	- typedef VectorContainer< unsigned int, vnl_vector_fixed< double, 3 > > GradientDirectionContainerType;
	-
	- typedef Image< Vector< TOdfPixelType, (NOrderL*NOrderL + NOrderL + 2)/2 + NOrderL >, 3 > CoefficientImageType;
	-
	- typedef std::map<unsigned int, std::vector<unsigned int> > BValueMap;
	- typedef std::map<unsigned int, std::vector<unsigned int> >::iterator BValueMapIteraotr;
	- typedef std::vector<unsigned int> IndiciesVector;
	-
	- // --------------------------------------------------------------------------------------------//
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- /** Runtime information support. */
	- itkTypeMacro(DiffusionMultiShellQballReconstructionImageFilter, ImageToImageFilter)
	-
	- /** Get reference image */
	- virtual typename Superclass::InputImageType * GetInputImage()
	- { return ( static_cast< typename Superclass::InputImageType *>(this->ProcessObject::GetInput(0)) ); }
	-
	- /** Replaces the Input method.
	- * Var vols = mitk::Image
	- * -----------------------------------------------------
	- * GradientDirectionContainerType-Input gradientDirectionContainer (e.g. GradientDirectionsContainerProperty)
	- * GradientImagesType-Input gradientImage (e.g. itkVectorImage)
	- * float-Input bvalue (e.g. ReferenceBValueProperty) */
	- void SetGradientImage( const GradientDirectionContainerType * gradientDirectionContainer, const GradientImagesType *gradientImage , float bvalue);//, std::vector<bool> listOfUserSelctedBValues );
	-
	- /** Set a BValue Map (key = bvalue, value = indicies splittet for each shell)
	- * If the input image containes more than three q-shells
	- * (e.g. b-Values of 0, 1000, 2000, 3000, 4000, ...).
	- * For the Analytical-Reconstruction it is needed to set a
	- * BValue Map containing three shells in an arithmetic series
	- * (e.g. 0, 1000, 2000, 3000).
	- */
	- inline void SetBValueMap(BValueMap map){this->m_BValueMap = map;}
	-
	- /** Threshold on the reference image data. The output ODF will be a null
	- * pdf for pixels in the reference image that have a value less than this
	- * threshold. */
	- itkSetMacro( Threshold, ReferencePixelType )
	- itkGetMacro( Threshold, ReferencePixelType )
	-
	- itkGetMacro( CoefficientImage, typename CoefficientImageType::Pointer )
	- /** Return non-diffusion weighted images */
	- itkGetMacro( BZeroImage, typename BZeroImageType::Pointer)
	-
	- /** Factor for Laplacian-Baltrami smoothing of the SH-coefficients*/
	- itkSetMacro( Lambda, double )
	- itkGetMacro( Lambda, double )
	-
	-protected:
	- DiffusionMultiShellQballReconstructionImageFilter();
	- ~DiffusionMultiShellQballReconstructionImageFilter() { }
	- void PrintSelf(std::ostream& os, Indent indent) const;
	- void BeforeThreadedGenerateData();
	- void AfterThreadedGenerateData();
	- void ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, ThreadIdType NumberOfThreads );
	-
	-
	-private:
	-
	- enum ReconstructionType
	- {
	- Mode_Analytical3Shells,
	- Mode_NumericalNShells,
	- Mode_Standard1Shell
	- };
	-
	- ReconstructionType m_ReconstructionType;
	-
	- // Interpolation
	- bool m_Interpolation_Flag;
	- vnl_matrix< double > * m_Interpolation_SHT1_inv;
	- vnl_matrix< double > * m_Interpolation_SHT2_inv;
	- vnl_matrix< double > * m_Interpolation_SHT3_inv;
	- vnl_matrix< double > * m_TARGET_SH_shell1;
	- vnl_matrix< double > * m_TARGET_SH_shell2;
	- vnl_matrix< double > * m_TARGET_SH_shell3;
	- unsigned int m_MaxDirections;
	-
	- vnl_matrix< double > * m_CoeffReconstructionMatrix;
	- vnl_matrix< double > * m_ODFSphericalHarmonicBasisMatrix;
	-
	- /** container to hold gradient directions */
	- GradientDirectionContainerType::Pointer m_GradientDirectionContainer;
	-
	- /** Number of gradient measurements */
	- unsigned int m_NumberOfGradientDirections;
	-
	- /** Number of baseline images */
	- unsigned int m_NumberOfBaselineImages;
	-
	- /** Threshold on the reference image data */
	- ReferencePixelType m_Threshold;
	-
	- typename BZeroImageType::Pointer m_BZeroImage;
	-
	- typename CoefficientImageType::Pointer m_CoefficientImage;
	-
	- float m_BValue;
	-
	- BValueMap m_BValueMap;
	-
	- double m_Lambda;
	-
	- bool m_IsHemisphericalArrangementOfGradientDirections;
	-
	- bool m_IsArithmeticProgession;
	-
	- void ComputeReconstructionMatrix(IndiciesVector const & refVector);
	- void ComputeODFSHBasis();
	- bool CheckDuplicateDiffusionGradients();
	- bool CheckForDifferingShellDirections();
	- IndiciesVector GetAllDirections();
	- void ComputeSphericalHarmonicsBasis(vnl_matrix<double>* QBallReference, vnl_matrix<double>* SHBasisOutput, int Lorder , vnl_matrix<double>* LaplaciaBaltramiOutput =0 , vnl_vector<int>* SHOrderAssociation =0 , vnl_matrix<double> * SHEigenvalues =0);
	- void Normalize(OdfPixelType & odf );
	- void S_S0Normalization( vnl_vector<double> & vec, double b0 = 0 );
	- void DoubleLogarithm(vnl_vector<double> & vec);
	- double CalculateThreashold(const double value, const double delta);
	- void Projection1(vnl_vector<double> & vec, double delta = 0.01);
	- void Projection2( vnl_vector<double> & E1, vnl_vector<double> & E2, vnl_vector<double> & E3, double delta = 0.01);
	- void Projection3( vnl_vector<double> & A, vnl_vector<double> & alpha, vnl_vector<double> & beta, double delta = 0.01);
	- void StandardOneShellReconstruction(const OutputImageRegionType& outputRegionForThread);
	- void AnalyticalThreeShellReconstruction(const OutputImageRegionType& outputRegionForThread);
	- void NumericalNShellReconstruction(const OutputImageRegionType& outputRegionForThread);
	- void GenerateAveragedBZeroImage(const OutputImageRegionType& outputRegionForThread);
	- void ComputeSphericalFromCartesian(vnl_matrix<double> * Q, const IndiciesVector & refShell);
	-
	-
	- //------------------------- VNL-function ------------------------------------
	-
	- template<typename CurrentValue, typename WntValue>
	- vnl_vector< WntValue> element_cast (vnl_vector< CurrentValue> const& v1)
	- {
	- vnl_vector<WntValue> result(v1.size());
	-
	- for(unsigned int i = 0 ; i < v1.size(); i++)
	- result[i] = static_cast< WntValue>(v1[i]);
	-
	- return result;
	- }
	-
	- template<typename type>
	- double dot (vnl_vector_fixed< type ,3> const& v1, vnl_vector_fixed< type ,3 > const& v2 )
	- {
	- double result = (v1[0] * v2[0] + v1[1] * v2[1] + v1[2] * v2[2]) / (v1.two_norm() * v2.two_norm());
	- return result ;
	- }
	-
	-
	-
	-
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkDiffusionMultiShellQballReconstructionImageFilter.cpp"
	-#endif
	-
	-#endif //__itkDiffusionMultiShellQballReconstructionImageFilter_h_
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionQballReconstructionImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionQballReconstructionImageFilter.h
	deleted file mode 100644
	index 121bbfae7a..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionQballReconstructionImageFilter.h
	+++ /dev/null
	@@ -1,341 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkDiffusionQballReconstructionImageFilter_h_
	-#define __itkDiffusionQballReconstructionImageFilter_h_
	-
	-#include "itkImageToImageFilter.h"
	-//#include "vnl/vnl_matrix.h"
	-#include "vnl/vnl_vector_fixed.h"
	-#include "vnl/vnl_matrix.h"
	-#include "vnl/algo/vnl_svd.h"
	-#include "itkVectorContainer.h"
	-#include "itkVectorImage.h"
	-
	-namespace itk{
	-/** \class DiffusionQballReconstructionImageFilter
	- * \brief This class takes as input one or more reference images (acquired in the
	- * absence of diffusion sensitizing gradients) and 'n' diffusion
	- * weighted images and their gradient directions and computes an image of
	- * orientation distribution functions (ODFs).
	- *
	- * \par Inputs and Usage
	- * There are two ways to use this class. When you have one reference image and \c n
	- * gradient images, you would use the class as
	- * \code
	- * filter->SetReferenceImage( image0 );
	- * filter->AddGradientImage( direction1, image1 );
	- * filter->AddGradientImage( direction2, image2 );
	- * ...
	- * \endcode
	- *
	- * \par
	- * When you have the 'n' gradient and one or more reference images in a single
	- * multi-component image (VectorImage), you can specify the images simply as
	- * \code
	- * filter->SetGradientImage( directionsContainer, vectorImage );
	- * \endcode
	- * Note that this method is used to specify both the reference and gradient images.
	- * This is convenient when the DWI images are read in using the
	- * <a href="http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format">NRRD</a>
	- * format. Like the Nrrd format, the reference images are those components of the
	- * vectorImage whose gradient direction is (0,0,0). If more than one reference image
	- * is present, they are averaged prior to the reconstruction.
	- *
	- * \par Outputs
	- * The output image is an image of vectors that must be understood as ODFs:
	- * \code
	- * Image< Vector< TPixelType, OdfNrDirections >, 3 >
	- * \endcode
	- *
	- * \par Parameters
	- * \li Threshold - Threshold on the reference image data. The output ODF will
	- * be a null pdf for pixels in the reference image that have a value less
	- * than this.
	- * \li BValue - See the documentation of SetBValue().
	- * \li At least 6 gradient images must be specified for the filter to be able
	- * to run. If the input gradient directions g_i are majorly sampled on one half
	- * of the sqhere, then each input image I_i will be duplicated and assign -g_i
	- * in order to guarantee stability of the Tuch-Algorithm.
	- * \li OdfDirections - directions of resulting orientation distribution function
	- * \li EquatorNrSamplingPoints - number of sampling points on equator when
	- * performing Funk Radeon Transform (FRT)
	- * \li BasisFunctionCenters - the centers of the basis functions are used for
	- * the sRBF (spherical radial basis functions interpolation). If not set, they
	- * will be defaulted to equal m_EquatorNrSamplingPoints
	- *
	- * \par Template parameters
	- * The class is templated over
	- * \li the pixel type of the reference and gradient images
	- * (expected to be scalar data types)
	- * \li the internal representation of the ODF pixels (double, float etc).
	- * \li the number of OdfDirections
	- * \li the number of basis function centers for the sRBF
	- *
	- * \par References:
	- * \li<a href="http://www3.interscience.wiley.com/cgi-bin/fulltext/109800293/PDFSTART">[1]</a>
	- * <em>Tuch DS,
	- * "Q-ball imaging", Magn Reson Med. 2004 Dec;52(6):1358-72.</em>
	- *
	- */
	-
	-template< class TReferenceImagePixelType,
	- class TGradientImagePixelType,
	- class TOdfPixelType,
	- int NrOdfDirections,
	- int NrBasisFunctionCenters = NrOdfDirections>
	-class DiffusionQballReconstructionImageFilter :
	- public ImageToImageFilter< Image< TReferenceImagePixelType, 3 >,
	- Image< Vector< TOdfPixelType, NrOdfDirections >, 3 > >
	-{
	-
	-public:
	-
	- /** \class DiffusionQballReconstructionImageFilter
	- * \brief This enum defines the normalization of the ODFs.
	- * \par
	- * Standard normalization simply divides by sum of ODF-values
	- * to ensure properties of a probability density function.
	- * \par
	- * B-zero/b-value normalization is ADC-style log of ratio
	- * between b-zero and b_i normalized by b-value.
	- * \par
	- * B-zero normalization simply divides by b-zero reference value
	- */
	- enum Normalization {
	- QBR_STANDARD,
	- QBR_B_ZERO_B_VALUE,
	- QBR_B_ZERO,
	- QBR_NONE
	- };
	-
	- typedef DiffusionQballReconstructionImageFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageToImageFilter< Image< TReferenceImagePixelType, 3>,
	- Image< Vector< TOdfPixelType, NrOdfDirections >, 3 > >
	- Superclass;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(DiffusionQballReconstructionImageFilter,
	- ImageToImageFilter);
	-
	- typedef TReferenceImagePixelType ReferencePixelType;
	-
	- typedef TGradientImagePixelType GradientPixelType;
	-
	- typedef Vector< TOdfPixelType, NrOdfDirections >
	- OdfPixelType;
	-
	- /** Reference image data, This image is aquired in the absence
	- * of a diffusion sensitizing field gradient */
	- typedef typename Superclass::InputImageType ReferenceImageType;
	-
	- typedef Image< OdfPixelType, 3 > OdfImageType;
	-
	- typedef OdfImageType OutputImageType;
	-
	- typedef TOdfPixelType BZeroPixelType;
	-
	- typedef Image< BZeroPixelType, 3 > BZeroImageType;
	-
	- typedef typename Superclass::OutputImageRegionType
	- OutputImageRegionType;
	-
	- /** Typedef defining one (of the many) gradient images. */
	- typedef Image< GradientPixelType, 3 > GradientImageType;
	-
	- /** An alternative typedef defining one (of the many) gradient images.
	- * It will be assumed that the vectorImage has the same dimension as the
	- * Reference image and a vector length parameter of \c n (number of
	- * gradient directions)*/
	- typedef VectorImage< GradientPixelType, 3 > GradientImagesType;
	-
	- /** Holds the ODF reconstruction matrix */
	- typedef vnl_matrix< TOdfPixelType >*
	- OdfReconstructionMatrixType;
	-
	- /** Holds each magnetic field gradient used to acquire one DWImage */
	- typedef vnl_vector_fixed< double, 3 > GradientDirectionType;
	-
	- /** Container to hold gradient directions of the 'n' DW measurements */
	- typedef VectorContainer< unsigned int,
	- GradientDirectionType > GradientDirectionContainerType;
	-
	- itkStaticConstMacro(NOdfDirections,int,NrOdfDirections);
	- itkStaticConstMacro(NBasisFunctionCenters,int,NrBasisFunctionCenters);
	-
	- /** Set method to add a gradient direction and its corresponding image. */
	- void AddGradientImage( const GradientDirectionType &, const GradientImageType *image);
	-
	- /** Another set method to add a gradient directions and its corresponding
	- * image. The image here is a VectorImage. The user is expected to pass the
	- * gradient directions in a container. The ith element of the container
	- * corresponds to the gradient direction of the ith component image the
	- * VectorImage. For the baseline image, a vector of all zeros
	- * should be set.*/
	- void SetGradientImage( const GradientDirectionContainerType *,
	- const GradientImagesType *image);
	-
	- /** Set method to set the reference image. */
	- void SetReferenceImage( ReferenceImageType *referenceImage )
	- {
	- if( m_GradientImageTypeEnumeration == GradientIsInASingleImage)
	- {
	- itkExceptionMacro( << "Cannot call both methods:"
	- << "AddGradientImage and SetGradientImage. Please call only one of them.");
	- }
	-
	- this->ProcessObject::SetNthInput( 0, referenceImage );
	-
	- m_GradientImageTypeEnumeration = GradientIsInManyImages;
	- }
	-
	- /** Get reference image */
	- virtual ReferenceImageType * GetReferenceImage()
	- { return ( static_cast< ReferenceImageType *>(this->ProcessObject::GetInput(0)) ); }
	-
	- /** Return the gradient direction. idx is 0 based */
	- virtual GradientDirectionType GetGradientDirection( unsigned int idx) const
	- {
	- if( idx >= m_NumberOfGradientDirections )
	- {
	- itkExceptionMacro( << "Gradient direction " << idx << "does not exist" );
	- }
	- return m_GradientDirectionContainer->ElementAt( idx+1 );
	- }
	-
	- /** Normalization performed on the reconstructed ODF according
	- * to method set in m_NormalizationMethod
	- */
	- OdfPixelType Normalize(OdfPixelType odf, typename NumericTraits<ReferencePixelType>::AccumulateType b0 );
	-
	- /** Normalization performed on diffusion signal vector according
	- * to method set in m_NormalizationMethod
	- */
	- vnl_vector<TOdfPixelType> PreNormalize( vnl_vector<TOdfPixelType> vec );
	-
	- /** Threshold on the reference image data. The output ODF will be a null
	- * pdf for pixels in the reference image that have a value less than this
	- * threshold. */
	- itkSetMacro( Threshold, ReferencePixelType );
	- itkGetMacro( Threshold, ReferencePixelType );
	-
	- /** Normalization applied to ODFs */
	- itkSetMacro( NormalizationMethod, Normalization);
	- itkGetMacro( NormalizationMethod, Normalization );
	-
	- /** Output image with b-zero weighted images */
	- itkGetMacro( BZeroImage, typename BZeroImageType::Pointer);
	-
	- /** B-value used to acquire the diffusion signal */
	- itkSetMacro( BValue, TOdfPixelType);
	-#ifdef GetBValue
	-#undef GetBValue
	-#endif
	- itkGetConstReferenceMacro( BValue, TOdfPixelType);
	-
	-#ifdef ITK_USE_CONCEPT_CHECKING
	- /** Begin concept checking */
	- itkConceptMacro(ReferenceEqualityComparableCheck,
	- (Concept::EqualityComparable<ReferencePixelType>));
	- itkConceptMacro(TensorEqualityComparableCheck,
	- (Concept::EqualityComparable<OdfPixelType>));
	- itkConceptMacro(GradientConvertibleToDoubleCheck,
	- (Concept::Convertible<GradientPixelType, double>));
	- itkConceptMacro(DoubleConvertibleToTensorCheck,
	- (Concept::Convertible<double, OdfPixelType>));
	- itkConceptMacro(GradientReferenceAdditiveOperatorsCheck,
	- (Concept::AdditiveOperators<GradientPixelType, GradientPixelType,
	- ReferencePixelType>));
	- itkConceptMacro(ReferenceOStreamWritableCheck,
	- (Concept::OStreamWritable<ReferencePixelType>));
	- itkConceptMacro(TensorOStreamWritableCheck,
	- (Concept::OStreamWritable<OdfPixelType>));
	- /** End concept checking */
	-#endif
	-
	-protected:
	- DiffusionQballReconstructionImageFilter();
	- ~DiffusionQballReconstructionImageFilter() override {};
	- void PrintSelf(std::ostream& os, Indent indent) const override;
	-
	- /** constructs reconstrion matrix according to Tuch's algorithm */
	- void ComputeReconstructionMatrix();
	-
	- void BeforeThreadedGenerateData() override;
	- void ThreadedGenerateData( const
	- OutputImageRegionType &outputRegionForThread, ThreadIdType) override;
	-
	- /** enum to indicate if the gradient image is specified as a single multi-
	- * component image or as several separate images */
	- typedef enum
	- {
	- GradientIsInASingleImage = 1,
	- GradientIsInManyImages,
	- Else
	- } GradientImageTypeEnumeration;
	-
	-private:
	-
	- /* Tensor basis coeffs */
	- OdfReconstructionMatrixType m_ReconstructionMatrix;
	-
	- /** container to hold gradient directions */
	- GradientDirectionContainerType::Pointer m_GradientDirectionContainer;
	-
	- /** Number of gradient measurements */
	- unsigned int m_NumberOfGradientDirections;
	-
	- /** Number of Equator Sampling Points (StdValue sqrt(8piNGradDirs)) */
	- unsigned int m_NumberOfEquatorSamplingPoints;
	-
	- /** Number of baseline images */
	- unsigned int m_NumberOfBaselineImages;
	-
	- /** Threshold on the reference image data */
	- ReferencePixelType m_Threshold;
	-
	- /** LeBihan's b-value for normalizing tensors */
	- TOdfPixelType m_BValue;
	-
	- /** Gradient image was specified in a single image or in multiple images */
	- GradientImageTypeEnumeration m_GradientImageTypeEnumeration;
	-
	- /** Output of b-zero reference image */
	- typename BZeroImageType::Pointer m_BZeroImage;
	-
	- /** Flag wether half shell was duplicated to ensure evenly
	- * distributed directions on the sphere
	- */
	- bool m_DirectionsDuplicated;
	-
	- /** Normalization method to be applied */
	- Normalization m_NormalizationMethod;
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkDiffusionQballReconstructionImageFilter.txx"
	-#endif
	-
	-#endif //__itkDiffusionQballReconstructionImageFilter_h_
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionQballReconstructionImageFilter.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionQballReconstructionImageFilter.txx
	deleted file mode 100644
	index 3f2e16ffb3..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkDiffusionQballReconstructionImageFilter.txx
	+++ /dev/null
	@@ -1,851 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef __itkDiffusionQballReconstructionImageFilter_txx
	-#define __itkDiffusionQballReconstructionImageFilter_txx
	-
	-#include "itkDiffusionQballReconstructionImageFilter.h"
	-#include "itkImageRegionConstIterator.h"
	-#include "itkImageRegionConstIteratorWithIndex.h"
	-#include "itkImageRegionIterator.h"
	-#include "itkArray.h"
	-#include "vnl/vnl_vector.h"
	-#include "itkPointShell.h"
	-
	-namespace itk {
	-
	- template< class TReferenceImagePixelType,
	- class TGradientImagePixelType,
	- class TOdfPixelType,
	- int NrOdfDirections,
	- int NrBasisFunctionCenters>
	- DiffusionQballReconstructionImageFilter< TReferenceImagePixelType,
	- TGradientImagePixelType, TOdfPixelType, NrOdfDirections,
	- NrBasisFunctionCenters>
	- ::DiffusionQballReconstructionImageFilter() :
	- m_GradientDirectionContainer(nullptr),
	- m_NumberOfGradientDirections(0),
	- m_NumberOfEquatorSamplingPoints(0),
	- m_NumberOfBaselineImages(1),
	- m_Threshold(NumericTraits< ReferencePixelType >::NonpositiveMin()),
	- m_BValue(1.0),
	- m_GradientImageTypeEnumeration(Else),
	- m_DirectionsDuplicated(false)
	- {
	- // At least 1 inputs is necessary for a vector image.
	- // For images added one at a time we need at least six
	- this->SetNumberOfRequiredInputs( 1 );
	- }
	-
	- template< class TReferenceImagePixelType,
	- class TGradientImagePixelType,
	- class TOdfPixelType,
	- int NrOdfDirections,
	- int NrBasisFunctionCenters>
	- void DiffusionQballReconstructionImageFilter< TReferenceImagePixelType,
	- TGradientImagePixelType, TOdfPixelType, NrOdfDirections,
	- NrBasisFunctionCenters>
	- ::BeforeThreadedGenerateData()
	- {
	- // If we have more than 2 inputs, then each input, except the first is a
	- // gradient image. The number of gradient images must match the number of
	- // gradient directions.
	- const unsigned int numberOfInputs = this->GetNumberOfInputs();
	-
	- // There need to be at least 6 gradient directions to be able to compute the
	- // tensor basis
	- if( m_NumberOfGradientDirections < 1 )
	- {
	- itkExceptionMacro( << "Your image contains no diffusion gradients!" );
	- }
	-
	- // If there is only 1 gradient image, it must be an itk::VectorImage. Otherwise
	- // we must have a container of (numberOfInputs-1) itk::Image. Check to make sure
	- if ( numberOfInputs == 1
	- && m_GradientImageTypeEnumeration != GradientIsInASingleImage )
	- {
	- std::string gradientImageClassName(
	- this->ProcessObject::GetInput(0)->GetNameOfClass());
	- if ( strcmp(gradientImageClassName.c_str(),"VectorImage") != 0 )
	- {
	- itkExceptionMacro( <<
	- "There is only one Gradient image. I expect that to be a VectorImage. "
	- << "But its of type: " << gradientImageClassName );
	- }
	- }
	-
	- // Compute reconstruction matrix that is multiplied to the data-vector
	- // each voxel in order to reconstruct the ODFs
	- this->ComputeReconstructionMatrix();
	-
	- // Allocate the b-zero image
	- m_BZeroImage = BZeroImageType::New();
	- if( m_GradientImageTypeEnumeration == GradientIsInManyImages )
	- {
	- typename ReferenceImageType::Pointer img = static_cast< ReferenceImageType * >(this->ProcessObject::GetInput(0));
	- m_BZeroImage->SetSpacing( img->GetSpacing() ); // Set the image spacing
	- m_BZeroImage->SetOrigin( img->GetOrigin() ); // Set the image origin
	- m_BZeroImage->SetDirection( img->GetDirection() ); // Set the image direction
	- m_BZeroImage->SetLargestPossibleRegion( img->GetLargestPossibleRegion());
	- m_BZeroImage->SetBufferedRegion( img->GetLargestPossibleRegion() );
	- }
	- // The gradients are specified in a single multi-component image
	- else if( m_GradientImageTypeEnumeration == GradientIsInASingleImage )
	- {
	- typename GradientImagesType::Pointer img = static_cast< GradientImagesType * >(
	- this->ProcessObject::GetInput(0) );
	- m_BZeroImage->SetSpacing( img->GetSpacing() ); // Set the image spacing
	- m_BZeroImage->SetOrigin( img->GetOrigin() ); // Set the image origin
	- m_BZeroImage->SetDirection( img->GetDirection() ); // Set the image direction
	- m_BZeroImage->SetLargestPossibleRegion( img->GetLargestPossibleRegion());
	- m_BZeroImage->SetBufferedRegion( img->GetLargestPossibleRegion() );
	- }
	-
	- m_BZeroImage->Allocate();
	-
	- }
	-
	- template< class TReferenceImagePixelType,
	- class TGradientImagePixelType,
	- class TOdfPixelType,
	- int NrOdfDirections,
	- int NrBasisFunctionCenters>
	- typename itk::DiffusionQballReconstructionImageFilter<TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NrOdfDirections, NrBasisFunctionCenters>::OdfPixelType
	- itk::DiffusionQballReconstructionImageFilter<TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NrOdfDirections, NrBasisFunctionCenters>::Normalize( OdfPixelType odf, typename NumericTraits<ReferencePixelType>::AccumulateType b0 )
	- {
	- switch( m_NormalizationMethod )
	- {
	-
	- // divide by sum to retreive a PDF
	- case QBR_STANDARD:
	- {
	- odf.Normalize();
	- return odf;
	- break;
	- }
	- // ADC style
	- case QBR_B_ZERO_B_VALUE:
	- {
	- for(int i=0; i<NrOdfDirections; i++)
	- {
	- odf[i] = ((TOdfPixelType)log((TOdfPixelType)b0)-odf[i])/m_BValue;
	- }
	- return odf;
	- break;
	- }
	- // divide by b-zero value of voxel
	- case QBR_B_ZERO:
	- {
	- odf *= 1.0/b0;
	- return odf;
	- break;
	- }
	- // no normalization of ODF
	- case QBR_NONE:
	- {
	- return odf;
	- break;
	- }
	- }
	-
	- return odf;
	- }
	-
	-
	- template< class TReferenceImagePixelType,
	- class TGradientImagePixelType,
	- class TOdfPixelType,
	- int NrOdfDirections,
	- int NrBasisFunctionCenters >
	- vnl_vector<TOdfPixelType> itk::DiffusionQballReconstructionImageFilter<TReferenceImagePixelType, TGradientImagePixelType, TOdfPixelType, NrOdfDirections, NrBasisFunctionCenters>::PreNormalize( vnl_vector<TOdfPixelType> vec )
	- {
	- switch( m_NormalizationMethod )
	- {
	- // standard: no normalization before reconstruction
	- case QBR_STANDARD:
	- {
	- return vec;
	- break;
	- }
	- // log of signal
	- case QBR_B_ZERO_B_VALUE:
	- {
	- int n = vec.size();
	- for(int i=0; i<n; i++)
	- {
	- vec[i] = log(vec[i]);
	- }
	- return vec;
	- break;
	- }
	- // no normalization before reconstruction here
	- case QBR_B_ZERO:
	- {
	- return vec;
	- break;
	- }
	- // no normalization before reconstruction here
	- case QBR_NONE:
	- {
	- return vec;
	- break;
	- }
	- }
	-
	- return vec;
	- }
	-
	- template< class TReferenceImagePixelType,
	- class TGradientImagePixelType,
	- class TOdfPixelType,
	- int NrOdfDirections,
	- int NrBasisFunctionCenters>
	- void DiffusionQballReconstructionImageFilter< TReferenceImagePixelType,
	- TGradientImagePixelType, TOdfPixelType, NrOdfDirections,
	- NrBasisFunctionCenters>
	- ::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread,
	- ThreadIdType )
	- {
	- // init output and b-zero iterators
	- typename OutputImageType::Pointer outputImage =
	- static_cast< OutputImageType * >(this->ProcessObject::GetPrimaryOutput());
	- ImageRegionIterator< OutputImageType > oit(outputImage, outputRegionForThread);
	- oit.GoToBegin();
	- ImageRegionIterator< BZeroImageType > oit2(m_BZeroImage, outputRegionForThread);
	- oit2.GoToBegin();
	- vnl_vector<TOdfPixelType> B(m_NumberOfGradientDirections);
	-
	- // Two cases here:
	- // 1. Gradients specified in multiple images
	- // 'n' iterators for each of the gradient images
	- // 2. Gradients specified in a single multi-component image
	- // one iterator for all gradient directions
	-
	- if( m_GradientImageTypeEnumeration == GradientIsInManyImages )
	- {
	- // b-zero reference image iterator
	- ImageRegionConstIterator< ReferenceImageType >
	- it(static_cast< ReferenceImageType * >(this->ProcessObject::GetInput(0)),
	- outputRegionForThread);
	- it.GoToBegin();
	-
	- // fill vector with gradient iterators
	- typedef ImageRegionConstIterator< GradientImageType > GradientIteratorType;
	- std::vector< GradientIteratorType * > gradientItContainer;
	- for( unsigned int i = 1; i<= m_NumberOfGradientDirections; i++ )
	- {
	- // adapt index in case we have a duplicated shell
	- int index = i;
	- if(m_DirectionsDuplicated)
	- index = i % (m_NumberOfGradientDirections/2);
	-
	- // init and pushback current input image iterator
	- typename GradientImageType::Pointer gradientImagePointer = nullptr;
	- // dynamic_cast would be nice, static because of SGI
	- gradientImagePointer = static_cast< GradientImageType * >(
	- this->ProcessObject::GetInput(index) );
	- GradientIteratorType *git = new GradientIteratorType(
	- gradientImagePointer, outputRegionForThread );
	- git->GoToBegin();
	- gradientItContainer.push_back(git);
	- }
	-
	- // Following loop does the actual reconstruction work in each voxel
	- // (Tuch, Q-Ball Reconstruction [1])
	- while( !it.IsAtEnd() )
	- {
	-
	- // b-zero reference value
	- ReferencePixelType b0 = it.Get();
	-
	- // init ODF
	- OdfPixelType odf(0.0);
	-
	- // threshold on reference value to suppress noisy regions
	- if( (b0 != 0) && (b0 >= m_Threshold) )
	- {
	-
	- // fill array of diffusion measurements
	- for( unsigned int i = 0; i< m_NumberOfGradientDirections; i++ )
	- {
	- GradientPixelType b = gradientItContainer[i]->Get();
	- B[i] = static_cast<TOdfPixelType>(b);
	- ++(*gradientItContainer[i]);
	- }
	-
	- // pre-normalization according to m_NormalizationMethod
	- B = PreNormalize(B);
	-
	- // actual reconstruction
	- odf = ( (m_ReconstructionMatrix) B ).data_block();
	-
	- // post-normalization according to m_NormalizationMethod
	- odf.Normalize();
	- }
	- else
	- {
	- // in case we fall below threshold, we just increment to next voxel
	- for( unsigned int i = 0; i< m_NumberOfGradientDirections; i++ )
	- {
	- ++(*gradientItContainer[i]);
	- }
	- }
	-
	- for (unsigned int i=0; i<odf.Size(); i++)
	- if (odf.GetElement(i)!=odf.GetElement(i))
	- odf.Fill(0.0);
	-
	- // set and increment output iterators
	- oit.Set( odf );
	- ++oit;
	- oit2.Set( b0 );
	- ++oit2;
	- ++it;
	- }
	-
	- // clean up
	- for( unsigned int i = 0; i< gradientItContainer.size(); i++ )
	- {
	- delete gradientItContainer[i];
	- }
	- }
	- // The gradients are specified in a single multi-component image
	- else if( m_GradientImageTypeEnumeration == GradientIsInASingleImage )
	- {
	-
	- // init input iterator
	- typedef ImageRegionConstIterator< GradientImagesType > GradientIteratorType;
	- typedef typename GradientImagesType::PixelType GradientVectorType;
	- typename GradientImagesType::Pointer gradientImagePointer = nullptr;
	- // dynamic_cast would be nice, static because of SGI
	- gradientImagePointer = static_cast< GradientImagesType * >(
	- this->ProcessObject::GetInput(0) );
	- GradientIteratorType git(gradientImagePointer, outputRegionForThread );
	- git.GoToBegin();
	-
	- // set of indicies each for the baseline images and gradient images
	- std::vector<unsigned int> baselineind; // contains baseline indicies
	- std::vector<unsigned int> gradientind; // contains gradient indicies
	- for(GradientDirectionContainerType::ConstIterator gdcit = this->m_GradientDirectionContainer->Begin();
	- gdcit != this->m_GradientDirectionContainer->End(); ++gdcit)
	- {
	- if(gdcit.Value().one_norm() <= 0.0)
	- {
	- baselineind.push_back(gdcit.Index());
	- }
	- else
	- {
	- gradientind.push_back(gdcit.Index());
	- }
	- }
	-
	- // in case we have a duplicated shell, we also duplicate or indices
	- if( m_DirectionsDuplicated )
	- {
	- int gradIndSize = gradientind.size();
	- for(int i=0; i<gradIndSize; i++)
	- gradientind.push_back(gradientind[i]);
	- }
	-
	- // Following loop does the actual reconstruction work in each voxel
	- // (Tuch, Q-Ball Reconstruction [1])
	- while( !git.IsAtEnd() )
	- {
	- // current vector of diffusion measurements
	- GradientVectorType b = git.Get();
	-
	- // average of current b-zero reference values
	- typename NumericTraits<ReferencePixelType>::AccumulateType b0 = NumericTraits<ReferencePixelType>::Zero;
	- for(unsigned int i = 0; i < baselineind.size(); ++i)
	- {
	- b0 += b[baselineind[i]];
	- }
	- b0 /= this->m_NumberOfBaselineImages;
	-
	- // init resulting ODF
	- OdfPixelType odf(0.0);
	-
	- // threshold on reference value to suppress noisy regions
	- if( (b0 != 0) && (b0 >= m_Threshold) )
	- {
	- for( unsigned int i = 0; i< m_NumberOfGradientDirections; i++ )
	- {
	- B[i] = static_cast<TOdfPixelType>(b[gradientind[i]]);
	- }
	-
	- // pre-normalization according to m_NormalizationMethod
	- B = PreNormalize(B);
	-
	- // actual reconstruction
	- odf = ( (m_ReconstructionMatrix) B ).data_block();
	-
	- // post-normalization according to m_NormalizationMethod
	- odf = Normalize(odf, b0);
	-
	- }
	-
	- for (unsigned int i=0; i<odf.Size(); i++)
	- if (odf.GetElement(i)!=odf.GetElement(i))
	- odf.Fill(0.0);
	-
	- // set and increment output iterators
	- oit.Set( odf );
	- ++oit;
	- oit2.Set( b0 );
	- ++oit2;
	- ++git; // Gradient image iterator
	- }
	- }
	-
	- std::cout << "One Thread finished reconstruction" << std::endl;
	- }
	-
	- template< class TReferenceImagePixelType,
	- class TGradientImagePixelType,
	- class TOdfPixelType,
	- int NrOdfDirections,
	- int NrBasisFunctionCenters>
	- void DiffusionQballReconstructionImageFilter< TReferenceImagePixelType,
	- TGradientImagePixelType, TOdfPixelType, NrOdfDirections,
	- NrBasisFunctionCenters>
	- ::ComputeReconstructionMatrix()
	- {
	-
	- if( m_NumberOfGradientDirections < 1 )
	- {
	- itkExceptionMacro( << "Your image contains no diffusion gradients!" );
	- }
	-
	- {
	- // check for duplicate diffusion gradients
	- bool warning = false;
	- for(GradientDirectionContainerType::ConstIterator gdcit1 = this->m_GradientDirectionContainer->Begin();
	- gdcit1 != this->m_GradientDirectionContainer->End(); ++gdcit1)
	- {
	- for(GradientDirectionContainerType::ConstIterator gdcit2 = this->m_GradientDirectionContainer->Begin();
	- gdcit2 != this->m_GradientDirectionContainer->End(); ++gdcit2)
	- {
	- if(gdcit1.Value() == gdcit2.Value() && gdcit1.Index() != gdcit2.Index())
	- {
	- itkWarningMacro( << "Some of the Diffusion Gradients equal each other. Corresponding image data should be averaged before calling this filter." );
	- warning = true;
	- break;
	- }
	- }
	- if (warning) break;
	- }
	-
	- // handle acquisition schemes where only half of the spherical
	- // shell is sampled by the gradient directions. In this case,
	- // each gradient direction is duplicated in negative direction.
	- vnl_vector<double> centerMass(3);
	- centerMass.fill(0.0);
	- int count = 0;
	- for(GradientDirectionContainerType::ConstIterator gdcit1 = this->m_GradientDirectionContainer->Begin();
	- gdcit1 != this->m_GradientDirectionContainer->End(); ++gdcit1)
	- {
	- if(gdcit1.Value().one_norm() > 0.0)
	- {
	- centerMass += gdcit1.Value();
	- count ++;
	- }
	- }
	- centerMass /= count;
	- if(centerMass.two_norm() > 0.1)
	- {
	- m_DirectionsDuplicated = true;
	- m_NumberOfGradientDirections *= 2;
	- }
	- }
	-
	- // set default number of equator sampling points if needed
	- if(!this->m_NumberOfEquatorSamplingPoints)
	- this->m_NumberOfEquatorSamplingPoints
	- = (int) ceil((double)sqrt(8itk::Math::pithis->m_NumberOfGradientDirections));
	-
	- vnl_matrix<double>* Q =
	- new vnl_matrix<double>(3, m_NumberOfGradientDirections);
	-
	- {
	- // Fill matrix Q with gradient directions
	- int i = 0;
	- for(GradientDirectionContainerType::ConstIterator gdcit = this->m_GradientDirectionContainer->Begin();
	- gdcit != this->m_GradientDirectionContainer->End(); ++gdcit)
	- {
	- if(gdcit.Value().one_norm() > 0.0)
	- {
	- (*Q)(0,i) = gdcit.Value().get(0);
	- (*Q)(1,i) = gdcit.Value().get(1);
	- (*Q)(2,i++) = gdcit.Value().get(2);
	- }
	- }
	- if(m_DirectionsDuplicated)
	- {
	- for(GradientDirectionContainerType::ConstIterator gdcit = this->m_GradientDirectionContainer->Begin();
	- gdcit != this->m_GradientDirectionContainer->End(); ++gdcit)
	- {
	- if(gdcit.Value().one_norm() > 0.0)
	- {
	- (*Q)(0,i) = -gdcit.Value().get(0);
	- (*Q)(1,i) = -gdcit.Value().get(1);
	- (*Q)(2,i++) = -gdcit.Value().get(2);
	- }
	- }
	- }
	-
	- }
	-
	- vnl_matrix_fixed<double, 3, NOdfDirections>* U =
	- itk::PointShell<NOdfDirections, vnl_matrix_fixed<double, 3, NOdfDirections> >::DistributePointShell();
	-
	- vnl_matrix_fixed<double, 3, NBasisFunctionCenters>* V =
	- itk::PointShell<NBasisFunctionCenters, vnl_matrix_fixed<double, 3, NBasisFunctionCenters> >::DistributePointShell();
	-
	- // calculate sampling points on the equator perpendicular to z-axis
	- vnl_matrix<double> *C
	- = new vnl_matrix<double>(3, m_NumberOfEquatorSamplingPoints);
	- for(unsigned int i=0; i<m_NumberOfEquatorSamplingPoints; i++)
	- {
	- double theta = i * (2*itk::Math::pi / m_NumberOfEquatorSamplingPoints);
	- (*C)(0,i) = cos(theta);
	- (*C)(1,i) = sin(theta);
	- (*C)(2,i) = NumericTraits<double>::Zero;
	- }
	-
	- // rotate the sampling points to each directions of interest
	- vnl_matrix<double> *S
	- = new vnl_matrix<double>(3,m_NumberOfEquatorSamplingPoints*NOdfDirections);
	-
	- {
	- vnl_vector_fixed<double,3> z(NumericTraits<double>::Zero);
	- z.put(2,NumericTraits<double>::One);
	- vnl_matrix_fixed<double,3,3> eye(NumericTraits<double>::Zero);
	- eye.fill_diagonal(NumericTraits<double>::One);
	- for(int i=0; i<NOdfDirections; i++)
	- {
	- vnl_vector_fixed<double,3> ui = (*U).get_column(i);
	- vnl_matrix<double> *RC
	- = new vnl_matrix<double>(3,m_NumberOfEquatorSamplingPoints);
	-
	- if( (z(0)ui(0)+z(1)ui(1)+z(2)*ui(2)+1) != 0 )
	- {
	- vnl_matrix_fixed<double,3,3> R;
	- R.set_column(0, (z+ui)*(z(0)+ui(0)));
	- R.set_column(1, (z+ui)*(z(1)+ui(1)));
	- R.set_column(2, (z+ui)*(z(2)+ui(2)));
	- R /= (z(0)ui(0)+z(1)ui(1)+z(2)*ui(2)+1);
	- R -= eye;
	- (RC) = R(*C);
	- }
	- else
	- {
	- RC = C;
	- }
	- (S).set_columns(im_NumberOfEquatorSamplingPoints, *RC);
	- }
	- }
	-
	- // determine interpolation kernel width first
	- // use to determine diffusion measurement contribution to each of the kernels
	- vnl_matrix<double> *H_plus
	- = new vnl_matrix<double>(NBasisFunctionCenters,m_NumberOfGradientDirections);
	-
	- double maxSigma = itk::Math::pi/6;
	- double bestSigma = maxSigma;
	-
	- {
	- double stepsize = 0.01;
	- double start = 0.01;
	- double minCondition = NumericTraits<double>::max();
	-
	- vnl_matrix<double> *H
	- = new vnl_matrix<double>(m_NumberOfGradientDirections,NBasisFunctionCenters,(double)0);
	-
	- {
	-
	- int increasing = 0;
	- for( double sigma=start; sigma<maxSigma; sigma+=stepsize)
	- {
	- vnl_matrix<double> *tmpH
	- = new vnl_matrix<double>(m_NumberOfGradientDirections,NBasisFunctionCenters);
	-
	- for(unsigned int r=0; r<m_NumberOfGradientDirections; r++)
	- {
	- for(int c=0; c<NBasisFunctionCenters; c++)
	- {
	- double qtv = (Q)(0,r)(*V)(0,c)
	- + (Q)(1,r)(*V)(1,c)
	- + (Q)(2,r)(*V)(2,c);
	- qtv = (qtv<-1.0) ? -1.0 : ( (qtv>1.0) ? 1.0 : qtv);
	- double x = acos(qtv);
	- (tmpH)(r,c) = (1.0/(sigmasqrt(2.0*itk::Math::pi)))
	- exp((-xx)/(2sigmasigma));
	- }
	- }
	-
	- vnl_svd<double> *solver;
	- if(m_NumberOfGradientDirections>NBasisFunctionCenters)
	- {
	- solver = new vnl_svd<double>(*tmpH);
	- }
	- else
	- {
	- solver = new vnl_svd<double>(tmpH->transpose());
	- }
	- double condition = solver->sigma_max() / solver->sigma_min();
	-
	- std::cout << sigma << ": " << condition << std::endl;
	-
	- if( condition < minCondition )
	- {
	- minCondition = condition;
	- bestSigma = sigma;
	- H->update(*tmpH);
	- }
	- else
	- {
	- // optimum assumed to be hit after condition increased 3 times
	- if (++increasing>3) break;
	- }
	- }
	- }
	-
	-
	- vnl_matrix_inverse<double> *pseudoInverse
	- = new vnl_matrix_inverse<double>(*H);
	- (*H_plus) = pseudoInverse->pinverse();
	-
	- std::cout << "choosing sigma = " << bestSigma << std::endl;
	-
	- }
	-
	- // this is the contribution of each kernel to each sampling point on the
	- // equator
	- vnl_matrix<double> *G
	- = new vnl_matrix<double>(m_NumberOfEquatorSamplingPoints*NOdfDirections,NBasisFunctionCenters);
	-
	- {
	- for(unsigned int r=0; r<m_NumberOfEquatorSamplingPoints*NOdfDirections; r++)
	- {
	- for(int c=0; c<NBasisFunctionCenters; c++)
	- {
	- double stv = (S)(0,r)(*V)(0,c)
	- + (S)(1,r)(*V)(1,c)
	- + (S)(2,r)(*V)(2,c);
	- stv = (stv<-1.0) ? -1.0 : ( (stv>1.0) ? 1.0 : stv);
	- double x = acos(stv);
	- (G)(r,c) = (1.0/(bestSigmasqrt(2.0*itk::Math::pi)))
	- exp((-xx)/(2bestSigmabestSigma));
	- }
	- }
	- }
	-
	- vnl_matrix<double> *GH_plus =
	- new vnl_matrix<double>(m_NumberOfEquatorSamplingPoints*NOdfDirections,m_NumberOfGradientDirections);
	-
	- // simple matrix multiplication, manual cause of stack overflow using operator
	- for (unsigned i = 0; i < m_NumberOfEquatorSamplingPoints*NOdfDirections; ++i)
	- {
	- for (unsigned j = 0; j < m_NumberOfGradientDirections; ++j)
	- {
	- double accum = (G)(i,0) (*H_plus)(0,j);
	- for (unsigned k = 1; k < NOdfDirections; ++k)
	- accum += (G)(i,k) (*H_plus)(k,j);
	- (*GH_plus)(i,j) = accum;
	- }
	- }
	-
	- typename vnl_matrix<double>::iterator it3;
	- for( it3 = (GH_plus).begin(); it3 != (GH_plus).end(); it3++)
	- {
	- if(*it3<0.0)
	- *it3 = 0;
	- }
	-
	- // this is an addition to the original tuch algorithm
	- for(unsigned int i=0; i<NOdfDirections*m_NumberOfEquatorSamplingPoints; i++)
	- {
	- vnl_vector< double > r = GH_plus->get_row(i);
	- r /= r.sum();
	- GH_plus->set_row(i,r);
	- }
	-
	- m_ReconstructionMatrix
	- = new vnl_matrix<TOdfPixelType>(NOdfDirections,m_NumberOfGradientDirections,0.0);
	- for(int i=0; i<NOdfDirections; i++)
	- {
	- for(unsigned int j=0; j<m_NumberOfGradientDirections; j++)
	- {
	- for(unsigned int k=0; k<m_NumberOfEquatorSamplingPoints; k++)
	- {
	- (m_ReconstructionMatrix)(i,j) += (TOdfPixelType)(GH_plus)(m_NumberOfEquatorSamplingPoints*i+k,j);
	- }
	- }
	- }
	-
	- // this is also an addition to the original tuch algorithm
	- for(int i=0; i<NOdfDirections; i++)
	- {
	- vnl_vector< TOdfPixelType > r = m_ReconstructionMatrix->get_row(i);
	- r /= r.sum();
	- m_ReconstructionMatrix->set_row(i,r);
	- }
	- std::cout << "Reconstruction Matrix computed." << std::endl;
	- }
	-
	- template< class TReferenceImagePixelType,
	- class TGradientImagePixelType,
	- class TOdfPixelType,
	- int NrOdfDirections,
	- int NrBasisFunctionCenters>
	- void DiffusionQballReconstructionImageFilter< TReferenceImagePixelType,
	- TGradientImagePixelType, TOdfPixelType, NrOdfDirections,
	- NrBasisFunctionCenters>
	- ::AddGradientImage( const GradientDirectionType &gradientDirection,
	- const GradientImageType *gradientImage )
	- {
	- // Make sure crazy users did not call both AddGradientImage and
	- // SetGradientImage
	- if( m_GradientImageTypeEnumeration == GradientIsInASingleImage)
	- {
	- itkExceptionMacro( << "Cannot call both methods:"
	- << "AddGradientImage and SetGradientImage. Please call only one of them.");
	- }
	-
	- // If the container to hold the gradient directions hasn't been allocated
	- // yet, allocate it.
	- if( !this->m_GradientDirectionContainer )
	- {
	- this->m_GradientDirectionContainer = GradientDirectionContainerType::New();
	- }
	-
	- this->m_NumberOfGradientDirections = m_GradientDirectionContainer->Size();
	-
	- m_GradientDirectionContainer->InsertElement( this->m_NumberOfGradientDirections,
	- gradientDirection / gradientDirection.two_norm() );
	-
	- this->ProcessObject::SetNthInput( this->m_NumberOfGradientDirections,
	- const_cast< GradientImageType* >(gradientImage) );
	-
	- m_GradientImageTypeEnumeration = GradientIsInManyImages;
	- }
	-
	- template< class TReferenceImagePixelType,
	- class TGradientImagePixelType,
	- class TOdfPixelType,
	- int NrOdfDirections,
	- int NrBasisFunctionCenters>
	- void DiffusionQballReconstructionImageFilter< TReferenceImagePixelType,
	- TGradientImagePixelType, TOdfPixelType, NrOdfDirections,
	- NrBasisFunctionCenters>
	- ::SetGradientImage(const GradientDirectionContainerType *gradientDirection,
	- const GradientImagesType *gradientImage )
	- {
	- // Make sure crazy users did not call both AddGradientImage and
	- // SetGradientImage
	- if( m_GradientImageTypeEnumeration == GradientIsInManyImages )
	- {
	- itkExceptionMacro( << "Cannot call both methods:"
	- << "AddGradientImage and SetGradientImage. Please call only one of them.");
	- }
	-
	- this->m_GradientDirectionContainer = GradientDirectionContainerType::New();
	- for(GradientDirectionContainerType::ConstIterator it = gradientDirection->Begin();
	- it != gradientDirection->End(); it++)
	- {
	- this->m_GradientDirectionContainer->push_back(it.Value());
	- }
	-
	- unsigned int numImages = gradientDirection->Size();
	- this->m_NumberOfBaselineImages = 0;
	- for(GradientDirectionContainerType::Iterator it = this->m_GradientDirectionContainer->Begin();
	- it != this->m_GradientDirectionContainer->End(); it++)
	- {
	- if(it.Value().one_norm() <= 0.0)
	- {
	- this->m_NumberOfBaselineImages++;
	- }
	- else // Normalize non-zero gradient directions
	- {
	- it.Value() = it.Value() / it.Value().two_norm();
	- }
	- }
	-
	- this->m_NumberOfGradientDirections = numImages - this->m_NumberOfBaselineImages;
	-
	- // ensure that the gradient image we received has as many components as
	- // the number of gradient directions
	- if( gradientImage->GetVectorLength() != this->m_NumberOfBaselineImages + m_NumberOfGradientDirections )
	- {
	- itkExceptionMacro( << m_NumberOfGradientDirections << " gradients + " << this->m_NumberOfBaselineImages
	- << "baselines = " << m_NumberOfGradientDirections + this->m_NumberOfBaselineImages
	- << " directions specified but image has " << gradientImage->GetVectorLength()
	- << " components.");
	- }
	-
	- this->ProcessObject::SetNthInput( 0,
	- const_cast< GradientImagesType* >(gradientImage) );
	- m_GradientImageTypeEnumeration = GradientIsInASingleImage;
	- }
	-
	-
	- template< class TReferenceImagePixelType,
	- class TGradientImagePixelType,
	- class TOdfPixelType,
	- int NrOdfDirections,
	- int NrBasisFunctionCenters>
	- void DiffusionQballReconstructionImageFilter< TReferenceImagePixelType,
	- TGradientImagePixelType, TOdfPixelType, NrOdfDirections,
	- NrBasisFunctionCenters>
	- ::PrintSelf(std::ostream& os, Indent indent) const
	- {
	- std::locale C("C");
	- std::locale originalLocale = os.getloc();
	- os.imbue(C);
	-
	- Superclass::PrintSelf(os,indent);
	-
	- os << indent << "OdfReconstructionMatrix: " << m_ReconstructionMatrix << std::endl;
	- if ( m_GradientDirectionContainer )
	- {
	- os << indent << "GradientDirectionContainer: "
	- << m_GradientDirectionContainer << std::endl;
	- }
	- else
	- {
	- os << indent <<
	- "GradientDirectionContainer: (Gradient directions not set)" << std::endl;
	- }
	- os << indent << "NumberOfGradientDirections: " <<
	- m_NumberOfGradientDirections << std::endl;
	- os << indent << "NumberOfBaselineImages: " <<
	- m_NumberOfBaselineImages << std::endl;
	- os << indent << "Threshold for reference B0 image: " << m_Threshold << std::endl;
	- os << indent << "BValue: " << m_BValue << std::endl;
	- if ( this->m_GradientImageTypeEnumeration == GradientIsInManyImages )
	- {
	- os << indent << "Gradient images haven been supplied " << std::endl;
	- }
	- else if ( this->m_GradientImageTypeEnumeration == GradientIsInManyImages )
	- {
	- os << indent << "A multicomponent gradient image has been supplied" << std::endl;
	- }
	-
	- os.imbue( originalLocale );
	- }
	-
	-}
	-
	-#endif // __itkDiffusionQballReconstructionImageFilter_txx
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkMultiTensorImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkMultiTensorImageFilter.h
	deleted file mode 100644
	index 2a9e491452..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkMultiTensorImageFilter.h
	+++ /dev/null
	@@ -1,200 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-/*===================================================================
	-
	-This file is based heavily on a corresponding ITK filter.
	-
	-===================================================================*/
	-#ifndef __itkMultiTensorImageFilter_h_
	-#define __itkMultiTensorImageFilter_h_
	-
	-#include "itkImageToImageFilter.h"
	-#include "itkVectorImage.h"
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <vnl/algo/vnl_levenberg_marquardt.h>
	-#include <mitkOdfImage.h>
	-#include <mitkPeakImage.h>
	-#include <mitkTensorImage.h>
	-
	-namespace itk{
	-/** \class MultiTensorImageFilter
	- */
	-
	-template< class TInPixelType, class TOutPixelType >
	-class MultiTensorImageFilter :
	- public ImageToImageFilter< VectorImage< TInPixelType, 3 >, Image< TOutPixelType, 3 > >
	-{
	-
	-public:
	-
	- typedef MultiTensorImageFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageToImageFilter< VectorImage< TInPixelType, 3 >, Image< TOutPixelType, 3 > > Superclass;
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionType GradientDirectionType;
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionsContainerType GradientContainerType;
	- typedef itk::Image< unsigned char, 3> ItkUcharImageType;
	- typedef mitk::PeakImage::ItkPeakImageType PeakImageType;
	- typedef mitk::TensorImage::PixelType TensorType;
	- typedef mitk::TensorImage::ItkTensorImageType TensorImageType;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(MultiTensorImageFilter, ImageToImageFilter)
	-
	- typedef typename Superclass::InputImageType InputImageType;
	- typedef typename Superclass::OutputImageType OutputImageType;
	- typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
	-
	- itkSetMacro( MaskImage, ItkUcharImageType::Pointer )
	- itkSetMacro( B_value, double )
	- itkSetMacro( GradientDirections, GradientContainerType::Pointer )
	-
	- itkGetMacro( PeakImage, PeakImageType::Pointer )
	- std::vector< TensorImageType::Pointer > GetTensorImages(){ return m_TensorImages; }
	-
	-protected:
	- MultiTensorImageFilter();
	- ~MultiTensorImageFilter() {}
	- void PrintSelf(std::ostream& os, Indent indent) const override;
	-
	- void BeforeThreadedGenerateData() override;
	- void ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, ThreadIdType) override;
	-
	- double m_B_value;
	- std::vector<double> m_B_values;
	- std::vector<int> m_WeightedIndices;
	- std::vector<int> m_UnWeightedIndices;
	-
	- GradientContainerType::Pointer m_GradientDirections;
	-
	- ItkUcharImageType::Pointer m_MaskImage;
	- PeakImageType::Pointer m_PeakImage;
	-
	- std::vector< TensorImageType::Pointer > m_TensorImages;
	- int m_NumTensors;
	-
	- vnl_vector<double> FitSingleVoxel( const typename InputImageType::PixelType &input);
	-
	-// struct multiTensorLeastSquaresFunction: public vnl_least_squares_function
	-// {
	-// GradientContainerType::Pointer gradientDirections;
	-// typename InputImageType::PixelType measurements;
	-// std::vector<double> bValues;
	-// double S0;
	-// int num_tensors;
	-// std::vector<int> weightedIndices;
	-
	-// void set_S0(double val)
	-// {
	-// S0 = val;
	-// }
	-
	-// void set_measurements(const typename InputImageType::PixelType& m)
	-// {
	-// measurements = m;
	-// }
	-
	-// void set_bvalues(std::vector<double>& x)
	-// {
	-// bValues = x;
	-// }
	-
	-// void set_weightedIndices(std::vector<int>& x)
	-// {
	-// weightedIndices = x;
	-// }
	-
	-// void set_gradient_directions(const GradientContainerType::Pointer& directions)
	-// {
	-// gradientDirections = directions;
	-// }
	-
	-// int check(int n)
	-// {
	-// if (n==1)
	-// return 6;
	-// return n*7;
	-// }
	-
	-// multiTensorLeastSquaresFunction(unsigned int number_of_tensors=2, unsigned int number_of_measurements=1) :
	-// vnl_least_squares_function(check(number_of_tensors), number_of_measurements, no_gradient)
	-// {
	-// num_tensors = number_of_tensors;
	-// }
	-
	-// void f(const vnl_vector<double>& x, vnl_vector<double>& fx) override
	-// {
	-// int elements = 7;
	-// for(auto s : weightedIndices)
	-// {
	-// GradientDirectionType g = gradientDirections->GetElement(s);
	-// g.normalize();
	-
	-// itk::DiffusionTensor3D< double > S;
	-// S[0] = g[0]*g[0];
	-// S[1] = g[1]*g[0];
	-// S[2] = g[2]*g[0];
	-// S[3] = g[1]*g[1];
	-// S[4] = g[2]*g[1];
	-// S[5] = g[2]*g[2];
	-
	-// double approx = 0;
	-// double penalty = 0;
	-// double f = 0;
	-// if (num_tensors==1 && x.size()==6)
	-// f = 1;
	-
	-// for (int i=0; i<num_tensors; i++)
	-// {
	-// if (num_tensors>1 && x.size()>6 && x[elements-1+i*elements]<0) // penalty if volume fractiuon is < 0
	-// penalty += 10e6;
	-
	-// if (num_tensors>1 && x.size()>6)
	-// f += fabs(x[elements-1+i*elements]);
	-
	-// double D = x[0+ielements]S[0] + x[1+ielements]S[1] + x[2+ielements]S[2] +
	-// x[1+ielements]S[1] + x[3+ielements]S[3] + x[4+ielements]S[4] +
	-// x[2+ielements]S[2] + x[4+ielements]S[4] + x[5+ielements]S[5];
	-// double signal = S0 * std::exp ( -bValues[s] * D );
	-// if (num_tensors>1 && x.size()>6)
	-// signal = x[elements-1+ielements];
	-// approx += signal;
	-// }
	-
	-// const double factor = measurements[s] - approx;
	-// penalty += fabs(f-1)*10e7; // penalty if volume fractiuon sum is != 1
	-
	-// fx[s] = factor*factor + penalty;
	-// }
	-// }
	-
	-// };
	-
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkMultiTensorImageFilter.txx"
	-#endif
	-
	-#endif //__itkMultiTensorImageFilter_h_
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkMultiTensorImageFilter.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkMultiTensorImageFilter.txx
	deleted file mode 100644
	index 18430b4405..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkMultiTensorImageFilter.txx
	+++ /dev/null
	@@ -1,253 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkMultiTensorImageFilter_txx
	-#define __itkMultiTensorImageFilter_txx
	-
	-#include <time.h>
	-#include <stdio.h>
	-#include <stdlib.h>
	-
	-#define _USE_MATH_DEFINES
	-#include <math.h>
	-
	-#include "itkImageRegionConstIterator.h"
	-#include "itkImageRegionConstIteratorWithIndex.h"
	-#include "itkImageRegionIterator.h"
	-#include <itkDiffusionTensor3D.h>
	-#include <mitkMultiTensorFitter.h>
	-
	-namespace itk {
	-
	-
	-template< class TInPixelType, class TOutPixelType >
	-MultiTensorImageFilter< TInPixelType, TOutPixelType>
	-::MultiTensorImageFilter()
	- : m_B_value(0)
	- , m_NumTensors(2)
	-{
	- this->SetNumberOfRequiredInputs( 1 );
	-}
	-
	-template< class TInPixelType, class TOutPixelType >
	-void
	-MultiTensorImageFilter< TInPixelType, TOutPixelType>
	-::BeforeThreadedGenerateData()
	-{
	- typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0));
	- outputImage->FillBuffer(0.0);
	-
	- m_UnWeightedIndices.clear();
	- m_WeightedIndices.clear();
	- m_B_values.clear();
	-
	- for (unsigned int i=0; i<m_GradientDirections->Size(); i++)
	- {
	- GradientDirectionType g = m_GradientDirections->GetElement(i);
	- double twonorm = g.two_norm();
	- double b = m_B_valuetwonormtwonorm;
	- m_B_values.push_back(b);
	-
	- if (b>100)
	- m_WeightedIndices.push_back(i);
	- else
	- m_UnWeightedIndices.push_back(i);
	- }
	-
	- if (m_UnWeightedIndices.empty())
	- mitkThrow() << "Unweighted (b=0 s/mm²) image volume missing!";
	-
	- itk::Vector<double, 3> spacing3 = outputImage->GetSpacing();
	- itk::Point<float, 3> origin3 = outputImage->GetOrigin();
	- itk::Matrix<double, 3, 3> direction3 = outputImage->GetDirection();
	- itk::ImageRegion<3> imageRegion3 = outputImage->GetLargestPossibleRegion();
	-
	- itk::Vector<double, 4> spacing4;
	- itk::Point<float, 4> origin4;
	- itk::Matrix<double, 4, 4> direction4;
	- itk::ImageRegion<4> imageRegion4;
	-
	- spacing4[0] = spacing3[0]; spacing4[1] = spacing3[1]; spacing4[2] = spacing3[2]; spacing4[3] = 1;
	- origin4[0] = origin3[0]; origin4[1] = origin3[1]; origin4[2] = origin3[2]; origin4[3] = 0;
	- for (int r=0; r<3; r++)
	- for (int c=0; c<3; c++)
	- direction4[r][c] = direction3[r][c];
	- direction4[3][3] = 1;
	- imageRegion4.SetSize(0, imageRegion3.GetSize()[0]);
	- imageRegion4.SetSize(1, imageRegion3.GetSize()[1]);
	- imageRegion4.SetSize(2, imageRegion3.GetSize()[2]);
	- imageRegion4.SetSize(3, 3*m_NumTensors);
	-
	- m_PeakImage = PeakImageType::New();
	- m_PeakImage->SetSpacing( spacing4 );
	- m_PeakImage->SetOrigin( origin4 );
	- m_PeakImage->SetDirection( direction4 );
	- m_PeakImage->SetRegions( imageRegion4 );
	- m_PeakImage->Allocate();
	- m_PeakImage->FillBuffer(0.0);
	-
	- m_TensorImages.clear();
	- for (int i=0; i<m_NumTensors; i++)
	- {
	- TensorImageType::Pointer tImg = TensorImageType::New();
	- tImg->SetSpacing( spacing3 );
	- tImg->SetOrigin( origin3 );
	- tImg->SetDirection( direction3 );
	- tImg->SetRegions( imageRegion3 );
	- tImg->Allocate();
	- m_TensorImages.push_back(tImg);
	- }
	-}
	-
	-template< class TInPixelType, class TOutPixelType >
	-vnl_vector<double>
	-MultiTensorImageFilter< TInPixelType, TOutPixelType>::FitSingleVoxel( const typename InputImageType::PixelType &input)
	-{
	- double S0 = 0;
	- for (auto i : m_UnWeightedIndices)
	- S0 += input[i];
	- S0 /= m_UnWeightedIndices.size();
	-
	- // signle tensor fit
	- mitk::MultiTensorFitter ls_fit(1, m_GradientDirections->size());
	- ls_fit.set_S0(S0);
	- ls_fit.set_weightedIndices(m_WeightedIndices);
	- ls_fit.set_bvalues(m_B_values);
	- ls_fit.set_gradient_directions(m_GradientDirections);
	- ls_fit.set_measurements(input);
	-
	- vnl_levenberg_marquardt lm(ls_fit);
	- vnl_vector<double> x;
	- x.set_size(6);
	- x.fill(0.0);
	-
	- lm.minimize(x);
	-
	-// TensorType tensor;
	-
	- vnl_vector<double> y;
	- y.set_size(7*m_NumTensors);
	- y.fill(0.0);
	- for (int i=0; i<6; i++)
	- {
	- y[i] = x[i];
	-// tensor[i] = x[i];
	- }
	- y[6]=1;
	-// double fa = tensor.GetFractionalAnisotropy();
	-
	- if (m_NumTensors>1)
	- {
	- mitk::MultiTensorFitter ls_fit(m_NumTensors, m_GradientDirections->size());
	- ls_fit.set_S0(S0);
	- ls_fit.set_weightedIndices(m_WeightedIndices);
	- ls_fit.set_bvalues(m_B_values);
	- ls_fit.set_gradient_directions(m_GradientDirections);
	- ls_fit.set_measurements(input);
	-
	- vnl_levenberg_marquardt lm(ls_fit);
	-
	- for (int i=0; i<m_NumTensors; i++)
	- y[6+i*7] = 1.0/m_NumTensors;
	-
	- lm.minimize(y);
	- }
	-
	- return y;
	-}
	-
	-template< class TInPixelType, class TOutPixelType >
	-void
	-MultiTensorImageFilter< TInPixelType, TOutPixelType>
	-::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, ThreadIdType )
	-{
	- typedef ImageRegionConstIterator< InputImageType > InputIteratorType;
	- typename InputImageType::Pointer inputImagePointer = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) );
	-
	- InputIteratorType git( inputImagePointer, outputRegionForThread );
	- git.GoToBegin();
	- while( !git.IsAtEnd() )
	- {
	- typename InputImageType::PixelType pix = git.Get();
	- vnl_vector<double> x = FitSingleVoxel(pix);
	-
	- typedef itk::DiffusionTensor3D<float> TensorType;
	-
	- int elements = 7;
	- for (int t=0; t<m_NumTensors; t++)
	- {
	- TensorType tensor;
	- double f = x[6+t*elements];
	- for (int i=0; i<6; i++)
	- tensor[i] = f * x[i+t*elements];
	- m_TensorImages.at(t)->SetPixel(git.GetIndex(), tensor);
	- }
	-
	-// TensorType tensor;
	-// tensor.Fill(0.0);
	-// tensor[0] = x[0]*x[1];
	-// tensor[3] = tensor[0];
	-// tensor[5] = tensor[0];
	-// m_TensorImages.at(m_NumTensors+1)->SetPixel(git.GetIndex(), tensor);
	-
	-// /// DWI from tensor
	-// int elements = 7;
	-// int num_ten = m_NumTensors;
	-// typename DiffusionImageType::PixelType dPix; dPix.SetSize(m_GradientDirections->Size()); dPix.Fill(0.0);
	-// for (unsigned int i=0; i<m_GradientDirections->Size(); i++)
	-// {
	-// GradientDirectionType g = m_GradientDirections->GetElement(i);
	-// double twonorm = g.two_norm();
	-// double b = m_B_valuetwonormtwonorm;
	-
	-// itk::DiffusionTensor3D< double > S;
	-// S[0] = g[0]*g[0];
	-// S[1] = g[1]*g[0];
	-// S[2] = g[2]*g[0];
	-// S[3] = g[1]*g[1];
	-// S[4] = g[2]*g[1];
	-// S[5] = g[2]*g[2];
	-
	-// double approx = 0;
	-// for (int i=0; i<num_ten; i++)
	-// {
	-// double D = x[0+ielements]S[0] + x[1+ielements]S[1] + x[2+ielements]S[2] +
	-// x[1+ielements]S[1] + x[3+ielements]S[3] + x[4+ielements]S[4] +
	-// x[2+ielements]S[2] + x[4+ielements]S[4] + x[5+ielements]S[5];
	-// approx += x[elements-1+ielements] 1000 * std::exp ( -b * D );
	-// }
	-
	-// dPix[i] = approx;
	-// }
	-// m_OutDwi->SetPixel(oit.GetIndex(), dPix);
	-
	- ++git;
	- }
	-
	- std::cout << "One Thread finished calculation" << std::endl;
	-}
	-
	-template< class TInPixelType, class TOutPixelType >
	-void
	-MultiTensorImageFilter< TInPixelType, TOutPixelType>
	-::PrintSelf(std::ostream& os, Indent indent) const
	-{
	- Superclass::PrintSelf(os,indent);
	-}
	-
	-}
	-
	-#endif // __itkMultiTensorImageFilter_txx
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkOrientationDistributionFunction.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkOrientationDistributionFunction.h
	deleted file mode 100644
	index c39cdc2079..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkOrientationDistributionFunction.h
	+++ /dev/null
	@@ -1,249 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkOrientationDistributionFunction_h
	-#define __itkOrientationDistributionFunction_h
	-
	-#include <MitkDiffusionCoreExports.h>
	-#include "itkIndent.h"
	-#include "itkFixedArray.h"
	-#include "itkMatrix.h"
	-#include "itkSymmetricEigenAnalysis.h"
	-#include "itkSimpleFastMutexLock.h"
	-#include "itkDiffusionTensor3D.h"
	-
	-#include "vtkPolyData.h"
	-#include "vtkPoints.h"
	-#include "vtkCellArray.h"
	-#include "vtkDelaunay2D.h"
	-#include "vtkCleanPolyData.h"
	-#include "vtkAppendPolyData.h"
	-#include "vtkPlane.h"
	-
	-namespace itk
	-{
	-
	-/** \class OrientationDistributionFunction
	- * \brief Represents an ODF
	- *
	- * Reference: David S. Tuch, Q-ball imaging,
	- * Magnetic Resonance in Medicine Volume 52 Issue 6, Pages 1358 - 1372
	- *
	- * \author Klaus Fritzsche, MBI
	- *
	- */
	-
	-template < typename TComponent, unsigned int NOdfDirections >
	-class OrientationDistributionFunction: public
	- FixedArray<TComponent,NOdfDirections>
	-{
	-public:
	-
	- enum InterpolationMethods {
	- ODF_NEAREST_NEIGHBOR_INTERP,
	- ODF_TRILINEAR_BARYCENTRIC_INTERP,
	- ODF_SPHERICAL_GAUSSIAN_BASIS_FUNCTIONS
	- };
	-
	- /** Standard class typedefs. */
	- typedef OrientationDistributionFunction Self;
	- typedef FixedArray<TComponent,NOdfDirections> Superclass;
	-
	- /** Dimension of the vector space. */
	- itkStaticConstMacro(InternalDimension, unsigned int, NOdfDirections);
	-
	- /** Convenience typedefs. */
	- typedef FixedArray<TComponent,
	- itkGetStaticConstMacro(InternalDimension)> BaseArray;
	-
	- /** Define the component type. */
	- typedef TComponent ComponentType;
	- typedef typename Superclass::ValueType ValueType;
	- typedef typename NumericTraits<ValueType>::RealType AccumulateValueType;
	- typedef typename NumericTraits<ValueType>::RealType RealValueType;
	-
	- typedef Matrix<TComponent, NOdfDirections, NOdfDirections> MatrixType;
	-
	- typedef vnl_matrix_fixed<double, 3, NOdfDirections> DirectionsType;
	-
	- /** Default constructor has nothing to do. */
	- OrientationDistributionFunction() {this->Fill(0); m_EigenAnalysisCalculated = false; }
	-
	- OrientationDistributionFunction (const ComponentType& r) { this->Fill(r); m_EigenAnalysisCalculated = false; }
	-
	- typedef ComponentType ComponentArrayType[ itkGetStaticConstMacro(InternalDimension) ];
	-
	- /** Pass-through constructor for the Array base class. */
	- OrientationDistributionFunction(const Self& r): BaseArray(r) { m_EigenAnalysisCalculated = false; }
	- OrientationDistributionFunction(const ComponentArrayType r): BaseArray(r) { m_EigenAnalysisCalculated = false; }
	-
	- /** Pass-through assignment operator for the Array base class. */
	- Self& operator= (const Self& r);
	- Self& operator= (const ComponentType& r);
	- Self& operator= (const ComponentArrayType r);
	-
	- /** Aritmetic operations between pixels. Return a new OrientationDistributionFunction. */
	- Self operator+(const Self &vec) const;
	- Self operator-(const Self &vec) const;
	- const Self & operator+=(const Self &vec);
	- const Self & operator-=(const Self &vec);
	-
	- /** Arithmetic operations between ODFs and scalars */
	- Self operator*(const RealValueType & scalar ) const;
	- Self operator/(const RealValueType & scalar ) const;
	- const Self & operator*=(const RealValueType & scalar );
	- const Self & operator/=(const RealValueType & scalar );
	-
	- /** Return the number of components. */
	- static DirectionsType* GetDirections()
	- {
	- return itkGetStaticConstMacro(m_Directions);
	- }
	-
	- /** Return the number of components. */
	- static unsigned int GetNumberOfComponents()
	- {
	- return itkGetStaticConstMacro(InternalDimension);
	- }
	-
	- /** Return the value for the Nth component. */
	- ComponentType GetNthComponent(int c) const
	- { return this->operator[](c); }
	-
	- /** Return the value for the Nth component. */
	- ComponentType GetInterpolatedComponent( vnl_vector_fixed<double,3> dir, InterpolationMethods method ) const;
	-
	- /** Set the Nth component to v. */
	- void SetNthComponent(int c, const ComponentType& v)
	- { this->operator[](c) = v; }
	-
	- /** Matrix notation, in const and non-const forms. */
	- ValueType & operator()( unsigned int row, unsigned int col );
	- const ValueType & operator()( unsigned int row, unsigned int col ) const;
	-
	- /** Set the distribution to isotropic.*/
	- void SetIsotropic();
	-
	- void InitFromTensor(itk::DiffusionTensor3D<TComponent> tensor);
	-
	- /** Evaluate diffusion tensor as ellipsoid. */
	- void InitFromEllipsoid(itk::DiffusionTensor3D<TComponent> tensor);
	-
	- /** Pre-Multiply by a Matrix as ResultingTensor = Matrix * ThisTensor. */
	- Self PreMultiply( const MatrixType & m ) const;
	-
	- /** Post-Multiply by a Matrix as ResultingTensor = ThisTensor * Matrix. */
	- Self PostMultiply( const MatrixType & m ) const;
	-
	- void Normalize();
	-
	- Self MinMaxNormalize() const;
	-
	- Self MaxNormalize() const;
	-
	- void L2Normalize();
	-
	- int GetPrincipalDiffusionDirectionIndex() const;
	-
	- vnl_vector_fixed<double,3> GetPrincipalDiffusionDirection() const;
	-
	- int GetNthDiffusionDirection(int n, vnl_vector_fixed<double,3> rndVec) const;
	-
	- TComponent GetGeneralizedFractionalAnisotropy() const;
	-
	- TComponent GetGeneralizedGFA(int k, int p) const;
	-
	- TComponent GetNormalizedEntropy() const;
	-
	- TComponent GetNematicOrderParameter() const;
	-
	- TComponent GetStdDevByMaxValue() const;
	-
	- ComponentType GetMaxValue() const;
	-
	- ComponentType GetMinValue() const;
	-
	- ComponentType GetMeanValue() const;
	-
	- TComponent GetPrincipleCurvature(double alphaMinDegree, double alphaMaxDegree, int invert) const;
	-
	- static std::vector<int> GetNeighbors(int idx);
	-
	- static vtkPolyData* GetBaseMesh(){ComputeBaseMesh(); return m_BaseMesh;}
	-
	- static void ComputeBaseMesh();
	-
	- static double GetMaxChordLength();
	-
	- static vnl_vector_fixed<double,3> GetDirection(int i);
	-
	-private:
	-
	- static vtkPolyData* m_BaseMesh;
	-
	- static double m_MaxChordLength;
	-
	- static DirectionsType* m_Directions;
	-
	- static std::vector< std::vector<int>* >* m_NeighborIdxs;
	-
	- static std::vector< std::vector<int>* >* m_AngularRangeIdxs;
	-
	- static std::vector<int>* m_HalfSphereIdxs;
	-
	- static itk::SimpleFastMutexLock m_MutexBaseMesh;
	- static itk::SimpleFastMutexLock m_MutexHalfSphereIdxs;
	- static itk::SimpleFastMutexLock m_MutexNeighbors;
	- static itk::SimpleFastMutexLock m_MutexAngularRange;
	- typename itk::DiffusionTensor3D<TComponent>::EigenValuesArrayType m_EigenValues;
	- typename itk::DiffusionTensor3D<TComponent>::EigenVectorsMatrixType m_EigenVectors;
	- bool m_EigenAnalysisCalculated;
	-
	-};
	-
	-/** This extra typedef is necessary for preventing an Internal Compiler Error in
	- * Microsoft Visual C++ 6.0. This typedef is not needed for any other compiler. */
	-typedef std::ostream OutputStreamType;
	-typedef std::istream InputStreamType;
	-
	-template< typename TComponent, unsigned int NOdfDirections >
	-MITKDIFFUSIONCORE_EXPORT OutputStreamType& operator<<(OutputStreamType& os,
	- const OrientationDistributionFunction<TComponent,NOdfDirections> & c);
	-template< typename TComponent, unsigned int NOdfDirections >
	-MITKDIFFUSIONCORE_EXPORT InputStreamType& operator>>(InputStreamType& is,
	- OrientationDistributionFunction<TComponent,NOdfDirections> & c);
	-
	-
	-
	-} // end namespace itk
	-
	-// Define instantiation macro for this template.
	-#define ITK_TEMPLATE_OrientationDistributionFunction(_, EXPORT, x, y) namespace itk { \
	- _(2(class MITKDIFFUSIONCORE_EXPORT EXPORT OrientationDistributionFunction< ITK_TEMPLATE_2 x >)) \
	- namespace Templates { typedef OrientationDistributionFunction< ITK_TEMPLATE_2 x > \
	- OrientationDistributionFunction##y; } \
	- }
	-
	-#if ITK_TEMPLATE_EXPLICIT
	-# include "Templates/itkOrientationDistributionFunction+-.h"
	-#endif
	-
	-#if ITK_TEMPLATE_TXX
	-# include "itkOrientationDistributionFunction.txx"
	-#endif
	-
	-
	-#endif //__itkOrientationDistributionFunction_h
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkOrientationDistributionFunction.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkOrientationDistributionFunction.txx
	deleted file mode 100644
	index c50bf289c1..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkOrientationDistributionFunction.txx
	+++ /dev/null
	@@ -1,1366 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _itkOrientationDistributionFunction_txx
	-#define _itkOrientationDistributionFunction_txx
	-
	-#include <cstdio>
	-#include <cstdlib>
	-#include <ctime>
	-#include <algorithm>
	-#include <vector>
	-#include <vnl/algo/vnl_matrix_inverse.h>
	-#include "itkPointShell.h"
	-
	-#ifdef _MSC_VER
	-#if _MSC_VER <= 1700
	-#define fmin(a,b) ((a<=b)?(a):(b))
	-#define fmax(a,b) ((a>=b)?(a):(b))
	-#define isnan(c) (c!=c)
	-#endif
	-#endif
	-
	-#include <itkMatrix.h>
	-#include <vnl/vnl_matrix.h>
	-#include <vnl/vnl_matrix_fixed.h>
	-#include <vnl/vnl_inverse.h>
	-#include <typeinfo>
	-#include <ciso646>
	-
	-namespace itk
	-{
	-
	-template<class T, unsigned int N>
	-vtkPolyData* itk::OrientationDistributionFunction<T,N>::m_BaseMesh = nullptr;
	-
	-template<class T, unsigned int N>
	-double itk::OrientationDistributionFunction<T,N>::m_MaxChordLength = -1.0;
	-
	-template<class T, unsigned int N>
	-vnl_matrix_fixed<double, 3, N>* itk::OrientationDistributionFunction<T,N>::m_Directions
	-= itk::PointShell<N, vnl_matrix_fixed<double, 3, N> >::DistributePointShell();
	-
	-template<class T, unsigned int N>
	-std::vector< std::vector<int>* >* itk::OrientationDistributionFunction<T,N>::m_NeighborIdxs = nullptr;
	-
	-template<class T, unsigned int N>
	-std::vector< std::vector<int>* >* itk::OrientationDistributionFunction<T,N>::m_AngularRangeIdxs = nullptr;
	-
	-template<class T, unsigned int N>
	-std::vector<int>* itk::OrientationDistributionFunction<T,N>::m_HalfSphereIdxs = nullptr;
	-
	-template<class T, unsigned int N>
	-itk::SimpleFastMutexLock itk::OrientationDistributionFunction<T,N>::m_MutexBaseMesh;
	-template<class T, unsigned int N>
	-itk::SimpleFastMutexLock itk::OrientationDistributionFunction<T,N>::m_MutexHalfSphereIdxs;
	-template<class T, unsigned int N>
	-itk::SimpleFastMutexLock itk::OrientationDistributionFunction<T,N>::m_MutexNeighbors;
	-template<class T, unsigned int N>
	-itk::SimpleFastMutexLock itk::OrientationDistributionFunction<T,N>::m_MutexAngularRange;
	-
	-/**
	- * Assignment Operator
	- */
	-template<class T, unsigned int NOdfDirections>
	-OrientationDistributionFunction<T, NOdfDirections>&
	-OrientationDistributionFunction<T, NOdfDirections>
	-::operator= (const Self& r)
	-{
	- BaseArray::operator=(r);
	- return *this;
	-}
	-
	-/**
	- * Assignment Operator from a scalar constant
	- */
	-template<class T, unsigned int NOdfDirections>
	-OrientationDistributionFunction<T, NOdfDirections>&
	-OrientationDistributionFunction<T, NOdfDirections>
	-::operator= (const ComponentType & r)
	-{
	- BaseArray::operator=(&r);
	- return *this;
	-}
	-
	-/**
	- * Assigment from a plain array
	- */
	-template<class T, unsigned int NOdfDirections>
	-OrientationDistributionFunction<T, NOdfDirections>&
	-OrientationDistributionFunction<T, NOdfDirections>
	-::operator= (const ComponentArrayType r )
	-{
	- BaseArray::operator=(r);
	- return *this;
	-}
	-
	-/**
	- * Returns a temporary copy of a vector
	- */
	-template<class T, unsigned int NOdfDirections>
	-OrientationDistributionFunction<T, NOdfDirections>
	-OrientationDistributionFunction<T, NOdfDirections>
	-::operator+(const Self & r) const
	-{
	- Self result;
	- for( unsigned int i=0; i<InternalDimension; i++)
	- {
	- result[i] = (*this)[i] + r[i];
	- }
	- return result;
	-}
	-
	-/**
	- * Returns a temporary copy of a vector
	- */
	-template<class T, unsigned int NOdfDirections>
	-OrientationDistributionFunction<T, NOdfDirections>
	-OrientationDistributionFunction<T, NOdfDirections>
	-::operator-(const Self & r) const
	-{
	- Self result;
	- for( unsigned int i=0; i<InternalDimension; i++)
	- {
	- result[i] = (*this)[i] - r[i];
	- }
	- return result;
	-}
	-
	-/**
	- * Performs addition in place
	- */
	-template<class T, unsigned int NOdfDirections>
	-const OrientationDistributionFunction<T, NOdfDirections> &
	-OrientationDistributionFunction<T, NOdfDirections>
	-::operator+=(const Self & r)
	-{
	- for( unsigned int i=0; i<InternalDimension; i++)
	- {
	- (*this)[i] += r[i];
	- }
	- return *this;
	-}
	-
	-/**
	- * Performs subtraction in place
	- */
	-template<class T, unsigned int NOdfDirections>
	-const OrientationDistributionFunction<T, NOdfDirections> &
	-OrientationDistributionFunction<T, NOdfDirections>
	-::operator-=(const Self & r)
	-{
	- for( unsigned int i=0; i<InternalDimension; i++)
	- {
	- (*this)[i] -= r[i];
	- }
	- return *this;
	-}
	-
	-/**
	- * Performs multiplication by a scalar, in place
	- */
	-template<class T, unsigned int NOdfDirections>
	-const OrientationDistributionFunction<T, NOdfDirections> &
	-OrientationDistributionFunction<T, NOdfDirections>
	-::operator*=(const RealValueType & r)
	-{
	- for( unsigned int i=0; i<InternalDimension; i++)
	- {
	- (this)[i] = r;
	- }
	- return *this;
	-}
	-
	-/**
	- * Performs division by a scalar, in place
	- */
	-template<class T, unsigned int NOdfDirections>
	-const OrientationDistributionFunction<T, NOdfDirections> &
	-OrientationDistributionFunction<T, NOdfDirections>
	-::operator/=(const RealValueType & r)
	-{
	- for( unsigned int i=0; i<InternalDimension; i++)
	- {
	- (*this)[i] /= r;
	- }
	- return *this;
	-}
	-
	-/**
	- * Performs multiplication with a scalar
	- */
	-template<class T, unsigned int NOdfDirections>
	-OrientationDistributionFunction<T, NOdfDirections>
	-OrientationDistributionFunction<T, NOdfDirections>
	-::operator*(const RealValueType & r) const
	-{
	- Self result;
	- for( unsigned int i=0; i<InternalDimension; i++)
	- {
	- result[i] = (this)[i] r;
	- }
	- return result;
	-}
	-
	-/**
	- * Performs division by a scalar
	- */
	-template<class T, unsigned int NOdfDirections>
	-OrientationDistributionFunction<T, NOdfDirections>
	-OrientationDistributionFunction<T, NOdfDirections>
	-::operator/(const RealValueType & r) const
	-{
	- Self result;
	- for( unsigned int i=0; i<InternalDimension; i++)
	- {
	- result[i] = (*this)[i] / r;
	- }
	- return result;
	-}
	-
	-/**
	- * Matrix notation access to elements
	- */
	-template<class T, unsigned int NOdfDirections>
	-const typename OrientationDistributionFunction<T, NOdfDirections>::ValueType &
	-OrientationDistributionFunction<T, NOdfDirections>
	-::operator()(unsigned int row, unsigned int col) const
	-{
	- unsigned int k;
	-
	- if( row < col )
	- {
	- k = row * InternalDimension + col - row * ( row + 1 ) / 2;
	- }
	- else
	- {
	- k = col * InternalDimension + row - col * ( col + 1 ) / 2;
	- }
	-
	-
	- if( k >= InternalDimension )
	- {
	- k = 0;
	- }
	-
	- return (*this)[k];
	-}
	-
	-/**
	- * Matrix notation access to elements
	- */
	-template<class T, unsigned int NOdfDirections>
	-typename OrientationDistributionFunction<T, NOdfDirections>::ValueType &
	-OrientationDistributionFunction<T, NOdfDirections>
	-::operator()(unsigned int row, unsigned int col)
	-{
	- unsigned int k;
	-
	- if( row < col )
	- {
	- k = row * InternalDimension + col - row * ( row + 1 ) / 2;
	- }
	- else
	- {
	- k = col * InternalDimension + row - col * ( col + 1 ) / 2;
	- }
	-
	-
	- if( k >= InternalDimension )
	- {
	- k = 0;
	- }
	-
	- return (*this)[k];
	-}
	-
	-/**
	- * Set the Tensor to an Identity.
	- * Set ones in the diagonal and zeroes every where else.
	- */
	-template<class T, unsigned int NOdfDirections>
	-void
	-OrientationDistributionFunction<T, NOdfDirections>
	-::SetIsotropic()
	-{
	- this->Fill(NumericTraits< T >::One / NOdfDirections);
	-}
	-
	-/**
	- * InitFromTensor()
	- */
	-template<class T, unsigned int NOdfDirections>
	-void
	-OrientationDistributionFunction<T, NOdfDirections>
	-::InitFromTensor(itk::DiffusionTensor3D<T> tensor)
	-{
	- m_EigenAnalysisCalculated = false;
	- for(unsigned int i=0; i<NOdfDirections; i++)
	- {
	- /*
	- * \| t0 t1 t2 \| g0
	- * g0 g1 g2 * \| t1 t3 t4 \| * g1
	- * \| t2 t4 t5 \| g2
	- *
	- * = g0 * (t0g0t1g1t2g2)
	- * + g1 * (t1g0+t3g1+t4g2)
	- * + g2 * (t2g0+t4g1+t5g2)
	- */
	- T g0 = (*m_Directions)(0,i);
	- T g1 = (*m_Directions)(1,i);
	- T g2 = (*m_Directions)(2,i);
	- T t0 = tensor[0];
	- T t1 = tensor[1];
	- T t2 = tensor[2];
	- T t3 = tensor[3];
	- T t4 = tensor[4];
	- T t5 = tensor[5];
	- (this)[i] = g0 (t0g0+t1g1+t2*g2)
	- + g1 * (t1g0+t3g1+t4*g2)
	- + g2 * (t2g0+t4g1+t5*g2);
	-
	- if ((this)[i]<0 \|\| (this)[i]!=(*this)[i])
	- (*this)[i] = 0;
	- }
	-}
	-
	-/**
	- * InitFromEllipsoid()
	- */
	-template<class T, unsigned int NOdfDirections>
	-void OrientationDistributionFunction<T, NOdfDirections>::
	-InitFromEllipsoid( itk::DiffusionTensor3D<T> tensor )
	-{
	- m_EigenAnalysisCalculated = false;
	- FixedArray<T, 6> nulltensor;
	- nulltensor.Fill(0.0);
	- if( tensor == nulltensor )
	- {
	- for ( unsigned int it=0; it < NOdfDirections; ++it ){ (*this)[it] = (T)0; }
	- MITK_DEBUG << "OrientationDistributionFunction<" << typeid(T).name() << ", " << NOdfDirections
	- << ">::InitFromEllipsoid(" << typeid(tensor).name()
	- << ") encountered a nulltensor as dti input point and ignorend it.";
	- return;
	- }
	-
	- tensor.ComputeEigenAnalysis( m_EigenValues, this->m_EigenVectors ); // gives normalized eigenvectors as lines i.e. rows.
	- m_EigenAnalysisCalculated = true;
	-
	- double a = m_EigenValues[0]; // those eigenvalues are the 3 \|axes of the ellipsoid\|,
	- double b = m_EigenValues[1]; // ComputeEigenAnalysis gives eigenValues in ascending < order per default,
	- double c = m_EigenValues[2]; // therefor the third eigenVector is the main direction of diffusion.
	-
	- if( a <= 0.0 \|\| b <= 0.0 \|\| c <= 0.0 )
	- {
	- for ( unsigned int it=0; it < NOdfDirections; ++it ){ (*this)[it] = (T)0; }
	- MITK_DEBUG << "OrientationDistributionFunction<" << typeid(T).name() << ", " << NOdfDirections
	- << ">::InitFromEllipsoid(" << typeid(tensor).name()
	- << ") encountered an eigenvalue <= 0 and ignored this input point.";
	- return;
	- }
	-
	- // check magnitude and scale towards 1 to minimize numerical condition kappa:
	-#ifdef _MSC_VER
	-#if _MSC_VER <= 1700
	- int exponent_a = floor(std::log(a)/std::log(2));
	- int exponent_b = floor(std::log(b)/std::log(2));
	- int exponent_c = floor(std::log(c)/std::log(2));
	-#else
	- int exponent_a = std::ilogb(a);
	- int exponent_b = std::ilogb(b);
	- int exponent_c = std::ilogb(c);
	-#endif
	-#else
	- int exponent_a = std::ilogb(a);
	- int exponent_b = std::ilogb(b);
	- int exponent_c = std::ilogb(c);
	-#endif
	-
	- T min_exponent= fmin(exponent_a, fmin(exponent_b, exponent_c) );
	- T max_exponent= fmax(exponent_c, fmax(exponent_b, exponent_a) );
	- int scale_exponent = floor(0.5 * (min_exponent + max_exponent));
	- double scaling = pow(2, scale_exponent);
	- a= a/scaling;
	- b= b/scaling;
	- c= c/scaling;
	-
	- vnl_matrix_fixed<double, 3, 3> eigenBase; // for change of base system.
	- for (int row = 0 ; row < 3; ++row) // Transposing because ComputeEigenAnalysis(,) gave us _row_ vectors.
	- {
	- for (int col = 0; col < 3; ++col)
	- {
	- eigenBase(row, col) = this->m_EigenVectors(col, row);
	- }
	- }
	- eigenBase= vnl_inverse(eigenBase); // Assuming canonical orthonormal system x=[1;0;0];y=[0;1;0];z=[0;0;1] for original DT.
	- eigenBase.assert_finite();
	-
	-#ifndef NDEBUG
	- double kappa=1.0;
	- { // calculate numerical condition kappa= \|\|f(x)-f(x~)\|\| approximately:
	- double gxaa = pow( a, -2.0); double gybb = pow( b, -2.0); double gzcc = pow( c, -2.0);
	- kappa = sqrt( pow( a, 2.0)+ pow( b, 2.0)+ pow( c, 2.0) + 1 ) / (gxaa + gybb + gzcc)
	- * sqrt( pow( a, -6.0)+ pow( b, -6.0)+ pow( c, -6.0) + pow( a, -4.0)+ pow( b, -4.0)+ pow( c, -4.0) );
	- MITK_DEBUG <<"kappa= "<< kappa << ", eigenvalues= [" << a <<", "<< b <<", "<< c <<"], eigenbase= ["
	- <<eigenBase(0,0)<<", "<<eigenBase(1,0)<<", "<<eigenBase(2,0)<<"; "
	- <<eigenBase(0,1)<<", "<<eigenBase(1,1)<<", "<<eigenBase(2,1)<<"; "
	- <<eigenBase(0,2)<<", "<<eigenBase(1,2)<<", "<<eigenBase(2,2)<<"] ";
	- if( std::isnan(kappa) )
	- {
	- MITK_DEBUG << "oh noes: kappa was NaN, setting kappa to 1e5"; // typical value kappa=1e5 for 1e-6<=a,b,c<=1e-4.
	- kappa=1e5;
	- };
	- }
	-#endif
	-
	- for( unsigned int i=0; i < NOdfDirections; ++i )
	- {
	- /// calculate probability p(g)=r as ellipsoids magnitude in direction of g' = B^-1 * g:
	- /// (g0r/evx)² + (g1r/evy)² + (g2*r/evz)² = 1, \|g'\|=1.
	-
	- vnl_vector_fixed<double, 3> g( (m_Directions)(0,i), (m_Directions)(1,i), (*m_Directions)(2,i) );
	- g = eigenBase*g; // passive change of base system of g.
	- g = g.normalize(); // unit vectors necessary.
	- (this)[i] = scaling / sqrt( (g[0]/a)(g[0]/a) + (g[1]/b)(g[1]/b) + (g[2]/c)(g[2]/c) );
	-
	-#ifndef NDEBUG
	- { // boundary check for numerical stability, assuming sigma=6, \|\|f(x~)-f~(x~)\|\| <= epskappasigma.
	- T min_ev= fmin(a, fmin(b, c) ); T max_ev= fmax(c, fmax(b, a) );
	- double eps= std::numeric_limits<T>::epsilon();
	- assert( scalingmin_ev <= ((this)[i] + epskappa6.0) ); // we should be between smallest and
	- assert( (this)[i] <= (scalingmax_ev + epskappa6.0) ); // biggest eigenvalue.
	- }
	-#endif
	- if ( (this)[i] < T(0) \|\| (this)[i] > T(1) \|\| std::isnan((*this)[i]) ) // P∈[0;1] sanity check.
	- { // C: NaN != NaN, C++11: isnan((*this)[i]).
	- MITK_DEBUG << "OrientationDistributionFunction<" << typeid(T).name() << ", " << NOdfDirections
	- << ">::InitFromEllipsoid(" << typeid(tensor).name()
	- << ") encountered a probability value out of range [0;1] and set it to zero: (*this)["
	- << i <<"]= " << (*this)[i];
	- (*this)[i] = T(0);
	- }
	- }
	-}
	-
	-/**
	- * L2-Normalization
	- */
	-template<class T, unsigned int NOdfDirections>
	-void
	-OrientationDistributionFunction<T, NOdfDirections>
	-::L2Normalize()
	-{
	- T sum = 0;
	- for( unsigned int i=0; i<InternalDimension; i++)
	- {
	- sum += (this)[i](*this)[i];
	- }
	- sum = std::sqrt(sum);
	- for( unsigned int i=0; i<InternalDimension; i++)
	- {
	- (this)[i] = (this)[i] / sum;
	- }
	-}
	-
	-/**
	- * Normalization to PDF
	- */
	-template<class T, unsigned int NOdfDirections>
	-void
	-OrientationDistributionFunction<T, NOdfDirections>
	-::Normalize()
	-{
	- T sum = 0;
	- for( unsigned int i=0; i<InternalDimension; i++)
	- {
	- sum += (*this)[i];
	- }
	- if (sum>0)
	- {
	- for( unsigned int i=0; i<InternalDimension; i++)
	- {
	- (this)[i] = (this)[i] / sum;
	- }
	- }
	-}
	-
	-/**
	- * Min/Max-Normalization
	- */
	-template<class T, unsigned int NOdfDirections>
	-OrientationDistributionFunction<T, NOdfDirections>
	-OrientationDistributionFunction<T, NOdfDirections>
	-::MinMaxNormalize() const
	-{
	- T max = NumericTraits<T>::NonpositiveMin();
	- T min = NumericTraits<T>::max();
	- for( unsigned int i=0; i<InternalDimension; i++)
	- {
	- max = (this)[i] > max ? (this)[i] : max;
	- min = (this)[i] < min ? (this)[i] : min;
	- }
	- Self retval;
	- for( unsigned int i=0; i<InternalDimension; i++)
	- {
	- retval[i] = ((*this)[i] - min) / (max - min);
	- }
	- return retval;
	-}
	-
	-/**
	- * Max-Normalization
	- */
	-template<class T, unsigned int NOdfDirections>
	-OrientationDistributionFunction<T, NOdfDirections>
	-OrientationDistributionFunction<T, NOdfDirections>
	-::MaxNormalize() const
	-{
	- T max = NumericTraits<T>::NonpositiveMin();
	- for( unsigned int i=0; i<InternalDimension; i++)
	- {
	- max = (this)[i] > max ? (this)[i] : max;
	- }
	- Self retval;
	- for( unsigned int i=0; i<InternalDimension; i++)
	- {
	- retval[i] = (*this)[i] / max;
	- }
	- return retval;
	-}
	-
	-template<class T, unsigned int NOdfDirections>
	-T
	-OrientationDistributionFunction<T, NOdfDirections>
	-::GetMaxValue() const
	-{
	- T max = NumericTraits<T>::NonpositiveMin();
	- for( unsigned int i=0; i<InternalDimension; i++)
	- {
	- if((*this)[i] >= max )
	- {
	- max = (*this)[i];
	- }
	- }
	- return max;
	-}
	-
	-template<class T, unsigned int NOdfDirections>
	-T
	-OrientationDistributionFunction<T, NOdfDirections>
	-::GetMinValue() const
	-{
	- T min = NumericTraits<T>::max();
	- for( unsigned int i=0; i<InternalDimension; i++)
	- {
	- if((*this)[i] >= min )
	- {
	- min = (*this)[i];
	- }
	- }
	- return min;
	-}
	-
	-template<class T, unsigned int NOdfDirections>
	-T
	-OrientationDistributionFunction<T, NOdfDirections>
	-::GetMeanValue() const
	-{
	- T sum = 0;
	- for( unsigned int i=0; i<InternalDimension; i++)
	- sum += (*this)[i];
	- return sum/InternalDimension;
	-}
	-
	-template<class T, unsigned int NOdfDirections>
	-double
	-OrientationDistributionFunction<T, NOdfDirections>
	-::GetMaxChordLength()
	-{
	- if(m_MaxChordLength<0.0)
	- {
	- ComputeBaseMesh();
	- double max_dist = -1;
	- vtkPoints* points = m_BaseMesh->GetPoints();
	- for(int i=0; i<NOdfDirections; i++)
	- {
	- double p[3];
	- points->GetPoint(i,p);
	- std::vector<int> neighbors = GetNeighbors(i);
	- for(std::size_t j=0; j<neighbors.size(); j++)
	- {
	- double n[3];
	- points->GetPoint(neighbors[j],n);
	- double d = sqrt(
	- (p[0]-n[0])*(p[0]-n[0]) +
	- (p[1]-n[1])*(p[1]-n[1]) +
	- (p[2]-n[2])*(p[2]-n[2]));
	- max_dist = d>max_dist ? d : max_dist;
	- }
	- }
	- m_MaxChordLength = max_dist;
	- }
	- return m_MaxChordLength;
	-}
	-
	-template<class T, unsigned int NOdfDirections>
	-void
	-OrientationDistributionFunction<T, NOdfDirections>
	-::ComputeBaseMesh()
	-{
	-
	- m_MutexBaseMesh.Lock();
	- if(m_BaseMesh == nullptr)
	- {
	-
	- vtkPoints* points = vtkPoints::New();
	- for(unsigned int j=0; j<NOdfDirections; j++){
	- double x = (*m_Directions)(0,j);
	- double y = (*m_Directions)(1,j);
	- double z = (*m_Directions)(2,j);
	- double az = atan2(y,x);
	- double elev = atan2(z,sqrt(xx+yy));
	- double r = sqrt(xx+yy+z*z);
	- points->InsertNextPoint(az,elev,r);
	- }
	-
	- vtkPolyData* polydata = vtkPolyData::New();
	- polydata->SetPoints( points );
	- vtkDelaunay2D *delaunay = vtkDelaunay2D::New();
	- delaunay->SetInputData( polydata );
	- delaunay->Update();
	-
	- vtkCellArray* vtkpolys = delaunay->GetOutput()->GetPolys();
	- vtkCellArray* vtknewpolys = vtkCellArray::New();
	- vtkIdType npts; vtkIdType *pts;
	- while(vtkpolys->GetNextCell(npts,pts))
	- {
	- bool insert = true;
	- for(int i=0; i<npts; i++)
	- {
	- double *tmpPoint = points->GetPoint(pts[i]);
	- double az = tmpPoint[0];
	- double elev = tmpPoint[1];
	- if((std::abs(az)>itk::Math::pi-0.5) \|\| (std::abs(elev)>itk::Math::pi/2-0.5))
	- insert = false;
	- }
	- if(insert)
	- vtknewpolys->InsertNextCell(npts, pts);
	- }
	-
	- vtkPoints* points2 = vtkPoints::New();
	- for(unsigned int j=0; j<NOdfDirections; j++){
	- double x = -(*m_Directions)(0,j);
	- double y = -(*m_Directions)(2,j);
	- double z = -(*m_Directions)(1,j);
	- double az = atan2(y,x);
	- double elev = atan2(z,sqrt(xx+yy));
	- double r = sqrt(xx+yy+z*z);
	- points2->InsertNextPoint(az,elev,r);
	- }
	-
	- vtkPolyData* polydata2 = vtkPolyData::New();
	- polydata2->SetPoints( points2 );
	- vtkDelaunay2D *delaunay2 = vtkDelaunay2D::New();
	- delaunay2->SetInputData( polydata2 );
	- delaunay2->Update();
	-
	- vtkpolys = delaunay2->GetOutput()->GetPolys();
	- while(vtkpolys->GetNextCell(npts,pts))
	- {
	- bool insert = true;
	- for(int i=0; i<npts; i++)
	- {
	- double *tmpPoint = points2->GetPoint(pts[i]);
	- double az = tmpPoint[0];
	- double elev = tmpPoint[1];
	- if((std::abs(az)>itk::Math::pi-0.5) \|\| (std::abs(elev)>itk::Math::pi/2-0.5))
	- insert = false;
	- }
	- if(insert)
	- vtknewpolys->InsertNextCell(npts, pts);
	- }
	-
	- polydata->SetPolys(vtknewpolys);
	-
	- for (unsigned int p = 0; p < NOdfDirections; p++)
	- {
	- points->SetPoint(p,m_Directions->get_column(p).data_block());
	- }
	- polydata->SetPoints( points );
	-
	- m_BaseMesh = polydata;
	- }
	- m_MutexBaseMesh.Unlock();
	-}
	-
	-/**
	- * Extract the index of the principal diffusion direction
	- */
	-template<class T, unsigned int NOdfDirections>
	-int OrientationDistributionFunction<T, NOdfDirections>::GetPrincipalDiffusionDirectionIndex() const
	-{
	- T max = NumericTraits<T>::NonpositiveMin();
	- int maxidx = -1;
	- for( unsigned int i=0; i<InternalDimension; i++)
	- {
	- if((*this)[i] >= max )
	- {
	- max = (*this)[i];
	- maxidx = i;
	- }
	- }
	-
	- return maxidx;
	-}
	-
	-/**
	- * Extract the principal diffusion direction
	- */
	-template<class T, unsigned int NOdfDirections>
	-vnl_vector_fixed<double,3> OrientationDistributionFunction<T, NOdfDirections>::GetPrincipalDiffusionDirection() const
	-{
	- if (m_EigenAnalysisCalculated)
	- {
	- vnl_vector_fixed<double,3> vec;
	- vec[0] = this->m_EigenVectors(2,0);
	- vec[1] = this->m_EigenVectors(2,1);
	- vec[2] = this->m_EigenVectors(2,2);
	- vec.normalize();
	- return vec;
	- }
	- else
	- {
	- int idx = GetPrincipalDiffusionDirectionIndex();
	- if (idx>0 && idx<(int)NOdfDirections)
	- return OrientationDistributionFunction<T, NOdfDirections>::GetDirection(idx);
	- vnl_vector_fixed<double,3> vec; vec.fill(0);
	- return vec;
	- }
	-}
	-
	-template<class T, unsigned int NOdfDirections>
	-std::vector<int>
	-OrientationDistributionFunction<T, NOdfDirections>
	-::GetNeighbors(int idx)
	-{
	- ComputeBaseMesh();
	-
	- m_MutexNeighbors.Lock();
	- if(m_NeighborIdxs == nullptr)
	- {
	- m_NeighborIdxs = new std::vector< std::vector<int>* >();
	- vtkCellArray* polys = m_BaseMesh->GetPolys();
	-
	- for(unsigned int i=0; i<NOdfDirections; i++)
	- {
	- auto idxs = new std::vector<int>();
	- polys->InitTraversal();
	- vtkIdType npts; vtkIdType *pts;
	- while(polys->GetNextCell(npts,pts))
	- {
	- if( pts[0] == i )
	- {
	- idxs->push_back(pts[1]);
	- idxs->push_back(pts[2]);
	- }
	- else if( pts[1] == i )
	- {
	- idxs->push_back(pts[0]);
	- idxs->push_back(pts[2]);
	- }
	- else if( pts[2] == i )
	- {
	- idxs->push_back(pts[0]);
	- idxs->push_back(pts[1]);
	- }
	- }
	- std::sort(idxs->begin(), idxs->end());
	- std::vector< int >::iterator endLocation;
	- endLocation = std::unique( idxs->begin(), idxs->end() );
	- idxs->erase(endLocation, idxs->end());
	- m_NeighborIdxs->push_back(idxs);
	- }
	- }
	- m_MutexNeighbors.Unlock();
	-
	- return *m_NeighborIdxs->at(idx);
	-}
	-
	-/**
	- * Extract the n-th diffusion direction
	- */
	-template<class T, unsigned int NOdfDirections>
	-int
	-OrientationDistributionFunction<T, NOdfDirections>
	-::GetNthDiffusionDirection(int n, vnl_vector_fixed<double,3> rndVec) const
	-{
	-
	- if( n == 0 )
	- return GetPrincipalDiffusionDirectionIndex();
	-
	- m_MutexHalfSphereIdxs.Lock();
	- if( !m_HalfSphereIdxs )
	- {
	- m_HalfSphereIdxs = new std::vector<int>();
	- for( unsigned int i=0; i<InternalDimension; i++)
	- {
	- if(dot_product(m_Directions->get_column(i),rndVec) > 0.0)
	- {
	- m_HalfSphereIdxs->push_back(i);
	- }
	- }
	- }
	- m_MutexHalfSphereIdxs.Unlock();
	-
	- // collect indices of directions
	- // that are local maxima
	- std::vector<int> localMaxima;
	- std::vector<int>::iterator it;
	- for( it=m_HalfSphereIdxs->begin();
	- it!=m_HalfSphereIdxs->end();
	- it++)
	- {
	- std::vector<int> nbs = GetNeighbors(*it);
	- std::vector<int>::iterator it2;
	- bool max = true;
	- for(it2 = nbs.begin();
	- it2 != nbs.end();
	- it2++)
	- {
	- if((this)[it2] > (this)[it])
	- {
	- max = false;
	- break;
	- }
	- }
	- if(max)
	- localMaxima.push_back(*it);
	- }
	-
	- // delete n highest local maxima from list
	- // and return remaining highest
	- int maxidx = -1;
	- for( int i=0; i<=n; i++ )
	- {
	- maxidx = -1;
	- T max = NumericTraits<T>::NonpositiveMin();
	- for(it = localMaxima.begin();
	- it != localMaxima.end();
	- it++)
	- {
	- if((this)[it]>max)
	- {
	- max = (this)[it];
	- maxidx = *it;
	- }
	- }
	- it = find(localMaxima.begin(), localMaxima.end(), maxidx);
	- if(it!=localMaxima.end())
	- localMaxima.erase(it);
	- }
	-
	- return maxidx;
	-}
	-
	-template < typename TComponent, unsigned int NOdfDirections >
	-vnl_vector_fixed<double,3> itk::OrientationDistributionFunction<TComponent, NOdfDirections>
	-::GetDirection( int i )
	-{
	- return m_Directions->get_column(i);
	-}
	-
	-/**
	- * Interpolate a position between sampled directions
	- */
	-template<class T, unsigned int NOdfDirections>
	-T
	-OrientationDistributionFunction<T, NOdfDirections>
	-::GetInterpolatedComponent(vnl_vector_fixed<double,3> dir, InterpolationMethods method) const
	-{
	-
	- ComputeBaseMesh();
	- double retval = -1.0;
	-
	- switch(method)
	- {
	- case ODF_NEAREST_NEIGHBOR_INTERP:
	- {
	-
	- vtkPoints* points = m_BaseMesh->GetPoints();
	- double current_min = NumericTraits<double>::max();
	- int current_min_idx = -1;
	- for(int i=0; i<NOdfDirections; i++)
	- {
	- vnl_vector_fixed<double,3> P(points->GetPoint(i));
	- double dist = (dir-P).two_norm();
	- current_min_idx = dist<current_min ? i : current_min_idx;
	- current_min = dist<current_min ? dist : current_min;
	- }
	- retval = this->GetNthComponent(current_min_idx);
	- break;
	-
	- }
	- case ODF_TRILINEAR_BARYCENTRIC_INTERP:
	- {
	-
	- double maxChordLength = GetMaxChordLength();
	- vtkCellArray* polys = m_BaseMesh->GetPolys();
	- vtkPoints* points = m_BaseMesh->GetPoints();
	- vtkIdType npts; vtkIdType *pts;
	- double current_min = NumericTraits<double>::max();
	- polys->InitTraversal();
	- while(polys->GetNextCell(npts,pts))
	- {
	- vnl_vector_fixed<double,3> A(points->GetPoint(pts[0]));
	- vnl_vector_fixed<double,3> B(points->GetPoint(pts[1]));
	- vnl_vector_fixed<double,3> C(points->GetPoint(pts[2]));
	-
	- vnl_vector_fixed<double,3> d1;
	- d1.put(0,(dir-A).two_norm());
	- d1.put(1,(dir-B).two_norm());
	- d1.put(2,(dir-C).two_norm());
	- double maxval = d1.max_value();
	- if(maxval>maxChordLength)
	- {
	- continue;
	- }
	-
	- // Compute vectors
	- vnl_vector_fixed<double,3> v0 = C - A;
	- vnl_vector_fixed<double,3> v1 = B - A;
	-
	- // Project direction to plane ABC
	- vnl_vector_fixed<double,3> v6 = dir;
	- vnl_vector_fixed<double,3> cross = vnl_cross_3d(v0, v1);
	- cross = cross.normalize();
	- vtkPlane::ProjectPoint(v6.data_block(),A.data_block(),cross.data_block(),v6.data_block());
	- v6 = v6-A;
	-
	- // Calculate barycentric coords
	- vnl_matrix_fixed<double,3,2> mat;
	- mat.set_column(0, v0);
	- mat.set_column(1, v1);
	- vnl_matrix_inverse<double> inv(mat);
	- vnl_matrix_fixed<double,2,3> inver = inv.pinverse();
	- vnl_vector<double> uv = inv.pinverse()*v6;
	-
	- // Check if point is in triangle
	- double eps = 0.01;
	- if( (uv(0) >= 0-eps) && (uv(1) >= 0-eps) && (uv(0) + uv(1) <= 1+eps) )
	- {
	- // check if minimum angle is the max so far
	- if(d1.two_norm() < current_min)
	- {
	- current_min = d1.two_norm();
	- vnl_vector<double> barycentricCoords(3);
	- barycentricCoords[2] = uv[0]<0 ? 0 : (uv[0]>1?1:uv[0]);
	- barycentricCoords[1] = uv[1]<0 ? 0 : (uv[1]>1?1:uv[1]);
	- barycentricCoords[0] = 1-(barycentricCoords[1]+barycentricCoords[2]);
	- retval = barycentricCoords[0]*this->GetNthComponent(pts[0]) +
	- barycentricCoords[1]*this->GetNthComponent(pts[1]) +
	- barycentricCoords[2]*this->GetNthComponent(pts[2]);
	- }
	- }
	- }
	-
	- break;
	- }
	- case ODF_SPHERICAL_GAUSSIAN_BASIS_FUNCTIONS:
	- {
	- double maxChordLength = GetMaxChordLength();
	- double sigma = asin(maxChordLength/2);
	-
	- // this is the contribution of each kernel to each sampling point on the
	- // equator
	- vnl_vector<double> contrib;
	- contrib.set_size(NOdfDirections);
	-
	- vtkPoints* points = m_BaseMesh->GetPoints();
	- double sum = 0;
	- for(int i=0; i<NOdfDirections; i++)
	- {
	- vnl_vector_fixed<double,3> P(points->GetPoint(i));
	- double stv = dir[0]*P[0]
	- + dir[1]*P[1]
	- + dir[2]*P[2];
	- stv = (stv<-1.0) ? -1.0 : ( (stv>1.0) ? 1.0 : stv);
	- double x = acos(stv);
	- contrib[i] = (1.0/(sigmasqrt(2.0itk::Math::pi)))
	- exp((-xx)/(2sigmasigma));
	- sum += contrib[i];
	- }
	-
	- retval = 0;
	- for(int i=0; i<NOdfDirections; i++)
	- {
	- retval += (contrib[i] / sum)*this->GetNthComponent(i);
	- }
	- break;
	- }
	-
	- }
	-
	- if(retval==-1)
	- {
	- std::cout << "Interpolation failed" << std::endl;
	- return 0;
	- }
	-
	- return retval;
	-
	-}
	-
	-/**
	- * Calculate Generalized Fractional Anisotropy
	- */
	-template<class T, unsigned int NOdfDirections>
	-T
	-OrientationDistributionFunction<T, NOdfDirections>
	-::GetGeneralizedFractionalAnisotropy() const
	-{
	- double mean = 0;
	- double std = 0;
	- double rms = 0;
	- for( unsigned int i=0; i<InternalDimension; i++)
	- {
	- T val = (*this)[i];
	- mean += val;
	- }
	- mean /= NOdfDirections;
	- for( unsigned int i=0; i<InternalDimension; i++)
	- {
	- T val = (*this)[i];
	- std += (val - mean) * (val - mean);
	- rms += val*val;
	- }
	- std *= NOdfDirections;
	- rms *= NOdfDirections - 1;
	-
	- if(rms == 0)
	- {
	- return 0;
	- }
	- else
	- {
	- return sqrt(std/rms);
	- }
	-}
	-
	-
	-template < typename T, unsigned int N>
	-T itk::OrientationDistributionFunction<T, N>
	-::GetGeneralizedGFA( int k, int p ) const
	-{
	- double mean = 0;
	- double std = 0;
	- double rms = 0;
	- double max = NumericTraits<double>::NonpositiveMin();
	- for( unsigned int i=0; i<InternalDimension; i++)
	- {
	- double val = (double)(*this)[i];
	- mean += pow(val,(double)p);
	- max = val > max ? val : max;
	- }
	- max = pow(max,(double)p);
	- mean /= N;
	- for( unsigned int i=0; i<InternalDimension; i++)
	- {
	- double val = (double)(*this)[i];
	- std += (pow(val,(double)p) - mean) * (pow(val,(double)p) - mean);
	- if(k>0)
	- {
	- rms += pow(val,(double)(p*k));
	- }
	- }
	- std /= N - 1;
	- std = sqrt(std);
	-
	- if(k>0)
	- {
	- rms /= N;
	- rms = pow(rms,(double)(1.0/k));
	- }
	- else if(k<0) // lim k->inf gives us the maximum
	- {
	- rms = max;
	- }
	- else // k==0 undefined, we define zeros root from 1 as 1
	- {
	- rms = 1;
	- }
	-
	- if(rms == 0)
	- {
	- return 0;
	- }
	- else
	- {
	- return (T)(std/rms);
	- }
	-}
	-
	-/**
	- * Calculate Nematic Order Parameter
	- */
	-template < typename T, unsigned int N >
	-T itk::OrientationDistributionFunction<T, N>
	-::GetNematicOrderParameter() const
	-{
	- // not yet implemented
	- return 0;
	-}
	-
	-/**
	- * Calculate StdDev by MaxValue
	- */
	-template < typename T, unsigned int N >
	-T itk::OrientationDistributionFunction<T, N>
	-::GetStdDevByMaxValue() const
	-{
	- double mean = 0;
	- double std = 0;
	- T max = NumericTraits<T>::NonpositiveMin();
	- for( unsigned int i=0; i<InternalDimension; i++)
	- {
	- T val = (*this)[i];
	- mean += val;
	- max = (this)[i] > max ? (this)[i] : max;
	- }
	- mean /= InternalDimension;
	- for( unsigned int i=0; i<InternalDimension; i++)
	- {
	- T val = (*this)[i];
	- std += (val - mean) * (val - mean);
	- }
	- std /= InternalDimension-1;
	-
	- if(max == 0)
	- {
	- return 0;
	- }
	- else
	- {
	- return (sqrt(std)/max);
	- }
	-}
	-
	-template < typename T, unsigned int N >
	-T itk::OrientationDistributionFunction<T, N>
	-::GetPrincipleCurvature(double alphaMinDegree, double alphaMaxDegree, int invert) const
	-{
	- // following loop only performed once
	- // (computing indices of each angular range)
	- m_MutexAngularRange.Lock();
	- if(m_AngularRangeIdxs == nullptr)
	- {
	- m_AngularRangeIdxs = new std::vector< std::vector<int>* >();
	- for(unsigned int i=0; i<N; i++)
	- {
	- vnl_vector_fixed<double,3> pDir = GetDirection(i);
	- auto idxs = new std::vector<int>();
	- for(unsigned int j=0; j<N; j++)
	- {
	- vnl_vector_fixed<double,3> cDir = GetDirection(j);
	- double angle = ( 180 / itk::Math::pi ) * acos( dot_product(pDir, cDir) );
	- if( (angle < alphaMaxDegree) && (angle > alphaMinDegree) )
	- {
	- idxs->push_back(j);
	- }
	- }
	- m_AngularRangeIdxs->push_back(idxs);
	- }
	- }
	- m_MutexAngularRange.Unlock();
	-
	- // find the maximum (or minimum) direction (remember index and value)
	- T mode;
	- int pIdx = -1;
	- if(invert == 0)
	- {
	- pIdx = GetPrincipalDiffusionDirectionIndex();
	- mode = (*this)[pIdx];
	- }
	- else
	- {
	- mode = NumericTraits<T>::max();
	- for( unsigned int i=0; i<N; i++)
	- {
	- if((*this)[i] < mode )
	- {
	- mode = (*this)[i];
	- pIdx = i;
	- }
	- }
	- }
	- //////////////////////
	- //////// compute median of mode and its neighbors to become more stable to noise
	- //////// compared to simply using the mode
	- //////////////////////
	-
	- //////// values of mode and its neighbors
	- //////std::vector<int> nbs = GetNeighbors(pIdx);
	- //////std::vector<T> modeAndNeighborVals;
	- //////modeAndNeighborVals.push_back(mode);
	- //////int numNeighbors = nbs.size();
	- //////for(int i=0; i<numNeighbors; i++)
	- //////{
	- ////// modeAndNeighborVals.push_back((*this)[nbs[i]]);
	- //////}
	-
	- //////// sort by value
	- //////std::sort( modeAndNeighborVals.begin(), modeAndNeighborVals.end() );
	-
	- //////// median of mode and neighbors
	- //////mode = modeAndNeighborVals[floor(0.5*(double)(numNeighbors+1)+0.5)];
	-
	- ////////////////
	- // computing a quantile of the angular range
	- ////////////////
	-
	- // define quantile
	- double quantile = 0.00;
	-
	- // collect all values in angular range of mode
	- std::vector<T> odfValuesInAngularRange;
	- int numInRange = m_AngularRangeIdxs->at(pIdx)->size();
	- for(int i=0; i<numInRange; i++)
	- {
	- odfValuesInAngularRange.push_back((this)[(m_AngularRangeIdxs->at(pIdx))[i] ]);
	- }
	-
	- // sort them by value
	- std::sort( odfValuesInAngularRange.begin(), odfValuesInAngularRange.end() );
	-
	- // median of angular range
	- T median = odfValuesInAngularRange[floor(quantile*(double)numInRange+0.5)];
	-
	- // compute and return final value
	- if(mode > median)
	- {
	- return mode/median - 1.0;
	- }
	- else
	- {
	- return median/mode - 1.0;
	- }
	-}
	-
	-/**
	- * Calculate Normalized Entropy
	- */
	-template < typename T, unsigned int N >
	-T itk::OrientationDistributionFunction<T, N>
	-::GetNormalizedEntropy() const
	-{
	- double mean = 0;
	- for( unsigned int i=0; i<InternalDimension; i++)
	- {
	- T val = (*this)[i];
	- if( val != 0 )
	- {
	- val = log(val);
	- }
	- else
	- {
	- val = log(0.0000001);
	- }
	- mean += val;
	- }
	- double _n = (double) InternalDimension;
	- mean /= _n;
	- return (T) (-_n / log(_n) * mean);
	-}
	-
	-/**
	- * Pre-multiply the Tensor by a Matrix
	- */
	-template<class T, unsigned int NOdfDirections>
	-OrientationDistributionFunction<T, NOdfDirections>
	-OrientationDistributionFunction<T, NOdfDirections>
	-::PreMultiply( const MatrixType & m ) const
	-{
	- Self result;
	- typedef typename NumericTraits<T>::AccumulateType AccumulateType;
	- for(unsigned int r=0; r<NOdfDirections; r++)
	- {
	- for(unsigned int c=0; c<NOdfDirections; c++)
	- {
	- AccumulateType sum = NumericTraits<AccumulateType>::ZeroValue();
	- for(unsigned int t=0; t<NOdfDirections; t++)
	- {
	- sum += m(r,t) * (*this)(t,c);
	- }
	- result(r,c) = static_cast<T>( sum );
	- }
	- }
	- return result;
	-}
	-
	-/**
	- * Post-multiply the Tensor by a Matrix
	- */
	-template<class T, unsigned int NOdfDirections>
	-OrientationDistributionFunction<T, NOdfDirections>
	-OrientationDistributionFunction<T, NOdfDirections>
	-::PostMultiply( const MatrixType & m ) const
	-{
	- Self result;
	- typedef typename NumericTraits<T>::AccumulateType AccumulateType;
	- for(unsigned int r=0; r<NOdfDirections; r++)
	- {
	- for(unsigned int c=0; c<NOdfDirections; c++)
	- {
	- AccumulateType sum = NumericTraits<AccumulateType>::ZeroValue();
	- for(unsigned int t=0; t<NOdfDirections; t++)
	- {
	- sum += (this)(r,t) m(t,c);
	- }
	- result(r,c) = static_cast<T>( sum );
	- }
	- }
	- return result;
	-}
	-
	-/**
	- * Print content to an ostream
	- */
	-template<class T, unsigned int NOdfDirections>
	-std::ostream &
	-operator<<(std::ostream& os,const OrientationDistributionFunction<T, NOdfDirections> & c )
	-{
	- for(unsigned int i=0; i<c.GetNumberOfComponents(); i++)
	- {
	- os << static_cast<typename NumericTraits<T>::PrintType>(c[i]) << " ";
	- }
	- return os;
	-}
	-
	-/**
	- * Read content from an istream
	- */
	-template<class T, unsigned int NOdfDirections>
	-std::istream &
	-operator>>(std::istream& is, OrientationDistributionFunction<T, NOdfDirections> & dt )
	-{
	- for(unsigned int i=0; i < dt.GetNumberOfComponents(); i++)
	- {
	- is >> dt[i];
	- }
	- return is;
	-}
	-} // end namespace itk
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkPointShell.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkPointShell.h
	deleted file mode 100644
	index a3b24e816a..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkPointShell.h
	+++ /dev/null
	@@ -1,47 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkPointShell_h__
	-#define __itkPointShell_h__
	-
	-#include "mitkOdfImage.h"
	-#include <MitkDiffusionCoreExports.h>
	-
	-
	-namespace itk
	-{
	- // generate by n-fold subdivisions of an icosahedron
	- template<int NPoints, class TMatrixType >
	- class PointShell
	- {
	- public:
	- static TMatrixType *DistributePointShell();
	- };
	-
	- template<int NpointsShell1, int NpointsShell2, int NpointsShell3, class TMatrixTypeshell1, class TMatrixTypeshell2, class TMatrixTypeshell3>
	- class ThreeLayerPointShell
	- {
	- public:
	- static TMatrixTypeshell1 *DistributePointShell1();
	- static TMatrixTypeshell2 *DistributePointShell2();
	- static TMatrixTypeshell3 *DistributePointShell3();
	- };
	-
	-}
	-
	-#include "itkPointShell.txx"
	-
	-#endif //__itkPointShell_h__
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkPointShell.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkPointShell.txx
	deleted file mode 100644
	index 6f9efcb9aa..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkPointShell.txx
	+++ /dev/null
	@@ -1,5242 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkPointShell_txx__
	-#define __itkPointShell_txx__
	-
	-#include "vnl/vnl_vector_fixed.h"
	-#include "vnl/vnl_matrix_fixed.h"
	-
	-namespace itk
	-{
	-template<int NPoints, class TMatrixType >
	-TMatrixType *
	-PointShell<NPoints, TMatrixType >
	-::DistributePointShell()
	-{
	-
	- auto theta
	- = new vnl_vector_fixed<double,NPoints>();
	-
	- auto phi
	- = new vnl_vector_fixed<double,NPoints>();
	-
	- double C = sqrt(4*itk::Math::pi);
	-
	- (*phi)(0) = 0.0;
	- (*phi)(NPoints-1) = 0.0;
	-
	- for(int i=0; i<NPoints; i++)
	- {
	- (theta)(i) = acos(-1.0+2.0i/(NPoints-1.0)) - itk::Math::pi / 2.0;
	- if( i>0 && i<NPoints-1)
	- {
	- (phi)(i) = ((phi)(i-1) + C /
	- sqrt(NPoints(1-(-1.0+2.0i/(NPoints-1.0))(-1.0+2.0i/(NPoints-1.0)))));
	- // % (2*itk::Math::pi);
	- }
	- }
	-
	- auto pointshell
	- = new vnl_matrix_fixed<double, 3, NPoints>();
	-
	- for(int i=0; i<NPoints; i++)
	- {
	- (pointshell)(0,i) = cos((theta)(i)) * cos((*phi)(i));
	- (pointshell)(1,i) = cos((theta)(i)) * sin((*phi)(i));
	- (pointshell)(2,i) = sin((theta)(i));
	- }
	-
	- return pointshell;
	-}
	-
	-// generate by n-fold subdivisions of an icosahedron
	-
	-// 1 - 12
	-// 2 - 42
	-// 3 - 92
	-// 4 - 162
	-// 5 - 252
	-// 6 - 362
	-// 7 - 492
	-// 8 - 642
	-// 9 - 812
	-// 10 - 1002
	-
	-template<> class PointShell<12, vnl_matrix_fixed<double, 3, 12> >
	-{
	-public:
	- static vnl_matrix_fixed<double, 3, 12>* DistributePointShell()
	- {
	- double coords[3*12] = {
	- 0.250254,0.320072,0.437594,
	- 0.550563,0.623196,0.975676,
	- -0.250253,-0.320073,-0.437593,
	- -0.550563,-0.6231950000000001,-0.975676,
	- -0.916162,-0.078054,-0.598061,
	- 0.758025,0.436642,-0.177816,
	- 0.916161,0.078054,0.598061,
	- -0.758024,-0.436643,0.177817,
	- -0.313083,-0.944171,0.671442,
	- -0.349682,0.648821,-0.128204,
	- 0.313082,0.944172,-0.671442,
	- 0.349683,-0.648822,0.128204 };
	-
	- auto pointshell
	- = new vnl_matrix_fixed<double, 3, 12>(coords);
	-
	- return pointshell;
	- }
	-};
	-
	-
	-template<> class PointShell<42, vnl_matrix_fixed<double, 3, 42> >
	-{
	-public:
	- static vnl_matrix_fixed<double, 3, 42>* DistributePointShell()
	- {
	- double coords[3*42] = {
	- 0.9756767549555488,0.9397937974509784,0.6231965669156312,
	- 0.8971014254962764,0.6899186612252972,0.5505632701289798,
	- 0.4375940376503738,0.06907711216819172,-0.3200730131503601,
	- 0.6235168560971455,0.1781713819192711,0.3200724178002418,
	- 0.7616224484252742,0.5117469206751248,0.2502538949373057,
	- 0.4043068999720243,0.7205836671095894,0.8306996157029517,
	- -0.4375932291383154,-0.06907715072573903,0.06640211724156461,
	- -0.6231952788307174,-0.2192092047974508,-0.1781713502362079,
	- 0.3352293490184233,-0.2502532651867688,-0.4043060780204903,
	- 0.1765178736510398,-0.975676581463901,-0.9397935597648752,
	- -0.8306992108488227,-0.6235158879179115,0.21921067448898,
	- -0.7616223457476226,-0.3352294641675141,-0.7205834943870382,
	- -0.5117470172320778,-0.06640153973221416,-0.5505634949474448,
	- -0.176517304179968,-0.6899183532182501,-0.8971016370404784,
	- -0.1778161375899129,0.1521341729788544,0.4366423972091847,
	- 0.3410385404813853,0.7022080829625521,0.7580253719184177,
	- -0.5980610514568759,-0.3056524524744078,0.07805400320688782,
	- -0.09487972868743588,0.3025309778153461,-0.07805410188638827,
	- -0.1503967869358663,0.3996773221825281,-0.9161616153729887,
	- -0.8900379255247358,-0.6430242175142256,-0.4560492515462431,
	- 0.5980613131647216,0.3056526230838691,0.797087559189558,
	- -0.4366431953633789,-0.7951587738972527,-0.3025315118038733,
	- -0.5843857415998933,0.9161619708326186,0.8900381161951118,
	- 0.9840623116657442,0.1778171059718252,-0.1521342296531137,
	- 0.4560499397602033,0.09487917246041,0.7951586652134927,
	- 0.1503972383762518,0.584385354546882,0.6430245879023526,
	- -0.399676350745083,-0.7970870947583816,-0.7580246814516085,
	- -0.9840624137666333,-0.7022083677250226,-0.3410374453295617,
	- -0.1282040992012935,0.3060111300013609,0.6488215902264565,
	- -0.2808945465452747,0.1758296024995542,-0.3496821715684524,
	- 0.6714420577705413,0.9496341036793501,0.9441720387917811,
	- 0.7760312926982584,0.9363385958760152,-0.9441722324566724,
	- -0.6303269409870232,-0.7605084662990487,-0.3130828685601688,
	- 0.2106381298878163,-0.2593820240207756,0.3193074202631062,
	- -0.671442351589465,-0.9496340459616871,-0.6002017842451572,
	- -0.648822290296783,-0.5653935344751363,-0.9363384293729856,
	- -0.7389956620788968,0.3130823317650696,-0.2106389019045293,
	- -0.02151295053653907,0.1282040764044601,-0.3060118317848469,
	- -0.3193074905789999,-0.7760321386045594,0.5653931175085022,
	- 0.6303269573377657,0.7389959159190775,0.2593815856416469,
	- 0.7605089118538748,0.6002024649156598,0.3496833143594963,
	- 0.02151295276860444,-0.175829673802738,0.2808952005684321 };
	-
	- auto pointshell
	- = new vnl_matrix_fixed<double, 3, 42>(coords);
	-
	- return pointshell;
	- }
	-};
	-
	-
	-template<> class PointShell<92, vnl_matrix_fixed<double, 3, 92> >
	-{
	-public:
	- static vnl_matrix_fixed<double, 3, 92>* DistributePointShell()
	- {
	- double coords[3*92] = {
	- 0.9756767549555487,0.9881046683022421,0.8528238339140162,
	- 0.6231965669156312,0.9602286065935876,0.9016229543668698,
	- 0.68966672282401,0.7970712198937139,0.6617902410567804,
	- 0.5505632701289798,0.4375940376503739,0.2130515669413184,
	- -0.07773888316805401,-0.3200730131503601,0.575075565563677,
	- 0.3107083252171692,-0.006505365777837463,0.6463093264667951,
	- 0.3555189519163455,0.3200724178002418,0.6201479032959075,
	- 0.8717669667532965,0.4569904905821254,0.7744719807282636,
	- 0.5454521871592555,0.2502538949373057,0.3600408236839538,
	- 0.4319414682718342,0.5665551499276381,0.697797754038698,
	- 0.7103565350090897,0.8449704612165639,0.9168712118355732,
	- -0.4375932291383153,-0.213051272338593,0.07773856031405026,
	- -0.1245894223683107,0.181648017057727,0.2546621526726748,
	- -0.6231952788307172,-0.3823142165271753,-0.04708691012811009,
	- -0.3555183995893311,-0.02217694060430831,0.3149362814931866,
	- 0.006504983859799645,0.3417324928044827,-0.2502532651867688,
	- -0.3600400745299253,-0.4319406005716204,0.01921174674137865,
	- -0.05758606025521316,0.3265627679363224,-0.9756765814639009,
	- -0.988104613901425,-0.8528232434185344,-0.9168708930751739,
	- -0.854235225343551,-0.6463082287051728,-0.7103560109842373,
	- -0.5750746905699001,0.3823157740702657,0.0470881327099307,
	- 0.3873829237054168,-0.6201479767677171,-0.8717667933239607,
	- -0.3417327749428254,-0.6485010946606566,-0.8449702640289916,
	- -0.3149361858566655,-0.5665549223826651,0.854235631268382,
	- -0.4569906864326022,-0.1816479322770386,0.1245901828483064,
	- -0.5454522916908328,-0.2546618495309371,-0.5505634949474448,
	- 0.6485010946606566,0.05758689641252078,-0.01921097131735245,
	- -0.3265625234832059,-0.3107079508004592,-0.3873820250532686,
	- -0.6896660583043277,-0.6617902107749167,-0.6977972953381247,
	- -0.9016230372124288,-0.9602286916122059,-0.7970714969272577,
	- 0.02217737847260294,-0.774471897882643,-0.1778161375899129,
	- 0.03109142233089637,0.2669187829195654,0.4366423972091846,
	- 0.1544374088220477,0.4265382311030135,0.6260922126282031,
	- 0.5136107375104821,0.7494380454402638,0.7580253719184178,
	- -0.5980610514568761,-0.4291113361140411,-0.1696203080333493,
	- 0.07805400320688781,-0.2914862882507431,-0.03496909012717316,
	- 0.2274959035287995,0.1056298518860434,0.3651211825280409,
	- -0.07805410188638827,-0.1281592432697842,-0.1664476243728032,
	- 0.2310143008479173,0.2106389321639752,0.5518992169467314,
	- -0.9161616153729886,-0.9327747060225072,-0.8106886470978539,
	- -0.771485918473268,-0.7097589298055721,-0.5273136421678301,
	- -0.4881111164997092,-0.3660248731570757,0.5980613131647216,
	- 0.4291115157626469,0.1696204410073287,0.7499962909367706,
	- 0.5360957563846484,0.8113900261915854,-0.4366431953633788,
	- -0.6867851479477911,-0.8708228680516066,-0.365121777041269,
	- -0.6002019152270697,-0.7331976694123558,-0.2274963530521035,
	- -0.4115345048612673,0.9161619708326186,0.9327749805257903,
	- 0.8106887957474585,0.9941684586829005,0.9531387910864955,
	- 0.9334760373935599,0.1778171059718252,-0.03109104889813258,
	- -0.266919222145987,0.3660256667153609,0.1422988506889488,
	- -0.1056306282458797,0.5273142067726671,0.2914860445503094,
	- 0.6867847261588661,0.8708230332223915,0.8854287054759334,
	- 0.1281594836202007,0.1664482855753907,0.4115339986401247,
	- 0.4916319868779721,0.4881116080953447,0.7331975726799166,
	- 0.7714862700692517,-0.1422987785572308,-0.2310136280273065,
	- -0.5360950867028047,-0.749995864312011,-0.551898166785698,
	- -0.8113895155772442,-0.7580246814516086,-0.4916319868779721,
	- -0.9531387450388693,-0.9941684373181742,-0.9334760519103793,
	- 0.03496867572798409,-0.885428988462601,-0.6260926899993671,
	- -0.7494380619781833,0.7097593165624652,-0.4265380492676017,
	- -0.154436271103469,-0.513609764630649,0.6002015742230613,
	- -0.2106379566061765,-0.1282040992012935,0.1506070646973712,
	- 0.448827218017063,0.6488215902264565,-0.232615798766268,
	- 0.07170206110196441,0.3638246180723771,-0.3176184514965804,
	- -0.01939827024983318,-0.3496821715684524,0.6714420577705416,
	- 0.8777656242085763,0.9824386073167399,0.9441720387917811,
	- 0.7644107780855932,0.9498618317294465,0.9737573075945113,
	- 0.7557291769626011,0.8604026946131842,-0.9441722324566724,
	- -0.7739455965390631,-0.4607792790679794,-0.8589482430980673,
	- -0.5965101770495287,-0.6307845637432553,-0.3130828685601688,
	- 0.01737679733452725,0.3952347219739472,-0.2895250242862085,
	- 0.09654302677976184,0.4661908578614318,-0.2185691140597737,
	- 0.1592889611288683,-0.671442351589465,-0.8777656078901646,
	- -0.982438609905361,-0.649602216294724,-0.8243817913354027,
	- -0.5261115978506249,-0.6488222902967828,-0.6181925269683732,
	- -0.4893366483035592,-0.8604026705465684,-0.7995410210009178,
	- -0.6026908960383706,-0.9737572051250643,-0.8449013283633929,
	- 0.3130823317650696,-0.01737758434298078,-0.3952353653550799,
	- 0.1061130743462423,-0.2970021727032599,-0.1482539922220807,
	- 0.1282040764044601,-0.1506074987015245,-0.4488280788164578,
	- -0.159288972427813,-0.5000332157715695,-0.7557300072673856,
	- -0.4661910177108468,-0.7644115292814133,0.6181920323103048,
	- 0.4893362367199527,0.2568082513095248,0.7739454978673308,
	- 0.4607793683387657,0.8449014608184471,0.5811577408091089,
	- 0.2185687785328751,0.6026910636921159,0.2895245326714229,
	- 0.5000325428335932,0.8589483198537152,0.8243822455102904,
	- 0.6496025629973337,0.6307853921801013,0.5261125320735169,
	- 0.3496833143594963,-0.5811577408091089,0.2970021583546204,
	- -0.1061134148983228,0.1482544392795429,-0.9498619694604108,
	- -0.2568086311939767,-0.3638250562458945,0.01939866440958929,
	- -0.0965434988571485,-0.07170210104888378,0.2326162031595532,
	- 0.3176193294845107,0.7995412648414353,0.5965106290979496 };
	-
	- auto pointshell
	- = new vnl_matrix_fixed<double, 3, 92>(coords);
	-
	- return pointshell;
	- }
	-};
	-
	-
	-template<> class PointShell<162, vnl_matrix_fixed<double, 3, 162> >
	-{
	-public:
	- static vnl_matrix_fixed<double, 3, 162>* DistributePointShell()
	- {
	- double coords[3*162] = {
	- 0.9756767549555488,0.9968737649581846,0.9397937974509784,
	- 0.7989268505692991,0.6231965669156312,0.9764792677814802,
	- 0.9657129396229355,0.8567905682573015,0.679558714000995,
	- 0.8971014254962764,0.8343457228904876,0.6899186612252972,
	- 0.7377425905504456,0.6387690340353133,0.5505632701289798,
	- 0.4375940376503738,0.2787444080680243,0.06907711216819172,
	- -0.1467487371786262,-0.3200730131503601,0.5436064763029955,
	- 0.3641181930198064,0.1299861910861632,-0.09463328683104604,
	- 0.6235168560971455,0.421472539809791,0.1781713819192711,
	- 0.6478378002177454,0.4350913076613168,0.3200724178002418,
	- 0.543583002477908,0.7616224484252742,0.9117594243665534,
	- 0.4242146396073646,0.6694499319211135,0.8720427891122669,
	- 0.5117469206751248,0.7406754453578036,0.5536544075493044,
	- 0.2502538949373057,0.3336803609057232,0.4043068999720243,
	- 0.438887490788423,0.4847692553550146,0.5913899314506929,
	- 0.6492812914734455,0.6425800233106177,0.7205836671095894,
	- 0.8155579470101821,0.8306996157029517,0.8921547074343706,
	- 0.9447583574027534,-0.4375932291383154,-0.278743955138478,
	- -0.06907715072573903,0.1467483093137361,-0.2140239599986307,
	- -0.001406336898152031,0.2327251986251803,0.06640211724156461,
	- 0.3039508137298482,0.3409081262151013,-0.6231952788307174,
	- -0.4546947222788382,-0.2192092047974508,0.03581973661208818,
	- -0.4350905112236564,-0.2089153242611869,0.0609953219830862,
	- 0.3006812043050254,-0.1781713502362079,0.08257031568712175,
	- 0.3352293490184233,0.09463277722176672,0.3398901915912972,
	- -0.2502532651867688,-0.3336796480610522,-0.4043060780204903,
	- -0.4388866188864613,-0.05621340666038893,-0.1197552832780665,
	- -0.1776465335448071,0.1765178736510398,0.1277105869872963,
	- 0.3935116760630417,-0.975676581463901,-0.9968737272214637,
	- -0.9397935597648752,-0.7989260596435309,-0.9447580743829742,
	- -0.9308031701048347,-0.8218804228775519,-0.6478366382006043,
	- -0.8306992108488227,-0.7645261844287355,-0.6235158879179115,
	- -0.6425794288509028,-0.543605629081954,0.4546962564744617,
	- 0.21921067448898,-0.03581866880653414,0.4779576265881325,
	- 0.2080468003445843,0.4555126388719097,-0.543583197615373,
	- -0.7616223457476226,-0.9117592443356049,-0.3398905505309818,
	- -0.5766491384642831,-0.7792417673233771,-0.8921544952781482,
	- -0.3352294641675141,-0.5550737397870624,-0.7205834943870382,
	- -0.3006809838192767,-0.4847689570296102,0.8218810203164033,
	- 0.9308033931946534,0.7645267056644409,-0.4242149221746557,
	- -0.2327253235991419,0.00140664545831139,0.2140247669633664,
	- -0.5117470172320778,-0.3039507303469009,-0.06640153973221416,
	- -0.5536545418185335,-0.3409079709201472,-0.5505634949474448,
	- 0.7792418677670352,0.5766490604842006,0.5550737528785307,
	- 0.1776474313398276,0.1197561650892531,0.05621421006516834,
	- -0.1277100030888262,-0.176517304179968,-0.3935115910448358,
	- -0.1299862309792015,-0.3641176806190365,-0.4214718858755578,
	- -0.2080457563809749,-0.477956563666828,-0.6795578679273953,
	- -0.4555121490743896,-0.6899183532182501,-0.6387691005409376,
	- -0.6492806993353901,-0.5913894852863821,-0.8155575864896008,
	- -0.8567903368462096,-0.9657130735429578,-0.9764792804081987,
	- -0.834345897568434,-0.8971016370404784,-0.7377428728490714,
	- -0.06099477310985241,0.2089161290281741,-0.08257033948198818,
	- -0.8720426859708773,-0.6694498734011487,-0.740675476302381,
	- -0.1778161375899129,-0.02718233037986957,0.1521341729788544,
	- 0.3178872248051531,0.4366423972091847,0.06305939500089614,
	- 0.2592762165236786,0.4491542846588709,0.5806638189836385,
	- 0.3410385404813853,0.5484671467389891,0.7022080829625521,
	- 0.5886123721388867,0.761147081998915,0.7580253719184177,
	- -0.5980610514568759,-0.4818747107897384,-0.3056524524744078,
	- -0.102179801407443,0.07805400320688782,-0.3811861908796716,
	- -0.2105722545208477,-0.001641189844283069,0.1883562467232593,
	- -0.09487972868743588,0.1091686599118738,0.3025309778153461,
	- 0.1998858588754617,0.3897335832229792,-0.07805410188638827,
	- -0.1156801299839266,-0.1503967869358663,-0.1717048170733874,
	- 0.1470965334761953,0.1310545667952879,0.100226360425432,
	- 0.3996773221825281,0.3894173756029716,0.6166247865338805,
	- -0.9161616153729887,-0.93968222548459,-0.8900379255247358,
	- -0.7610423024299814,-0.8216809647863927,-0.8059784419089511,
	- -0.7076799521032789,-0.5537209611836944,-0.6430242175142256,
	- -0.577817181345379,-0.4560492515462431,-0.4070385900414059,
	- -0.3177184789930138,0.5980613131647216,0.4818748986235024,
	- 0.3056526230838691,0.1021798945147061,0.7166389355513205,
	- 0.5797448495418049,0.3708138719979267,0.797087559189558,
	- 0.6291765311790336,0.8064720598658887,-0.4366431953633789,
	- -0.6250679008877252,-0.7951587738972527,-0.894357332660672,
	- -0.3897342152274581,-0.5770900179397438,-0.7252694054566711,
	- -0.7936687210308288,-0.3025315118038733,-0.4662800296194353,
	- -0.5843857415998933,-0.1883566309643827,-0.3230016809603438,
	- 0.9161619708326186,0.9396825386256142,0.8900381161951118,
	- 0.7610424573388179,0.98459889389352,0.985272860446651,
	- 0.8869743499570832,0.9840623116657442,0.9364058649128151,
	- 0.8957919700911449,0.1778171059718252,0.02718289859111821,
	- -0.1521342296531137,-0.3178878068603045,0.31771932061924,
	- 0.1597779786826127,-0.03010074909289372,-0.1998866892639353,
	- 0.4560499397602033,0.2896405921772683,0.09487917246041,
	- 0.5537214556082512,0.3811861035860583,0.6250673427588886,
	- 0.7951586652134927,0.8943575917970892,0.7872122199392447,
	- 0.9353918603084618,0.8865248509843126,0.1156802730367007,
	- 0.1503972383762518,0.1717055726654157,0.3230012075937738,
	- 0.3862979863651042,0.4171265008378126,0.4070391829394841,
	- 0.584385354546882,0.6452876111171104,0.6430245879023526,
	- 0.7936687790069655,0.8216813253645509,0.03010042800399446,
	- -0.159777601870924,-0.2896404384341761,-0.1470960585711635,
	- -0.3708132697350703,-0.5797443521912047,-0.7166385361913998,
	- -0.399676350745083,-0.6291757405426562,-0.7970870947583816,
	- -0.6166237809711579,-0.8064715143730887,-0.7580246814516085,
	- -0.417126245587897,-0.3862981411371962,-0.6452875761129986,
	- -0.8869742038831786,-0.9852727972566903,-0.9845987728990332,
	- -0.9364058061885231,-0.9840624137666333,-0.8957918541675716,
	- 0.001640881330767951,0.2105720065923513,-0.109169268647464,
	- -0.9353919526972201,-0.7872126141915534,-0.5806643774075225,
	- -0.8865251005609038,-0.7022083677250226,-0.7611469342493191,
	- 0.707680317140174,0.8059787882713181,0.577817672809353,
	- -0.4491544873380491,-0.2592757174096171,-0.063058272648828,
	- -0.5484668466671915,-0.3410374453295617,-0.5886114742048517,
	- 0.7252693007743299,0.5770896067011005,0.4662795459560942,
	- -0.1002253860034311,-0.1310538163159151,-0.3894163023521484,
	- -0.1282040992012935,0.07418771901881034,0.3060111300013609,
	- 0.5105522497698926,0.6488215902264565,-0.2061837828129686,
	- 0.01320461245153456,0.2533186742384155,0.4483631157317138,
	- -0.2808945465452747,-0.05523589088936585,0.1758296024995542,
	- -0.3305621657917769,-0.1123798946526014,-0.3496821715684524,
	- 0.6714420577705413,0.8307215647087252,0.9496341036793501,
	- 0.983882155708098,0.9441720387917811,0.7477894668983293,
	- 0.9072360592139173,0.9915144459980433,0.9775308002021622,
	- 0.7760312926982584,0.9002461340540874,0.9363385958760152,
	- 0.7350862725086435,0.8116669810370153,-0.9441722324566724,
	- -0.8313456723553714,-0.6303269409870232,-0.3731115220313701,
	- -0.8935348618728204,-0.7312055040636086,-0.4790574606800003,
	- -0.7605084662990487,-0.5474979380988695,-0.5596790773588694,
	- -0.3130828685601688,-0.07519795113003093,0.2106381298878163,
	- 0.4776948653078811,-0.299731815412124,-0.02562616156907596,
	- 0.2786088475509629,0.5296074119458033,-0.2593820240207756,
	- 0.03150460300683353,0.3193074202631062,-0.1959070295313489,
	- 0.08053951964108649,-0.671442351589465,-0.8307216077305004,
	- -0.9496340459616871,-0.9838822098556939,-0.6637939293172054,
	- -0.8147968652653733,-0.8990751104656249,-0.6002017842451572,
	- -0.7153675946298389,-0.4830988161196208,-0.648822290296783,
	- -0.6344626299567083,-0.5653935344751363,-0.4459169294668335,
	- -0.8116671044980045,-0.7895071237697285,-0.6857578728711079,
	- -0.5288485365725882,-0.9363384293729856,-0.8807752703984302,
	- -0.7389956620788968,-0.9775307754986758,-0.8832579304805722,
	- 0.3130823317650696,0.07519720122433592,-0.2106389019045293,
	- -0.4776954195825031,0.1655447705464922,-0.1220494268493898,
	- -0.4262841911656161,-0.02151295053653907,-0.3268548028226648,
	- -0.2066526242811376,0.1282040764044601,-0.07418801789892716,
	- -0.3060118317848469,-0.51055312502423,-0.08053951945115613,
	- -0.3287498381001709,-0.5688642328312289,-0.7350870708018485,
	- -0.3193074905789999,-0.5758541835274278,-0.7760321386045594,
	- -0.5296076162752261,-0.7477901272839138,0.6344620803203709,
	- 0.5653931175085022,0.4459164955009389,0.389683753785766,
	- 0.2859346018498913,0.08112906023855893,0.831345524857385,
	- 0.6303269573377657,0.3731116142445962,0.8832579654623612,
	- 0.7198955735651289,0.467747528435525,0.1959067638111305,
	- 0.7389959159190775,0.5248781214125594,0.2593815856416469,
	- 0.5288485749239231,0.2997313094215869,0.5688633866559212,
	- 0.3287493895928871,0.5758535688432742,0.8935348059013593,
	- 0.8990753265127792,0.8147972186077681,0.6637941002839092,
	- 0.7605089118538748,0.7153683254339585,0.6002024649156598,
	- 0.5596800524090022,0.4830998363360157,0.3496833143594963,
	- -0.4677475887278177,-0.7198955529773995,-0.5248781506021705,
	- 0.4262841209617862,0.1220490717256491,-0.165545217365127,
	- 0.326855199205205,0.02151295276860444,0.2066532886754674,
	- -0.9915144412787341,-0.9072363224101446,-0.9002463663906001,
	- -0.2859350592025221,-0.3896842610441149,-0.4483636748755489,
	- -0.0811290830782055,-0.175829673802738,0.1123805173372347,
	- -0.2786093002807504,0.02562556437243592,-0.03150492197167008,
	- -0.253319097564816,-0.01320461850800903,0.2061840662709727,
	- 0.05523623192861417,0.2808952005684321,0.3305631346577989,
	- 0.6857580324047194,0.78950721141067,0.8807755242176112,
	- 0.4790578522946484,0.7312056921497674,0.5474986596025796 };
	-
	- auto pointshell
	- = new vnl_matrix_fixed<double, 3, 162>(coords);
	-
	- return pointshell;
	- }
	-};
	-
	-
	-template<> class PointShell<252, vnl_matrix_fixed<double, 3, 252> >
	-{
	-public:
	- static vnl_matrix_fixed<double, 3, 252>* DistributePointShell()
	- {
	- double coords[3*252] = {
	- 0.9756767549555488,0.9977154378498742,0.9738192119472443,
	- 0.8915721200771204,0.7646073555341725,0.6231965669156312,
	- 0.9817040172417226,0.9870396762453547,0.9325589150767597,
	- 0.8173592116492303,0.6708930871960926,0.9399233672993689,
	- 0.9144882783890762,0.8267930935417315,0.6931818659696647,
	- 0.8407280774774689,0.782394344826989,0.6762337155773353,
	- 0.7005607434301688,0.6228579759074076,0.5505632701289798,
	- 0.4375940376503738,0.3153040621970065,0.1569517536476641,
	- -0.01984099037382634,-0.1857690950088067,-0.3200730131503601,
	- 0.5232435944036425,0.3889403678268736,0.2135250052622625,
	- 0.02420694871807206,-0.1448539951504302,0.5971534158422009,
	- 0.4482053228282282,0.2597018771197477,0.06677517278138323,
	- 0.6404616222418184,0.4782876117785159,0.2868761951248767,
	- 0.6459894362878276,0.4789651252338281,0.3200724178002418,
	- 0.4973180497018747,0.6793811951363423,0.8323587928990375,
	- 0.9308933612987835,0.4036036036586492,0.5984781165037405,
	- 0.7817280923310203,0.9140795130247613,0.4809905907165384,
	- 0.6759621154318279,0.8390728924802671,0.5347729120192694,
	- 0.7094340284155564,0.5560356639783846,0.2502538949373057,
	- 0.3171352000240629,0.3793963897789465,0.4231100429674418,
	- 0.4410301813437042,0.4357529867703999,0.5208717223808415,
	- 0.5850086433327374,0.611055499882272,0.6009463532173235,
	- 0.6305067000562991,0.7188806066405239,0.7654898954879897,
	- 0.7616477696596397,0.7997756996573342,0.8700831379830764,
	- 0.8872031228985237,0.9155019734809123,0.9568003701205341,
	- -0.4375932291383153,-0.3153035222278598,-0.1569515927579475,
	- 0.0198407706589918,0.1857686171195431,-0.2644927501381796,
	- -0.1064219080255857,0.07849995612144045,0.2583107784678281,
	- -0.04938676750055992,0.1358448755096817,0.3243479900672576,
	- 0.1811879481039926,0.3692668145365748,0.3890115016151001,
	- -0.6231952788307174,-0.4943551945928708,-0.319458133528771,
	- -0.1156489798772063,0.08328895892415776,-0.4789641985801549,
	- -0.3127252940830145,-0.1059392282183739,0.1077444781964869,
	- 0.2912280153186658,-0.2868758523956744,-0.08856892011805101,
	- 0.1287405357080231,0.3245517154572714,-0.06677541204276306,
	- 0.1413542883070481,0.3408430926744944,0.1448534358763926,
	- 0.3374016489097037,-0.2502532651867688,-0.3171345072414974,
	- -0.3793956104585266,-0.4231091882680272,-0.4410293135613324,
	- -0.09929959410007272,-0.1535127609134815,-0.2052877394623771,
	- -0.2436963810571767,0.08175409117371149,0.04056025153798869,
	- -0.006048944565669369,0.2686152102237028,0.2319923070602857,
	- 0.430309819720559,-0.975676581463901,-0.9977153903038788,
	- -0.9738191090293654,-0.8915716840571059,-0.7646064477130079,
	- -0.9568001079664734,-0.9598482725023617,-0.9044523389503778,
	- -0.7901672201648241,-0.6459882395962464,-0.8872027729137049,
	- -0.8582754834679532,-0.7705800268610806,-0.6404605781008121,
	- -0.7616472974254324,-0.7008201753656432,-0.5971525097007422,
	- -0.6009457148226922,-0.5232427588825813,0.4943566966479628,
	- 0.3194596781650836,0.1156503154178581,-0.0832879858164388,
	- 0.5222841738261358,0.3225497922064885,0.1018140973507329,
	- 0.5217885230992481,0.3044789836562512,0.4873191346491355,
	- -0.4973183240635209,-0.6793811856410323,-0.8323586364840968,
	- -0.9308931819742911,-0.3374020539278631,-0.5261951664998159,
	- -0.7070125356849136,-0.8417962075837926,-0.9155017573317124,
	- -0.3408433114184408,-0.5265312606271311,-0.6896418460594331,
	- -0.7997755164970677,-0.3245517106425898,-0.4925847482169691,
	- -0.6305065080228541,-0.2912277152063287,-0.4357526334612896,
	- 0.7901679726328494,0.9044526665335126,0.9598484396937114,
	- 0.7705806468939737,0.858275831469383,0.7008207681995118,
	- -0.4036039458806759,-0.2583110138480089,-0.0784999126587471,
	- 0.1064223584250461,0.264493571710179,-0.4809907334514471,
	- -0.3243480295764106,-0.1358446002697818,0.04938746901646566,
	- -0.5347730026038946,-0.3692667658371347,-0.1811875286592425,
	- -0.5560358190148772,-0.3890114324926668,-0.5505634949474449,
	- 0.8417963565884857,0.7070125813068046,0.5261950179989611,
	- 0.6896418985458221,0.5265311900255359,0.4925848265160583,
	- 0.2436972866599269,0.2052886581368649,0.153513629451971,
	- 0.09930039009433847,0.006049691633511915,-0.04055950638179381,
	- -0.08175337578691833,-0.2319919155781195,-0.2686148310916902,
	- -0.430309819678344,-0.02420720081803753,-0.2135248270679241,
	- -0.3889397838050994,-0.2597016312374675,-0.4482046405142344,
	- -0.4782867918076852,-0.1018130528605821,-0.322548598821141,
	- -0.5222830294256716,-0.6708921376896406,-0.304478224282928,
	- -0.5217878437313506,-0.6931813485878851,-0.4873188675145023,
	- -0.6762335873429084,-0.6228580878699612,-0.6110548409057,
	- -0.5850080622199078,-0.5208712693637837,-0.7654894328832393,
	- -0.7188802647693375,-0.8700828159137221,-0.8173587433845655,
	- -0.9325588839421305,-0.9870397834787261,-0.9817039872478999,
	- -0.8267930492778305,-0.9144884914916022,-0.9399235077793813,
	- -0.7823945479956939,-0.8407283372889187,-0.7005610213599369,
	- -0.1077438933887955,0.1059400956623477,0.3127262866621893,
	- -0.1287403742204129,0.08856921814263634,-0.1413545191115968,
	- -0.9140794058749131,-0.7817279594934516,-0.5984781448346268,
	- -0.8390728949381593,-0.6759620794963979,-0.709434131000089,
	- -0.1778161375899129,-0.06053925384414331,0.07929679392711581,
	- 0.222673458561735,0.3458247516791153,0.4366423972091846,
	- 0.01030826616734189,0.1591522280204451,0.3173816763430465,
	- 0.4549463955350546,0.5521270265729551,0.2292788658415479,
	- 0.3973400932411465,0.5502139834879405,0.6594089221868847,
	- 0.4476465561008348,0.6096570464011057,0.7343998566036512,
	- 0.629214796874201,0.7646693979379596,0.7580253719184178,
	- -0.5980610514568761,-0.5101530988159087,-0.382225667160838,
	- -0.2244621267538426,-0.06301328229424107,0.07805400320688782,
	- -0.4311039309963852,-0.3079662136138592,-0.1501157132113724,
	- 0.01750888497279251,0.1650825345160538,-0.2148810450151756,
	- -0.06090095222676627,0.1073128739652992,0.2584097661066967,
	- 0.02655484252908358,0.1901297170957776,0.3420822257932489,
	- 0.2531835106264871,0.4022303494272352,-0.07805410188638827,
	- -0.1080255529483224,-0.1376217050758367,-0.1609000070073124,
	- -0.1740018618448228,0.09827676798573926,0.083291898217249,
	- 0.06127443921955168,0.03526739273256396,0.2991139104294396,
	- 0.2941068360088736,0.2692865316145088,0.4942032775296958,
	- 0.4857723178878524,0.6512069539966677,-0.9161616153729886,
	- -0.9396953110011561,-0.9204280785344878,-0.8462030522374957,
	- -0.7293237120999879,-0.8470541513588044,-0.8482966176587544,
	- -0.7977006542517769,-0.6951661565374421,-0.566558592627622,
	- -0.7243096319272092,-0.6931460376496088,-0.6140043047773551,
	- -0.5016343691560573,-0.5520254073275178,-0.4928644880867128,
	- -0.403575153350467,-0.3587591578566765,-0.2886351685087218,
	- 0.5980613131647216,0.5101532951859686,0.382225843595672,
	- 0.2244622808787926,0.06301334452030186,0.6944632949786616,
	- 0.5955168212825119,0.4473425940100297,0.2700417838303327,
	- 0.7724043956082883,0.6553545192922715,0.4871408620353512,
	- 0.8097301284690857,0.6725220182496192,0.8002534097038426,
	- -0.4366431953633789,-0.5869882376922511,-0.7332080507197046,
	- -0.8450980113065225,-0.9041113586460733,-0.4022310083998925,
	- -0.554596445154436,-0.6925605687496104,-0.7854318984598006,
	- -0.8250621271173465,-0.3420827953668352,-0.4840440064641756,
	- -0.6033456975789954,-0.6777531805937266,-0.2584102557043402,
	- -0.3819753792546441,-0.4821906665520286,-0.1650828712784331,
	- -0.270790845781693,0.9161619708326184,0.9396956424389374,
	- 0.9204283182965946,0.8462032095340455,0.7293238793541417,
	- 0.9749588444840027,0.9879501207294071,0.942053498973333,
	- 0.8348196077814718,0.9950795014807369,0.9818515654328379,
	- 0.9027098746674149,0.9581801446138297,0.9118246030313639,
	- 0.8703772282258925,0.1778171059718252,0.06053992567271226,
	- -0.07929659020903117,-0.2226737578340799,-0.345825401239635,
	- 0.2886360377097776,0.1672516508448342,0.02000533874392893,
	- -0.1285435155191929,-0.2531843553864728,0.403575906447316,
	- 0.2774342678683828,0.1245598363284875,-0.02655554762561945,
	- 0.5016349858535857,0.3695530582277636,0.2148806720954671,
	- 0.5665590425344393,0.431103930292903,0.5869876102086139,
	- 0.7332077514676827,0.845098078457225,0.9041116580482536,
	- 0.7182616282077119,0.8617334421407644,0.9490975365686583,
	- 0.8223898048944452,0.9416915744235097,0.8729720010540123,
	- 0.1080256414522809,0.1376220280275969,0.1609005865750696,
	- 0.1740026689030255,0.2707904196202965,0.3196768235430837,
	- 0.3552546724685221,0.3677018240803483,0.3587598208776521,
	- 0.4821901792282771,0.5389508449256169,0.5637713635689835,
	- 0.5520258363563475,0.6777529577987501,0.7231337276202411,
	- 0.724309982145211,0.8250622687013296,0.8470545173149734,
	- 0.1285429999155006,-0.02000532948058562,-0.1672511147059996,
	- -0.1245600244829796,-0.2774338902981233,-0.3695528631494325,
	- -0.09827641615811868,-0.2700412859530667,-0.4473420975374328,
	- -0.5955164071695848,-0.6944629164413806,-0.2991130971968019,
	- -0.4871400501186961,-0.6553538941234454,-0.7724039524031648,
	- -0.4942022299541438,-0.6725212074710563,-0.8097296395344389,
	- -0.6512059956089504,-0.8002528392148971,-0.7580246814516085,
	- -0.3677014077761052,-0.3552545716101517,-0.3196770257819652,
	- -0.5637712030900536,-0.5389510214534028,-0.7231336172569296,
	- -0.8348194119106425,-0.9420533966954356,-0.9879499956150448,
	- -0.9749586635216289,-0.9027097279159257,-0.9818515951566739,
	- -0.9950795477220543,-0.9118244750171576,-0.9581802235578871,
	- -0.8703770126934449,-0.0175091339170676,0.1501155140512474,
	- 0.3079660822386824,-0.1073133727582037,0.06090046334304851,
	- -0.1901304002696938,-0.9490974969653682,-0.8617336589899791,
	- -0.7182621005240754,-0.5521276321758419,-0.941691783045487,
	- -0.8223901593137167,-0.6594093292610237,-0.872972144171723,
	- -0.7343999908188845,-0.7646691446910742,0.6951665021597787,
	- 0.7977009700656229,0.8482969664746548,0.6140047811934269,
	- 0.6931464276818936,0.4928650597255946,-0.4549467775084718,
	- -0.3173815862988101,-0.1591515620353438,-0.01030716362341688,
	- -0.5502140363721867,-0.3973395475484636,-0.2292777334167206,
	- -0.609656670182737,-0.4476455277450017,-0.6292139442700462,
	- 0.7854319364049284,0.6925603649758249,0.5545959620739339,
	- 0.6033453603619342,0.4840435291285519,0.3819748711371402,
	- -0.03526641653115874,-0.06127364342066123,-0.0832913202753871,
	- -0.2692854573778917,-0.2941058574917593,-0.4857712605383084,
	- -0.1282040992012934,0.02998172476739921,0.2130449739264662,
	- 0.394354771181159,0.5438573645627299,0.6488215902264565,
	- -0.1901340637026595,-0.02057293935230464,0.1720544722828635,
	- 0.3534794142829396,0.4950335464190314,-0.252933321812349,
	- -0.07636778766011496,0.1169519253626288,0.2909961752861106,
	- -0.304612640171253,-0.1271903099934383,0.0580070042064605,
	- -0.3366056805211806,-0.1653138037361849,-0.3496821715684524,
	- 0.6714420577705413,0.8002044514563711,0.9106424580428781,
	- 0.9742808059046055,0.9805708386415104,0.9441720387917811,
	- 0.7350956003099328,0.8682639008659977,0.9653353535299492,
	- 0.9995536316680411,0.9755844796257857,0.7728091190204586,
	- 0.8918537226509272,0.9597077065970592,0.9637247890765801,
	- 0.767530944505584,0.857374860312736,0.8948082473172733,
	- 0.7201359303293944,0.7802583897718675,-0.9441722324566724,
	- -0.8608166107545396,-0.7207644955095487,-0.5303678229575245,
	- -0.3211867088850157,-0.9096404828216634,-0.7967975927156801,
	- -0.620601831095295,-0.4039985827676406,-0.8241231220089414,
	- -0.6757043639889994,-0.4726959329165278,-0.6854057579633669,
	- -0.5106159168102177,-0.5164821811548767,-0.3130828685601688,
	- -0.128054626578418,0.09418349997750548,0.3239109228229815,
	- 0.523048087763098,-0.3043330399192493,-0.09531787499064681,
	- 0.146419102006115,0.3786227553496849,0.5638039035645359,
	- -0.2789925774668332,-0.05252850546893189,0.1924160430438771,
	- 0.4101897544477446,-0.2358533016570041,-0.006318969895916147,
	- 0.2236016867495729,-0.1820659309330632,0.03496843200875603,
	- -0.6714423515894649,-0.8002045390283683,-0.9106424117173109,
	- -0.9742807748705438,-0.9805709251787237,-0.6691519386893557,
	- -0.79626257796142,-0.8909109722488041,-0.9275521423149625,
	- -0.6332080201962388,-0.7430051304270751,-0.8108589038018792,
	- -0.5581290590099237,-0.6413705283620924,-0.4563600901355626,
	- -0.648822290296783,-0.6411378559950974,-0.600293640880965,
	- -0.5219527418637842,-0.4191009430775375,-0.7802586188950914,
	- -0.7711197529973893,-0.713538182957094,-0.6094980396194888,
	- -0.4842093859996422,-0.8948081394501657,-0.8705497953564927,
	- -0.7870195954857328,-0.6597854273844109,-0.9637246412193355,
	- -0.9132982945459158,-0.8070428410352181,-0.975584505681221,
	- -0.9015722073987464,0.3130823317650696,0.1280539101236855,
	- -0.09418429615654819,-0.3239116283455282,-0.523048586255087,
	- 0.1989845274738189,-0.01970764286946627,-0.2653151882168217,
	- -0.4936479477555078,0.05597369301027853,-0.1852629737758222,
	- -0.4302072668465533,-0.09867461327158224,-0.3387557568094476,
	- -0.2393260112020272,0.1282040764044601,-0.0299819504088954,
	- -0.2130455201840074,-0.3943555879655132,-0.5438582278251758,
	- -0.03496843048443223,-0.2252069693946209,-0.4261053308619027,
	- -0.5992598174372795,-0.720136706807033,-0.2236017161594696,
	- -0.4317330442416767,-0.6250530132529536,-0.7675317913865697,
	- -0.4101898771205939,-0.6101488498350025,-0.7728099228904255,
	- -0.5638041319099237,-0.7350961954485662,0.6411372723067146,
	- 0.6002931843810706,0.5219523372221417,0.4191004905746099,
	- 0.4596949806286311,0.3916338931244087,0.2980734064957148,
	- 0.226741584116328,0.1432114770939381,-0.02097489882147943,
	- 0.8608164411414747,0.7207644427956729,0.5303678926086439,
	- 0.3211867913977836,0.9015721838250796,0.7879881821713033,
	- 0.6114960278478284,0.3951892122332402,0.1820657113417612,
	- 0.8070430398170311,0.6574928275930984,0.4544842943197335,
	- 0.2358529185889448,0.6597856586149884,0.4841878538357612,
	- 0.2789921022280572,0.4842093252521232,0.3043325272261384,
	- 0.5992589358516202,0.4261046359672609,0.2252066549797059,
	- 0.6250522113657903,0.4317325950511361,0.6101482870567641,
	- 0.9096403689902206,0.9275522217134882,0.8909112253661301,
	- 0.796262827475376,0.6691520068054228,0.8241233338640371,
	- 0.810859375773786,0.7430057321681839,0.6332085061147845,
	- 0.6854064426268304,0.6413714065577412,0.5581299045184589,
	- 0.5164832226272315,0.4563611494403301,0.3496833143594963,
	- -0.3951892821849063,-0.6114960336943951,-0.787988199289983,
	- -0.4544844137443082,-0.657492739431111,-0.484187939006181,
	- 0.4936478319326018,0.2653148405479006,0.01970714938077021,
	- -0.1989850169013517,0.4302075642722875,0.1852629793843341,
	- -0.0559739158243807,0.3387563694841473,0.09867487876932232,
	- 0.2393267951217032,-0.999553621201999,-0.9653354239158236,
	- -0.8682642090770526,-0.9597077173597477,-0.8918540989344099,
	- -0.8573751662344773,-0.2980738893651726,-0.3916343988495664,
	- -0.4596955428592778,-0.4950341577852201,-0.1432117197792371,
	- -0.2267418620329016,-0.2909964852939082,0.02097514873862574,
	- -0.05800679989935065,0.1653145532988453,-0.3786231842883476,
	- -0.1464197032303796,0.09531724619007391,-0.1924163631703616,
	- 0.05252803743712917,0.006318730357784829,-0.3534800054422614,
	- -0.1720548071373146,0.02057294660420643,0.190134278339324,
	- -0.1169519894866824,0.07636807502743861,0.2529338262925594,
	- 0.1271908635410245,0.3046134343217798,0.3366066958443542,
	- 0.6094980941008995,0.7135382519498201,0.7711196978950583,
	- 0.7870198804193677,0.8705500304441893,0.9132984713369965,
	- 0.403998910419839,0.62060207699311,0.7967976318501995,
	- 0.4726965405256068,0.6757048258462731,0.5106167801856609 };
	-
	- auto pointshell
	- = new vnl_matrix_fixed<double, 3, 252>(coords);
	-
	- return pointshell;
	- }
	-
	-};
	-
	-template<> class PointShell<362, vnl_matrix_fixed<double, 3, 362> >
	-{
	-public:
	- static vnl_matrix_fixed<double, 3, 362>* DistributePointShell()
	- {
	- double coords[3*362] = {
	- 0.9756767549555487,0.9966345256373878,0.9881046683022421,
	- 0.9397937974509782,0.8528238339140162,0.7412214378486838,
	- 0.6231965669156312,0.9834769262997924,0.9946239689739521,
	- 0.9675363014408187,0.8953435882073797,0.7874413200090197,
	- 0.6642104349774659,0.9602286065935876,0.9526601679743949,
	- 0.9016229543668698,0.8082746868815032,0.68966672282401,
	- 0.8971014254962764,0.865591182877164,0.7933984257386667,
	- 0.6899186612252972,0.7970712198937139,0.7447486127431006,
	- 0.6617902410567804,0.6754324093484999,0.6115790799976598,
	- 0.5505632701289798,0.4375940376503739,0.3383775196739809,
	- 0.2130515669413184,0.06907711216819173,-0.07773888316805401,
	- -0.2106409255960856,-0.3200730131503601,0.5092547181142852,
	- 0.4023388431564537,0.265404014577164,0.1102235177567159,
	- -0.04300669133613336,-0.1770183828831563,0.575075565563677,
	- 0.4585983658816588,0.3107083252171692,0.1482373789939068,
	- -0.006505365777837463,0.6235168560971455,0.4966123011343984,
	- 0.3414318272800055,0.178171381919271,0.6463093264667951,
	- 0.5114333072914884,0.3555189519163455,0.6437455132939696,
	- 0.5064909697503934,0.3200724178002418,0.4666605048128079,
	- 0.6201479032959075,0.7616224484252742,0.8717669667532965,
	- 0.9417225609211535,0.3896493566867455,0.5498790773446007,
	- 0.7090922337204692,0.8433688828589941,0.9352336066902967,
	- 0.4569904905821254,0.6220231833138386,0.7744719807282636,
	- 0.8905764752647638,0.5117469206751248,0.6692307929647209,
	- 0.8035074327650433,0.5454521871592555,0.6853580997057199,
	- 0.5566669166856135,0.2502538949373057,0.3059448167491349,
	- 0.3600408236839538,0.4043068999720242,0.4319414682718342,
	- 0.441694708443188,0.4034206272561209,0.4730271557866856,
	- 0.532848297654098,0.5712181400125941,0.5831430197408345,
	- 0.573108039637807,0.5665551499276381,0.6430548267994817,
	- 0.697797754038698,0.7197945422057391,0.7103565350090897,
	- 0.7205836671095895,0.7916313033238946,0.830001177910469,
	- 0.8306996157029517,0.8449704612165639,0.8994200667307424,
	- 0.9168712118355732,0.9290744770112713,0.9630120083465428,
	- -0.4375932291383153,-0.3383769257894378,-0.213051272338593,
	- -0.069077150725739,0.07773856031405026,0.210640419502912,
	- -0.2966224671809508,-0.1723655417522876,-0.02500201334267453,
	- 0.1301781584808292,0.2729791005675229,-0.1245894223683107,
	- 0.02220568982766716,0.181648017057727,0.3325661017840546,
	- 0.06640211724156465,0.224593525159963,0.3797737583307059,
	- 0.2546621526726748,0.4084582460890006,0.4194124862841989,
	- -0.6231952788307172,-0.5191377313825043,-0.3823142165271753,
	- -0.2192092047974507,-0.04708691012811009,0.1137784201343049,
	- -0.5064899646320268,-0.3766634899185586,-0.2148504892229182,
	- -0.03595624973804722,0.1367370476543766,0.2846552253706529,
	- -0.3555183995893311,-0.2005508680670486,-0.02217694060430831,
	- 0.1572376520619428,0.3149362814931866,-0.1781713502362079,
	- -0.007356907961155389,0.1715373930872541,0.3352293490184234,
	- 0.006504983859799645,0.1777752170237141,0.3417324928044827,
	- 0.1770178009419758,0.3352469806136632,-0.2502532651867688,
	- -0.305944136422603,-0.3600400745299253,-0.4043060780204903,
	- -0.4319406005716204,-0.4416938460694254,-0.1269352612818317,
	- -0.1739928009393344,-0.2202529758737042,-0.2586227459701909,
	- -0.284108486127532,0.01921174674137865,-0.0178650781598001,
	- -0.05758606025521316,-0.0946046496972474,0.1765178736510398,
	- 0.1461529703905971,0.1077831731751904,0.3265627679363224,
	- 0.2967152689909496,0.4533499532981318,-0.9756765814639009,
	- -0.9966344649740785,-0.988104613901425,-0.9397935597648753,
	- -0.8528232434185344,-0.7412204556286736,-0.9630117602017364,
	- -0.9724898559386537,-0.9443983719046766,-0.872205391539895,
	- -0.7653064930405823,-0.6437442957669286,-0.9168708930751739,
	- -0.9063844772960285,-0.854235225343551,-0.7619985358162277,
	- -0.6463082287051728,-0.8306992108488227,-0.7961776618828416,
	- -0.7239846967363567,-0.6235158879179115,-0.7103560109842373,
	- -0.6562122899574033,-0.5750746905699001,-0.57310737178428,
	- -0.5092538887995088,0.5191392058051657,0.3823157740702657,
	- 0.21921067448898,0.0470881327099307,-0.1137775092906953,
	- 0.5472470006444878,0.3931697400830757,0.2142753542688524,
	- 0.03384607877300972,0.5571877569557013,0.3873829237054168,
	- 0.1993990574966068,0.5423114310655514,0.3634170963876792,
	- 0.5045541233354154,-0.4666608333315146,-0.6201479767677171,
	- -0.7616223457476226,-0.8717667933239607,-0.9417223829869568,
	- -0.3352474166348553,-0.4910400536375052,-0.6475846838452103,
	- -0.7818611891844719,-0.8763941477411082,-0.9290742611527086,
	- -0.3417327749428254,-0.4990082491682611,-0.6485010946606566,
	- -0.7675612257958812,-0.8449702640289916,-0.3352294641675141,
	- -0.4847082676062016,-0.6189847486203324,-0.7205834943870382,
	- -0.3149361858566655,-0.4500011545486986,-0.5665549223826651,
	- -0.2846548708446658,-0.4034202330037945,0.7653073532861547,
	- 0.872205859792842,0.9443985741044771,0.9724900050827093,
	- 0.761999264311147,0.854235631268382,0.9063847463761845,
	- 0.7239853440497003,0.7961780994118357,0.656212928522132,
	- -0.3896497406159066,-0.2729794041072619,-0.1301782703739063,
	- 0.02500220716165068,0.1723660797382231,0.2966232936614225,
	- -0.4569906864326022,-0.3325662253633467,-0.1816479322770386,
	- -0.02220527620210722,0.1245901828483064,-0.5117470172320778,
	- -0.379773775950072,-0.2245933008307449,-0.0664015397322142,
	- -0.5454522916908328,-0.4084582325525932,-0.2546618495309371,
	- -0.5566670856360056,-0.4194124724547443,-0.5505634949474448,
	- 0.8763943198737287,0.7818612997205676,0.6475846717443501,
	- 0.4910398461057182,0.7675613256844861,0.6485010946606566,
	- 0.4990081234589473,0.6189848075516286,0.4847082388524531,
	- 0.450001299655162,0.2841093866952762,0.2586236728290179,
	- 0.2202538772848093,0.1739936456875063,0.1269360432434686,
	- 0.09460546886511037,0.05758689641252078,0.01786589383219402,
	- -0.01921097131735245,-0.1077825867383485,-0.1461523912078012,
	- -0.176517304179968,-0.2967150069434516,-0.3265625234832059,
	- -0.4533500040307881,0.04300632519905166,-0.1102235647973928,
	- -0.2654036978528873,-0.4023382153059064,-0.148237402516883,
	- -0.3107079508004592,-0.4585976694770509,-0.341431363569028,
	- -0.4966114955495211,-0.5114323842282982,-0.0338450669354788,
	- -0.2142741518944354,-0.3931684703578905,-0.5472458119265531,
	- -0.6642094200020999,-0.1993981773021475,-0.3873820250532686,
	- -0.5571869441797634,-0.6896660583043277,-0.3634165630969035,
	- -0.5423109973324143,-0.6899183532182501,-0.504553984174398,
	- -0.6617902107749167,-0.6115792176515682,-0.5831423229868272,
	- -0.5712174808640838,-0.5328477301676857,-0.4730266887482617,
	- -0.7197940112087894,-0.6977972953381247,-0.643054488612089,
	- -0.8300007800598662,-0.7916309980553373,-0.8994197666839766,
	- -0.787440689562144,-0.8953433656420341,-0.9675363415293142,
	- -0.9946240407011416,-0.9834768689460589,-0.8082744359221968,
	- -0.9016230372124288,-0.9526603585193832,-0.9602286916122059,
	- -0.7933984756354565,-0.8655914258905276,-0.8971016370404785,
	- -0.7447488265146829,-0.7970714969272577,-0.6754326817805886,
	- -0.1367364480221615,0.03595711502889169,0.2148515425621942,
	- 0.3766645834143537,-0.1572373865760062,0.02217737847260294,
	- 0.2005514111744157,-0.1715374471229988,0.007356909834687842,
	- -0.1777755545457471,-0.9352334959045954,-0.8433687324667886,
	- -0.7090921450939843,-0.5498791863597017,-0.8905764592918793,
	- -0.774471897882643,-0.6220231689320465,-0.8035075122026962,
	- -0.6692308066909014,-0.6853582437416091,-0.1778161375899129,
	- -0.08196112014272428,0.03109142233089637,0.1521341729788544,
	- 0.2669187829195654,0.3632859224072412,0.4366423972091846,
	- -0.02374119024204515,0.09471244259515242,0.2248569419991813,
	- 0.350706344617783,0.4558820271112225,0.5328176919569597,
	- 0.1544374088220477,0.290680604004569,0.4265382311030135,
	- 0.5423794137964371,0.6260922126282031,0.3410385404813853,
	- 0.4823536424782295,0.6082030290912097,0.702208082962552,
	- 0.5136107375104821,0.6447862719396159,0.7494380454402638,
	- 0.6543855332308085,0.7656972306146125,0.7580253719184178,
	- -0.5980610514568761,-0.5275667073977156,-0.4291113361140411,
	- -0.3056524524744078,-0.1696203080333493,-0.0376422258299667,
	- 0.07805400320688781,-0.4626069507186271,-0.367865039277211,
	- -0.2460698157210856,-0.1075922772772709,0.02954542570643959,
	- 0.1497986786591435,-0.2914862882507431,-0.1726261297241735,
	- -0.03496909012717316,0.1043290137555473,0.2274959035287995,
	- -0.09487972868743588,0.03929513959897087,0.1777727700059916,
	- 0.3025309778153461,0.1056298518860434,0.2403183339972744,
	- 0.3651211825280409,0.2871566925727233,0.4096380159360284,
	- -0.07805410188638827,-0.1029113333575652,-0.1281592432697842,
	- -0.1503967869358663,-0.1664476243728032,-0.1752005995696255,
	- 0.06662046905832243,0.05250750966401235,0.0344560317246887,
	- 0.01402339491018058,-0.006131193542750579,0.2310143008479173,
	- 0.2261291767278549,0.2106389321639752,0.1852638684253743,
	- 0.399677322182528,0.3973696146518023,0.3769369479489949,
	- 0.5518992169467314,0.5439427436094942,0.6724578932085956,
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	- 0.2241327483663198,0.02151295276860445,0.3442643233016264,
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	- -0.5013199694054605,-0.5243381301130434,-0.1820189194073548,
	- -0.2568086311939767,-0.319546898969995,-0.3638250562458945,
	- -0.04627540884770265,-0.1150393837809054,-0.1758296738027379,
	- 0.08558690678521951,0.01939866440958929,0.1991961595715477,
	- -0.4397580914639075,-0.2580566866135989,-0.05641266799084353,
	- 0.1389310087452558,-0.295922215665352,-0.0965434988571485,
	- 0.107365815243832,-0.1321437542333658,0.06950025525528913,
	- 0.03026233882278601,-0.4148593732748149,-0.2745272477919344,
	- -0.1153816305493603,0.04186543327713237,0.1794701997231261,
	- -0.2291653183673072,-0.07170210104888378,0.08912594410177796,
	- 0.2326162031595532,-0.02465773800362392,0.134487905062478,
	- 0.2808952005684321,0.1720476740810845,0.3176193294845107,
	- 0.3399578552959914,0.5574798958328108,0.6515250645580214,
	- 0.7202890442609949,0.754822534930785,0.7120168974234773,
	- 0.7995412648414353,0.8495448706478895,0.841272643210163,
	- 0.9100366384710021,0.9284251625234463,0.3539783956892765,
	- 0.5371522584244614,0.7042734954121332,0.8335921603240184,
	- 0.4153929051801631,0.5965106290979496,0.7496353473630305,
	- 0.4607548496345096,0.6278760663083329,0.4841605931432954 };
	-
	- auto pointshell
	- = new vnl_matrix_fixed<double, 3, 362>(coords);
	-
	- return pointshell;
	- }
	-};
	-
	-
	-template<> class PointShell<492, vnl_matrix_fixed<double, 3, 492> >
	-{
	-public:
	- static vnl_matrix_fixed<double, 3, 492>* DistributePointShell()
	- {
	- double coords[3*492] = {
	- 0.9756767549555487,0.995129146382046,0.9942990656144199,
	- 0.9656349505028294,0.906669314667086,0.8226336999568686,
	- 0.7243638464104109,0.6231965669156312,0.9839703767589784,
	- 0.997142038124067,0.984428692964357,0.9391662760580684,
	- 0.862670051560969,0.7648456045484533,0.6590519021583431,
	- 0.9707167715611407,0.9718838371878742,0.9426229117731289,
	- 0.8796306184740903,0.7892458129328142,0.6846076300785651,
	- 0.929183358966584,0.9136522029381524,0.8666502644050813,
	- 0.7898345918065129,0.693320589737796,0.8580670030245058,
	- 0.8250351905308677,0.7641558269670571,0.6811699046825979,
	- 0.7636773150775941,0.7169778531093051,0.6492336193335421,
	- 0.6574101272386674,0.6032570204852985,0.5505632701289798,
	- 0.4375940376503738,0.3542026794336651,0.2512745383622963,
	- 0.1321836977435469,0.005435183516526082,-0.1177256014717769,
	- -0.2278158095071639,-0.3200730131503601,0.499121216713679,
	- 0.4104288008617515,0.2993922246212043,0.1713800199472592,
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	- 0.03960267796661452,0.1738084474791471,0.2983321411535529,
	- 0.2022902215891641,0.3254642982361922,0.3420368325512359,
	- 0.5203743808147369,0.603498584268205,0.6726720548002406,
	- 0.719474396239089,0.741638033276861,0.6545106949482685,
	- 0.7372275485364457,0.7972280664875324,0.8284744266242357,
	- 0.7764214244136933,0.8500106167743341,0.8943583778920716,
	- 0.8725105875877179,0.9304985104221231,0.9362840195367765,
	- 0.3187873126271887,0.4751176460530464,0.6264663831892676,
	- 0.7569806648964799,0.8565378137633573,0.3724393069541885,
	- 0.5311885746144091,0.6770114116120104,0.7952337966915513,
	- 0.4176372345893317,0.5707694457794332,0.7042664250854263,
	- 0.4489457715859918,0.5898772631309003,0.4647496441635906 };
	-
	- auto pointshell
	- = new vnl_matrix_fixed<double, 3, 492>(coords);
	-
	- return pointshell;
	- }
	-};
	-
	-
	-template<> class PointShell<642, vnl_matrix_fixed<double, 3, 642> >
	-{
	-public:
	- static vnl_matrix_fixed<double, 3, 642>* DistributePointShell()
	- {
	- double coords[3*642] = {
	- 0.9756767549555488,0.9936273045965159,0.9968737649581846,
	- 0.9799612120178374,0.9397937974509784,0.8775847359538656,
	- 0.7989268505692991,0.7116707502187636,0.6231965669156312,
	- 0.9839439883131955,0.997606269193783,0.9928389431247303,
	- 0.9642927845075879,0.9105363959854476,0.8355633282696746,
	- 0.7474316403407526,0.6549945735140008,0.9764792677814802,
	- 0.98203616585628,0.9657129396229355,0.9235205478703636,
	- 0.8567905682573015,0.7723352820545265,0.679558714000995,
	- 0.9483175267842808,0.9421385440112533,0.9121470670895898,
	- 0.8569526200134567,0.7808692882316954,0.6923761132322002,
	- 0.8971014254962764,0.8773049187483365,0.8343457228904876,
	- 0.7697920647699087,0.6899186612252972,0.8248449061833976,
	- 0.7923517869921962,0.7399265426789414,0.6712800260218211,
	- 0.7377425905504456,0.6958798370509692,0.6387690340353133,
	- 0.6438863846345996,0.5968935863094567,0.5505632701289798,
	- 0.4375940376503738,0.3657089664269339,0.2787444080680243,
	- 0.1782978006253255,0.06907711216819172,-0.04176369281672855,
	- -0.1467487371786262,-0.2403654598146251,-0.3200730131503601,
	- 0.4914658799359538,0.415730180051685,0.322900981562039,
	- 0.2155490838668689,0.09999803429967301,-0.01516787889370763,
	- -0.1220279512352428,-0.2156209889399338,0.5436064763029955,
	- 0.4631956410318647,0.3641181930198064,0.2503784412304452,
	- 0.1299861910861632,0.01243715490308354,-0.09463328683104604,
	- 0.5892511755529848,0.5032632034506475,0.398083833846048,
	- 0.2794416963056139,0.1566100659016669,0.03909742267488438,
	- 0.6235168560971455,0.5315692770219257,0.421472539809791,
	- 0.300467209121473,0.1781713819192711,0.6431587521468424,
	- 0.5460109940101698,0.4333214055893837,0.3130665794035795,
	- 0.6478378002177454,0.547462575328819,0.4350913076613168,
	- 0.6399334332955604,0.5389210845670883,0.3200724178002418,
	- 0.4287826750526064,0.543583002477908,0.6574820925009807,
	- 0.7616224484252742,0.84789985457486,0.9117594243665534,
	- 0.9532148993238304,0.3721063927495636,0.4892591428502506,
	- 0.6101418466998186,0.7256202393614284,0.8256057937005235,
	- 0.9026705854615993,0.9545776898360481,0.4242146396073646,
	- 0.5469136809977159,0.6694499319211135,0.7811234805255704,
	- 0.8720427891122669,0.9369519951934821,0.4722731360977363,
	- 0.595952912761318,0.7145554586697968,0.8172157093145741,
	- 0.8959095653312069,0.5117469206751248,0.6311048134383331,
	- 0.7406754453578036,0.8310759079383635,0.5392182936767531,
	- 0.6497579584113991,0.7472675269245613,0.5536544075493044,
	- 0.6528511281517397,0.5564810307882812,0.2502538949373057,
	- 0.2918876561725356,0.3336803609057232,0.3723595102048779,
	- 0.4043068999720243,0.4267717639621923,0.438887490788423,
	- 0.4417451579814044,0.3636248847448722,0.4137579266740147,
	- 0.4613876866690337,0.5016743933949674,0.5302454776050456,
	- 0.5449783839335098,0.5467236437808158,0.5384586718996058,
	- 0.4847692553550146,0.5414178984405463,0.5913899314506929,
	- 0.6286876371986284,0.6492812914734455,0.6528721916210272,
	- 0.6425800233106177,0.6067853073481849,0.6657991451456106,
	- 0.7129452846304364,0.742280692335758,0.7515124484581964,
	- 0.7428160470273413,0.7205836671095894,0.7764326916323942,
	- 0.8155579470101821,0.8335749126408774,0.8306996157029517,
	- 0.8174816717930142,0.8650995515806045,0.8929631510323212,
	- 0.8991001659430972,0.8921547074343706,0.9286306144549926,
	- 0.9447583574027534,0.943906557149077,0.9688828514077716,
	- -0.4375932291383154,-0.3657083101776577,-0.278743955138478,
	- -0.1782975892372044,-0.06907715072573903,0.04176343253822806,
	- 0.1467483093137361,0.2403649238452659,-0.334979155028856,
	- -0.249113234922861,-0.1483246071802934,-0.03654010765740752,
	- 0.07901069585299947,0.1897435516910367,0.2886438308249422,
	- -0.2140239599986307,-0.114043112737167,-0.001406336898152031,
	- 0.1172166109444462,0.2327251986251803,0.3367145075141528,
	- -0.07787968046152194,0.03376382657255556,0.153308912419789,
	- 0.2719508349268641,0.3804163499145621,0.06640211724156461,
	- 0.1844665658852621,0.3039508137298482,0.4155682770935452,
	- 0.2091265361205084,0.3268694132891478,0.4395588586722926,
	- 0.3409081262151013,0.4522359229770948,0.4554687573578106,
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	- 0.2196681717134536,0.3398901915912972,0.2156203893390849,
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	- -0.299731815412124,-0.1710988752936458,-0.02562616156907596,
	- 0.1281943739657924,0.2786088475509629,0.4146241489277275,
	- 0.5296074119458033,-0.2831889282507517,-0.1472477576556685,
	- 0.002978788421451789,0.1571443739074394,0.3031991278501129,
	- 0.4316900017871718,-0.2593820240207756,-0.1190520671608967,
	- 0.03150460300683353,0.1812458940061291,0.3193074202631062,
	- -0.229491624834242,-0.08860645786522432,0.05782435035907074,
	- 0.1994358494400003,-0.1959070295313489,-0.05832274784344905,
	- 0.08053951964108649,-0.1613858092941266,-0.03012854522533278,
	- -0.671442351589465,-0.7524955042654247,-0.8307216077305004,
	- -0.8988911324269672,-0.9496340459616871,-0.9781045247295723,
	- -0.9838822098556939,-0.9706581405182357,-0.6732379910932457,
	- -0.7555353929734253,-0.8321927576733623,-0.8949176301047361,
	- -0.9365114268652753,-0.9538841305299445,-0.949106939734586,
	- -0.6637939293172054,-0.7437729138119192,-0.8147968652653733,
	- -0.8684734875620626,-0.8990751104656249,-0.906028082404147,
	- -0.6398902977415805,-0.7135875679260879,-0.7753830615613055,
	- -0.8180895331241328,-0.8383689548572043,-0.6002017842451572,
	- -0.6645162706136697,-0.7153675946298389,-0.747703849697991,
	- -0.5464363016035276,-0.6002045214061834,-0.6407682965760649,
	- -0.4830988161196208,-0.5271645300902241,-0.4158550110968205,
	- -0.648822290296783,-0.6472486014147985,-0.6344626299567083,
	- -0.6075203746111165,-0.5653935344751363,-0.5100061066600627,
	- -0.4459169294668335,-0.3786832614419487,-0.7313855414086173,
	- -0.7310744930343959,-0.7160642832118092,-0.6830433558919348,
	- -0.6318400429346884,-0.5662582509809229,-0.492781618346183,
	- -0.418059300054038,-0.8116671044980045,-0.8099276517898805,
	- -0.7895071237697285,-0.74756375917153,-0.6857578728711079,
	- -0.6101862708902825,-0.5288485365725882,-0.882466459585,
	- -0.8755369303175729,-0.8463852653947486,-0.7938122127531423,
	- -0.7219269876119373,-0.6386807736786417,-0.9363384293729856,
	- -0.920580474049937,-0.8807752703984302,-0.8181738478934094,
	- -0.7389956620788968,-0.9682497764059059,-0.9417119830617079,
	- -0.8917766410561483,-0.8219783739569782,-0.9775307754986758,
	- -0.9407006676234038,-0.8832579304805722,-0.9676424743883053,
	- -0.9228815898031446,0.3130823317650696,0.2026646799488628,
	- 0.07519720122433592,-0.06519302988114704,-0.2106389019045293,
	- -0.3511444697687643,-0.4776954195825031,-0.5848781397282268,
	- 0.2455618355531619,0.1217043818280624,-0.01891222872758066,
	- -0.1695413327023869,-0.3196901877897432,-0.4582042349710876,
	- -0.5770670118160844,0.1655447705464922,0.0289439344448441,
	- -0.1220494268493898,-0.2778581225722938,-0.4262841911656161,
	- -0.5567786600361208,0.07498802093385774,-0.07139865292607843,
	- -0.2274740800198117,-0.3816395081442781,-0.5218451060581218,
	- -0.02151295053653907,-0.1724761631672423,-0.3268548028226648,
	- -0.4727737792825113,-0.1175093448034605,-0.2667795638863601,
	- -0.413210185645996,-0.2066526242811376,-0.3486960301430706,
	- -0.2845979196243639,0.1282040764044601,0.03314425179116901,
	- -0.07418801789892716,-0.1895810572320515,-0.3060118317848469,
	- -0.4152654547344749,-0.51055312502423,-0.5884161844630592,
	- 0.03012854220925541,-0.07822075478791662,-0.1975265605100549,
	- -0.3210457437412529,-0.4395492890997685,-0.5442335497807274,
	- -0.6297193044589443,-0.6950252371327137,-0.08053951945115613,
	- -0.2008908777469321,-0.3287498381001709,-0.454849657793549,
	- -0.5688642328312289,-0.6631668267266261,-0.7350870708018485,
	- -0.1994358711312821,-0.3279452265433291,-0.4583916832350944,
	- -0.5800652917395807,-0.683455813944916,-0.7636467367251844,
	- -0.3193074905789999,-0.4498985165051642,-0.5758541835274278,
	- -0.6869055692486817,-0.7760321386045594,-0.4316901383846216,
	- -0.5576908306091364,-0.6732598101682218,-0.7702166526708257,
	- -0.5296076162752261,-0.6457739738857279,-0.7477901272839138,
	- -0.6095261314476621,-0.7131195245736661,0.6472479688324123,
	- 0.6344620803203709,0.6075199046816795,0.5653931175085022,
	- 0.5100057007389891,0.4459164955009389,0.3786827774326808,
	- 0.5474099886510654,0.5236257914257873,0.4857185197867951,
	- 0.4345152489333596,0.3738198763531287,0.3091172837171857,
	- 0.4250511511939136,0.389683753785766,0.3423573476615138,
	- 0.2859346018498913,0.2253099468416643,0.2835632478824897,
	- 0.2385758256608239,0.1860028309402729,0.1299534657091715,
	- 0.1312824242313411,0.08112906023855893,0.02887591783637235,
	- -0.02047837605993849,-0.07041365620347247,-0.1612832799773341,
	- 0.8982333732257657,0.831345524857385,0.7414325451852105,
	- 0.6303269573377657,0.5044378109359756,0.3731116142445962,
	- 0.2455228128124526,0.9228814872695982,0.8667983517234625,
	- 0.7868465046935174,0.6823837598597929,0.5579412946135831,
	- 0.4227639330815517,0.2876608055402039,0.1613856625640601,
	- 0.8832579654623612,0.8143439687072217,0.7198955735651289,
	- 0.6018165967179313,0.467747528435525,0.3289004093680582,
	- 0.1959067638111305,0.8219785498827571,0.7387750958937861,
	- 0.6307665078242817,0.5029950256220953,0.3654474931658011,
	- 0.2294912586325793,0.7389959159190775,0.6425282428469168,
	- 0.5248781214125594,0.3936431094566906,0.2593815856416469,
	- 0.6386809855643202,0.5327535820451708,0.4113926019080829,
	- 0.2831884462269615,0.5288485749239231,0.4188791724037085,
	- 0.2997313094215869,0.418059069948,0.3092738247890606,
	- 0.6297184498311313,0.5442326731425132,0.4395485037972626,
	- 0.3210451478850294,0.1975261966743493,0.07822060158766293,
	- 0.6631659475585863,0.5688633866559212,0.4548489689298922,
	- 0.3287493895928871,0.2008906793070462,0.6834549460780991,
	- 0.5800645299836926,0.4583911438911752,0.3279449596345045,
	- 0.6869047733719595,0.5758535688432742,0.449898169624651,
	- 0.6732591535970365,0.5576904114999332,0.6457735063412144,
	- 0.9277609198709332,0.949106860839256,0.9538841631800392,
	- 0.9365115581247451,0.8949178072878723,0.8321929059126493,
	- 0.755535446210326,0.6732379126875105,0.8935348059013593,
	- 0.9060281564869469,0.8990753265127792,0.8684738109832391,
	- 0.8147972186077681,0.7437732084300421,0.6637941002839092,
	- 0.8379239537972928,0.8383692759036656,0.8180900037577743,
	- 0.7753836155369005,0.7135881068095284,0.639890731966599,
	- 0.7605089118538748,0.747704461889213,0.7153683254339585,
	- 0.664517027376214,0.6002024649156598,0.6652570996829634,
	- 0.6407691682823238,0.6002054473372921,0.5464371824658241,
	- 0.5596800524090022,0.5271655706244485,0.4830998363360157,
	- 0.4522165310007144,0.4158561136906575,0.3496833143594963,
	- -0.2876608652754351,-0.4227639382532795,-0.5579412897306785,
	- -0.6823837835510913,-0.7868465717409772,-0.8667984500087526,
	- -0.3289005616515215,-0.4677475887278177,-0.6018165999573247,
	- -0.7198955529773995,-0.8143439414326642,-0.3654477029697049,
	- -0.5029950893382186,-0.6307664561929963,-0.7387749669914671,
	- -0.3936433402523272,-0.5248781506021705,-0.6425281057326593,
	- -0.4113928310116375,-0.5327535685472626,-0.4188793967911134,
	- 0.577066822550539,0.4582039092088336,0.3196897246958904,
	- 0.169540766109225,0.01891161845986538,-0.1217049732030892,
	- -0.2455623627393322,0.5567787306370593,0.4262841209617862,
	- 0.2778578974521733,0.1220490717256491,-0.02894436515050694,
	- -0.165545217365127,0.5218454423524129,0.3816396895816639,
	- 0.2274740807377008,0.07139849210836301,-0.07498829123147716,
	- 0.4727743520975624,0.326855199205205,0.1724763529977552,
	- 0.02151295276860444,0.4132109394322543,0.2667801205874505,
	- 0.1175096785325448,0.3486969033343195,0.2066532886754674,
	- 0.2845988618411943,-0.9915701323913838,-0.9983759139464571,
	- -0.9821329817122836,-0.9405392168410572,-0.8766846298252051,
	- -0.7979987142017131,-0.9950116201913212,-0.9915144412787341,
	- -0.9621574590524813,-0.9072363224101446,-0.8327566769720253,
	- -0.9752335225013484,-0.9586154363208594,-0.9159090584602802,
	- -0.8504523952727223,-0.9301899969464084,-0.9002463663906001,
	- -0.8470026365747616,-0.863227339500068,-0.8226636840857314,
	- -0.7819440310902068,-0.3091177896659217,-0.3738203674077975,
	- -0.4345157440029583,-0.4857190441849699,-0.5236263640902669,
	- -0.5474106128468904,-0.5588885443532919,-0.2253103954606045,
	- -0.2859350592025221,-0.3423578252345214,-0.3896842610441149,
	- -0.4250516888435538,-0.4483636748755489,-0.1299537462879293,
	- -0.1860031284708927,-0.2385761459990237,-0.2835635916740772,
	- -0.3187738370923436,-0.02887592341002545,-0.0811290830782055,
	- -0.1312824709082232,-0.175829673802738,0.07041398450649188,
	- 0.02047868355036482,-0.02876160928094873,0.1612839336168132,
	- 0.1123805173372347,0.2398380094723457,-0.5092306348673886,
	- -0.3871271308997349,-0.2468082566335953,-0.09665937383397012,
	- 0.05216495245602301,0.189540870507144,-0.4146244745670597,
	- -0.2786093002807504,-0.1281949271302634,0.02562556437243592,
	- 0.1710982989127918,-0.3031993859046618,-0.1571447546490307,
	- -0.00297925984664287,0.147247252029971,-0.1812460903983632,
	- -0.03150492197167008,0.119051661271318,-0.05782450627681404,
	- 0.08860617741886109,0.05832260658459812,-0.4847695337402862,
	- -0.3923591556376936,-0.2838184503258238,-0.1653148824643805,
	- -0.04565210375030839,0.06672910665806144,0.1662653402185898,
	- -0.3594180507425287,-0.253319097564816,-0.1350560618895416,
	- -0.01320461850800903,0.1028580486723768,0.2061840662709727,
	- -0.2162633298539993,-0.1003749112365929,0.02129875586186771,
	- 0.139247419944916,0.2454372621958313,-0.06398217348632655,
	- 0.05523623192861417,0.17302500577526,0.2808952005684321,
	- 0.08611242071710691,0.2016814632806757,0.3097650809527805,
	- 0.2239251562628219,0.3305631346577989,0.3434314452768145,
	- 0.4927814627145429,0.5662581542385627,0.6318399645986254,
	- 0.683043240780333,0.7160640841376876,0.7310741891309572,
	- 0.6101863849438733,0.6857580324047194,0.7475639112793486,
	- 0.78950721141067,0.8099276375885235,0.7219272504872226,
	- 0.7938124902720932,0.8463855099577528,0.8755371018531016,
	- 0.8181741141101887,0.8807755242176112,0.9205806914487843,
	- 0.8917768010350154,0.9417121277771469,0.9407006846750625,
	- 0.2928563777418555,0.4282076937835696,0.5635232482078705,
	- 0.6879656610506216,0.7922901195775008,0.8719937126447483,
	- 0.3397879564876633,0.4790578522946484,0.6132791099941464,
	- 0.7312056921497674,0.8252311496217807,0.3821934817691987,
	- 0.520188888877212,0.6479602207299933,0.7555206677931847,
	- 0.415971059154168,0.5474986596025796,0.6648558465528478,
	- 0.4386113475958364,0.5599721413103722,0.4500523932965443 };
	-
	- auto pointshell
	- = new vnl_matrix_fixed<double, 3, 642>(coords);
	-
	- return pointshell;
	- }
	-};
	-
	-
	-template<> class PointShell<812, vnl_matrix_fixed<double, 3, 812> >
	-{
	-public:
	- static vnl_matrix_fixed<double, 3, 812>* DistributePointShell()
	- {
	- double coords[3*812] = {
	- 0.9756767549555487,0.9922508097125681,0.9977223655964853,
	- 0.9881046683022422,0.9605519470607568,0.9146195529015363,
	- 0.8528238339140162,0.7799959774035472,0.7017828679367573,
	- 0.6231965669156313,0.9837002757017411,0.9971982264747434,
	- 0.9970195212545997,0.9790578176231792,0.9411837637692063,
	- 0.8844913295435498,0.8132898830804115,0.733693935416079,
	- 0.6517368229295557,0.9797764734635961,0.9875546637606186,
	- 0.9791028733313679,0.9508425500024201,0.9020818068674743,
	- 0.8358206809420552,0.757892552927626,0.6749593629473696,
	- 0.9602286065935876,0.9595713376770644,0.9407948278222147,
	- 0.9016229543668696,0.8432733179563544,0.7704382634077368,
	- 0.6896667228240099,0.9226923908191266,0.9116587851060941,
	- 0.8819863001926875,0.833225536765196,0.7683765355083914,
	- 0.693030195174853,0.8672949635738141,0.8455181303237055,
	- 0.8062955359163166,0.7509515682311381,0.6835651897016059,
	- 0.7970712198937139,0.7659650471206068,0.7200326020746473,
	- 0.6617902410567805,0.7171844959174759,0.6793953685069648,
	- 0.6300938559406523,0.6333774065241421,0.5918819525326566,
	- 0.5505632701289798,0.4375940376503738,0.3744427273176402,
	- 0.2993381563954681,0.2130515669413183,0.1182813882301629,
	- 0.01954824200640591,-0.07773888316805401,-0.1686715778074173,
	- -0.2499271804752164,-0.32007301315036,0.4854882574576871,
	- 0.4194229010537701,0.3399338752288831,0.2482942679442456,
	- 0.1481384200976902,0.04502062388977755,-0.05499873367858239,
	- -0.1469877513574829,-0.2280773868570659,0.5324004751734927,
	- 0.4628532125512143,0.3786136701220479,0.2817283713716202,
	- 0.1769156386035929,0.07062416136199023,-0.03081255771979229,
	- -0.1228131994141411,0.5750755655636769,0.5013629074790578,
	- 0.4122166091807719,0.3107083252171691,0.2025911492637849,
	- 0.09481562164394035,-0.006505365777837463,0.6099587706972414,
	- 0.5315747218240751,0.4378921540503243,0.3330794318970117,
	- 0.2235852429888137,0.1162930447896056,0.6341450324413492,
	- 0.5511580300049011,0.4540605894555947,0.3478844246654598,
	- 0.2392124945153528,0.6463093264667951,0.5595982440953389,
	- 0.46086512448968,0.3555189519163455,0.647046909800018,
	- 0.5581741842011717,0.4598430939447178,0.6384375755240163,
	- 0.5492419252084272,0.3200724178002418,0.4163027723501219,
	- 0.5178612432225475,0.6201479032959074,0.7171164359379398,
	- 0.8025495773806206,0.8717669667532965,0.9228269911622408,
	- 0.9565659576168886,0.3662566345969678,0.4693191708546967,
	- 0.5762858482292442,0.6811797034275579,0.7768921407658641,
	- 0.8570710368648269,0.9180184145424319,0.9594305591455454,
	- 0.4128244293574089,0.5208884118196857,0.6304558785383466,
	- 0.7343501607073976,0.8250439179808262,0.8969571451990621,
	- 0.9480541165102998,0.4569904905821253,0.5671264332790738,
	- 0.6755415775491402,0.7744719807282637,0.8569290887080647,
	- 0.9189090911818834,0.4955267041670984,0.6040846468052238,
	- 0.7074267562469234,0.7981205092043148,0.8705859012982401,
	- 0.5255624261223592,0.6289645166670731,0.7241496615411406,
	- 0.804855834362468,0.5454521871592556,0.6410312785579098,
	- 0.7264644091774437,0.5551982228864044,0.641627582268501,
	- 0.5561969667017818,0.2502538949373057,0.2872027754172267,
	- 0.3245344712904296,0.3600408236839537,0.3911506315330521,
	- 0.4155633223527059,0.4319414682718341,0.4402542183539166,
	- 0.4415840008368697,0.3505479885894233,0.3943500788462172,
	- 0.43685649380825,0.4748347886538213,0.5050141859852789,
	- 0.5250961060909611,0.5345072780254662,0.5344003893389805,
	- 0.5269837056592495,0.4574833953114167,0.5069750581222974,
	- 0.5525393550046852,0.5900243847437713,0.6159403270481748,
	- 0.6286926742607352,0.6290385665487288,0.6194911060068102,
	- 0.5665551499276381,0.6191962274832306,0.6644606027057701,
	- 0.6977977540386979,0.7162925017359711,0.7197189132272425,
	- 0.7103565350090897,0.6716249671619864,0.7237430894816727,
	- 0.7648128117488485,0.7907287689487973,0.7998964507309693,
	- 0.7936885378432519,0.7661563418365048,0.813819159923423,
	- 0.8474217166041815,0.864080531689031,0.8638072256614686,
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	- -0.3366780195432001,-0.2347914812056201,-0.1282104074092338,
	- -0.0232916058381637,0.07454407090624685,0.1619078867980062,
	- -0.3994539622273614,-0.310067650345868,-0.2090689910564566,
	- -0.101578111712534,0.005791506035575475,0.1068257468493955,
	- 0.1972675814170221,-0.2772576433388097,-0.1784304214682155,
	- -0.07170210104888376,0.0365513498207285,0.1396776293169983,
	- 0.2326162031595532,-0.1447608377351292,-0.04030095729466294,
	- 0.06718993398467658,0.1710983522944223,0.2658045221403088,
	- -0.009369596982657442,0.09582219059763358,0.1990980586833061,
	- 0.2946659462714916,0.1210154650283388,0.2222714245712332,
	- 0.3176193294845107,0.2401157501920485,0.3340749869695284,
	- 0.3444220768905359,0.4715398981500615,0.5369261966393798,
	- 0.5977544079195963,0.6492830104914913,0.6878295422870739,
	- 0.7119297300805439,0.7225291958412279,0.5754139764385705,
	- 0.6438104077520811,0.703735439041779,0.7501803284162304,
	- 0.7802875102236209,0.7941684049065568,0.6769937335137454,
	- 0.7445931056463463,0.7995412648414352,0.8374828910500066,
	- 0.8571440245657689,0.7693422116354997,0.8318956310273866,
	- 0.8783405275925528,0.9058193343789728,0.8463080799206776,
	- 0.900346626617332,0.936383240514816,0.9043683688324304,
	- 0.948119268339247,0.9433248910510675,0.2730237834281818,
	- 0.3918812540743772,0.512863760525918,0.6286055997510109,
	- 0.7317788088844818,0.817202970027369,0.883018402482024,
	- 0.3144121837974857,0.4374900830135051,0.559528090412838,
	- 0.6724058856901879,0.7691785827023693,0.8460642869454081,
	- 0.3533690330364157,0.4772888327771027,0.5965106290979496,
	- 0.7030444104060292,0.7911990697093608,0.3869476434981415,
	- 0.5079274002472546,0.6208051861357136,0.718636116718038,
	- 0.4127894497989522,0.5275207205127158,0.631704463913464,
	- 0.4298578384111184,0.536188255170367,0.4385954324163403 };
	-
	- auto pointshell
	- = new vnl_matrix_fixed<double, 3, 812>(coords);
	-
	- return pointshell;
	- }
	-};
	-
	-
	-template<> class PointShell<1002, vnl_matrix_fixed<double, 3, 1002> >
	-{
	-public:
	- static vnl_matrix_fixed<double, 3, 1002>* DistributePointShell()
	- {
	- double coords[3*1002] = {
	- 0.9756767549555488,0.9910244201339067,0.9977154378498742,
	- 0.9927800993607139,0.9738192119472443,0.9397937974509784,
	- 0.8915721200771204,0.8318778673129345,0.7646073555341725,
	- 0.693869346809198,0.6231965669156312,0.9833704607135893,
	- 0.9964241736681655,0.9989802553190876,0.987902775761947,
	- 0.9610864540427623,0.9183225885811028,0.8616492668438125,
	- 0.7948923552800862,0.7226196323725681,0.6490709211350905,
	- 0.9817040172417226,0.9905693687720445,0.9870396762453547,
	- 0.9681598062324672,0.9325589150767597,0.881205326354676,
	- 0.8173592116492303,0.7456638277324369,0.6708930871960926,
	- 0.9679134019101711,0.9705588332310378,0.959200825309353,
	- 0.9315264271335991,0.8872988802116832,0.8287690756632178,
	- 0.7601362175694236,0.6863342915062906,0.9399233672993689,
	- 0.934650496070032,0.9144882783890762,0.8781852416959071,
	- 0.8267930935417315,0.7635949206829796,0.6931818659696647,
	- 0.8971014254962764,0.8830745457598012,0.8543282347786828,
	- 0.8108509720355672,0.754782849204541,0.6899186612252973,
	- 0.8407280774774689,0.8182890571891552,0.782394344826989,
	- 0.7341199823031558,0.6762337155773353,0.7738549713477869,
	- 0.7444263912611687,0.7036087793266443,0.6531781708866408,
	- 0.7005607434301688,0.6661985543964391,0.6228579759074076,
	- 0.6249824933683414,0.5878380796842572,0.5505632701289798,
	- 0.4375940376503738,0.3812939184075813,0.3153040621970065,
	- 0.2399906033000567,0.1569517536476641,0.06907711216819173,
	- -0.01984099037382634,-0.1058738447453135,-0.1857690950088067,
	- -0.2574501777461976,-0.3200730131503601,0.4806956770236153,
	- 0.4221182950629059,0.3527542025586833,0.2732412963568581,
	- 0.1857299193159225,0.09380763985613347,0.001855404825389049,
	- -0.08593912303271299,-0.1664330628904374,-0.2378914640002027,
	- 0.5232435944036425,0.4619857831524665,0.3889403678268736,
	- 0.305177254463085,0.2135250052622625,0.1182658918935892,
	- 0.02420694871807206,-0.06444621903648747,-0.1448539951504302,
	- 0.5629325029626137,0.4984853033494325,0.4215263456365218,
	- 0.3337322884960374,0.2386638182445053,0.1411593054699449,
	- 0.04617547921974115,-0.04233031957129997,0.5971534158422009,
	- 0.5290500940108692,0.4482053228282282,0.3570208135159443,
	- 0.2597018771197477,0.1613609902081595,0.06677517278138323,
	- 0.6235168560971456,0.5515679242489461,0.4673132571654228,
	- 0.3738575901923395,0.2758011201251887,0.1781713819192711,
	- 0.6404616222418184,0.5649656062523414,0.4782876117785159,
	- 0.3840417218310146,0.2868761951248767,0.6476575150457713,
	- 0.5694506961858633,0.481712063543859,0.388259258354853,
	- 0.6459894362878276,0.566293293292668,0.4789651252338281,
	- 0.6371661773752719,0.5573232120043787,0.3200724178002418,
	- 0.4063802566221164,0.4973180497018747,0.5897273522875156,
	- 0.6793811951363423,0.7616224484252742,0.8323587928990375,
	- 0.889001584581435,0.9308933612987835,0.9590813334864968,
	- 0.3615817483188572,0.4535168742898277,0.5491779429163389,
	- 0.64449992308253,0.7344437631005388,0.8139835008962493,
	- 0.8793283338489147,0.9287763706314454,0.9627864725173401,
	- 0.4036036036586492,0.499949320334643,0.5984781165037405,
	- 0.6942590478190055,0.7817280923310203,0.8559922020830166,
	- 0.9140795130247613,0.9554674311422222,0.4441835036049274,
	- 0.5429866860840018,0.6418227066741695,0.7351609508563529,
	- 0.8174230627001258,0.8844224346157006,0.9343673632346869,
	- 0.4809905907165384,0.5797158369815773,0.6759621154318279,
	- 0.7640818148143264,0.8390728924802671,0.897874775015538,
	- 0.5117469206751248,0.6076796078041039,0.6986831899155831,
	- 0.7795497616193484,0.8462988042859838,0.5347729120192694,
	- 0.6255452713743446,0.7094340284155564,0.7820975288082114,
	- 0.5493993272212266,0.633404689923654,0.7093243648499448,
	- 0.5560356639783846,0.6325607438661257,0.5558948726075613,
	- 0.2502538949373057,0.2834596649308375,0.3171352000240629,
	- 0.3497321770767574,0.3793963897789465,0.4043068999720242,
	- 0.4231100429674418,0.4352503773152589,0.4410301813437042,
	- 0.4413950384816501,0.3401627625801983,0.3789979847088327,
	- 0.4171897539368579,0.4525063773118708,0.4825397797856335,
	- 0.5052684266816663,0.5196090830694199,0.5256607773912181,
	- 0.5245227828309349,0.5178400854028183,0.4357529867703999,
	- 0.479500221024681,0.5208717223808415,0.5569598687552583,
	- 0.5850086433327374,0.6031754713474787,0.611055499882272,
	- 0.6096654752354952,0.6009463532173235,0.5339523560360242,
	- 0.5809954188619362,0.6233304915365264,0.6575940739282847,
	- 0.6811006607903708,0.6926539121832439,0.6928333109300957,
	- 0.6836092937706954,0.6305067000562991,0.6783846661286849,
	- 0.7188806066405239,0.7486166997908829,0.7654898954879897,
	- 0.7692993175005894,0.7616477696596397,0.7205836671095895,
	- 0.7663950141411601,0.8022874547238388,0.8253952737866894,
	- 0.8345810205360885,0.8306996157029517,0.7997756996573342,
	- 0.8408319454787708,0.8700831379830764,0.8855671363619817,
	- 0.8872031228985237,0.8650978792558638,0.8995240516802058,
	- 0.921218286608597,0.9292366279325103,0.9155019734809123,
	- 0.9425022788739567,0.9568003701205341,0.951723763021908,
	- 0.9714657198391669,-0.4375932291383153,-0.3812932275173999,
	- -0.3153035222278598,-0.2399902437364576,-0.1569515927579475,
	- -0.06907715072573904,0.0198407706589918,0.1058734766109667,
	- 0.1857686171195431,0.257449626507278,-0.3570040493097855,
	- -0.2918648787974354,-0.2168311251285635,-0.1330995445648626,
	- -0.04332608784719146,0.04859599442048472,0.1382857743932946,
	- 0.2218613031927873,0.2966853245585511,-0.2644927501381796,
	- -0.1901399993818987,-0.1064219080255857,-0.01561852722247663,
	- 0.07849995612144045,0.1712924506084217,0.2583107784678281,
	- 0.3362909838861173,-0.1610782390926968,-0.0780603807507026,
	- 0.01281177251559359,0.1081011253085713,0.2031694108248999,
	- 0.2931782765634202,0.3742486038435638,-0.04938676750055992,
	- 0.04056537812597379,0.1358448755096817,0.232090324110116,
	- 0.3243479900672576,0.4082538491780348,0.06640211724156458,
	- 0.1604512568352431,0.2565833049862117,0.3500388266409877,
	- 0.436217636937124,0.1811879481039926,0.2758835926122972,
	- 0.3692668145365748,0.4568072375603044,0.2900013554556395,
	- 0.3820078910424991,0.4697464271137876,0.3890115016151001,
	- 0.4757292848583335,0.4760519631420977,-0.6231952788307174,
	- -0.5646794654796425,-0.4943551945928708,-0.4121616924667699,
	- -0.319458133528771,-0.2192092047974507,-0.1156489798772063,
	- -0.01344431006605927,0.08328895892415776,0.1716736688754058,
	- -0.5573220717056252,-0.4899613221250736,-0.4101426439397438,
	- -0.3185871044669488,-0.2177607050610849,-0.1117914195951733,
	- -0.005729665044898873,0.09558913699521315,0.1885288856066103,
	- 0.2710751964644532,-0.4789641985801549,-0.402057686424166,
	- -0.3127252940830145,-0.2127814923512051,-0.1059392282183739,
	- 0.002692533596869102,0.1077444781964869,0.2048204657664428,
	- 0.2912280153186658,-0.3882586050506625,-0.3019152874380811,
	- -0.2041697091828281,-0.09809683500613878,0.01149943312218195,
	- 0.1190413522149791,0.2195138260022026,0.3094968646292108,
	- -0.2868758523956744,-0.1923492526670043,-0.08856892011805101,
	- 0.02025987059937257,0.1287405357080231,0.2315279747463358,
	- 0.3245517154572714,-0.1781713502362079,-0.07790941981152795,
	- 0.02852799618806018,0.136265045008317,0.2399985475821452,
	- 0.3352293490184233,-0.06677541204276306,0.035950103618558,
	- 0.1413542883070481,0.2445218382684434,0.3408430926744944,
	- 0.04232987969953258,0.1440992946503647,0.2452457212250337,
	- 0.3413681152295799,0.1448534358763926,0.2427634183836315,
	- 0.3374016489097037,0.2378908589603879,0.3299350928268919,
	- -0.2502532651867688,-0.2834590071461157,-0.3171345072414974,
	- -0.3497314427767591,-0.3793956104585266,-0.4043060780204903,
	- -0.4231091882680272,-0.43524950627169,-0.4410293135613324,
	- -0.4413941927799012,-0.1793269230918291,-0.2096296374650262,
	- -0.2404488793458187,-0.2702796532141552,-0.2973713527283103,
	- -0.3200999575733405,-0.3373822412281449,-0.3489197313348205,
	- -0.3551542383465527,-0.09929959410007272,-0.1260192341590947,
	- -0.1535127609134815,-0.1804461251889914,-0.2052877394623771,
	- -0.2266616403246165,-0.2436963810571767,-0.2561842894548281,
	- -0.01142151773467507,-0.034316887225212,-0.05856032689489409,
	- -0.08307746147223684,-0.1065840014642066,-0.1278836167145054,
	- -0.1461545898453977,0.08175409117371149,0.06228642306456245,
	- 0.04056025153798869,0.01740518175433122,-0.006048944565669369,
	- -0.02862806146519492,0.1765178736510397,0.1594436875323896,
	- 0.1389956691289133,0.1158878972138483,0.09125781311736192,
	- 0.2686152102237028,0.2525244737680689,0.2319923070602857,
	- 0.2077893717181683,0.3541399826172473,0.3376577748776239,
	- 0.3159635830269856,0.430309819720559,0.4124399032037845,
	- 0.4957938830064738,-0.975676581463901,-0.9910243213530433,
	- -0.9977153903038788,-0.9927800571163499,-0.9738191090293654,
	- -0.9397935597648752,-0.8915716840571059,-0.8318771966689975,
	- -0.7646064477130079,-0.6938682276631534,-0.9714655004610564,
	- -0.983887723902267,-0.9858981447798461,-0.9744145976009966,
	- -0.9473804480134012,-0.9046164166427493,-0.8481606115014303,
	- -0.7818095106057968,-0.7100822624036758,-0.6371649246085965,
	- -0.9568001079664734,-0.9644051676944579,-0.9598482725023617,
	- -0.9402907381732713,-0.9044523389503778,-0.8533359449908623,
	- -0.7901672201648241,-0.7194988284538555,-0.6459882395962464,
	- -0.9292363237529666,-0.9300944286029187,-0.9173973041924147,
	- -0.8890014167596085,-0.844773720173384,-0.7869651249304563,
	- -0.7196711542084638,-0.6476563908917461,-0.8872027729137049,
	- -0.8798270414245473,-0.8582754834679532,-0.8214852287823353,
	- -0.7705800268610806,-0.7087709559526547,-0.6404605781008121,
	- -0.8306992108488226,-0.8145452502402749,-0.7846557072154475,
	- -0.7411783184941589,-0.6862531911113832,-0.6235158879179116,
	- -0.7616472974254324,-0.73736034048619,-0.7008201753656432,
	- -0.6531910402117445,-0.5971525097007422,-0.6836087421746132,
	- -0.652851924507533,-0.612034208511092,-0.5629316404694558,
	- -0.6009457148226922,-0.5659076360456838,-0.5232427588825813,
	- -0.5178393593330568,-0.4806948574024101,0.5646808729466086,
	- 0.4943566966479628,0.4121632456350594,0.3194596781650836,
	- 0.21921067448898,0.1156503154178581,0.013445471844618,
	- -0.0832879858164388,-0.1716728777368211,0.5865775784632071,
	- 0.5109645672417243,0.4225383974740667,0.323390011818691,
	- 0.2174206286797427,0.1096806787773226,0.005232361633134523,
	- -0.09191315247018395,0.6036999320472409,0.5222841738261358,
	- 0.4275626351684279,0.3225497922064885,0.2120884454656291,
	- 0.1018140973507329,-0.003178626653090429,0.6137659240175044,
	- 0.5263406106031267,0.4258274919194899,0.3162311593161161,
	- 0.2031293654582096,0.09233653282973062,0.6148617703985678,
	- 0.5217885230992481,0.4167137837086616,0.3044789836562512,
	- 0.190984387847104,0.6060496757760786,0.5084224141934828,
	- 0.4006853449688581,0.2881416501332511,0.5877496225758772,
	- 0.4873191346491355,0.3791778875849738,0.5616447830131567,
	- 0.460498372897877,0.5301563765120954,-0.4063806941036804,
	- -0.4973183240635209,-0.5897274724251101,-0.6793811856410323,
	- -0.7616223457476226,-0.8323586364840968,-0.8890014069516364,
	- -0.9308931819742911,-0.9590811587055613,-0.3299355917757612,
	- -0.4201916721510849,-0.5144019383498233,-0.6086443620415749,
	- -0.6980092714824531,-0.7775489279696631,-0.8434725272922868,
	- -0.8939999530932097,-0.9294606883512702,-0.9517235558231533,
	- -0.3374020539278631,-0.4303972015599547,-0.5261951664998159,
	- -0.6201746406216091,-0.7070125356849136,-0.7819076179156583,
	- -0.8417962075837926,-0.8859147779324957,-0.9155017573317124,
	- -0.3413684282280401,-0.4354200733480757,-0.5306961815651272,
	- -0.6221165659419365,-0.7043785843697545,-0.7732956289121359,
	- -0.8268002829198581,-0.8650976752328781,-0.3408433114184408,
	- -0.4339783095259441,-0.5265312606271311,-0.6133559560669121,
	- -0.6896418460594331,-0.752136864699832,-0.7997755164970677,
	- -0.3352294641675141,-0.4255076064827776,-0.5134721858345982,
	- -0.594338662260662,-0.6641265172984932,-0.7205834943870382,
	- -0.3245517106425898,-0.4104116666038574,-0.4925847482169691,
	- -0.5669637398252093,-0.6305065080228541,-0.3094967204309826,
	- -0.3899712787954628,-0.4658908667926167,-0.5339521035735905,
	- -0.2912277152063287,-0.3659561925975448,-0.4357526334612896,
	- -0.2710747314715586,-0.3401622786069621,0.7100833249889532,
	- 0.78181034476627,0.8481612032420389,0.9046167870637368,
	- 0.9473806530146282,0.9744147135590244,0.9858982469324079,
	- 0.9838878689052019,0.7194998173208004,0.7901679726328494,
	- 0.8533364642620689,0.9044526665335126,0.9402909454666769,
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	- 0.1416474750285941,0.02151295276860444,0.4536241369952758,
	- 0.3387563694841473,0.2185284943201295,0.09867487876932232,
	- 0.4027080566573236,0.2886989329203987,0.1721561104744125,
	- 0.3502038519557472,0.2393267951217032,0.298654161645374,
	- -0.984713259051105,-0.9959947612173518,-0.9943464342167785,
	- -0.9773096457316496,-0.9442212908026748,-0.8966583408378461,
	- -0.8380826821486993,-0.772858299407996,-0.9933753694301851,
	- -0.999553621201999,-0.9908225482912788,-0.9653354239158236,
	- -0.9235419454230499,-0.8682642090770526,-0.8038809644055149,
	- -0.9889450353591552,-0.9880324674077218,-0.9708623496514911,
	- -0.9366415263248317,-0.8871116184521261,-0.8261317121277938,
	- -0.9690767381494427,-0.9597077173597477,-0.9338032828335274,
	- -0.8918540989344099,-0.8367235291009597,-0.9332440544501512,
	- -0.9151716624555581,-0.881531417418751,-0.8339792023300259,
	- -0.8831547498989281,-0.8573751662344773,-0.8180295248104962,
	- -0.8223661602728524,-0.7907838386634013,-0.7552871860588483,
	- -0.3111396248637522,-0.3635623115811258,-0.4149325617880891,
	- -0.4623636071651684,-0.503096462804278,-0.5351898259002444,
	- -0.5579572907903124,-0.5719400747815568,-0.5785069283639182,
	- -0.2479344056308305,-0.2980738893651726,-0.3469143327715778,
	- -0.3916343988495664,-0.4297390036046975,-0.4596955428592778,
	- -0.4812083484887336,-0.4950341577852201,-0.1764988082863052,
	- -0.2237521076309895,-0.2697404459306319,-0.3118674408741246,
	- -0.3479890956417611,-0.3769275248330646,-0.3985931343359159,
	- -0.09893938901501213,-0.1432117197792371,-0.186579712833973,
	- -0.2267418620329016,-0.2618707421483436,-0.2909964852939082,
	- -0.01853073419918189,-0.06025216482046628,-0.1016644832117871,
	- -0.1407292340032114,-0.1758296738027379,0.06089493100791283,
	- 0.02097514873862574,-0.01927652693035482,-0.05800679989935065,
	- 0.1358108258261833,0.09693185715603557,0.0572108907410362,
	- 0.2036932746994002,0.1653145532988453,0.2632739407438701,
	- -0.5471131012749936,-0.4569196340994406,-0.3535541587646317,
	- -0.2398162730231354,-0.1203709912173413,-0.0009109877496780188,
	- 0.1131254888510733,0.2176599356582619,-0.478328705556794,
	- -0.3786231842883476,-0.2666208448402719,-0.1464197032303796,
	- -0.02374523314186032,0.09531724619007391,0.2057254392916539,
	- -0.3977013270678494,-0.2894249268534429,-0.1708861328457008,
	- -0.04735264212838212,0.07488848723411734,0.1900372836013431,
	- -0.3071060284643041,-0.1924163631703616,-0.07055027067676212,
	- 0.05252803743712917,0.1706750855887899,-0.2100906838592314,
	- -0.0921575105240425,0.02928029003178066,0.1482451448989572,
	- -0.1112789754160983,0.006318730357784829,0.123816455924515,
	- -0.01532906198457091,0.09867995232819112,0.07404761591340303,
	- -0.5229702552542058,-0.455754381535759,-0.3771270572800299,
	- -0.2889439451759633,-0.194672902916372,-0.09880682824059986,
	- -0.005851780927923981,0.08061942171187554,0.1584410564110822,
	- -0.4301068723700084,-0.3534800054422614,-0.2664452641642683,
	- -0.1720548071373146,-0.07475800001082551,0.02057294660420643,
	- 0.1097762759917693,0.190134278339324,-0.324239892584746,
	- -0.2391265604455334,-0.1457556026172962,-0.04825796103784657,
	- 0.04840435106572794,0.1396272041512353,0.2221350978923813,
	- -0.2083325524549613,-0.1169519894866824,-0.02046779780351893,
	- 0.07636807502743861,0.1687516747481361,0.2529338262925594,
	- -0.08719102201021951,0.007198147474544054,0.1030417934166896,
	- 0.1956221602390349,0.2808952005684322,0.03341116907881747,
	- 0.1271908635410245,0.2189580303556818,0.3046134343217798,
	- 0.1480334302314487,0.2380139721282078,0.323237313179716,
	- 0.2526632136782334,0.3366066958443542,0.3451570696887505,
	- 0.4547190651923899,0.5133917435529424,0.5694125552964621,
	- 0.6193373643788831,0.6600701990863211,0.6896697595590643,
	- 0.7077866317530298,0.7155194029861072,0.5475936980371527,
	- 0.6094980941008995,0.6660993907770576,0.7135382519498201,
	- 0.748924034855715,0.7711196978950583,0.7808675744788959,
	- 0.6399396139686974,0.7025299057553986,0.7567806697847073,
	- 0.7989076596939885,0.8267668794191896,0.8403683088289017,
	- 0.7268356797799225,0.7870198804193677,0.8359668400797895,
	- 0.8705500304441893,0.8897670473314109,0.803401239536944,
	- 0.858215507236093,0.8996278379610205,0.9255997745502057,
	- 0.8659872391476647,0.9132984713369965,0.9461587349139229,
	- 0.9129980537560551,0.9518770467134829,0.9449458910860361,
	- 0.2573950079345842,0.363089267383967,0.4717819390919956,
	- 0.5783933464143868,0.6773888186481814,0.7640503132419058,
	- 0.835538996354342,0.8912340245126464,0.2942468056901541,
	- 0.403998910419839,0.5147136234231619,0.62060207699311,
	- 0.7160073275453937,0.7967976318501995,0.8611864392751584,
	- 0.3298234714814622,0.4413854454351217,0.5513863234589741,
	- 0.6537700563672823,0.7433259842576552,0.8169373645440049,
	- 0.3620182543235557,0.4726965405256068,0.5791764634315589,
	- 0.6757048258462731,0.7580000771779366,0.3888887347419664,
	- 0.4960228623929952,0.5966697046150125,0.685875099677583,
	- 0.4091542831822379,0.5106167801856609,0.6039998362037971,
	- 0.422484479771868,0.5169744155067602,0.4294387727293252 };
	-
	- auto pointshell
	- = new vnl_matrix_fixed<double, 3, 1002>(coords);
	-
	- return pointshell;
	- }
	-};
	-
	-
	-// ThreeLayerPointShell using a staggered-distribution
	-#include <itkMacro.h>
	-
	-template<int NpointsShell1, int NpointsShell2, int NpointsShell3, class TMatrixTypeshell1, class TMatrixTypeshell2, class TMatrixTypeshell3>
	-TMatrixTypeshell1 *
	-ThreeLayerPointShell< NpointsShell1, NpointsShell2, NpointsShell3, TMatrixTypeshell1, TMatrixTypeshell2, TMatrixTypeshell3>
	-::DistributePointShell1()
	-{
	- itkGenericExceptionMacro(<<"This type of PointShell is not Supported and should not be used!");
	- return 0;
	-}
	-
	-template<int NpointsShell1, int NpointsShell2, int NpointsShell3, class TMatrixTypeshell1, class TMatrixTypeshell2, class TMatrixTypeshell3>
	-TMatrixTypeshell2 *
	-ThreeLayerPointShell< NpointsShell1, NpointsShell2, NpointsShell3, TMatrixTypeshell1, TMatrixTypeshell2, TMatrixTypeshell3>
	-::DistributePointShell2()
	-{
	-itkGenericExceptionMacro(<<"This type of PointShell is not Supported and should not be used!");
	-return 0;
	-}
	-
	-template<int NpointsShell1, int NpointsShell2, int NpointsShell3, class TMatrixTypeshell1, class TMatrixTypeshell2, class TMatrixTypeshell3>
	-TMatrixTypeshell3 *
	-ThreeLayerPointShell< NpointsShell1, NpointsShell2, NpointsShell3, TMatrixTypeshell1, TMatrixTypeshell2, TMatrixTypeshell3>
	-::DistributePointShell3()
	-{
	- itkGenericExceptionMacro(<<"This type of PointShell is not Supported and should not be used!");
	- return 0;
	-}
	-
	-
	-
	-//Distributed Pointshell 7 - 16 - 22
	-
	-template<> class ThreeLayerPointShell<7,16,22, vnl_matrix_fixed<double, 3, 7>,vnl_matrix_fixed<double, 3, 16>,vnl_matrix_fixed<double, 3, 22> >
	-{
	-public:
	- static vnl_matrix_fixed<double, 3, 7>* DistributePointShell1()
	- {
	- double coords[3*7] = {
	- 0.8134386897688890,-0.4341253640420510,0.3871080808797820,
	- -0.4587290424636170,-0.8386718051774130,-0.2935937138306440,
	- 0.9664216428893120,0.2069240694656700,-0.1523536597226610,
	- 0.2351246687899070,-0.9681943247699460,0.0855344352275928,
	- 0.3639220075873960,0.5047564346894090,-0.7828037519284090,
	- 0.5319989685716170,-0.4881652317616310,-0.6918611160759410,
	- 0.3581867553682760,0.1086899080235520,0.9273018668009770
	- };
	- auto pointshell
	- = new vnl_matrix_fixed<double, 3, 7>(coords);
	-
	- // List sorted for each row [x,y,z]
	- // pointshell need [x...x
	- // y...y
	- // z...z]
	- int i=0;
	- for(int c =0; c < 7; c++)
	- {
	- for(int r=0; r<3; r++){
	- pointshell->put(r,c,coords[i++]);
	- }
	- }
	-
	- return pointshell;
	- }
	-
	- static vnl_matrix_fixed<double, 3, 16>* DistributePointShell2()
	- {
	- double coords[3*16] = {
	- -0.5452474978820280,0.0761974966412968,0.8348048320170320,
	- 0.2927980757498900,-0.6773379396203400,0.6748945120446840,
	- -0.1417004162163040,-0.9633970491958960,0.2275678308653590,
	- -0.6140671213404080,0.1662941114081500,-0.7715360257302810,
	- -0.7535977994952050,0.5644302557976330,0.3369107343736630,
	- 0.6046201505721580,-0.7556729189381400,0.2517794930204040,
	- -0.5761191698601790,-0.6394532899960390,0.5091033215692650,
	- -0.8771756234198420,-0.0996725024517006,0.4697108876032420,
	- 0.1777092608486050,-0.9423569168215250,-0.2835187117762620,
	- -0.9768429239415920,0.1642087829444060,-0.1371618662353210,
	- -0.1487223091187880,0.6561163072920720,0.7398601665691900,
	- 0.8263922468011810,0.2709995685589460,0.4935940520992520,
	- 0.0308686015665059,0.1530129849183750,0.9877419480227090,
	- 0.4225700117384330,0.6462523317724860,0.6354467002495210,
	- 0.7837589636894810,0.6201599634850410,0.0335187488821074,
	- 0.0539036789368123,0.3663544585938050,-0.9289126999161520
	- };
	- auto pointshell
	- = new vnl_matrix_fixed<double, 3, 16>(coords);
	- // List sorted for each row [x,y,z]
	- // pointshell need [x...x
	- // y...y
	- // z...z]
	- int i=0;
	- for(int c =0; c < 16; c++)
	- {
	- for(int r=0; r<3; r++){
	- pointshell->put(r,c,coords[i++]);
	- }
	- }
	-
	- return pointshell;
	- }
	-
	- static vnl_matrix_fixed<double, 3, 22>* DistributePointShell3()
	- {
	- double coords[3*22] = {
	- -0.8173635684245140,-0.4833486694613540,0.3135137329404920,
	- -0.2868452120883920,-0.8216012153929990,0.4926370541957950,
	- -0.7664861123034300,0.2467518351336330,0.5929692837779680,
	- -0.6473847770633690,-0.2749696442612980,0.7108337676007140,
	- -0.8434413337089970,0.5359848183688930,-0.0364278886191929,
	- -0.6982955004575730,-0.6008181795242910,-0.3891026974897790,
	- -0.1840600867015900,-0.4748774851820570,-0.8605889021772050,
	- -0.5838330320870200,0.5227863025561340,-0.6211549504783510,
	- 0.2399013062530760,-0.8837050331449780,0.4018865233524250,
	- 0.2572284397529420,0.1068009420516400,-0.9604306786849050,
	- 0.0228576846453402,0.6541700548957510,-0.7560020274644400,
	- 0.2865351008629760,-0.2558878809381770,0.9232654159895800,
	- -0.9589554732993380,0.1841748711215180,0.2156015238272050,
	- -0.1416546797498710,-0.9826949020935590,-0.1193510833813020,
	- 0.5319624136210260,0.8404508833828820,-0.1032390580905500,
	- -0.9539866018255820,-0.2464051857069770,-0.1708626582784740,
	- -0.5967074337720730,-0.2735711735415940,-0.7543865398376490,
	- -0.8579620414436700,0.0965216321209641,-0.5045638809650520,
	- 0.4190874972849550,-0.7580966160880540,-0.4996550713194790,
	- -0.1112620377459570,-0.8350080959462270,-0.5388712635322760,
	- 0.2732684357685670,-0.3457098692283190,-0.8976686740277500,
	- -0.5333383595673660,0.8405849409324210,0.0946950436486956
	- };
	- auto pointshell
	- = new vnl_matrix_fixed<double, 3, 22>();
	-
	- // List sorted for each row [x,y,z]
	- // pointshell need [x...x
	- // y...y
	- // z...z]
	- int i=0;
	- for(int c =0; c < 22; c++)
	- {
	- for(int r=0; r<3; r++){
	- pointshell->put(r,c,coords[i++]);
	- }
	- }
	-
	- return pointshell;
	- }
	-};
	-
	-//Distributed Pointshell 15 - 30 - 45
	-
	-template<> class ThreeLayerPointShell<15,30,45, vnl_matrix_fixed<double, 3, 15>,vnl_matrix_fixed<double, 3, 30>,vnl_matrix_fixed<double, 3, 45> >
	-{
	-public:
	- static vnl_matrix_fixed<double, 3, 15>* DistributePointShell1()
	- {
	- double coords[3*15] = {
	- -0.8262066830854160,-0.4726354124122490,0.3065913954417130,
	- -0.1648544111105980,-0.8594278487393920,-0.4839491666988980,
	- -0.0358642514967783,-0.3860637871945480,-0.9217746512470260,
	- -0.7684991573547760,0.6362727605963740,-0.0675723261999100,
	- 0.1470231744209000,-0.2445782513554300,0.9584183142798970,
	- -0.4269215415769730,0.7783400701208900,0.4603528348796690,
	- 0.3354375712062210,0.5671194195694440,-0.7522348036155240,
	- 0.4782763791345030,0.8758625019989820,-0.0641606012602034,
	- 0.9898549006984430,0.0293790674196844,0.1390113159452260,
	- -0.6942246846812260,0.1045517495672360,-0.7121243001342390,
	- -0.5002034766634700,0.0396563572397201,0.8649993383027830,
	- -0.3370551539814700,0.7499893159794020,-0.5691307838197430,
	- -0.8609008763099680,0.2402687527531810,0.4484647228257290,
	- -0.6557865116475140,-0.4999608118385060,-0.5656706088944040,
	- -0.0693103556967315,0.9875634181798020,-0.1411189911607090
	- };
	- auto pointshell
	- = new vnl_matrix_fixed<double, 3, 15>(coords);
	-
	- // List sorted for each row [x,y,z]
	- // pointshell need [x...x
	- // y...y
	- // z...z]
	- int i=0;
	- for(int c =0; c < 15; c++)
	- {
	- for(int r=0; r<3; r++){
	- pointshell->put(r,c,coords[i++]);
	- }
	- }
	-
	- return pointshell;
	- }
	-
	- static vnl_matrix_fixed<double, 3, 30>* DistributePointShell2()
	- {
	- double coords[3*30] = {
	- 0.2837014644823930,-0.2206420544708420,-0.9331830275189480,
	- 0.6952056236193340,-0.1366087970901870,-0.7057104062188850,
	- -0.3982427056422320,-0.8946622247526970,-0.2024407345454680,
	- 0.6912813662578750,0.2350369054844600,0.6832918305709010,
	- 0.3004304980870820,0.2618613453462440,0.9171532868788080,
	- -0.8122424463478870,0.2721420733854360,-0.5159466060013130,
	- 0.9419343376574850,0.3217426374876110,-0.0961320901898529,
	- 0.7896221636664980,0.5657937790715650,0.2374325971945600,
	- 0.4752045378048260,-0.5551457462701800,0.6826374203395420,
	- 0.7035350948936570,-0.6486284012073840,0.2903783177169470,
	- -0.9657370911439440,0.2516454388878180,-0.0634542660172643,
	- 0.4335627021602730,0.7069616605804370,-0.5587741885277380,
	- -0.8057237269560320,0.4981857033689590,0.3203440038128640,
	- 0.9405564452144110,-0.0095010729465114,-0.3395044962566700,
	- 0.1927525893653990,0.9455549503304530,-0.2622446857393060,
	- 0.0977862568275677,-0.8610667582542970,-0.4990008875794600,
	- -0.9244603975979140,-0.1428771862175540,-0.3534955203841470,
	- -0.0587838438498267,0.9919184790835770,0.1124374962135020,
	- 0.0413372764424745,-0.4921846796379190,0.8695087525183610,
	- -0.0416085831127836,0.5985263605884460,0.8000218256348350,
	- -0.0355639978656969,-0.0871145642116132,0.9955632851597270,
	- 0.4117279464778380,0.2997527998928850,-0.8605976743203040,
	- -0.3489182251383090,0.9011702877335440,-0.2571928938998360,
	- -0.4466362970172200,0.1524928751735680,-0.8816246033363880,
	- 0.7474002986676580,0.3366743112988240,-0.5727505579769920,
	- 0.0459516120636567,-0.8054328299457180,0.5909030426342220,
	- -0.6709586581555420,-0.7177574233281400,0.1861149115559070,
	- 0.4102749262480260,0.6499693688374480,0.6396986043952450,
	- 0.4840608825017460,-0.5520432393197750,-0.6789207052027200,
	- 0.4932109057185150,-0.8496377203461870,-0.1867049722028180
	- };
	- auto pointshell
	- = new vnl_matrix_fixed<double, 3, 30>(coords);
	- // List sorted for each row [x,y,z]
	- // pointshell need [x...x
	- // y...y
	- // z...z]
	- int i=0;
	- for(int c =0; c < 30; c++)
	- {
	- for(int r=0; r<3; r++){
	- pointshell->put(r,c,coords[i++]);
	- }
	- }
	-
	- return pointshell;
	- }
	-
	- static vnl_matrix_fixed<double, 3, 45>* DistributePointShell3()
	- {
	- double coords[3*45] = {
	- -0.5319244251302650,-0.0924062555950406,-0.8417348097095310,
	- -0.1568078023044440,-0.3505682049930730,0.9233164391390330,
	- -0.0268033601770698,0.1671912039337100,0.9855600850330810,
	- -0.8635644949706830,0.4302558439150240,-0.2629377717312540,
	- -0.1232991287092530,-0.6582015219317060,0.7426762965022680,
	- 0.2376788616301610,0.5073218686335690,0.8283316246168160,
	- -0.2566320540992200,0.7153437906464810,0.6499409588511380,
	- -0.2043674419674510,0.6455892128571940,-0.7358318536908470,
	- 0.4526173742466210,0.8360898783655450,-0.3099858510073980,
	- 0.6836009409422150,-0.5146343588192300,0.5175337962545400,
	- -0.2416560443524480,-0.0050416195905518,-0.9703488745290690,
	- 0.6217071536966980,0.1629149642421430,-0.7661193963530300,
	- 0.3925487362456630,0.8090879125984540,0.4373582505898420,
	- 0.9937673576390050,0.0621775579881003,-0.0925223766114162,
	- -0.6145262933579910,0.6346672434383510,0.4685668841030610,
	- 0.8259615790179220,0.5617603544414460,-0.0470401335461508,
	- -0.9322660404149650,-0.3254138676429420,-0.1580691134746520,
	- 0.1164156506796110,-0.9181409097759250,0.3787672980507660,
	- 0.3168138266596370,-0.3901334055493560,0.8645374052704360,
	- 0.2176339314862630,0.9758048396839600,-0.0209853929005879,
	- -0.8962471871878890,-0.2522993236544900,0.3648095814822890,
	- -0.6612497786305060,-0.6092040683197140,0.4377432277075390,
	- 0.6864998437314790,-0.7035766895855040,-0.1835696228371040,
	- 0.5089165208574290,0.4070575405636090,0.7584906943850230,
	- -0.8813116916999880,0.4680173236355270,0.0651880882519394,
	- -0.2012114505332470,-0.8431942495440670,0.4985352642593330,
	- 0.5022346836643460,-0.7613661632799880,0.4099779115231480,
	- 0.2920837705654530,0.0626526547841476,-0.9543383654767130,
	- 0.9371632886212690,-0.1374669688206610,0.3206677454060930,
	- 0.5505816317240350,0.4677412077906900,-0.6914318689087190,
	- -0.7167807102053720,0.3777968874482810,0.5860844011845660,
	- -0.2932320783275170,0.9560381526252190,-0.0024492784000661,
	- 0.6321152281530360,0.6671359233891630,0.3941573265343710,
	- 0.8208025699405450,0.0279728493062268,-0.5705266522088930,
	- -0.2446598581934500,0.4624912733458210,0.8521991409686590,
	- 0.5981132830055560,-0.3201976866112960,0.7346658711149490,
	- 0.5635872282435520,-0.8205568040328310,0.0951628473521853,
	- 0.8170510623081950,0.3573123713720030,0.4524990948560730,
	- -0.1077825148871900,-0.7347609483441290,-0.6697083531456270,
	- -0.9500761846368700,0.2288974134306240,0.2120406034480560,
	- -0.2525195159846320,0.9165943360942510,0.3099818012187580,
	- -0.1132939165725980,-0.9559551317814730,-0.2707660881430790,
	- 0.6286490080714330,0.7713217806218580,0.0993133192936744,
	- 0.8227143106676380,0.0339170261757165,0.5674423304249230,
	- -0.5076617466917020,0.3007946007639900,0.8073426528415060
	- };
	- auto pointshell
	- = new vnl_matrix_fixed<double, 3, 45>();
	-
	- // List sorted for each row [x,y,z]
	- // pointshell need [x...x
	- // y...y
	- // z...z]
	- int i=0;
	- for(int c =0; c < 45; c++)
	- {
	- for(int r=0; r<3; r++){
	- pointshell->put(r,c,coords[i++]);
	- }
	- }
	-
	- return pointshell;
	- }
	-};
	-
	-//Distributed Pointshell 22 - 46 - 67
	-
	-template<> class ThreeLayerPointShell<22,46,67, vnl_matrix_fixed<double, 3, 22>,vnl_matrix_fixed<double, 3, 46>,vnl_matrix_fixed<double, 3, 67> >
	-{
	-public:
	- static vnl_matrix_fixed<double, 3, 22>* DistributePointShell1()
	- {
	- double coords[3*22] = {
	- 0.25642497332897700,0.69733994966702500,-0.66930055106179500,
	- -0.63587617425647900,0.60181880252846700,-0.48319314971980300,
	- 0.02750479511080110,-0.49812287900990700,-0.86667011235694100,
	- -0.35667911834084000,-0.89655924253456900,0.26260527634729500,
	- -0.97064232445283100,-0.10849397816068500,0.21466842963899700,
	- 0.13668042906880200,-0.37888572303413600,0.91529452592620000,
	- 0.51081097493717800,0.82410825259274000,0.24478099577432200,
	- 0.56937377655062700,-0.82148556938178300,-0.03122437948083380,
	- -0.70712711556887700,0.17758768051548200,-0.68442228058149100,
	- 0.77448769645207600,-0.17248893945546000,-0.60861841395893200,
	- -0.10740168736203100,0.99190238197584200,0.06778305232459120,
	- 0.33092898900280500,0.01295617559776370,-0.94356671293102500,
	- 0.96250467033690100,-0.16189196397475400,0.21765971510605600,
	- -0.45033217736158200,0.66660174976094400,0.59400592358024700,
	- -0.85650276118059000,-0.36171210207403600,-0.36819475186809100,
	- 0.27465477100258400,0.05835151655784800,0.95977073162340000,
	- 0.11563788475332800,0.85791228608919200,0.50061401197628500,
	- -0.54693056940441200,-0.44061696250608900,-0.71184523922189100,
	- -0.84737370301991400,0.46653338404151400,0.25358314022247300,
	- 0.81343236730821000,0.56190972107245100,-0.15028389527703900,
	- -0.18653146496488500,0.84209830314271900,-0.50603997907498000,
	- -0.63212021995023600,-0.37635030041830100,0.67733631152118100,
	- };
	- auto pointshell
	- = new vnl_matrix_fixed<double, 3, 22>(coords);
	-
	- // List sorted for each row [x,y,z]
	- // pointshell need [x...x
	- // y...y
	- // z...z]
	- int i=0;
	- for(int c =0; c < 22; c++)
	- {
	- for(int r=0; r<3; r++){
	- pointshell->put(r,c,coords[i++]);
	- }
	- }
	-
	- return pointshell;
	- }
	-
	- static vnl_matrix_fixed<double, 3, 46>* DistributePointShell2()
	- {
	- double coords[3*46] = {
	- -0.23824007219091700,-0.86075578881685600,0.44982345428038400,
	- -0.51769500181405200,-0.84172584112854800,0.15326282482449900,
	- 0.44541900890312100,0.24566021345088800,0.86096049040302900,
	- -0.07063199679231950,-0.74435681728880700,-0.66403618093053200,
	- 0.28462319785348100,0.44431638677441600,-0.84945428581377100,
	- -0.64536739671188300,-0.00105803610891677,-0.76387158856768400,
	- 0.99957798463419400,-0.02741827295649930,0.00959640259292167,
	- 0.25010658086046200,-0.76013925657241700,-0.59969576355667200,
	- 0.39532812932947400,-0.74907082575728600,0.53160941315984400,
	- -0.34325878056226200,-0.92866133182164700,-0.14057574593845400,
	- -0.26920408631492800,0.17274923523146300,0.94746338274272500,
	- -0.54467024543405600,0.38808975702695900,-0.74345185737178700,
	- 0.52496025794034400,0.62807129953803100,-0.57440679860166600,
	- -0.78050768202914100,-0.24385280423360000,-0.57562450274541400,
	- -0.71694800106757700,-0.61231043102019300,0.33325890810159900,
	- -0.79056173292908700,0.40623831712611600,-0.45823855809687000,
	- -0.01131173053347560,-0.71410951594821100,0.69994260049274700,
	- 0.51711028616473900,-0.41981678757221700,-0.74588927919307400,
	- 0.09293538971980670,0.99313719503650500,-0.07100369830262170,
	- 0.06305806394427750,0.10620573522794300,0.99234269402071500,
	- -0.33630459418638300,0.16690245213556600,-0.92684561357340800,
	- -0.91315571223437600,0.04840489638883500,-0.40472658822878600,
	- 0.93648363925049100,-0.29927660444831100,-0.18284394287491200,
	- -0.05612562081659480,-0.20305248576816200,0.97755797920702400,
	- -0.37275429556215800,0.89636189167834400,0.23997832045161700,
	- -0.67013076748237900,0.05267398640468540,0.74037166722512800,
	- -0.71746069173368600,-0.55944913994429100,-0.41505037722258700,
	- 0.32124017988313500,-0.93693212076753000,0.13770601984920100,
	- 0.28299823115899100,-0.54968353921141900,0.78597710391644900,
	- 0.15427673771645000,0.42717011000338400,0.89091210863881800,
	- 0.73177570493927800,-0.66613283838403200,-0.14412272300735500,
	- -0.75153823442269900,-0.65477491803088400,-0.08037467834125450,
	- 0.48366214065856300,0.15108779957940700,-0.86211565959088600,
	- 0.93951136227144300,0.29289842100589400,0.17756383397277200,
	- -0.87960856796377400,0.45546435899697500,-0.13726246700461500,
	- -0.64569564311752200,0.72655108088168600,-0.23494821414239600,
	- -0.78338372249755100,-0.28544299520279600,0.55211614703387900,
	- -0.21774715968345700,0.47658876151730000,0.85173313123606500,
	- -0.02304329061227880,-0.94618817341094000,-0.32279551926107200,
	- -0.57374791604915700,0.69666566365718000,0.43066260797792600,
	- -0.07108119393689040,0.93003463387864700,-0.36053161255944900,
	- 0.76657473659095900,-0.39315791656506800,-0.50773026880688800,
	- -0.92597907090953600,-0.32929755574671300,0.18473191390972800,
	- 0.91121096468807600,-0.03396316106949220,-0.41053755190286000,
	- -0.43706646286549800,-0.78947199903364200,-0.43093719934587400,
	- -0.40196779675371200,-0.59965623521593900,-0.69197853286038600,
	- };
	- auto pointshell
	- = new vnl_matrix_fixed<double, 3, 46>(coords);
	- // List sorted for each row [x,y,z]
	- // pointshell need [x...x
	- // y...y
	- // z...z]
	- int i=0;
	- for(int c =0; c < 46; c++)
	- {
	- for(int r=0; r<3; r++){
	- pointshell->put(r,c,coords[i++]);
	- }
	- }
	-
	- return pointshell;
	- }
	-
	- static vnl_matrix_fixed<double, 3, 67>* DistributePointShell3()
	- {
	- double coords[3*67] = {
	- 0.56913096982886400,-0.78778656243185400,-0.23554674957098500,
	- -0.83141868259485000,-0.50643545944750500,-0.22861780255797400,
	- 0.66520728747741500,0.16406099937578400,-0.72841145870363500,
	- 0.89843444153226500,-0.32337141111972700,0.29706309891846700,
	- 0.10682918210921600,-0.98310908722825000,0.14860702695065500,
	- 0.47695410914339100,0.34004755151800200,-0.81048284403671700,
	- 0.73195863370355600,-0.57860748500094100,-0.35979151858778900,
	- -0.34693446874899500,0.36681507780719100,-0.86318200461267500,
	- 0.69155604307511300,0.71307629015228000,-0.11520609232567700,
	- 0.46165051573275700,0.03834019742989470,0.88623294374826500,
	- -0.97397281635692200,0.09418099894164960,0.20617199721620300,
	- -0.29851857051594800,0.88978611904209300,-0.34520620709530000,
	- -0.35435497259052800,0.57535527165268900,0.73715592976101400,
	- 0.81483656941218300,0.03423671864623110,-0.57867885069779600,
	- 0.09093817184312330,-0.56161837808076500,0.82238375853597700,
	- -0.38426863203906100,-0.76843844817080100,0.51170300937524000,
	- -0.73642722235150800,0.67410491319471600,-0.05707461945896040,
	- -0.54419758869133900,-0.83725684681843000,-0.05338498776051840,
	- -0.21793670722020900,0.72064410859729600,-0.65816081651069200,
	- -0.86994783943189000,0.48926427520412000,0.06173512514583880,
	- 0.10775852899571900,-0.66193658502334100,-0.74177358866187400,
	- 0.64544044927716800,-0.27486614918135400,-0.71263961893168700,
	- -0.11695347642120100,0.01614429356247260,0.99300616621366600,
	- -0.76804280354387200,0.56311186828017900,-0.30498405815136400,
	- -0.89852079402656700,-0.17264968995044600,-0.40354983243941700,
	- 0.15476743176759600,0.59389894762264400,-0.78951319309861900,
	- -0.08940325110166170,0.85346959988929000,0.51341669310343500,
	- -0.70606292132486000,-0.42769174553909800,-0.56440669904592900,
	- -0.07667441970353810,-0.38529704221355400,0.91960166519238700,
	- 0.97761562873568900,0.05518196801914950,0.20303357568948200,
	- 0.27057965262888700,0.90009485795734400,0.34149070011052800,
	- -0.07518696164793450,0.30024488370383200,0.95089427940640300,
	- 0.13690225805945900,0.94909731680809600,-0.28367596825584700,
	- -0.50251469982969000,0.85107263931481100,-0.15216549893059300,
	- 0.21156984762048800,0.24711360232026500,0.94560724781811200,
	- 0.54655302079371500,0.64091673556772900,0.53898565243470900,
	- -0.55776925354389300,-0.75378730237748100,0.34741641091860700,
	- 0.33541827007282600,-0.94032512320547200,-0.05729962277332840,
	- 0.67560875362133500,-0.41311684917543700,0.61064497128657700,
	- 0.89999152407210300,0.19323788395138500,-0.39073568662762600,
	- -0.98068938405211500,-0.19462539941972600,0.01921681316436500,
	- -0.83571217382768900,-0.43205465164452500,0.33898958761077700,
	- 0.17146282600716700,-0.94464169246048600,-0.27973661212473500,
	- -0.54059787517480200,0.19148492705680600,-0.81919927982545100,
	- -0.11323347366714700,-0.98395720927995300,-0.13786366724876500,
	- -0.96778324010342800,0.25052610173143600,-0.02514502985004660,
	- -0.37464301489130600,0.81614231968582300,0.43994809399632100,
	- 0.87643936365442000,-0.25855236763220800,-0.40620772398960400,
	- 0.52679822663262800,-0.75204791987234000,0.39611558241554000,
	- -0.83302160989998000,0.19922527352743200,-0.51612429494024400,
	- -0.36881247628488900,-0.43365274990848600,-0.82214515131661200,
	- -0.68494199482737100,-0.50458868526765800,0.52558988044078300,
	- -0.47018702426243700,0.58505538166360200,-0.66078314340008000,
	- -0.37416836671127000,0.32358269311843500,0.86907552840178400,
	- -0.27722979680714700,-0.21344561523946000,0.93679485966636000,
	- -0.42391010237203500,-0.55511199435901700,0.71564718879185400,
	- 0.14056187290120700,-0.12797911064355400,0.98176560701900200,
	- 0.65560180621904000,0.70152916060800800,0.27936196680821600,
	- 0.31456644451092300,0.94702007926960300,-0.06481451571947000,
	- 0.17066405874813200,0.60471657508100000,0.77794064225615400,
	- 0.79129808311628700,0.03500830070119940,0.61042752439458600,
	- 0.89399321972683600,0.44808044136416500,-0.00020285300027376,
	- 0.62673064388188000,0.22888439553392000,0.74486282864731200,
	- 0.04867785807210680,0.84066847580244300,-0.53935793303288600,
	- -0.61746764544761500,0.52381468179607700,0.58681503556082400,
	- 0.28885209645735200,0.75743720323072100,0.58553680459405300,
	- -0.49988083572550200,0.08893492748180820,0.86151594805214000,
	- };
	- auto pointshell
	- = new vnl_matrix_fixed<double, 3, 67>();
	-
	- // List sorted for each row [x,y,z]
	- // pointshell need [x...x
	- // y...y
	- // z...z]
	- int i=0;
	- for(int c =0; c < 67; c++)
	- {
	- for(int r=0; r<3; r++){
	- pointshell->put(r,c,coords[i++]);
	- }
	- }
	-
	- return pointshell;
	- }
	-};
	-
	-// Distributed Pointshell 30-60-90
	-template<> class ThreeLayerPointShell<30,60,90, vnl_matrix_fixed<double, 3, 30>,vnl_matrix_fixed<double, 3, 60>,vnl_matrix_fixed<double, 3, 90> >
	-{
	-public:
	- static vnl_matrix_fixed<double, 3, 30>* DistributePointShell1()
	- {
	- double coords[3*30] = {
	- -0.0384531292653293 ,0.0948025501623591 ,-0.9947531519590260,
	- 0.5110816729083550,0.5146956026128700,0.6883923011395250,
	- -0.1446942037238470,0.9515456918526300,0.2713381354056610,
	- -0.4478957210732550,0.8874427193875220,-0.1087880639148770,
	- 0.0234550198951957,-0.3332336016908820,-0.9425525071558810,
	- 0.9229881949625620,0.3842551764058190,0.0209940792863651,
	- -0.6911807120917000,-0.6043864949901590,0.3962148254494260,
	- -0.0316674103891205,-0.6829866700288160,-0.7297440535435660,
	- 0.8018580068378580,-0.1378458982057450,0.5813968053041460,
	- 0.3973142766999960,0.4262411104325310,-0.8126868285555020,
	- -0.8315080441618440,0.3951380066705710,0.3904616859290430,
	- -0.8752414233521170,-0.2348057149272050,-0.4228696336769560,
	- -0.2818275522720080,-0.8725715270267310,-0.3989889234084150,
	- 0.2217711399465410,0.7995959805053020,-0.5580894457401740,
	- -0.3678809968698430,-0.0344850464711680,0.9292332073876450,
	- 0.6642059344014850,0.6635911630050780,0.3442052368680880,
	- -0.8248962619923230,0.5292990045320030,-0.1984659183651500,
	- -0.1835415051538410,0.8857989535243100,-0.4262308410017950,
	- -0.1166555399998580,-0.9878457938197680,0.1027237685247790,
	- -0.5153844228415700,-0.8501138123201320,0.1080990415997830,
	- 0.5451858248749490,-0.3086757610614890,-0.7794175330902750,
	- -0.5671903126002800,0.6003393592309330,-0.5638153980254410,
	- -0.4890503721480340,-0.1375661511749660,-0.8613392406902020,
	- 0.3976996460860260,-0.6740608343992310,-0.6224764919513510,
	- 0.4349956952359570,-0.3316293950165250,0.8371383932702870,
	- 0.6340600901853650,-0.7334511285536860,-0.2449841710344760,
	- 0.9845956419603380,-0.1475029048111290,0.0938845828929696,
	- 0.9610090220995200,0.0558414999946514,-0.2708198410782880,
	- -0.7632149908465080,-0.1335295186020360,0.6321967616249480,
	- 0.0826215834627986,-0.6217188595585800,0.7788705499730220,
	- };
	- auto pointshell
	- = new vnl_matrix_fixed<double, 3, 30>(coords);
	-
	- // List sorted for each row [x,y,z]
	- // pointshell need [x...x
	- // y...y
	- // z...z]
	- int i=0;
	- for(int c =0; c < 30; c++)
	- {
	- for(int r=0; r<3; r++){
	- pointshell->put(r,c,coords[i++]);
	- }
	- }
	-
	- return pointshell;
	- }
	-
	- static vnl_matrix_fixed<double, 3, 60>* DistributePointShell2()
	- {
	- double coords[3*60] = {
	- -0.9757323531821020,0.1141645636029930,0.1868497454401630,
	- -0.3081645385608390,-0.9413175847225490,0.1376801433239040,
	- 0.2268128430936140,0.3605118823065700,-0.9047580433041550,
	- 0.0053723381344127,-0.9527141369992010,0.3038205245615180,
	- 0.4997098468405750,0.8591889901243150,0.1099288325223530,
	- 0.2826871445408290,-0.5384236997311110,0.7938437490332800,
	- -0.9169656502561230,0.3927426788378230,0.0701939062145264,
	- -0.4122096064130160,-0.6082501787985420,0.6783177429290540,
	- 0.8689901348066610,0.0966091330875035,-0.4853069348492570,
	- 0.9016117108528340,-0.0311940714365313,0.4314200421401830,
	- 0.0602430803117106,-0.3322121265937110,0.9412788504044060,
	- -0.7401273323624760,0.6637816179074090,-0.1077288058887970,
	- 0.2609246136270950,0.8706803367668190,-0.4169341640729010,
	- -0.3416095796360020,0.1763315450422400,-0.9231522525152230,
	- 0.2417187698627780,-0.7721496224459510,-0.5876708235505650,
	- 0.0613208945746505,0.1158091933659950,0.9913768096039370,
	- 0.6752331524032520,0.5192825815894980,0.5238375610371130,
	- 0.1859160712558880,0.0545608595018432,-0.9810496047902950,
	- -0.8705635614786970,-0.3824245858905910,-0.3096296522168640,
	- -0.7511998187032470,-0.2098339818012360,-0.6258342691652840,
	- -0.3238272471878560,0.9093048344891080,0.2613438959560160,
	- 0.0312467158098265,-0.9020995865833540,-0.4303951424415010,
	- 0.1997844244448850,-0.2949296496204980,-0.9343996390859500,
	- 0.0993378318350216,0.6282103369083360,-0.7716759473819500,
	- 0.7029961904247910,-0.5712633600352550,0.4236207380776580,
	- 0.6081885222938300,-0.0369636906278732,0.7929315272614730,
	- -0.8386908835040670,-0.4071869261928720,0.3616578618871240,
	- -0.6722483496885470,-0.0353283318457414,0.7394822954675930,
	- 0.0999489360975153,-0.5914665380137460,-0.8001109576696270,
	- 0.1502553918254090,0.7709976382621730,0.6188585937203620,
	- -0.2288419561759350,-0.9457701920389410,-0.2305430609326490,
	- 0.2000892573988740,0.4465173368776440,0.8721161373012560,
	- 0.6810481798116100,0.7159072717862530,-0.1537860688711920,
	- -0.9675337290891160,-0.1992515487286990,0.1554905251265250,
	- -0.6915973408017530,0.2529246583829880,0.6765517240963850,
	- 0.4051983586769120,-0.6954173613750950,0.5934719737474010,
	- 0.3828531024787670,0.6364092429998630,0.6696318222327270,
	- 0.5431852686098420,0.7191354072485380,-0.4333520854994610,
	- -0.4766435443833670,-0.7756897459394560,-0.4136621201440160,
	- -0.2634864894153490,0.9592084977706880,-0.1024398735848210,
	- -0.7706589629193440,0.6046810772525520,0.2011108094677480,
	- -0.5074055034405280,0.8063323635715170,-0.3039206714513410,
	- -0.5457935890943380,0.8354998025106060,0.0636351955151979,
	- 0.3190257966006890,0.1393790695388820,0.9374412067312650,
	- -0.4883735140357740,-0.2538251441534990,0.8349036513178050,
	- 0.7814334110960810,-0.3206898482390990,0.5352754853896490,
	- 0.5674042808667500,-0.3889648144620360,0.7257814789346710,
	- 0.7365968935987790,0.6532051494950900,0.1753512161740710,
	- 0.5454313517376770,-0.7269270773618580,-0.4172309489236830,
	- 0.9213613541912860,-0.2944856448350440,0.2537153128782090,
	- 0.8605683113688990,0.5039629381095560,-0.0737803393843139,
	- 0.9884254663736010,0.0653918314621231,0.1368904883553190,
	- -0.6908004715469640,0.4998012720691420,0.5224877002844740,
	- 0.6727955231552780,0.3943331152249490,-0.6259772985174470,
	- -0.4586010376503450,0.1473697927994620,0.8763373964611290,
	- -0.0145240600324916,0.9964844905654110,0.0825088585714514,
	- 0.5144395480682960,0.3368539248460700,0.7885945629403520,
	- 0.4119578382931460,-0.5109788900305280,-0.7544476876576700,
	- -0.1166393819714400,0.8099047244599660,-0.5748474509561170,
	- 0.8653655945438620,-0.2118053715810700,-0.4541815411805620,
	- };
	- auto pointshell
	- = new vnl_matrix_fixed<double, 3, 60>(coords);
	-
	- // List sorted for each row [x,y,z]
	- // pointshell need [x...x
	- // y...y
	- // z...z]
	- int i=0;
	- for(int c =0; c < 60; c++)
	- {
	- for(int r=0; r<3; r++){
	- pointshell->put(r,c,coords[i++]);
	- }
	- }
	-
	- return pointshell;
	- }
	-
	- static vnl_matrix_fixed<double, 3, 90>* DistributePointShell3()
	- {
	- double coords[3*90] = {
	- 0.7830306271444820,0.5716685391117410,-0.2450675791359720,
	- -0.3870553382696590,0.9200004222080310,0.0615417602445897,
	- 0.9237963183374240,-0.2584997104179900,-0.2824504592668160,
	- -0.5842983723039450,-0.7712899205183550,-0.2524029925134570,
	- 0.3359998847225240,0.7641041306124860,0.5506804473080420,
	- -0.9783788169663750,-0.2066075720365220,-0.0093915754081947,
	- -0.0445468908163855,-0.8801917861335100,0.4725230091135180,
	- 0.8775085322085220,-0.2202272889989130,0.4260031890507770,
	- -0.5808389302765810,0.4437425367947590,0.6824358564100420,
	- 0.5331596759297140,0.4366496520639920,-0.7246225509290440,
	- 0.6151687893470670,-0.1325993633208080,-0.7771645703840200,
	- 0.4011147552907920,0.8712537751236570,-0.2828848041531790,
	- 0.7304993029031530,-0.0076263316203289,0.6828708571348050,
	- -0.5475051350669790,0.6162612183405430,0.5660920754123990,
	- 0.8023122911715880,0.2709359026259910,-0.5318728458036140,
	- 0.2336323077450560,-0.6929349377840680,0.6820975859625270,
	- 0.1689148924284850,-0.9486250397707260,0.2675411987635920,
	- -0.8314637780782760,0.5554909857699080,0.0098868838455222,
	- -0.1011517806960660,-0.2148730146317450,0.9713896771353290,
	- 0.3877486434569820,-0.3420676320990350,-0.8559443466531150,
	- -0.3648694025982520,0.8893842897839550,-0.2754376592499350,
	- 0.1726950806932710,0.9829215274686680,0.0635742081586933,
	- -0.3959729941386110,-0.7643798871495520,0.5088504456460080,
	- -0.9617290799445310,0.1062410103220330,-0.2525668713723110,
	- -0.0327316740125812,-0.4982367497870410,-0.8664229790800670,
	- 0.1706515883535990,-0.2008209194778680,0.9646496740747160,
	- 0.2501225023053060,0.6910620770273610,-0.6781385843138260,
	- 0.3654852701417630,0.4920313286800810,0.7901428281688790,
	- 0.9153163381057960,-0.3852897569037580,0.1172510316442380,
	- -0.6881847644097410,0.7218125899083820,0.0734051434441835,
	- -0.6873457829778960,0.2458189841721520,-0.6834682155324220,
	- -0.3219850147738870,0.8095000604196670,-0.4909534626027350,
	- -0.5632523312637280,-0.5973559275989310,0.5708876483936170,
	- -0.9084685052242310,-0.3740631899713040,0.1864449112315510,
	- -0.7845198100635990,-0.3605738415896990,-0.5044949676448910,
	- -0.2000039873810240,-0.6330205581036100,-0.7478525108936150,
	- -0.9148801969792540,0.0534543198667285,0.4001710395103400,
	- 0.7664323664233560,-0.3341914416639150,-0.5485412546174510,
	- 0.4872976306941970,-0.8343714235123850,-0.2576147254054740,
	- -0.6413753405832620,-0.2298206308844890,0.7319973702900570,
	- 0.7054813742936480,-0.6006428992790810,-0.3761969405382820,
	- -0.1929691654472430,0.9760562116682670,0.1003851226546300,
	- -0.9439691512808960,-0.1047955385010510,-0.3129538888403490,
	- -0.4276451629474120,0.0186575235064224,-0.9037541211105420,
	- -0.7344812627593790,-0.4734265259198780,0.4862145608790640,
	- 0.6377710213710160,0.3906960864871740,0.6637806055489840,
	- 0.0474387462958210,0.9621772979130640,0.2682618361425920,
	- 0.7913486901745450,-0.0748105169885527,-0.6067706626946760,
	- -0.0982434620561768,0.1155119940049920,0.9884357345848060,
	- -0.2883901942644810,0.3703318191063880,-0.8829979839215070,
	- 0.3295292140825860,0.2147146585289090,-0.9194063913628870,
	- -0.5210574847572160,-0.0609880081835259,0.8513398618861260,
	- 0.1729068266771900,0.9459249066560850,-0.2744618375222680,
	- -0.2062545956858610,0.4593595720405990,0.8639721206920620,
	- 0.6720182971610780,-0.4607369705129640,0.5797524060176540,
	- -0.2554108625029320,0.6389014951165470,0.7256515491979250,
	- 0.4500266667406290,-0.5361016246739610,0.7141925841425810,
	- -0.9983559681192810,-0.0042300087224308,0.0571617699762653,
	- -0.8406688842019840,-0.0901045876756096,-0.5340009273535010,
	- -0.3909575963129450,0.7939675140678560,0.4655832304648770,
	- -0.9713179118089640,0.2320449947116890,0.0519291308258172,
	- -0.0612195458720222,0.7850603547539780,0.6163865723689800,
	- -0.6242925102191230,-0.1774216962215860,-0.7607761848232110,
	- -0.0802679405745239,-0.4570324492769940,0.8858207482463910,
	- -0.3609460670444700,-0.2996972708558150,-0.8831191779860200,
	- 0.1285945459353310,0.8707004556055770,0.4747042862287270,
	- 0.5951730348219600,-0.7933110389121110,0.1281665095140040,
	- 0.2033751954557950,0.0131770863036256,0.9790122033304090,
	- -0.2052893840274300,0.8803381043882250,0.4276226032002800,
	- -0.3731942266334910,-0.9275730588324440,-0.0182835919789316,
	- 0.2685955896736170,0.5262799019911600,-0.8067749834793190,
	- 0.9390948774123210,0.2816262184669510,0.1969453840280110,
	- -0.9130820847807490,-0.2162790214867180,0.3456942164936930,
	- -0.7722185508796150,-0.6352920195758570,0.0090862280741177,
	- 0.1460103850487270,0.2737759341802480,0.9506459410956610,
	- -0.7668676175868570,-0.5322707367226740,-0.3586110984414160,
	- 0.5327000875787680,-0.1961334068751380,0.8232632042069670,
	- -0.8210993253048930,0.4385794796816200,-0.3652997919326650,
	- -0.6255762780977020,-0.7798597751409450,-0.0217497447925055,
	- 0.2991048825976350,-0.1334972919760040,-0.9448358281952090,
	- 0.0606298744362150,-0.9937831824740320,0.0933756100790349,
	- 0.8564420120030050,-0.4610622959465800,-0.2322254063032560,
	- -0.5455890340730230,-0.6468991032576630,-0.5327796506096080,
	- -0.8522969529983180,-0.5007967009121140,-0.1509720777671300,
	- -0.0228411934161264,-0.7512799112567760,0.6595883373933590,
	- 0.5854881600260220,0.7616691389056020,-0.2776035614111240,
	- -0.1213541141003080,0.4896966102871260,-0.8634062826179960,
	- 0.5356517245344040,-0.7170045054372250,0.4460737261776780,
	- -0.3912157018163170,-0.8815613582567070,-0.2641966053547140,
	- -0.6919685152992150,0.6644155090244570,-0.2823678544069240,
	- };
	- auto pointshell
	- = new vnl_matrix_fixed<double, 3, 90>(coords);
	-
	- // List sorted for each row [x,y,z]
	- // pointshell need [x...x
	- // y...y
	- // z...z]
	- int i=0;
	- for(int c =0; c < 90; c++)
	- {
	- for(int r=0; r<3; r++){
	- pointshell->put(r,c,coords[i++]);
	- }
	- }
	-
	- return pointshell;
	- }
	-};
	-
	-// Optimal PointDistribution For Multishell Scheme 50 - 100 - 150
	-// Generated by Emmanuel Caruyer
	-template<> class ThreeLayerPointShell<50,100,150, vnl_matrix_fixed<double, 3, 50>,vnl_matrix_fixed<double, 3, 100>,vnl_matrix_fixed<double, 3, 150> >
	-{
	-public:
	- static vnl_matrix_fixed<double, 3, 50>* DistributePointShell1()
	- {
	-
	- double coords[3*50] = {
	- 0.913310030405731,-0.305436511654557,-0.269394368368340,
	- 0.274520611983463,-0.931497424367645,-0.238644048726690,
	- 0.724295307031846,-0.291296816682609,-0.624933974754310,
	- 0.179546279617146,0.559467539325302,-0.809171926055848,
	- 0.333306860790720,0.932650091766363,0.138095412226576,
	- -0.423224047088266,0.854335111704236,-0.301650332132319,
	- -0.057337449880758,-0.311676405763001,-0.948456764924911,
	- -0.167285210491163,0.516195511070583,0.839974911947675,
	- 0.763325168891534,0.512093536284904,-0.393820894102804,
	- 0.457619183693223,-0.672231259407514,0.581970632069466,
	- -0.246793802164352,-0.050216662420050,-0.967766038889902,
	- 0.927994874653326,0.242210812920042,-0.283124415622830,
	- 0.613792300977422,0.763214386431347,0.201898022786412,
	- 0.720951430921191,-0.550579081664088,-0.420822657525251,
	- -0.566617724460163,-0.603447657535153,-0.561066198360694,
	- 0.575968738378302,-0.783648913166458,-0.232710965156210,
	- -0.532150073708023,-0.619733926203769,0.576841537828723,
	- -0.911227494753416,-0.409216343893830,-0.046972722888692,
	- 0.243129633174557,0.820980315213879,-0.516603623200345,
	- 0.429059425848317,0.332137825141317,-0.839995520345857,
	- -0.862659530206915,0.023610632091113,0.505233681572638,
	- 0.837291268298631,-0.163164674031590,0.521843483411485,
	- 0.803588479073049,0.456397841392963,0.382029536388100,
	- 0.303630079812031,0.840160692576492,0.449375995445604,
	- 0.558311152322438,-0.044011396373360,-0.828463429598227,
	- 0.238930415896487,-0.057120162540996,-0.969355220438215,
	- 0.246985899213630,-0.326331770359038,0.912417416122670,
	- 0.837050631211904,-0.547095262685976,0.005745810152941,
	- -0.554571420346131,0.053288087401785,-0.830428154313384,
	- 0.751372177673996,-0.530499886791399,0.392440722570616,
	- 0.204389904673926,0.615196807070163,0.761418186963024,
	- 0.106700970850229,-0.867025439314806,0.486705034287282,
	- 0.717231391359855,0.239339763160166,-0.654442976139587,
	- 0.069544882069961,0.220289919002015,-0.972952137036535,
	- 0.648780744604385,-0.754349357811800,0.100202753452702,
	- -0.727376323458570,-0.175112683983955,-0.663520332755394,
	- 0.726060483848279,0.676802250037960,-0.121551997669954,
	- 0.580156273414571,-0.371836855429485,0.724676514978945,
	- -0.060890718603115,0.804268669172008,0.591138078773718,
	- -0.386606299473394,0.736073310034347,0.555636258232458,
	- 0.171832268210408,-0.620770257189966,0.764930035617617,
	- 0.030029178348917,0.973024956515624,0.228737147060675,
	- 0.197806050466708,-0.977284832169067,0.076073143822506,
	- 0.941717594278340,-0.292439497987513,0.166274209195007,
	- 0.103620708501302,0.975442422157789,-0.194357479466658,
	- -0.999930437744010,0.003907201094968,0.011128946611211,
	- -0.453284936431437,-0.867544703290094,0.204692340349242,
	- -0.939310554852217,-0.109134901287686,-0.325246452500478,
	- 0.453912788215515,0.373549749748161,0.808964625405526,
	- 0.446853673336740,-0.414239447718517,-0.792923372451158
	- };
	-
	- auto pointshell
	- = new vnl_matrix_fixed<double, 3, 50>();
	-
	-
	- // List sorted for each row [x,y,z]
	- // pointshell need [x...x
	- // y...y
	- // z...z]
	- int i=0;
	- for(int c =0; c < 50; c++)
	- {
	- for(int r=0; r<3; r++){
	- pointshell->put(r,c,coords[i++]);
	- }
	- }
	-
	- return pointshell;
	- }
	-
	- static vnl_matrix_fixed<double, 3, 100>* DistributePointShell2()
	- {
	- double coords[3*100] = {
	- -0.6783406728914600,-0.6757825732021540,-0.2883952934037510,
	- -0.7868810762760640,0.3417432912343670,0.5138381989448860,
	- 0.1812675472397420,0.9341812435603770,0.3073230881298610,
	- 0.4392152776431420,0.8556891913232610,0.2736529695387940,
	- -0.6296241987663400,0.2128741188301860,0.7471666332620290,
	- 0.6170474427091470,0.0980582575477010,-0.7807925662894150,
	- 0.3935013484893500,0.9192019551005550,0.0149818048438275,
	- -0.3269299998796330,-0.4401580515926610,0.8362880274145110,
	- -0.2869929508839660,0.8309767335503890,0.4765634421992920,
	- 0.5088992607891730,-0.7072946217461350,-0.4906687889169470,
	- 0.5806843974003410,0.3583450335309360,-0.7310228912691540,
	- 0.9491724956627390,-0.1834420594707910,0.2557744793650880,
	- 0.0153560310858227,0.1752309003794950,0.9844076004691760,
	- -0.0479773456177447,0.9905464575577180,-0.1285141615828030,
	- 0.0693843127112566,-0.5942844228507240,-0.8012564145806050,
	- -0.3165721030432440,-0.4164032785066600,-0.8522854059666170,
	- 0.4896581521634270,0.7211168510820520,0.4901279232051600,
	- 0.7776461071669160,-0.0320557656217032,-0.6278845115931320,
	- 0.2300492326525960,0.8027977937856420,0.5500845869944510,
	- -0.3766021271868230,-0.7564724591162180,0.5347151170455350,
	- -0.1790056555604940,-0.2983809560973960,0.9375104161105410,
	- -0.5841988205464850,-0.8089448753434100,-0.0657261494972090,
	- -0.8551587253793000,0.4448943753338720,0.2660311057074570,
	- -0.7752975795230930,0.6190258715864510,0.1253819504245550,
	- -0.6764680634440770,-0.5064314530534920,0.5347131403830920,
	- 0.7501893689724760,0.6048830482657770,-0.2670812771449510,
	- -0.5138286280086930,-0.4945630265573110,-0.7009904092076970,
	- 0.5804145400895790,0.7956021922609330,-0.1735975613947330,
	- -0.1755232810907650,0.3977545839146920,0.9005458726627870,
	- 0.0397560432054666,0.4921914390519250,-0.8695786590945290,
	- 0.5538585716719580,-0.8081611673456340,0.2002903147434720,
	- 0.8992305597521990,0.1140934067118160,-0.4223352873637700,
	- 0.7698402757004470,0.6378303091348330,0.0227694237612964,
	- -0.4412960658520300,0.8971893864056890,0.0175780313033856,
	- -0.0811198993955311,0.2753962213738170,-0.9579021260938310,
	- -0.8572077886102190,-0.3790625619618600,0.3485776545690900,
	- 0.6857756541322800,0.5415157578159610,0.4862843162558790,
	- 0.8549241931498690,-0.2861863354061220,0.4326684705335710,
	- -0.4182775751481730,0.7970464185340600,-0.4356155149098700,
	- 0.3499190445152290,0.8866592889390710,-0.3023110444949170,
	- -0.0132033510852791,-0.8749575867614390,-0.4840195170535130,
	- 0.9116379197252770,-0.0091996476760664,0.4108913114214080,
	- -0.6490542475593910,-0.0530061128719349,-0.7588932307797450,
	- 0.2036777677589340,-0.7982257583158190,0.5668782988277740,
	- 0.3791318665509280,0.1705982429677800,-0.9094807679450480,
	- -0.1470179365181320,0.9220511216311460,-0.3580606868125770,
	- -0.3344979114418210,-0.6343147268032640,-0.6969619606560740,
	- -0.6076879381877640,0.5109764367904180,0.6079625406438060,
	- -0.5844013508588990,-0.7109052658706510,0.3912655927521240,
	- 0.9862110505381910,-0.1637207304543020,0.0241513191330477,
	- -0.2051748270057740,0.7136488133907960,0.6697825479281010,
	- 0.9069081158736650,-0.4209955960690930,0.0167444752950723,
	- -0.1319432828456750,0.9392959075033450,0.3167241201098720,
	- 0.7549548594926640,-0.1430122887152190,0.6399926916808070,
	- 0.2084074643614400,-0.1965342739298880,-0.9580921709153480,
	- -0.4579812060622150,-0.5603838600979070,0.6900892291838540,
	- -0.5044451924143650,-0.2283097986021220,-0.8327122454439420,
	- -0.1632507891313170,0.0595367888203028,-0.9847865507941140,
	- 0.6304967444231040,-0.7732039721298140,-0.0680402289424677,
	- -0.4189905487906070,0.2950674433427220,0.8587095690065030,
	- -0.1064870135377420,-0.0503578524476393,0.9930380670672570,
	- -0.9594694024759230,-0.2706424081220130,-0.0785566842376365,
	- 0.6572248348109010,-0.6577047684772120,0.3680760166461810,
	- 0.8938413333977800,-0.1605095289995250,-0.4186697526810690,
	- 0.9676575561375490,0.2066292219530930,-0.1447177207012450,
	- 0.8845432302365500,0.4553528053106210,-0.1011785379338700,
	- 0.3127824838603270,-0.9329319353982300,0.1783399049687880,
	- 0.0538977574368990,0.9943600559842480,0.0913406306430770,
	- -0.8270410405970430,-0.3169506321051900,-0.4642686872666290,
	- -0.3836295436457290,0.5570493630789800,0.7365625433970090,
	- -0.4341709114900190,0.8573912849439030,0.2763617269416430,
	- -0.6794088494430530,-0.3329865853053170,-0.6538528498868610,
	- -0.3373613680825300,0.6537103259033100,-0.6773847629913670,
	- 0.3577142489860180,-0.2395141136991300,0.9025926575212580,
	- 0.0475306676831556,-0.6921666442661880,0.7201709326228570,
	- -0.9238533114270850,-0.2442810637733990,-0.2946554273162900,
	- -0.7702042751707540,0.6239784781621260,-0.1320463301238260,
	- -0.1058068553327490,-0.9342834914303710,0.3404691865723970,
	- -0.6712641876558270,0.6601081560713440,0.3371373795040410,
	- -0.9902933383503500,-0.0392378960032633,-0.1333397597723740,
	- 0.2680611017833540,0.2096519795061000,0.9403134015847410,
	- -0.2193780563994170,0.9713963546921800,0.0908976922763060,
	- 0.4259546539557210,-0.0086224931160314,0.9047034239937000,
	- -0.7126278602910880,0.4094408405402170,-0.5696663328955520,
	- -0.2175209712545230,0.4840278946263750,-0.8475857622022950,
	- 0.5687366838665980,-0.5871979617261380,0.5759662647838790,
	- 0.0944273658455115,0.8302981465345910,-0.5492617412861550,
	- 0.2132739207069970,0.6628352636620030,-0.7177490146230690,
	- 0.9572113632369580,-0.2441349912405500,-0.1553850447823740,
	- -0.8451592214984760,-0.4858715283504990,-0.2227885729889170,
	- -0.8457073503037060,0.4544256488253640,-0.2797792117580030,
	- -0.4568229734634650,0.4521433068383050,-0.7660804141846460,
	- 0.2161513748810380,0.9712225012944180,-0.1000271768893380,
	- -0.9727568289959310,0.0233660996838811,0.2306473000651490,
	- 0.0955550598977780,0.4497094877292240,0.8880487639618950,
	- -0.5803054956345510,0.2185728470394220,-0.7845198801008280,
	- 0.0802960854964209,0.7085380275275620,0.7010894395163160,
	- -0.8170365471147090,-0.1054124160886850,-0.5668681532889450,
	- -0.7903491223400260,-0.2661789011279690,0.5518125201648250,
	- -0.4240807031724980,0.0532021972358502,0.9040603317290260
	- };
	- auto pointshell
	- = new vnl_matrix_fixed<double, 3, 100>();
	-
	- // List sorted for each row [x,y,z]
	- // pointshell need [x...x
	- // y...y
	- // z...z]
	- int i=0;
	- for(int c =0; c < 100; c++)
	- {
	- for(int r=0; r<3; r++){
	- pointshell->put(r,c,coords[i++]);
	- }
	- }
	-
	- return pointshell;
	- }
	-
	- static vnl_matrix_fixed<double, 3, 150>* DistributePointShell3()
	- {
	- double coords[3*150] = {
	- -0.5818137157755120,-0.5030550053652260,0.6390840803153230,
	- 0.9670851419246870,0.1662861674810110,0.1926012429165080,
	- 0.0578846316476645,-0.7976809936025330,0.6002952622370840,
	- 0.4660628327321890,-0.1511747542980830,0.8717405747173640,
	- 0.6902368719591830,0.3748091607024440,-0.6189435787222700,
	- -0.1997955747625600,-0.1526408912355860,0.9678752433181160,
	- 0.9511193914166630,0.1151598714233260,-0.2865486124289540,
	- 0.0822444520102396,-0.5510970245321980,0.8303781787025070,
	- 0.7452339673590670,0.4163359900238880,0.5208557163985940,
	- 0.7753251365196900,0.6018341048080190,0.1914853596770620,
	- 0.1116030335825260,-0.9761251513556840,-0.1863449805764000,
	- -0.3170679847245510,0.9480932422722550,-0.0242300850265728,
	- -0.1215812147248450,0.4013080511364970,-0.9078380121580370,
	- 0.8680201958339400,-0.2937180126790240,-0.4003381928473620,
	- 0.7117815464094280,-0.4555489837210150,-0.5346420799205320,
	- -0.4221584476961910,-0.8100472693071080,-0.4069467612929700,
	- 0.0186640877956507,-0.9603335901627470,0.2782284087434000,
	- -0.5396677502633030,0.3145543091567380,0.7809060800868890,
	- -0.4898321413919820,-0.0679885797782780,0.8691616801718060,
	- -0.6750918694436950,0.2756900693390990,-0.6842849943399450,
	- -0.4765551297163720,-0.8680896906246820,-0.1389802049651460,
	- -0.8007926338965610,0.4138072508780090,-0.4330066011249610,
	- 0.6252172011926140,0.2326499546399870,-0.7449680865237690,
	- 0.6824097373557610,-0.7075614150231750,-0.1835042079420600,
	- -0.7485107920414520,-0.0179476036655747,-0.6628796857048340,
	- 0.6619059872141820,-0.0443716919725870,-0.7482724216764290,
	- -0.0389254961022405,0.4513344326841560,0.8915054882763560,
	- 0.6705154952625320,-0.7056948744571640,0.2289185767423150,
	- -0.0421968777730212,-0.3582833631874890,0.9326588096240070,
	- -0.0859685420644288,0.2858229400217130,0.9544184914033570,
	- 0.9471108604678190,0.3162982815144110,-0.0541886989596281,
	- -0.5550008908723820,-0.7690560878042730,-0.3170595290194690,
	- -0.9104090909480310,-0.3561208782301570,0.2105545231234920,
	- -0.8278006128591360,-0.4943059810149400,0.2653445731174760,
	- 0.9608962244735380,-0.0205957379787835,0.2761417414474080,
	- 0.2202282819057040,-0.6075951351306100,-0.7631039612100540,
	- 0.6244544517901810,0.4795352369175020,0.6165246095606390,
	- -0.1883106968238980,-0.4391326823901580,0.8784654624505860,
	- -0.2302051549830810,-0.9409736043275990,0.2481416179884810,
	- -0.0791847103092564,-0.9956294659870780,0.0495151301272986,
	- 0.3432876609136320,-0.1606450217698800,-0.9253900576756810,
	- 0.6910132782044240,0.7150303514681560,0.1059822901455680,
	- -0.3743211784491260,-0.1177211051182680,-0.9197963887590500,
	- -0.0638117734968980,-0.6201179359188230,0.7819090759896310,
	- -0.6081942748353220,0.4670488067500740,-0.6418451029421870,
	- -0.9237110100984830,0.0253860825460826,0.3822479779355320,
	- -0.9551685142832210,0.2944878574922000,-0.0304960835458829,
	- 0.2047274908347290,-0.2027142615186940,0.9575978188537430,
	- 0.4664286040672840,0.4413500991724570,-0.7665862295060520,
	- 0.2436221916378790,0.7468678862924580,-0.6187378994102360,
	- 0.7739427622698460,-0.5762620863418250,0.2625540107769950,
	- -0.8824775950813450,-0.1623522085699230,-0.4414465477857010,
	- -0.5674249283656180,-0.3593537766554100,-0.7408736828048120,
	- 0.6114933730446530,0.6602715260117740,0.4360245023626030,
	- 0.6580967800369840,-0.1033246068935280,0.7458100654424360,
	- -0.0651725243592964,-0.5903861242505850,-0.8044854046911040,
	- 0.6288524174560490,0.2026776272049530,0.7506440011684980,
	- -0.5594322362469380,0.7479956050065880,0.3571248352307300,
	- 0.5065956414163710,-0.4948790783785480,-0.7060138482219270,
	- -0.7796248885518470,0.2823581769849720,-0.5589802259832120,
	- 0.1069521912958730,-0.0945188164394620,-0.9897612955232660,
	- -0.1677987609066020,-0.9702091453514290,-0.1747506512567480,
	- 0.6497726089471500,0.7581321700271420,-0.0550560571776502,
	- -0.7436099555683260,-0.5675313008756160,-0.3534861475448520,
	- 0.8705569853960000,-0.4718161643221160,0.1397141448193180,
	- -0.7367938401263080,0.6760868762135980,-0.0064321818744716,
	- -0.8709771462534060,-0.3550310615284370,-0.3396347391746950,
	- -0.5568793244548770,0.8296552833726470,-0.0394655389742952,
	- 0.8255863288934740,-0.1743226461918030,-0.5366738567965490,
	- 0.5123909885019620,-0.8475608044158260,-0.1381888480304350,
	- 0.3892383734256480,0.6628221159035160,-0.6396564166192190,
	- -0.3850734793456500,-0.5125887952201850,-0.7674445533843810,
	- -0.0303214011502939,0.1349348899639910,-0.9903904220572250,
	- -0.1951010042782680,-0.3408158110301630,-0.9196630801991900,
	- -0.7299481699543050,0.1633700135838910,0.6636911238233930,
	- -0.3764204298254850,-0.8272654006443230,0.4170606873187450,
	- -0.0207934145254701,-0.9354136997804840,-0.3529431174783800,
	- 0.0530508631426718,0.0286917551417508,0.9981795375115150,
	- -0.9893103145653900,-0.1443535615447680,-0.0206676259852998,
	- 0.3520785503091250,-0.7515903016454040,0.5578106424986840,
	- 0.4646561319602880,-0.5645009731359150,0.6822267440963500,
	- -0.3638080873049480,-0.7397671945737120,-0.5660284210567990,
	- 0.8993857269815550,-0.3263912150460360,0.2908162458368350,
	- -0.1700781261443220,0.9625883335514640,-0.2109434310848530,
	- -0.3098321331013300,-0.2959672665364290,0.9035526694315240,
	- 0.3772438334691890,0.2858348804818840,0.8809003980072750,
	- 0.4170539029542560,-0.8070208930488820,-0.4180709511712160,
	- 0.3535382771055950,0.9267047409094850,-0.1273931308865980,
	- 0.0162686253194627,0.8954558957620720,-0.4448528639619620,
	- -0.4409570938666000,0.8843580437434560,-0.1531916833087520,
	- 0.1659388260557630,0.8826574008153690,0.4397501777067190,
	- -0.6722877318211110,0.5534153014066750,-0.4916916816581130,
	- -0.5022690191279730,-0.7127108731518800,0.4896621730492420,
	- -0.2994694405516180,0.9013048000637180,-0.3129979417788570,
	- -0.3172838107693270,-0.5624673796012650,0.7635191093274480,
	- 0.7315837873258040,0.0963804929381182,-0.6749044100485910,
	- -0.2068469360516820,0.7944607239234560,0.5710048188842610,
	- 0.5378470897916880,-0.7741067897070790,0.3338849893780950,
	- 0.1257284809109600,-0.8835082232405290,-0.4512267374105670,
	- 0.3130995324769140,-0.4640943924714670,-0.8286042949679160,
	- 0.9894576229982930,0.0690358063959267,-0.1273093465768750,
	- -0.0845800025595276,-0.7421395656655050,0.6648872748375060,
	- 0.5451534912742490,-0.6927392692238080,0.4721440202170950,
	- -0.5063313485711320,0.1671271448910190,0.8459888196038490,
	- 0.9140701463180970,0.3632958280951350,0.1802551216988890,
	- 0.8112330574743470,0.5738372376167550,-0.1123020533436160,
	- 0.8691548124260960,0.2553703834185790,-0.4235042848770290,
	- 0.2587208365075750,-0.8528680460626400,0.4535191558932370,
	- -0.7810165842314370,-0.4032429479626940,0.4768733794979690,
	- 0.6386218421663880,-0.3771596505315350,-0.6707553508686590,
	- 0.6209847697030420,-0.6181456007191380,-0.4819480595545900,
	- 0.1495129959273720,0.1671684875068860,0.9745258133233210,
	- 0.8500517134843810,0.5236094820204760,0.0569666107515227,
	- 0.2831566624639810,-0.3165192184973970,-0.9053385492864280,
	- -0.9842250831135330,0.1106121936986040,-0.1380794277774220,
	- 0.5302801835192860,0.0861689235342689,0.8434321807849740,
	- 0.8470084161413430,-0.0276085553364133,0.5308620448458990,
	- -0.2172067203511410,-0.5051072452535100,-0.8352771464769700,
	- 0.3204407112933310,0.0455278779726987,-0.9461738544649850,
	- -0.4935635772769070,0.6256485875038120,0.6041182335769260,
	- 0.4980559918394660,0.2263222843527210,-0.8370892739715230,
	- 0.2021779827202400,-0.7110486153559470,0.6734492778996520,
	- 0.6602958653226490,0.7044162570524200,-0.2603979781758510,
	- 0.4825507527225460,-0.3146110298685950,0.8174134027112130,
	- -0.8074813189441350,0.4434122850213180,0.3890494377947510,
	- 0.7706009639641810,-0.5764170340352260,-0.2718778350868380,
	- 0.9877213210351460,-0.1170482811531720,-0.1034712126713200,
	- 0.9471546743930560,-0.1633313871864270,-0.2760812937073770,
	- 0.9072494495203930,-0.1579003412593720,0.3898280628368310,
	- -0.3139240581363140,0.0802169066474812,-0.9460533460704720,
	- 0.2464642940724080,0.9686222614596370,0.0320353921812441,
	- -0.3117655950297000,-0.9062547169400450,-0.2854901080242450,
	- 0.0608632767228376,-0.7075111154985250,-0.7040764752444090,
	- -0.4607335862628370,-0.6188008149745030,-0.6362468969482480,
	- 0.2190580158109430,0.7137403609578260,0.6652730889257150,
	- -0.0823847846664380,-0.8044875371365980,-0.5882283143876660,
	- -0.8295547427688960,-0.1162092353369240,0.5461999106298320,
	- -0.0852410700430401,0.9961766497246490,0.0191322377491922,
	- 0.3131894593955590,-0.5541595443573950,0.7712454615238390,
	- -0.2053809775103630,-0.8866791538596230,0.4142689128907330,
	- -0.2803794157477670,0.8920364641234400,0.3544831870471280,
	- 0.3607197436800900,-0.9212300461377630,-0.1456587402540090,
	- 0.5099563266151200,0.8025819147395540,-0.3095267598741700,
	- 0.3434662076553160,-0.3991341139236100,0.8501311212402990,
	- -0.8525024407450160,0.5081350695533460,0.1226309080689130,
	- -0.7808884875619300,-0.2500741633167730,-0.5724299807266000,
	- -0.5053813675827790,-0.8611316666645480,0.0551536577907309,
	- -0.9210719657807660,0.3672285791438610,0.1294975077471940,
	- 0.6652607437466560,0.6063117536090580,-0.4356767153121150,
	- 0.3394557649489950,-0.6705912128459400,-0.6596038272301810
	- };
	- auto pointshell
	- = new vnl_matrix_fixed<double, 3, 150>();
	-
	- // List sorted for each row [x,y,z]
	- // pointshell need [x...x
	- // y...y
	- // z...z]
	- int i=0;
	- for(int c =0; c < 150; c++)
	- {
	- for(int r=0; r<3; r++){
	- pointshell->put(r,c,coords[i++]);
	- }
	- }
	-
	- return pointshell;
	- }
	-};
	-
	-}
	-
	-#endif //__itkPointShell_txx__
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/mitkTeemDiffusionTensor3DReconstructionImageFilter.cpp b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/mitkTeemDiffusionTensor3DReconstructionImageFilter.cpp
	deleted file mode 100644
	index 6e6d3b1e06..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/mitkTeemDiffusionTensor3DReconstructionImageFilter.cpp
	+++ /dev/null
	@@ -1,220 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <cstdlib>
	-#include <ctime>
	-
	-#include <iostream>
	-#include <fstream>
	-
	-#include <itksys/SystemTools.hxx>
	-#include "mitkPixelType.h"
	-#include "itkImageRegionIterator.h"
	-#include "itkImageFileReader.h"
	-#include <mitkIOUtil.h>
	-#include <mitkLocaleSwitch.h>
	-#include <itkMersenneTwisterRandomVariateGenerator.h>
	-
	-template< class D, class T >
	-mitk::TeemDiffusionTensor3DReconstructionImageFilter<D,T>
	-::TeemDiffusionTensor3DReconstructionImageFilter():
	-m_EstimateErrorImage(false),m_Sigma(-19191919),
	-m_EstimationMethod(TeemTensorEstimationMethodsLLS),
	-m_NumIterations(1),m_ConfidenceThreshold(-19191919.0),
	-m_ConfidenceFuzzyness(0.0),m_MinPlausibleValue(1.0)
	-{
	-}
	-
	-template< class D, class T >
	-mitk::TeemDiffusionTensor3DReconstructionImageFilter<D,T>
	-::~TeemDiffusionTensor3DReconstructionImageFilter()
	-{
	-}
	-
	-void file_replace(std::string filename, std::string what, std::string with)
	-{
	- ofstream myfile2;
	-
	- std::locale C("C");
	- std::locale originalLocale2 = myfile2.getloc();
	- myfile2.imbue(C);
	-
	- char filename2[512];
	- sprintf(filename2, "%s2",filename.c_str());
	- myfile2.open (filename2);
	-
	- std::string line;
	- ifstream myfile (filename.c_str());
	-
	- std::locale originalLocale = myfile.getloc();
	- myfile.imbue(C);
	-
	- if (myfile.is_open())
	- {
	- while (! myfile.eof() )
	- {
	- getline (myfile,line);
	- itksys::SystemTools::ReplaceString(line,what.c_str(),with.c_str());
	- myfile2 << line << std::endl;
	- }
	- myfile.close();
	- }
	- myfile2.close();
	- itksys::SystemTools::RemoveFile(filename.c_str());
	- rename(filename2,filename.c_str());
	-
	- myfile.imbue( originalLocale );
	- myfile2.imbue( originalLocale2 );
	-}
	-
	-// do the work
	-template< class D, class T >
	-void
	-mitk::TeemDiffusionTensor3DReconstructionImageFilter<D,T>
	-::Update()
	-{
	- itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer randgen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New();
	- randgen->SetSeed();
	-
	- // save input image to nrrd file in temp-folder
	- char filename[512];
	- int random_integer = randgen->GetIntegerVariate();
	- sprintf( filename, "dwi_%d.nhdr",random_integer);
	-
	- try
	- {
	- mitk::IOUtil::Save(m_Input, filename);
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.GetDescription() << std::endl;
	- }
	-
	- file_replace(filename,"vector","list");
	-
	- // build up correct command from input params
	- char command[4096];
	- sprintf( command, "tend estim -i %s -B kvp -o tensors_%d.nhdr -knownB0 true",
	- filename, random_integer);
	-
	- //m_DiffusionImages;
	- if(m_EstimateErrorImage)
	- {
	- sprintf( command, "%s -ee error_image_%d.nhdr", command, random_integer);
	- }
	-
	- if(m_Sigma != -19191919)
	- {
	- sprintf( command, "%s -sigma %f", command, m_Sigma);
	- }
	-
	- switch(m_EstimationMethod)
	- {
	- case TeemTensorEstimationMethodsLLS:
	- sprintf( command, "%s -est lls", command);
	- break;
	- case TeemTensorEstimationMethodsMLE:
	- sprintf( command, "%s -est mle", command);
	- break;
	- case TeemTensorEstimationMethodsNLS:
	- sprintf( command, "%s -est nls", command);
	- break;
	- case TeemTensorEstimationMethodsWLS:
	- sprintf( command, "%s -est wls", command);
	- break;
	- }
	-
	- sprintf( command, "%s -wlsi %d", command, m_NumIterations);
	-
	- if(m_ConfidenceThreshold != -19191919.0)
	- {
	- sprintf( command, "%s -t %f", command, m_ConfidenceThreshold);
	- }
	-
	- sprintf( command, "%s -soft %f", command, m_ConfidenceFuzzyness);
	- sprintf( command, "%s -mv %f", command, m_MinPlausibleValue);
	-
	- // call tend estim command
	- std::cout << "Calling <" << command << ">" << std::endl;
	- int success = system(command);
	- if(!success)
	- {
	- MITK_ERROR << "system command could not be called!";
	- }
	-
	- remove(filename);
	- sprintf( filename, "dwi_%d.raw", random_integer);
	- remove(filename);
	-
	- // change kind from tensor to vector
	- sprintf( filename, "tensors_%d.nhdr", random_integer);
	- file_replace(filename,"3D-masked-symmetric-matrix","vector");
	-
	- mitk::LocaleSwitch localeSwitch("C");
	- // read result as mitk::Image and provide it in m_Output
	- typedef itk::ImageFileReader<VectorImageType> FileReaderType;
	- typename FileReaderType::Pointer reader = FileReaderType::New();
	- reader->SetFileName(filename);
	- reader->Update();
	- typename VectorImageType::Pointer vecImage = reader->GetOutput();
	-
	- remove(filename);
	- sprintf( filename, "tensors_%d.raw", random_integer);
	- remove(filename);
	-
	- typename ItkTensorImageType::Pointer itkTensorImage = ItkTensorImageType::New();
	- itkTensorImage->SetSpacing( vecImage->GetSpacing() ); // Set the image spacing
	- itkTensorImage->SetOrigin( vecImage->GetOrigin() ); // Set the image origin
	- itkTensorImage->SetDirection( vecImage->GetDirection() ); // Set the image direction
	- itkTensorImage->SetLargestPossibleRegion( vecImage->GetLargestPossibleRegion() );
	- itkTensorImage->SetBufferedRegion( vecImage->GetLargestPossibleRegion() );
	- itkTensorImage->SetRequestedRegion( vecImage->GetLargestPossibleRegion() );
	- itkTensorImage->Allocate();
	-
	- itk::ImageRegionIterator<VectorImageType> it(vecImage,
	- vecImage->GetLargestPossibleRegion());
	-
	- itk::ImageRegionIterator<ItkTensorImageType> it2(itkTensorImage,
	- itkTensorImage->GetLargestPossibleRegion());
	- it2 = it2.Begin();
	-
	- //#pragma omp parallel private (it)
	- {
	- for(it=it.Begin();!it.IsAtEnd(); ++it, ++it2)
	- {
	- //#pragma omp single nowait
	- {
	- VectorType vec = it.Get();
	- TensorType tensor;
	- for(int i=1;i<7;i++)
	- tensor[i-1] = vec[i] * vec[0];
	- it2.Set( tensor );
	- }
	- } // end for
	- } // end ompparallel
	-
	- m_OutputItk = mitk::TensorImage::New();
	- m_OutputItk->InitializeByItk(itkTensorImage.GetPointer());
	- m_OutputItk->SetVolume( itkTensorImage->GetBufferPointer() );
	-
	- // in case: read resulting error-image and provide it in m_ErrorImage
	- if(m_EstimateErrorImage)
	- {
	- // open error image here
	- }
	-
	-}
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/mitkTeemDiffusionTensor3DReconstructionImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/mitkTeemDiffusionTensor3DReconstructionImageFilter.h
	deleted file mode 100644
	index 4cc5dcb4e1..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/mitkTeemDiffusionTensor3DReconstructionImageFilter.h
	+++ /dev/null
	@@ -1,116 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef __mitkTeemDiffusionTensor3DReconstructionImageFilter_h__
	-#define __mitkTeemDiffusionTensor3DReconstructionImageFilter_h__
	-
	-#include "mitkImage.h"
	-#include "mitkTensorImage.h"
	-#include "itkDiffusionTensor3D.h"
	-
	-namespace mitk
	-{
	-
	- enum TeemTensorEstimationMethods{
	- TeemTensorEstimationMethodsLLS,
	- TeemTensorEstimationMethodsNLS,
	- TeemTensorEstimationMethodsWLS,
	- TeemTensorEstimationMethodsMLE,
	- };
	-
	- template< class DiffusionImagePixelType = short,
	- class TTensorPixelType=float >
	- class TeemDiffusionTensor3DReconstructionImageFilter : public itk::Object
	- {
	- public:
	-
	- typedef TTensorPixelType TensorPixelType;
	-
	- typedef itk::Vector<TensorPixelType,7> VectorType;
	- typedef itk::Image<VectorType,3> VectorImageType;
	-
	- typedef itk::DiffusionTensor3D<TensorPixelType> TensorType;
	- typedef itk::Image<TensorType,3 > ItkTensorImageType;
	-
	- typedef itk::Vector<TensorPixelType,6> ItkTensorVectorType;
	- typedef itk::Image<ItkTensorVectorType,3> ItkTensorVectorImageType;
	-
	- typedef DiffusionImagePixelType DiffusionPixelType;
	- typedef itk::VectorImage< DiffusionPixelType, 3 > DiffusionImageType;
	-
	- mitkClassMacroItkParent( TeemDiffusionTensor3DReconstructionImageFilter,
	- itk::Object );
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- itkGetMacro(Input,
	- mitk::Image::Pointer);
	- itkSetMacro(Input,
	- mitk::Image::Pointer);
	-
	- itkGetMacro(EstimateErrorImage, bool);
	- itkSetMacro(EstimateErrorImage, bool);
	-
	- itkGetMacro(Sigma, float);
	- itkSetMacro(Sigma, float);
	-
	- itkGetMacro(EstimationMethod, TeemTensorEstimationMethods);
	- itkSetMacro(EstimationMethod, TeemTensorEstimationMethods);
	-
	- itkGetMacro(NumIterations, int);
	- itkSetMacro(NumIterations, int);
	-
	- itkGetMacro(ConfidenceThreshold, double);
	- itkSetMacro(ConfidenceThreshold, double);
	-
	- itkGetMacro(ConfidenceFuzzyness, float);
	- itkSetMacro(ConfidenceFuzzyness, float);
	-
	- itkGetMacro(MinPlausibleValue, double);
	- itkSetMacro(MinPlausibleValue, double);
	-
	- itkGetMacro(Output, mitk::TensorImage::Pointer);
	- itkGetMacro(OutputItk, mitk::TensorImage::Pointer);
	-
	- // do the work
	- virtual void Update();
	-
	- protected:
	-
	- TeemDiffusionTensor3DReconstructionImageFilter();
	- virtual ~TeemDiffusionTensor3DReconstructionImageFilter();
	-
	- mitk::Image::Pointer m_Input;
	- bool m_EstimateErrorImage;
	- float m_Sigma;
	- TeemTensorEstimationMethods m_EstimationMethod;
	- int m_NumIterations;
	- double m_ConfidenceThreshold;
	- float m_ConfidenceFuzzyness;
	- double m_MinPlausibleValue;
	- mitk::TensorImage::Pointer m_Output;
	- mitk::TensorImage::Pointer m_OutputItk;
	- mitk::Image::Pointer m_ErrorImage;
	- };
	-
	-}
	-
	-#include "mitkTeemDiffusionTensor3DReconstructionImageFilter.cpp"
	-
	-#endif
	-
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Registration/mitkDWIHeadMotionCorrectionFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Registration/mitkDWIHeadMotionCorrectionFilter.h
	deleted file mode 100644
	index e5202cd56c..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Registration/mitkDWIHeadMotionCorrectionFilter.h
	+++ /dev/null
	@@ -1,80 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef MITKDWIHEADMOTIONCORRECTIONFILTER_H
	-#define MITKDWIHEADMOTIONCORRECTIONFILTER_H
	-
	-#include "mitkImageToImageFilter.h"
	-
	-#include <itkAccumulateImageFilter.h>
	-#include <itkExtractImageFilter.h>
	-
	-#include "mitkITKImageImport.h"
	-#include <itkVectorImage.h>
	-#include <MitkDiffusionCoreExports.h>
	-
	-namespace mitk
	-{
	-
	-/**
	- * @class DWIHeadMotionCorrectionFilter
	- *
	- * @brief Performs standard head-motion correction by using affine registration of the gradient images.
	- *
	- * (Head) motion correction is a essential pre-processing step before performing any further analysis of a diffusion-weighted
	- * images since all model fits ( tensor, ODF ) rely on an aligned diffusion-weighted dataset. The correction is done in two steps. First the
	- * unweighted images ( if multiple present ) are separately registered on the first one by means of rigid registration and normalized correlation
	- * as error metric. Second, the weighted gradient images are registered to the unweighted reference ( computed as average from the aligned images from first step )
	- * by an affine transformation using the MattesMutualInformation metric as optimizer guidance.
	- *
	- */
	-
	-class MITKDIFFUSIONCORE_EXPORT DWIHeadMotionCorrectionFilter
	- : public ImageToImageFilter
	-{
	-public:
	-
	- // class macros
	- mitkClassMacro( DWIHeadMotionCorrectionFilter,
	- ImageToImageFilter )
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- // public typedefs
	- typedef short DiffusionPixelType;
	- typedef Superclass::InputImageType InputImageType;
	- typedef Superclass::OutputImageType OutputImageType;
	- typedef itk::VectorImage<DiffusionPixelType, 3> ITKDiffusionImageType;
	- typedef itk::Image<DiffusionPixelType, 3> ITKDiffusionVolumeType;
	-
	- mitk::Image::Pointer GetCorrectedImage() const;
	- void UpdateOutputInformation() override;
	-
	-protected:
	- DWIHeadMotionCorrectionFilter();
	- ~DWIHeadMotionCorrectionFilter() override {}
	-
	- mitk::Image::Pointer m_CorrectedImage;
	-
	- void GenerateData() override;
	-
	-};
	-
	-} //end namespace mitk
	-
	-
	-#endif // MITKDWIHEADMOTIONCORRECTIONFILTER_H
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Registration/mitkPyramidImageRegistrationMethod.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Registration/mitkPyramidImageRegistrationMethod.h
	deleted file mode 100644
	index 742d34d742..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Registration/mitkPyramidImageRegistrationMethod.h
	+++ /dev/null
	@@ -1,343 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef MITKPYRAMIDIMAGEREGISTRATION_H
	-#define MITKPYRAMIDIMAGEREGISTRATION_H
	-
	-#include <MitkDiffusionCoreExports.h>
	-
	-#include <itkObject.h>
	-#include "itkImageMaskSpatialObject.h"
	-#include "itkNotImageFilter.h"
	-#include <itkCenteredVersorTransformInitializer.h>
	-#include <itkOptimizerParameters.h>
	-
	-#include <vnl/vnl_matrix_fixed.h>
	-
	-#include "mitkImage.h"
	-#include "mitkBaseProcess.h"
	-
	-#include "mitkPyramidRegistrationMethodHelper.h"
	-#include <itkWindowedSincInterpolateImageFunction.h>
	-
	-#include "mitkImageToItk.h"
	-#include "mitkImageCast.h"
	-#include "mitkImageCaster.h"
	-#include "mitkITKImageImport.h"
	-#include "mitkIOUtil.h"
	-
	-
	-namespace mitk
	-{
	-
	-/**
	- * @brief The PyramidImageRegistration class implements a multi-scale registration method
	- *
	- * The PyramidImageRegistration class is suitable for aligning (f.e.) brain MR images. The method offers two
	- * transform types
	- * - Rigid: optimizing translation and rotation only and
	- * - Affine ( default ): with scaling in addition ( 12 DOF )
	- *
	- * The error metric is internally chosen based on the selected task type : \sa SetCrossModalityOn
	- *
	- * It uses
	- * - MattesMutualInformation for CrossModality=on ( default ) and
	- * - NormalizedCorrelation for CrossModality=off.
	- */
	-class MITKDIFFUSIONCORE_EXPORT PyramidImageRegistrationMethod :
	- public itk::Object
	-{
	-public:
	-
	- /** Typedefs */
	- mitkClassMacroItkParent(PyramidImageRegistrationMethod, itk::Object)
	-
	- /** Smart pointer support */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- typedef itk::OptimizerParameters<double> ParametersType;
	-
	- /** Typedef for the transformation matrix, corresponds to the InternalMatrixType from ITK transforms */
	- typedef vnl_matrix_fixed< double, 3, 3> TransformMatrixType;
	-
	- typedef itk::AffineTransform< double > AffineTransformType;
	- typedef itk::Euler3DTransform< double > RigidTransformType;
	-
	- /** Registration is between modalities - will take MattesMutualInformation as error metric */
	- void SetCrossModalityOn()
	- {
	- m_CrossModalityRegistration = true;
	- }
	-
	- /** Registration is between modalities - will take NormalizedCorrelation as error metric */
	- void SetCrossModalityOff()
	- {
	- m_CrossModalityRegistration = false;
	- }
	-
	- /** Turn the cross-modality on/off */
	- void SetCrossModality(bool flag)
	- {
	- if( flag )
	- this->SetCrossModalityOn();
	- else
	- this->SetCrossModalityOff();
	- }
	-
	- /** Controll the verbosity of the registration output
	- *
	- * for true, each iteration step of the optimizer is watched and passed to the std::cout
	- */
	- void SetVerbose(bool flag)
	- {
	- if( flag )
	- this->SetVerboseOn();
	- else
	- this->SetVerboseOff();
	- }
	-
	- /** Turn verbosity on, \sa SetVerbose */
	- void SetVerboseOn()
	- {
	- m_Verbose = true;
	- }
	-
	- /** Turn verbosity off, \sa SetVerbose */
	- void SetVerboseOff()
	- {
	- m_Verbose = false;
	- }
	-
	- /** A rigid ( 6dof : translation + rotation ) transform is optimized */
	- void SetTransformToRigid()
	- {
	- m_UseAffineTransform = false;
	- }
	-
	- /** An affine ( 12dof : Rigid + scale + skew ) transform is optimized */
	- void SetTransformToAffine()
	- {
	- m_UseAffineTransform = true;
	- }
	-
	- /** Input image, the reference one */
	- void SetFixedImage( mitk::Image::Pointer );
	-
	- /** Input image, the one to be transformed */
	- void SetMovingImage( mitk::Image::Pointer );
	-
	- /** Fixed image mask, excludes the masked voxels from the registration metric*/
	- void SetFixedImageMask( mitk::Image::Pointer mask);
	-
	- /** \brief Use the itk::CenteredVersorTransformInitializer to perform initialization step for the registration
	- *
	- * The initializer takes the geometries and their features to perform an initialization for the successive registration
	- */
	- void SetInitializeByGeometry(bool flag)
	- {
	- m_InitializeByGeometry = flag;
	- }
	-
	- void Update();
	-
	- /**
	- * @brief Get the number of parameters optimized ( 12 or 6 )
	- *
	- * @return number of paramters
	- */
	- unsigned int GetNumberOfParameters()
	- {
	- unsigned int retValue = 12;
	- if(!m_UseAffineTransform)
	- retValue = 6;
	-
	- return retValue;
	- }
	-
	- /**
	- * @brief Copies the estimated parameters to the given array
	- * @param paramArray, target array for copy, make sure to allocate enough space
	- */
	- void GetParameters( double* paramArray)
	- {
	- if( m_EstimatedParameters == nullptr )
	- {
	- mitkThrow() << "No parameters were estimated yet, call Update() first.";
	- }
	-
	- unsigned int dim = 12;
	- if( !m_UseAffineTransform )
	- dim = 6;
	-
	- for( unsigned int i=0; i<dim; i++)
	- {
	- *(paramArray+i) = m_EstimatedParameters[i];
	- }
	- }
	-
	- /**
	- * @brief Retrieve the parameters of the last registration computed
	- *
	- * @return Parameters array ( as an itk::Array )
	- */
	- ParametersType GetLastRegistrationParameters()
	- {
	- if( m_EstimatedParameters == nullptr )
	- {
	- mitkThrow() << "No parameters were estimated yet, call Update() first.";
	- }
	-
	- unsigned int dim = 12;
	- if( !m_UseAffineTransform )
	- dim = 6;
	-
	- ParametersType params(dim);
	-
	- params.SetDataSameSize( m_EstimatedParameters );
	- return params;
	- }
	-
	- /**
	- * @brief Set the starting position of the registration
	- *
	- * @param params make sure the parameters have the same dimension as the selected transform type
	- * otherwise the update call will throw an exception
	- */
	- void SetInitialParameters( ParametersType& params )
	- {
	- m_InitialParameters = params;
	- }
	-
	- /**
	- * @brief Control the interpolator used for resampling.
	- *
	- * The Windowed Sinc Interpolator is more time consuming, but the interpolation preserves more structure
	- * in the data
	- *
	- * The class uses the
	- * - Linear interpolator on default ( flag = false )
	- * - WindowedSinc interpolator if called with true
	- */
	- void SetUseAdvancedInterpolation( bool flag)
	- {
	- m_UseWindowedSincInterpolator = flag;
	- }
	-
	- /**
	- * @brief Control the interpolator used for resampling.
	- *
	- * The class uses the
	- * - Linear interpolator on default ( flag = false )
	- * - Nearest neighbor interpolation if this is true
	- *
	- * used to resample e.g. segmentations.
	- */
	- void SetUseNearestNeighborInterpolation( bool flag)
	- {
	- m_UseNearestNeighborInterpolator = flag;
	- }
	-
	- /**
	- * @brief Set if fixed image mask is used to exclude a region.
	- * @param flag , true if mask is to be used, false if mask is to be ignored (default)
	- */
	- void SetUseFixedImageMask( bool flag)
	- {
	- m_UseMask = flag;
	- }
	-
	- /**
	- * @brief Returns the moving image transformed according to the estimated transformation and resampled
	- * to the geometry of the fixed/resampling reference image
	- *
	- */
	- mitk::Image::Pointer GetResampledMovingImage();
	-
	- /**
	- * @brief Returns a provided moving image transformed according to the given transformation and resampled
	- * to the geometry of the fixed/resampling reference image
	- */
	- mitk::Image::Pointer GetResampledMovingImage(mitk::Image::Pointer movingImage, double *transform );
	-
	- /**
	- * @brief Get the rotation part of the transformation as a vnl_fixed_matrix<double, 3,3>
	- *
	- * It returns identity if the internal parameters are not-yet allocated ( i.e. the filter did not run yet )
	- *
	- * @return \sa TransformMatrixType
	- */
	- TransformMatrixType GetLastRotationMatrix();
	-
	-
	-protected:
	- PyramidImageRegistrationMethod();
	-
	- ~PyramidImageRegistrationMethod() override;
	-
	- /** Fixed image, used as reference for registration */
	- mitk::Image::Pointer m_FixedImage;
	-
	- /** Moving image, will be transformed */
	- mitk::Image::Pointer m_MovingImage;
	-
	- mitk::Image::Pointer m_FixedImageMask;
	-
	- bool m_CrossModalityRegistration;
	-
	- bool m_UseAffineTransform;
	-
	- bool m_UseWindowedSincInterpolator;
	-
	- bool m_UseNearestNeighborInterpolator;
	-
	- bool m_UseMask;
	-
	- double* m_EstimatedParameters;
	-
	- ParametersType m_InitialParameters;
	-
	- /** Control the verbosity of the regsitistration output */
	- bool m_Verbose;
	-
	- bool m_InitializeByGeometry;
	-
	- /**
	- * @brief The method takes two itk::Images and performs a multi-scale registration on them
	- *
	- * Can be accessed by the AccessTwoImagesFixedDimensionByItk macro.
	- *
	- * @note Currently the access is currently reduced only for short and float ( the only types occuring with mitk::DiffusionImage ) and
	- * hence the method is accessed by means of the \sa AccessTwoImagesFixedDimensionTypeSubsetByItk macro.
	- */
	-template <typename TPixel1, unsigned int VImageDimension1, typename TPixel2, unsigned int VImageDimension2>
	- void RegisterTwoImagesV4(itk::Image<TPixel1, VImageDimension1>* itkImage1, itk::Image<TPixel2, VImageDimension2>* itkImage2);
	-
	- /**
	- * @brief ResampleMitkImage applies the functionality of an the itk::ResampleImageFilter to the given
	- * mitk::Image.
	- *
	- * The API of the function is conform to the interface of \sa AccessByItk_1 macros.
	- */
	- template< typename TPixel, unsigned int VDimension>
	- void ResampleMitkImage( itk::Image<TPixel, VDimension>* itkImage,
	- mitk::Image::Pointer& outputImage );
	-
	-};
	-
	-} // end namespace
	-
	-#endif // MITKPYRAMIDIMAGEREGISTRATION_H
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Registration/mitkPyramidRegistrationMethodHelper.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Registration/mitkPyramidRegistrationMethodHelper.h
	deleted file mode 100644
	index 4b3a670b0e..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Registration/mitkPyramidRegistrationMethodHelper.h
	+++ /dev/null
	@@ -1,212 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef MITKPYRAMIDREGISTRATIONMETHODHELPER_H
	-#define MITKPYRAMIDREGISTRATIONMETHODHELPER_H
	-
	-#include <MitkDiffusionCoreExports.h>
	-
	-#include <itkCommand.h>
	-
	-#include <itkRegularStepGradientDescentOptimizer.h>
	-#include <itkMattesMutualInformationImageToImageMetricv4.h>
	-#include <itkCorrelationImageToImageMetricv4.h>
	-#include <itkGradientDescentLineSearchOptimizerv4.h>
	-
	-#include <itkImageRegistrationMethodv4.h>
	-
	-#include <itkAffineTransform.h>
	-#include <itkEuler3DTransform.h>
	-
	-#include <itkMattesMutualInformationImageToImageMetric.h>
	-#include <itkNormalizedCorrelationImageToImageMetric.h>
	-
	-#include <itkMultiResolutionImageRegistrationMethod.h>
	-#include <itkImageMomentsCalculator.h>
	-
	-#include "mitkImageAccessByItk.h"
	-
	-/**
	- * @brief Provides same functionality as \a AccessTwoImagesFixedDimensionByItk for a subset of types
	- *
	- * For now, the subset defined is only short and float.
	- */
	-#define AccessTwoImagesFixedDimensionTypeSubsetByItk(mitkImage1, mitkImage2, itkImageTypeFunction, dimension) \
	-{ \
	- const mitk::PixelType& pixelType1 = mitkImage1->GetPixelType(); \
	- const mitk::PixelType& pixelType2 = mitkImage2->GetPixelType(); \
	- const mitk::Image* constImage1 = mitkImage1; \
	- const mitk::Image* constImage2 = mitkImage2; \
	- mitk::Image* nonConstImage1 = const_cast<mitk::Image*>(constImage1); \
	- mitk::Image* nonConstImage2 = const_cast<mitk::Image*>(constImage2); \
	- nonConstImage1->Update(); \
	- nonConstImage2->Update(); \
	- _checkSpecificDimension(mitkImage1, (dimension)); \
	- _checkSpecificDimension(mitkImage2, (dimension)); \
	- _accessTwoImagesByItkForEach(itkImageTypeFunction, ((short, dimension))((unsigned short, dimension))((float, dimension))((double, dimension)), ((short, dimension))((unsigned short, dimension))((float, dimension))((double, dimension)) ) \
	- { \
	- std::string msg("Pixel type "); \
	- msg.append(pixelType1.GetComponentTypeAsString() ); \
	- msg.append(" or pixel type "); \
	- msg.append(pixelType2.GetComponentTypeAsString() ); \
	- msg.append(" is not in " BOOST_PP_STRINGIZE(MITK_ACCESSBYITK_TYPES_DIMN_SEQ(dimension))); \
	- throw mitk::AccessByItkException(msg); \
	- } \
	-}
	-
	-
	-/**
	- * @brief The PyramidOptControlCommand class stears the step lenght of the
	- * gradient descent optimizer in multi-scale registration methods
	- */
	-template <typename RegistrationType >
	-class PyramidOptControlCommand : public itk::Command
	-{
	-public:
	-
	- typedef itk::RegularStepGradientDescentOptimizer OptimizerType;
	-
	- mitkClassMacroItkParent(PyramidOptControlCommand<RegistrationType>, itk::Command)
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- void Execute(itk::Object caller, const itk::EventObject & /event*/) override
	- {
	- RegistrationType* registration = dynamic_cast< RegistrationType* >( caller );
	-
	- if( registration == nullptr)
	- return;
	-
	- MITK_DEBUG << "\t - Pyramid level " << registration->GetCurrentLevel();
	- if( registration->GetCurrentLevel() == 0 )
	- { MITK_WARN("OptCommand") << "Cast to registration failed";
	- return;
	- }
	-
	- OptimizerType* optimizer = dynamic_cast< OptimizerType* >(registration->GetOptimizer());
	-
	- if( optimizer == nullptr)
	- { MITK_WARN("OptCommand") << "Cast to optimizer failed";
	- return;
	- }
	-
	- MITK_DEBUG /<< optimizer->GetStopConditionDescription() << "\n"/
	- << optimizer->GetValue() << " : " << optimizer->GetCurrentPosition();
	-
	- optimizer->SetMaximumStepLength( optimizer->GetMaximumStepLength() * 0.25f );
	- optimizer->SetMinimumStepLength( optimizer->GetMinimumStepLength() * 0.1f );
	- // optimizer->SetNumberOfIterations( optimizer->GetNumberOfIterations() * 1.5f );
	- }
	-
	- void Execute(const itk::Object * /object/, const itk::EventObject & /event/) override{}
	-};
	-
	-#include <itkGradientDescentLineSearchOptimizerv4.h>
	-
	-template <typename RegistrationType >
	-class PyramidOptControlCommandv4 : public itk::Command
	-{
	-public:
	-
	- typedef itk::GradientDescentLineSearchOptimizerv4 OptimizerType;
	-
	- mitkClassMacroItkParent(PyramidOptControlCommandv4<RegistrationType>, itk::Command)
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- void Execute(itk::Object caller, const itk::EventObject & /event*/) override
	- {
	- RegistrationType* registration = dynamic_cast< RegistrationType* >( caller );
	-
	- if( registration == nullptr)
	- return;
	-
	- MITK_DEBUG << "\t - Pyramid level " << registration->GetCurrentLevel();
	- if( registration->GetCurrentLevel() == 0 )
	- return;
	-
	- OptimizerType* optimizer = dynamic_cast< OptimizerType* >( registration->GetOptimizer() );
	-
	- if( optimizer == nullptr)
	- { MITK_WARN("OptCommand4") << "Cast to optimizer failed";
	- return;
	- }
	-
	- optimizer->SetNumberOfIterations( optimizer->GetNumberOfIterations() * 2.5 );
	- optimizer->SetMaximumStepSizeInPhysicalUnits( optimizer->GetMaximumStepSizeInPhysicalUnits() * 0.4);
	-
	- MITK_INFO("Pyramid.Command.Iter") << optimizer->GetNumberOfIterations();
	- MITK_INFO("Pyramid.Command.MaxStep") << optimizer->GetMaximumStepSizeInPhysicalUnits();
	-
	- }
	-
	- void Execute(const itk::Object * /object/, const itk::EventObject & /event/) override{}
	-};
	-
	-
	-template <typename OptimizerType>
	-class OptimizerIterationCommand : public itk::Command
	-{
	-public:
	- mitkClassMacroItkParent(OptimizerIterationCommand<OptimizerType>, itk::Command)
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- void Execute(itk::Object caller, const itk::EventObject & /event*/) override
	- {
	-
	- OptimizerType* optimizer = dynamic_cast< OptimizerType* >( caller );
	-
	- unsigned int currentIter = optimizer->GetCurrentIteration();
	- MITK_INFO << "[" << currentIter << "] : " << optimizer->GetValue() << " : " << optimizer->GetCurrentPosition();
	-
	- }
	-
	- void Execute(const itk::Object * /object/, const itk::EventObject & /event/) override
	- {
	-
	- }
	-};
	-
	-template <typename OptimizerType>
	-class OptimizerIterationCommandv4 : public itk::Command
	-{
	-public:
	- itkNewMacro( OptimizerIterationCommandv4 )
	-
	- void Execute(itk::Object *object, const itk::EventObject & event) override
	- {
	- OptimizerType* optimizer = dynamic_cast< OptimizerType* >( object );
	-
	- if( typeid( event ) != typeid( itk::IterationEvent ) )
	- { return; }
	-
	- unsigned int currentIter = optimizer->GetCurrentIteration();
	- MITK_INFO << "[" << currentIter << "] : " << optimizer->GetCurrentMetricValue() << " : "
	- << optimizer->GetMetric()->GetParameters() ;
	- //<< " : " << optimizer->GetScales();
	-
	- }
	-
	- void Execute(const itk::Object * /object/, const itk::EventObject & /event/) override
	- {
	-
	-
	- }
	-};
	-
	-
	-#endif // MITKPYRAMIDREGISTRATIONMETHODHELPER_H
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Registration/mitkRegistrationWrapper.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Registration/mitkRegistrationWrapper.h
	deleted file mode 100644
	index 768a9b9c9e..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Registration/mitkRegistrationWrapper.h
	+++ /dev/null
	@@ -1,70 +0,0 @@
	-#ifndef MITKBATCHEDREGISTRATION_H
	-#define MITKBATCHEDREGISTRATION_H
	-
	-// MITK
	-#include <MitkDiffusionCoreExports.h>
	-#include "mitkCommon.h"
	-#include "mitkImage.h"
	-
	-
	-namespace mitk
	-{
	-/**
	- * @brief The RegistrationWrapper class wraps the pyramid registration to calculate and apply a reference transformation to several images.
	- *
	- * Use if several pictures with the same world geometry are to be registered
	- * to one reference image, the registration is only computed once (for the moving image) and the geometry can be transformed for the complete
	- * image batch accordingly. Can handle image types that are usually not supported by registrations filters, e.g. fiber bundles and segmentations:
	- * these can be registered if a "registerable" image such as B0/T2 from which they are derived is supplied, since the transformation can be calculated
	- * on those and applied to the derived objects.
	- *
	- * For DWI images a registerable B0 Image will automatically be extracted.
	- *
	- */
	-class MITKDIFFUSIONCORE_EXPORT RegistrationWrapper
	-{
	-public:
	-
	- typedef itk::Image<double,3> ItkImageType;
	- typedef itk::Image<unsigned char,3> ItkBinaryImageType;
	- typedef double* RidgidTransformType;
	-
	-
	- /**
	- * @brief ApplyTransformationToImage Applies transformation from GetTransformation to provided image.
	- *
	- * Transforms image according to previously calculated transformation. Can be applied to derived resources also (e.g. binary images).
	- * Handles DWI Data and rotates the gradients according to the transformation.
	- * Images are resampled to provided reference, if no reference it supplied a copy of the input image is used as reference.
	- *
	- * @param img - image on which the transformation is to be applied
	- * @param transformation - transformation returned from GetTransformation
	- * @param offset - offset transformation returned from GetTransformation
	- * @param resampleReference - image to which is to be resampled
	- * @param binary - resampling will be done using nearest neighbor interpolation
	- */
	- static void ApplyTransformationToImage(mitk::Image::Pointer img, const RidgidTransformType& transformation, double offset, mitk::Image resampleReference = nullptr , bool binary = false);
	-
	- /**
	- * @brief GetTransformation Registeres the moving to the fixed image and returns the according transformation
	- *
	- * \note Does not return a registered image \see ApplyTransformationToImage for this.
	- *
	- * Both images are set to the same origin (the one of the fixed image), this is supposed to ensure overlapping,
	- * the correction of the moving image is returned in the offset.
	- *
	- * It is possible mask a certain area and thereby excluding it from the registration metric (e.g. a tumor that is operated on),
	- * this can be set as mitk::Image where all non-zero voxels are excluded.
	- *
	- * @param fixedImage
	- * @param movingImage
	- * @param transformation
	- * @param offset - stores offset that has been applied to match origin of both images
	- * @param useSameOrigin -
	- * @param mask - optional, provide a mask that is excluded from registration metric
	- */
	- static void GetTransformation(Image::Pointer fixedImage , Image::Pointer movingImage, RidgidTransformType transformation, double* offset, bool useSameOrigin = true, mitk::Image* mask = nullptr);
	-};
	-
	-}
	-#endif // MITKBATCHEDREGISTRATION_H
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkAdcImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkAdcImageFilter.h
	deleted file mode 100644
	index 9d20dd89d6..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkAdcImageFilter.h
	+++ /dev/null
	@@ -1,136 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-/*===================================================================
	-
	-This file is based heavily on a corresponding ITK filter.
	-
	-===================================================================*/
	-#ifndef __itkAdcImageFilter_h_
	-#define __itkAdcImageFilter_h_
	-
	-#include "itkImageToImageFilter.h"
	-#include "itkVectorImage.h"
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <vnl/algo/vnl_levenberg_marquardt.h>
	-#include <vnl/vnl_least_squares_function.h>
	-
	-namespace itk{
	-/** \class AdcImageFilter
	- */
	-
	-template< class TInPixelType, class TOutPixelType >
	-class AdcImageFilter :
	- public ImageToImageFilter< VectorImage< TInPixelType, 3 >, Image< TOutPixelType, 3 > >
	-{
	-
	-public:
	-
	- typedef AdcImageFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageToImageFilter< VectorImage< TInPixelType, 3 >, Image< TOutPixelType, 3 > > Superclass;
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionType GradientDirectionType;
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer GradientContainerType;
	- typedef itk::Image< unsigned char, 3> ItkUcharImageType;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(AdcImageFilter, ImageToImageFilter)
	-
	- typedef typename Superclass::InputImageType InputImageType;
	- typedef typename Superclass::OutputImageType OutputImageType;
	- typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
	-
	- itkSetMacro( MaskImage, ItkUcharImageType::Pointer )
	- itkSetMacro( FitSignal, bool )
	- itkSetMacro( B_value, double )
	- itkSetMacro( GradientDirections, GradientContainerType )
	-
	- /**
	- * \brief The lestSquaresFunction struct for Non-Linear-Least-Squres fit of monoexponential model Si = S0exp(-bADC)
	- */
	- struct adcLeastSquaresFunction: public vnl_least_squares_function
	- {
	-
	- void set_S0(double val)
	- {
	- S0 = val;
	- }
	-
	- void set_measurements(const vnl_vector<double>& m)
	- {
	- measurements.set_size(m.size());
	- measurements.copy_in(m.data_block());
	- }
	-
	- void set_bvalues(const vnl_vector<double>& x)
	- {
	- bValues.set_size(x.size());
	- bValues.copy_in(x.data_block());
	- }
	-
	- vnl_vector<double> measurements;
	- vnl_vector<double> bValues;
	- double S0;
	-
	- adcLeastSquaresFunction(unsigned int number_of_measurements=1) :
	- vnl_least_squares_function(1, number_of_measurements, no_gradient)
	- {
	- }
	-
	- void f(const vnl_vector<double>& x, vnl_vector<double>& fx) override {
	-
	- const double & ADC = x[0];
	-
	- for(unsigned int s=0; s<measurements.size(); s++)
	- {
	- double approx = S0 * std::exp(-bValues[s] * ADC);
	- fx[s] = vnl_math_abs( measurements[s] - approx );
	- }
	- }
	- };
	-
	- protected:
	- AdcImageFilter();
	- ~AdcImageFilter() override {}
	- void PrintSelf(std::ostream& os, Indent indent) const override;
	-
	- void BeforeThreadedGenerateData() override;
	- void ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, ThreadIdType) override;
	-
	- bool m_FitSignal;
	- double m_B_value;
	- vnl_vector<double> m_B_values;
	- vnl_vector<double> m_Nonzero_B_values;
	- GradientContainerType m_GradientDirections;
	- ItkUcharImageType::Pointer m_MaskImage;
	-
	- double FitSingleVoxel( const typename InputImageType::PixelType &input);
	-
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkAdcImageFilter.txx"
	-#endif
	-
	-#endif //__itkAdcImageFilter_h_
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkAdcImageFilter.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkAdcImageFilter.txx
	deleted file mode 100644
	index ba2041be3c..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkAdcImageFilter.txx
	+++ /dev/null
	@@ -1,208 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkAdcImageFilter_txx
	-#define __itkAdcImageFilter_txx
	-
	-#include <ctime>
	-#include <cstdio>
	-#include <cstdlib>
	-
	-#define _USE_MATH_DEFINES
	-#include <cmath>
	-
	-#include "itkImageRegionConstIterator.h"
	-#include "itkImageRegionConstIteratorWithIndex.h"
	-#include "itkImageRegionIterator.h"
	-
	-namespace itk {
	-
	-
	-template< class TInPixelType, class TOutPixelType >
	-AdcImageFilter< TInPixelType, TOutPixelType>
	-::AdcImageFilter()
	- : m_FitSignal(true)
	- , m_B_value(0)
	-{
	- this->SetNumberOfRequiredInputs( 1 );
	-}
	-
	-template< class TInPixelType, class TOutPixelType >
	-void
	-AdcImageFilter< TInPixelType, TOutPixelType>
	-::BeforeThreadedGenerateData()
	-{
	- typename OutputImageType::Pointer outputImage =
	- static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0));
	- outputImage->FillBuffer(0.0);
	-
	- m_B_values.set_size(m_GradientDirections->Size());
	- int nonzero = 0;
	- for (unsigned int i=0; i<m_GradientDirections->Size(); i++)
	- {
	- GradientDirectionType g = m_GradientDirections->GetElement(i);
	- double twonorm = g.two_norm();
	- double b = m_B_valuetwonormtwonorm;
	- m_B_values[i] = b;
	-
	- if (g.magnitude()>0.001)
	- nonzero++;
	- }
	-
	- m_Nonzero_B_values.set_size(nonzero);
	- nonzero = 0;
	- for (unsigned int i=0; i<m_B_values.size(); i++)
	- {
	- if (m_B_values[i]>1)
	- {
	- m_Nonzero_B_values[nonzero] = m_B_values[i];
	- nonzero++;
	- }
	- }
	-
	- if (m_B_values.size() == m_Nonzero_B_values.size())
	- mitkThrow() << "Unweighted (b=0 s/mm²) image volume missing!";
	-
	-}
	-
	-template< class TInPixelType, class TOutPixelType >
	-double
	-AdcImageFilter< TInPixelType, TOutPixelType>::FitSingleVoxel( const typename InputImageType::PixelType &input)
	-{
	- double S0 = 0;
	- int nonzero = 0;
	- vnl_vector<double> m; m.set_size(m_Nonzero_B_values.size());
	- for (unsigned int i=0; i<m_B_values.size(); i++)
	- {
	- if (m_B_values[i]>1)
	- {
	- m[nonzero] = input[i];
	- nonzero++;
	- }
	- else
	- S0 += input[i];
	- }
	- S0 /= (m_B_values.size() - m_Nonzero_B_values.size());
	-
	- adcLeastSquaresFunction f(m_Nonzero_B_values.size());
	- f.set_bvalues(m_Nonzero_B_values);
	- f.set_S0(S0);
	- f.set_measurements(m);
	-
	- vnl_levenberg_marquardt lm(f);
	-
	- vnl_vector_fixed<double, 1> x; x.fill(0);
	- lm.minimize(x);
	-
	- return x[0];
	-}
	-
	-template< class TInPixelType, class TOutPixelType >
	-void
	-AdcImageFilter< TInPixelType, TOutPixelType>
	-::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, ThreadIdType )
	-{
	- typename OutputImageType::Pointer outputImage =
	- static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0));
	-
	- ImageRegionIterator< OutputImageType > oit(outputImage, outputRegionForThread);
	- oit.GoToBegin();
	-
	- typedef ImageRegionConstIterator< InputImageType > InputIteratorType;
	- typename InputImageType::Pointer inputImagePointer = NULL;
	- inputImagePointer = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) );
	-
	- InputIteratorType git( inputImagePointer, outputRegionForThread );
	- git.GoToBegin();
	- while( !git.IsAtEnd() )
	- {
	- typename InputImageType::PixelType pix = git.Get();
	- TOutPixelType outval = 0;
	-
	- if (!m_FitSignal)
	- {
	- double S0 = 0;
	- int c = 0;
	- for (unsigned int i=0; i<inputImagePointer->GetVectorLength(); i++)
	- {
	- GradientDirectionType g = m_GradientDirections->GetElement(i);
	- if (g.magnitude()<0.001)
	- {
	- if (pix[i]>0)
	- {
	- S0 += pix[i];
	- c++;
	- }
	- }
	- }
	- if (c>0)
	- S0 /= c;
	-
	- if (S0>0)
	- {
	- c = 0;
	- for (unsigned int i=0; i<inputImagePointer->GetVectorLength(); i++)
	- {
	- GradientDirectionType g = m_GradientDirections->GetElement(i);
	- if (g.magnitude()>0.001)
	- {
	- double twonorm = g.two_norm();
	- double b = m_B_valuetwonormtwonorm;
	- if (b>0)
	- {
	- double S = pix[i];
	- if (S>0 && S0>0)
	- {
	- outval -= std::log(S/S0)/b;
	- c++;
	- }
	- }
	- }
	- }
	-
	- if (c>0)
	- outval /= c;
	- }
	- }
	- else
	- {
	- outval = FitSingleVoxel(pix);
	- }
	-
	- // if (outval<-0.00001)
	- // outval = -0.00001;
	-
	- if (outval==outval && outval<1000)
	- oit.Set( outval );
	- // else
	- // oit.Set( -0.00001 );
	-
	- ++oit;
	- ++git;
	- }
	-}
	-
	-template< class TInPixelType, class TOutPixelType >
	-void
	-AdcImageFilter< TInPixelType, TOutPixelType>
	-::PrintSelf(std::ostream& os, Indent indent) const
	-{
	- Superclass::PrintSelf(os,indent);
	-}
	-
	-}
	-
	-#endif // __itkAdcImageFilter_txx
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkB0ImageExtractionImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkB0ImageExtractionImageFilter.h
	deleted file mode 100644
	index 87985622a4..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkB0ImageExtractionImageFilter.h
	+++ /dev/null
	@@ -1,90 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkB0ImageExtractionImageFilter_h_
	-#define __itkB0ImageExtractionImageFilter_h_
	-
	-#include "itkImageToImageFilter.h"
	-
	-namespace itk{
	- /** \class B0ImageExtractionImageFilter
	- * \brief This class takes as input a T2-weighted image and computes a brainmask.
	- *
	- */
	-
	- template< class TInputImagePixelType,
	- class TOutputImagePixelType >
	- class B0ImageExtractionImageFilter :
	- public ImageToImageFilter< VectorImage<TInputImagePixelType, 3>,
	- Image< TOutputImagePixelType, 3 > >
	- {
	-
	- public:
	-
	- typedef B0ImageExtractionImageFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageToImageFilter< VectorImage< TInputImagePixelType, 3 >,
	- Image< TOutputImagePixelType, 3 > >
	- Superclass;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(B0ImageExtractionImageFilter,
	- ImageToImageFilter);
	-
	- typedef TInputImagePixelType InputPixelType;
	-
	- typedef TOutputImagePixelType OutputPixelType;
	-
	- typedef typename Superclass::InputImageType InputImageType;
	- typedef typename Superclass::OutputImageType OutputImageType;
	-
	- typedef typename Superclass::OutputImageRegionType
	- OutputImageRegionType;
	-
	- typedef vnl_vector_fixed< double, 3 > GradientDirectionType;
	-
	- typedef itk::VectorContainer< unsigned int, GradientDirectionType >
	- GradientDirectionContainerType;
	-
	- GradientDirectionContainerType::Pointer GetDirections()
	- { return m_Directions; }
	- void SetDirections( GradientDirectionContainerType::Pointer directions )
	- { this->m_Directions = directions; }
	-
	- protected:
	-
	- B0ImageExtractionImageFilter();
	- ~B0ImageExtractionImageFilter() override {};
	-
	- void GenerateData() override;
	-
	- GradientDirectionContainerType::Pointer m_Directions;
	-
	- };
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkB0ImageExtractionImageFilter.txx"
	-#endif
	-
	-#endif //__itkB0ImageExtractionImageFilter_h_
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkB0ImageExtractionImageFilter.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkB0ImageExtractionImageFilter.txx
	deleted file mode 100644
	index 76f4609353..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkB0ImageExtractionImageFilter.txx
	+++ /dev/null
	@@ -1,126 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-/*===================================================================
	-
	-This file is based heavily on a corresponding ITK filter.
	-
	-===================================================================*/
	-#ifndef __itkB0ImageExtractionImageFilter_txx
	-#define __itkB0ImageExtractionImageFilter_txx
	-
	-#include "itkB0ImageExtractionImageFilter.h"
	-
	-#include "itkImageRegionIterator.h"
	-
	-namespace itk {
	-
	- template< class TInputImagePixelType,
	- class TOutputImagePixelType >
	- B0ImageExtractionImageFilter< TInputImagePixelType,
	- TOutputImagePixelType >
	- ::B0ImageExtractionImageFilter()
	- {
	- // At least 1 inputs is necessary for a vector image.
	- // For images added one at a time we need at least six
	- this->SetNumberOfRequiredInputs( 1 );
	- }
	-
	- template< class TInputImagePixelType,
	- class TOutputImagePixelType >
	- void B0ImageExtractionImageFilter< TInputImagePixelType,
	- TOutputImagePixelType >
	- ::GenerateData()
	- {
	-
	- typename GradientDirectionContainerType::Iterator begin = m_Directions->Begin();
	- typename GradientDirectionContainerType::Iterator end = m_Directions->End();
	-
	- // Find the index of the b0 image
	- std::vector<int> indices;
	- int index = 0;
	- while(begin!=end)
	- {
	- GradientDirectionType grad = begin->Value();
	-
	- if(grad[0] == 0 && grad[1] == 0 && grad[2] == 0)
	- {
	- indices.push_back(index);
	- }
	- ++index;
	- ++begin;
	- }
	-
	- typedef itk::Image<float,3> TempImageType;
	- TempImageType::Pointer tmp = TempImageType::New();
	- typename TempImageType::RegionType region = this->GetInput()->GetLargestPossibleRegion();
	-
	- tmp->SetSpacing(this->GetInput()->GetSpacing());
	- tmp->SetOrigin(this->GetInput()->GetOrigin());
	- tmp->SetDirection(this->GetInput()->GetDirection());
	- tmp->SetRegions(region);
	- tmp->Allocate();
	-
	- itk::ImageRegionIterator<TempImageType> it(tmp.GetPointer(), tmp->GetLargestPossibleRegion() );
	- itk::ImageRegionConstIterator<InputImageType> vectorIt(this->GetInput(), this->GetInput()->GetLargestPossibleRegion() );
	-
	- it.GoToBegin();
	- while(!it.IsAtEnd())
	- {
	- it.Set(0);
	- ++it;
	- }
	-
	- //Sum all images that have zero diffusion weighting (indices stored in vector index)
	- for(std::vector<int>::iterator indexIt = indices.begin();
	- indexIt != indices.end();
	- indexIt++)
	- {
	- it.GoToBegin();
	- vectorIt.GoToBegin();
	-
	- while(!it.IsAtEnd() && !vectorIt.IsAtEnd())
	- {
	- typename InputImageType::PixelType vec = vectorIt.Get();
	- it.Set((1.0 * it.Get()) + (1.0 * vec[indexIt]) / (1.0 indices.size()));
	- ++it;
	- ++vectorIt;
	- }
	- }
	-
	- typename OutputImageType::Pointer b0Image =
	- static_cast< OutputImageType * >(this->ProcessObject::GetPrimaryOutput());
	- typename OutputImageType::RegionType outregion = this->GetInput()->GetLargestPossibleRegion();
	- b0Image->SetSpacing(this->GetInput()->GetSpacing());
	- b0Image->SetOrigin(this->GetInput()->GetOrigin());
	- b0Image->SetDirection(this->GetInput()->GetDirection());
	- b0Image->SetRegions(outregion);
	- b0Image->Allocate();
	- itk::ImageRegionIterator<TempImageType> itIn(tmp, tmp->GetLargestPossibleRegion() );
	- itk::ImageRegionIterator<OutputImageType> itOut(b0Image, b0Image->GetLargestPossibleRegion() );
	- itIn.GoToBegin();
	- itOut.GoToBegin();
	- while(!itIn.IsAtEnd())
	- {
	- itOut.Set(itIn.Get());
	- ++itIn;
	- ++itOut;
	- }
	- }
	-
	-}
	-
	-#endif // __itkB0ImageExtractionImageFilter_txx
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkB0ImageExtractionToSeparateImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkB0ImageExtractionToSeparateImageFilter.h
	deleted file mode 100644
	index 0d85e3cd74..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkB0ImageExtractionToSeparateImageFilter.h
	+++ /dev/null
	@@ -1,107 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef ITKB0IMAGEEXTRACTIONTOSEPARATEIMAGEFILTER_H
	-#define ITKB0IMAGEEXTRACTIONTOSEPARATEIMAGEFILTER_H
	-
	-#include "itkImageToImageFilter.h"
	-
	-namespace itk
	-{
	-/** \class B0ImageExtractionToSeparateImageFilter
	- \brief This class has an advanced functionality to the B0ImageExtractionImageFilter, however the b0 images are
	- stored in a 3D+t image with each b0 image beeing a separate timestep and not averaged to a single 3D volume
	- */
	-
	-template< class TInputImagePixelType,
	- class TOutputImagePixelType >
	-class B0ImageExtractionToSeparateImageFilter :
	- public ImageToImageFilter< VectorImage<TInputImagePixelType, 3>,
	- Image< TOutputImagePixelType, 4 > >
	-{
	-public:
	-
	- typedef B0ImageExtractionToSeparateImageFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	-
	- typedef TInputImagePixelType InputPixelType;
	- typedef TOutputImagePixelType OutputPixelType;
	-
	- typedef ImageToImageFilter< VectorImage<TInputImagePixelType, 3>,
	- Image< TOutputImagePixelType, 4 > > Superclass;
	-
	- /** typedefs from superclass */
	- typedef typename Superclass::InputImageType InputImageType;
	- //typedef typename Superclass::OutputImageType OutputImageType;
	- typedef Image< TOutputImagePixelType, 4 > OutputImageType;
	-
	- typedef typename OutputImageType::RegionType OutputImageRegionType;
	-
	- typedef vnl_vector_fixed< double, 3 > GradientDirectionType;
	-
	- typedef itk::VectorContainer< unsigned int, GradientDirectionType >
	- GradientDirectionContainerType;
	-
	- typedef typename GradientDirectionContainerType::Iterator GradContainerIteratorType;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(B0ImageExtractionToSeparateImageFilter,
	- ImageToImageFilter);
	-
	- GradientDirectionContainerType::Pointer GetDirections()
	- {
	- return m_Directions;
	- }
	-
	- void SetDirections( GradientDirectionContainerType::Pointer directions )
	- {
	- this->m_Directions = directions;
	- }
	-
	-protected:
	-
	- B0ImageExtractionToSeparateImageFilter();
	- virtual ~B0ImageExtractionToSeparateImageFilter(){};
	-
	- void GenerateData();
	-
	- /** The dimension of the output does not match the dimension of the input
	- hence we need to re-implement the CopyInformation method to avoid
	- executing the default implementation which tries to copy the input information to the
	- output
	- */
	- virtual void CopyInformation( const DataObject *data);
	-
	- /** Override of the ProcessObject::GenerateOutputInformation() because of different
	- dimensionality of the input and the output
	- */
	- virtual void GenerateOutputInformation();
	-
	- GradientDirectionContainerType::Pointer m_Directions;
	-};
	-
	-} // end namespace itk
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkB0ImageExtractionToSeparateImageFilter.txx"
	-#endif
	-
	-#endif // ITKB0IMAGEEXTRACTIONTOSEPARATEIMAGEFILTER_H
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkB0ImageExtractionToSeparateImageFilter.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkB0ImageExtractionToSeparateImageFilter.txx
	deleted file mode 100644
	index 95808e5ddb..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkB0ImageExtractionToSeparateImageFilter.txx
	+++ /dev/null
	@@ -1,165 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef __itkB0ImageExtractionToSeparateImageFilter_txx
	-#define __itkB0ImageExtractionToSeparateImageFilter_txx
	-
	-#include "itkB0ImageExtractionToSeparateImageFilter.h"
	-
	-#include <itkImageRegionConstIterator.h>
	-#include <itkImageRegionIterator.h>
	-
	-template< class TInputImagePixelType,
	- class TOutputImagePixelType>
	-itk::B0ImageExtractionToSeparateImageFilter< TInputImagePixelType, TOutputImagePixelType >
	-::B0ImageExtractionToSeparateImageFilter()
	-{
	- this->SetNumberOfRequiredInputs( 1 );
	-}
	-
	-template< class TInputImagePixelType,
	- class TOutputImagePixelType>
	-void itk::B0ImageExtractionToSeparateImageFilter<
	-TInputImagePixelType, TOutputImagePixelType >::CopyInformation( const DataObject *)
	-{
	-
	-}
	-
	-template< class TInputImagePixelType,
	- class TOutputImagePixelType>
	-void itk::B0ImageExtractionToSeparateImageFilter<
	-TInputImagePixelType, TOutputImagePixelType >::GenerateOutputInformation()
	-{
	-
	-}
	-
	-template< class TInputImagePixelType,
	- class TOutputImagePixelType>
	-void itk::B0ImageExtractionToSeparateImageFilter<
	-TInputImagePixelType, TOutputImagePixelType >::GenerateData()
	-{
	-
	- GradContainerIteratorType begin = m_Directions->Begin();
	- GradContainerIteratorType end = m_Directions->End();
	-
	- // Find the indices of the b0 images in the diffusion image
	- std::vector<int> indices;
	- int index = 0;
	- while(begin!=end)
	- {
	- GradientDirectionType grad = begin->Value();
	-
	- if(grad[0] == 0 && grad[1] == 0 && grad[2] == 0)
	- {
	- indices.push_back(index);
	- }
	- ++index;
	- ++begin;
	- }
	-
	- // declare the output image
	- // this will have the b0 images stored as timesteps
	- typename OutputImageType::Pointer outputImage = this->GetOutput();
	- //OutputImageType::New();
	-
	- // get the input region
	- typename Superclass::InputImageType::RegionType inputRegion =
	- this->GetInput()->GetLargestPossibleRegion();
	-
	- // allocate image with
	- // - dimension: [DimX, DimY, DimZ, NumOfb0 ]
	- // - spacing: old one, 1.0 time
	-
	- typename OutputImageType::SpacingType spacing;
	- spacing.Fill(1);
	-
	- typename OutputImageType::PointType origin;
	- origin.Fill(0);
	-
	- OutputImageRegionType outputRegion;
	-
	- // the spacing and origin corresponds to the respective values in the input image (3D)
	- // the same for the region
	- for (unsigned int i=0; i< 3; i++)
	- {
	- spacing[i] = (this->GetInput()->GetSpacing())[i];
	- origin[i] = (this->GetInput()->GetOrigin())[i];
	- outputRegion.SetSize(i, this->GetInput()->GetLargestPossibleRegion().GetSize()[i]);
	- outputRegion.SetIndex(i, this->GetInput()->GetLargestPossibleRegion().GetIndex()[i]);
	- }
	-
	- // number of timesteps = number of b0 images
	- outputRegion.SetSize(3, indices.size());
	- outputRegion.SetIndex( 3, 0 );
	-
	- // output image direction (4x4)
	- typename OutputImageType::DirectionType outputDirection;
	- //initialize to identity
	- outputDirection.SetIdentity();
	- // get the input image direction ( 3x3 matrix )
	- typename InputImageType::DirectionType inputDirection = this->GetInput()->GetDirection();
	-
	- for( unsigned int i=0; i< 3; i++)
	- {
	- outputDirection(0,i) = inputDirection(0,i);
	- outputDirection(1,i) = inputDirection(1,i);
	- outputDirection(2,i) = inputDirection(2,i);
	- }
	-
	- outputImage->SetSpacing( spacing );
	- outputImage->SetOrigin( origin );
	- outputImage->SetDirection( outputDirection );
	- outputImage->SetRegions( outputRegion );
	- outputImage->Allocate();
	-
	- // input iterator
	- itk::ImageRegionConstIterator<InputImageType> inputIt( this->GetInput(), this->GetInput()->GetLargestPossibleRegion() );
	-
	- // we want to iterate separately over each 3D volume of the output image
	- // so reset the regions last dimension
	- outputRegion.SetSize(3,1);
	- unsigned int currentTimeStep = 0;
	-
	-
	- // extract b0 and insert them as a new time step
	- for(std::vector<int>::iterator indexIt = indices.begin();
	- indexIt != indices.end();
	- indexIt++)
	- {
	- // set the time step
	- outputRegion.SetIndex(3, currentTimeStep);
	- itk::ImageRegionIterator< OutputImageType> outputIt( outputImage.GetPointer(), outputRegion );
	-
	- // iterate over the current b0 image and store it to corresponding place
	- outputIt.GoToBegin();
	- inputIt.GoToBegin();
	- while( !outputIt.IsAtEnd() && !inputIt.IsAtEnd() )
	- {
	- // the input vector
	- typename InputImageType::PixelType vec = inputIt.Get();
	-
	- outputIt.Set( vec[*indexIt]);
	- ++outputIt;
	- ++inputIt;
	- }
	-
	- // increase time step
	- currentTimeStep++;
	- }
	-
	-
	-}
	-
	-#endif // ifndef __itkB0ImageExtractionToSeparateImageFilter_txx
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkBrainMaskExtractionImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkBrainMaskExtractionImageFilter.h
	deleted file mode 100644
	index a0f98760b3..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkBrainMaskExtractionImageFilter.h
	+++ /dev/null
	@@ -1,84 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkBrainMaskExtractionImageFilter_h_
	-#define __itkBrainMaskExtractionImageFilter_h_
	-
	-#include "itkImageToImageFilter.h"
	-
	-namespace itk{
	-/** \class BrainMaskExtractionImageFilter
	- * \brief This class takes as input a T2-weighted image and computes a brainmask.
	- *
	- */
	-
	-template< class TOutputImagePixelType >
	-class BrainMaskExtractionImageFilter :
	- public ImageToImageFilter< Image< unsigned short, 3 >,
	- Image< TOutputImagePixelType, 3 > >
	-{
	-
	-public:
	-
	- typedef BrainMaskExtractionImageFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageToImageFilter< Image< unsigned short, 3 >,
	- Image< TOutputImagePixelType, 3 > >
	- Superclass;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(BrainMaskExtractionImageFilter,
	- ImageToImageFilter);
	-
	- typedef unsigned short InputPixelType;
	-
	- typedef TOutputImagePixelType OutputPixelType;
	-
	- typedef typename Superclass::InputImageType InputImageType;
	- typedef typename Superclass::OutputImageType OutputImageType;
	-
	- typedef typename Superclass::OutputImageRegionType
	- OutputImageRegionType;
	-
	- itkSetMacro( MaxNumIterations, int )
	- itkGetMacro( MaxNumIterations, int )
	-
	-protected:
	- BrainMaskExtractionImageFilter();
	- ~BrainMaskExtractionImageFilter() {};
	-
	- void GenerateData();
	-
	- bool CompareImages( typename OutputImageType::Pointer im1, typename OutputImageType::Pointer im2);
	- int ComputeHistogram( typename InputImageType::Pointer image);
	- void CopyImage( typename OutputImageType::Pointer target, typename OutputImageType::Pointer source);
	-
	- int m_MaxNumIterations;
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkBrainMaskExtractionImageFilter.txx"
	-#endif
	-
	-#endif //__itkBrainMaskExtractionImageFilter_h_
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkBrainMaskExtractionImageFilter.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkBrainMaskExtractionImageFilter.txx
	deleted file mode 100644
	index e195403710..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkBrainMaskExtractionImageFilter.txx
	+++ /dev/null
	@@ -1,444 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-/*===================================================================
	-
	-This file is based heavily on a corresponding ITK filter.
	-
	-===================================================================*/
	-#ifndef __itkBrainMaskExtractionImageFilter_txx
	-#define __itkBrainMaskExtractionImageFilter_txx
	-
	-#include "itkBrainMaskExtractionImageFilter.h"
	-
	-#include <itkBinaryThresholdImageFilter.h>
	-#include <itkBinaryErodeImageFilter.h>
	-#include <itkBinaryDilateImageFilter.h>
	-#include <itkVotingBinaryHoleFillingImageFilter.h>
	-#include <itkVotingBinaryIterativeHoleFillingImageFilter.h>
	-#include <itkBinaryBallStructuringElement.h>
	-#include <itkBinaryCrossStructuringElement.h>
	-#include <itkAndImageFilter.h>
	-#include <itkRecursiveGaussianImageFilter.h>
	-#include <itkMaskImageFilter.h>
	-
	-namespace itk {
	-
	- template< class TOutputImagePixelType >
	- BrainMaskExtractionImageFilter< TOutputImagePixelType >
	- ::BrainMaskExtractionImageFilter()
	- : m_MaxNumIterations(itk::NumericTraits<int>::max())
	- {
	- // At least 1 inputs is necessary for a vector image.
	- // For images added one at a time we need at least six
	- this->SetNumberOfRequiredInputs( 1 );
	- }
	-
	- template< class TOutputImagePixelType >
	- void BrainMaskExtractionImageFilter< TOutputImagePixelType >
	- ::GenerateData()
	- {
	-
	- // gaussian filter
	- typename itk::RecursiveGaussianImageFilter<InputImageType,InputImageType>::Pointer gaussian
	- = itk::RecursiveGaussianImageFilter<InputImageType,InputImageType>::New();
	- gaussian->SetInput( this->GetInput(0) );
	- gaussian->SetSigma( 1.0 );
	-
	- try
	- {
	- gaussian->Update();
	- }
	- catch( itk::ExceptionObject &e)
	- {
	- std::cerr << e;
	- return;
	- }
	-
	- // threshold the image
	- typename itk::BinaryThresholdImageFilter<InputImageType,OutputImageType>::Pointer threshold =
	- itk::BinaryThresholdImageFilter<InputImageType,OutputImageType>::New();
	-
	- threshold->SetInput( gaussian->GetOutput() );
	-
	- int seuil = static_cast<int>( ComputeHistogram( gaussian->GetOutput() ) );
	- threshold->SetLowerThreshold( seuil );
	-
	- std::cout << "Thresholding..." << std::flush;
	- try
	- {
	- threshold->Update();
	- }
	- catch( itk::ExceptionObject &e)
	- {
	- std::cerr << e;
	- return;
	- }
	- std::cout << "Done." << std::endl;
	-
	-#ifdef DEBUG_ME
	- {
	- WriterType::Pointer writer = WriterType::New();
	- writer->SetInput( threshold->GetOutput() );
	- writer->SetFileName( "AfterThreshold.hdr" );
	- writer->Update();
	- }
	-#endif
	-
	- // erode to remove background noise
	- typedef itk::BinaryBallStructuringElement<int, 3> StructuralElementType;
	- StructuralElementType ball;
	-
	- typename itk::BinaryErodeImageFilter<OutputImageType,OutputImageType,StructuralElementType>::Pointer erode =
	- itk::BinaryErodeImageFilter<OutputImageType,OutputImageType,StructuralElementType>::New();
	-
	- ball.SetRadius( 3 );
	-
	- erode->SetInput( threshold->GetOutput() );
	- erode->SetKernel( ball );
	-
	- std::cout << "Eroding..." << std::flush;
	- try
	- {
	- erode->Update();
	- }
	- catch( itk::ExceptionObject &e)
	- {
	- std::cerr << e;
	- return;
	- }
	- std::cout << "Done." << std::endl;
	-
	-#ifdef DEBUG_ME
	- {
	- WriterType::Pointer writer = WriterType::New();
	- writer->SetInput( erode->GetOutput() );
	- writer->SetFileName( "AfterErode.hdr" );
	- writer->Update();
	- }
	-#endif
	-
	-
	- typedef BinaryCrossStructuringElement<int, 3> CrossType;
	-
	- typedef BinaryDilateImageFilter<OutputImageType,OutputImageType,CrossType> DilateFilterType;
	- typedef AndImageFilter<OutputImageType,OutputImageType,OutputImageType> AndFilterType;
	-
	- typename OutputImageType::Pointer M0 = threshold->GetOutput();
	- typename OutputImageType::Pointer Mn = OutputImageType::New();
	- Mn->SetRegions( M0->GetLargestPossibleRegion() );
	- Mn->SetSpacing( M0->GetSpacing() );
	- Mn->SetOrigin( M0->GetOrigin() );
	- Mn->SetDirection( M0->GetDirection() );
	- Mn->Allocate();
	-
	- typename OutputImageType::Pointer Mnplus1 = erode->GetOutput();
	-
	-
	- CrossType cross;
	- cross.SetRadius( 1 );
	- //unsigned long rad[3]={3,3,3};
	-
	- //ball2.SetRadius( rad );
	-
	- std::cout << "Conditional reconstruction..." << std::flush;
	- int iter = 0;
	- do
	- {
	- std::cout << "Iteration: " << iter++ << std::endl;
	- CopyImage( Mn, Mnplus1);
	-
	- typename DilateFilterType::Pointer dilater = DilateFilterType::New();
	- dilater->SetInput( Mn );
	- dilater->SetKernel( cross );
	-
	- try
	- {
	- dilater->Update();
	- }
	- catch( itk::ExceptionObject &e)
	- {
	- std::cerr << e;
	- return;
	- }
	-
	- typename AndFilterType::Pointer andfilter = AndFilterType::New();
	- andfilter->SetInput(0, M0);
	- andfilter->SetInput(1, dilater->GetOutput() );
	-
	- try
	- {
	- andfilter->Update();
	- }
	- catch( itk::ExceptionObject &e)
	- {
	- std::cerr << e;
	- return;
	- }
	-
	- Mnplus1 = andfilter->GetOutput();
	-
	- /*
	- #ifdef DEBUG_ME
	- {
	- WriterType::Pointer writer = WriterType::New();
	- writer->SetInput( andfilter->GetOutput() );
	- char filename[512];
	- sprintf( filename, "CondReconstruction_iter_%d.hdr", iter);
	- writer->SetFileName( filename );
	- writer->Update();
	- }
	- #endif*/
	-
	- } while( !CompareImages( Mn, Mnplus1) && iter < m_MaxNumIterations );
	-
	- std::cout << "Done." << std::endl;
	-
	-#ifdef DEBUG_ME
	- {
	- WriterType::Pointer writer = WriterType::New();
	- writer->SetInput( Mn );
	- writer->SetFileName( "AfterCondReconstruction.hdr" );
	- writer->Update();
	- }
	-#endif
	- // now fill the holes
	-
	- typename itk::VotingBinaryIterativeHoleFillingImageFilter< OutputImageType >::Pointer filler =
	- itk::VotingBinaryIterativeHoleFillingImageFilter< OutputImageType >::New();
	- filler->SetInput( Mn );
	- filler->SetMaximumNumberOfIterations (1000);
	-
	- std::cout << "Filling the holes..." << std::flush;
	- try
	- {
	- filler->Update();
	- }
	- catch( itk::ExceptionObject &e)
	- {
	- std::cerr << e;
	- return;
	- }
	- std::cout << "Done." << std::endl;
	-
	- typename OutputImageType::Pointer outputImage =
	- static_cast< OutputImageType * >(this->ProcessObject::GetPrimaryOutput());
	-
	- outputImage->SetSpacing( filler->GetOutput()->GetSpacing() ); // Set the image spacing
	- outputImage->SetOrigin( filler->GetOutput()->GetOrigin() ); // Set the image origin
	- outputImage->SetLargestPossibleRegion( filler->GetOutput()->GetLargestPossibleRegion());
	- outputImage->SetBufferedRegion( filler->GetOutput()->GetLargestPossibleRegion() );
	- outputImage->SetDirection( filler->GetOutput()->GetDirection() );
	- outputImage->Allocate();
	-
	- itk::ImageRegionIterator<OutputImageType> itIn( filler->GetOutput(), filler->GetOutput()->GetLargestPossibleRegion() );
	- itk::ImageRegionIterator<OutputImageType> itOut( outputImage, outputImage->GetLargestPossibleRegion() );
	-
	- while( !itIn.IsAtEnd() )
	- {
	- itOut.Set(itIn.Get());
	- ++itIn;
	- ++itOut;
	- }
	-
	- }
	-
	-
	- template< class TOutputImagePixelType >
	- void BrainMaskExtractionImageFilter< TOutputImagePixelType >
	- ::CopyImage( typename OutputImageType::Pointer target, typename OutputImageType::Pointer source)
	- {
	- itk::ImageRegionConstIterator<OutputImageType> itIn( source, source->GetLargestPossibleRegion() );
	- itk::ImageRegionIterator<OutputImageType> itOut( target, target->GetLargestPossibleRegion() );
	-
	- while( !itOut.IsAtEnd() )
	- {
	- itOut.Set( itIn.Get() );
	- ++itIn;
	- ++itOut;
	- }
	- }
	-
	-
	- template< class TOutputImagePixelType >
	- bool BrainMaskExtractionImageFilter< TOutputImagePixelType >
	- ::CompareImages( typename OutputImageType::Pointer im1, typename OutputImageType::Pointer im2)
	- {
	- itk::ImageRegionConstIterator<OutputImageType> itIn( im1, im1->GetLargestPossibleRegion() );
	- itk::ImageRegionConstIterator<OutputImageType> itOut( im2, im2->GetLargestPossibleRegion() );
	-
	- while( !itOut.IsAtEnd() )
	- {
	- if( itOut.Value() != itIn.Value() )
	- {
	- return false;
	- }
	- ++itOut;
	- ++itIn;
	- }
	-
	- return true;
	- }
	-
	-
	- template< class TOutputImagePixelType >
	- int BrainMaskExtractionImageFilter< TOutputImagePixelType >
	- ::ComputeHistogram( typename InputImageType::Pointer image)
	- {
	- // IMPORTANT: IMAGE MUST BE UNSIGNED SHORT
	- int N=65535;
	- int* histogram = new int[N];
	- for( int i=0; i<N; i++)
	- {
	- histogram[i] = 0;
	- }
	-
	- itk::ImageRegionConstIterator<InputImageType> itIn( image, image->GetLargestPossibleRegion() );
	-
	- long totVoxels = 0;
	-
	- int max = -1;
	- int min = 9999999;
	- while( !itIn.IsAtEnd() )
	- {
	- histogram[ (int)(itIn.Value()) ]++;
	-
	- if( itIn.Value()>max )
	- {
	- max = itIn.Value();
	- }
	-
	- if( itIn.Value()<min )
	- {
	- min = itIn.Value();
	- }
	- ++itIn;
	- ++totVoxels;
	- }
	-
	-
	- //int EPS = 1;
	- int seuil = 0;
	- //int newseuil = (max + min)/2;
	-
	- N = max;
	-
	- double V = 0.0;
	- int S = 0;
	-
	- double mean = 0.0;
	- for( int i=min; i<=max; i++)
	- {
	- mean += (double)(i) * (double)histogram[i];
	- }
	- mean /= (double)totVoxels;
	-
	- //std::cout << "Min/Max/Mean: " << min << "/" << max << "/" << mean << std::endl;
	-
	- //while( abs(newseuil - seuil)>EPS )
	- for( seuil = min; seuil<=max; seuil++)
	- {
	- //seuil = newseuil;
	-
	- // compute the classes:
	- double mean0 = 0.0;
	- double mean1 = 0.0;
	- //double std0 = 0.0;
	- //double std1 = 0.0;
	-
	- double num0 = 0.0;
	- double num1 = 0.0;
	- for( int i=min; i<seuil; i++)
	- {
	- //mean0 += (double)(histogram[i])/(double)(totVoxels) * (double)(i);
	- mean0 += (double)histogram[i] * (double)i;
	- num0 += (double)histogram[i];
	- }
	-
	- for( int i=seuil; i<max; i++)
	- {
	- //mean1 += (double)(histogram[i])/(double)(totVoxels) * (double)(i);
	- mean1 += (double)histogram[i] * (double)i;
	- num1 += (double)histogram[i];
	- }
	-
	- if( num0 )
	- {
	- mean0/=num0;
	- }
	- if( num1 )
	- {
	- mean1/=num1;
	- }
	-
	- /*
	- for( int i=0; i<seuil; i++)
	- {
	- std0 += (double)histogram[i]/(double)totVoxels* ((double)i - mean0)*((double)i - mean0);
	- //std0 += (double)histogram[i]/num0* ((double)i - mean0)*((double)i - mean0);
	- }
	-
	- for( int i=seuil; i<65536; i++)
	- {
	- std1 += (double)histogram[i]/(double)totVoxels* ((double)i - mean1)* ((double)i - mean1);
	- //std1 += (double)histogram[i]/num1* ((double)i - mean1)* ((double)i - mean1);
	- }
	- */
	-
	-
	- //std0 = sqrt(std0);
	- //std1 = sqrt(std1);
	-
	- //std::cout << "Classe 0: " << mean0 << " " << std0 << std::endl;
	- //std::cout << "Classe 1: " << mean1 << " " << std1 << std::endl;
	-
	- //std::cout << "Classe 0: " << mean0 << std::endl;
	- //std::cout << "Classe 1: " << mean1 << std::endl;
	-
	- //double alpha = std0*std1/(std0+std1);
	-
	- //std::cout << "alpha: " << alpha << " " << std0 << " " << std1 << std::endl;
	- //newseuil = (int) (alpha*(mean0/std0 + mean1/std1));
	-
	- //std::cout << "New threshold: " << newseuil << std::endl;
	-
	- /*
	- if( newseuil > 65535 \|\| newseuil<0)
	- {
	- std::cerr << "Error: threshold is too low or high, exiting" << std::endl;
	- return -1;
	- }*/
	-
	- double Vm = num0 * (mean0 - mean)(mean0 - mean) + num1(mean1 - mean)*(mean1 - mean);
	- if( Vm > V )
	- {
	- V = Vm;
	- S = seuil;
	- //std::cout << "New seuil: " << S << std::endl;
	- //getchar();
	- }
	-
	- }
	-
	- delete [] histogram;
	-
	- std::cout << "Seuil: " << S << std::endl;
	-
	- return S;
	- }
	-}
	-
	-#endif // __itkBrainMaskExtractionImageFilter_txx
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkCartesianToPolarVectorImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkCartesianToPolarVectorImageFilter.h
	deleted file mode 100644
	index 16f7205ee4..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkCartesianToPolarVectorImageFilter.h
	+++ /dev/null
	@@ -1,130 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkCartesianToPolarVectorImageFilter_h
	-#define __itkCartesianToPolarVectorImageFilter_h
	-
	-#include "itkUnaryFunctorImageFilter.h"
	-
	-namespace itk
	-{
	-
	- namespace Functor {
	-
	- template< typename TInput, typename TOutput, bool symmetric >
	- class CartesianToPolarFunction
	- {
	- public:
	- CartesianToPolarFunction() {}
	- ~CartesianToPolarFunction() {}
	- bool operator!=( const CartesianToPolarFunction & ) const
	- {
	- return false;
	- }
	- bool operator==( const CartesianToPolarFunction & other ) const
	- {
	- return !(*this != other);
	- }
	- inline TOutput operator()( const TInput & x )
	- {
	-
	- TOutput opoint;
	-
	- if(x[0] \|\| x[1] \|\| x[2])
	- {
	- opoint[0] = sqrt( x[0] * x[0] + x[1] * x[1] + x[2] * x[2] );
	- opoint[1] = atan2( x[1], x[0] );
	- opoint[2] = 0.5itk::Math::pi - atan( x[2] / sqrt( x[0] x[0] + x[1] * x[1] ) );
	-
	- if(symmetric && opoint[1]>itk::Math::pi)
	- {
	- opoint[1] = opoint[1] - itk::Math::pi;
	- }
	- }
	- else
	- {
	- opoint[0] = 0;
	- opoint[1] = 0;
	- opoint[2] = 0;
	- }
	- return opoint;
	-
	- }
	- };
	-
	- } // end namespace functor
	-
	-
	- /** \class CartesianToPolarVectorImageFilter
	- *
	- */
	- template <typename TInputImage, typename TOutputImage, bool symmetric>
	- class CartesianToPolarVectorImageFilter :
	- public
	- UnaryFunctorImageFilter<TInputImage,TOutputImage,
	- Functor::CartesianToPolarFunction<
	- typename TInputImage::PixelType,
	- typename TOutputImage::PixelType, symmetric> >
	- {
	- public:
	- /** Standard class typedefs. */
	- typedef CartesianToPolarVectorImageFilter Self;
	- typedef UnaryFunctorImageFilter<
	- TInputImage,TOutputImage,
	- Functor::CartesianToPolarFunction<
	- typename TInputImage::PixelType,
	- typename TOutputImage::PixelType, symmetric > > Superclass;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	-
	- typedef typename Superclass::OutputImageType OutputImageType;
	- typedef typename OutputImageType::PixelType OutputPixelType;
	- typedef typename TInputImage::PixelType InputPixelType;
	- typedef typename InputPixelType::ValueType InputValueType;
	-
	- /** Run-time type information (and related methods). */
	- itkTypeMacro( CartesianToPolarVectorImageFilter, UnaryFunctorImageFilter );
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Print internal ivars */
	- void PrintSelf(std::ostream& os, Indent indent) const
	- { this->Superclass::PrintSelf( os, indent ); }
	-
	-#ifdef ITK_USE_CONCEPT_CHECKING
	- /** Begin concept checking */
	- itkConceptMacro(InputHasNumericTraitsCheck,
	- (Concept::HasNumericTraits<InputValueType>));
	- /** End concept checking */
	-#endif
	-
	- protected:
	- CartesianToPolarVectorImageFilter() {};
	- virtual ~CartesianToPolarVectorImageFilter() {};
	-
	- private:
	- CartesianToPolarVectorImageFilter(const Self&); //purposely not implemented
	- void operator=(const Self&); //purposely not implemented
	-
	- };
	-
	-
	-
	-} // end namespace itk
	-
	-#endif // __itkCartesianToPolarVectorImageFilter_h
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDiffusionOdfGeneralizedFaImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDiffusionOdfGeneralizedFaImageFilter.h
	deleted file mode 100644
	index 06dde43046..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDiffusionOdfGeneralizedFaImageFilter.h
	+++ /dev/null
	@@ -1,128 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-/*===================================================================
	-
	-This file is based heavily on a corresponding ITK filter.
	-
	-===================================================================*/
	-#ifndef __itkDiffusionOdfGeneralizedFaImageFilter_h_
	-#define __itkDiffusionOdfGeneralizedFaImageFilter_h_
	-
	-//#include "MitkDiffusionImagingMBIExports.h"
	-#include "itkImageToImageFilter.h"
	-//#include "vnl/vnl_matrix.h"
	-#include "vnl/vnl_vector_fixed.h"
	-#include "vnl/vnl_matrix.h"
	-#include "vnl/algo/vnl_svd.h"
	-#include "itkVectorContainer.h"
	-#include "itkVectorImage.h"
	-
	-namespace itk{
	-/** \class DiffusionOdfGeneralizedFaImageFilter
	- */
	-
	-template< class TOdfPixelType,
	- class TGfaPixelType,
	- int NrOdfDirections>
	-class DiffusionOdfGeneralizedFaImageFilter :
	- public ImageToImageFilter< Image< Vector< TOdfPixelType, NrOdfDirections >, 3 >,
	- Image< TGfaPixelType, 3 > >
	-{
	-
	-public:
	-
	- enum GfaComputationMethod
	- {
	- GFA_STANDARD,
	- GFA_QUANTILES_HIGH_LOW,
	- GFA_QUANTILE_HIGH,
	- GFA_MAX_ODF_VALUE,
	- GFA_DECONVOLUTION_COEFFS,
	- GFA_MIN_MAX_NORMALIZED_STANDARD,
	- GFA_NORMALIZED_ENTROPY,
	- GFA_NEMATIC_ORDER_PARAMETER,
	- GFA_QUANTILE_LOW,
	- GFA_MIN_ODF_VALUE,
	- GFA_QUANTILES_LOW_HIGH,
	- GFA_STD_BY_MAX,
	- GFA_PRINCIPLE_CURVATURE,
	- GFA_GENERALIZED_GFA
	- };
	-
	- typedef DiffusionOdfGeneralizedFaImageFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageToImageFilter< Image< Vector< TOdfPixelType, NrOdfDirections >, 3 >,
	- Image< TGfaPixelType, 3 > >
	- Superclass;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(DiffusionOdfGeneralizedFaImageFilter,
	- ImageToImageFilter);
	-
	- typedef TOdfPixelType OdfComponentType;
	-
	- typedef TGfaPixelType DirectionPixelType;
	-
	- typedef typename Superclass::InputImageType InputImageType;
	-
	- typedef typename Superclass::OutputImageType OutputImageType;
	-
	- typedef typename Superclass::OutputImageRegionType
	- OutputImageRegionType;
	-
	- itkStaticConstMacro(NOdfDirections,int,NrOdfDirections);
	-
	- void SetOdfImage( const InputImageType *image );
	-
	- itkGetMacro(ComputationMethod, GfaComputationMethod);
	- itkSetMacro(ComputationMethod, GfaComputationMethod);
	-
	- itkGetMacro(Param1, double);
	- itkSetMacro(Param1, double);
	-
	- itkGetMacro(Param2, double);
	- itkSetMacro(Param2, double);
	-
	-protected:
	- DiffusionOdfGeneralizedFaImageFilter();
	- ~DiffusionOdfGeneralizedFaImageFilter() override {};
	- void PrintSelf(std::ostream& os, Indent indent) const override;
	-
	- void BeforeThreadedGenerateData() override;
	- void ThreadedGenerateData( const
	- OutputImageRegionType &outputRegionForThread, ThreadIdType) override;
	-
	- GfaComputationMethod m_ComputationMethod;
	-
	- double m_Param1;
	- double m_Param2;
	-
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkDiffusionOdfGeneralizedFaImageFilter.txx"
	-#endif
	-
	-#endif //__itkDiffusionOdfGeneralizedFaImageFilter_h_
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDiffusionOdfGeneralizedFaImageFilter.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDiffusionOdfGeneralizedFaImageFilter.txx
	deleted file mode 100644
	index f43e1fa529..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDiffusionOdfGeneralizedFaImageFilter.txx
	+++ /dev/null
	@@ -1,220 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkDiffusionOdfGeneralizedFaImageFilter_txx
	-#define __itkDiffusionOdfGeneralizedFaImageFilter_txx
	-
	-#include <ctime>
	-#include <cstdio>
	-#include <cstdlib>
	-
	-#define _USE_MATH_DEFINES
	-#include <cmath>
	-
	-#include "itkImageRegionConstIterator.h"
	-#include "itkImageRegionConstIteratorWithIndex.h"
	-#include "itkImageRegionIterator.h"
	-#include "itkArray.h"
	-#include "vnl/vnl_vector.h"
	-#include "itkOrientationDistributionFunction.h"
	-
	-namespace itk {
	-
	- template< class TOdfPixelType,
	- class TGfaPixelType,
	- int NrOdfDirections>
	- DiffusionOdfGeneralizedFaImageFilter< TOdfPixelType,
	- TGfaPixelType, NrOdfDirections>
	- ::DiffusionOdfGeneralizedFaImageFilter() :
	- m_ComputationMethod(GFA_STANDARD)
	- {
	- // At least 1 inputs is necessary for a vector image.
	- // For images added one at a time we need at least six
	- this->SetNumberOfRequiredInputs( 1 );
	- }
	-
	- template< class TOdfPixelType,
	- class TGfaPixelType,
	- int NrOdfDirections>
	- void DiffusionOdfGeneralizedFaImageFilter< TOdfPixelType,
	- TGfaPixelType, NrOdfDirections>
	- ::BeforeThreadedGenerateData()
	- {
	- }
	-
	- template< class TOdfPixelType,
	- class TGfaPixelType,
	- int NrOdfDirections>
	- void DiffusionOdfGeneralizedFaImageFilter< TOdfPixelType,
	- TGfaPixelType, NrOdfDirections>
	- ::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread,
	- ThreadIdType )
	- {
	- typename OutputImageType::Pointer outputImage =
	- static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0));
	-
	- ImageRegionIterator< OutputImageType > oit(outputImage, outputRegionForThread);
	- oit.GoToBegin();
	-
	- typedef itk::OrientationDistributionFunction<TOdfPixelType,NrOdfDirections> OdfType;
	- typedef ImageRegionConstIterator< InputImageType > InputIteratorType;
	- typedef typename InputImageType::PixelType OdfVectorType;
	- typename InputImageType::Pointer inputImagePointer = nullptr;
	- inputImagePointer = static_cast< InputImageType * >(
	- this->ProcessObject::GetInput(0) );
	-
	- InputIteratorType git(inputImagePointer, outputRegionForThread );
	- git.GoToBegin();
	- while( !git.IsAtEnd() )
	- {
	- OdfVectorType b = git.Get();
	- TGfaPixelType outval = -1;
	-
	- switch( m_ComputationMethod )
	- {
	- case GFA_STANDARD:
	- {
	- OdfType odf = b.GetDataPointer();
	- outval = odf.GetGeneralizedFractionalAnisotropy();
	- break;
	- }
	- case GFA_QUANTILES_HIGH_LOW:
	- {
	- vnl_vector_fixed<TOdfPixelType,NrOdfDirections> sorted;
	- for(int i=0; i<NrOdfDirections; i++)
	- {
	- sorted[i] = b[i];
	- }
	- std::sort( sorted.begin(), sorted.end() );
	- double q60 = sorted[floor(0.6*(double)NrOdfDirections+0.5)];
	- double q95 = sorted[floor(0.95*(double)NrOdfDirections+0.5)];
	- outval = q95/q60 - 1.0;
	- break;
	- }
	- case GFA_QUANTILE_HIGH:
	- {
	- vnl_vector_fixed<TOdfPixelType,NrOdfDirections> sorted;
	- for(int i=0; i<NrOdfDirections; i++)
	- {
	- sorted[i] = b[i];
	- }
	- std::sort( sorted.begin(), sorted.end() );
	- //double q40 = sorted[floor(0.4*(double)NrOdfDirections+0.5)];
	- double q95 = sorted[floor(0.95*(double)NrOdfDirections+0.5)];
	- outval = q95;
	- break;
	- }
	- case GFA_MAX_ODF_VALUE:
	- {
	- outval = b.GetVnlVector().max_value();
	- break;
	- }
	- case GFA_DECONVOLUTION_COEFFS:
	- {
	- break;
	- }
	- case GFA_MIN_MAX_NORMALIZED_STANDARD:
	- {
	- OdfType odf = b.GetDataPointer();
	- odf = odf.MinMaxNormalize();
	- outval = odf.GetGeneralizedFractionalAnisotropy();
	- break;
	- }
	- case GFA_NORMALIZED_ENTROPY:
	- {
	- OdfType odf = b.GetDataPointer();
	- outval = odf.GetNormalizedEntropy();
	- break;
	- }
	- case GFA_NEMATIC_ORDER_PARAMETER:
	- {
	- OdfType odf = b.GetDataPointer();
	- outval = odf.GetNematicOrderParameter();
	- break;
	- }
	- case GFA_QUANTILE_LOW:
	- {
	- vnl_vector_fixed<TOdfPixelType,NrOdfDirections> sorted;
	- for(int i=0; i<NrOdfDirections; i++)
	- {
	- sorted[i] = b[i];
	- }
	- std::sort( sorted.begin(), sorted.end() );
	- //double q40 = sorted[floor(0.4*(double)NrOdfDirections+0.5)];
	- double q05 = sorted[floor(0.05*(double)NrOdfDirections+0.5)];
	- outval = q05;
	- break;
	- }
	- case GFA_MIN_ODF_VALUE:
	- {
	- outval = b.GetVnlVector().min_value();
	- break;
	- }
	- case GFA_QUANTILES_LOW_HIGH:
	- {
	- vnl_vector_fixed<TOdfPixelType,NrOdfDirections> sorted;
	- for(int i=0; i<NrOdfDirections; i++)
	- {
	- sorted[i] = b[i];
	- }
	- std::sort( sorted.begin(), sorted.end() );
	- double q05 = sorted[floor(0.05*(double)NrOdfDirections+0.5)];
	- double q40 = sorted[floor(0.4*(double)NrOdfDirections+0.5)];
	- outval = q40/q05 - 1.0;
	- break;
	- }
	- case GFA_STD_BY_MAX:
	- {
	- OdfType odf = b.GetDataPointer();
	- outval = odf.GetStdDevByMaxValue();
	- break;
	- }
	- case GFA_PRINCIPLE_CURVATURE:
	- {
	- OdfType odf = b.GetDataPointer();
	- outval = odf.GetPrincipleCurvature(m_Param1, m_Param2, 0);
	- break;
	- }
	- case GFA_GENERALIZED_GFA:
	- {
	- OdfType odf = b.GetDataPointer();
	- outval = odf.GetGeneralizedGFA(m_Param1, m_Param2);
	- break;
	- }
	- }
	-
	- oit.Set( outval );
	-
	- ++oit;
	- ++git; // Gradient image iterator
	- }
	-
	- std::cout << "One Thread finished calculation" << std::endl;
	- }
	-
	- template< class TOdfPixelType,
	- class TGfaPixelType,
	- int NrOdfDirections>
	- void DiffusionOdfGeneralizedFaImageFilter< TOdfPixelType,
	- TGfaPixelType, NrOdfDirections>
	- ::PrintSelf(std::ostream& os, Indent indent) const
	- {
	- Superclass::PrintSelf(os,indent);
	- }
	-
	-}
	-
	-#endif // __itkDiffusionOdfGeneralizedFaImageFilter_txx
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDiffusionOdfPrepareVisualizationImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDiffusionOdfPrepareVisualizationImageFilter.h
	deleted file mode 100644
	index 84b31dc4c4..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDiffusionOdfPrepareVisualizationImageFilter.h
	+++ /dev/null
	@@ -1,142 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-/*===================================================================
	-
	-This file is based heavily on a corresponding ITK filter.
	-
	-===================================================================*/
	-#ifndef __itkDiffusionOdfPrepareVisualizationImageFilter_h_
	-#define __itkDiffusionOdfPrepareVisualizationImageFilter_h_
	-
	-#include <MitkDiffusionCoreExports.h>
	-#include "itkImageToImageFilter.h"
	-//#include "vnl/vnl_matrix.h"
	-#include "vnl/vnl_vector_fixed.h"
	-#include "vnl/vnl_matrix.h"
	-#include "vnl/algo/vnl_svd.h"
	-#include "itkVectorContainer.h"
	-#include "itkVectorImage.h"
	-#include "itkDiffusionOdfGeneralizedFaImageFilter.h"
	-
	-namespace itk{
	-/** \class DiffusionOdfPrepareVisualizationImageFilter
	- */
	-
	-template< class TOdfPixelType,
	- int NrOdfDirections>
	-class MITKDIFFUSIONCORE_EXPORT DiffusionOdfPrepareVisualizationImageFilter :
	- public ImageToImageFilter< Image< Vector< TOdfPixelType, NrOdfDirections >, 3 >,
	- Image< Vector< TOdfPixelType, NrOdfDirections >, 3 > >
	-{
	-
	-public:
	-
	- enum NormalizationMethods
	- {
	- PV_NONE,
	- PV_MAX,
	- PV_MIN_MAX,
	- PV_GLOBAL_MAX,
	- PV_MIN_MAX_INVERT
	- };
	-
	- typedef DiffusionOdfPrepareVisualizationImageFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageToImageFilter< Image< Vector< TOdfPixelType, NrOdfDirections >, 3 >,
	- Image< Vector< TOdfPixelType, NrOdfDirections >, 3 > >
	- Superclass;
	-
	- typedef DiffusionOdfGeneralizedFaImageFilter<TOdfPixelType,TOdfPixelType,NrOdfDirections>
	- GfaFilterType;
	- typedef typename GfaFilterType::OutputImageType GfaImageType;
	- typedef typename GfaFilterType::GfaComputationMethod GfaComputationMethod;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(DiffusionOdfPrepareVisualizationImageFilter,
	- ImageToImageFilter);
	-
	- typedef TOdfPixelType OdfComponentType;
	-
	- typedef typename Superclass::InputImageType InputImageType;
	-
	- typedef typename Superclass::OutputImageType OutputImageType;
	-
	- typedef typename Superclass::OutputImageRegionType
	- OutputImageRegionType;
	-
	- itkStaticConstMacro(NOdfDirections,int,NrOdfDirections);
	-
	- itkSetMacro( Threshold, OdfComponentType );
	- itkGetMacro( Threshold, OdfComponentType );
	-
	- itkSetMacro( NormalizationMethod, NormalizationMethods );
	- itkGetMacro( NormalizationMethod, NormalizationMethods );
	-
	- itkSetMacro( ScaleByGfaType, GfaComputationMethod );
	- itkGetMacro( ScaleByGfaType, GfaComputationMethod );
	-
	- itkSetMacro( DoScaleGfa, bool );
	- itkGetMacro( DoScaleGfa, bool );
	-
	- itkSetMacro( GfaParam1, double );
	- itkGetMacro( GfaParam1, double );
	-
	- itkSetMacro( GfaParam2, double );
	- itkGetMacro( GfaParam2, double );
	-
	-protected:
	- DiffusionOdfPrepareVisualizationImageFilter();
	- ~DiffusionOdfPrepareVisualizationImageFilter() {};
	- void PrintSelf(std::ostream& os, Indent indent) const;
	-
	- void BeforeThreadedGenerateData();
	- void ThreadedGenerateData( const
	- OutputImageRegionType &outputRegionForThread, ThreadIdType);
	-
	-private:
	-
	- /** Threshold on the reference image data */
	- OdfComponentType m_Threshold;
	-
	- NormalizationMethods m_NormalizationMethod;
	-
	- OdfComponentType m_GlobalInputMaximum;
	-
	- GfaComputationMethod m_ScaleByGfaType;
	-
	- bool m_DoScaleGfa;
	-
	- typename GfaImageType::Pointer m_GfaImage;
	-
	- double m_GfaParam1;
	-
	- double m_GfaParam2;
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkDiffusionOdfPrepareVisualizationImageFilter.cpp"
	-#endif
	-
	-#endif //__itkDiffusionOdfPrepareVisualizationImageFilter_h_
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDiffusionTensorPrincipalDirectionImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDiffusionTensorPrincipalDirectionImageFilter.h
	deleted file mode 100644
	index 761f6e5a6d..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDiffusionTensorPrincipalDirectionImageFilter.h
	+++ /dev/null
	@@ -1,102 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-/*===================================================================
	-
	-This file is based heavily on a corresponding ITK filter.
	-
	-===================================================================*/
	-#ifndef __itkDiffusionTensorPrincipalDirectionImageFilter_h_
	-#define __itkDiffusionTensorPrincipalDirectionImageFilter_h_
	-
	-#include <MitkDiffusionCoreExports.h>
	-#include <itkImageToImageFilter.h>
	-#include <vnl/vnl_vector_fixed.h>
	-#include <vnl/vnl_matrix.h>
	-#include <vnl/algo/vnl_svd.h>
	-#include <itkVectorContainer.h>
	-#include <itkVectorImage.h>
	-#include <itkDiffusionTensor3D.h>
	-#include <mitkFiberBundle.h>
	-
	-namespace itk{
	-/** \brief Extracts principal eigenvectors of the input tensors
	- */
	-
	-template< class TTensorPixelType>
	-class DiffusionTensorPrincipalDirectionImageFilter : public ImageToImageFilter< Image< DiffusionTensor3D<TTensorPixelType>, 3 >, Image< unsigned char, 3 > >
	-{
	-
	-public:
	-
	- typedef DiffusionTensorPrincipalDirectionImageFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageToImageFilter< Image< DiffusionTensor3D<TTensorPixelType>, 3 >, Image< unsigned char, 3 > >
	- Superclass;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(DiffusionTensorPrincipalDirectionImageFilter, ImageToImageFilter)
	-
	- typedef TTensorPixelType TensorComponentType;
	- typedef typename Superclass::InputImageType InputImageType;
	- typedef typename Superclass::OutputImageType OutputImageType;
	- typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
	- typedef itk::Image<unsigned char, 3> ItkUcharImgType;
	- typedef vnl_vector_fixed< double, 3 > DirectionType;
	- typedef Image< float, 4 > PeakImageType;
	-
	- void SetImage( const InputImageType *image );
	-
	- // input
	- itkSetMacro( MaskImage, ItkUcharImgType::Pointer)
	- itkSetMacro( NormalizeVectors, bool)
	- itkSetMacro( UsePolarCoordinates, bool)
	- itkSetMacro( FaThreshold, float)
	-
	- // output
	- itkGetMacro( PeakImage, PeakImageType::Pointer)
	-
	- protected:
	- DiffusionTensorPrincipalDirectionImageFilter();
	- ~DiffusionTensorPrincipalDirectionImageFilter() {}
	- void PrintSelf(std::ostream& os, Indent indent) const;
	-
	- void BeforeThreadedGenerateData();
	- void ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, ThreadIdType );
	- void AfterThreadedGenerateData();
	-
	-private:
	-
	- bool m_NormalizeVectors; ///< Normalizes the output vector to length 1
	- ItkUcharImgType::Pointer m_MaskImage; ///< Extraction is only performed inside of the binary mask
	- PeakImageType::Pointer m_PeakImage;
	- bool m_UsePolarCoordinates;
	- float m_FaThreshold;
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkDiffusionTensorPrincipalDirectionImageFilter.txx"
	-#endif
	-
	-#endif //__itkDiffusionTensorPrincipalDirectionImageFilter_h_
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDiffusionTensorPrincipalDirectionImageFilter.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDiffusionTensorPrincipalDirectionImageFilter.txx
	deleted file mode 100644
	index 0e9c2b634a..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDiffusionTensorPrincipalDirectionImageFilter.txx
	+++ /dev/null
	@@ -1,215 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkDiffusionTensorPrincipalDirectionImageFilter_txx
	-#define __itkDiffusionTensorPrincipalDirectionImageFilter_txx
	-
	-#include <time.h>
	-#include <stdio.h>
	-#include <stdlib.h>
	-
	-#include "itkDiffusionTensorPrincipalDirectionImageFilter.h"
	-#include "itkImageRegionConstIterator.h"
	-#include "itkImageRegionConstIteratorWithIndex.h"
	-#include "itkImageRegionIterator.h"
	-#include "itkArray.h"
	-#include "vnl/vnl_vector.h"
	-#include <boost/progress.hpp>
	-
	-#include <vtkSmartPointer.h>
	-#include <vtkPolyData.h>
	-#include <vtkCellArray.h>
	-#include <vtkPoints.h>
	-#include <vtkPolyLine.h>
	-
	-namespace itk {
	-
	-template< class TTensorPixelType>
	-DiffusionTensorPrincipalDirectionImageFilter< TTensorPixelType>::DiffusionTensorPrincipalDirectionImageFilter()
	- : m_NormalizeVectors(true)
	- , m_UsePolarCoordinates(false)
	- , m_FaThreshold(0.2)
	-{
	- this->SetNumberOfRequiredInputs( 1 );
	-}
	-
	-template< class TTensorPixelType>
	-void DiffusionTensorPrincipalDirectionImageFilter< TTensorPixelType>::BeforeThreadedGenerateData()
	-{
	- typename InputImageType::Pointer inputImagePointer = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) );
	- Vector<double,3> spacing3 = inputImagePointer->GetSpacing();
	- mitk::Point3D origin3 = inputImagePointer->GetOrigin();
	- itk::Matrix<double, 3, 3> direction3 = inputImagePointer->GetDirection();
	- ImageRegion<3> imageRegion3 = inputImagePointer->GetLargestPossibleRegion();
	-
	- if (m_MaskImage.IsNull())
	- {
	- m_MaskImage = ItkUcharImgType::New();
	- m_MaskImage->SetSpacing( spacing3 );
	- m_MaskImage->SetOrigin( origin3 );
	- m_MaskImage->SetDirection( direction3 );
	- m_MaskImage->SetRegions( imageRegion3 );
	- m_MaskImage->Allocate();
	- m_MaskImage->FillBuffer(1);
	- }
	-
	- typename OutputImageType::Pointer outputImage = OutputImageType::New();
	- outputImage->SetSpacing( spacing3 );
	- outputImage->SetOrigin( origin3 );
	- outputImage->SetDirection( direction3 );
	- outputImage->SetRegions( imageRegion3 );
	- outputImage->Allocate();
	- outputImage->FillBuffer(0);
	- this->SetNthOutput(0, outputImage);
	-
	-
	- itk::Vector<double, 4> spacing4;
	- itk::Point<float, 4> origin4;
	- itk::Matrix<double, 4, 4> direction4;
	- itk::ImageRegion<4> imageRegion4;
	-
	- spacing4[0] = spacing3[0]; spacing4[1] = spacing3[1]; spacing4[2] = spacing3[2]; spacing4[3] = 1;
	- origin4[0] = origin3[0]; origin4[1] = origin3[1]; origin4[2] = origin3[2]; origin3[3] = 0;
	- for (int r=0; r<3; r++)
	- for (int c=0; c<3; c++)
	- direction4[r][c] = direction3[r][c];
	- direction4[3][3] = 1;
	- imageRegion4.SetSize(0, imageRegion3.GetSize()[0]);
	- imageRegion4.SetSize(1, imageRegion3.GetSize()[1]);
	- imageRegion4.SetSize(2, imageRegion3.GetSize()[2]);
	- imageRegion4.SetSize(3, 3);
	-
	- m_PeakImage = PeakImageType::New();
	- m_PeakImage->SetSpacing( spacing4 );
	- m_PeakImage->SetOrigin( origin4 );
	- m_PeakImage->SetDirection( direction4 );
	- m_PeakImage->SetRegions( imageRegion4 );
	- m_PeakImage->Allocate();
	- m_PeakImage->FillBuffer(0.0);
	-}
	-
	-template< class TTensorPixelType>
	-void DiffusionTensorPrincipalDirectionImageFilter< TTensorPixelType>
	-::AfterThreadedGenerateData()
	-{
	-
	-}
	-
	-template< class TTensorPixelType>
	-void DiffusionTensorPrincipalDirectionImageFilter< TTensorPixelType>
	-::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, ThreadIdType )
	-{
	-
	- typedef itk::DiffusionTensor3D<TTensorPixelType> TensorType;
	- typedef ImageRegionConstIterator< InputImageType > InputIteratorType;
	- typename InputImageType::Pointer inputImagePointer = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) );
	-
	- typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetPrimaryOutput());
	-
	- ImageRegionIterator< OutputImageType > numDirectionsIterator(outputImage, outputRegionForThread);
	- InputIteratorType tensorIterator(inputImagePointer, outputRegionForThread );
	-
	- while( !tensorIterator.IsAtEnd() )
	- {
	- typename InputImageType::IndexType index = tensorIterator.GetIndex();
	- if (m_MaskImage->GetPixel(index)==0)
	- {
	- ++tensorIterator;
	- ++numDirectionsIterator;
	- continue;
	- }
	-
	- typename InputImageType::PixelType b = tensorIterator.Get();
	- TensorType tensor = b.GetDataPointer();
	-
	- typename PeakImageType::IndexType peakIndex;
	- peakIndex[0] = tensorIterator.GetIndex()[0];
	- peakIndex[1] = tensorIterator.GetIndex()[1];
	- peakIndex[2] = tensorIterator.GetIndex()[2];
	-
	- typename TensorType::EigenValuesArrayType eigenvalues;
	- typename TensorType::EigenVectorsMatrixType eigenvectors;
	- if(tensor.GetTrace()!=0)
	- {
	- tensor.ComputeEigenAnalysis(eigenvalues, eigenvectors);
	-
	- vnl_vector_fixed<float,3> vec;
	- vec[0] = eigenvectors(2,0);
	- vec[1] = eigenvectors(2,1);
	- vec[2] = eigenvectors(2,2);
	- vec.normalize();
	-
	- vnl_vector_fixed<float,3> out; out.fill(0);
	-
	- float fa = tensor.GetFractionalAnisotropy();
	- if (fa<m_FaThreshold)
	- vec.fill(0.0);
	- else
	- {
	- if (!m_NormalizeVectors)
	- vec *= fa;
	-
	- if (m_UsePolarCoordinates)
	- {
	- if(vec[0] \|\| vec[1] \|\| vec[2])
	- {
	- out[0] = sqrt( vec[0] * vec[0] + vec[1] * vec[1] + vec[2] * vec[2] );
	- out[1] = atan2( vec[1], vec[0] );
	- out[2] = 0.5itk::Math::pi - atan( vec[2] / sqrt( vec[0] vec[0] + vec[1] * vec[1] ) );
	-
	- if(out[1]>itk::Math::pi)
	- {
	- out[1] = out[1] - itk::Math::pi;
	- }
	- }
	- else
	- {
	- out[0] = 0;
	- out[1] = 0;
	- out[2] = 0;
	- }
	- }
	- else
	- {
	- out = vec;
	- }
	- }
	-
	- peakIndex[3] = 0;
	- m_PeakImage->SetPixel(peakIndex, out[0]);
	- peakIndex[3] = 1;
	- m_PeakImage->SetPixel(peakIndex, out[1]);
	- peakIndex[3] = 2;
	- m_PeakImage->SetPixel(peakIndex, out[2]);
	-
	- numDirectionsIterator.Set( 1 );
	- }
	-
	- ++numDirectionsIterator;
	- ++tensorIterator;
	- }
	-
	- std::cout << "One Thread finished extraction" << std::endl;
	-}
	-
	-template< class TTensorPixelType>
	-void DiffusionTensorPrincipalDirectionImageFilter< TTensorPixelType>
	-::PrintSelf(std::ostream& , Indent ) const
	-{
	-}
	-
	-}
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDistanceMapFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDistanceMapFilter.h
	deleted file mode 100644
	index e07cf0cf24..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDistanceMapFilter.h
	+++ /dev/null
	@@ -1,94 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef ITKDISTANCEMAPFILTER_H_
	-#define ITKDISTANCEMAPFILTER_H_
	-
	-#include "itkImageToImageFilter.h"
	-#include "itkImage.h"
	-#include "mitkImage.h"
	-
	-
	-namespace itk
	-{
	-template < class TInputImage, class TOutputImage >
	-class DistanceMapFilter : public ImageToImageFilter<TInputImage, TOutputImage>
	-{
	- /**
	- * \brief This filter creates a map of the distance to the nearest point on a binary mask.
	- *
	- */
	-
	-public:
	-
	- /** Typedef for input ImageType. */
	- typedef TInputImage InputImageType;
	-
	- /** Typedef for input imageType Pointer. */
	- typedef typename InputImageType::Pointer InputImagePointer;
	-
	- /** Typedef for output ImageType. */
	- typedef TOutputImage OutputImageType;
	-
	- /** Typedef for input imageType Pointer. */
	- typedef typename OutputImageType::Pointer OutputImagePointer;
	-
	-public:
	-
	- /** */
	- typedef DistanceMapFilter Self;
	-
	- /** Superclass */
	- typedef ImageToImageFilter<InputImageType, OutputImageType> Superclass;
	-
	- /** Smart Pointer */
	- typedef SmartPointer<Self> Pointer;
	-
	- /** Smart Pointer */
	- typedef SmartPointer<const Self> ConstPointer;
	-
	- /** */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Generate Data. The image will be divided into a number of pieces, a number of threads
	- will be spawned and Threaded GenerateData() will be called in each thread. */
	- void GenerateData() override;
	-
	-
	-protected:
	-
	- /** Constructor */
	- DistanceMapFilter();
	-
	- /** Destructor */
	- ~DistanceMapFilter() override;
	-
	-
	-
	-protected:
	-
	-
	-
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkDistanceMapFilter.txx"
	-#endif
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDistanceMapFilter.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDistanceMapFilter.txx
	deleted file mode 100644
	index f80ce05286..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDistanceMapFilter.txx
	+++ /dev/null
	@@ -1,79 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef _itkDistanceMapFilter_txx
	-#define _itkDistanceMapFilter_txx
	-
	-#include "itkDistanceMapFilter.h"
	-
	-#include <itkSignedMaurerDistanceMapImageFilter.h>
	-
	-
	-namespace itk
	-{
	-
	- template< class TInputImage, class TOutputImage >
	- DistanceMapFilter<TInputImage, TOutputImage>::DistanceMapFilter()
	- {
	-
	- }
	-
	- template< class TInputImage, class TOutputImage >
	- DistanceMapFilter<TInputImage, TOutputImage>::~DistanceMapFilter()
	- {
	-
	-
	- }
	-
	-
	-
	-
	- template< class TInputImage, class TOutputImage >
	- void DistanceMapFilter<TInputImage, TOutputImage>::GenerateData()
	- {
	-
	-
	- typedef itk::SignedMaurerDistanceMapImageFilter<InputImageType, OutputImageType> DistanceFilterType;
	- typename DistanceFilterType::Pointer dFilter = DistanceFilterType::New();
	- dFilter->SetInput(this->GetInput());
	- dFilter->SetUseImageSpacing(true);
	- dFilter->SetSquaredDistance(false);
	- dFilter->SetInsideIsPositive(true);
	- dFilter->Update();
	-
	- typename OutputImageType::Pointer outputImg = dFilter->GetOutput();
	-
	- typedef itk::ImageRegionIterator<OutputImageType> ImageIteratorType;
	-
	- ImageIteratorType outIt(outputImg, outputImg->GetRequestedRegion());
	- outIt.GoToBegin();
	- while(!outIt.IsAtEnd())
	- {
	- typename OutputImageType::PixelType p = outIt.Get();
	- p *= -1;
	- outIt.Set(p);
	- ++outIt;
	- }
	-
	- Superclass::SetNthOutput( 0, outputImg );
	-
	- }
	-
	-
	-
	-
	-
	-}
	-#endif // _itkDistanceMapFilter_txx
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDwiGradientLengthCorrectionFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDwiGradientLengthCorrectionFilter.h
	deleted file mode 100644
	index 1272613832..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDwiGradientLengthCorrectionFilter.h
	+++ /dev/null
	@@ -1,75 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _itk_DwiGradientLengthCorrectionFilter_h_
	-#define _itk_DwiGradientLengthCorrectionFilter_h_
	-
	-#include <itkProcessObject.h>
	-#include <vnl/vnl_vector_fixed.h>
	-#include <itkVectorContainer.h>
	-#include <MitkDiffusionCoreExports.h>
	-
	-namespace itk
	-{
	-
	-class MITKDIFFUSIONCORE_EXPORT DwiGradientLengthCorrectionFilter : public ProcessObject
	-{
	-
	-public:
	- typedef DwiGradientLengthCorrectionFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ProcessObject Superclass;
	-
	- typedef vnl_vector_fixed< double, 3 > GradientDirectionType;
	- typedef itk::VectorContainer< unsigned int, GradientDirectionType > GradientDirectionContainerType;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- itkTypeMacro(DwiGradientLengthCorrectionFilter,ProcessObject)
	-
	- void GenerateData() override;
	-
	- void Update() override{
	- this->GenerateData();
	- }
	-
	- // input
	- itkSetMacro(RoundingValue, int)
	- itkSetMacro(ReferenceBValue, double)
	- itkSetMacro(ReferenceGradientDirectionContainer, GradientDirectionContainerType::Pointer)
	-
	- // output
	- itkGetMacro(OutputGradientDirectionContainer, GradientDirectionContainerType::Pointer)
	- itkGetMacro(NewBValue, double)
	-
	- protected:
	- DwiGradientLengthCorrectionFilter();
	- ~DwiGradientLengthCorrectionFilter() override;
	-
	- double m_NewBValue;
	- double m_ReferenceBValue;
	- int m_RoundingValue;
	-
	- GradientDirectionContainerType::Pointer m_ReferenceGradientDirectionContainer;
	- GradientDirectionContainerType::Pointer m_OutputGradientDirectionContainer;
	-};
	-
	-
	-} // end of namespace
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDwiNormilzationFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDwiNormilzationFilter.h
	deleted file mode 100644
	index d614feb423..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDwiNormilzationFilter.h
	+++ /dev/null
	@@ -1,101 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-/*===================================================================
	-
	-This file is based heavily on a corresponding ITK filter.
	-
	-===================================================================*/
	-#ifndef __itkDwiNormilzationFilter_h_
	-#define __itkDwiNormilzationFilter_h_
	-
	-#include "itkImageToImageFilter.h"
	-#include "itkVectorImage.h"
	-#include <itkLabelStatisticsImageFilter.h>
	-#include <itkImageRegionIteratorWithIndex.h>
	-#include <itkShiftScaleImageFilter.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-
	-namespace itk{
	-/** \class DwiNormilzationFilter
	- * \brief Normalizes the data vectors either using the specified reference value or the voxelwise baseline value.
	- */
	-
	-template< class TInPixelType >
	-class DwiNormilzationFilter :
	- public ImageToImageFilter< VectorImage< TInPixelType, 3 >, VectorImage< TInPixelType, 3 > >
	-{
	-
	-public:
	-
	- typedef DwiNormilzationFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageToImageFilter< VectorImage< TInPixelType, 3 >, VectorImage< TInPixelType, 3 > > Superclass;
	-
	- typedef typename Superclass::InputImageType InputImageType;
	- typedef typename Superclass::OutputImageType OutputImageType;
	- typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(DwiNormilzationFilter, ImageToImageFilter)
	-
	- typedef itk::Image< double, 3 > DoubleImageType;
	- typedef itk::Image< unsigned char, 3 > UcharImageType;
	- typedef itk::Image< unsigned short, 3 > BinImageType;
	- typedef itk::Image< TInPixelType, 3 > TInPixelImageType;
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionType GradientDirectionType;
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer GradientContainerType;
	-
	- typedef ImageRegionConstIterator< InputImageType > InputIteratorType;
	- typedef ImageRegionConstIterator< UcharImageType > MaskIteratorType;
	-
	-
	- itkSetMacro( GradientDirections, GradientContainerType )
	- itkSetMacro( ScalingFactor, TInPixelType )
	- itkSetMacro( MaskImage, UcharImageType::Pointer )
	- itkSetMacro( NewMean, double )
	- itkSetMacro( NewStdev, double )
	-
	- protected:
	- DwiNormilzationFilter();
	- ~DwiNormilzationFilter() {}
	- void PrintSelf(std::ostream& os, Indent indent) const;
	-
	- void BeforeThreadedGenerateData();
	- void ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, ThreadIdType);
	-
	- UcharImageType::Pointer m_MaskImage;
	- GradientContainerType m_GradientDirections;
	- int m_B0Index;
	- TInPixelType m_ScalingFactor;
	- double m_Mean;
	- double m_Stdev;
	- double m_NewMean;
	- double m_NewStdev;
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkDwiNormilzationFilter.txx"
	-#endif
	-
	-#endif //__itkDwiNormilzationFilter_h_
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDwiNormilzationFilter.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDwiNormilzationFilter.txx
	deleted file mode 100644
	index d27b8af8db..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkDwiNormilzationFilter.txx
	+++ /dev/null
	@@ -1,183 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkDwiNormilzationFilter_txx
	-#define __itkDwiNormilzationFilter_txx
	-
	-#include <time.h>
	-#include <stdio.h>
	-#include <stdlib.h>
	-
	-#define _USE_MATH_DEFINES
	-#include <math.h>
	-
	-#include "itkImageRegionConstIterator.h"
	-#include "itkImageRegionConstIteratorWithIndex.h"
	-#include "itkImageRegionIterator.h"
	-#include <itkNumericTraits.h>
	-
	-namespace itk {
	-
	-
	-template< class TInPixelType >
	-DwiNormilzationFilter< TInPixelType>::DwiNormilzationFilter()
	- : m_B0Index(-1)
	- , m_NewMean(1000)
	- , m_NewStdev(500)
	-{
	- this->SetNumberOfRequiredInputs( 1 );
	-}
	-
	-template< class TInPixelType >
	-void DwiNormilzationFilter< TInPixelType>::BeforeThreadedGenerateData()
	-{
	- typename InputImageType::Pointer inputImagePointer = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) );
	-
	- m_B0Index = -1;
	- for (unsigned int i=0; i<inputImagePointer->GetVectorLength(); i++)
	- {
	- GradientDirectionType g = m_GradientDirections->GetElement(i);
	- if (g.magnitude()<0.001)
	- m_B0Index = i;
	- }
	- if (m_B0Index==-1)
	- itkExceptionMacro(<< "DwiNormilzationFilter: No b-Zero indecies found!");
	-
	- if (m_MaskImage.IsNull())
	- {
	- // initialize mask image
	- m_MaskImage = UcharImageType::New();
	- m_MaskImage->SetSpacing( inputImagePointer->GetSpacing() );
	- m_MaskImage->SetOrigin( inputImagePointer->GetOrigin() );
	- m_MaskImage->SetDirection( inputImagePointer->GetDirection() );
	- m_MaskImage->SetRegions( inputImagePointer->GetLargestPossibleRegion() );
	- m_MaskImage->Allocate();
	- m_MaskImage->FillBuffer(1);
	- }
	- else
	- std::cout << "DwiNormilzationFilter: using mask image" << std::endl;
	-
	- InputIteratorType git( inputImagePointer, inputImagePointer->GetLargestPossibleRegion() );
	- MaskIteratorType mit( m_MaskImage, m_MaskImage->GetLargestPossibleRegion() );
	- git.GoToBegin();
	- mit.GoToBegin();
	-
	- int n = 0;
	- m_Mean = 0;
	- m_Stdev = 0;
	- while( !git.IsAtEnd() )
	- {
	- if (mit.Get()>0)
	- {
	- for (unsigned int i=0; i<inputImagePointer->GetVectorLength(); i++)
	- {
	- if ((int)i==m_B0Index)
	- continue;
	- m_Mean += git.Get()[i];
	- n++;
	- }
	- }
	- ++git;
	- ++mit;
	- }
	- m_Mean /= n;
	-
	- git.GoToBegin();
	- mit.GoToBegin();
	-
	- while( !git.IsAtEnd() )
	- {
	- if (mit.Get()>0)
	- {
	- for (unsigned int i=0; i<inputImagePointer->GetVectorLength(); i++)
	- {
	- if ((int)i==m_B0Index)
	- continue;
	- double diff = (double)(git.Get()[i]) - m_Mean;
	- m_Stdev += diff*diff;
	- }
	- }
	- ++git;
	- ++mit;
	- }
	-
	- m_Stdev = std::sqrt(m_Stdev/(n-1));
	-
	- MITK_INFO << "Mean: " << m_Mean;
	- MITK_INFO << "Stdev: " << m_Stdev;
	-}
	-
	-template< class TInPixelType >
	-void DwiNormilzationFilter< TInPixelType>::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, ThreadIdType )
	-{
	- typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0));
	-
	- ImageRegionIterator< OutputImageType > oit(outputImage, outputRegionForThread);
	- oit.GoToBegin();
	-
	- typename InputImageType::Pointer inputImagePointer = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) );
	-
	- MaskIteratorType mit( m_MaskImage, outputRegionForThread );
	- mit.GoToBegin();
	- InputIteratorType git( inputImagePointer, outputRegionForThread );
	- git.GoToBegin();
	-
	- while( !git.IsAtEnd() )
	- {
	- typename InputImageType::PixelType pix = git.Get();
	- typename OutputImageType::PixelType outPix;
	- outPix.SetSize(inputImagePointer->GetVectorLength());
	-
	- for (unsigned int i=0; i<inputImagePointer->GetVectorLength(); i++)
	- {
	- double val = (double)pix[i] - m_Mean;
	- val /= m_Stdev;
	- val *= m_NewStdev;
	- val += m_NewMean;
	- if (val<0)
	- {
	- val = 0;
	- MITK_INFO << "Negative value.";
	- }
	- if (val>32767)
	- {
	- val = 32767;
	- MITK_INFO << "Range overflow. Value is too large for datatype short.";
	- }
	- outPix[i] = (TInPixelType)val;
	- }
	-
	- oit.Set(outPix);
	-
	- ++mit;
	- ++oit;
	- ++git;
	- }
	-
	- std::cout << "One Thread finished calculation" << std::endl;
	-}
	-
	-template< class TInPixelType >
	-void
	-DwiNormilzationFilter< TInPixelType>
	-::PrintSelf(std::ostream& os, Indent indent) const
	-{
	- Superclass::PrintSelf(os,indent);
	-}
	-
	-}
	-
	-#endif // __itkDwiNormilzationFilter_txx
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.h
	deleted file mode 100644
	index 7ff7cb21f7..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.h
	+++ /dev/null
	@@ -1,128 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-/*=========================================================================
	-
	-Program: Tensor ToolKit - TTK
	-Module: $URL: svn://scm.gforge.inria.fr/svn/ttk/trunk/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.h $
	-Language: C++
	-Date: $Date: 2010-06-07 13:39:13 +0200 (Mo, 07 Jun 2010) $
	-Version: $Revision: 68 $
	-
	-Copyright (c) INRIA 2010. All rights reserved.
	-See LICENSE.txt for details.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without even
	-the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
	-PURPOSE. See the above copyright notices for more information.
	-
	-=========================================================================*/
	-#ifndef _itk_ElectrostaticRepulsionDiffusionGradientReductionFilter_h_
	-#define _itk_ElectrostaticRepulsionDiffusionGradientReductionFilter_h_
	-
	-#include <itkImageToImageFilter.h>
	-#include <itkVectorImage.h>
	-#include <itkPointShell.h>
	-
	-namespace itk
	-{
	-
	-/**
	-* \brief Select subset of the input vectors equally distributed over the sphere using an iterative electrostatic repulsion strategy. */
	-
	- template <class TInputScalarType, class TOutputScalarType>
	- class ElectrostaticRepulsionDiffusionGradientReductionFilter
	- : public ImageToImageFilter<itk::VectorImage<TInputScalarType,3>, itk::VectorImage<TOutputScalarType,3> >
	- {
	-
	- public:
	-
	- typedef ElectrostaticRepulsionDiffusionGradientReductionFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageToImageFilter< itk::VectorImage<TOutputScalarType,3>, itk::VectorImage<TOutputScalarType,3> >
	- Superclass;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(ElectrostaticRepulsionDiffusionGradientReductionFilter, ImageToImageFilter)
	-
	- typedef TInputScalarType InputScalarType;
	- typedef itk::VectorImage<InputScalarType,3> InputImageType;
	- typedef typename InputImageType::PixelType InputPixelType;
	-
	- typedef TOutputScalarType OutputScalarType;
	- typedef itk::VectorImage<OutputScalarType,3> OutputImageType;
	- typedef typename OutputImageType::PixelType OutputPixelType;
	-
	- typedef OutputScalarType BaselineScalarType;
	- typedef BaselineScalarType BaselinePixelType;
	- typedef typename itk::Image<BaselinePixelType,3> BaselineImageType;
	-
	- typedef vnl_vector_fixed< double, 3 > GradientDirectionType;
	- typedef itk::VectorContainer< unsigned int, GradientDirectionType > GradientDirectionContainerType;
	-
	- typedef std::vector<unsigned int> IndicesVector;
	- typedef std::map<unsigned int, IndicesVector> BValueMap;
	-
	- itkGetMacro(OriginalGradientDirections, GradientDirectionContainerType::Pointer)
	- itkSetMacro(OriginalGradientDirections, GradientDirectionContainerType::Pointer)
	-
	- itkGetMacro(GradientDirections, GradientDirectionContainerType::Pointer)
	- itkSetMacro(GradientDirections, GradientDirectionContainerType::Pointer)
	- itkSetMacro(UseFirstN, bool)
	-
	- IndicesVector GetUsedGradientIndices(){return m_UsedGradientIndices;}
	- void SetOriginalBValueMap(BValueMap inp){m_OriginalBValueMap = inp;}
	- void SetShellSelectionBValueMap(BValueMap inp){m_InputBValueMap = inp;}
	- void SetNumGradientDirections(std::vector<unsigned int> numDirs){m_NumGradientDirections = numDirs;}
	-
	-
	- void UpdateOutputInformation() override;
	-
	- protected:
	- ElectrostaticRepulsionDiffusionGradientReductionFilter();
	- ~ElectrostaticRepulsionDiffusionGradientReductionFilter() override {}
	-
	- void GenerateData() override;
	- double Costs(); ///< calculates electrostatic energy of current direction set
	-
	- GradientDirectionContainerType::Pointer m_GradientDirections; ///< container for the subsampled output gradient directions
	- GradientDirectionContainerType::Pointer m_OriginalGradientDirections; ///< input gradient directions
	-
	- IndicesVector m_UsedGradientIndices;
	- IndicesVector m_UnusedGradientIndices;
	- IndicesVector m_BaselineImageIndices;
	-
	- BValueMap m_OriginalBValueMap;
	- BValueMap m_InputBValueMap;
	- bool m_UseFirstN;
	-
	- std::vector<unsigned int> m_NumGradientDirections;
	- };
	-
	-
	-} // end of namespace
	-
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkElectrostaticRepulsionDiffusionGradientReductionFilter.txx"
	-#endif
	-
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.txx
	deleted file mode 100644
	index b8751e8145..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.txx
	+++ /dev/null
	@@ -1,270 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-/*=========================================================================
	-
	-Program: Tensor ToolKit - TTK
	-Module: $URL: svn://scm.gforge.inria.fr/svn/ttk/trunk/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.txx $
	-Language: C++
	-Date: $Date: 2010-06-07 13:39:13 +0200 (Mo, 07 Jun 2010) $
	-Version: $Revision: 68 $
	-
	-Copyright (c) INRIA 2010. All rights reserved.
	-See LICENSE.txt for details.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without even
	-the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
	-PURPOSE. See the above copyright notices for more information.
	-
	-=========================================================================*/
	-#ifndef _itk_ElectrostaticRepulsionDiffusionGradientReductionFilter_txx_
	-#define _itk_ElectrostaticRepulsionDiffusionGradientReductionFilter_txx_
	-#endif
	-
	-#include "itkElectrostaticRepulsionDiffusionGradientReductionFilter.h"
	-#include <itkMersenneTwisterRandomVariateGenerator.h>
	-#include <ctime>
	-#include <itkImageRegionIterator.h>
	-#include <itkImageRegion.h>
	-
	-namespace itk
	-{
	-
	-template <class TInputScalarType, class TOutputScalarType>
	-ElectrostaticRepulsionDiffusionGradientReductionFilter<TInputScalarType, TOutputScalarType>
	-::ElectrostaticRepulsionDiffusionGradientReductionFilter()
	- : m_UseFirstN(false)
	-{
	- this->SetNumberOfRequiredInputs( 1 );
	-}
	-
	-template <class TInputScalarType, class TOutputScalarType>
	-double
	-ElectrostaticRepulsionDiffusionGradientReductionFilter<TInputScalarType, TOutputScalarType>
	-::Costs()
	-{
	- double costs = 2*itk::Math::pi;
	- for (IndicesVector::iterator it = m_UsedGradientIndices.begin(); it!=m_UsedGradientIndices.end(); ++it)
	- {
	- for (IndicesVector::iterator it2 = m_UsedGradientIndices.begin(); it2!=m_UsedGradientIndices.end(); ++it2)
	- if (it != it2)
	- {
	- vnl_vector_fixed<double,3> v1 = m_OriginalGradientDirections->at(*it);
	- vnl_vector_fixed<double,3> v2 = m_OriginalGradientDirections->at(*it2);
	-
	- v1.normalize(); v2.normalize();
	- double temp = dot_product(v1,v2);
	- if (temp>1)
	- temp = 1;
	- else if (temp<-1)
	- temp = -1;
	-
	- double angle = acos(temp);
	-
	- if (angle<costs)
	- costs = angle;
	-
	- temp = dot_product(-v1,v2);
	- if (temp>1)
	- temp = 1;
	- else if (temp<-1)
	- temp = -1;
	-
	- angle = acos(temp);
	- if (angle<costs)
	- costs = angle;
	- }
	- }
	-
	- return costs;
	-}
	-
	-template <class TInputScalarType, class TOutputScalarType>
	-void
	-ElectrostaticRepulsionDiffusionGradientReductionFilter<TInputScalarType, TOutputScalarType>
	-::GenerateData()
	-{
	- itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer randgen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New();
	-
	- if(m_InputBValueMap.empty() \|\| m_NumGradientDirections.size()!=m_InputBValueMap.size())
	- mitkThrow() << "Vector of the number of desired gradient directions contains more elements than the specified target b-value map.";
	-
	- BValueMap manipulatedMap = m_InputBValueMap;
	-
	- IndicesVector final_gradient_indices;
	- int shellCounter = 0;
	- for(BValueMap::iterator it = m_InputBValueMap.begin(); it != m_InputBValueMap.end(); it++ )
	- {
	- randgen->SetSeed();
	-
	- m_UsedGradientIndices.clear();
	- m_UnusedGradientIndices.clear();
	-
	- MITK_INFO << "Shell number: " << shellCounter;
	- unsigned int c=0;
	- for (unsigned int i=0; i<it->second.size(); i++)
	- {
	- if (c<m_NumGradientDirections[shellCounter])
	- m_UsedGradientIndices.push_back(it->second.at(i));
	- else
	- m_UnusedGradientIndices.push_back(it->second.at(i));
	- c++;
	- }
	-
	- if ( it->second.size() <= m_NumGradientDirections[shellCounter] )
	- {
	- itkWarningMacro( << "current directions: " << it->second.size() << " wanted directions: " << m_NumGradientDirections[shellCounter]);
	- m_NumGradientDirections[shellCounter] = it->second.size();
	- }
	- else if (!m_UseFirstN)
	- {
	- double minAngle = Costs();
	- double newMinAngle = 0;
	-
	- MITK_INFO << "minimum angle: " << 180*minAngle/itk::Math::pi;
	- int stagnationCount = 0;
	- int rejectionCount = 0;
	- int maxRejections = m_NumGradientDirections[shellCounter] * 1000;
	- if (maxRejections<10000)
	- maxRejections = 10000;
	- int iUsed = 0;
	- if (m_UsedGradientIndices.size()>0)
	- {
	- while ( stagnationCount<1000 && rejectionCount<maxRejections )
	- {
	- // make proposal for new gradient configuration by randomly removing one of the currently used directions and instead adding one of the unused directions
	- int iUnUsed = randgen->GetIntegerVariate() % m_UnusedGradientIndices.size();
	- int vUsed = m_UsedGradientIndices.at(iUsed);
	- int vUnUsed = m_UnusedGradientIndices.at(iUnUsed);
	- m_UsedGradientIndices.at(iUsed) = vUnUsed;
	- m_UnusedGradientIndices.at(iUnUsed) = vUsed;
	-
	- newMinAngle = Costs(); // calculate costs of proposed configuration
	- if (newMinAngle > minAngle) // accept or reject proposal
	- {
	- MITK_INFO << "minimum angle: " << 180*newMinAngle/itk::Math::pi;
	-
	- if ( (newMinAngle-minAngle)<0.01 )
	- stagnationCount++;
	- else
	- stagnationCount = 0;
	-
	- minAngle = newMinAngle;
	- rejectionCount = 0;
	- }
	- else
	- {
	- rejectionCount++;
	- m_UsedGradientIndices.at(iUsed) = vUsed;
	- m_UnusedGradientIndices.at(iUnUsed) = vUnUsed;
	- }
	- iUsed++;
	- iUsed = iUsed % m_UsedGradientIndices.size();
	- }
	- }
	- }
	- manipulatedMap[it->first] = m_UsedGradientIndices;
	- shellCounter++;
	-
	- for (auto gidx : m_UsedGradientIndices)
	- final_gradient_indices.push_back(gidx);
	- }
	- std::sort(final_gradient_indices.begin(), final_gradient_indices.end());
	-
	- int vecLength = 0 ;
	- for(BValueMap::iterator it = manipulatedMap.begin(); it != manipulatedMap.end(); it++)
	- vecLength += it->second.size();
	-
	- // initialize output image
	- typename OutputImageType::Pointer outImage = OutputImageType::New();
	- outImage->SetSpacing( this->GetInput()->GetSpacing() ); // Set the image spacing
	- outImage->SetOrigin( this->GetInput()->GetOrigin() ); // Set the image origin
	- outImage->SetDirection( this->GetInput()->GetDirection() ); // Set the image direction
	- outImage->SetLargestPossibleRegion( this->GetInput()->GetLargestPossibleRegion());
	- outImage->SetBufferedRegion( this->GetInput()->GetLargestPossibleRegion() );
	- outImage->SetRequestedRegion( this->GetInput()->GetLargestPossibleRegion() );
	- outImage->SetVectorLength( final_gradient_indices.size() ); // Set the vector length
	- outImage->Allocate();
	-
	- itk::ImageRegionIterator< OutputImageType > newIt(outImage, outImage->GetLargestPossibleRegion());
	- newIt.GoToBegin();
	-
	- typename InputImageType::Pointer inImage = const_cast<InputImageType*>(this->GetInput(0));
	- itk::ImageRegionIterator< InputImageType > oldIt(inImage, inImage->GetLargestPossibleRegion());
	- oldIt.GoToBegin();
	-
	- // initial new value of voxel
	- OutputPixelType newVec;
	- newVec.SetSize( final_gradient_indices.size() );
	- newVec.AllocateElements( final_gradient_indices.size() );
	-
	- // generate new pixel values
	- while(!newIt.IsAtEnd())
	- {
	- // init new vector with zeros
	- newVec.Fill(0.0);
	- InputPixelType oldVec = oldIt.Get();
	-
	- for (unsigned int i=0; i<final_gradient_indices.size(); ++i)
	- newVec[i] = oldVec[final_gradient_indices.at(i)];
	-
	- // int index = 0;
	- // for(BValueMap::iterator it=manipulatedMap.begin(); it!=manipulatedMap.end(); it++)
	- // for(unsigned int j=0; j<it->second.size(); j++)
	- // {
	- // newVec[index] = oldVec[it->second.at(j)];
	- // index++;
	- // }
	- newIt.Set(newVec);
	-
	- ++newIt;
	- ++oldIt;
	- }
	-
	- // set new gradient directions
	- m_GradientDirections = GradientDirectionContainerType::New();
	- for (unsigned int i=0; i<final_gradient_indices.size(); ++i)
	- m_GradientDirections->InsertElement(i, m_OriginalGradientDirections->at(final_gradient_indices.at(i)));
	-
	- // int index = 0;
	- // for(BValueMap::iterator it = manipulatedMap.begin(); it != manipulatedMap.end(); it++)
	- // for(unsigned int j = 0; j < it->second.size(); j++)
	- // {
	- // m_GradientDirections->InsertElement(index, m_OriginalGradientDirections->at(it->second.at(j)));
	- // index++;
	- // }
	-
	- this->SetNumberOfRequiredOutputs (1);
	- this->SetNthOutput (0, outImage);
	- MITK_INFO << "...done";
	-}
	-
	-template <class TInputScalarType, class TOutputScalarType>
	-void
	-ElectrostaticRepulsionDiffusionGradientReductionFilter<TInputScalarType, TOutputScalarType>
	-::UpdateOutputInformation()
	-{
	- Superclass::UpdateOutputInformation();
	-
	- int vecLength = 0 ;
	- for(unsigned int index = 0; index < m_NumGradientDirections.size(); index++)
	- {
	- vecLength += m_NumGradientDirections[index];
	- }
	-
	- this->GetOutput()->SetVectorLength( vecLength );
	-}
	-
	-} // end of namespace
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkExtractChannelFromRgbaImageFilter.cpp b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkExtractChannelFromRgbaImageFilter.cpp
	deleted file mode 100644
	index afc9b02bfc..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkExtractChannelFromRgbaImageFilter.cpp
	+++ /dev/null
	@@ -1,171 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#include "itkExtractChannelFromRgbaImageFilter.h"
	-
	-// VTK
	-#include <vtkPolyLine.h>
	-#include <vtkCellArray.h>
	-#include <vtkCellData.h>
	-
	-// misc
	-#include <math.h>
	-
	-namespace itk{
	-
	- template< class ReferenceImageType, class OutputImageType >
	- ExtractChannelFromRgbaImageFilter< ReferenceImageType, OutputImageType >::ExtractChannelFromRgbaImageFilter():
	- m_Channel(RED)
	- {
	-
	- }
	-
	- template< class ReferenceImageType, class OutputImageType >
	- ExtractChannelFromRgbaImageFilter< ReferenceImageType, OutputImageType >::~ExtractChannelFromRgbaImageFilter()
	- {
	- }
	-
	- template< class ReferenceImageType, class OutputImageType >
	- void ExtractChannelFromRgbaImageFilter< ReferenceImageType, OutputImageType >::GenerateData()
	- {
	-
	- typename InputImageType::Pointer rgbaImage = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) );
	-
	- typename OutputImageType::Pointer outputImage =
	- static_cast< OutputImageType * >(this->ProcessObject::GetPrimaryOutput());
	-
	- typename InputImageType::RegionType region = rgbaImage->GetLargestPossibleRegion();
	- outputImage->SetSpacing( m_ReferenceImage->GetSpacing() ); // Set the image spacing
	- outputImage->SetOrigin( m_ReferenceImage->GetOrigin() ); // Set the image origin
	- outputImage->SetDirection( m_ReferenceImage->GetDirection() ); // Set the image direction
	- outputImage->SetRegions( m_ReferenceImage->GetLargestPossibleRegion());
	- outputImage->Allocate();
	- outputImage->FillBuffer(0);
	- float* outImageBufferPointer = outputImage->GetBufferPointer();
	-
	- itk::Image< short, 3 >::Pointer counterImage = itk::Image< short, 3 >::New();
	- counterImage->SetSpacing( m_ReferenceImage->GetSpacing() ); // Set the image spacing
	- counterImage->SetOrigin( m_ReferenceImage->GetOrigin() ); // Set the image origin
	- counterImage->SetDirection( m_ReferenceImage->GetDirection() ); // Set the image direction
	- counterImage->SetRegions( m_ReferenceImage->GetLargestPossibleRegion());
	- counterImage->Allocate();
	- counterImage->FillBuffer(0);
	- short* counterImageBufferPointer = counterImage->GetBufferPointer();
	-
	- int w = m_ReferenceImage->GetLargestPossibleRegion().GetSize().GetElement(0);
	- int h = m_ReferenceImage->GetLargestPossibleRegion().GetSize().GetElement(1);
	- int d = m_ReferenceImage->GetLargestPossibleRegion().GetSize().GetElement(2);
	-
	- typedef ImageRegionConstIterator< InputImageType > InImageIteratorType;
	- InImageIteratorType rgbaIt(rgbaImage, region);
	- rgbaIt.GoToBegin();
	- while(!rgbaIt.IsAtEnd()){
	-
	- InPixelType x = rgbaIt.Get();
	- ++rgbaIt;
	-
	- itk::Point<float, 3> vertex;
	- itk::Index<3> index = rgbaIt.GetIndex();
	-
	- rgbaImage->TransformIndexToPhysicalPoint(index, vertex);
	- outputImage->TransformPhysicalPointToIndex(vertex, index);
	-
	- itk::ContinuousIndex<float, 3> contIndex;
	- outputImage->TransformPhysicalPointToContinuousIndex(vertex, contIndex);
	-
	- float frac_x = contIndex[0] - index[0];
	- float frac_y = contIndex[1] - index[1];
	- float frac_z = contIndex[2] - index[2];
	- int px = index[0];
	- if (frac_x<0)
	- {
	- px -= 1;
	- frac_x += 1;
	- }
	- int py = index[1];
	- if (frac_y<0)
	- {
	- py -= 1;
	- frac_y += 1;
	- }
	- int pz = index[2];
	- if (frac_z<0)
	- {
	- pz -= 1;
	- frac_z += 1;
	- }
	- frac_x = 1-frac_x;
	- frac_y = 1-frac_y;
	- frac_z = 1-frac_z;
	-
	- // int coordinates inside image?
	- if (px < 0 \|\| px >= w-1)
	- continue;
	- if (py < 0 \|\| py >= h-1)
	- continue;
	- if (pz < 0 \|\| pz >= d-1)
	- continue;
	-
	- OutPixelType out = 0.0f;
	- switch (m_Channel)
	- {
	- case RED:
	- out = (float)x.GetRed()/255;
	- break;
	- case GREEN:
	- out = (float)x.GetGreen()/255;
	- break;
	- case BLUE:
	- out = (float)x.GetBlue()/255;
	- break;
	- case ALPHA:
	- out = (float)x.GetAlpha()/255;
	- }
	-
	- outImageBufferPointer[( px + w(py + hpz ))] += out( frac_x)( frac_y)*( frac_z);
	- outImageBufferPointer[( px + w(py+1+ hpz ))] += out( frac_x)(1-frac_y)*( frac_z);
	- outImageBufferPointer[( px + w(py + hpz+h))] += out( frac_x)( frac_y)*(1-frac_z);
	- outImageBufferPointer[( px + w(py+1+ hpz+h))] += out( frac_x)(1-frac_y)*(1-frac_z);
	- outImageBufferPointer[( px+1 + w(py + hpz ))] += out(1-frac_x)( frac_y)*( frac_z);
	- outImageBufferPointer[( px+1 + w(py + hpz+h))] += out(1-frac_x)( frac_y)*(1-frac_z);
	- outImageBufferPointer[( px+1 + w(py+1+ hpz ))] += out(1-frac_x)(1-frac_y)*( frac_z);
	- outImageBufferPointer[( px+1 + w(py+1+ hpz+h))] += out(1-frac_x)(1-frac_y)*(1-frac_z);
	-
	- counterImageBufferPointer[( px + w(py + hpz ))] += 1;
	- counterImageBufferPointer[( px + w(py+1+ hpz ))] += 1;
	- counterImageBufferPointer[( px + w(py + hpz+h))] += 1;
	- counterImageBufferPointer[( px + w(py+1+ hpz+h))] += 1;
	- counterImageBufferPointer[( px+1 + w(py + hpz ))] += 1;
	- counterImageBufferPointer[( px+1 + w(py + hpz+h))] += 1;
	- counterImageBufferPointer[( px+1 + w(py+1+ hpz ))] += 1;
	- counterImageBufferPointer[( px+1 + w(py+1+ hpz+h))] += 1;
	-
	- }
	-
	- typedef ImageRegionIterator< OutputImageType > OutImageIteratorType;
	- OutImageIteratorType outIt(outputImage, outputImage->GetLargestPossibleRegion());
	- outIt.GoToBegin();
	- typedef ImageRegionConstIterator< itk::Image< short, 3 > > CountImageIteratorType;
	- CountImageIteratorType counterIt(counterImage, counterImage->GetLargestPossibleRegion());
	- counterIt.GoToBegin();
	-
	- while(!outIt.IsAtEnd() && !counterIt.IsAtEnd()){
	- if (counterIt.Value()>0)
	- outIt.Set(outIt.Value()/counterIt.Value());
	- ++outIt;
	- ++counterIt;
	- }
	- }
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkExtractChannelFromRgbaImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkExtractChannelFromRgbaImageFilter.h
	deleted file mode 100644
	index 1411b1ab8e..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkExtractChannelFromRgbaImageFilter.h
	+++ /dev/null
	@@ -1,73 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef __itkExtractChannelFromRgbaImageFilter_h__
	-#define __itkExtractChannelFromRgbaImageFilter_h__
	-
	-#include <itkImageToImageFilter.h>
	-#include <itkImage.h>
	-#include <itkRGBAPixel.h>
	-#include <itkVectorImage.h>
	-
	-namespace itk{
	-
	-template< class ReferenceImageType, class OutputImageType >
	-class ExtractChannelFromRgbaImageFilter : public ImageToImageFilter< itk::Image<itk::RGBAPixel<unsigned char>,3>, OutputImageType >
	-{
	-
	-public:
	-
	- enum Channel {
	- RED,
	- GREEN,
	- BLUE,
	- ALPHA
	- };
	-
	- typedef ExtractChannelFromRgbaImageFilter Self;
	- typedef ProcessObject Superclass;
	- typedef SmartPointer< Self > Pointer;
	- typedef SmartPointer< const Self > ConstPointer;
	-
	- typedef itk::Image<itk::RGBAPixel<unsigned char>,3> InputImageType;
	- typedef typename OutputImageType::PixelType OutPixelType;
	- typedef typename InputImageType::PixelType InPixelType;
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- itkTypeMacro( ExtractChannelFromRgbaImageFilter, ImageSource );
	-
	- / Upsampling factor /
	-
	- void GenerateData();
	-
	- itkSetMacro(Channel, Channel)
	- itkSetMacro(ReferenceImage, typename ReferenceImageType::Pointer)
	-
	-protected:
	-
	- ExtractChannelFromRgbaImageFilter();
	- virtual ~ExtractChannelFromRgbaImageFilter();
	- Channel m_Channel;
	- typename ReferenceImageType::Pointer m_ReferenceImage;
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkExtractChannelFromRgbaImageFilter.cpp"
	-#endif
	-
	-#endif // __itkExtractChannelFromRgbaImageFilter_h__
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkExtractDwiChannelFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkExtractDwiChannelFilter.h
	deleted file mode 100644
	index c4dfaecb5f..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkExtractDwiChannelFilter.h
	+++ /dev/null
	@@ -1,77 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-/*===================================================================
	-
	-This file is based heavily on a corresponding ITK filter.
	-
	-===================================================================*/
	-#ifndef __itkExtractDwiChannelFilter_h_
	-#define __itkExtractDwiChannelFilter_h_
	-
	-#include "itkImageToImageFilter.h"
	-#include "itkVectorImage.h"
	-#include <itkImageRegionIteratorWithIndex.h>
	-#include <mitkImage.h>
	-
	-namespace itk{
	-/** \class ExtractDwiChannelFilter
	- * \brief Remove specified channels from diffusion-weighted image.
	- */
	-
	-template< class TInPixelType >
	-class ExtractDwiChannelFilter :
	- public ImageToImageFilter< VectorImage< TInPixelType, 3 >, Image< TInPixelType, 3 > >
	-{
	-
	-public:
	-
	- typedef ExtractDwiChannelFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageToImageFilter< VectorImage< TInPixelType, 3 >, Image< TInPixelType, 3 > > Superclass;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(ExtractDwiChannelFilter, ImageToImageFilter)
	-
	- typedef typename Superclass::InputImageType InputImageType;
	- typedef typename Superclass::OutputImageType OutputImageType;
	- typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
	-
	- itkSetMacro( ChannelIndex, unsigned int )
	-
	- protected:
	- ExtractDwiChannelFilter();
	- ~ExtractDwiChannelFilter() override {}
	-
	- void BeforeThreadedGenerateData() override;
	- void ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, ThreadIdType ) override;
	-
	- unsigned int m_ChannelIndex;
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkExtractDwiChannelFilter.txx"
	-#endif
	-
	-#endif //__itkExtractDwiChannelFilter_h_
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkExtractDwiChannelFilter.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkExtractDwiChannelFilter.txx
	deleted file mode 100644
	index 6ab8d1e179..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkExtractDwiChannelFilter.txx
	+++ /dev/null
	@@ -1,71 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkExtractDwiChannelFilter_txx
	-#define __itkExtractDwiChannelFilter_txx
	-
	-#include <ctime>
	-#include <cstdio>
	-#include <cstdlib>
	-
	-#define _USE_MATH_DEFINES
	-#include <cmath>
	-
	-#include "itkImageRegionConstIterator.h"
	-#include "itkImageRegionConstIteratorWithIndex.h"
	-#include "itkImageRegionIterator.h"
	-
	-namespace itk {
	-
	-
	-template< class TInPixelType >
	-ExtractDwiChannelFilter< TInPixelType>::ExtractDwiChannelFilter()
	-{
	- this->SetNumberOfRequiredInputs( 1 );
	-}
	-
	-template< class TInPixelType >
	-void ExtractDwiChannelFilter< TInPixelType>::BeforeThreadedGenerateData()
	-{
	- typename InputImageType::Pointer inputImagePointer = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) );
	- if ( inputImagePointer->GetVectorLength()<=m_ChannelIndex )
	- itkExceptionMacro("Index out of bounds!");
	-}
	-
	-template< class TInPixelType >
	-void ExtractDwiChannelFilter< TInPixelType>::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, ThreadIdType )
	-{
	- typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0));
	-
	- ImageRegionIterator< OutputImageType > oit(outputImage, outputRegionForThread);
	- oit.GoToBegin();
	-
	- typedef ImageRegionConstIterator< InputImageType > InputIteratorType;
	- typename InputImageType::Pointer inputImagePointer = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) );
	-
	- InputIteratorType git( inputImagePointer, outputRegionForThread );
	- git.GoToBegin();
	- while( !git.IsAtEnd() )
	- {
	- oit.Set( git.Get()[m_ChannelIndex] );
	- ++oit;
	- ++git;
	- }
	-}
	-
	-}
	-
	-#endif // __itkExtractDwiChannelFilter_txx
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkFlipPeaksFilter.cpp b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkFlipPeaksFilter.cpp
	deleted file mode 100644
	index 0e1fc33aa9..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkFlipPeaksFilter.cpp
	+++ /dev/null
	@@ -1,99 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef __itkFlipPeaksFilter_cpp
	-#define __itkFlipPeaksFilter_cpp
	-
	-#include "itkFlipPeaksFilter.h"
	-#include <itkImageRegionConstIterator.h>
	-#include <itkImageRegionConstIteratorWithIndex.h>
	-#include <itkImageRegionIterator.h>
	-#include <vnl/vnl_vector.h>
	-#include <itkOrientationDistributionFunction.h>
	-#include <itkContinuousIndex.h>
	-
	-#include <vtkSmartPointer.h>
	-#include <vtkPolyData.h>
	-#include <vtkCellArray.h>
	-#include <vtkPoints.h>
	-#include <vtkPolyLine.h>
	-
	-#include <boost/math/special_functions.hpp>
	-#include <boost/progress.hpp>
	-
	-
	-using namespace boost::math;
	-
	-namespace itk {
	-
	-template< class PixelType >
	-FlipPeaksFilter< PixelType>::FlipPeaksFilter()
	-{
	- this->SetNumberOfRequiredInputs(1);
	-}
	-
	-
	-template< class PixelType >
	-void FlipPeaksFilter< PixelType>
	-::BeforeThreadedGenerateData()
	-{
	- typename InputImageType::Pointer input = static_cast< InputImageType* >( this->ProcessObject::GetInput(0) );
	-
	-// typename OutputImageType::Pointer output = OutputImageType::New();
	-// output->SetSpacing( input->GetSpacing() );
	-// output->SetOrigin( input->GetOrigin() );
	-// output->SetDirection( input->GetDirection() );
	-// output->SetRegions( input->GetLargestPossibleRegion() );
	-// output->Allocate();
	-// output->FillBuffer(0.0);
	-}
	-
	-template< class PixelType >
	-void FlipPeaksFilter< PixelType>
	-::AfterThreadedGenerateData()
	-{
	-
	-}
	-
	-template< class PixelType >
	-void FlipPeaksFilter< PixelType>
	-::ThreadedGenerateData( const OutputImageRegionType& outputRegionForThread, ThreadIdType )
	-{
	- typename InputImageType::Pointer input_image = static_cast< InputImageType* >( this->ProcessObject::GetInput(0) );
	- typename OutputImageType::Pointer output_image = static_cast< OutputImageType* >( this->ProcessObject::GetOutput(0) );
	-
	- ImageRegionIterator< InputImageType > iit(input_image, outputRegionForThread );
	- ImageRegionIterator< OutputImageType > oit(output_image, outputRegionForThread );
	-
	- while( !iit.IsAtEnd() )
	- {
	- typename InputImageType::IndexType idx = iit.GetIndex();
	-
	- oit.Set(iit.Get());
	- if (m_FlipX && idx[3]%3==0)
	- oit.Set(-1*iit.Get());
	- if (m_FlipY && idx[3]%3==1)
	- oit.Set(-1*iit.Get());
	- if (m_FlipZ && idx[3]%3==2)
	- oit.Set(-1*iit.Get());
	-
	- ++iit;
	- ++oit;
	- }
	-}
	-
	-}
	-
	-#endif // __itkFlipPeaksFilter_cpp
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkFlipPeaksFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkFlipPeaksFilter.h
	deleted file mode 100644
	index 64ca3625d8..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkFlipPeaksFilter.h
	+++ /dev/null
	@@ -1,84 +0,0 @@
	-/*=========================================================================
	-
	- Program: Insight Segmentation & Registration Toolkit
	- Module: $RCSfile: itkDiffusionTensor3DReconstructionImageFilter.h,v $
	- Language: C++
	- Date: $Date: 2006-03-27 17:01:06 $
	- Version: $Revision: 1.12 $
	-
	- Copyright (c) Insight Software Consortium. All rights reserved.
	- See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
	-
	- This software is distributed WITHOUT ANY WARRANTY; without even
	- the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
	- PURPOSE. See the above copyright notices for more information.
	-
	-=========================================================================*/
	-#ifndef __itkFlipPeaksFilter_h_
	-#define __itkFlipPeaksFilter_h_
	-
	-#include "itkImageToImageFilter.h"
	-#include "vnl/vnl_vector_fixed.h"
	-#include "vnl/vnl_matrix.h"
	-#include "vnl/algo/vnl_svd.h"
	-#include "itkVectorContainer.h"
	-#include "itkVectorImage.h"
	-#include <mitkFiberBundle.h>
	-#include <itkOrientationDistributionFunction.h>
	-#include <mitkPeakImage.h>
	-
	-namespace itk{
	-
	-/**
	-* \brief Flip peaks along specified axes
	-*/
	-
	-template< class PixelType >
	-class FlipPeaksFilter : public ImageToImageFilter< mitk::PeakImage::ItkPeakImageType, mitk::PeakImage::ItkPeakImageType >
	-{
	-
	- public:
	-
	- typedef FlipPeaksFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageToImageFilter< mitk::PeakImage::ItkPeakImageType, mitk::PeakImage::ItkPeakImageType > Superclass;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(FlipPeaksFilter, ImageToImageFilter)
	-
	- typedef typename Superclass::InputImageType InputImageType;
	- typedef typename Superclass::OutputImageType OutputImageType;
	- typedef typename OutputImageType::RegionType OutputImageRegionType;
	-
	- itkSetMacro( FlipX, bool) ///< flip peaks in x direction
	- itkSetMacro( FlipY, bool) ///< flip peaks in y direction
	- itkSetMacro( FlipZ, bool) ///< flip peaks in z direction
	-
	- protected:
	- FlipPeaksFilter();
	- ~FlipPeaksFilter(){}
	-
	- void BeforeThreadedGenerateData();
	- void ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, ThreadIdType threadID );
	- void AfterThreadedGenerateData();
	-
	- private:
	-
	- bool m_FlipX;
	- bool m_FlipY;
	- bool m_FlipZ;
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkFlipPeaksFilter.cpp"
	-#endif
	-
	-#endif //__itkFlipPeaksFilter_h_
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkFourDToVectorImageFilter.cpp b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkFourDToVectorImageFilter.cpp
	deleted file mode 100644
	index 94d27a76b5..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkFourDToVectorImageFilter.cpp
	+++ /dev/null
	@@ -1,101 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef __itkFourDToVectorImageFilter_cpp
	-#define __itkFourDToVectorImageFilter_cpp
	-
	-#include "itkFourDToVectorImageFilter.h"
	-#include <itkImageRegionConstIterator.h>
	-#include <itkImageRegionConstIteratorWithIndex.h>
	-#include <itkImageRegionIterator.h>
	-#include <vnl/vnl_vector.h>
	-#include <itkOrientationDistributionFunction.h>
	-#include <itkContinuousIndex.h>
	-
	-#include <vtkSmartPointer.h>
	-#include <vtkPolyData.h>
	-#include <vtkCellArray.h>
	-#include <vtkPoints.h>
	-#include <vtkPolyLine.h>
	-
	-#include <boost/math/special_functions.hpp>
	-#include <boost/progress.hpp>
	-
	-
	-using namespace boost::math;
	-
	-namespace itk {
	-
	-template< class PixelType >
	-FourDToVectorImageFilter< PixelType>::FourDToVectorImageFilter()
	-{
	-
	-}
	-
	-
	-template< class PixelType >
	-void FourDToVectorImageFilter< PixelType>
	-::GenerateData()
	-{
	- Vector<float, 4> spacing4 = m_InputImage->GetSpacing();
	- Point<float, 4> origin4 = m_InputImage->GetOrigin();
	- Matrix<double, 4, 4> direction4 = m_InputImage->GetDirection();
	- ImageRegion<4> imageRegion4 = m_InputImage->GetLargestPossibleRegion();
	-
	- Vector<double, 3> spacing3;
	- Point<float, 3> origin3;
	- Matrix<double, 3, 3> direction3;
	- ImageRegion<3> imageRegion3;
	-
	- spacing3[0] = spacing4[0]; spacing3[1] = spacing4[1]; spacing3[2] = spacing4[2];
	- origin3[0] = origin4[0]; origin3[1] = origin4[1]; origin3[2] = origin4[2];
	- for (int r=0; r<3; r++)
	- for (int c=0; c<3; c++)
	- direction3[r][c] = direction4[r][c];
	- imageRegion3.SetSize(0, imageRegion4.GetSize()[0]);
	- imageRegion3.SetSize(1, imageRegion4.GetSize()[1]);
	- imageRegion3.SetSize(2, imageRegion4.GetSize()[2]);
	-
	- m_OutputImage = OutputImageType::New();
	- m_OutputImage->SetSpacing( spacing3 );
	- m_OutputImage->SetOrigin( origin3 );
	- m_OutputImage->SetDirection( direction3 );
	- m_OutputImage->SetRegions( imageRegion3 );
	- m_OutputImage->SetVectorLength(imageRegion4.GetSize()[3]);
	- m_OutputImage->Allocate();
	- typename OutputImageType::PixelType pix; pix.SetSize(imageRegion4.GetSize()[3]); pix.Fill(0.0);
	- m_OutputImage->FillBuffer(pix);
	- ImageRegionIterator< OutputImageType > oit(m_OutputImage, m_OutputImage->GetLargestPossibleRegion() );
	-
	- while( !oit.IsAtEnd() )
	- {
	- auto idx3 = oit.GetIndex();
	-
	- typename OutputImageType::PixelType pix = oit.Get();
	- for (unsigned int i=0; i<pix.GetSize(); ++i)
	- {
	- typename InputImageType::IndexType idx4;
	- idx4[0] = idx3[0]; idx4[1] = idx3[1]; idx4[2] = idx3[2]; idx4[3] = i;
	- pix[i] = m_InputImage->GetPixel(idx4);
	- }
	- oit.Set(pix);
	-
	- ++oit;
	- }
	-}
	-
	-}
	-
	-#endif // __itkFourDToVectorImageFilter_cpp
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkFourDToVectorImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkFourDToVectorImageFilter.h
	deleted file mode 100644
	index f4c29d9082..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkFourDToVectorImageFilter.h
	+++ /dev/null
	@@ -1,74 +0,0 @@
	-/*=========================================================================
	-
	- Program: Insight Segmentation & Registration Toolkit
	- Module: $RCSfile: itkDiffusionTensor3DReconstructionImageFilter.h,v $
	- Language: C++
	- Date: $Date: 2006-03-27 17:01:06 $
	- Version: $Revision: 1.12 $
	-
	- Copyright (c) Insight Software Consortium. All rights reserved.
	- See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
	-
	- This software is distributed WITHOUT ANY WARRANTY; without even
	- the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
	- PURPOSE. See the above copyright notices for more information.
	-
	-=========================================================================*/
	-#ifndef __itkFourDToVectorImageFilter_h_
	-#define __itkFourDToVectorImageFilter_h_
	-
	-#include "itkImageToImageFilter.h"
	-#include <itkImage.h>
	-#include <itkVectorImage.h>
	-
	-namespace itk{
	-
	-/**
	-* \brief Flip peaks along specified axes
	-*/
	-
	-template< class PixelType >
	-class FourDToVectorImageFilter : public ProcessObject
	-{
	-
	-public:
	-
	- typedef FourDToVectorImageFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ProcessObject Superclass;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(FourDToVectorImageFilter, ProcessObject)
	-
	- typedef Image<PixelType, 4> InputImageType;
	- typedef VectorImage<PixelType, 3> OutputImageType;
	- typedef typename OutputImageType::RegionType OutputImageRegionType;
	-
	- itkSetMacro(InputImage, typename InputImageType::Pointer)
	- itkGetMacro(OutputImage, typename OutputImageType::Pointer)
	-
	- void GenerateData();
	-
	-protected:
	- FourDToVectorImageFilter();
	- ~FourDToVectorImageFilter(){}
	-
	- typename InputImageType::Pointer m_InputImage;
	- typename OutputImageType::Pointer m_OutputImage;
	-
	-private:
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkFourDToVectorImageFilter.cpp"
	-#endif
	-
	-#endif //__itkFourDToVectorImageFilter_h_
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkGaussianInterpolateImageFunction.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkGaussianInterpolateImageFunction.h
	deleted file mode 100644
	index ac1c9ab798..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkGaussianInterpolateImageFunction.h
	+++ /dev/null
	@@ -1,186 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-/*===================================================================
	-
	-This file is based heavily on a corresponding ITK filter.
	-
	-===================================================================*/
	-#ifndef __itkGaussianInterpolateImageFunction_h
	-#define __itkGaussianInterpolateImageFunction_h
	-
	-#include "itkInterpolateImageFunction.h"
	-
	-#include "itkConceptChecking.h"
	-#include "itkFixedArray.h"
	-#include "vnl/vnl_erf.h"
	-
	-namespace itk
	-{
	-
	-/** \class GaussianInterpolateImageFunction
	- * \brief Evaluates the Gaussian interpolation of an image.
	- *
	- * This class defines an N-dimensional Gaussian interpolation function using
	- * the vnl error function. The two parameters associated with this function
	- * are:
	- * 1. Sigma - a scalar array of size ImageDimension determining the width
	- * of the interpolation function.
	- * 2. Alpha - a scalar specifying the cutoff distance over which the function
	- * is calculated.
	- *
	- * \ingroup ImageFunctions ImageInterpolators
	- */
	-
	-template <class TInputImage, class TCoordRep = double>
	-class ITK_EXPORT GaussianInterpolateImageFunction :
	- public InterpolateImageFunction<TInputImage, TCoordRep>
	-{
	-public:
	- /** Standard class typedefs. */
	- typedef GaussianInterpolateImageFunction Self;
	- typedef InterpolateImageFunction<TInputImage, TCoordRep> Superclass;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	-
	- /** Run-time type information (and related methods). */
	- itkTypeMacro( GaussianInterpolateImageFunction, InterpolateImageFunction );
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** ImageDimension constant */
	- itkStaticConstMacro( ImageDimension, unsigned int,
	- TInputImage::ImageDimension );
	-
	-
	- /** OutputType typedef support. */
	- typedef typename Superclass::OutputType OutputType;
	-
	- /** InputImageType typedef support. */
	- typedef typename Superclass::InputImageType InputImageType;
	-
	- /** RealType typedef support. */
	- typedef typename Superclass::RealType RealType;
	-
	- /** Index typedef support. */
	- typedef typename Superclass::IndexType IndexType;
	-
	- /** ContinuousIndex typedef support. */
	- typedef typename Superclass::ContinuousIndexType ContinuousIndexType;
	-
	- /** Array typedef support */
	- typedef FixedArray<RealType,
	- itkGetStaticConstMacro( ImageDimension )> ArrayType;
	-
	- /**
	- * Set input image
	- */
	- void SetInputImage( const TInputImage *image ) override
	- {
	- Superclass::SetInputImage( image );
	- this->ComputeBoundingBox();
	- }
	-
	- /**
	- * Set/Get ivars
	- */
	- virtual void SetSigma( const ArrayType s )
	- {
	- itkDebugMacro( "setting Sigma to " << s );
	- if( this->m_Sigma != s )
	- {
	- this->m_Sigma = s;
	- this->ComputeBoundingBox();
	- this->Modified();
	- }
	- }
	- itkGetConstMacro( Sigma, ArrayType );
	- void SetSigma( RealType *s )
	- {
	- ArrayType sigma;
	- for( unsigned int d = 0; d < ImageDimension; d++ )
	- {
	- sigma[d] = s[d];
	- }
	- this->SetSigma( sigma );
	- }
	-
	- virtual void SetAlpha( const RealType a )
	- {
	- itkDebugMacro( "setting Alpha to " << a );
	- if( this->m_Alpha != a )
	- {
	- this->m_Alpha = a;
	- this->ComputeBoundingBox();
	- this->Modified();
	- }
	- }
	- itkGetConstMacro( Alpha, RealType );
	-
	- void SetParameters( RealType *sigma, RealType alpha )
	- {
	- this->SetSigma( sigma );
	- this->SetAlpha( alpha );
	- }
	-
	- /**
	- * Evaluate at the given index
	- */
	- OutputType EvaluateAtContinuousIndex(
	- const ContinuousIndexType & cindex ) const override
	- {
	- return this->EvaluateAtContinuousIndex( cindex, nullptr );
	- }
	-
	- /**
	- * Evaluate function value and gradient at the given index
	- */
	- virtual OutputType EvaluateAtContinuousIndex(
	- const ContinuousIndexType &, OutputType * ) const;
	-
	-protected:
	- GaussianInterpolateImageFunction();
	- ~GaussianInterpolateImageFunction() override{};
	- void PrintSelf( std::ostream& os, Indent indent ) const override;
	-
	-private:
	- GaussianInterpolateImageFunction( const Self& ); //purposely not implemented
	- void operator=( const Self& ); //purposely not implemented
	-
	- void ComputeBoundingBox();
	-
	- void ComputeErrorFunctionArray( unsigned int dimension, RealType cindex,
	- vnl_vector<RealType> &erfArray, vnl_vector<RealType> &gerfArray,
	- bool evaluateGradient = false ) const;
	-
	- ArrayType m_Sigma;
	- RealType m_Alpha;
	-
	- ArrayType m_BoundingBoxStart;
	- ArrayType m_BoundingBoxEnd;
	- ArrayType m_ScalingFactor;
	- ArrayType m_CutoffDistance;
	-};
	-
	-} // end namespace itk
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkGaussianInterpolateImageFunction.txx"
	-#endif
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkGaussianInterpolateImageFunction.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkGaussianInterpolateImageFunction.txx
	deleted file mode 100644
	index 3400eed649..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkGaussianInterpolateImageFunction.txx
	+++ /dev/null
	@@ -1,230 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-/*===================================================================
	-
	-This file is based heavily on a corresponding ITK filter.
	-
	-===================================================================*/
	-#ifndef __itkGaussianInterpolateImageFunction_txx
	-#define __itkGaussianInterpolateImageFunction_txx
	-
	-#include "itkGaussianInterpolateImageFunction.h"
	-
	-#include "itkImageRegionConstIteratorWithIndex.h"
	-
	-namespace itk
	-{
	-
	-/**
	- * Constructor
	- */
	-template <class TImageType, class TCoordRep>
	-GaussianInterpolateImageFunction<TImageType, TCoordRep>
	-::GaussianInterpolateImageFunction()
	-{
	- this->m_Alpha = 1.0;
	- this->m_Sigma.Fill( 1.0 );
	-}
	-
	-/**
	- * Standard "PrintSelf" method
	- */
	-template <class TImageType, class TCoordRep>
	-void
	-GaussianInterpolateImageFunction<TImageType, TCoordRep>
	-::PrintSelf( std::ostream& os, Indent indent ) const
	-{
	- Superclass::PrintSelf( os, indent );
	- os << indent << "Alpha: " << this->m_Alpha << std::endl;
	- os << indent << "Sigma: " << this->m_Sigma << std::endl;
	-}
	-
	-template <class TImageType, class TCoordRep>
	-void
	-GaussianInterpolateImageFunction<TImageType, TCoordRep>
	-::ComputeBoundingBox()
	-{
	- if( !this->GetInputImage() )
	- {
	- return;
	- }
	-
	- for( unsigned int d = 0; d < ImageDimension; d++ )
	- {
	- this->m_BoundingBoxStart[d] = -0.5;
	- this->m_BoundingBoxEnd[d] = static_cast<RealType>(
	- this->GetInputImage()->GetBufferedRegion().GetSize()[d] ) - 0.5;
	- this->m_ScalingFactor[d] = 1.0 / ( vnl_math::sqrt2 * this->m_Sigma[d] /
	- this->GetInputImage()->GetSpacing()[d] );
	- this->m_CutoffDistance[d] = this->m_Sigma[d] * this->m_Alpha /
	- this->GetInputImage()->GetSpacing()[d];
	- }
	-}
	-
	-template <class TImageType, class TCoordRep>
	-typename GaussianInterpolateImageFunction<TImageType, TCoordRep>
	-::OutputType
	-GaussianInterpolateImageFunction<TImageType, TCoordRep>
	-::EvaluateAtContinuousIndex( const ContinuousIndexType &cindex,
	- OutputType *grad ) const
	-{
	- vnl_vector<RealType> erfArray[ImageDimension];
	- vnl_vector<RealType> gerfArray[ImageDimension];
	-
	- // Compute the ERF difference arrays
	- for( unsigned int d = 0; d < ImageDimension; d++ )
	- {
	- bool evaluateGradient = false;
	- if( grad )
	- {
	- evaluateGradient = true;
	- }
	- this->ComputeErrorFunctionArray( d, cindex[d], erfArray[d],
	- gerfArray[d], evaluateGradient );
	- }
	-
	- RealType sum_me = 0.0;
	- RealType sum_m = 0.0;
	- ArrayType dsum_me;
	- ArrayType dsum_m;
	- ArrayType dw;
	-
	- dsum_m.Fill( 0.0 );
	- dsum_me.Fill( 0.0 );
	-
	- // Loop over the voxels in the region identified
	- ImageRegion<ImageDimension> region;
	- for( unsigned int d = 0; d < ImageDimension; d++ )
	- {
	- int boundingBoxSize = static_cast<int>(
	- this->m_BoundingBoxEnd[d] - this->m_BoundingBoxStart[d] + 0.5 );
	- int begin = vnl_math_max( 0, static_cast<int>( vcl_floor( cindex[d] -
	- this->m_BoundingBoxStart[d] - this->m_CutoffDistance[d] ) ) );
	- int end = vnl_math_min( boundingBoxSize, static_cast<int>( vcl_ceil(
	- cindex[d] - this->m_BoundingBoxStart[d] + this->m_CutoffDistance[d] ) ) );
	- region.SetIndex( d, begin );
	- region.SetSize( d, end - begin );
	- }
	-
	- ImageRegionConstIteratorWithIndex<InputImageType> It(
	- this->GetInputImage(), region );
	- for( It.GoToBegin(); !It.IsAtEnd(); ++It )
	- {
	- unsigned int j = It.GetIndex()[0];
	- RealType w = erfArray[0][j];
	- if( grad )
	- {
	- dw[0] = gerfArray[0][j];
	- for( unsigned int d = 1; d < ImageDimension; d++ )
	- {
	- dw[d] = erfArray[0][j];
	- }
	- }
	- for( unsigned int d = 1; d < ImageDimension; d++)
	- {
	- j = It.GetIndex()[d];
	- w *= erfArray[d][j];
	- if( grad )
	- {
	- for( unsigned int q = 0; q < ImageDimension; q++ )
	- {
	- if( d == q )
	- {
	- dw[q] *= gerfArray[d][j];
	- }
	- else
	- {
	- dw[q] *= erfArray[d][j];
	- }
	- }
	- }
	- }
	- RealType V = It.Get();
	- sum_me += V * w;
	- sum_m += w;
	- if( grad )
	- {
	- for( unsigned int q = 0; q < ImageDimension; q++ )
	- {
	- dsum_me[q] += V * dw[q];
	- dsum_m[q] += dw[q];
	- }
	- }
	- }
	- RealType rc = sum_me / sum_m;
	-
	- if( grad )
	- {
	- for( unsigned int q = 0; q < ImageDimension; q++ )
	- {
	- grad[q] = ( dsum_me[q] - rc * dsum_m[q] ) / sum_m;
	- grad[q] /= -vnl_math::sqrt2 * this->m_Sigma[q];
	- }
	- }
	-
	- return rc;
	-}
	-
	-template <class TImageType, class TCoordRep>
	-void
	-GaussianInterpolateImageFunction<TImageType, TCoordRep>
	-::ComputeErrorFunctionArray( unsigned int dimension, RealType cindex,
	- vnl_vector<RealType> &erfArray, vnl_vector<RealType> &gerfArray,
	- bool evaluateGradient ) const
	-{
	- // Determine the range of voxels along the line where to evaluate erf
	- int boundingBoxSize = static_cast<int>(
	- this->m_BoundingBoxEnd[dimension] - this->m_BoundingBoxStart[dimension] +
	- 0.5 );
	- int begin = vnl_math_max( 0, static_cast<int>( vcl_floor( cindex -
	- this->m_BoundingBoxStart[dimension] -
	- this->m_CutoffDistance[dimension] ) ) );
	- int end = vnl_math_min( boundingBoxSize, static_cast<int>( vcl_ceil( cindex -
	- this->m_BoundingBoxStart[dimension] +
	- this->m_CutoffDistance[dimension] ) ) );
	-
	- erfArray.set_size( boundingBoxSize );
	- gerfArray.set_size( boundingBoxSize );
	-
	- // Start at the first voxel
	- RealType t = ( this->m_BoundingBoxStart[dimension] - cindex +
	- static_cast<RealType>( begin ) ) * this->m_ScalingFactor[dimension];
	- RealType e_last = vnl_erf( t );
	- RealType g_last = 0.0;
	- if( evaluateGradient )
	- {
	- g_last = vnl_math::two_over_sqrtpi * vcl_exp( -vnl_math_sqr( t ) );
	- }
	-
	- for( int i = begin; i < end; i++ )
	- {
	- t += this->m_ScalingFactor[dimension];
	- RealType e_now = vnl_erf( t );
	- erfArray[i] = e_now - e_last;
	- if( evaluateGradient )
	- {
	- RealType g_now = vnl_math::two_over_sqrtpi * vcl_exp( -vnl_math_sqr( t ) );
	- gerfArray[i] = g_now - g_last;
	- g_last = g_now;
	- }
	- e_last = e_now;
	- }
	-}
	-
	-} // namespace itk
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkMergeDiffusionImagesFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkMergeDiffusionImagesFilter.h
	deleted file mode 100644
	index bd8c584053..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkMergeDiffusionImagesFilter.h
	+++ /dev/null
	@@ -1,108 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-/*=========================================================================
	-
	-Program: Tensor ToolKit - TTK
	-Module: $URL: svn://scm.gforge.inria.fr/svn/ttk/trunk/Algorithms/itkMergeDiffusionImagesFilter.h $
	-Language: C++
	-Date: $Date: 2010-06-07 13:39:13 +0200 (Mo, 07 Jun 2010) $
	-Version: $Revision: 68 $
	-
	-Copyright (c) INRIA 2010. All rights reserved.
	-See LICENSE.txt for details.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without even
	-the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
	-PURPOSE. See the above copyright notices for more information.
	-
	-=========================================================================*/
	-#ifndef _itk_MergeDiffusionImagesFilter_h_
	-#define _itk_MergeDiffusionImagesFilter_h_
	-
	-#include "itkImageToImageFilter.h"
	-#include <itkDiffusionTensor3D.h>
	-#include <itkVectorImage.h>
	-#include <itkVectorContainer.h>
	-
	-namespace itk
	-{
	-
	-/**
	-* \brief Merges diffusion weighted images, e.g. to generate one multishell volume from several single shell volumes. */
	-
	-template <class TScalarType>
	-class MergeDiffusionImagesFilter
	- : public ImageSource<itk::VectorImage<TScalarType,3> >
	-{
	-
	-public:
	-
	-
	- typedef MergeDiffusionImagesFilter Self;
	- typedef ImageSource< itk::VectorImage<TScalarType,3> > Superclass;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(MergeDiffusionImagesFilter, ImageSource)
	-
	- typedef itk::VectorImage<TScalarType,3> DwiImageType;
	- typedef typename DwiImageType::PixelType DwiPixelType;
	- typedef typename DwiImageType::RegionType DwiRegionType;
	- typedef typename std::vector< typename DwiImageType::Pointer > DwiImageContainerType;
	-
	- typedef vnl_vector_fixed< double, 3 > GradientType;
	- typedef itk::VectorContainer< unsigned int, GradientType > GradientListType;
	- typedef typename std::vector< GradientListType::Pointer > GradientListContainerType;
	-
	- // input
	- void SetImageVolumes(DwiImageContainerType cont); ///< input DWI image volume container
	- void SetGradientLists(GradientListContainerType cont); ///< gradients of all input images
	- void SetBValues(std::vector< double > bvals); ///< b-values of all input images
	-
	- // output
	- GradientListType::Pointer GetOutputGradients(); ///< gradient list of the merged output image
	- double GetB_Value(); ///< main b-value of the merged output image
	-
	-protected:
	-
	- MergeDiffusionImagesFilter();
	- ~MergeDiffusionImagesFilter();
	-
	- void GenerateData() override;
	-
	- DwiImageContainerType m_ImageVolumes; ///< contains input images
	- GradientListContainerType m_GradientLists; ///< contains gradients of all input images
	- std::vector< double > m_BValues; ///< contains b-values of all input images
	- int m_NumGradients; ///< number of gradients in the output image
	- GradientListType::Pointer m_OutputGradients; ///< container for output gradients
	- double m_BValue; ///< main output b-value
	-};
	-
	-
	-} // end of namespace
	-
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkMergeDiffusionImagesFilter.txx"
	-#endif
	-
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkMergeDiffusionImagesFilter.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkMergeDiffusionImagesFilter.txx
	deleted file mode 100644
	index 6d8c0909e0..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkMergeDiffusionImagesFilter.txx
	+++ /dev/null
	@@ -1,179 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-/*=========================================================================
	- 2
	- 3 Program: Tensor ToolKit - TTK
	- 4 Module: $URL: svn://scm.gforge.inria.fr/svn/ttk/trunk/Algorithms/itkMergeDiffusionImagesFilter.txx $
	- 5 Language: C++
	- 6 Date: $Date: 2010-06-07 13:39:13 +0200 (Mo, 07 Jun 2010) $
	- 7 Version: $Revision: 68 $
	- 8
	- 9 Copyright (c) INRIA 2010. All rights reserved.
	- 10 See LICENSE.txt for details.
	- 11
	- 12 This software is distributed WITHOUT ANY WARRANTY; without even
	- 13 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
	- 14 PURPOSE. See the above copyright notices for more information.
	- 15
	- 16 =========================================================================*/
	-#ifndef _itk_MergeDiffusionImagesFilter_txx_
	-#define _itk_MergeDiffusionImagesFilter_txx_
	-#endif
	-
	-#include "itkMergeDiffusionImagesFilter.h"
	-#include "itkTensorToL2NormImageFilter.h"
	-#include "itkRescaleIntensityImageFilter.h"
	-#include <itkImageRegionIterator.h>
	-#include <itkImageRegionConstIterator.h>
	-#include <boost/progress.hpp>
	-
	-namespace itk
	-{
	-
	-template <class TScalarType>
	-MergeDiffusionImagesFilter<TScalarType>::MergeDiffusionImagesFilter()
	-{
	-
	-}
	-
	-template <class TScalarType>
	-MergeDiffusionImagesFilter<TScalarType>::~MergeDiffusionImagesFilter()
	-{
	-
	-}
	-
	-template <class TScalarType>
	-void MergeDiffusionImagesFilter<TScalarType>
	-::SetImageVolumes(DwiImageContainerType cont)
	-{
	- m_ImageVolumes=cont;
	-}
	-
	-template <class TScalarType>
	-void MergeDiffusionImagesFilter<TScalarType>
	-::SetGradientLists(GradientListContainerType cont)
	-{
	- m_GradientLists=cont;
	-}
	-
	-template <class TScalarType>
	-void MergeDiffusionImagesFilter<TScalarType>
	-::SetBValues(std::vector< double > bvals)
	-{
	- m_BValues=bvals;
	-}
	-
	-template <class TScalarType>
	-MergeDiffusionImagesFilter<TScalarType>::GradientListType::Pointer MergeDiffusionImagesFilter<TScalarType>
	-::GetOutputGradients()
	-{
	- return m_OutputGradients;
	-}
	-
	-template <class TScalarType>
	-double MergeDiffusionImagesFilter<TScalarType>
	-::GetB_Value()
	-{
	- return m_BValue;
	-}
	-
	-template <class TScalarType>
	-void
	-MergeDiffusionImagesFilter<TScalarType>
	-::GenerateData ()
	-{
	-
	- if( m_ImageVolumes.size()<2 )
	- throw itk::ExceptionObject (__FILE__,__LINE__,"Error: cannot combine less than two DWIs.");
	-
	- if( m_GradientLists.size()!=m_ImageVolumes.size() \|\| m_ImageVolumes.size()!=m_BValues.size() \|\| m_BValues.size()!=m_GradientLists.size() )
	- throw itk::ExceptionObject (__FILE__,__LINE__,"Error: need same number of b-values, image volumes and gradient containers.");
	-
	- typename DwiImageType::Pointer img = m_ImageVolumes.at(0);
	-
	- m_NumGradients = 0;
	- for (unsigned int i=0; i<m_GradientLists.size(); i++)
	- {
	- m_NumGradients += m_GradientLists.at(i)->Size();
	- typename DwiImageType::Pointer tmp = m_ImageVolumes.at(i);
	- if ( img->GetLargestPossibleRegion()!=tmp->GetLargestPossibleRegion() )
	- throw itk::ExceptionObject (__FILE__,__LINE__,"Error: images are not of same size.");
	- }
	-
	- m_BValue = 0;
	- for (auto bval : m_BValues)
	- if (bval>m_BValue)
	- m_BValue = bval;
	- m_OutputGradients = GradientListType::New();
	-
	- typename DwiImageType::Pointer outImage = DwiImageType::New();
	- outImage->SetSpacing( img->GetSpacing() ); // Set the image spacing
	- outImage->SetOrigin( img->GetOrigin() ); // Set the image origin
	- outImage->SetDirection( img->GetDirection() ); // Set the image direction
	- outImage->SetLargestPossibleRegion( img->GetLargestPossibleRegion());
	- outImage->SetBufferedRegion( img->GetLargestPossibleRegion() );
	- outImage->SetRequestedRegion( img->GetLargestPossibleRegion() );
	- outImage->SetVectorLength(m_NumGradients);
	- outImage->Allocate();
	-
	- this->SetNumberOfRequiredOutputs(1);
	- this->SetNthOutput (0, outImage);
	-
	- typedef ImageRegionIterator<DwiImageType> IteratorOutputType;
	- IteratorOutputType itOut (this->GetOutput(), this->GetOutput()->GetLargestPossibleRegion());
	-
	- MITK_INFO << "MergeDiffusionImagesFilter: merging images";
	- GradientType zeroG; zeroG.fill(0.0);
	- boost::progress_display disp(this->GetOutput()->GetLargestPossibleRegion().GetNumberOfPixels());
	- while(!itOut.IsAtEnd())
	- {
	- ++disp;
	- DwiPixelType out;
	- out.SetSize(m_NumGradients);
	- out.Fill(0);
	-
	- int c=0;
	- for (unsigned int i=0; i<m_GradientLists.size(); i++)
	- {
	- GradientListType::Pointer gradients = m_GradientLists.at(i);
	- typename DwiImageType::Pointer img = m_ImageVolumes.at(i);
	-
	- for (unsigned int j=0; j<gradients->Size(); j++)
	- {
	- GradientType g = gradients->GetElement(j);
	- double mag = g.two_norm();
	-
	- if (mag>0.0001)
	- {
	- double frac = m_BValues.at(i)magmag/m_BValue;
	- g.normalize();
	- g *= sqrt(frac);
	- }
	- else
	- g = zeroG;
	-
	- m_OutputGradients->InsertElement(c, g);
	- out[c] = static_cast<TScalarType>(img->GetPixel(itOut.GetIndex())[j]);
	- c++;
	- }
	- }
	-
	- itOut.Set(out);
	- ++itOut;
	- }
	-}
	-
	-} // end of namespace
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkNonLocalMeansDenoisingFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkNonLocalMeansDenoisingFilter.h
	deleted file mode 100644
	index 4fd2d6cdc1..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkNonLocalMeansDenoisingFilter.h
	+++ /dev/null
	@@ -1,145 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkNonLocalMeansDenoisingFilter_h_
	-#define __itkNonLocalMeansDenoisingFilter_h_
	-
	-#include "itkImageToImageFilter.h"
	-#include "itkVectorImage.h"
	-
	-
	-namespace itk{
	- /** @class NonLocalMeansDenoisingFilter
	- * @brief This class denoises a vectorimage according to the non-local means procedure.
	- *
	- * This Filter needs as an input a diffusion weigthed image, which will be denoised unsing the non-local means principle.
	- * An input mask is optional to denoise only inside the mask range. All other voxels will be set to 0.
	- */
	-
	- template< class TPixelType >
	- class NonLocalMeansDenoisingFilter :
	- public ImageToImageFilter< VectorImage < TPixelType, 3 >, VectorImage < TPixelType, 3 > >
	- {
	- public:
	-
	- /** Typedefs */
	- typedef NonLocalMeansDenoisingFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageToImageFilter< VectorImage < TPixelType, 3 >, VectorImage < TPixelType, 3 > > Superclass;
	- typedef typename Superclass::InputImageType InputImageType;
	- typedef typename Superclass::OutputImageType OutputImageType;
	- typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
	- typedef Image <TPixelType, 3> MaskImageType;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(NonLocalMeansDenoisingFilter, ImageToImageFilter)
	-
	- /**
	- * @brief Set flag to use joint information
	- */
	- itkSetMacro(UseJointInformation, bool)
	- /**
	- * @brief Set the searchradius
	- *
	- * The searchradius generates a neighborhood of size (2 * searchradius + 1)³.
	- * Default is 4.
	- */
	- itkSetMacro(SearchRadius, int)
	- /**
	- * @brief Set the comparisonradius
	- *
	- * The comparisonradius generates neighborhoods of size (2 * comparisonradius +1)³.
	- * Default is 1.
	- */
	- itkSetMacro(ComparisonRadius, int)
	- /**
	- * @brief Set the variance of the noise
	- *
	- * The variance of the noise needs to be estimated to use this filter properly.
	- * Default is 1.
	- */
	- itkSetMacro(Variance, double)
	- /**
	- * @brief Set flag to use a rician adaption
	- *
	- * If this flag is true the filter uses a method which is optimized for Rician distributed noise.
	- */
	- itkSetMacro(UseRicianAdaption, bool)
	- /**
	- * @brief Get the amount of calculated Voxels
	- *
	- * @return the number of calculated Voxels until yet, useful for the use of a progressbars.
	- */
	- itkGetMacro(CurrentVoxelCount, unsigned int)
	-
	-
	- / @brief Set the input image. /
	- void SetInputImage(const InputImageType* image);
	- /**
	- * @brief Set a denoising mask
	- *
	- * optional
	- *
	- * Set a mask to denoise only the masked area, all voxel outside this area will be set to 0.
	- */
	- void SetInputMask(MaskImageType* mask);
	-
	- protected:
	- NonLocalMeansDenoisingFilter();
	- ~NonLocalMeansDenoisingFilter() override {}
	-
	- /**
	- * @brief Calculations which need to be done before the denoising starts
	- *
	- * This method is called before the denoising starts. It calculates the ROI if a mask is used
	- * and sets the number of processed voxels to zero.
	- */
	- void BeforeThreadedGenerateData() override;
	-
	- /**
	- * @brief Denoising procedure
	- *
	- * This method calculates the denoised voxelvalue for each voxel in the image in multiple threads.
	- * If a mask is used, voxels outside the masked area will be set to 0.
	- *
	- * @param outputRegionForThread Region to denoise for each thread.
	- */
	- void ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, ThreadIdType) override;
	-
	-
	-
	- private:
	-
	- int m_SearchRadius; ///< Radius of the searchblock.
	- int m_ComparisonRadius; ///< Radius of the comparisonblock.
	- bool m_UseJointInformation; ///< Flag to use joint information.
	- bool m_UseRicianAdaption; ///< Flag to use rician adaption.
	- unsigned int m_CurrentVoxelCount; ///< Amount of processed voxels.
	- double m_Variance; ///< Estimated noise variance.
	- typename MaskImageType::Pointer m_Mask; ///< Pointer to the mask image.
	- };
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkNonLocalMeansDenoisingFilter.txx"
	-#endif
	-
	-#endif //__itkNonLocalMeansDenoisingFilter_h_
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkNonLocalMeansDenoisingFilter.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkNonLocalMeansDenoisingFilter.txx
	deleted file mode 100644
	index 40f7212c9f..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkNonLocalMeansDenoisingFilter.txx
	+++ /dev/null
	@@ -1,388 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkNonLocalMeansDenoisingFilter_txx
	-#define __itkNonLocalMeansDenoisingFilter_txx
	-
	-#include <ctime>
	-#include <cstdio>
	-#include <cstdlib>
	-
	-#define _USE_MATH_DEFINES
	-#include <cmath>
	-
	-#include "itkImageRegionIterator.h"
	-#include "itkNeighborhoodIterator.h"
	-#include <itkImageRegionIteratorWithIndex.h>
	-#include <vector>
	-
	-namespace itk {
	-
	-
	-template< class TPixelType >
	-NonLocalMeansDenoisingFilter< TPixelType >
	-::NonLocalMeansDenoisingFilter()
	- : m_SearchRadius(4),
	- m_ComparisonRadius(1),
	- m_UseJointInformation(false),
	- m_UseRicianAdaption(false),
	- m_Variance(1),
	- m_Mask(nullptr)
	-{
	- this->SetNumberOfRequiredInputs( 1 );
	-}
	-
	-template< class TPixelType >
	-void
	-NonLocalMeansDenoisingFilter< TPixelType >
	-::BeforeThreadedGenerateData()
	-{
	-
	- MITK_INFO << "SearchRadius: " << m_SearchRadius;
	- MITK_INFO << "ComparisonRadius: " << m_ComparisonRadius;
	- MITK_INFO << "Noisevariance: " << m_Variance;
	- MITK_INFO << "Use Rician Adaption: " << std::boolalpha << m_UseRicianAdaption;
	- MITK_INFO << "Use Joint Information: " << std::boolalpha << m_UseJointInformation;
	-
	-
	- typename InputImageType::Pointer inputImagePointer = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) );
	- if (m_Mask.IsNull())
	- {
	- // If no mask is used generate a mask of the complete image
	-
	- m_Mask = MaskImageType::New();
	- m_Mask->SetRegions(inputImagePointer->GetLargestPossibleRegion());
	- m_Mask->Allocate();
	- m_Mask->FillBuffer(1);
	- }
	- else
	- {
	- // Calculation of the smallest masked region
	-
	- typename OutputImageType::Pointer outputImage =
	- static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0));
	- ImageRegionIterator< OutputImageType > oit(outputImage, inputImagePointer->GetLargestPossibleRegion());
	- oit.GoToBegin();
	- ImageRegionIterator< MaskImageType > mit(m_Mask, m_Mask->GetLargestPossibleRegion());
	- mit.GoToBegin();
	- typename MaskImageType::IndexType minIndex;
	- typename MaskImageType::IndexType maxIndex;
	- minIndex.Fill(10000);
	- maxIndex.Fill(0);
	- typename OutputImageType::PixelType outpix;
	- outpix.SetSize(inputImagePointer->GetVectorLength());
	- outpix.Fill(0);
	- while (!mit.IsAtEnd())
	- {
	-
	- if (mit.Get())
	- {
	- // calculation of the start & end index of the smallest masked region
	- minIndex[0] = minIndex[0] < mit.GetIndex()[0] ? minIndex[0] : mit.GetIndex()[0];
	- minIndex[1] = minIndex[1] < mit.GetIndex()[1] ? minIndex[1] : mit.GetIndex()[1];
	- minIndex[2] = minIndex[2] < mit.GetIndex()[2] ? minIndex[2] : mit.GetIndex()[2];
	-
	- maxIndex[0] = maxIndex[0] > mit.GetIndex()[0] ? maxIndex[0] : mit.GetIndex()[0];
	- maxIndex[1] = maxIndex[1] > mit.GetIndex()[1] ? maxIndex[1] : mit.GetIndex()[1];
	- maxIndex[2] = maxIndex[2] > mit.GetIndex()[2] ? maxIndex[2] : mit.GetIndex()[2];
	- }
	- else
	- {
	- oit.Set(outpix);
	- }
	- ++mit;
	- ++oit;
	- }
	-
	-
	- // calculation of the masked region
	- typename OutputImageType::SizeType size;
	- size[0] = maxIndex[0] - minIndex[0] + 1;
	- size[1] = maxIndex[1] - minIndex[1] + 1;
	- size[2] = maxIndex[2] - minIndex[2] + 1;
	-
	- typename OutputImageType::RegionType region (minIndex, size);
	-
	- outputImage->SetRequestedRegion(region);
	- }
	-
	- m_CurrentVoxelCount = 0;
	-}
	-
	-template< class TPixelType >
	-void
	-NonLocalMeansDenoisingFilter< TPixelType >
	-::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, ThreadIdType )
	-{
	-
	-
	- // initialize iterators
	- typename OutputImageType::Pointer outputImage =
	- static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0));
	-
	- ImageRegionIterator< OutputImageType > oit(outputImage, outputRegionForThread);
	- oit.GoToBegin();
	-
	- ImageRegionIterator< MaskImageType > mit(m_Mask, outputRegionForThread);
	- mit.GoToBegin();
	-
	-
	-
	- typedef ImageRegionIteratorWithIndex <InputImageType> InputIteratorType;
	- typename InputImageType::Pointer inputImagePointer = nullptr;
	- inputImagePointer = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) );
	-
	- InputIteratorType git(inputImagePointer, outputRegionForThread );
	- git.GoToBegin();
	-
	- // iterate over complete image region
	- while( !git.IsAtEnd() )
	- {
	- typename OutputImageType::PixelType outpix;
	- outpix.SetSize (inputImagePointer->GetVectorLength());
	-
	- if (mit.Get() != 0 && !this->GetAbortGenerateData())
	- {
	- if(!m_UseJointInformation)
	- {
	- for (int i = 0; i < (int)inputImagePointer->GetVectorLength(); ++i)
	- {
	- double summw = 0;
	- double sumj = 0;
	- double w = 0;
	- std::vector<double> wj;
	- std::vector<double> p;
	- typename InputIteratorType::IndexType index;
	- index = git.GetIndex();
	-
	- for (int x = index.GetElement(0) - m_SearchRadius; x <= index.GetElement(0) + m_SearchRadius; ++x)
	- {
	- for (int y = index.GetElement(1) - m_SearchRadius; y <= index.GetElement(1) + m_SearchRadius; ++y)
	- {
	- for (int z = index.GetElement(2) - m_SearchRadius; z <= index.GetElement(2) + m_SearchRadius; ++z)
	- {
	- typename InputIteratorType::IndexType indexV;
	- indexV.SetElement(0, x);
	- indexV.SetElement(1, y);
	- indexV.SetElement(2, z);
	- if (inputImagePointer->GetLargestPossibleRegion().IsInside(indexV))
	- {
	- TPixelType pixelJ = inputImagePointer->GetPixel(indexV)[i];
	- double sumk = 0;
	- double size = 0;
	- for (int xi = index.GetElement(0) - m_ComparisonRadius, xj = x - m_ComparisonRadius; xi <= index.GetElement(0) + m_ComparisonRadius; ++xi, ++xj)
	- {
	- for (int yi = index.GetElement(1) - m_ComparisonRadius, yj = y - m_ComparisonRadius; yi <= index.GetElement(1) + m_ComparisonRadius; ++yi, ++yj)
	- {
	- for (int zi = index.GetElement(2) - m_ComparisonRadius, zj = z - m_ComparisonRadius; zi <= index.GetElement(2) + m_ComparisonRadius; ++zi, ++zj)
	- {
	- typename InputIteratorType::IndexType indexI, indexJ;
	- indexI.SetElement(0, xi);
	- indexI.SetElement(1, yi);
	- indexI.SetElement(2, zi);
	- indexJ.SetElement(0, xj);
	- indexJ.SetElement(1, yj);
	- indexJ.SetElement(2, zj);
	-
	-
	- // Compare neighborhoods ni & nj
	- if (inputImagePointer->GetLargestPossibleRegion().IsInside(indexI) && inputImagePointer->GetLargestPossibleRegion().IsInside(indexJ))
	- {
	- int diff = inputImagePointer->GetPixel(indexI)[i] - inputImagePointer->GetPixel(indexJ)[i];
	- sumk += (double)(diff*diff);
	- ++size;
	- }
	- }
	- }
	- }
	- // weight all neighborhoods
	- w = std::exp( - sumk / size / m_Variance);
	- wj.push_back(w);
	- if (m_UseRicianAdaption)
	- {
	- p.push_back((double)(pixelJ*pixelJ));
	- }
	- else
	- {
	- p.push_back((double)(pixelJ));
	- }
	- summw += w;
	- }
	- }
	- }
	- }
	- for (unsigned int n = 0; n < wj.size(); ++n)
	- {
	- sumj += (wj[n]/summw) * p[n];
	- }
	- if (m_UseRicianAdaption)
	- {
	- sumj -=2 * m_Variance;
	- }
	-
	- if (sumj < 0)
	- {
	- sumj = 0;
	- }
	-
	- TPixelType outval;
	- if (m_UseRicianAdaption)
	- {
	- outval = std::floor(std::sqrt(sumj) + 0.5);
	- }
	- else
	- {
	- outval = std::floor(sumj + 0.5);
	- }
	- outpix.SetElement(i, outval);
	- }
	- }
	-
	- else
	- {
	- // same procedure for vektoranalysis
	-
	- double Z = 0;
	- itk::VariableLengthVector<double> sumj;
	- sumj.SetSize(inputImagePointer->GetVectorLength());
	- sumj.Fill(0.0);
	- double w = 0;
	- std::vector<double> wj;
	- std::vector<itk::VariableLengthVector <double> > p;
	- typename InputIteratorType::IndexType index;
	- index = git.GetIndex();
	-
	- for (int x = index.GetElement(0) - m_SearchRadius; x <= index.GetElement(0) + m_SearchRadius; ++x)
	- {
	- for (int y = index.GetElement(1) - m_SearchRadius; y <= index.GetElement(1) + m_SearchRadius; ++y)
	- {
	- for (int z = index.GetElement(2) - m_SearchRadius; z <= index.GetElement(2) + m_SearchRadius; ++z)
	- {
	- typename InputIteratorType::IndexType indexV;
	- indexV.SetElement(0, x);
	- indexV.SetElement(1, y);
	- indexV.SetElement(2, z);
	- if (inputImagePointer->GetLargestPossibleRegion().IsInside(indexV))
	- {
	- typename InputImageType::PixelType pixelJ = inputImagePointer->GetPixel(indexV);
	- double sumk = 0;
	- double size = 0;
	- for (int xi = index.GetElement(0) - m_ComparisonRadius, xj = x - m_ComparisonRadius; xi <= index.GetElement(0) + m_ComparisonRadius; ++xi, ++xj)
	- {
	- for (int yi = index.GetElement(1) - m_ComparisonRadius, yj = y - m_ComparisonRadius; yi <= index.GetElement(1) + m_ComparisonRadius; ++yi, ++yj)
	- {
	- for (int zi = index.GetElement(2) - m_ComparisonRadius, zj = z - m_ComparisonRadius; zi <= index.GetElement(2) + m_ComparisonRadius; ++zi, ++zj)
	- {
	- typename InputIteratorType::IndexType indexI, indexJ;
	- indexI.SetElement(0, xi);
	- indexI.SetElement(1, yi);
	- indexI.SetElement(2, zi);
	- indexJ.SetElement(0, xj);
	- indexJ.SetElement(1, yj);
	- indexJ.SetElement(2, zj);
	- // Compare neighborhoods ni & nj
	- if (inputImagePointer->GetLargestPossibleRegion().IsInside(indexI) && inputImagePointer->GetLargestPossibleRegion().IsInside(indexJ))
	- {
	- typename InputImageType::PixelType diff = inputImagePointer->GetPixel(indexI) - inputImagePointer->GetPixel(indexJ);
	- sumk += (double)(diff.GetSquaredNorm());
	- ++size;
	- }
	- }
	- }
	- }
	- // weight all neighborhoods
	- size *= inputImagePointer->GetVectorLength() + 1;
	- w = std::exp( - (sumk / size) / m_Variance);
	- wj.push_back(w);
	- if (m_UseRicianAdaption)
	- {
	- itk::VariableLengthVector <double> m;
	- m.SetSize(inputImagePointer->GetVectorLength());
	- for (unsigned int i = 0; i < inputImagePointer->GetVectorLength(); ++i)
	- {
	- double sp = (double)(pixelJ.GetElement(i) * pixelJ.GetElement(i));
	- m.SetElement(i,sp);
	- }
	- p.push_back(m);
	- }
	- else
	- ++size;
	- {
	- p.push_back(pixelJ);
	- }
	- Z += w;
	- }
	- }
	- }
	- }
	- for (unsigned int n = 0; n < wj.size(); ++n)
	- {
	- sumj = sumj + ((wj[n]/Z) * p[n]);
	- }
	- if (m_UseRicianAdaption)
	- {
	- sumj = sumj - (2 * m_Variance);
	- }
	-
	- for (unsigned int i = 0; i < inputImagePointer->GetVectorLength(); ++i)
	- {
	- double a = sumj.GetElement(i);
	- if (a < 0)
	- {
	- a = 0;
	- }
	- TPixelType outval;
	- if (m_UseRicianAdaption)
	- {
	- outval = std::floor(std::sqrt(a) + 0.5);
	- }
	- else
	- {
	- outval = std::floor(a + 0.5);
	- }
	- outpix.SetElement(i, outval);
	- }
	- }
	- }
	- else
	- {
	- outpix.Fill(0);
	- }
	-
	- oit.Set(outpix);
	- ++oit;
	- ++m_CurrentVoxelCount;
	- ++git;
	- ++mit;
	- }
	-
	- MITK_INFO << "One Thread finished calculation";
	-}
	-
	-template< class TPixelType >
	-void NonLocalMeansDenoisingFilter< TPixelType >::SetInputImage(const InputImageType* image)
	-{
	- this->SetNthInput(0, const_cast< InputImageType* >(image));
	-}
	-
	-template< class TPixelType >
	-void NonLocalMeansDenoisingFilter< TPixelType >::SetInputMask(MaskImageType* mask)
	-{
	- m_Mask = mask;
	-}
	-}
	-
	-#endif // __itkNonLocalMeansDenoisingFilter_txx
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkOdfMaximaExtractionFilter.cpp b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkOdfMaximaExtractionFilter.cpp
	deleted file mode 100644
	index e53de6545c..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkOdfMaximaExtractionFilter.cpp
	+++ /dev/null
	@@ -1,362 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef __itkOdfMaximaExtractionFilter_cpp
	-#define __itkOdfMaximaExtractionFilter_cpp
	-
	-#include "itkOdfMaximaExtractionFilter.h"
	-#include <itkImageRegionConstIterator.h>
	-#include <itkImageRegionConstIteratorWithIndex.h>
	-#include <itkImageRegionIterator.h>
	-#include <vnl/vnl_vector.h>
	-#include <itkOrientationDistributionFunction.h>
	-#include <itkContinuousIndex.h>
	-
	-#include <vtkSmartPointer.h>
	-#include <vtkPolyData.h>
	-#include <vtkCellArray.h>
	-#include <vtkPoints.h>
	-#include <vtkPolyLine.h>
	-
	-#include <boost/math/special_functions.hpp>
	-#include <boost/progress.hpp>
	-
	-using namespace boost::math;
	-
	-namespace itk {
	-
	-
	-static bool CompareVectors(const vnl_vector_fixed< double, 3 >& v1, const vnl_vector_fixed< double, 3 >& v2)
	-{
	- return (v1.magnitude()>v2.magnitude());
	-}
	-
	-template< class PixelType, int ShOrder, int NrOdfDirections >
	-OdfMaximaExtractionFilter< PixelType, ShOrder, NrOdfDirections>
	-::OdfMaximaExtractionFilter()
	- : m_NormalizationMethod(MAX_VEC_NORM)
	- , m_MaxNumPeaks(2)
	- , m_RelativePeakThreshold(0.4)
	- , m_AbsolutePeakThreshold(0)
	- , m_AngularThreshold(0.9)
	- , m_NumCoeffs((ShOrder*ShOrder + ShOrder + 2)/2 + ShOrder)
	- , m_Toolkit(MRTRIX)
	- , m_FlipX(false)
	- , m_FlipY(false)
	- , m_FlipZ(false)
	- , m_ApplyDirectionMatrix(false)
	- , m_ScaleByGfa(false)
	- , m_Iterations(10)
	-{
	- this->SetNumberOfRequiredInputs(1);
	-}
	-
	-template< class PixelType, int ShOrder, int NrOdfDirections >
	-double OdfMaximaExtractionFilter< PixelType, ShOrder, NrOdfDirections>
	-::FindCandidatePeaks(OdfType& odf, double thr, std::vector< DirectionType >& container)
	-{
	- double gfa = 1.0;
	- if (m_ScaleByGfa)
	- gfa = odf.GetGeneralizedFractionalAnisotropy();
	-
	- //Find the peaks using a finite difference method
	- bool flag = true;
	- vnl_vector_fixed< bool, NrOdfDirections > used; used.fill(false);
	- //Find the peaks
	- for (int i=0; i<NrOdfDirections; i++)
	- {
	- if (used[i])
	- continue;
	-
	- double val = odf.GetElement(i);
	- if (val>thr0.9 && gfaval>m_AbsolutePeakThreshold*0.9)
	- {
	- flag = true;
	- std::vector< int > neighbours = odf.GetNeighbors(i);
	- for (unsigned int j=0; j<neighbours.size(); j++)
	- if (val<odf.GetElement(neighbours.at(j)))
	- {
	- flag = false;
	- break;
	- }
	- if (flag) // point is a peak
	- {
	- container.push_back(odf.GetDirection(i).normalize());
	- used[i] = true;
	- for (unsigned int j=0; j<neighbours.size(); j++)
	- used[neighbours.at(j)] = true;
	- }
	- }
	- }
	- return gfa;
	-}
	-
	-template< class PixelType, int ShOrder, int NrOdfDirections >
	-void OdfMaximaExtractionFilter< PixelType, ShOrder, NrOdfDirections>
	-::BeforeThreadedGenerateData()
	-{
	- typename CoefficientImageType::Pointer ShCoeffImage = static_cast< CoefficientImageType* >( this->ProcessObject::GetInput(0) );
	- itk::Vector<double,3> spacing = ShCoeffImage->GetSpacing();
	- double minSpacing = spacing[0];
	- if (spacing[1]<minSpacing)
	- minSpacing = spacing[1];
	- if (spacing[2]<minSpacing)
	- minSpacing = spacing[2];
	-
	- mitk::Point3D origin = ShCoeffImage->GetOrigin();
	- itk::Matrix<double, 3, 3> direction = ShCoeffImage->GetDirection();
	- ImageRegion<3> imageRegion = ShCoeffImage->GetLargestPossibleRegion();
	-
	- if (m_MaskImage.IsNotNull())
	- {
	- origin = m_MaskImage->GetOrigin();
	- direction = m_MaskImage->GetDirection();
	- imageRegion = m_MaskImage->GetLargestPossibleRegion();
	- }
	-
	- itk::Vector<double, 3> spacing3 = ShCoeffImage->GetSpacing();
	- itk::Point<float, 3> origin3 = ShCoeffImage->GetOrigin();
	- itk::Matrix<double, 3, 3> direction3 = ShCoeffImage->GetDirection();
	- itk::ImageRegion<3> imageRegion3 = ShCoeffImage->GetLargestPossibleRegion();
	-
	- itk::Vector<double, 4> spacing4;
	- itk::Point<float, 4> origin4;
	- itk::Matrix<double, 4, 4> direction4;
	- itk::ImageRegion<4> imageRegion4;
	-
	- spacing4[0] = spacing3[0]; spacing4[1] = spacing3[1]; spacing4[2] = spacing3[2]; spacing4[3] = 1;
	- origin4[0] = origin3[0]; origin4[1] = origin3[1]; origin4[2] = origin3[2]; origin4[3] = 0;
	- for (int r=0; r<3; r++)
	- for (int c=0; c<3; c++)
	- direction4[r][c] = direction3[r][c];
	- direction4[3][3] = 1;
	- imageRegion4.SetSize(0, imageRegion3.GetSize()[0]);
	- imageRegion4.SetSize(1, imageRegion3.GetSize()[1]);
	- imageRegion4.SetSize(2, imageRegion3.GetSize()[2]);
	- imageRegion4.SetSize(3, m_MaxNumPeaks*3);
	-
	- m_PeakImage = PeakImageType::New();
	- m_PeakImage->SetSpacing( spacing4 );
	- m_PeakImage->SetOrigin( origin4 );
	- m_PeakImage->SetDirection( direction4 );
	- m_PeakImage->SetRegions( imageRegion4 );
	- m_PeakImage->Allocate();
	- m_PeakImage->FillBuffer(0.0);
	-
	- if (m_MaskImage.IsNull())
	- {
	- m_MaskImage = ItkUcharImgType::New();
	- m_MaskImage->SetSpacing( spacing );
	- m_MaskImage->SetOrigin( origin );
	- m_MaskImage->SetDirection( direction );
	- m_MaskImage->SetRegions( imageRegion );
	- m_MaskImage->Allocate();
	- m_MaskImage->FillBuffer(1);
	- }
	- m_NumDirectionsImage = ItkUcharImgType::New();
	- m_NumDirectionsImage->SetSpacing( spacing );
	- m_NumDirectionsImage->SetOrigin( origin );
	- m_NumDirectionsImage->SetDirection( direction );
	- m_NumDirectionsImage->SetRegions( imageRegion );
	- m_NumDirectionsImage->Allocate();
	- m_NumDirectionsImage->FillBuffer(0);
	-
	- // calculate SH basis
	- OdfType odf;
	- vnl_matrix< double > dir_matrix;
	- dir_matrix.set_size(3, NrOdfDirections);
	- for (int i=0; i<NrOdfDirections; i++)
	- {
	- dir_matrix(0, i) = odf.GetDirection(i)[0];
	- dir_matrix(1, i) = odf.GetDirection(i)[1];
	- dir_matrix(2, i) = odf.GetDirection(i)[2];
	- }
	-
	- if (m_Toolkit==Toolkit::MRTRIX)
	- m_ShBasis = mitk::sh::CalcShBasisForDirections(ShOrder, dir_matrix);
	- else
	- m_ShBasis = mitk::sh::CalcShBasisForDirections(ShOrder, dir_matrix, false);
	-
	- MITK_INFO << "Starting peak extraction";
	- MITK_INFO << "SH order: " << ShOrder;
	- MITK_INFO << "Maximum peaks: " << m_MaxNumPeaks;
	- MITK_INFO << "Relative threshold: " << m_RelativePeakThreshold;
	- MITK_INFO << "Absolute threshold: " << m_AbsolutePeakThreshold;
	- MITK_INFO << "Angular threshold: " << m_AngularThreshold;
	- this->SetNumberOfThreads(1);
	-}
	-
	-template< class PixelType, int ShOrder, int NrOdfDirections >
	-void OdfMaximaExtractionFilter< PixelType, ShOrder, NrOdfDirections>
	-::AfterThreadedGenerateData()
	-{
	-
	-}
	-
	-template< class PixelType, int ShOrder, int NrOdfDirections >
	-void OdfMaximaExtractionFilter< PixelType, ShOrder, NrOdfDirections>
	-::ThreadedGenerateData( const OutputImageRegionType& outputRegionForThread, ThreadIdType threadID )
	-{
	- typename CoefficientImageType::Pointer ShCoeffImage = static_cast< CoefficientImageType* >( this->ProcessObject::GetInput(0) );
	-
	- ImageRegionConstIterator< CoefficientImageType > cit(ShCoeffImage, outputRegionForThread );
	-
	- boost::progress_display disp(outputRegionForThread.GetSize()[0]outputRegionForThread.GetSize()[1]outputRegionForThread.GetSize()[2]);
	- OdfType odf;
	- while( !cit.IsAtEnd() )
	- {
	- typename CoefficientImageType::IndexType idx3 = cit.GetIndex();
	- if (m_MaskImage->GetPixel(idx3)==0)
	- {
	- ++disp;
	- ++cit;
	- continue;
	- }
	-
	- CoefficientPixelType c = cit.Get();
	- vnl_vector<float> coeffs; coeffs.set_size((ShOrder*ShOrder + ShOrder + 2)/2 + ShOrder);
	- for (int j=0; j<m_NumCoeffs; j++)
	- coeffs[j] = c[j];
	-
	- double max = 0;
	- for (int i=0; i<NrOdfDirections; i++)
	- {
	- odf[i] = 0;
	- for (int j=0; j<m_NumCoeffs; j++)
	- odf[i] += c[j]*m_ShBasis(i,j);
	- if (odf[i]>max)
	- max = odf[i];
	- }
	- if (max<0.0001)
	- {
	- ++disp;
	- ++cit;
	- continue;
	- }
	-
	- std::vector< DirectionType > candidates, final_peaks;
	- double scale = FindCandidatePeaks(odf, max*m_RelativePeakThreshold, candidates); // find all local maxima
	-
	- max = 0;
	- for (unsigned int i=0; i<candidates.size(); ++i)
	- {
	- double spherical[3];
	- mitk::sh::Cart2Sph(candidates[i][0], candidates[i][1], candidates[i][2], spherical);
	- vnl_vector<double> x;
	- x.set_size(2);
	- x[0] = spherical[1]; // theta
	- x[1] = spherical[0]; // phi
	-
	- VnlCostFunction cost;
	- if (m_Toolkit==Toolkit::MRTRIX)
	- cost.SetProblem(coeffs, ShOrder, true, max);
	- else
	- cost.SetProblem(coeffs, ShOrder, false, max);
	-
	- vnl_lbfgsb minimizer(cost);
	- minimizer.set_f_tolerance(1e-6);
	-// minimizer.set_trace(true);
	-
	- vnl_vector<double> l; l.set_size(2); l[0] = 0; l[1] = -itk::Math::pi;
	- vnl_vector<double> u; u.set_size(2); u[0] = itk::Math::pi; u[1] = itk::Math::pi;
	- vnl_vector<long> bound_selection; bound_selection.set_size(2); bound_selection.fill(2);
	- minimizer.set_bound_selection(bound_selection);
	- minimizer.set_lower_bound(l);
	- minimizer.set_upper_bound(u);
	- if (m_Iterations>0)
	- minimizer.set_max_function_evals(m_Iterations);
	- minimizer.minimize(x);
	-
	- float v = -minimizer.get_end_error()*scale;
	- candidates[i] = mitk::sh::Sph2Cart(x[0], x[1], v);
	- if (v>max)
	- max = v;
	- }
	-
	- std::sort( candidates.begin(), candidates.end(), CompareVectors ); // sort peaks
	-
	- // kick out directions to close to a larger direction
	- for (unsigned int i=0; i<candidates.size(); i++)
	- {
	- DirectionType v1 = candidates.at(i);
	- double val = v1.magnitude();
	- if (val<max*m_RelativePeakThreshold \|\| val<m_AbsolutePeakThreshold)
	- break;
	-
	- bool flag = true;
	- for (unsigned int j=0; j<candidates.size(); j++)
	- if (i!=j)
	- {
	- DirectionType v2 = candidates.at(j);
	- double val2 = v2.magnitude();
	- double angle = fabs(dot_product(v1,v2)/(val*val2));
	- if (angle>m_AngularThreshold && val<val2)
	- {
	- flag = false;
	- break;
	- }
	- }
	-
	- if (flag)
	- final_peaks.push_back(v1);
	- }
	-
	- itk::Index<4> idx4; idx4[0] = idx3[0]; idx4[1] = idx3[1]; idx4[2] = idx3[2];
	-
	- // fill output image
	- unsigned int num = final_peaks.size();
	- if ( num>m_MaxNumPeaks )
	- num = m_MaxNumPeaks;
	- for (unsigned int i=0; i<num; i++)
	- {
	- DirectionType dir = final_peaks.at(i);
	- switch (m_NormalizationMethod)
	- {
	- case NO_NORM:
	- break;
	- case SINGLE_VEC_NORM:
	- dir.normalize();
	- break;
	- case MAX_VEC_NORM:
	- dir /= max;
	- break;
	- }
	-
	- if (m_ApplyDirectionMatrix)
	- dir = m_MaskImage->GetDirection()*dir;
	-
	- if (m_FlipX)
	- dir[0] = -dir[0];
	- if (m_FlipY)
	- dir[1] = -dir[1];
	- if (m_FlipZ)
	- dir[2] = -dir[2];
	-
	- for (unsigned int j = 0; j<3; j++)
	- {
	- idx4[3] = i*3 + j;
	- m_PeakImage->SetPixel(idx4, dir[j]);
	- }
	- }
	- m_NumDirectionsImage->SetPixel(idx3, num);
	- ++disp;
	- ++cit;
	- }
	- MITK_INFO << "Thread " << threadID << " finished extraction";
	-}
	-
	-}
	-
	-#endif // __itkOdfMaximaExtractionFilter_cpp
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkOdfMaximaExtractionFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkOdfMaximaExtractionFilter.h
	deleted file mode 100644
	index e82badce66..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkOdfMaximaExtractionFilter.h
	+++ /dev/null
	@@ -1,182 +0,0 @@
	-/*=========================================================================
	-
	- Program: Insight Segmentation & Registration Toolkit
	- Module: $RCSfile: itkDiffusionTensor3DReconstructionImageFilter.h,v $
	- Language: C++
	- Date: $Date: 2006-03-27 17:01:06 $
	- Version: $Revision: 1.12 $
	-
	- Copyright (c) Insight Software Consortium. All rights reserved.
	- See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
	-
	- This software is distributed WITHOUT ANY WARRANTY; without even
	- the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
	- PURPOSE. See the above copyright notices for more information.
	-
	-=========================================================================*/
	-#ifndef __itkOdfMaximaExtractionFilter_h_
	-#define __itkOdfMaximaExtractionFilter_h_
	-
	-#include "itkImageToImageFilter.h"
	-#include "vnl/vnl_vector_fixed.h"
	-#include "vnl/vnl_matrix.h"
	-#include "vnl/algo/vnl_svd.h"
	-#include "itkVectorContainer.h"
	-#include "itkVectorImage.h"
	-#include <mitkFiberBundle.h>
	-#include <mitkPeakImage.h>
	-#include <mitkShImage.h>
	-#include <itkOrientationDistributionFunction.h>
	-#include <vnl/algo/vnl_lbfgsb.h>
	-#include <mitkDiffusionFunctionCollection.h>
	-
	-class VnlCostFunction : public vnl_cost_function
	-{
	-public:
	-
	- bool mrtrix;
	- int ShOrder;
	- vnl_vector<float> coeffs;
	- double max;
	- void SetProblem(vnl_vector<float>& coeffs, int ShOrder, bool mrtrix, double max)
	- {
	- this->coeffs = coeffs;
	- this->ShOrder = ShOrder;
	- this->mrtrix = mrtrix;
	- this->max = max;
	- }
	-
	- VnlCostFunction(const int NumVars=2) : vnl_cost_function(NumVars)
	- {
	- }
	-
	- // cost function
	- double f(vnl_vector<double> const &x)
	- {
	- return -mitk::sh::GetValue(coeffs, ShOrder, x[0], x[1], mrtrix);
	- }
	-
	- // gradient of cost function
	- void gradf(vnl_vector<double> const &x, vnl_vector<double> &dx)
	- {
	- fdgradf(x, dx);
	- }
	-};
	-
	-
	-namespace itk{
	-
	-/**
	-* \brief Extract ODF peaks by searching all local maxima on a roughly sampled sphere and a successive gradient descent optimization
	-*/
	-
	-template< class PixelType, int ShOrder, int NrOdfDirections >
	-class OdfMaximaExtractionFilter : public ImageToImageFilter< Image< Vector< PixelType, (ShOrder*ShOrder + ShOrder + 2)/2 + ShOrder >, 3 >,
	-Image< unsigned char, 3 > >
	-{
	-
	- public:
	-
	- enum Toolkit { ///< SH coefficient convention (depends on toolkit)
	- FSL,
	- MRTRIX
	- };
	-
	- enum NormalizationMethods {
	- NO_NORM, ///< no length normalization of the output peaks
	- SINGLE_VEC_NORM, ///< normalize the single peaks to length 1
	- MAX_VEC_NORM ///< normalize all peaks according to their length in comparison to the largest peak in the respective voxel (0-1)
	- };
	-
	- typedef OdfMaximaExtractionFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageToImageFilter< Image< Vector< PixelType, (ShOrder*ShOrder + ShOrder + 2)/2 + ShOrder >, 3 >,
	- Image< unsigned char, 3 > > Superclass;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(OdfMaximaExtractionFilter, ImageToImageFilter)
	-
	- typedef typename Superclass::InputImageType CoefficientImageType;
	- typedef typename CoefficientImageType::RegionType CoefficientImageRegionType;
	- typedef typename CoefficientImageType::PixelType CoefficientPixelType;
	- typedef typename Superclass::OutputImageType OutputImageType;
	- typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
	- typedef typename Superclass::InputImageRegionType InputImageRegionType;
	- typedef mitk::PeakImage::ItkPeakImageType PeakImageType;
	-
	- typedef OrientationDistributionFunction<PixelType, NrOdfDirections> OdfType;
	- typedef itk::Image<unsigned char, 3> ItkUcharImgType;
	-
	- typedef vnl_vector_fixed< double, 3 > DirectionType;
	-
	- // input
	- itkSetMacro( MaxNumPeaks, unsigned int) ///< maximum number of peaks per voxel. if more peaks are detected, only the largest are kept.
	- itkSetMacro( RelativePeakThreshold, double) ///< threshold on the peak length relative to the largest peak inside the current voxel
	- itkSetMacro( AbsolutePeakThreshold, double) ///< hard threshold on the peak length of all local maxima
	- itkSetMacro( AngularThreshold, double) ///< directions closer together than the specified threshold are discarded
	- itkSetMacro( MaskImage, ItkUcharImgType::Pointer) ///< only voxels inside the binary mask are processed
	- itkSetMacro( NormalizationMethod, NormalizationMethods) ///< normalization method of ODF peaks
	- itkSetMacro( FlipX, bool) ///< flip peaks in x direction
	- itkSetMacro( FlipY, bool) ///< flip peaks in y direction
	- itkSetMacro( FlipZ, bool) ///< flip peaks in z direction
	- itkSetMacro( ApplyDirectionMatrix, bool)
	- itkSetMacro( ScaleByGfa, bool)
	- itkSetMacro( Iterations, int)
	-
	- // output
	- itkGetMacro( NumDirectionsImage, ItkUcharImgType::Pointer )
	- itkGetMacro( PeakImage, PeakImageType::Pointer )
	-
	- itkSetMacro( Toolkit, Toolkit) ///< define SH coefficient convention (depends on toolkit)
	- itkGetMacro( Toolkit, Toolkit) ///< SH coefficient convention (depends on toolkit)
	-
	- protected:
	- OdfMaximaExtractionFilter();
	- ~OdfMaximaExtractionFilter(){}
	-
	- void BeforeThreadedGenerateData();
	- void ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, ThreadIdType threadID );
	- void AfterThreadedGenerateData();
	-
	- / Extract all local maxima from the densely sampled ODF surface. Thresholding possible. /
	- double FindCandidatePeaks(OdfType& odf, double odfMax, std::vector< DirectionType >& inDirs);
	-
	- / Cluster input directions within a certain angular threshold /
	- std::vector< DirectionType > MeanShiftClustering(std::vector< DirectionType >& inDirs);
	-
	- private:
	-
	- NormalizationMethods m_NormalizationMethod; ///< normalization method of ODF peaks
	- unsigned int m_MaxNumPeaks; ///< maximum number of peaks per voxel. if more peaks are detected, only the largest are kept.
	- double m_RelativePeakThreshold; ///< threshold on the peak length relative to the largest peak inside the current voxel
	- double m_AbsolutePeakThreshold;///< hard threshold on the peak length of all local maxima
	- vnl_matrix< float > m_ShBasis; ///< container for evaluated SH base functions
	- double m_AngularThreshold;
	- const int m_NumCoeffs; ///< number of spherical harmonics coefficients
	-
	- PeakImageType::Pointer m_PeakImage;
	- ItkUcharImgType::Pointer m_NumDirectionsImage; ///< number of peaks per voxel
	- ItkUcharImgType::Pointer m_MaskImage; ///< only voxels inside the binary mask are processed
	-
	- Toolkit m_Toolkit;
	- bool m_FlipX;
	- bool m_FlipY;
	- bool m_FlipZ;
	- bool m_ApplyDirectionMatrix;
	- bool m_ScaleByGfa;
	- int m_Iterations;
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkOdfMaximaExtractionFilter.cpp"
	-#endif
	-
	-#endif //__itkOdfMaximaExtractionFilter_h_
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkOdfToRgbImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkOdfToRgbImageFilter.h
	deleted file mode 100644
	index 04f7ec93b5..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkOdfToRgbImageFilter.h
	+++ /dev/null
	@@ -1,148 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkOdfToRgbImageFilter_h
	-#define __itkOdfToRgbImageFilter_h
	-
	-#include "itkUnaryFunctorImageFilter.h"
	-#include "itkOrientationDistributionFunction.h"
	-#include "itkRGBAPixel.h"
	-#include "itkImageRegionConstIterator.h"
	-#include "itkImageRegionIterator.h"
	-
	-namespace itk
	-{
	-
	- #define __IMG_DAT_ITEM__CEIL_ZERO_ONE__(val) (val) = \
	- ( (val) < 0 ) ? ( 0 ) : ( ( (val)>1 ) ? ( 1 ) : ( (val) ) );
	-
	-
	-/** \class OdfToRgbImageFilter
	-*
	-*/
	-template <typename TInputImage,
	-typename TOutputImage=itk::Image<itk::RGBAPixel<unsigned char>,3> >
	- class OdfToRgbImageFilter :
	- public ImageToImageFilter<TInputImage,TOutputImage>
	- {
	- public:
	- /** Standard class typedefs. */
	- typedef OdfToRgbImageFilter Self;
	- typedef ImageToImageFilter<TInputImage,TOutputImage>
	- Superclass;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	-
	- typedef typename Superclass::InputImageType InputImageType;
	- typedef typename Superclass::OutputImageType OutputImageType;
	- typedef typename OutputImageType::PixelType OutputPixelType;
	- typedef typename TInputImage::PixelType InputPixelType;
	- typedef typename InputPixelType::ValueType InputValueType;
	-
	- /** Run-time type information (and related methods). */
	- itkTypeMacro( OdfToRgbImageFilter, ImageToImageFilter )
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Print internal ivars */
	- void PrintSelf(std::ostream& os, Indent indent) const override
	- { this->Superclass::PrintSelf( os, indent ); }
	-
	-#ifdef ITK_USE_CONCEPT_CHECKING
	- /** Begin concept checking */
	- itkConceptMacro(InputHasNumericTraitsCheck,
	- (Concept::HasNumericTraits<InputValueType>));
	- /** End concept checking */
	-#endif
	-
	-protected:
	- OdfToRgbImageFilter(){}
	- ~OdfToRgbImageFilter() override{}
	-
	- void GenerateData() override
	- {
	-
	- typename InputImageType::Pointer OdfImage = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) );
	-
	- typename OutputImageType::Pointer outputImage =
	- static_cast< OutputImageType * >(this->ProcessObject::GetPrimaryOutput());
	-
	- typename InputImageType::RegionType region = OdfImage->GetLargestPossibleRegion();
	-
	- outputImage->SetSpacing( OdfImage->GetSpacing() ); // Set the image spacing
	- outputImage->SetOrigin( OdfImage->GetOrigin() ); // Set the image origin
	- outputImage->SetDirection( OdfImage->GetDirection() ); // Set the image direction
	- outputImage->SetRegions( OdfImage->GetLargestPossibleRegion());
	- outputImage->Allocate();
	-
	- typedef ImageRegionConstIterator< InputImageType > OdfImageIteratorType;
	- OdfImageIteratorType OdfIt(OdfImage, OdfImage->GetLargestPossibleRegion());
	-
	- typedef ImageRegionIterator< OutputImageType > OutputImageIteratorType;
	- OutputImageIteratorType outputIt(outputImage, outputImage->GetLargestPossibleRegion());
	-
	- OdfIt.GoToBegin();
	- outputIt.GoToBegin();
	-
	- while(!OdfIt.IsAtEnd() && !outputIt.IsAtEnd()){
	-
	- InputPixelType x = OdfIt.Get();
	- typedef itk::OrientationDistributionFunction<float,ODF_SAMPLING_SIZE> OdfType;
	- OdfType odf(x.GetDataPointer());
	-
	- vnl_vector_fixed<double,3> dir;
	- int pd = odf.GetPrincipalDiffusionDirectionIndex();
	- if (pd==-1)
	- dir.fill(0);
	- else
	- dir = OdfType::GetDirection(pd);
	-
	- const float fa = odf.GetGeneralizedFractionalAnisotropy();
	- float r = fabs(dir[0]) * fa;
	- float g = fabs(dir[1]) * fa;
	- float b = fabs(dir[2]) * fa;
	-// float a = (fa-(m_OpacLevel-m_OpacWindow/2.0f))/m_OpacWindow;
	- float a = fa;
	-
	- __IMG_DAT_ITEM__CEIL_ZERO_ONE__(r);
	- __IMG_DAT_ITEM__CEIL_ZERO_ONE__(g);
	- __IMG_DAT_ITEM__CEIL_ZERO_ONE__(b);
	- __IMG_DAT_ITEM__CEIL_ZERO_ONE__(a);
	-
	- OutputPixelType out;
	- out.SetRed( r * 255.0f);
	- out.SetGreen( g * 255.0f);
	- out.SetBlue( b * 255.0f);
	- out.SetAlpha( a * 255.0f);
	-
	- outputIt.Set(out);
	-
	- ++OdfIt;
	- ++outputIt;
	- }
	-
	- }
	-
	-private:
	- OdfToRgbImageFilter(const Self&); //purposely not implemented
	- void operator=(const Self&); //purposely not implemented
	-};
	-
	-} // end namespace itk
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkPolarToCartesianVectorImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkPolarToCartesianVectorImageFilter.h
	deleted file mode 100644
	index 4a88210532..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkPolarToCartesianVectorImageFilter.h
	+++ /dev/null
	@@ -1,121 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkPolarToCartesianVectorImageFilter_h
	-#define __itkPolarToCartesianVectorImageFilter_h
	-
	-#include "itkUnaryFunctorImageFilter.h"
	-
	-namespace itk
	-{
	-
	- namespace Functor {
	-
	- template< typename TInput, typename TOutput, bool symmetric >
	- class PolarToCartesianFunction
	- {
	- public:
	- PolarToCartesianFunction() {}
	- ~PolarToCartesianFunction() {}
	- bool operator!=( const PolarToCartesianFunction & ) const
	- {
	- return false;
	- }
	- bool operator==( const PolarToCartesianFunction & other ) const
	- {
	- return !(*this != other);
	- }
	- inline TOutput operator()( const TInput & x )
	- {
	-
	- TOutput opoint;
	- opoint[0] = x[0] * cos( x[1] ) * sin( x[2] );
	- opoint[1] = x[0] * sin( x[1] ) * sin( x[2] );
	- opoint[2] = x[0] * cos( x[2] );
	-
	- if(symmetric && opoint[2]<0)
	- {
	- opoint[2] = -opoint[2];
	- }
	-
	- return opoint;
	- ;
	- }
	- };
	-
	- } // end namespace functor
	-
	-
	- /** \class PolarToCartesianVectorImageFilter
	- *
	- */
	- template <typename TInputImage, typename TOutputImage, bool symmetric>
	- class PolarToCartesianVectorImageFilter :
	- public
	- UnaryFunctorImageFilter<TInputImage,TOutputImage,
	- Functor::PolarToCartesianFunction<
	- typename TInputImage::PixelType,
	- typename TOutputImage::PixelType, symmetric> >
	- {
	- public:
	- /** Standard class typedefs. */
	- typedef PolarToCartesianVectorImageFilter Self;
	- typedef UnaryFunctorImageFilter<
	- TInputImage,TOutputImage,
	- Functor::PolarToCartesianFunction<
	- typename TInputImage::PixelType,
	- typename TOutputImage::PixelType, symmetric > > Superclass;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	-
	- typedef typename Superclass::OutputImageType OutputImageType;
	- typedef typename OutputImageType::PixelType OutputPixelType;
	- typedef typename TInputImage::PixelType InputPixelType;
	- typedef typename InputPixelType::ValueType InputValueType;
	-
	- /** Run-time type information (and related methods). */
	- itkTypeMacro( PolarToCartesianVectorImageFilter, UnaryFunctorImageFilter );
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Print internal ivars */
	- void PrintSelf(std::ostream& os, Indent indent) const
	- { this->Superclass::PrintSelf( os, indent ); }
	-
	-#ifdef ITK_USE_CONCEPT_CHECKING
	- /** Begin concept checking */
	- itkConceptMacro(InputHasNumericTraitsCheck,
	- (Concept::HasNumericTraits<InputValueType>));
	- /** End concept checking */
	-#endif
	-
	- protected:
	- PolarToCartesianVectorImageFilter() {};
	- virtual ~PolarToCartesianVectorImageFilter() {};
	-
	- private:
	- PolarToCartesianVectorImageFilter(const Self&); //purposely not implemented
	- void operator=(const Self&); //purposely not implemented
	-
	- };
	-
	-
	-
	-} // end namespace itk
	-
	-#endif // __itkPolarToCartesianVectorImageFilter_h
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkProjectionFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkProjectionFilter.h
	deleted file mode 100644
	index 20db22d01d..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkProjectionFilter.h
	+++ /dev/null
	@@ -1,159 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef ITKPROJECTIONFILTER_H_
	-#define ITKPROJECTIONFILTER_H_
	-
	-#include "itkObject.h"
	-#include "itkImage.h"
	-#include "mitkImage.h"
	-#include "mitkTbssImage.h"
	-
	-namespace itk
	-{
	-
	-
	-/**
	- * \brief Projection part of the TBSS pipeline
	- *
	- * This class performs the projection step of the TBSS pipeline
	- * (see Smith et al., 2009. http://dx.doi.org/10.1016/j.neuroimage.2006.02.024 )
	- * As input it takes a binary skeleton, a distance map, and a vector image containing the image gradients
	- * that are typically provided by the itkSkeletonizationFilter and the itkDistanceMapFilter.
	- * Furthermore it requires a 4d dataset with patient data registered to the same space as the mean FA image.
	- * This 4D dataset is typically created by the TBSS pipeline (see http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/tbss/index),
	- * in which case it is often named all_FA.nii.gz
	- */
	-
	-
	-class ProjectionFilter : public Object
	-{
	-
	-public:
	-
	- typedef itk::Image<float, 3> RealImageType;
	-
	- typedef itk::CovariantVector<int,3> VectorType;
	-
	- typedef itk::Image<VectorType, 3> VectorImageType;
	-
	- typedef itk::Image<char,3> CharImageType;
	-
	- typedef itk::Image<float, 4> Float4DImageType;
	- typedef itk::Image<float, 3> FloatImageType;
	-
	-
	-
	-public:
	-
	- /** */
	- typedef ProjectionFilter Self;
	-
	- /** Superclass */
	- typedef Object Superclass;
	-
	- /** Smart Pointer */
	- typedef SmartPointer<Self> Pointer;
	-
	- /** Smart Pointer */
	- typedef SmartPointer<const Self> ConstPointer;
	-
	- /** */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	-
	- /** \brief Does the actual projection */
	- void Project();
	-
	-
	- /** \brief Set the distance map
	- *
	- * Sets the distance map that decodes for every voxel the distance to the nearest point on the skeleton.
	- */
	- itkSetMacro(DistanceMap, RealImageType::Pointer)
	-
	-
	- /** \brief Set the directions
	- *
	- * Sets the direction calculated by the TBSS skeletonization algorithm in itkSkeletonizationFilter.
	- */
	- itkSetMacro(Directions, VectorImageType::Pointer)
	-
	-
	- /** \brief Set the binary skeleton
	- *
	- * Sets the binary skeleton that defines on which voxels must be projected.
	- */
	- itkSetMacro(Skeleton, CharImageType::Pointer)
	-
	-
	- /** \brief Set the mask defining tubular structures on the skeleton
	- *
	- * Sets a binary mask that defines wich part of the white matter skeleton are tubular instead of sheet like.
	- * This is important because the a different projection method is used for sheet like structues and
	- * tubular structures.
	- */
	- itkSetMacro(Tube, CharImageType::Pointer)
	-
	-
	- /** \brief Set a 4D image containing the 3D registered FA maps of all study subjects. */
	- itkSetMacro(AllFA, Float4DImageType::Pointer)
	-
	-
	- /** \brief Returns a 4D image containing the skeleton projections of all subjects */
	- itkGetMacro(Projections, Float4DImageType::Pointer)
	-
	-
	-protected:
	-
	- /** Constructor */
	- ProjectionFilter();
	-
	- /** Destructor */
	- ~ProjectionFilter() override;
	-
	- RealImageType::Pointer m_DistanceMap;
	-
	- VectorImageType::Pointer m_Directions;
	-
	- CharImageType::Pointer m_Skeleton;
	-
	- CharImageType::Pointer m_Tube;
	-
	- Float4DImageType::Pointer m_Projections;
	-
	- Float4DImageType::Pointer m_AllFA;
	-
	- int round(float x)
	- {
	- if (x>0.0) return ((int) (x+0.5));
	- else return ((int) (x-0.5));
	- }
	-
	-protected:
	-
	-
	-
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkProjectionFilter.txx"
	-#endif
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkProjectionFilter.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkProjectionFilter.txx
	deleted file mode 100644
	index 16d9de6a53..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkProjectionFilter.txx
	+++ /dev/null
	@@ -1,196 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef _itkProjectionFilter_txx
	-#define _itkProjectionFilter_txx
	-
	-#include "itkProjectionFilter.h"
	-
	-#include "mitkProgressBar.h"
	-//#include <itkSignedMaurerDistanceMapImageFilter.h>
	-
	-#define SEARCHSIGMA 10 /* length in linear voxel dimensions */
	-#define MAXSEARCHLENGTH (3*SEARCHSIGMA)
	-
	-
	-namespace itk
	-{
	-
	-
	- ProjectionFilter::ProjectionFilter()
	- {
	-
	- }
	-
	- ProjectionFilter::~ProjectionFilter()
	- {
	-
	-
	- }
	-
	- void ProjectionFilter::Project()
	- {
	- // Contains only code for the projection of FA data. The original FSL code contains some extra lines
	- // For projection of other measurements than FA
	-
	- mitk::ProgressBar::GetInstance()->AddStepsToDo( 3 );
	-
	- Float4DImageType::Pointer data_4d_projected = Float4DImageType::New();
	- data_4d_projected->SetRegions(m_AllFA->GetRequestedRegion());
	- data_4d_projected->SetDirection(m_AllFA->GetDirection());
	- data_4d_projected->SetSpacing(m_AllFA->GetSpacing());
	- data_4d_projected->SetOrigin(m_AllFA->GetOrigin());
	- data_4d_projected->Allocate();
	- data_4d_projected->FillBuffer(0.0);
	-
	- Float4DImageType::SizeType size = m_AllFA->GetRequestedRegion().GetSize();
	- long s0 = size[0], s1 = size[1], s2 = size[2], s3 = size[3];
	-
	- for(int t=0; t<s3; t++)
	- {
	- for(int z=1; z<s2-1; z++)
	- {
	- for(int y=1; y<s1-1; y++)
	- {
	-
	- for(int x=1; x<s0-1; x++)
	- {
	-
	- VectorImageType::IndexType ix;
	- ix[0] = x; ix[1] = y; ix[2] = z;
	-
	- if(m_Skeleton->GetPixel(ix) != 0)
	- {
	- VectorImageType::PixelType dir = m_Directions->GetPixel(ix);
	-
	- Float4DImageType::IndexType ix4d;
	- ix4d[0]=x; ix4d[1]=y; ix4d[2]=z; ix4d[3]=t;
	- float maxval = m_AllFA->GetPixel(ix4d);
	- float maxval_weighted = maxval;
	- float exponentfactor = -0.5 * (dir[0]dir[0]+dir[1]dir[1]+dir[2]dir[2]) / (float)(SEARCHSIGMASEARCHSIGMA);
	-
	-
	- // No tubular structure here
	- if(m_Tube->GetPixel(ix) == 0)
	- {
	- for(int iters=0;iters<2;iters++)
	- {
	- float distance=0;
	-
	- for(int d=1;d<MAXSEARCHLENGTH;d++)
	- {
	- int D=d;
	- if (iters==1) D=-d;
	-
	- FloatImageType::IndexType ix3d;
	- int dx = x+dir[0]D, dy = y+dir[1]D, dz = z+dir[2]*D;
	- ix3d[0] = dx; ix3d[1] = dy; ix3d[2] = dz;
	-
	- if(dx<0 \|\| dy<0 \|\| dz<0
	- \|\| (dx>=s0 && dy<=s1 && dz<=s2))
	- {
	- d=MAXSEARCHLENGTH;
	- }
	- else if(m_DistanceMap->GetPixel(ix3d)>=distance)
	- {
	- float distanceweight = exp(d * d * exponentfactor);
	- distance = m_DistanceMap->GetPixel(ix3d);
	-
	- ix4d[0]=x+dir[0]D; ix4d[1]=y+dir[1]D; ix4d[2]=z+dir[2]*D; ix4d[3]=t;
	-
	- if(distanceweight*m_AllFA->GetPixel(ix4d)>maxval_weighted)
	- {
	- maxval = m_AllFA->GetPixel(ix4d);
	- maxval_weighted = maxval*distanceweight;
	- }
	- }
	- else{
	- d=MAXSEARCHLENGTH;
	- }
	-
	-
	-
	- }
	-
	- }
	- }
	-
	- // Tubular structure
	- else
	- {
	- for(int dy=-MAXSEARCHLENGTH; dy<=MAXSEARCHLENGTH;dy++) {
	- for(int dx=-MAXSEARCHLENGTH; dx<=MAXSEARCHLENGTH; dx++) {
	-
	- float distanceweight = exp(-0.5 * (dxdx+dydy) / (float)(SEARCHSIGMA*SEARCHSIGMA) );
	- float r=sqrt((float)(dxdx+dydy));
	-
	- if (r>0)
	- {
	- int allok=1;
	-
	- for(float rr=1; rr<=r+0.1; rr++) /* search outwards from centre to current voxel - test that distancemap always increasing */
	- {
	-
	- int dx1=round(rr*dx/r);
	- int dy1=round(rr*dy/r);
	- int dx2=round((rr+1)*dx/r);
	- int dy2=round((rr+1)*dy/r);
	-
	- RealImageType::IndexType ix1, ix2;
	- ix1[0]=x+dx1; ix1[1]=y+dy1; ix1[2]=z;
	- ix2[0]=x+dx2; ix2[1]=y+dy2; ix2[2]=z;
	- if(m_DistanceMap->GetPixel(ix1) > m_DistanceMap->GetPixel(ix2) )
	- {
	- allok=0;
	- }
	-
	- }
	-
	- ix4d[0]=x+dx; ix4d[1]=y+dy, ix4d[2]=z; ix4d[3]=t;
	- if( allok && (distanceweight * m_AllFA->GetPixel(ix4d) > maxval_weighted) )
	- {
	- maxval = m_AllFA->GetPixel(ix4d);
	- maxval_weighted = maxval * distanceweight;
	- }
	-
	-
	- }
	-
	- }
	- }
	- }
	-
	- ix4d[0]=x; ix4d[1]=y; ix4d[2]=z; ix4d[3]=t;
	-
	- data_4d_projected->SetPixel(ix4d, maxval);
	-
	- }
	- }
	- }
	- }
	- }
	-
	- m_Projections = data_4d_projected;
	-
	-
	-
	- }
	-
	-
	-
	-
	-
	-}
	-#endif // _itkProjectionFilter_txx
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkRemoveDwiChannelFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkRemoveDwiChannelFilter.h
	deleted file mode 100644
	index aeec9c0f37..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkRemoveDwiChannelFilter.h
	+++ /dev/null
	@@ -1,84 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-/*===================================================================
	-
	-This file is based heavily on a corresponding ITK filter.
	-
	-===================================================================*/
	-#ifndef __itkRemoveDwiChannelFilter_h_
	-#define __itkRemoveDwiChannelFilter_h_
	-
	-#include "itkImageToImageFilter.h"
	-#include "itkVectorImage.h"
	-#include <itkImageRegionIteratorWithIndex.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-
	-namespace itk{
	-/** \class RemoveDwiChannelFilter
	- * \brief Remove spcified channels from diffusion-weighted image.
	- */
	-
	-template< class TInPixelType >
	-class RemoveDwiChannelFilter :
	- public ImageToImageFilter< VectorImage< TInPixelType, 3 >, VectorImage< TInPixelType, 3 > >
	-{
	-
	-public:
	-
	- typedef RemoveDwiChannelFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageToImageFilter< VectorImage< TInPixelType, 3 >, VectorImage< TInPixelType, 3 > > Superclass;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(RemoveDwiChannelFilter, ImageToImageFilter)
	-
	- typedef typename Superclass::InputImageType InputImageType;
	- typedef typename Superclass::OutputImageType OutputImageType;
	- typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
	- typedef typename mitk::DiffusionPropertyHelper::GradientDirectionType DirectionType;
	- typedef typename mitk::DiffusionPropertyHelper::GradientDirectionsContainerType DirectionContainerType;
	-
	- void SetChannelIndices( std::vector< unsigned int > indices ){ m_ChannelIndices = indices; }
	- void SetDirections( typename DirectionContainerType::Pointer directions ){ m_Directions = directions; }
	- typename DirectionContainerType::Pointer GetNewDirections(){ return m_NewDirections; }
	-
	- protected:
	- RemoveDwiChannelFilter();
	- ~RemoveDwiChannelFilter() {}
	- void PrintSelf(std::ostream& os, Indent indent) const override;
	-
	- void BeforeThreadedGenerateData() override;
	- void ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, ThreadIdType id ) override;
	-
	- std::vector< unsigned int > m_ChannelIndices;
	- typename DirectionContainerType::Pointer m_Directions;
	- typename DirectionContainerType::Pointer m_NewDirections;
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkRemoveDwiChannelFilter.txx"
	-#endif
	-
	-#endif //__itkRemoveDwiChannelFilter_h_
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkRemoveDwiChannelFilter.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkRemoveDwiChannelFilter.txx
	deleted file mode 100644
	index f7eb3006d4..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkRemoveDwiChannelFilter.txx
	+++ /dev/null
	@@ -1,133 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkRemoveDwiChannelFilter_txx
	-#define __itkRemoveDwiChannelFilter_txx
	-
	-#include <time.h>
	-#include <stdio.h>
	-#include <stdlib.h>
	-
	-#define _USE_MATH_DEFINES
	-#include <math.h>
	-
	-#include "itkImageRegionConstIterator.h"
	-#include "itkImageRegionConstIteratorWithIndex.h"
	-#include "itkImageRegionIterator.h"
	-
	-namespace itk {
	-
	-
	-template< class TInPixelType >
	-RemoveDwiChannelFilter< TInPixelType>::RemoveDwiChannelFilter()
	-{
	- this->SetNumberOfRequiredInputs( 1 );
	-}
	-
	-template< class TInPixelType >
	-void RemoveDwiChannelFilter< TInPixelType>::BeforeThreadedGenerateData()
	-{
	- typename InputImageType::Pointer inputImagePointer = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) );
	- if ( inputImagePointer->GetVectorLength()-m_ChannelIndices.size()<=0 )
	- itkExceptionMacro("No channels remaining!");
	-
	- typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0));
	- outputImage->SetSpacing( inputImagePointer->GetSpacing() );
	- outputImage->SetOrigin( inputImagePointer->GetOrigin() );
	- outputImage->SetDirection( inputImagePointer->GetDirection() );
	- outputImage->SetLargestPossibleRegion( inputImagePointer->GetLargestPossibleRegion() );
	- outputImage->SetBufferedRegion( inputImagePointer->GetLargestPossibleRegion() );
	- outputImage->SetRequestedRegion( inputImagePointer->GetLargestPossibleRegion() );
	- outputImage->Allocate();
	- outputImage->SetVectorLength( inputImagePointer->GetVectorLength()-m_ChannelIndices.size() );
	- typename OutputImageType::PixelType nullPix;
	- nullPix.SetSize(outputImage->GetVectorLength());
	- nullPix.Fill(0);
	- outputImage->FillBuffer(nullPix);
	- this->SetNthOutput(0, outputImage);
	-
	- m_NewDirections = DirectionContainerType::New();
	-
	- int chIdx = 0;
	- for (unsigned int i=0; i<inputImagePointer->GetVectorLength(); i++)
	- {
	- bool use = true;
	- for (unsigned int j=0; j<m_ChannelIndices.size(); j++)
	- if (m_ChannelIndices.at(j)==i)
	- {
	- use = false;
	- break;
	- }
	- if (use)
	- {
	- m_NewDirections->InsertElement(chIdx, m_Directions->GetElement(i));
	- ++chIdx;
	- MITK_INFO << "Using channel " << i;
	- }
	- }
	-}
	-
	-template< class TInPixelType >
	-void RemoveDwiChannelFilter< TInPixelType>::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, ThreadIdType )
	-{
	- typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0));
	-
	- ImageRegionIterator< OutputImageType > oit(outputImage, outputRegionForThread);
	- oit.GoToBegin();
	-
	- typedef ImageRegionConstIterator< InputImageType > InputIteratorType;
	- typename InputImageType::Pointer inputImagePointer = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) );
	-
	- InputIteratorType git( inputImagePointer, outputRegionForThread );
	- git.GoToBegin();
	- while( !git.IsAtEnd() )
	- {
	- int chIdx = 0;
	- typename OutputImageType::PixelType pix = oit.Get();
	- for (unsigned int i=0; i<inputImagePointer->GetVectorLength(); i++)
	- {
	- bool use = true;
	- for (unsigned int j=0; j<m_ChannelIndices.size(); j++)
	- if (m_ChannelIndices.at(j)==i)
	- {
	- use = false;
	- break;
	- }
	- if (use)
	- {
	- pix[chIdx] = git.Get()[i];
	- ++chIdx;
	- }
	- }
	- oit.Set(pix);
	- ++oit;
	- ++git;
	- }
	-
	- std::cout << "One Thread finished calculation" << std::endl;
	-}
	-
	-template< class TInPixelType >
	-void
	-RemoveDwiChannelFilter< TInPixelType>
	-::PrintSelf(std::ostream& os, Indent indent) const
	-{
	- Superclass::PrintSelf(os,indent);
	-}
	-
	-}
	-
	-#endif // __itkRemoveDwiChannelFilter_txx
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkResampleDwiImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkResampleDwiImageFilter.h
	deleted file mode 100644
	index 605743b66a..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkResampleDwiImageFilter.h
	+++ /dev/null
	@@ -1,146 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-/*=========================================================================
	-
	-Program: Tensor ToolKit - TTK
	-Module: $URL: svn://scm.gforge.inria.fr/svn/ttk/trunk/Algorithms/itkResampleDwiImageFilter.h $
	-Language: C++
	-Date: $Date: 2010-06-07 13:39:13 +0200 (Mo, 07 Jun 2010) $
	-Version: $Revision: 68 $
	-
	-Copyright (c) INRIA 2010. All rights reserved.
	-See LICENSE.txt for details.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without even
	-the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
	-PURPOSE. See the above copyright notices for more information.
	-
	-=========================================================================*/
	-#ifndef _itk_ResampleDwiImageFilter_h_
	-#define _itk_ResampleDwiImageFilter_h_
	-
	-#include <itkImageToImageFilter.h>
	-#include <itkVectorImage.h>
	-#include <itkPointShell.h>
	-
	-namespace itk
	-{
	-
	-/**
	-* \brief Resample DWI channel by channel. */
	-
	-template <class TScalarType>
	-class ResampleDwiImageFilter
	- : public ImageToImageFilter<itk::VectorImage<TScalarType,3>, itk::VectorImage<TScalarType,3> >
	-{
	-
	-public:
	-
	- enum Interpolation {
	- Interpolate_NearestNeighbour,
	- Interpolate_Linear,
	- Interpolate_BSpline,
	- Interpolate_WindowedSinc
	- };
	-
	- typedef ResampleDwiImageFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageToImageFilter< itk::VectorImage<TScalarType,3>, itk::VectorImage<TScalarType,3> >
	- Superclass;
	-
	- typedef itk::Vector< double, 3 > DoubleVectorType;
	- typedef itk::VectorImage<TScalarType,3> DwiImageType;
	- typedef itk::Image<TScalarType,3> DwiChannelType;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(ResampleDwiImageFilter, ImageToImageFilter)
	-
	- itkSetMacro( Interpolation, Interpolation )
	-
	- void SetSamplingFactor(DoubleVectorType sampling)
	- {
	- m_NewSpacing = this->GetInput()->GetSpacing();
	- m_NewSpacing[0] /= sampling[0];
	- m_NewSpacing[1] /= sampling[1];
	- m_NewSpacing[2] /= sampling[2];
	- m_NewImageRegion = this->GetInput()->GetLargestPossibleRegion();
	- m_NewImageRegion.SetSize(0, m_NewImageRegion.GetSize(0)*sampling[0]);
	- m_NewImageRegion.SetSize(1, m_NewImageRegion.GetSize(1)*sampling[1]);
	- m_NewImageRegion.SetSize(2, m_NewImageRegion.GetSize(2)*sampling[2]);
	- }
	- void SetNewSpacing(DoubleVectorType spacing)
	- {
	- DoubleVectorType oldSpacing = this->GetInput()->GetSpacing();
	- DoubleVectorType sampling;
	- sampling[0] = oldSpacing[0]/spacing[0];
	- sampling[1] = oldSpacing[1]/spacing[1];
	- sampling[2] = oldSpacing[2]/spacing[2];
	-
	- m_NewSpacing = spacing;
	- m_NewImageRegion = this->GetInput()->GetLargestPossibleRegion();
	- m_NewImageRegion.SetSize(0, m_NewImageRegion.GetSize(0)*sampling[0]);
	- m_NewImageRegion.SetSize(1, m_NewImageRegion.GetSize(1)*sampling[1]);
	- m_NewImageRegion.SetSize(2, m_NewImageRegion.GetSize(2)*sampling[2]);
	- }
	- void SetNewImageSize(ImageRegion<3> region)
	- {
	- ImageRegion<3> oldRegion = this->GetInput()->GetLargestPossibleRegion();
	- DoubleVectorType sampling;
	- sampling[0] = (double)region.GetSize(0)/oldRegion.GetSize(0);
	- sampling[1] = (double)region.GetSize(1)/oldRegion.GetSize(1);
	- sampling[2] = (double)region.GetSize(2)/oldRegion.GetSize(2);
	-
	- m_NewImageRegion = region;
	- m_NewSpacing = this->GetInput()->GetSpacing();
	- m_NewSpacing[0] /= sampling[0];
	- m_NewSpacing[1] /= sampling[1];
	- m_NewSpacing[2] /= sampling[2];
	- }
	-
	- void UpdateOutputInformation() override;
	-
	- virtual void PropagateRequestedRegion(){}
	-
	- void PropagateRequestedRegion(itk::DataObject *) override{}
	-
	- void VerifyInputInformation() override{}
	-
	- protected:
	- ResampleDwiImageFilter();
	- ~ResampleDwiImageFilter() override{}
	-
	- void GenerateData() override;
	-
	- DoubleVectorType m_NewSpacing;
	- ImageRegion<3> m_NewImageRegion;
	- Interpolation m_Interpolation;
	-};
	-
	-
	-} // end of namespace
	-
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkResampleDwiImageFilter.txx"
	-#endif
	-
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkResampleDwiImageFilter.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkResampleDwiImageFilter.txx
	deleted file mode 100644
	index b317f88f4d..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkResampleDwiImageFilter.txx
	+++ /dev/null
	@@ -1,176 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-/*=========================================================================
	-
	-Program: Tensor ToolKit - TTK
	-Module: $URL: svn://scm.gforge.inria.fr/svn/ttk/trunk/Algorithms/itkResampleDwiImageFilter.txx $
	-Language: C++
	-Date: $Date: 2010-06-07 13:39:13 +0200 (Mo, 07 Jun 2010) $
	-Version: $Revision: 68 $
	-
	-Copyright (c) INRIA 2010. All rights reserved.
	-See LICENSE.txt for details.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without even
	-the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
	-PURPOSE. See the above copyright notices for more information.
	-
	-=========================================================================*/
	-#ifndef _itk_ResampleDwiImageFilter_txx_
	-#define _itk_ResampleDwiImageFilter_txx_
	-#endif
	-
	-#define _USE_MATH_DEFINES
	-
	-#include "itkResampleDwiImageFilter.h"
	-#include <itkImageRegionIterator.h>
	-#include <itkImageRegion.h>
	-#include <itkResampleImageFilter.h>
	-#include <itkBSplineInterpolateImageFunction.h>
	-#include <itkNearestNeighborInterpolateImageFunction.h>
	-#include <itkLinearInterpolateImageFunction.h>
	-#include <itkWindowedSincInterpolateImageFunction.h>
	-
	-namespace itk
	-{
	-
	-template <class TScalarType>
	-ResampleDwiImageFilter<TScalarType>
	-::ResampleDwiImageFilter()
	- : m_Interpolation(Interpolate_Linear)
	-{
	- this->SetNumberOfRequiredInputs( 1 );
	-}
	-
	-template <class TScalarType>
	-void
	-ResampleDwiImageFilter<TScalarType>
	-::GenerateData()
	-{
	-// // initialize output image
	-// itk::Vector< double, 3 > spacing = this->GetInput()->GetSpacing();
	-// spacing[0] /= m_SamplingFactor[0];
	-// spacing[1] /= m_SamplingFactor[1];
	-// spacing[2] /= m_SamplingFactor[2];
	-// ImageRegion<3> region = this->GetInput()->GetLargestPossibleRegion();
	-// region.SetSize(0, region.GetSize(0)*m_SamplingFactor[0]);
	-// region.SetSize(1, region.GetSize(1)*m_SamplingFactor[1]);
	-// region.SetSize(2, region.GetSize(2)*m_SamplingFactor[2]);
	-
	- itk::Point<double,3> origin = this->GetInput()->GetOrigin();
	- origin[0] -= this->GetInput()->GetSpacing()[0]/2;
	- origin[1] -= this->GetInput()->GetSpacing()[1]/2;
	- origin[2] -= this->GetInput()->GetSpacing()[2]/2;
	-
	- origin[0] += m_NewSpacing[0]/2;
	- origin[1] += m_NewSpacing[1]/2;
	- origin[2] += m_NewSpacing[2]/2;
	-
	- typename DwiImageType::Pointer outImage = DwiImageType::New();
	- outImage->SetSpacing( m_NewSpacing );
	- outImage->SetOrigin( origin );
	- outImage->SetDirection( this->GetInput()->GetDirection() );
	- outImage->SetLargestPossibleRegion( m_NewImageRegion );
	- outImage->SetBufferedRegion( m_NewImageRegion );
	- outImage->SetRequestedRegion( m_NewImageRegion );
	- outImage->SetVectorLength( this->GetInput()->GetVectorLength() );
	- outImage->Allocate();
	-
	- typename itk::ResampleImageFilter<DwiChannelType, DwiChannelType>::Pointer resampler = itk::ResampleImageFilter<DwiChannelType, DwiChannelType>::New();
	- resampler->SetOutputParametersFromImage(outImage);
	-
	- switch (m_Interpolation)
	- {
	- case Interpolate_NearestNeighbour:
	- {
	- typename itk::NearestNeighborInterpolateImageFunction<DwiChannelType>::Pointer interp = itk::NearestNeighborInterpolateImageFunction<DwiChannelType>::New();
	- resampler->SetInterpolator(interp);
	- break;
	- }
	- case Interpolate_Linear:
	- {
	- typename itk::LinearInterpolateImageFunction<DwiChannelType>::Pointer interp = itk::LinearInterpolateImageFunction<DwiChannelType>::New();
	- resampler->SetInterpolator(interp);
	- break;
	- }
	- case Interpolate_BSpline:
	- {
	- typename itk::BSplineInterpolateImageFunction<DwiChannelType>::Pointer interp = itk::BSplineInterpolateImageFunction<DwiChannelType>::New();
	- resampler->SetInterpolator(interp);
	- break;
	- }
	- case Interpolate_WindowedSinc:
	- {
	- typename itk::WindowedSincInterpolateImageFunction<DwiChannelType, 3>::Pointer interp = itk::WindowedSincInterpolateImageFunction<DwiChannelType, 3>::New();
	- resampler->SetInterpolator(interp);
	- break;
	- }
	- default:
	- {
	- typename itk::LinearInterpolateImageFunction<DwiChannelType>::Pointer interp = itk::LinearInterpolateImageFunction<DwiChannelType>::New();
	- resampler->SetInterpolator(interp);
	- }
	- }
	-
	- for (unsigned int i=0; i<this->GetInput()->GetVectorLength(); i++)
	- {
	- typename DwiChannelType::Pointer channel = DwiChannelType::New();
	- channel->SetSpacing( this->GetInput()->GetSpacing() );
	- channel->SetOrigin( this->GetInput()->GetOrigin() );
	- channel->SetDirection( this->GetInput()->GetDirection() );
	- channel->SetLargestPossibleRegion( this->GetInput()->GetLargestPossibleRegion() );
	- channel->SetBufferedRegion( this->GetInput()->GetLargestPossibleRegion() );
	- channel->SetRequestedRegion( this->GetInput()->GetLargestPossibleRegion() );
	- channel->Allocate();
	-
	- ImageRegionIterator<DwiChannelType> it(channel, channel->GetLargestPossibleRegion());
	- while(!it.IsAtEnd())
	- {
	- typename DwiImageType::PixelType pix = this->GetInput()->GetPixel(it.GetIndex());
	- it.Set(pix[i]);
	- ++it;
	- }
	-
	- resampler->SetInput(channel);
	- resampler->Update();
	- channel = resampler->GetOutput();
	-
	- ImageRegionIterator<DwiImageType> it2(outImage, outImage->GetLargestPossibleRegion());
	- while(!it2.IsAtEnd())
	- {
	- typename DwiImageType::PixelType pix = it2.Get();
	- pix[i] = channel->GetPixel(it2.GetIndex());
	- it2.Set(pix);
	- ++it2;
	- }
	- }
	-
	- this->SetNthOutput(0, outImage);
	-}
	-
	-template <class TScalarType>
	-void
	-ResampleDwiImageFilter<TScalarType>
	-::UpdateOutputInformation()
	-{
	- // Calls to superclass updateoutputinformation
	- //Superclass::UpdateOutputInformation();
	-
	- this->GetOutput()->SetSpacing(m_NewSpacing);
	- this->GetOutput()->SetLargestPossibleRegion(m_NewImageRegion);
	-}
	-
	-} // end of namespace
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkResidualImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkResidualImageFilter.h
	deleted file mode 100644
	index 78f8656688..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkResidualImageFilter.h
	+++ /dev/null
	@@ -1,177 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-/*=========================================================================
	-
	-Program: Tensor ToolKit - TTK
	-Module: $URL: svn://scm.gforge.inria.fr/svn/ttk/trunk/Algorithms/itkTensorImageToDiffusionImageFilter.h $
	-Language: C++
	-Date: $Date: 2010-06-07 13:39:13 +0200 (Mo, 07 Jun 2010) $
	-Version: $Revision: 68 $
	-
	-Copyright (c) INRIA 2010. All rights reserved.
	-See LICENSE.txt for details.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without even
	-the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
	-PURPOSE. See the above copyright notices for more information.
	-
	-=========================================================================*/
	-#ifndef _itk_ResidualImageFilter_h_
	-#define _itk_ResidualImageFilter_h_
	-
	-#include "itkImageToImageFilter.h"
	-#include <itkDiffusionTensor3D.h>
	-
	-
	-namespace itk
	-{
	-
	- template <class TInputScalarType, class TOutputScalarType>
	- class ResidualImageFilter
	- : public ImageToImageFilter<itk::VectorImage<TInputScalarType,3>, itk::Image<TOutputScalarType,3> >
	- {
	-
	- public:
	-
	- typedef TInputScalarType InputScalarType;
	- typedef itk::VectorImage<InputScalarType,3> InputImageType;
	- typedef typename InputImageType::PixelType InputPixelType;
	- typedef typename InputImageType::RegionType InputImageRegionType;
	-
	- typedef TOutputScalarType OutputScalarType;
	- typedef itk::Image<OutputScalarType,3> OutputImageType;
	- typedef typename OutputImageType::PixelType OutputPixelType;
	- typedef typename OutputImageType::RegionType OutputImageRegionType;
	-
	- typedef ResidualImageFilter Self;
	- typedef ImageToImageFilter<InputImageType, OutputImageType> Superclass;
	-
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	-
	- typedef vnl_vector_fixed< double, 3 > GradientDirectionType;
	- typedef itk::VectorContainer< unsigned int,
	- GradientDirectionType > GradientDirectionContainerType;
	-
	-
	- typedef itk::Image<InputScalarType,3> BaselineImageType;
	-
	- itkTypeMacro (ResidualImageFilter, ImageToImageFilter);
	-
	- itkStaticConstMacro (ImageDimension, unsigned int,
	- OutputImageType::ImageDimension);
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- void SetSecondDiffusionImage(typename InputImageType::Pointer diffImage)
	- {
	- m_SecondDiffusionImage = diffImage;
	- }
	-
	-
	- std::vector<double> GetQ1()
	- {
	- return m_Q1;
	- }
	-
	- std::vector<double> GetQ3()
	- {
	- return m_Q3;
	- }
	-
	- std::vector<double> GetMeans()
	- {
	- return m_Means;
	- }
	-
	- std::vector<double> GetPercentagesOfOutliers()
	- {
	- return m_PercentagesOfOutliers;
	- }
	-
	- std::vector< std::vector<double> > GetOutliersPerSlice()
	- {
	- return m_OutliersPerSlice;
	- }
	-
	- void SetGradients(GradientDirectionContainerType* grads)
	- {
	- m_Gradients = grads;
	- }
	-
	- void SetBaseLineImage(BaselineImageType* baseline)
	- {
	- m_BaseLineImage = baseline;
	- }
	-
	- void SetB0Threshold(InputScalarType threshold)
	- {
	- m_B0Threshold = threshold;
	- }
	-
	- itkSetMacro(B0Index, int)
	-
	-
	- protected:
	- ResidualImageFilter()
	- {
	- m_B0Threshold = 30.0; // default value. allow user to redefine
	- };
	- ~ResidualImageFilter(){};
	-
	- void PrintSelf (std::ostream& os, Indent indent) const override
	- {
	- Superclass::PrintSelf (os, indent);
	- }
	-
	-
	- void GenerateData() override;
	-
	- private:
	-
	- ResidualImageFilter (const Self&);
	- void operator=(const Self&);
	-
	- typename InputImageType::Pointer m_SecondDiffusionImage;
	-
	- std::vector<double> m_Means, m_Q1, m_Q3, m_PercentagesOfOutliers;
	-
	-
	-
	- // 'Outer' vector: slices, 'Inner' volumes
	- std::vector< std::vector<double> > m_OutliersPerSlice;
	-
	- GradientDirectionContainerType* m_Gradients;
	-
	- typename BaselineImageType::Pointer m_BaseLineImage;
	-
	- InputScalarType m_B0Threshold;
	-
	- int m_B0Index;
	-
	- };
	-
	-
	-} // end of namespace
	-
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkResidualImageFilter.txx"
	-#endif
	-
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkResidualImageFilter.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkResidualImageFilter.txx
	deleted file mode 100644
	index fb1c06a99a..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkResidualImageFilter.txx
	+++ /dev/null
	@@ -1,285 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-/*=========================================================================
	-
	-Program: Tensor ToolKit - TTK
	-Module: $URL: svn://scm.gforge.inria.fr/svn/ttk/trunk/Algorithms/itkTensorImageToDiffusionImageFilter.txx $
	-Language: C++
	-Date: $Date: 2010-06-07 13:39:13 +0200 (Mo, 07 Jun 2010) $
	-Version: $Revision: 68 $
	-
	-Copyright (c) INRIA 2010. All rights reserved.
	-See LICENSE.txt for details.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without even
	-the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
	-PURPOSE. See the above copyright notices for more information.
	-
	-=========================================================================*/
	-#ifndef _itk_ResidualImageFilter_txx_
	-#define _itk_ResidualImageFilter_txx_
	-#endif
	-
	-#include "itkResidualImageFilter.h"
	-#include <mitkCommon.h>
	-#include <cmath>
	-
	-namespace itk
	-{
	-
	-
	-
	-
	- template <class TInputScalarType, class TOutputScalarType>
	- void
	- ResidualImageFilter<TInputScalarType, TOutputScalarType>
	- ::GenerateData()
	- {
	- typename InputImageType::SizeType size = this->GetInput()->GetLargestPossibleRegion().GetSize();
	- typename InputImageType::SizeType size2 = m_SecondDiffusionImage->GetLargestPossibleRegion().GetSize();
	-
	- if(size != size2)
	- {
	- MITK_ERROR << "Sizes do not match";
	- return;
	- }
	-
	- // Initialize output image
	- typename OutputImageType::Pointer outputImage =
	- static_cast< OutputImageType * >(this->ProcessObject::GetPrimaryOutput());
	-
	- outputImage->SetSpacing( this->GetInput()->GetSpacing() ); // Set the image spacing
	- outputImage->SetOrigin( this->GetInput()->GetOrigin() ); // Set the image origin
	- outputImage->SetDirection( this->GetInput()->GetDirection() ); // Set the image direction
	- outputImage->SetRegions( this->GetInput()->GetLargestPossibleRegion() );
	- outputImage->Allocate();
	- outputImage->FillBuffer(0.0);
	-
	-
	-
	-
	-
	- std::vector< std::vector<double> > residuals;
	-
	- // per slice, per volume
	- std::vector< std::vector <std::vector<double> > > residualsPerSlice;
	-
	- // Detrmine number of B0 images
	- int numberB0=0;
	- for(unsigned int i=0; i<m_Gradients->Size(); i++)
	- {
	- GradientDirectionType grad = m_Gradients->ElementAt(i);
	-
	- if(fabs(grad[0]) < 0.001 && fabs(grad[1]) < 0.001 && fabs(grad[2]) < 0.001)
	- {
	- numberB0++;
	- }
	- }
	-
	- residuals.resize(this->GetInput()->GetVectorLength()-numberB0);
	-
	- // Calculate the standard residual image and for each volume put all residuals in a vector
	- for(unsigned int z=0; z<size[2]; z++)
	- {
	- std::vector< std::vector<double> > sliceResiduals; // residuals per volume for this slice
	- sliceResiduals.resize(this->GetInput()->GetVectorLength()-numberB0);
	-
	- for(unsigned int y=0; y<size[1]; y++)
	- {
	- for(unsigned int x=0; x<size[0]; x++)
	- {
	-
	- // Check if b0 exceeds threshold
	- itk::Index<3> ix;
	- ix[0] = x;
	- ix[1] = y;
	- ix[2] = z;
	-
	-
	- typename InputImageType::PixelType p1 = this->GetInput()->GetPixel(ix);
	- typename InputImageType::PixelType p2 = m_SecondDiffusionImage->GetPixel(ix);
	-
	- if(p1.GetSize() != p2.GetSize())
	- {
	- MITK_ERROR << "Vector sizes do not match";
	- return;
	- }
	-
	-
	- if(p1.GetElement(m_B0Index) <= m_B0Threshold)
	- {
	- continue;
	- }
	-
	-
	-
	- double res = 0;
	- int shift = 0; // correction for the skipped B0 images
	-
	- for(unsigned int i = 0; i<p1.GetSize(); i++)
	- {
	-
	-
	-
	- GradientDirectionType grad = m_Gradients->ElementAt(i);
	- if(!(fabs(grad[0]) < 0.001 && fabs(grad[1]) < 0.001 && fabs(grad[2]) < 0.001))
	- {
	- double val1 = (double)p1.GetElement(i);
	- double val2 = (double)p2.GetElement(i);
	-
	- res += abs(val1-val2);
	-
	- residuals[i-shift].push_back(val1-val2);
	- sliceResiduals[i-shift].push_back(val1-val2);
	-
	- }
	- else
	- {
	- shift++;
	- }
	-
	-
	-
	- }
	-
	-
	- res = res/p1.GetSize();
	-
	- outputImage->SetPixel(ix, res);
	-
	- }
	- }
	-
	- residualsPerSlice.push_back(sliceResiduals);
	- }
	-
	-
	-
	-
	-
	- // for each dw volume: sort the the measured residuals (for each voxel) to enable determining Q1 and Q3; calculate means
	- // determine percentage of errors as described in QUALITY ASSESSMENT THROUGH ANALYSIS OF RESIDUALS OF DIFFUSION IMAGE FITTING
	- // Leemans et al 2008
	-
	- double q1,q3, median;
	- std::vector< std::vector<double> >::iterator it = residuals.begin();
	- while(it != residuals.end())
	- {
	- std::vector<double> res = *it;
	-
	- // sort
	- std::sort(res.begin(), res.end());
	-
	- q1 = res[0.25*res.size()];
	- m_Q1.push_back(q1);
	- q3 = res[0.75*res.size()];
	- m_Q3.push_back(q3);
	-
	-
	-
	- median = res[0.5*res.size()];
	- double iqr = q3-q1;
	- double outlierThreshold = median + 1.5*iqr;
	- double numberOfOutliers = 0.0;
	-
	- std::vector<double>::iterator resIt = res.begin();
	- double mean = 0;
	- while(resIt != res.end())
	- {
	- double f = *resIt;
	- if(f>outlierThreshold)
	- {
	- numberOfOutliers++;
	- }
	- mean += f;
	- ++resIt;
	- }
	-
	- double percOfOutliers = 100 * numberOfOutliers / res.size();
	- m_PercentagesOfOutliers.push_back(percOfOutliers);
	-
	- mean /= res.size();
	- m_Means.push_back(mean);
	-
	- ++it;
	- }
	-
	-
	-
	- // Calculate for each slice the number of outliers per volume(dw volume)
	- std::vector< std::vector <std::vector<double> > >::iterator sliceIt = residualsPerSlice.begin();
	-
	- while(sliceIt != residualsPerSlice.end())
	- {
	- std::vector< std::vector<double> > currentSlice = *sliceIt;
	- std::vector<double> percentages;
	-
	- std::vector< std::vector<double> >::iterator volIt = currentSlice.begin();
	- while(volIt != currentSlice.end())
	- {
	-
	-
	- std::vector<double> currentVolume = *volIt;
	-
	- //sort
	- std::sort(currentVolume.begin(), currentVolume.end());
	-
	-
	-
	- q1 = currentVolume[0.25*currentVolume.size()];
	- q3 = currentVolume[0.75*currentVolume.size()];
	- median = currentVolume[0.5*currentVolume.size()];
	- double iqr = q3-q1;
	- double outlierThreshold = median + 1.5*iqr;
	- double numberOfOutliers = 0.0;
	-
	- std::vector<double>::iterator resIt = currentVolume.begin();
	- double mean(0.0);
	- while(resIt != currentVolume.end())
	- {
	- double f = *resIt;
	- if(f>outlierThreshold)
	- {
	- numberOfOutliers++;
	- }
	- mean += f;
	- ++resIt;
	- }
	-
	- double percOfOutliers = 100 * numberOfOutliers / currentVolume.size();
	- percentages.push_back(percOfOutliers);
	-
	- ++volIt;
	- }
	-
	- m_OutliersPerSlice.push_back(percentages);
	-
	-
	-
	- ++sliceIt;
	- }
	-
	-
	-
	-
	- }
	-
	-
	-
	-
	-
	-
	-} // end of namespace
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkShCoefficientImageExporter.cpp b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkShCoefficientImageExporter.cpp
	deleted file mode 100644
	index e8ec5d8bc4..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkShCoefficientImageExporter.cpp
	+++ /dev/null
	@@ -1,111 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef __itkShCoefficientImageExporter_cpp
	-#define __itkShCoefficientImageExporter_cpp
	-
	-#include <ctime>
	-#include <cstdio>
	-#include <cstdlib>
	-
	-#include "itkShCoefficientImageExporter.h"
	-#include <itkImageRegionIterator.h>
	-#include <boost/math/special_functions.hpp>
	-
	-using namespace boost::math;
	-
	-namespace itk {
	-
	-template< class PixelType, int ShOrder >
	-ShCoefficientImageExporter< PixelType, ShOrder >::ShCoefficientImageExporter()
	-{
	-
	-}
	-
	-template< class PixelType, int ShOrder >
	-void ShCoefficientImageExporter< PixelType, ShOrder >
	-::GenerateData()
	-{
	- if (m_InputImage.IsNull())
	- return;
	-
	- Vector<double, 4> spacing4;
	- Point<float, 4> origin4;
	- Matrix<double, 4, 4> direction4; direction4.SetIdentity();
	- ImageRegion<4> imageRegion4;
	-
	- Vector<double, 3> spacing3 = m_InputImage->GetSpacing();
	- Point<float, 3> origin3 = m_InputImage->GetOrigin();
	- Matrix<double, 3, 3> direction3 = m_InputImage->GetDirection();
	- ImageRegion<3> imageRegion3 = m_InputImage->GetLargestPossibleRegion();
	-
	- spacing4[0] = spacing3[0]; spacing4[1] = spacing3[1]; spacing4[2] = spacing3[2]; spacing4[3] = 1;
	- origin4[0] = origin3[0]; origin4[1] = origin3[1]; origin4[2] = origin3[2]; origin4[3] = 0;
	- for (int r=0; r<3; r++)
	- for (int c=0; c<3; c++)
	- direction4[r][c] = direction3[r][c];
	-
	- imageRegion4.SetSize(0, imageRegion3.GetSize()[0]);
	- imageRegion4.SetSize(1, imageRegion3.GetSize()[1]);
	- imageRegion4.SetSize(2, imageRegion3.GetSize()[2]);
	- imageRegion4.SetSize(3, (ShOrder*ShOrder + ShOrder + 2)/2 + ShOrder );
	-
	- m_OutputImage = CoefficientImageType::New();
	- m_OutputImage->SetSpacing( spacing4 );
	- m_OutputImage->SetOrigin( origin4 );
	- m_OutputImage->SetDirection( direction4 );
	- m_OutputImage->SetRegions( imageRegion4 );
	- m_OutputImage->Allocate();
	- m_OutputImage->FillBuffer(0.0);
	-
	- typedef ImageRegionConstIterator< InputImageType > InputIteratorType;
	- InputIteratorType it(m_InputImage, m_InputImage->GetLargestPossibleRegion());
	- int numCoeffs = imageRegion4.GetSize(3);
	-
	- int x = imageRegion3.GetSize(0);
	- int y = imageRegion3.GetSize(1);
	- int z = imageRegion3.GetSize(2);
	-
	-#ifdef WIN32
	-#pragma omp parallel for
	-#else
	-#pragma omp parallel for collapse(3)
	-#endif
	- for (int a=0; a<x; a++)
	- for (int b=0; b<y; b++)
	- for (int c=0; c<z; c++)
	- {
	- typename InputImageType::IndexType index3;
	- index3.SetElement(0,a);
	- index3.SetElement(1,b);
	- index3.SetElement(2,c);
	-
	- CoefficientImageType::IndexType index4;
	- index4[0] = index3[0];
	- index4[1] = index3[1];
	- index4[2] = index3[2];
	-
	- typename InputImageType::PixelType pix = m_InputImage->GetPixel(index3);
	- for (int i=0; i<numCoeffs; i++)
	- {
	- index4[3] = i;
	- m_OutputImage->SetPixel(index4, pix[i]);
	- }
	- }
	-}
	-
	-}
	-
	-#endif // __itkShCoefficientImageExporter_cpp
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkShCoefficientImageExporter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkShCoefficientImageExporter.h
	deleted file mode 100644
	index e517bd04d3..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkShCoefficientImageExporter.h
	+++ /dev/null
	@@ -1,80 +0,0 @@
	-/*=========================================================================
	-
	- Program: Insight Segmentation & Registration Toolkit
	- Module: $RCSfile: itkDiffusionTensor3DReconstructionImageFilter.h,v $
	- Language: C++
	- Date: $Date: 2006-03-27 17:01:06 $
	- Version: $Revision: 1.12 $
	-
	- Copyright (c) Insight Software Consortium. All rights reserved.
	- See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
	-
	- This software is distributed WITHOUT ANY WARRANTY; without even
	- the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
	- PURPOSE. See the above copyright notices for more information.
	-
	-=========================================================================*/
	-#ifndef __itkShCoefficientImageExporter_h_
	-#define __itkShCoefficientImageExporter_h_
	-
	-#include <itkOrientationDistributionFunction.h>
	-
	-namespace itk{
	-/** \class ShCoefficientImageExporter
	- Converts FSL reconstructions of diffusionweighted images (4D images containing the sh coefficients) to Odf images or 3D sh-coefficient images.
	-*/
	-
	-template< class PixelType, int ShOrder >
	-class ShCoefficientImageExporter : public ProcessObject
	-{
	-
	-public:
	-
	- enum NormalizationMethods {
	- NO_NORM,
	- SINGLE_VEC_NORM,
	- SPACING_COMPENSATION
	- };
	-
	-
	- typedef ShCoefficientImageExporter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ProcessObject Superclass;
	- typedef itk::Image< float, 4 > CoefficientImageType;
	- typedef Image< Vector< PixelType, (ShOrder*ShOrder + ShOrder + 2)/2 + ShOrder >, 3 > InputImageType;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(ShCoefficientImageExporter, ProcessObject)
	-
	- // input
	- itkSetMacro( InputImage, typename InputImageType::Pointer) ///< sh coefficient image in FSL file format
	-
	- // output
	- itkGetMacro( OutputImage, typename CoefficientImageType::Pointer) ///< mitk style image containing the SH coefficients
	-
	- void GenerateData() override;
	-
	-protected:
	- ShCoefficientImageExporter();
	- ~ShCoefficientImageExporter() override{}
	-
	- typename InputImageType::Pointer m_InputImage;
	- CoefficientImageType::Pointer m_OutputImage;
	-
	-private:
	-
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkShCoefficientImageExporter.cpp"
	-#endif
	-
	-#endif //__itkShCoefficientImageExporter_h_
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkShCoefficientImageImporter.cpp b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkShCoefficientImageImporter.cpp
	deleted file mode 100644
	index 6a179e84c2..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkShCoefficientImageImporter.cpp
	+++ /dev/null
	@@ -1,104 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef __itkShCoefficientImageImporter_cpp
	-#define __itkShCoefficientImageImporter_cpp
	-
	-#include <ctime>
	-#include <cstdio>
	-#include <cstdlib>
	-
	-#include "itkShCoefficientImageImporter.h"
	-#include <itkImageRegionIterator.h>
	-#include <mitkDiffusionFunctionCollection.h>
	-
	-namespace itk {
	-
	-template< class PixelType, int ShOrder >
	-ShCoefficientImageImporter< PixelType, ShOrder >::ShCoefficientImageImporter()
	-{
	-
	-}
	-
	-template< class PixelType, int ShOrder >
	-void ShCoefficientImageImporter< PixelType, ShOrder >
	-::GenerateData()
	-{
	- if (m_InputImage.IsNull())
	- return;
	-
	- Vector<float, 4> spacing4 = m_InputImage->GetSpacing();
	- Point<float, 4> origin4 = m_InputImage->GetOrigin();
	- Matrix<double, 4, 4> direction4 = m_InputImage->GetDirection();
	- ImageRegion<4> imageRegion4 = m_InputImage->GetLargestPossibleRegion();
	-
	- Vector<double, 3> spacing3;
	- Point<float, 3> origin3;
	- Matrix<double, 3, 3> direction3;
	- ImageRegion<3> imageRegion3;
	-
	- spacing3[0] = spacing4[0]; spacing3[1] = spacing4[1]; spacing3[2] = spacing4[2];
	- origin3[0] = origin4[0]; origin3[1] = origin4[1]; origin3[2] = origin4[2];
	- for (int r=0; r<3; r++)
	- for (int c=0; c<3; c++)
	- direction3[r][c] = direction4[r][c];
	- imageRegion3.SetSize(0, imageRegion4.GetSize()[0]);
	- imageRegion3.SetSize(1, imageRegion4.GetSize()[1]);
	- imageRegion3.SetSize(2, imageRegion4.GetSize()[2]);
	-
	- m_CoefficientImage = CoefficientImageType::New();
	- m_CoefficientImage->SetSpacing( spacing3 );
	- m_CoefficientImage->SetOrigin( origin3 );
	- m_CoefficientImage->SetDirection( direction3 );
	- m_CoefficientImage->SetRegions( imageRegion3 );
	- m_CoefficientImage->Allocate();
	- Vector< PixelType, (ShOrder*ShOrder + ShOrder + 2)/2 + ShOrder > nullVec2; nullVec2.Fill(0.0);
	- m_CoefficientImage->FillBuffer(nullVec2);
	-
	- int x = imageRegion4.GetSize(0);
	- int y = imageRegion4.GetSize(1);
	- int z = imageRegion4.GetSize(2);
	- int numCoeffs = imageRegion4.GetSize(3);
	-
	-#ifdef WIN32
	-#pragma omp parallel for
	-#else
	-#pragma omp parallel for collapse(3)
	-#endif
	- for (int a=0; a<x; a++)
	- for (int b=0; b<y; b++)
	- for (int c=0; c<z; c++)
	- {
	- typename InputImageType::IndexType index;
	- index.SetElement(0,a);
	- index.SetElement(1,b);
	- index.SetElement(2,c);
	- typename CoefficientImageType::PixelType pix;
	- for (int d=0; d<numCoeffs; d++)
	- {
	- index.SetElement(3,d);
	- pix[d] = m_InputImage->GetPixel(index);
	- }
	- typename CoefficientImageType::IndexType index2;
	- index2.SetElement(0,a);
	- index2.SetElement(1,b);
	- index2.SetElement(2,c);
	- m_CoefficientImage->SetPixel(index2, pix);
	- }
	-}
	-
	-}
	-
	-#endif // __itkShCoefficientImageImporter_cpp
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkShCoefficientImageImporter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkShCoefficientImageImporter.h
	deleted file mode 100644
	index 1556a00436..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkShCoefficientImageImporter.h
	+++ /dev/null
	@@ -1,74 +0,0 @@
	-/*=========================================================================
	-
	- Program: Insight Segmentation & Registration Toolkit
	- Module: $RCSfile: itkDiffusionTensor3DReconstructionImageFilter.h,v $
	- Language: C++
	- Date: $Date: 2006-03-27 17:01:06 $
	- Version: $Revision: 1.12 $
	-
	- Copyright (c) Insight Software Consortium. All rights reserved.
	- See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
	-
	- This software is distributed WITHOUT ANY WARRANTY; without even
	- the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
	- PURPOSE. See the above copyright notices for more information.
	-
	-=========================================================================*/
	-#ifndef __itkShCoefficientImageImporter_h_
	-#define __itkShCoefficientImageImporter_h_
	-
	-#include <itkOrientationDistributionFunction.h>
	-
	-namespace itk{
	-/** \class ShCoefficientImageImporter
	- Converts converts 4D SH coefficient images (MRtrix) to 3D vector images containing the SH coefficients
	-*/
	-
	-template< class PixelType, int ShOrder >
	-class ShCoefficientImageImporter : public ProcessObject
	-{
	-
	-public:
	-
	- typedef ShCoefficientImageImporter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ProcessObject Superclass;
	- typedef itk::Image< float, 4 > InputImageType;
	- typedef Image< Vector< PixelType, (ShOrder*ShOrder + ShOrder + 2)/2 + ShOrder >, 3 > CoefficientImageType;
	- typedef Image< Vector< PixelType, ODF_SAMPLING_SIZE >, 3 > OdfImageType;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(ShCoefficientImageImporter, ProcessObject)
	-
	- // input
	- itkSetMacro( InputImage, InputImageType::Pointer) ///< sh coefficient image in FSL file format
	-
	- // output
	- itkGetMacro( CoefficientImage, typename CoefficientImageType::Pointer) ///< mitk style image containing the SH coefficients
	-
	- void GenerateData() override;
	-
	-protected:
	- ShCoefficientImageImporter();
	- ~ShCoefficientImageImporter() override{}
	-
	- InputImageType::Pointer m_InputImage;
	- typename CoefficientImageType::Pointer m_CoefficientImage; ///< mitk style image containing the SH coefficients
	-
	-private:
	-
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkShCoefficientImageImporter.cpp"
	-#endif
	-
	-#endif //__itkShCoefficientImageImporter_h_
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkShToOdfImageFilter.cpp b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkShToOdfImageFilter.cpp
	deleted file mode 100644
	index 1243cd100e..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkShToOdfImageFilter.cpp
	+++ /dev/null
	@@ -1,80 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef __itkShToOdfImageFilter_cpp
	-#define __itkShToOdfImageFilter_cpp
	-
	-#include <time.h>
	-#include <stdio.h>
	-#include <stdlib.h>
	-
	-#include "itkShToOdfImageFilter.h"
	-#include <itkImageRegionIterator.h>
	-#include <mitkDiffusionFunctionCollection.h>
	-
	-namespace itk {
	-
	-template< class PixelType, int ShOrder >
	-ShToOdfImageFilter< PixelType, ShOrder >::ShToOdfImageFilter()
	- : m_Toolkit(Toolkit::MRTRIX)
	-{
	-
	-}
	-
	-template< class PixelType, int ShOrder >
	-void ShToOdfImageFilter< PixelType, ShOrder >::BeforeThreadedGenerateData()
	-{
	- CalcShBasis();
	-}
	-
	-template< class PixelType, int ShOrder >
	-void ShToOdfImageFilter< PixelType, ShOrder >::ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, ThreadIdType)
	-{
	- typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetPrimaryOutput());
	-
	- typename InputImageType::Pointer inputImage = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) );
	-
	- typedef ImageRegionConstIterator< InputImageType > InputIteratorType;
	- InputIteratorType it(inputImage, outputRegionForThread);
	-
	- typedef ImageRegionIterator< OutputImageType > OutputIteratorType;
	- OutputIteratorType oit(outputImage, outputRegionForThread);
	-
	- while(!it.IsAtEnd())
	- {
	- auto pix = it.Get();
	- vnl_vector<PixelType> coeffs = pix.GetVnlVector();
	- OutputPixelType odf = (m_ShBasis * coeffs).data_block();
	- oit.Set(odf);
	-
	- ++it;
	- ++oit;
	- }
	-}
	-
	-// generate spherical harmonic values of the desired order for each input direction
	-template< class PixelType, int ShOrder >
	-void ShToOdfImageFilter< PixelType, ShOrder >::CalcShBasis()
	-{
	- vnl_matrix_fixed<double, 3, ODF_SAMPLING_SIZE>* U = itk::PointShell<ODF_SAMPLING_SIZE, vnl_matrix_fixed<double, 3, ODF_SAMPLING_SIZE> >::DistributePointShell();
	- if (m_Toolkit==Toolkit::MRTRIX)
	- m_ShBasis = mitk::sh::CalcShBasisForDirections(ShOrder, U->as_matrix());
	- else
	- m_ShBasis = mitk::sh::CalcShBasisForDirections(ShOrder, U->as_matrix(), false);
	-}
	-
	-}
	-
	-#endif // __itkShToOdfImageFilter_cpp
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkShToOdfImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkShToOdfImageFilter.h
	deleted file mode 100644
	index dea8d8a8e5..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkShToOdfImageFilter.h
	+++ /dev/null
	@@ -1,87 +0,0 @@
	-/*=========================================================================
	-
	- Program: Insight Segmentation & Registration Toolkit
	- Module: $RCSfile: itkDiffusionTensor3DReconstructionImageFilter.h,v $
	- Language: C++
	- Date: $Date: 2006-03-27 17:01:06 $
	- Version: $Revision: 1.12 $
	-
	- Copyright (c) Insight Software Consortium. All rights reserved.
	- See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
	-
	- This software is distributed WITHOUT ANY WARRANTY; without even
	- the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
	- PURPOSE. See the above copyright notices for more information.
	-
	-=========================================================================*/
	-#ifndef __itkShToOdfImageFilter_h_
	-#define __itkShToOdfImageFilter_h_
	-
	-#include <itkOrientationDistributionFunction.h>
	-#include <itkImageToImageFilter.h>
	-
	-namespace itk{
	-/** \class ShToOdfImageFilter
	-
	-*/
	-
	-template< class PixelType, int ShOrder >
	-class ShToOdfImageFilter : public
	- ImageToImageFilter< itk::Image< itk::Vector< PixelType, (ShOrder*ShOrder + ShOrder + 2)/2 + ShOrder >, 3 >, itk::Image< itk::Vector<PixelType,ODF_SAMPLING_SIZE>,3> >
	-{
	-
	-public:
	-
	- enum Toolkit { ///< SH coefficient convention (depends on toolkit)
	- FSL,
	- MRTRIX
	- };
	-
	- typedef itk::Vector< PixelType, (ShOrder*ShOrder + ShOrder + 2)/2 + ShOrder > InputPixelType;
	- typedef itk::Image<InputPixelType,3> InputImageType;
	- typedef typename InputImageType::RegionType InputImageRegionType;
	-
	- typedef itk::Vector<PixelType,ODF_SAMPLING_SIZE> OutputPixelType;
	- typedef itk::Image<OutputPixelType,3> OutputImageType;
	- typedef typename OutputImageType::RegionType OutputImageRegionType;
	-
	- typedef ShToOdfImageFilter Self;
	- typedef itk::ImageToImageFilter<InputImageType, OutputImageType> Superclass;
	-
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(ShToOdfImageFilter, ImageToImageFilter)
	-
	- itkSetMacro( Toolkit, Toolkit) ///< define SH coefficient convention (depends on toolkit)
	- itkGetMacro( Toolkit, Toolkit) ///< SH coefficient convention (depends on toolkit)
	-
	- void BeforeThreadedGenerateData();
	- void ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, ThreadIdType);
	-
	-protected:
	- ShToOdfImageFilter();
	- ~ShToOdfImageFilter(){}
	-
	- void CalcShBasis();
	-
	- vnl_matrix<float> m_ShBasis;
	- Toolkit m_Toolkit;
	-
	-private:
	-
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkShToOdfImageFilter.cpp"
	-#endif
	-
	-#endif //__itkShToOdfImageFilter_h_
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkShToRgbImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkShToRgbImageFilter.h
	deleted file mode 100644
	index 771a1127d9..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkShToRgbImageFilter.h
	+++ /dev/null
	@@ -1,154 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkShToRgbImageFilter_h
	-#define __itkShToRgbImageFilter_h
	-
	-#include "itkUnaryFunctorImageFilter.h"
	-#include "itkOrientationDistributionFunction.h"
	-#include "itkRGBAPixel.h"
	-#include "itkImageRegionConstIterator.h"
	-#include "itkImageRegionIterator.h"
	-#include <mitkDiffusionFunctionCollection.h>
	-
	-namespace itk
	-{
	-
	- #define __IMG_DAT_ITEM__CEIL_ZERO_ONE__(val) (val) = \
	- ( (val) < 0 ) ? ( 0 ) : ( ( (val)>1 ) ? ( 1 ) : ( (val) ) );
	-
	-
	-/** \class ShToRgbImageFilter
	-*
	-*/
	-template <typename TInputImage, int ShOrder,
	-typename TOutputImage=itk::Image<itk::RGBAPixel<unsigned char>,3> >
	- class ShToRgbImageFilter :
	- public ImageToImageFilter<TInputImage,TOutputImage>
	- {
	- public:
	- /** Standard class typedefs. */
	- typedef ShToRgbImageFilter Self;
	- typedef ImageToImageFilter<TInputImage,TOutputImage>
	- Superclass;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	-
	- typedef typename Superclass::InputImageType InputImageType;
	- typedef typename Superclass::OutputImageType OutputImageType;
	- typedef typename OutputImageType::PixelType OutputPixelType;
	- typedef typename TInputImage::PixelType InputPixelType;
	- typedef typename InputPixelType::ValueType InputValueType;
	-
	- /** Run-time type information (and related methods). */
	- itkTypeMacro( ShToRgbImageFilter, ImageToImageFilter )
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Print internal ivars */
	- void PrintSelf(std::ostream& os, Indent indent) const override
	- { this->Superclass::PrintSelf( os, indent ); }
	-
	-#ifdef ITK_USE_CONCEPT_CHECKING
	- /** Begin concept checking */
	- itkConceptMacro(InputHasNumericTraitsCheck,
	- (Concept::HasNumericTraits<InputValueType>));
	- /** End concept checking */
	-#endif
	-
	-protected:
	- ShToRgbImageFilter(){}
	- ~ShToRgbImageFilter() override{}
	-
	- void ThreadedGenerateData( const typename OutputImageType::RegionType &outputRegionForThread, ThreadIdType) override
	- {
	- typename InputImageType::Pointer coeff_image = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) );
	- typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetPrimaryOutput());
	-
	- outputImage->SetSpacing( coeff_image->GetSpacing() ); // Set the image spacing
	- outputImage->SetOrigin( coeff_image->GetOrigin() ); // Set the image origin
	- outputImage->SetDirection( coeff_image->GetDirection() ); // Set the image direction
	- outputImage->SetRegions( coeff_image->GetLargestPossibleRegion());
	- outputImage->Allocate();
	-
	- typedef ImageRegionConstIterator< InputImageType > OdfImageIteratorType;
	- OdfImageIteratorType it(coeff_image, outputRegionForThread);
	-
	- typedef ImageRegionIterator< OutputImageType > OutputImageIteratorType;
	- OutputImageIteratorType oit(outputImage, outputRegionForThread);
	-
	- it.GoToBegin();
	- oit.GoToBegin();
	-
	- typedef itk::OrientationDistributionFunction<float,ODF_SAMPLING_SIZE> OdfType;
	- vnl_matrix<float> sh2Basis = mitk::sh::CalcShBasisForDirections(ShOrder, itk::PointShell<ODF_SAMPLING_SIZE, vnl_matrix_fixed<double, 3, ODF_SAMPLING_SIZE> >::DistributePointShell()->as_matrix());
	-
	- while(!it.IsAtEnd() && !oit.IsAtEnd())
	- {
	- InputPixelType x = it.Get();
	-
	- Vector< float, ODF_SAMPLING_SIZE > odf_vals;
	- vnl_vector< float > coeffs(x.GetNumberOfComponents());
	- for(unsigned int i=0; i<x.GetNumberOfComponents(); i++)
	- coeffs[i] = (float)x[i];
	- odf_vals = ( sh2Basis * coeffs ).data_block();
	-
	- OdfType odf;
	- for(int i=0; i<ODF_SAMPLING_SIZE; i++)
	- odf[i] = odf_vals[i];
	-
	- vnl_vector_fixed<double,3> dir;
	- int pd = odf.GetPrincipalDiffusionDirectionIndex();
	- if (pd==-1)
	- dir.fill(0);
	- else
	- dir = OdfType::GetDirection(pd);
	-
	- const float fa = odf.GetGeneralizedFractionalAnisotropy();
	- float r = fabs(dir[0]) * fa;
	- float g = fabs(dir[1]) * fa;
	- float b = fabs(dir[2]) * fa;
	- float a = fa;
	-
	- __IMG_DAT_ITEM__CEIL_ZERO_ONE__(r);
	- __IMG_DAT_ITEM__CEIL_ZERO_ONE__(g);
	- __IMG_DAT_ITEM__CEIL_ZERO_ONE__(b);
	- __IMG_DAT_ITEM__CEIL_ZERO_ONE__(a);
	-
	- OutputPixelType out;
	- out.SetRed( r * 255.0f);
	- out.SetGreen( g * 255.0f);
	- out.SetBlue( b * 255.0f);
	- out.SetAlpha( a * 255.0f);
	-
	- oit.Set(out);
	-
	- ++it;
	- ++oit;
	- }
	-
	- }
	-
	-private:
	- ShToRgbImageFilter(const Self&); //purposely not implemented
	- void operator=(const Self&); //purposely not implemented
	-};
	-
	-} // end namespace itk
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkSplitDWImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkSplitDWImageFilter.h
	deleted file mode 100644
	index 66ad3f8f24..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkSplitDWImageFilter.h
	+++ /dev/null
	@@ -1,153 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef ITKSPLITDWIMAGEFILTER_H
	-#define ITKSPLITDWIMAGEFILTER_H
	-
	-#include "itkImageToImageFilter.h"
	-#include <itkVectorImage.h>
	-
	-namespace itk
	-{
	-
	-/** \class SplitDWImageFilter
	- *
	- * \brief Splits a DW-Image passed in as input into a 3D-t image where each volume coresponds to a
	- * gradient image ( or the unweighted b0 )
	- *
	- * Several applications require to get the gradient images as a separate volume, f.e. the registration for
	- * head-motion correction. Also a reduction of the DW Image is possible when combined with its counterpart filter,
	- * the \sa mitkImageToDiffusionImageSource, which can reinterpret a 3d+t (scalar) image into a diffusion weighted image.
	- */
	-
	-template< class TInputImagePixelType,
	- class TOutputImagePixelType >
	-class SplitDWImageFilter :
	- public ImageToImageFilter< VectorImage<TInputImagePixelType, 3>,
	- Image< TOutputImagePixelType, 4 > >
	-{
	-public:
	-
	- typedef SplitDWImageFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	-
	- typedef TInputImagePixelType InputPixelType;
	- typedef TOutputImagePixelType OutputPixelType;
	-
	- typedef ImageToImageFilter< VectorImage<TInputImagePixelType, 3>,
	- Image< TOutputImagePixelType, 4 > > Superclass;
	-
	- /** typedefs from superclass */
	- typedef typename Superclass::InputImageType InputImageType;
	- //typedef typename Superclass::OutputImageType OutputImageType;
	- typedef Image< TOutputImagePixelType, 4 > OutputImageType;
	- typedef typename OutputImageType::RegionType OutputImageRegionType;
	-
	- typedef std::vector< unsigned int > IndexListType;
	- typedef std::map< unsigned int, IndexListType> BValueMapType;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(SplitDWImageFilter, ImageToImageFilter);
	-
	- /**
	- * @brief Set the indices of the images to be extracted.
	- *
	- *
	- */
	- void SetExtractIndices( IndexListType list)
	- {
	- m_IndexList = list;
	- }
	-
	- /**
	- * @brief Extract all images
	- *
	- * The same as setting SetExtractIndices( ) with [0,1,2,...,N]
	- */
	- void SetExtractAll()
	- {
	- m_ExtractAllImages = true;
	- }
	-
	- /**
	- * @brief Selects only the weighted images with b-value above the given b_threshold to be extracted
	- *
	- * Setting b_threshold to 0 will do the same as \sa SetExtractAll. Please note that some images have no true
	- * unweighted images as the minimal b-value is something like 5 so for extracting all.
	- *
	- * @note It will reorder the images!
	- *
	- * @param b_threshold the minimal b-value to be extracted
	- * @param map the map with b-values to the corresponding image
	- *
	- * @sa GetIndexList
	- */
	- void SetExtractAllAboveThreshold( double b_threshold, BValueMapType map);
	-
	- /**
	- * @brief SetExtractSingleShell
	- * @param b_value b-value of the shell to be extracted
	- * @param tol the tolerance of the shell choice, i.e. all shells within [ b_value - tol, b_value + tol ] will be extracted
	- */
	- void SetExtractSingleShell( double b_value, BValueMapType map, double tol );
	-
	- /**
	- * @brief Returns the index list used for extraction
	- *
	- * The list is necessary for further processing, especially when a b-value threshold is used ( like in \sa SetExtractAllAboveThreshold )
	- *
	- * @return The index list used during the extraction
	- */
	- const IndexListType GetIndexList() const
	- {
	- return m_IndexList;
	- }
	-
	-protected:
	-
	- SplitDWImageFilter();
	- virtual ~SplitDWImageFilter(){};
	-
	- void GenerateData();
	-
	- /** The dimension of the output does not match the dimension of the input
	- hence we need to re-implement the CopyInformation method to avoid
	- executing the default implementation which tries to copy the input information to the
	- output
	- */
	- virtual void CopyInformation( const DataObject *data);
	-
	- /** Override of the ProcessObject::GenerateOutputInformation() because of different
	- dimensionality of the input and the output
	- */
	- virtual void GenerateOutputInformation();
	-
	- IndexListType m_IndexList;
	- bool m_ExtractAllImages;
	-};
	-
	-} //end namespace itk
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkSplitDWImageFilter.txx"
	-#endif
	-
	-#endif // ITKSPLITDWIMAGEFILTER_H
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkSplitDWImageFilter.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkSplitDWImageFilter.txx
	deleted file mode 100644
	index 338f2c5e4e..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkSplitDWImageFilter.txx
	+++ /dev/null
	@@ -1,212 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef __itkSplitDWImageFilter_txx
	-#define __itkSplitDWImageFilter_txx
	-
	-#include "itkSplitDWImageFilter.h"
	-
	-#include <itkImageRegionConstIterator.h>
	-#include <itkImageRegionIterator.h>
	-
	-template< class TInputImagePixelType,
	- class TOutputImagePixelType>
	-itk::SplitDWImageFilter< TInputImagePixelType, TOutputImagePixelType >
	-::SplitDWImageFilter()
	- : m_IndexList(0),
	- m_ExtractAllImages(true)
	-{
	- this->SetNumberOfRequiredInputs(1);
	-}
	-
	-template< class TInputImagePixelType,
	- class TOutputImagePixelType>
	-void itk::SplitDWImageFilter< TInputImagePixelType, TOutputImagePixelType >
	-::CopyInformation( const DataObject* /data/)
	-{
	-
	-}
	-
	-template< class TInputImagePixelType,
	- class TOutputImagePixelType>
	-void itk::SplitDWImageFilter<
	-TInputImagePixelType, TOutputImagePixelType >::GenerateOutputInformation()
	-{
	-
	-}
	-
	-template< class TInputImagePixelType,
	- class TOutputImagePixelType>
	-void itk::SplitDWImageFilter< TInputImagePixelType, TOutputImagePixelType >
	-::SetExtractAllAboveThreshold(double b_threshold, BValueMapType map)
	-{
	- m_ExtractAllImages = false;
	- m_IndexList.clear();
	-
	- // create the index list following the given threshold
	- // iterate over the b-value map
	- BValueMapType::const_iterator bvalueIt = map.begin();
	- while( bvalueIt != map.end() )
	- {
	- // check threshold
	- if (bvalueIt->first > b_threshold)
	- {
	- // the map contains an index container, this needs to be inserted into the
	- // index list
	- IndexListType::const_iterator listIt = bvalueIt->second.begin();
	- while( listIt != bvalueIt->second.end() )
	- {
	- m_IndexList.push_back( *listIt );
	- ++listIt;
	- }
	- }
	-
	- ++bvalueIt;
	- }
	-}
	-
	-template< class TInputImagePixelType,
	- class TOutputImagePixelType>
	-void itk::SplitDWImageFilter< TInputImagePixelType, TOutputImagePixelType >
	-::SetExtractSingleShell(double b_value, BValueMapType map, double tol)
	-{
	- m_ExtractAllImages = false;
	- m_IndexList.clear();
	-
	- // create index list
	- BValueMapType::const_iterator bvalueIt = map.begin();
	- while( bvalueIt != map.end() )
	- {
	- IndexListType::const_iterator listIt = bvalueIt->second.begin();
	- if( std::fabs( bvalueIt->first - b_value) < tol)
	- {
	- m_IndexList.insert( m_IndexList.begin(), bvalueIt->second.begin(), bvalueIt->second.end() );
	- ++listIt;
	- }
	-
	- ++bvalueIt;
	- }
	-}
	-
	-template< class TInputImagePixelType,
	- class TOutputImagePixelType>
	-void itk::SplitDWImageFilter<
	-TInputImagePixelType, TOutputImagePixelType >::GenerateData()
	-{
	-
	- if( m_IndexList.empty() && !m_ExtractAllImages )
	- {
	- itkExceptionMacro(<<"The index list is empty and the option to extract all images is disabled. ");
	- }
	-
	- // construct the index list (for each component)
	- if( m_ExtractAllImages )
	- {
	- m_IndexList.clear();
	-
	- for( unsigned int i=0; i< this->GetInput()->GetNumberOfComponentsPerPixel(); i++)
	- m_IndexList.push_back(i);
	- }
	-
	- // declare the output image
	- // this will have the b0 images stored as timesteps
	- typename OutputImageType::Pointer outputImage = this->GetOutput();
	- //OutputImageType::New();
	-
	- // allocate image with
	- // - dimension: [DimX, DimY, DimZ, size(IndexList) ]
	- // - spacing: old one, 1.0 time
	-
	- typename OutputImageType::SpacingType spacing;
	- spacing.Fill(1);
	-
	- typename OutputImageType::PointType origin;
	- origin.Fill(0);
	-
	- OutputImageRegionType outputRegion;
	-
	- // the spacing and origin corresponds to the respective values in the input image (3D)
	- // the same for the region
	- for (unsigned int i=0; i< 3; i++)
	- {
	- spacing[i] = (this->GetInput()->GetSpacing())[i];
	- origin[i] = (this->GetInput()->GetOrigin())[i];
	- outputRegion.SetSize(i, this->GetInput()->GetLargestPossibleRegion().GetSize()[i]);
	- outputRegion.SetIndex(i, this->GetInput()->GetLargestPossibleRegion().GetIndex()[i]);
	- }
	-
	- // number of timesteps = number of b0 images
	- outputRegion.SetSize(3, m_IndexList.size());
	- outputRegion.SetIndex( 3, 0 );
	-
	- // output image direction (4x4)
	- typename OutputImageType::DirectionType outputDirection;
	- //initialize to identity
	- outputDirection.SetIdentity();
	- // get the input image direction ( 3x3 matrix )
	- typename InputImageType::DirectionType inputDirection = this->GetInput()->GetDirection();
	-
	- for( unsigned int i=0; i< 3; i++)
	- {
	- outputDirection(0,i) = inputDirection(0,i);
	- outputDirection(1,i) = inputDirection(1,i);
	- outputDirection(2,i) = inputDirection(2,i);
	- }
	-
	- outputImage->SetSpacing( spacing );
	- outputImage->SetOrigin( origin );
	- outputImage->SetDirection( outputDirection );
	- outputImage->SetRegions( outputRegion );
	- outputImage->Allocate();
	-
	- // input iterator
	- itk::ImageRegionConstIterator<InputImageType> inputIt( this->GetInput(),
	- this->GetInput()->GetLargestPossibleRegion() );
	-
	-
	- // we want to iterate separately over each 3D volume of the output image
	- // so reset the regions last dimension
	- outputRegion.SetSize(3,1);
	- unsigned int currentTimeStep = 0;
	-
	- // for each index in the iterator list, extract the image and insert it as a new time step
	- for(IndexListType::const_iterator indexIt = m_IndexList.begin();
	- indexIt != m_IndexList.end();
	- indexIt++)
	- {
	- // set the time step
	- outputRegion.SetIndex(3, currentTimeStep);
	- itk::ImageRegionIterator< OutputImageType> outputIt( outputImage.GetPointer(), outputRegion );
	-
	- // iterate over the current b0 image and store it to corresponding place
	- outputIt.GoToBegin();
	- inputIt.GoToBegin();
	- while( !outputIt.IsAtEnd() && !inputIt.IsAtEnd() )
	- {
	- // the input vector
	- typename InputImageType::PixelType vec = inputIt.Get();
	-
	- outputIt.Set( vec[*indexIt]);
	- ++outputIt;
	- ++inputIt;
	- }
	-
	- // increase time step
	- currentTimeStep++;
	- }
	-}
	-
	-
	-#endif // __itkSplitDWImageFilter_txx
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkSplitVectorImageFilter.cpp b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkSplitVectorImageFilter.cpp
	deleted file mode 100644
	index cad351efe0..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkSplitVectorImageFilter.cpp
	+++ /dev/null
	@@ -1,79 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef __itkSplitVectorImageFilter_cpp
	-#define __itkSplitVectorImageFilter_cpp
	-
	-#include "itkSplitVectorImageFilter.h"
	-#include <itkImageRegionConstIterator.h>
	-#include <itkImageRegionConstIteratorWithIndex.h>
	-#include <itkImageRegionIterator.h>
	-#include <vnl/vnl_vector.h>
	-#include <itkOrientationDistributionFunction.h>
	-#include <itkContinuousIndex.h>
	-
	-#include <vtkSmartPointer.h>
	-#include <vtkPolyData.h>
	-#include <vtkCellArray.h>
	-#include <vtkPoints.h>
	-#include <vtkPolyLine.h>
	-
	-#include <boost/math/special_functions.hpp>
	-#include <boost/progress.hpp>
	-
	-
	-using namespace boost::math;
	-
	-namespace itk {
	-
	-template< class PixelType >
	-SplitVectorImageFilter< PixelType>::SplitVectorImageFilter()
	-{
	-
	-}
	-
	-
	-template< class PixelType >
	-void SplitVectorImageFilter< PixelType>
	-::GenerateData()
	-{
	- m_OutputImages.clear();
	- for (unsigned int i=0; i<m_InputImage->GetVectorLength(); ++i)
	- {
	- typename OutputImageType::Pointer m_OutputImage = OutputImageType::New();
	- m_OutputImage->SetSpacing( m_InputImage->GetSpacing() );
	- m_OutputImage->SetOrigin( m_InputImage->GetOrigin() );
	- m_OutputImage->SetDirection( m_InputImage->GetDirection() );
	- m_OutputImage->SetRegions( m_InputImage->GetLargestPossibleRegion() );
	- m_OutputImage->Allocate();
	- m_OutputImage->FillBuffer(0);
	- m_OutputImages.push_back(m_OutputImage);
	- }
	-
	- ImageRegionIterator< InputImageType > iit(m_InputImage, m_InputImage->GetLargestPossibleRegion() );
	-
	- while( !iit.IsAtEnd() )
	- {
	- auto idx = iit.GetIndex();
	- typename InputImageType::PixelType pix = iit.Get();
	- for (unsigned int i=0; i<pix.GetSize(); ++i)
	- m_OutputImages.at(i)->SetPixel(idx, pix[i]);
	- ++iit;
	- }
	-}
	-
	-}
	-
	-#endif // __itkSplitVectorImageFilter_cpp
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkSplitVectorImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkSplitVectorImageFilter.h
	deleted file mode 100644
	index 21599950bb..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkSplitVectorImageFilter.h
	+++ /dev/null
	@@ -1,73 +0,0 @@
	-/*=========================================================================
	-
	- Program: Insight Segmentation & Registration Toolkit
	- Module: $RCSfile: itkDiffusionTensor3DReconstructionImageFilter.h,v $
	- Language: C++
	- Date: $Date: 2006-03-27 17:01:06 $
	- Version: $Revision: 1.12 $
	-
	- Copyright (c) Insight Software Consortium. All rights reserved.
	- See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
	-
	- This software is distributed WITHOUT ANY WARRANTY; without even
	- the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
	- PURPOSE. See the above copyright notices for more information.
	-
	-=========================================================================*/
	-#ifndef __itkSplitVectorImageFilter_h_
	-#define __itkSplitVectorImageFilter_h_
	-
	-#include "itkImageToImageFilter.h"
	-#include <itkImage.h>
	-#include <itkVectorImage.h>
	-
	-namespace itk{
	-
	-/**
	-* \brief Flip peaks along specified axes
	-*/
	-
	-template< class PixelType >
	-class SplitVectorImageFilter : public ProcessObject
	-{
	-
	-public:
	-
	- typedef SplitVectorImageFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ProcessObject Superclass;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(SplitVectorImageFilter, ProcessObject)
	-
	- typedef VectorImage<PixelType, 3> InputImageType;
	- typedef Image<PixelType, 3> OutputImageType;
	- typedef typename OutputImageType::RegionType OutputImageRegionType;
	-
	- itkSetMacro(InputImage, typename InputImageType::Pointer)
	- std::vector< typename OutputImageType::Pointer > GetOutputImages(){ return m_OutputImages; }
	- void GenerateData();
	-
	-protected:
	- SplitVectorImageFilter();
	- ~SplitVectorImageFilter(){}
	-
	- typename InputImageType::Pointer m_InputImage;
	- std::vector< typename OutputImageType::Pointer > m_OutputImages;
	-
	-private:
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkSplitVectorImageFilter.cpp"
	-#endif
	-
	-#endif //__itkSplitVectorImageFilter_h_
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorDerivedMeasurementsFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorDerivedMeasurementsFilter.h
	deleted file mode 100644
	index c08a604dae..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorDerivedMeasurementsFilter.h
	+++ /dev/null
	@@ -1,93 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-/*===================================================================
	-
	-This file is based heavily on a corresponding ITK filter.
	-
	-===================================================================*/
	-#ifndef __itkTensorDerivedMeasurementsFilter_h_
	-#define __itkTensorDerivedMeasurementsFilter_h_
	-
	-#include "itkDiffusionTensor3D.h"
	-#include "itkImageToImageFilter.h"
	-
	-
	-
	-namespace itk{
	-/** \class TensorDerivedMeasurementsFilter
	- */
	-
	-template <class TPixel>
	-class TensorDerivedMeasurementsFilter :
	- public ImageToImageFilter< itk::Image< itk::DiffusionTensor3D<TPixel>, 3 >,
	- itk::Image< TPixel, 3 > >
	-{
	-
	-public:
	-
	- enum Measure
	- {
	- FA,// Fractional anisotropy
	- RA,// Relative anisotropy
	- AD,// Axial diffusivity
	- RD,// Radial diffusivity
	- CA, // Clustering anisotropy 1-(λ2+λ3)/(2*λ1)
	- L2,
	- L3,
	- MD // mean diffusivity
	- };
	-
	- typedef itk::DiffusionTensor3D<TPixel> TensorType;
	- typedef itk::Image< TensorType, 3 > TensorImageType;
	- typedef itk::Image< TPixel, 3 > OutputImageType;
	-
	- typedef TensorDerivedMeasurementsFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageToImageFilter< TensorType,
	- OutputImageType >
	- SuperClass;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(TensorDerivedMeasurementsFilter, ImageToImageFilter);
	-
	- itkSetMacro(Measure, Measure);
	-
	-
	-protected:
	- TensorDerivedMeasurementsFilter();
	- ~TensorDerivedMeasurementsFilter() {};
	- //void PrintSelf(std::ostream& os, Indent indent) const;
	-
	- Measure m_Measure;
	-
	- void GenerateData() override;
	-
	-}; // end class
	-
	-} // end namespace
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkTensorDerivedMeasurementsFilter.txx"
	-#endif
	-
	-#endif //__itkTensorDerivedMeasurements_h_
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorDerivedMeasurementsFilter.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorDerivedMeasurementsFilter.txx
	deleted file mode 100644
	index ad119b1a73..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorDerivedMeasurementsFilter.txx
	+++ /dev/null
	@@ -1,145 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkTensorDerivedMeasurementsFilter_txx
	-#define __itkTensorDerivedMeasurementsFilter_txx
	-
	-
	-#include <itkImageRegionIterator.h>
	-
	-
	-namespace itk {
	-
	- template <class TPixel>
	- TensorDerivedMeasurementsFilter<TPixel>::TensorDerivedMeasurementsFilter() : m_Measure(AD)
	- {
	- }
	-
	- template <class TPixel>
	- void TensorDerivedMeasurementsFilter<TPixel>::GenerateData()
	- {
	- typename TensorImageType::Pointer tensorImage = static_cast< TensorImageType * >( this->ProcessObject::GetInput(0) );
	- typedef ImageRegionConstIterator< TensorImageType > TensorImageIteratorType;
	- typedef ImageRegionIterator< OutputImageType > OutputImageIteratorType;
	-
	-
	- typename OutputImageType::Pointer outputImage =
	- static_cast< OutputImageType * >(this->ProcessObject::GetPrimaryOutput());
	-
	- typename TensorImageType::RegionType region = tensorImage->GetLargestPossibleRegion();
	-
	-
	- outputImage->SetSpacing( tensorImage->GetSpacing() ); // Set the image spacing
	- outputImage->SetOrigin( tensorImage->GetOrigin() ); // Set the image origin
	- outputImage->SetDirection( tensorImage->GetDirection() ); // Set the image direction
	- outputImage->SetRegions( tensorImage->GetLargestPossibleRegion());
	- outputImage->Allocate();
	-
	- TensorImageIteratorType tensorIt(tensorImage, tensorImage->GetLargestPossibleRegion());
	- OutputImageIteratorType outputIt(outputImage, outputImage->GetLargestPossibleRegion());
	-
	- tensorIt.GoToBegin();
	- outputIt.GoToBegin();
	-
	- while(!tensorIt.IsAtEnd() && !outputIt.IsAtEnd()){
	-
	- TensorType tensor = tensorIt.Get();
	-
	- switch(m_Measure)
	- {
	- case FA:
	- {
	- TPixel diffusionIndex = tensor.GetFractionalAnisotropy();
	- outputIt.Set(diffusionIndex);
	- break;
	- }
	- case RA:
	- {
	- TPixel diffusionIndex = tensor.GetRelativeAnisotropy();
	- outputIt.Set(diffusionIndex);
	- break;
	- }
	- case AD:
	- {
	- // eigenvalues are sorted in ascending order by default because the
	- // itk::SymmetricEigenAnalysis defaults are not touched in the tensor implementation
	- typename TensorType::EigenValuesArrayType evs;
	- tensor.ComputeEigenValues(evs);
	- outputIt.Set(evs[2]);
	- break;
	- }
	- case RD:
	- {
	- // eigenvalues are sorted in ascending order by default because the
	- // itk::SymmetricEigenAnalysis defaults are not touched in the tensor implementation
	- typename TensorType::EigenValuesArrayType evs;
	- tensor.ComputeEigenValues(evs);
	- outputIt.Set((evs[0]+evs[1])/2.0);
	-
	- break;
	- }
	- case CA:
	- {
	- // eigenvalues are sorted in ascending order by default because the
	- // itk::SymmetricEigenAnalysis defaults are not touched in the tensor implementation
	- typename TensorType::EigenValuesArrayType evs;
	- tensor.ComputeEigenValues(evs);
	- if (evs[2] == 0)
	- {
	- outputIt.Set(0);
	- break;
	- }
	- outputIt.Set(1.0-(evs[0]+evs[1])/(2.0*evs[2]));
	- break;
	- }
	- case L2:
	- {
	- // eigenvalues are sorted in ascending order by default because the
	- // itk::SymmetricEigenAnalysis defaults are not touched in the tensor implementation
	- typename TensorType::EigenValuesArrayType evs;
	- tensor.ComputeEigenValues(evs);
	- outputIt.Set(evs[1]);
	- break;
	- }
	- case L3:
	- {
	- // eigenvalues are sorted in ascending order by default because the
	- // itk::SymmetricEigenAnalysis defaults are not touched in the tensor implementation
	- typename TensorType::EigenValuesArrayType evs;
	- tensor.ComputeEigenValues(evs);
	- outputIt.Set(evs[0]);
	- break;
	- }
	- case MD:
	- {
	- typename TensorType::EigenValuesArrayType evs;
	- tensor.ComputeEigenValues(evs);
	- outputIt.Set((evs[0]+evs[1]+evs[2])/3.0);
	- break;
	- }
	- }
	-
	- ++tensorIt;
	- ++outputIt;
	- }
	-
	-
	- }
	-
	-
	-}
	-
	-#endif // __itkTensorDerivedMeasurements_txx
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorImageToDiffusionImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorImageToDiffusionImageFilter.h
	deleted file mode 100644
	index 4906264554..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorImageToDiffusionImageFilter.h
	+++ /dev/null
	@@ -1,170 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-/*=========================================================================
	-
	-Program: Tensor ToolKit - TTK
	-Module: $URL: svn://scm.gforge.inria.fr/svn/ttk/trunk/Algorithms/itkTensorImageToDiffusionImageFilter.h $
	-Language: C++
	-Date: $Date: 2010-06-07 13:39:13 +0200 (Mo, 07 Jun 2010) $
	-Version: $Revision: 68 $
	-
	-Copyright (c) INRIA 2010. All rights reserved.
	-See LICENSE.txt for details.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without even
	-the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
	-PURPOSE. See the above copyright notices for more information.
	-
	-=========================================================================*/
	-#ifndef _itk_TensorImageToDiffusionImageFilter_h_
	-#define _itk_TensorImageToDiffusionImageFilter_h_
	-
	-#include "itkImageToImageFilter.h"
	-
	-#include <itkDiffusionTensor3D.h>
	-#include <itkVectorContainer.h>
	-
	-namespace itk
	-{
	-
	- template <class TInputScalarType, class TOutputScalarType>
	- class TensorImageToDiffusionImageFilter
	- : public ImageToImageFilter<itk::Image<itk::DiffusionTensor3D<TInputScalarType>,3>, itk::VectorImage<TOutputScalarType,3> >
	- {
	-
	- public:
	-
	- typedef TInputScalarType InputScalarType;
	- typedef itk::DiffusionTensor3D<InputScalarType> InputPixelType;
	- typedef itk::Image<InputPixelType,3> InputImageType;
	- typedef typename InputImageType::RegionType InputImageRegionType;
	-
	- typedef TOutputScalarType OutputScalarType;
	- typedef itk::VectorImage<OutputScalarType,3> OutputImageType;
	- typedef typename OutputImageType::PixelType OutputPixelType;
	- typedef typename OutputImageType::RegionType OutputImageRegionType;
	-
	- typedef OutputScalarType BaselineScalarType;
	- typedef BaselineScalarType BaselinePixelType;
	- typedef typename itk::Image<BaselinePixelType,3> BaselineImageType;
	- typedef typename BaselineImageType::RegionType BaselineImageRegionType;
	-
	- typedef itk::Image< short, 3> MaskImageType;
	- typedef MaskImageType::RegionType MaskImageRegionType;
	-
	- typedef TensorImageToDiffusionImageFilter Self;
	- typedef ImageToImageFilter<InputImageType, OutputImageType> Superclass;
	-
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	-
	- itkTypeMacro (TensorImageToDiffusionImageFilter, ImageToImageFilter);
	-
	- itkStaticConstMacro (ImageDimension, unsigned int,
	- OutputImageType::ImageDimension);
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- typedef vnl_vector_fixed<double,3> GradientType;
	- typedef VectorContainer<unsigned int, GradientType> GradientListType;
	- typedef GradientListType::Pointer GradientListPointerType;
	-
	- /** Manually Set/Get a list of gradients */
	- void SetGradientList(const GradientListPointerType list)
	- {
	- m_GradientList = list;
	- this->Modified();
	- }
	- GradientListPointerType GetGradientList(void) const
	- {return m_GradientList;}
	-
	-
	- void SetBValue( const double& bval)
	- { m_BValue = bval; }
	-
	- void SetMaskImage( MaskImageType::Pointer maskimage )
	- {
	- m_MaskImage = maskimage;
	- }
	-
	-
	- /**
	- * @brief Set an external baseline image for signal generation (optional)
	- *
	- * An option to enforce a specific baseline image. If none provided (default) the filter uses
	- * the itk::TensorToL2NormImageFilter to generate the modelled baseline image.
	- */
	- void SetExternalBaselineImage( typename BaselineImageType::Pointer bimage)
	- {
	- m_BaselineImage = bimage;
	- }
	-
	- itkSetMacro(Min, OutputScalarType);
	- itkSetMacro(Max, OutputScalarType);
	-
	-
	- protected:
	- TensorImageToDiffusionImageFilter()
	- {
	- m_BValue = 1.0;
	- m_BaselineImage = 0;
	- m_Min = 0.0;
	- m_Max = 10000.0;
	- }
	-
	- virtual ~TensorImageToDiffusionImageFilter(){}
	-
	- void PrintSelf (std::ostream& os, Indent indent) const override
	- {
	- Superclass::PrintSelf (os, indent);
	- }
	-
	- virtual void BeforeThreadedGenerateData( void ) override;
	-
	- virtual void ThreadedGenerateData(const OutputImageRegionType &outputRegionForThread, ThreadIdType) override;
	-
	- //void GenerateData();
	-
	- virtual void UpdateOutputInformation() override;
	-
	-
	- private:
	-
	- TensorImageToDiffusionImageFilter (const Self&);
	- void operator=(const Self&);
	-
	- GradientListType::Pointer m_GradientList;
	- double m_BValue;
	- typename BaselineImageType::Pointer m_BaselineImage;
	-
	- OutputScalarType m_Min;
	- OutputScalarType m_Max;
	-
	- MaskImageType::Pointer m_MaskImage;
	-
	- };
	-
	-
	-} // end of namespace
	-
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkTensorImageToDiffusionImageFilter.txx"
	-#endif
	-
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorImageToDiffusionImageFilter.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorImageToDiffusionImageFilter.txx
	deleted file mode 100644
	index 67a9b355d2..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorImageToDiffusionImageFilter.txx
	+++ /dev/null
	@@ -1,244 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-/*=========================================================================
	- 2
	- 3 Program: Tensor ToolKit - TTK
	- 4 Module: $URL: svn://scm.gforge.inria.fr/svn/ttk/trunk/Algorithms/itkTensorImageToDiffusionImageFilter.txx $
	- 5 Language: C++
	- 6 Date: $Date: 2010-06-07 13:39:13 +0200 (Mo, 07 Jun 2010) $
	- 7 Version: $Revision: 68 $
	- 8
	- 9 Copyright (c) INRIA 2010. All rights reserved.
	- 10 See LICENSE.txt for details.
	- 11
	- 12 This software is distributed WITHOUT ANY WARRANTY; without even
	- 13 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
	- 14 PURPOSE. See the above copyright notices for more information.
	- 15
	- 16 =========================================================================*/
	-#ifndef _itk_TensorImageToDiffusionImageFilter_txx_
	-#define _itk_TensorImageToDiffusionImageFilter_txx_
	-#endif
	-
	-#include "itkTensorImageToDiffusionImageFilter.h"
	-#include "itkTensorToL2NormImageFilter.h"
	-#include "itkRescaleIntensityImageFilter.h"
	-#include <itkImageRegionIterator.h>
	-#include <itkImageRegionConstIterator.h>
	-
	-namespace itk
	-{
	-
	-template <class TInputScalarType, class TOutputScalarType>
	-void
	-TensorImageToDiffusionImageFilter<TInputScalarType, TOutputScalarType>
	-::BeforeThreadedGenerateData()
	-{
	-
	- if( m_GradientList->Size()==0 )
	- {
	- throw itk::ExceptionObject (__FILE__,__LINE__,"Error: gradient list is empty, cannot generate DWI.");
	- }
	-
	- if( m_BaselineImage.IsNull() )
	- {
	- // create a B0 image by taking the norm of the tensor field * scale:
	- typedef itk::TensorToL2NormImageFilter<InputImageType, itk::Image<InputScalarType,3> >
	- TensorToL2NormFilterType;
	-
	- typename TensorToL2NormFilterType::Pointer myFilter1 = TensorToL2NormFilterType::New();
	- myFilter1->SetInput (this->GetInput());
	-
	- try
	- {
	- myFilter1->Update();
	- }
	- catch (itk::ExceptionObject &e)
	- {
	- std::cerr << e;
	- return;
	- }
	-
	- typename itk::RescaleIntensityImageFilter< itk::Image<InputScalarType,3>, BaselineImageType>::Pointer rescaler=
	- itk::RescaleIntensityImageFilter<itk::Image<InputScalarType,3>, BaselineImageType>::New();
	-
	- rescaler->SetOutputMinimum ( m_Min );
	- rescaler->SetOutputMaximum ( m_Max );
	- rescaler->SetInput ( myFilter1->GetOutput() );
	- try
	- {
	- rescaler->Update();
	- }
	- catch (itk::ExceptionObject &e)
	- {
	- std::cerr << e;
	- return;
	- }
	-
	- m_BaselineImage = rescaler->GetOutput();
	- }
	-
	- typename OutputImageType::Pointer outImage = OutputImageType::New();
	- outImage->SetSpacing( this->GetInput()->GetSpacing() ); // Set the image spacing
	- outImage->SetOrigin( this->GetInput()->GetOrigin() ); // Set the image origin
	- outImage->SetDirection( this->GetInput()->GetDirection() ); // Set the image direction
	- outImage->SetLargestPossibleRegion( this->GetInput()->GetLargestPossibleRegion());
	- outImage->SetBufferedRegion( this->GetInput()->GetLargestPossibleRegion() );
	- outImage->SetRequestedRegion( this->GetInput()->GetLargestPossibleRegion() );
	- outImage->SetVectorLength(m_GradientList->Size());
	- outImage->Allocate();
	-
	- this->SetNumberOfRequiredOutputs (1);
	- this->SetNthOutput (0, outImage);
	-
	-}
	-
	-template <class TInputScalarType, class TOutputScalarType>
	-void TensorImageToDiffusionImageFilter<TInputScalarType, TOutputScalarType>
	-::ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, ThreadIdType threadId )
	-{
	- typedef ImageRegionIterator<OutputImageType> IteratorOutputType;
	- typedef ImageRegionConstIterator<InputImageType> IteratorInputType;
	- typedef ImageRegionConstIterator<BaselineImageType> IteratorBaselineType;
	-
	- unsigned long numPixels = outputRegionForThread.GetNumberOfPixels();
	- unsigned long step = numPixels/100;
	- unsigned long progress = 0;
	-
	- IteratorOutputType itOut (this->GetOutput(), outputRegionForThread);
	- IteratorInputType itIn (this->GetInput(), outputRegionForThread);
	- IteratorBaselineType itB0 (m_BaselineImage, outputRegionForThread);
	-
	- typedef ImageRegionConstIterator< MaskImageType > IteratorMaskImageType;
	- IteratorMaskImageType itMask;
	-
	- if( m_MaskImage.IsNotNull() )
	- {
	- itMask = IteratorMaskImageType( m_MaskImage, outputRegionForThread);
	- itMask.GoToBegin();
	- }
	-
	- if( threadId==0 )
	- {
	- this->UpdateProgress (0.0);
	- }
	-
	- while(!itIn.IsAtEnd())
	- {
	-
	- if( this->GetAbortGenerateData() )
	- {
	- throw itk::ProcessAborted(__FILE__,__LINE__);
	- }
	-
	- InputPixelType T = itIn.Get();
	-
	- BaselinePixelType b0 = itB0.Get();
	-
	- OutputPixelType out;
	- out.SetSize(m_GradientList->Size());
	- out.Fill(0);
	-
	- short maskvalue = 1;
	- if( m_MaskImage.IsNotNull() )
	- {
	- maskvalue = itMask.Get();
	- ++itMask;
	- }
	-
	- std::vector<unsigned int> b0_indices;
	- if( b0 > 0)
	- {
	- for( unsigned int i=0; i<m_GradientList->Size(); i++)
	- {
	- GradientType g = m_GradientList->at(i);
	-
	- // normalize vector so the following computations work
	- const double twonorm = g.two_norm();
	- if( twonorm < vnl_math::eps )
	- {
	- b0_indices.push_back(i);
	- continue;
	- }
	-
	- GradientType gn = g.normalize();
	-
	- InputPixelType S;
	- S[0] = gn[0]*gn[0];
	- S[1] = gn[1]*gn[0];
	- S[2] = gn[2]*gn[0];
	- S[3] = gn[1]*gn[1];
	- S[4] = gn[2]*gn[1];
	- S[5] = gn[2]*gn[2];
	-
	- const double res =
	- T[0]*S[0] +
	- 2 * T[1]S[1] + T[3]S[3] +
	- 2 * T[2]S[2] + 2 T[4]S[4] + T[5]S[5];
	-
	- // check for corrupted tensor
	- if (res>=0)
	- {
	- // estimate the bvalue from the base value and the norm of the gradient
	- // - because of this estimation the vector have to be normalized beforehand
	- // otherwise the modelled signal is wrong ( i.e. not scaled properly )
	- const double bval = m_BValue * twonorm * twonorm;
	- out[i] = static_cast<OutputScalarType>( maskvalue * 1.0 * b0 * exp ( -1.0 * bval * res ) );
	- }
	- }
	- }
	-
	- for(unsigned int idx = 0; idx < b0_indices.size(); idx++ )
	- {
	- out[b0_indices.at(idx)] = b0;
	- }
	-
	-
	- itOut.Set(out);
	-
	- if( threadId==0 && step>0)
	- {
	- if( (progress%step)==0 )
	- {
	- this->UpdateProgress ( double(progress)/double(numPixels) );
	- }
	- }
	-
	- ++progress;
	- ++itB0;
	- ++itIn;
	- ++itOut;
	-
	- }
	-
	- if( threadId==0 )
	- {
	- this->UpdateProgress (1.0);
	- }
	-}
	-
	-template <class TInputScalarType, class TOutputScalarType>
	-void
	-TensorImageToDiffusionImageFilter<TInputScalarType, TOutputScalarType>
	-::UpdateOutputInformation()
	-{
	- // Calls to superclass updateoutputinformation
	- Superclass::UpdateOutputInformation();
	-
	- this->GetOutput()->SetVectorLength( m_GradientList->size() );
	-}
	-
	-} // end of namespace
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorImageToOdfImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorImageToOdfImageFilter.h
	deleted file mode 100644
	index 430b5ad426..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorImageToOdfImageFilter.h
	+++ /dev/null
	@@ -1,108 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-/*=========================================================================
	-
	-Program: Tensor ToolKit - TTK
	-Module: $URL: svn://scm.gforge.inria.fr/svn/ttk/trunk/Algorithms/itkTensorImageToOdfImageFilter.h $
	-Language: C++
	-Date: $Date: 2010-06-07 13:39:13 +0200 (Mo, 07 Jun 2010) $
	-Version: $Revision: 68 $
	-
	-Copyright (c) INRIA 2010. All rights reserved.
	-See LICENSE.txt for details.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without even
	-the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
	-PURPOSE. See the above copyright notices for more information.
	-
	-=========================================================================*/
	-#ifndef _itk_TensorImageToOdfImageFilter_h_
	-#define _itk_TensorImageToOdfImageFilter_h_
	-
	-#include "itkImageToImageFilter.h"
	-#include <mitkOdfImage.h>
	-#include <itkDiffusionTensor3D.h>
	-
	-
	-namespace itk
	-{
	-
	- template <class TInputScalarType, class TOutputScalarType>
	- class TensorImageToOdfImageFilter
	- : public ImageToImageFilter<itk::Image<itk::DiffusionTensor3D<TInputScalarType>,3>, itk::Image<itk::Vector<TOutputScalarType,ODF_SAMPLING_SIZE>,3> >
	- {
	-
	- public:
	-
	- typedef TInputScalarType InputScalarType;
	- typedef itk::DiffusionTensor3D<InputScalarType> InputPixelType;
	- typedef itk::Image<InputPixelType,3> InputImageType;
	- typedef typename InputImageType::RegionType InputImageRegionType;
	-
	- typedef TOutputScalarType OutputScalarType;
	- typedef itk::Vector<OutputScalarType,ODF_SAMPLING_SIZE> OutputPixelType;
	- typedef itk::Image<OutputPixelType,3> OutputImageType;
	- typedef typename OutputImageType::RegionType OutputImageRegionType;
	-
	- typedef TensorImageToOdfImageFilter Self;
	- typedef ImageToImageFilter<InputImageType, OutputImageType> Superclass;
	-
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	-
	- itkTypeMacro (TensorImageToOdfImageFilter, ImageToImageFilter);
	-
	- itkStaticConstMacro (ImageDimension, unsigned int,
	- OutputImageType::ImageDimension);
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	-
	- protected:
	- TensorImageToOdfImageFilter(){};
	- ~TensorImageToOdfImageFilter() override{};
	-
	- void PrintSelf (std::ostream& os, Indent indent) const override
	- {
	- Superclass::PrintSelf (os, indent);
	- }
	-
	- void BeforeThreadedGenerateData( void ) override;
	-
	- void ThreadedGenerateData( const
	- OutputImageRegionType &outputRegionForThread, ThreadIdType) override;
	-
	- //void GenerateData();
	-
	- private:
	-
	- TensorImageToOdfImageFilter (const Self&);
	- void operator=(const Self&);
	-
	- typename InputImageType::Pointer m_ItkTensorImage;
	- typename OutputImageType::Pointer m_ItkOdfImage;
	- };
	-
	-} // end of namespace
	-
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkTensorImageToOdfImageFilter.txx"
	-#endif
	-
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorImageToOdfImageFilter.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorImageToOdfImageFilter.txx
	deleted file mode 100644
	index def89d52b4..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorImageToOdfImageFilter.txx
	+++ /dev/null
	@@ -1,131 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-/*=========================================================================
	-
	-Program: Tensor ToolKit - TTK
	-Module: $URL: svn://scm.gforge.inria.fr/svn/ttk/trunk/Algorithms/itkTensorImageToOdfImageFilter.txx $
	-Language: C++
	-Date: $Date: 2010-06-07 13:39:13 +0200 (Mo, 07 Jun 2010) $
	-Version: $Revision: 68 $
	-
	-Copyright (c) INRIA 2010. All rights reserved.
	-See LICENSE.txt for details.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without even
	-the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
	-PURPOSE. See the above copyright notices for more information.
	-
	-=========================================================================*/
	-#ifndef _itk_TensorImageToOdfImageFilter_txx_
	-#define _itk_TensorImageToOdfImageFilter_txx_
	-#endif
	-
	-#include "itkTensorImageToOdfImageFilter.h"
	-#include <itkImageRegionIterator.h>
	-#include <itkImageRegionConstIterator.h>
	-#include <itkOrientationDistributionFunction.h>
	-
	-namespace itk
	-{
	- template <class TInputScalarType, class TOutputScalarType>
	- void
	- TensorImageToOdfImageFilter<TInputScalarType, TOutputScalarType>
	- ::BeforeThreadedGenerateData()
	- {
	- typename OutputImageType::Pointer outImage = OutputImageType::New();
	- outImage->SetSpacing( this->GetInput()->GetSpacing() ); // Set the image spacing
	- outImage->SetOrigin( this->GetInput()->GetOrigin() ); // Set the image origin
	- outImage->SetDirection( this->GetInput()->GetDirection() ); // Set the image direction
	- outImage->SetLargestPossibleRegion( this->GetInput()->GetLargestPossibleRegion());
	- outImage->SetBufferedRegion( this->GetInput()->GetLargestPossibleRegion() );
	- outImage->SetRequestedRegion( this->GetInput()->GetLargestPossibleRegion() );
	- outImage->Allocate();
	- outImage->FillBuffer(0.0);
	-
	- this->SetNumberOfRequiredOutputs (1);
	- this->SetNthOutput (0, outImage);
	- }
	-
	- template <class TInputScalarType, class TOutputScalarType>
	- void
	- TensorImageToOdfImageFilter<TInputScalarType, TOutputScalarType>
	- ::ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, ThreadIdType threadId )
	- {
	-
	- typedef ImageRegionIterator<OutputImageType> IteratorOutputType;
	- typedef ImageRegionConstIterator<InputImageType> IteratorInputType;
	-
	- unsigned long numPixels = outputRegionForThread.GetNumberOfPixels();
	- unsigned long step = numPixels/100;
	- unsigned long progress = 0;
	-
	- IteratorOutputType itOut (this->GetOutput(), outputRegionForThread);
	- IteratorInputType itIn (this->GetInput(), outputRegionForThread);
	-
	- if( threadId==0 )
	- this->UpdateProgress (0.0);
	-
	-
	- while(!itIn.IsAtEnd())
	- {
	- if( this->GetAbortGenerateData() )
	- {
	- throw itk::ProcessAborted(__FILE__,__LINE__);
	- }
	-
	- InputPixelType T = itIn.Get();
	-
	- OutputPixelType out;
	-
	- float tensorelems[6] = {
	- (float)T[0],
	- (float)T[1],
	- (float)T[2],
	- (float)T[3],
	- (float)T[4],
	- (float)T[5],
	- };
	- itk::DiffusionTensor3D<float> tensor(tensorelems);
	-
	- itk::OrientationDistributionFunction<TOutputScalarType, ODF_SAMPLING_SIZE> odf;
	- odf.InitFromTensor(tensor);
	- odf.Normalize();
	-
	- for( unsigned int i=0; i<ODF_SAMPLING_SIZE; i++)
	- out[i] = odf.GetElement(i);
	-
	- itOut.Set(out);
	-
	- if( threadId==0 && step>0)
	- {
	- if( (progress%step)==0 )
	- {
	- this->UpdateProgress ( double(progress)/double(numPixels) );
	- }
	- }
	-
	- ++progress;
	- ++itIn;
	- ++itOut;
	- }
	-
	- if( threadId==0 )
	- {
	- this->UpdateProgress (1.0);
	- }
	- MITK_INFO << "one thread finished ODF estimation";
	- }
	-} // end of namespace
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorReconstructionWithEigenvalueCorrectionFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorReconstructionWithEigenvalueCorrectionFilter.h
	deleted file mode 100644
	index ffbe263c4f..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorReconstructionWithEigenvalueCorrectionFilter.h
	+++ /dev/null
	@@ -1,227 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef _itk_TensorReconstructionWithEigenvalueCorrectionFilter_h_
	-#define _itk_TensorReconstructionWithEigenvalueCorrectionFilter_h_
	-
	-#include "itkImageToImageFilter.h"
	-#include <itkDiffusionTensor3D.h>
	-#include <itkVectorImage.h>
	-#include <vnl/algo/vnl_symmetric_eigensystem.h>
	-
	-#include <math.h>
	-
	-
	-
	-namespace itk
	-{
	-
	-template <class TDiffusionPixelType, class TTensorPixelType>
	-class TensorReconstructionWithEigenvalueCorrectionFilter
	- : public ImageToImageFilter< itk::Image< TDiffusionPixelType, 3 >, itk::Image<itk::DiffusionTensor3D<TTensorPixelType>,3> >
	-{
	-
	-public:
	-
	-
	- typedef itk::VectorImage<short, 3> ImageType;
	-
	-
	-
	- typedef TensorReconstructionWithEigenvalueCorrectionFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	-
	-
	-
	- typedef ImageToImageFilter< Image< TDiffusionPixelType, 3>,
	- Image< DiffusionTensor3D< TTensorPixelType >, 3 > >
	- Superclass;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(TensorReconstructionWithEigenvalueCorrectionFilter, ImageToImageFilter)
	-
	-
	- typedef typename itk::Image<itk::DiffusionTensor3D<TTensorPixelType>,3> OutputType;
	- typedef TDiffusionPixelType GradientPixelType;
	- typedef DiffusionTensor3D< TTensorPixelType > TensorPixelType;
	-
	- typedef Image< TensorPixelType, 3 > TensorImageType;
	-
	- typedef typename Superclass::OutputImageRegionType
	- OutputImageRegionType;
	-
	-
	- /** An alternative typedef defining one (of the many) gradient images.
	- * It will be assumed that the vectorImage has the same dimension as the
	- * Reference image and a vector length parameter of \c n (number of
	- * gradient directions) */
	- typedef VectorImage< GradientPixelType, 3 > GradientImagesType;
	- typedef typename GradientImagesType::PixelType GradientVectorType;
	-
	-
	-
	- /** Holds each magnetic field gradient used to acquire one DWImage */
	- typedef vnl_vector_fixed< double, 3 > GradientDirectionType;
	-
	- /** Container to hold gradient directions of the 'n' DW measurements */
	- typedef VectorContainer< unsigned int,
	- GradientDirectionType > GradientDirectionContainerType;
	-
	-
	-
	- /** Another set method to add a gradient directions and its corresponding
	- * image. The image here is a VectorImage. The user is expected to pass the
	- * gradient directions in a container. The ith element of the container
	- * corresponds to the gradient direction of the ith component image the
	- * VectorImage. For the baseline image, a vector of all zeros
	- * should be set. */
	- void SetGradientImage( GradientDirectionContainerType *,
	- const GradientImagesType *image);
	-
	-
	-
	-
	-
	- itkSetMacro( BValue, TTensorPixelType)
	-
	- /** Set the b0 threshold */
	- itkSetMacro( B0Threshold, double)
	-
	- /** Get the pseudeInverse that was calculated in the process of tensor estimation */
	- itkGetMacro(PseudoInverse, vnl_matrix<double>)
	-
	- /** FIXME: added by Sebastian Wirkert due to compile error otherwise. */
	- itkGetMacro(CorrectedDiffusionVolumes, ImageType::Pointer)
	-
	- /** Outputs the design matrix that was calculated in the process of tensor estimation */
	- itkGetMacro(H, vnl_matrix<double>)
	-
	- /** Outputs the normalized b-vector */
	- itkGetMacro(BVec, vnl_vector<double>)
	-
	- /** Outputs the mask created by thresholding the B0 weighted volume*/
	- itkGetMacro(B0Mask, vnl_vector<short>)
	-
	-
	- /** Returns the dwi image volumes with smoothed voxels on positions were there were negative eigenvalues in the tensir*/
	- ImageType::Pointer GetGradientImagePointer()
	- {
	- return m_GradientImagePointer;
	- }
	-
	- /** Get the mask image*/
	- itk::Image<short, 3>::Pointer GetMask()
	- {
	- return m_MaskImage;
	- }
	-
	-
	-protected:
	-
	- TensorReconstructionWithEigenvalueCorrectionFilter();
	- ~TensorReconstructionWithEigenvalueCorrectionFilter() {}
	-
	- void GenerateData() override;
	-
	- typedef enum
	- {
	- GradientIsInASingleImage = 1,
	- GradientIsInManyImages,
	- Else
	- } GradientImageTypeEnumeration;
	-
	-private:
	-
	- double CheckNeighbours(int x, int y, int z,int f, itk::Size<3> size, itk::Image<short, 3> ::Pointer mask,typename GradientImagesType::Pointer corrected_diffusion_temp);
	-
	- /** Calculates the attenuation for a voxel*/
	- void CalculateAttenuation(vnl_vector<double> org_data, vnl_vector<double> &atten,int nof,int numberb0);
	-
	- /** Correct the diffusion data set for voxels that contain negative eigenvalues in the tensor*/
	- void CorrectDiffusionImage(int nof,int numberb0,itk::Size<3> size,typename GradientImagesType::Pointer corrected_diffusion,itk::Image<short, 3>::Pointer mask,vnl_vector< double> pixel_max,vnl_vector< double> pixel_min);
	-
	- /** Calculte a tensor iamge from a diffusion data set*/
	- void GenerateTensorImage(int nof,int numberb0,itk::Size<3> size,itk::VectorImage<short, 3>::Pointer corrected_diffusion,itk::Image<short, 3>::Pointer mask,double what_mask, typename itk::Image< itk::DiffusionTensor3D<TTensorPixelType>, 3 >::Pointer tensorImg );
	-
	- //void DeepCopyTensorImage(itk::Image< itk::DiffusionTensor3D<double>, 3 >::Pointer tensorImg, itk::Image< itk::DiffusionTensor3D<double>, 3 >::Pointer temp_tensorImg);
	-
	- //void DeepCopyDiffusionImage(itk::VectorImage<short, 3>::Pointer corrected_diffusion, itk::VectorImage<short, 3>::Pointer corrected_diffusion_temp,int nof);
	-
	-
	- void TurnMask( itk::Size<3> size, itk::Image<short, 3>::Pointer mask, double previous_mask, double set_mask);
	-
	- double CheckNegatives ( itk::Size<3> size, itk::Image<short, 3>::Pointer mask, typename itk::Image< itk::DiffusionTensor3D<TTensorPixelType>, 3 >::Pointer tensorImg );
	-
	-
	- /** Gradient image was specified in a single image or in multiple images */
	- GradientImageTypeEnumeration m_GradientImageTypeEnumeration;
	-
	- /** Number of gradient measurements */
	- unsigned int m_NumberOfGradientDirections;
	-
	- /** container to hold gradient directions */
	- GradientDirectionContainerType::Pointer m_GradientDirectionContainer;
	-
	-
	- /** b-value */
	- TTensorPixelType m_BValue;
	-
	- /** Number of baseline images */
	- unsigned int m_NumberOfBaselineImages;
	-
	- ImageType::Pointer m_CorrectedDiffusionVolumes;
	-
	- double m_B0Threshold;
	-
	-
	- /** decodes what is to be done with every single voxel */
	- itk::Image<short, 3>::Pointer m_MaskImage;
	-
	- /** Pseudoinverse calculated in the process of calculating a tensor */
	- vnl_matrix<double> m_PseudoInverse;
	-
	- /** design matrix */
	- vnl_matrix<double> m_H;
	-
	- /** normalized b-vector */
	- vnl_vector<double> m_BVec;
	-
	- /** m_B0Mask indicates whether a volume identified by an index is B0-weighted or not */
	- vnl_vector<short> m_B0Mask;
	-
	- /** volumes of the diffusion data set */
	- typename GradientImagesType::Pointer m_GradientImagePointer;
	-
	-};
	-
	-
	-
	-
	-
	-
	-} // end of namespace
	-
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkTensorReconstructionWithEigenvalueCorrectionFilter.txx"
	-#endif
	-
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorReconstructionWithEigenvalueCorrectionFilter.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorReconstructionWithEigenvalueCorrectionFilter.txx
	deleted file mode 100644
	index c358796bbf..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorReconstructionWithEigenvalueCorrectionFilter.txx
	+++ /dev/null
	@@ -1,863 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef _itk_TensorReconstructionWithEigenvalueCorrectionFilter_txx_
	-#define _itk_TensorReconstructionWithEigenvalueCorrectionFilter_txx_
	-#endif
	-#include "itkImageRegionConstIterator.h"
	-#include <math.h>
	-#include "itkImage.h"
	-#include "itkImageRegionIterator.h"
	-#include <itkImageDuplicator.h>
	-
	-namespace itk
	-{
	-
	-template <class TDiffusionPixelType, class TTensorPixelType>
	-TensorReconstructionWithEigenvalueCorrectionFilter<TDiffusionPixelType, TTensorPixelType>
	-::TensorReconstructionWithEigenvalueCorrectionFilter()
	-{
	- m_B0Threshold = 50.0;
	-}
	-
	-template <class TDiffusionPixelType, class TTensorPixelType>
	-void
	-TensorReconstructionWithEigenvalueCorrectionFilter<TDiffusionPixelType, TTensorPixelType>
	-::GenerateData ()
	-{
	- typename GradientImagesType::Pointer input_image = static_cast< GradientImagesType * >( this->ProcessObject::GetInput(0) );
	- typename itk::ImageDuplicator<GradientImagesType>::Pointer duplicator = itk::ImageDuplicator<GradientImagesType>::New();
	- duplicator->SetInputImage(input_image);
	- duplicator->Update();
	- m_GradientImagePointer = duplicator->GetOutput();
	-
	- typename GradientImagesType::SizeType size = m_GradientImagePointer->GetLargestPossibleRegion().GetSize();
	-
	- // number of volumes
	- int nof = m_GradientDirectionContainer->Size();
	-
	- // determine the number of b-zero values
	- int numberb0=0;
	- for(int i=0; i<nof; i++)
	- {
	- vnl_vector_fixed <double, 3 > vec = m_GradientDirectionContainer->ElementAt(i);
	-
	- float bval = vec.magnitude();
	- bval = bvalbvalm_BValue;
	-
	- if(bval<100)
	- numberb0++;
	- }
	-
	-
	- // Matrix to store all diffusion encoding gradients
	- vnl_matrix<double> directions(nof-numberb0,3);
	-
	- m_B0Mask.set_size(nof);
	-
	-
	- int cnt=0;
	- for(int i=0; i<nof; i++)
	- {
	- vnl_vector_fixed <double, 3 > vec = m_GradientDirectionContainer->ElementAt(i);
	-
	- float bval = vec.magnitude();
	- bval = bvalbvalm_BValue;
	-
	- if(bval<100)
	- {
	- // the diffusion encoding gradient is approximately zero, wo we are dealing with a non-diffusion weighted volume
	- m_B0Mask[i]=1;
	- }
	- else
	- {
	- // dealing with a diffusion weighted volume
	- m_B0Mask[i]=0;
	-
	- // set the diffusion encoding gradient to the directions matrix
	- directions[cnt][0] = vec[0];
	- directions[cnt][1] = vec[1];
	- directions[cnt][2] = vec[2];
	-
	- cnt++;
	- }
	- }
	-
	- // looking for maximal norm among gradients.
	- // The norm is calculated with use of spectral radius theorem- based on determination of eigenvalue.
	-
	- vnl_matrix<double> dirsTimesDirsTrans = directions*directions.transpose();
	-
	- vnl_vector< double> diagonal(nof-numberb0);
	- vnl_vector< double> b_vec(nof-numberb0);
	- vnl_vector< double> temporary(3);
	-
	-
	- for (int i=0;i<nof-numberb0;i++)
	- diagonal[i]=dirsTimesDirsTrans[i][i];
	-
	- // normalization: free-water method assumes that directions matrix norm 1 is equal to b=1000
	- directions=directions*sqrt(m_BValue/1000.0);
	-
	- //calculation of norms and storing them in vector
	-
	- dirsTimesDirsTrans = directions*directions.transpose();
	-
	- for (int i=0;i<nof-numberb0;i++)
	- b_vec[i]= dirsTimesDirsTrans[i][i];
	-
	- // Calculation of so called design matrix that is used to obtain expected signal.
	- vnl_matrix<double> H(nof-numberb0, 6);
	- vnl_matrix<double> H_org(nof-numberb0, 6);
	- vnl_vector<double> pre_tensor(9);
	-
	- //H is matrix that contains covariances for directions. It is stored twice because its original value is needed later
	- // while H is changed
	-
	- int etbt[6] = { 0, 4, 8, 1, 5, 2 };// tensor order
	-
	- for (int i = 0; i < nof-numberb0; i++)
	- {
	- for (int j = 0; j < 3; j++)
	- {
	- temporary[j] = -directions[i][j];
	- }
	- for (int j = 0; j < 3; j++)
	- {
	- for (int k = 0; k < 3; k++)
	- {
	- pre_tensor[k + 3 * j] = temporary[k] * directions[i][j];
	- }
	- }
	- for (int j = 0; j < 6; j++)
	- {
	- H[i][j] = pre_tensor[etbt[j]];
	- }
	- for (int j = 0; j < 3; j++)
	- {
	- H[i][3 + j] *= 2.0;
	- }
	- }
	-
	- H_org=H;
	-
	- // calculation of inverse matrix by means of pseudoinverse
	-
	- vnl_matrix<double> inputtopseudoinverse=H.transpose()*H;
	- vnl_symmetric_eigensystem<double> eig( inputtopseudoinverse);
	- vnl_matrix<double> pseudoInverse = eig.pinverse()*H.transpose();
	-
	-
	- typedef itk::Image<short, 3> MaskImageType;
	- MaskImageType::Pointer mask = MaskImageType::New();
	- mask->SetRegions(m_GradientImagePointer->GetLargestPossibleRegion().GetSize());
	- mask->SetSpacing(m_GradientImagePointer->GetSpacing());
	- mask->SetOrigin(m_GradientImagePointer->GetOrigin());
	- mask->SetDirection( m_GradientImagePointer->GetDirection() ); // Set the image direction
	- mask->SetLargestPossibleRegion( m_GradientImagePointer->GetLargestPossibleRegion() );
	- mask->SetBufferedRegion( m_GradientImagePointer->GetLargestPossibleRegion() );
	- mask->SetRequestedRegion( m_GradientImagePointer->GetLargestPossibleRegion() );
	- mask->Allocate();
	-
	- // Image thresholding: For every voxel mean B0 image is calculated and then voxels of mean B0 less than the
	- // treshold on the B0 image proviced by the userare excluded from the dataset with use of defined mask image.
	- // 1 in mask voxel means that B0 > assumed treshold.
	-
	- int mask_cnt=0;
	-#ifdef WIN32
	-#pragma omp parallel for
	-#else
	-#pragma omp parallel for collapse(3)
	-#endif
	- for(int x=0;x<(int)size[0];x++)
	- for(int y=0;y<(int)size[1];y++)
	- for(int z=0;z<(int)size[2];z++)
	- {
	- double mean_b=0.0;
	- itk::Index<3> ix = {{(itk::IndexValueType)x,(itk::IndexValueType)y,(itk::IndexValueType)z}};
	-
	- GradientVectorType pixel = m_GradientImagePointer->GetPixel(ix);
	- for (int i=0;i<nof;i++)
	- {
	- if(m_B0Mask[i]==1)
	- {
	- mean_b = mean_b + pixel[i];
	- }
	- }
	- mean_b=mean_b/numberb0;
	- if(mean_b > m_B0Threshold)
	- {
	-#pragma omp critical
	- {
	- mask->SetPixel(ix, 1);
	- mask_cnt++;
	- }
	- }
	- else
	- {
	-#pragma omp critical
	- mask->SetPixel(ix, 0);
	- }
	- }
	-
	-#ifdef WIN32
	-#pragma omp parallel for
	-#else
	-#pragma omp parallel for collapse(3)
	-#endif
	- for (int x=0;x<(int)size[0];x++)
	- for (int y=0;y<(int)size[1];y++)
	- for (int z=0;z<(int)size[2];z++)
	- {
	- vnl_vector<double> org_vec(nof);
	- itk::Index<3> ix = {{(itk::IndexValueType)x,(itk::IndexValueType)y,(itk::IndexValueType)z}};
	-
	- double mask_val = mask->GetPixel(ix);
	-
	- GradientVectorType pixel2 = m_GradientImagePointer->GetPixel(ix);
	-
	- for (int i=0;i<nof;i++)
	- org_vec[i]=pixel2[i];
	-
	- if(mask_val >0)
	- {
	- for( int f=0;f<nof;f++)
	- if(org_vec[f] <= 0)
	- org_vec[f] = CheckNeighbours(x,y,z,f,size,mask,m_GradientImagePointer);
	-
	- for (int i=0;i<nof;i++)
	- pixel2[i]=org_vec[i];
	-
	-#pragma omp critical
	- m_GradientImagePointer->SetPixel(ix, pixel2);
	- }
	- }
	-
	- typename TensorImageType::Pointer tensorImg;
	- tensorImg = TensorImageType::New();
	- tensorImg->SetSpacing( m_GradientImagePointer->GetSpacing() ); // Set the image spacing
	- tensorImg->SetOrigin( m_GradientImagePointer->GetOrigin() ); // Set the image origin
	- tensorImg->SetDirection( m_GradientImagePointer->GetDirection() ); // Set the image direction
	- tensorImg->SetLargestPossibleRegion( m_GradientImagePointer->GetLargestPossibleRegion() );
	- tensorImg->SetBufferedRegion( m_GradientImagePointer->GetLargestPossibleRegion() );
	- tensorImg->SetRequestedRegion( m_GradientImagePointer->GetLargestPossibleRegion() );
	- tensorImg->Allocate();
	-
	- //Declaration of vectors that contains too high or too low atenuation for each gradient. Attenuation is only calculated for
	- //non B0 images so nof-numberb0.
	-
	- vnl_vector< double> pixel_max(nof-numberb0);
	- vnl_vector< double> pixel_min(nof-numberb0);
	-
	- // to high and to low attenuation is calculated with use of highest allowed =5 and lowest allowed =0.01 diffusion coefficient
	-
	- for (int i=0;i<nof-numberb0;i++)
	- {
	- pixel_max[i]=exp(-b_vec[i]*0.01);
	- pixel_min[i]= exp(-b_vec[i]*5);
	- }
	-
	- m_PseudoInverse = pseudoInverse;
	- m_H = H_org;
	- m_BVec=b_vec;
	-
	- // in preprocessing we are dealing with 3 types of voxels: voxels excluded = 0 in mask, voxels correct =1 and voxels under correction
	- //= 2. During pre processing most of voxels should be switched from 2 to 1.
	-
	- // what mask is a variable declared to simplify tensor calculaton. Tensors are obtained only for voxels that have a mask value bigger
	- // than what_mask. Sometimes it is 1 sometimes 2.
	-
	- // initialization of required variables
	- double what_mask=1.0;
	- double set_mask=2.0;
	- double previous_mask=0;
	-
	- int old_number_negative_eigs=0;
	- int new_number_negative_eigs=0;
	-
	- bool stil_correcting = true;
	-
	- TurnMask(size,mask,previous_mask,set_mask);
	- // simply defining all possible tensors as with negative eigenvalues
	-
	- //Preprocessing is performed in multiple iterations as long as the next iteration does not increase the number of bad voxels.
	- //The final DWI should be the one that has a smaller or equal number of bad voxels as in the
	- //previous iteration. To obtain this temporary DWI image must be stored in memory.
	-
	- // ! Initial Calculation of Tensors
	- std::cout << "Initial tensor calculation" << std::endl;
	- GenerateTensorImage(nof,numberb0,size,m_GradientImagePointer,mask,what_mask,tensorImg);
	-
	- std::cout << "Check negatives" << std::endl;
	- // checking how many tensors have problems, this is working only for mask =2
	- old_number_negative_eigs = CheckNegatives (size,mask,tensorImg);
	-
	- //info for the user printed in the consol-debug information to be removed in the future
	- std::cout << "Number of negative eigenvalues: " << old_number_negative_eigs << std::endl;
	-
	- CorrectDiffusionImage(nof,numberb0,size,m_GradientImagePointer,mask,pixel_max,pixel_min);
	- while (stil_correcting == true)
	- {
	- //info for the user printed in the consol-debug information to be removed in the future
	- std::cout << "Number of negative eigenvalues: " << old_number_negative_eigs << std::endl;
	-
	- GenerateTensorImage(nof,numberb0,size,m_GradientImagePointer,mask,what_mask,tensorImg);
	-
	- new_number_negative_eigs = CheckNegatives (size,mask,tensorImg);
	-
	- if(new_number_negative_eigs<old_number_negative_eigs)
	- {
	- // if the correction does not introduce new negative eigenvalues and corrects some of negative detected n previous iteration
	- // smoothed DWI is used to substitute DWI from previous iteration
	- stil_correcting=true;
	- old_number_negative_eigs=new_number_negative_eigs;
	-
	- }
	-
	- else
	- {
	- stil_correcting=false;
	- }
	-
	- //14.10.2013
	- //CorrectDiffusionImage(nof,numberb0,size,corrected_diffusion_temp,mask,pixel_max,pixel_min);
	- CorrectDiffusionImage(nof,numberb0,size,m_GradientImagePointer,mask,pixel_max,pixel_min);
	- }
	-
	- // Changing the mask value for voxels that are still not corrcted. Original idea is to take them into analysis even though
	- // eigenvalues are still negative
	- TurnMask(size, mask,1,1);
	-
	- // Generation of final pre-processed tensor image that might be used as an input for FWE method
	-
	- // Final Tensor Reconstruction
	- std::cout << "Final tensors " << std::endl;
	- GenerateTensorImage(nof,numberb0,size,m_GradientImagePointer,mask,what_mask,tensorImg);
	-
	- m_MaskImage = mask;
	-
	-
	-
	- // Change diffusivity representation to standard convention
	- itk::ImageRegionIterator<OutputType> outputIterator(tensorImg, tensorImg->GetLargestPossibleRegion());
	- outputIterator.GoToBegin();
	- while(!outputIterator.IsAtEnd())
	- {
	- TensorPixelType tens = outputIterator.Get();
	-
	- tens/= 1000.0;
	-
	- outputIterator.Set(tens);
	- ++outputIterator;
	- }
	-
	- this->SetNthOutput(0, tensorImg);
	-}
	-
	-
	-
	-template <class TDiffusionPixelType, class TTensorPixelType>
	-void
	-TensorReconstructionWithEigenvalueCorrectionFilter<TDiffusionPixelType, TTensorPixelType>
	-::SetGradientImage( GradientDirectionContainerType *gradientDirection,
	- const GradientImagesType *gradientImage )
	-{
	-
	- if( m_GradientImageTypeEnumeration == GradientIsInManyImages )
	- {
	- itkExceptionMacro( << "Cannot call both methods:"
	- << "AddGradientImage and SetGradientImage. Please call only one of them.");
	- }
	-
	- this->m_GradientDirectionContainer = gradientDirection;
	-
	-
	- unsigned int numImages = gradientDirection->Size();
	- this->m_NumberOfBaselineImages = 0;
	-
	- this->m_NumberOfGradientDirections = numImages - this->m_NumberOfBaselineImages;
	-
	- // ensure that the gradient image we received has as many components as
	- // the number of gradient directions
	- if( gradientImage->GetVectorLength() != this->m_NumberOfBaselineImages + this->m_NumberOfGradientDirections )
	- {
	- itkExceptionMacro( << this->m_NumberOfGradientDirections << " gradients + " << this->m_NumberOfBaselineImages
	- << "baselines = " << this->m_NumberOfGradientDirections + this->m_NumberOfBaselineImages
	- << " directions specified but image has " << gradientImage->GetVectorLength()
	- << " components.");
	- }
	-
	- this->ProcessObject::SetNthInput( 0,
	- const_cast< GradientImagesType* >(gradientImage) );
	- m_GradientImageTypeEnumeration = GradientIsInASingleImage;
	-}
	-
	-template <class TDiffusionPixelType, class TTensorPixelType>
	-double
	-TensorReconstructionWithEigenvalueCorrectionFilter<TDiffusionPixelType, TTensorPixelType>
	-::CheckNeighbours(int x, int y, int z,int f, itk::Size<3> size, itk::Image<short, 3>::Pointer mask, typename GradientImagesType::Pointer corrected_diffusion_temp)
	-{
	- // method is used for finding a new value for the voxel with use of its 27 neighborhood. To perform such a smoothing correct voxels are
	- // counted an arithmetical mean is calculated and stored as a new value for the voxel. If there is no proper neigborhood voxel is turned
	- // to the value of 0.
	-
	- // Definition of neighbourhood avoiding crossing the image boundaries
	- int x_max=size[0]-1;
	- int y_max=size[1]-1;
	- int z_max=size[2]-1;
	-
	- double back_x=std::max(0,x-1);
	- double back_y=std::max(0,y-1);
	- double back_z=std::max(0,z-1);
	-
	- double forth_x=std::min((x+1),x_max);
	- double forth_y=std::min((y+1),y_max);
	- double forth_z=std::min((z+1),z_max);
	-
	-
	- double tempsum=0;
	- double temp_number=0;
	-
	- for(int i=back_x; i<=forth_x; i++)
	- {
	- for (int j=back_y; j<=forth_y; j++)
	- {
	- for (int k=back_z; k<=forth_z; k++)
	- {
	- itk::Index<3> ix = {{i,j,k}};
	-
	- GradientVectorType p = corrected_diffusion_temp->GetPixel(ix);
	-
	- if (p[f] > 0.0 )// taking only positive values and counting them
	- {
	- if(!(i==x && j==y && k== z))
	- {
	- tempsum=tempsum+p[f];
	- temp_number++;
	- }
	- }
	- }
	- }
	- }
	-
	- //getting back to the original position of the voxel
	-
	- itk::Index<3> ix = {{x,y,z}};
	- if (temp_number <= 0.0)
	- {
	- tempsum=0;
	-#pragma omp critical
	- mask->SetPixel(ix,0);
	- }
	- else
	- {
	- tempsum=tempsum/temp_number;
	- }
	-
	- return tempsum;// smoothed value of voxel
	-}
	-
	-
	-template <class TDiffusionPixelType, class TTensorPixelType>
	-void
	-TensorReconstructionWithEigenvalueCorrectionFilter<TDiffusionPixelType, TTensorPixelType>
	-::CalculateAttenuation(vnl_vector<double> org_data,vnl_vector<double> &atten,int nof, int numberb0)
	-{
	- double mean_b=0.0;
	-
	- for (int i=0;i<nof;i++)
	- if(m_B0Mask[i]>0)
	- mean_b=mean_b+org_data[i];
	-
	- mean_b=mean_b/numberb0;
	- int cnt=0;
	- for (int i=0;i<nof;i++)
	- if(m_B0Mask[i]==0)
	- {
	- //if(org_data[i]<0.001){org_data[i]=0.01;}
	- atten[cnt]=org_data[i]/mean_b;
	- cnt++;
	- }
	-}
	-
	-template <class TDiffusionPixelType, class TTensorPixelType>
	-double
	-TensorReconstructionWithEigenvalueCorrectionFilter<TDiffusionPixelType, TTensorPixelType>
	-::CheckNegatives ( itk::Size<3> size, itk::Image<short, 3>::Pointer mask, typename itk::Image< itk::DiffusionTensor3D<TTensorPixelType>, 3 >::Pointer tensorImg )
	-{
	- // The method was created to simplif the flow of negative eigenvalue correction process. The method itself just return the number
	- // of voxels (tensors) with negative eigenvalues. Then if the voxel was previously bad ( mask=2 ) but it is not bad anymore mask is
	- //changed to 1.
	-
	- // declaration of important structures and variables
	- double badvoxels=0;
	-
	-#ifdef WIN32
	-#pragma omp parallel for
	-#else
	-#pragma omp parallel for collapse(3)
	-#endif
	- for (int x=0;x<(int)size[0];x++)
	- for (int y=0;y<(int)size[1];y++)
	- for (int z=0;z<(int)size[2];z++)
	- {
	- double pixel=0;
	-
	- itk::Index<3> ix = {{(itk::IndexValueType)x,(itk::IndexValueType)y,(itk::IndexValueType)z}};
	- pixel = mask->GetPixel(ix);
	-
	- // but only if previously marked as bad one-negative eigen value
	- if(pixel > 1)
	- {
	-#pragma omp critical
	- {
	- itk::DiffusionTensor3D<double>::EigenValuesArrayType eigenvalues;
	- itk::DiffusionTensor3D<double>::EigenVectorsMatrixType eigenvectors;
	- itk::DiffusionTensor3D<double> ten = tensorImg->GetPixel(ix);
	- ten.ComputeEigenAnalysis(eigenvalues, eigenvectors);
	-
	- //comparison to 0.01 instead of 0 was proposed by O.Pasternak
	- if( eigenvalues[0]>0.01 && eigenvalues[1]>0.01 && eigenvalues[2]>0.01)
	- mask->SetPixel(ix,1);
	- else
	- badvoxels++;
	- }
	- }
	- }
	-
	- return badvoxels;
	-}
	-
	-
	-template <class TDiffusionPixelType, class TTensorPixelType>
	-void
	-TensorReconstructionWithEigenvalueCorrectionFilter<TDiffusionPixelType, TTensorPixelType>
	-::CorrectDiffusionImage(int nof, int numberb0, itk::Size<3> size, typename GradientImagesType::Pointer corrected_diffusion,itk::Image<short, 3>::Pointer mask,vnl_vector< double> pixel_max,vnl_vector< double> pixel_min)
	-{
	- // in this method the voxels that has tensor negative eigenvalues are smoothed. Smoothing is done on DWI image.For the voxel
	- //detected as bad one, B0 image is smoothed obligatory. All other gradient images are smoothed only when value of attenuation
	- //is out of declared bounds for too high or too low attenuation.
	-
	- // declaration of important variables
	-
	-#ifdef WIN32
	-#pragma omp parallel for
	-#else
	-#pragma omp parallel for collapse(3)
	-#endif
	- for (int z=0;z<(int)size[2];z++)
	- for (int x=0;x<(int)size[0];x++)
	- for (int y=0;y<(int)size[1];y++)
	- {
	- vnl_vector<double> org_data(nof);
	- vnl_vector<double> atten(nof-numberb0);
	- double cnt_atten=0;
	-
	- itk::Index<3> ix = {{(itk::IndexValueType)x, (itk::IndexValueType)y, (itk::IndexValueType)z}};
	-
	- if(mask->GetPixel(ix) > 1.0)
	- {
	- GradientVectorType pt = corrected_diffusion->GetPixel(ix);
	-
	- for (int i=0;i<nof;i++)
	- org_data[i]=pt[i];
	-
	- double mean_b=0.0;
	-
	- for (int i=0;i<nof;i++)
	- if(m_B0Mask[i]>0)
	- {
	- mean_b=mean_b+org_data[i];
	- }
	-
	- mean_b=mean_b/numberb0;
	- int cnt=0;
	- for (int i=0;i<nof;i++)
	- if(m_B0Mask[i]==0)
	- {
	- atten[cnt]=org_data[i]/mean_b;
	- cnt++;
	- }
	-
	- cnt_atten=0;
	-
	- //smoothing certain gradient images that are out of declared constraints
	- for (int f=0;f<nof;f++)
	- {
	- if(m_B0Mask[f]==0)
	- {
	- if(atten[cnt_atten]<pixel_min[cnt_atten] \|\| atten[cnt_atten]> pixel_max[cnt_atten])
	- {
	-
	- int x_max=size[0]-1;
	- int y_max=size[1]-1;
	- int z_max=size[2]-1;
	-
	- double back_x=std::max(0,(int)x-1);
	- double back_y=std::max(0,(int)y-1);
	- double back_z=std::max(0,(int)z-1);
	-
	- double forth_x=std::min(((int)x+1),x_max);
	- double forth_y=std::min(((int)y+1),y_max);
	- double forth_z=std::min(((int)z+1),z_max);
	-
	- double tempsum=0;
	- double temp_number=0;
	-
	- for(int i=back_x; i<=forth_x; i++)
	- for (int j=back_y; j<=forth_y; j++)
	- for (int k=back_z; k<=forth_z; k++)
	- {
	- itk::Index<3> ix = {{i,j,k}};
	-
	- GradientVectorType p = corrected_diffusion->GetPixel(ix);
	-
	- if(p[f] > 0.0 && !(i==x && j==y && k== z))
	- {
	- tempsum=tempsum+p[f];
	- temp_number++;
	- }
	- }
	-
	- //getting back to the original position of the voxel
	- itk::Index<3> ix = {{(itk::IndexValueType)x,(itk::IndexValueType)y,(itk::IndexValueType)z}};
	- if (temp_number <= 0.0)
	- {
	- tempsum=0;
	-#pragma omp critical
	- mask->SetPixel(ix,0);
	- }
	- else
	- tempsum=tempsum/temp_number;
	-
	- org_data[f] = tempsum;
	- }
	-
	- cnt_atten++;
	- }
	-
	- //smoothing B0
	- if(m_B0Mask[f]==1)
	- {
	- int x_max=size[0] - 1;
	- int y_max=size[1] - 1;
	- int z_max=size[2] - 1;
	-
	- double back_x=std::max(0,(int)x-1);
	- double back_y=std::max(0,(int)y-1);
	- double back_z=std::max(0,(int)z-1);
	-
	- double forth_x=std::min(((int)x+1),x_max);
	- double forth_y=std::min(((int)y+1),y_max);
	- double forth_z=std::min(((int)z+1),z_max);
	-
	- double tempsum=0;
	- double temp_number=0;
	-
	- for(int i=back_x; i<=forth_x; i++)
	- for (int j=back_y; j<=forth_y; j++)
	- for (int k=back_z; k<=forth_z; k++)
	- {
	- itk::Index<3> ix = {{i,j,k}};
	-
	- GradientVectorType p = corrected_diffusion->GetPixel(ix);
	-
	- //double test= p[f];
	-
	- if (p[f] > 0.0 )// taking only positive values and counting them
	- {
	- if(!(i==x && j==y && k== z))
	- {
	- tempsum=tempsum+p[f];
	- temp_number++;
	- }
	- }
	- }
	-
	- //getting back to the original position of the voxel
	- itk::Index<3> ix = {{(itk::IndexValueType)x,(itk::IndexValueType)y,(itk::IndexValueType)z}};
	- if (temp_number <= 0.0)
	- {
	- tempsum=0;
	-#pragma omp critical
	- mask->SetPixel(ix,0);
	- }
	- else
	- {
	- tempsum=tempsum/temp_number;
	- }
	-
	- org_data[f] = tempsum;
	- }
	- }
	-
	- for (int i=0;i<nof;i++)
	- {
	- pt[i]=org_data[i];
	- }
	-
	-#pragma omp critical
	- corrected_diffusion->SetPixel(ix, pt);
	- }
	- else
	- {
	- GradientVectorType pt = corrected_diffusion->GetPixel(ix);
	-#pragma omp critical
	- corrected_diffusion->SetPixel(ix, pt);
	- }
	- }
	-}
	-
	-template <class TDiffusionPixelType, class TTensorPixelType>
	-void
	-TensorReconstructionWithEigenvalueCorrectionFilter<TDiffusionPixelType, TTensorPixelType>
	-::GenerateTensorImage(int nof,int numberb0,itk::Size<3> size,itk::VectorImage<short, 3>::Pointer corrected_diffusion,itk::Image<short, 3>::Pointer mask,double , typename itk::Image< itk::DiffusionTensor3D<TTensorPixelType>, 3 >::Pointer tensorImg)
	-{
	- // in this method the whole tensor image is updated with a tensors for defined voxels ( defined by a value of mask);
	-
	-#ifdef WIN32
	-#pragma omp parallel for
	-#else
	-#pragma omp parallel for collapse(3)
	-#endif
	- for (int x=0;x<(int)size[0];x++)
	- for (int y=0;y<(int)size[1];y++)
	- for (int z=0;z<(int)size[2];z++)
	- {
	- itk::Index<3> ix;
	-
	- vnl_vector<double> org_data(nof);
	- vnl_vector<double> atten(nof-numberb0);
	- vnl_vector<double> tensor(6);
	- itk::DiffusionTensor3D<double> ten;
	- double mask_val=0;
	-
	- ix[0] = x; ix[1] = y; ix[2] = z;
	-
	- mask_val= mask->GetPixel(ix);
	-
	- //Tensors are calculated only for voxels above theshold for B0 image.
	- if( mask_val > 0.0 )
	- {
	-
	- // calculation of attenuation with use of gradient image and and mean B0 image
	- GradientVectorType pt = corrected_diffusion->GetPixel(ix);
	-
	- for (int i=0;i<nof;i++)
	- {
	- org_data[i]=pt[i];
	- }
	-
	- double mean_b=0.0;
	-
	- for (int i=0;i<nof;i++)
	- {
	- if(m_B0Mask[i]>0)
	- {
	- mean_b=mean_b+org_data[i];
	- }
	-
	- }
	- mean_b=mean_b/numberb0;
	- int cnt=0;
	- for (int i=0;i<nof;i++)
	- {
	- if (org_data[i]<= 0)
	-
	- {
	- org_data[i]=0.1;
	- }
	- if(m_B0Mask[i]==0)
	- {
	- atten[cnt]=org_data[i]/mean_b;
	- cnt++;
	- }
	- }
	-
	- for (int i=0;i<nof-numberb0;i++)
	- {
	-
	- atten[i]=log((double)atten[i]);
	- }
	-
	- // Calculation of tensor with use of previously calculated inverse of design matrix and attenuation
	- tensor = m_PseudoInverse*atten;
	-
	- ten(0,0) = tensor[0];
	- ten(0,1) = tensor[3];
	- ten(0,2) = tensor[5];
	- ten(1,1) = tensor[1];
	- ten(1,2) = tensor[4];
	- ten(2,2) = tensor[2];
	-
	-#pragma omp critical
	- tensorImg->SetPixel(ix, ten);
	- }
	- // for voxels with mask value 0 - tensor is simply 0 ( outside brain value)
	- else if (mask_val < 1.0)
	- {
	- ten(0,0) = 0;
	- ten(0,1) = 0;
	- ten(0,2) = 0;
	- ten(1,1) = 0;
	- ten(1,2) = 0;
	- ten(2,2) = 0;
	-
	-#pragma omp critical
	- tensorImg->SetPixel(ix, ten);
	- }
	- }
	-
	-}// end of Generate Tensor
	-
	-
	-template <class TDiffusionPixelType, class TTensorPixelType>
	-void
	-TensorReconstructionWithEigenvalueCorrectionFilter<TDiffusionPixelType, TTensorPixelType>
	-::TurnMask( itk::Size<3> size, itk::Image<short, 3>::Pointer mask, double previous_mask, double set_mask)
	-{
	- // The method changes voxels in the mask that poses a certain value with other value.
	-
	- itk::Index<3> ix;
	- double temp_mask_value=0;
	-
	-#ifdef WIN32
	-#pragma omp parallel for
	-#else
	-#pragma omp parallel for collapse(3)
	-#endif
	- for(int x=0;x<(int)size[0];x++)
	- for(int y=0;y<(int)size[1];y++)
	- for(int z=0;z<(int)size[2];z++)
	- {
	- ix[0] = x; ix[1] = y; ix[2] = z;
	- temp_mask_value=mask->GetPixel(ix);
	-
	- if(temp_mask_value>previous_mask)
	- {
	-#pragma omp critical
	- mask->SetPixel(ix,set_mask);
	- }
	- }
	-}
	-
	-} // end of namespace
	-
	-
	-
	-
	-
	-
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorToL2NormImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorToL2NormImageFilter.h
	deleted file mode 100644
	index d9b591654a..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorToL2NormImageFilter.h
	+++ /dev/null
	@@ -1,79 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef _itk_TensorToL2NormImageFilter_h_
	-#define _itk_TensorToL2NormImageFilter_h_
	-
	-#include "itkImageToImageFilter.h"
	-
	-namespace itk
	-{
	-
	- template <class TInputImage, class TOutputImage>
	- class ITK_EXPORT TensorToL2NormImageFilter
	- : public ImageToImageFilter<TInputImage, TOutputImage>
	- {
	-
	- public:
	-
	- typedef TensorToL2NormImageFilter Self;
	- typedef ImageToImageFilter<TInputImage, TOutputImage> Superclass;
	-
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	-
	- itkTypeMacro (TensorToL2NormImageFilter, ImageToImageFilter);
	-
	- itkStaticConstMacro (ImageDimension, unsigned int,
	- TOutputImage::ImageDimension);
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- typedef TInputImage InputImageType;
	- typedef typename InputImageType::PixelType InputPixelType;
	- typedef TOutputImage OutputImageType;
	- typedef typename OutputImageType::PixelType OutputPixelType;
	- typedef typename OutputImageType::RegionType OutputImageRegionType;
	-
	- protected:
	- TensorToL2NormImageFilter(){};
	- ~TensorToL2NormImageFilter(){};
	-
	- void PrintSelf (std::ostream& os, Indent indent) const override
	- {
	- Superclass::PrintSelf (os, indent);
	- }
	-
	-
	- void ThreadedGenerateData(const OutputImageRegionType &outputRegionForThread, ThreadIdType threadId) override;
	-
	-
	- private:
	- TensorToL2NormImageFilter (const Self&);
	- void operator=(const Self&);
	-
	- };
	-
	-
	-} // end of namespace
	-
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkTensorToL2NormImageFilter.txx"
	-#endif
	-
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorToL2NormImageFilter.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorToL2NormImageFilter.txx
	deleted file mode 100644
	index 4be0eb3dc8..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorToL2NormImageFilter.txx
	+++ /dev/null
	@@ -1,97 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-/*=========================================================================
	-
	- Program: Tensor ToolKit - TTK
	- Module: $URL: svn://scm.gforge.inria.fr/svn/ttk/trunk/Algorithms/itkTensorToL2NormImageFilter.txx $
	- Language: C++
	- Date: $Date: 2010-06-07 13:39:13 +0200 (Mo, 07 Jun 2010) $
	- Version: $Revision: 68 $
	-
	- Copyright (c) INRIA 2010. All rights reserved.
	- See LICENSE.txt for details.
	-
	- This software is distributed WITHOUT ANY WARRANTY; without even
	- the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
	- PURPOSE. See the above copyright notices for more information.
	-
	-=========================================================================*/
	-#ifndef _itk_TensorToL2NormImageFilter_txx_
	-#define _itk_TensorToL2NormImageFilter_txx_
	-#endif
	-
	-#include "itkTensorToL2NormImageFilter.h"
	-#include <itkImageRegionIterator.h>
	-#include <itkImageRegionConstIterator.h>
	-
	-namespace itk
	-{
	-
	- template <class TInputImage, class TOutputImage>
	- void TensorToL2NormImageFilter<TInputImage, TOutputImage>::ThreadedGenerateData(const OutputImageRegionType &outputRegionForThread, ThreadIdType threadId )
	- {
	- typedef ImageRegionIterator<OutputImageType> IteratorOutputType;
	- typedef ImageRegionConstIterator<InputImageType> IteratorInputType;
	-
	- unsigned long numPixels = outputRegionForThread.GetNumberOfPixels();
	- unsigned long step = numPixels/100;
	- unsigned long progress = 0;
	-
	- IteratorOutputType itOut(this->GetOutput(), outputRegionForThread);
	- IteratorInputType itIn(this->GetInput(), outputRegionForThread);
	-
	- if( threadId==0 )
	- this->UpdateProgress (0.0);
	-
	- while(!itOut.IsAtEnd())
	- {
	- if( this->GetAbortGenerateData() )
	- throw itk::ProcessAborted(__FILE__,__LINE__);
	-
	-
	- OutputPixelType out = static_cast<OutputPixelType>( 0.0 ); // be careful, overload in MedINRIA
	-
	- InputPixelType T = itIn.Get();
	-
	- if ( !(T[0]==0 && T[1]==0 && T[2]==0 && T[3]==0 && T[4]==0 && T[5]==0) )
	- {
	- double sum = T[0]T[0] + T[3]T[3] + T[5]*T[5]
	- + T[1]T[2]2.0 + T[2]T[4]2.0 + T[1]T[4]2.0;
	- out = static_cast<OutputPixelType>( vcl_sqrt( sum ));
	- }
	-
	- if( threadId==0 && step>0)
	- {
	- if( (progress%step)==0 )
	- this->UpdateProgress ( double(progress)/double(numPixels) );
	- }
	-
	-
	- itOut.Set (out);
	- ++progress;
	- ++itOut;
	- ++itIn;
	-
	- }
	-
	- if( threadId==0 )
	- this->UpdateProgress (1.0);
	-
	- }
	-
	-
	-
	-} // end of namespace
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorToRgbImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorToRgbImageFilter.h
	deleted file mode 100644
	index cb75cdaf91..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkTensorToRgbImageFilter.h
	+++ /dev/null
	@@ -1,153 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkTensorToRgbImageFilter_h
	-#define __itkTensorToRgbImageFilter_h
	-
	-#include "itkUnaryFunctorImageFilter.h"
	-#include "itkRGBAPixel.h"
	-#include "itkImageRegionConstIterator.h"
	-#include "itkImageRegionIterator.h"
	-
	-namespace itk
	-{
	-
	-#define __IMG_DAT_ITEM__CEIL_ZERO_ONE__(val) (val) = \
	- ( (val) < 0 ) ? ( 0 ) : ( ( (val)>1 ) ? ( 1 ) : ( (val) ) );
	-
	- /** \class TensorToRgbImageFilter
	- *
	- */
	- template <typename TInputImage,
	- typename TOutputImage=itk::Image<itk::RGBAPixel<unsigned char>,3> >
	- class TensorToRgbImageFilter :
	- public ImageToImageFilter<TInputImage,TOutputImage>
	- {
	- public:
	- /** Standard class typedefs. */
	- typedef TensorToRgbImageFilter Self;
	- typedef ImageToImageFilter<TInputImage,TOutputImage>
	- Superclass;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	-
	- typedef typename Superclass::InputImageType InputImageType;
	- typedef typename Superclass::OutputImageType OutputImageType;
	- typedef typename OutputImageType::PixelType OutputPixelType;
	- typedef typename TInputImage::PixelType InputPixelType;
	- typedef typename InputPixelType::ValueType InputValueType;
	-
	- /** Run-time type information (and related methods). */
	- itkTypeMacro( TensorToRgbImageFilter, ImageToImageFilter );
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Print internal ivars */
	- void PrintSelf(std::ostream& os, Indent indent) const override
	- { this->Superclass::PrintSelf( os, indent ); }
	-
	-#ifdef ITK_USE_CONCEPT_CHECKING
	- /** Begin concept checking */
	- itkConceptMacro(InputHasNumericTraitsCheck,
	- (Concept::HasNumericTraits<InputValueType>));
	- /** End concept checking */
	-#endif
	-
	-protected:
	- TensorToRgbImageFilter() {};
	- ~TensorToRgbImageFilter() override {};
	-
	- void GenerateData() override
	- {
	-
	- typename InputImageType::Pointer tensorImage = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) );
	-
	- typename OutputImageType::Pointer outputImage =
	- static_cast< OutputImageType * >(this->ProcessObject::GetPrimaryOutput());
	-
	- typename InputImageType::RegionType region = tensorImage->GetLargestPossibleRegion();
	-
	- outputImage->SetSpacing( tensorImage->GetSpacing() ); // Set the image spacing
	- outputImage->SetOrigin( tensorImage->GetOrigin() ); // Set the image origin
	- outputImage->SetDirection( tensorImage->GetDirection() ); // Set the image direction
	- outputImage->SetRegions( tensorImage->GetLargestPossibleRegion());
	- outputImage->Allocate();
	-
	- typedef ImageRegionConstIterator< InputImageType > TensorImageIteratorType;
	- TensorImageIteratorType tensorIt(tensorImage, tensorImage->GetLargestPossibleRegion());
	-
	- typedef ImageRegionIterator< OutputImageType > OutputImageIteratorType;
	- OutputImageIteratorType outputIt(outputImage, outputImage->GetLargestPossibleRegion());
	-
	- tensorIt.GoToBegin();
	- outputIt.GoToBegin();
	-
	- while(!tensorIt.IsAtEnd() && !outputIt.IsAtEnd()){
	-
	- InputPixelType x = tensorIt.Get();
	-
	- // eigenvalues are sorted in ascending order by default because the
	- // itk::SymmetricEigenAnalysis defaults are not touched in the tensor implementation
	-
	- typename InputPixelType::EigenValuesArrayType eigenvalues;
	- typename InputPixelType::EigenVectorsMatrixType eigenvectors;
	- x.ComputeEigenAnalysis(eigenvalues, eigenvectors);
	-
	- // int index = 2;
	- // if( (eigenvalues[0] >= eigenvalues[1])
	- // && (eigenvalues[0] >= eigenvalues[2]) )
	- // index = 0;
	- // else if(eigenvalues[1] >= eigenvalues[2])
	- // index = 1;
	-
	- const float fa = x.GetFractionalAnisotropy();
	- float r = fabs(eigenvectors(2/index/,0)) * fa;
	- float g = fabs(eigenvectors(2/index/,1)) * fa;
	- float b = fabs(eigenvectors(2/index/,2)) * fa;
	-// float a = (fa-(m_OpacLevel-m_OpacWindow/2.0f))/m_OpacWindow;
	- float a = fa;
	-
	- __IMG_DAT_ITEM__CEIL_ZERO_ONE__(r);
	- __IMG_DAT_ITEM__CEIL_ZERO_ONE__(g);
	- __IMG_DAT_ITEM__CEIL_ZERO_ONE__(b);
	- __IMG_DAT_ITEM__CEIL_ZERO_ONE__(a);
	-
	- OutputPixelType out;
	- out.SetRed( r * 255.0f);
	- out.SetGreen( g * 255.0f);
	- out.SetBlue( b * 255.0f);
	- out.SetAlpha( a * 255.0f);
	-
	- outputIt.Set(out);
	-
	- ++tensorIt;
	- ++outputIt;
	- }
	-
	- }
	-
	- private:
	- TensorToRgbImageFilter(const Self&); //purposely not implemented
	- void operator=(const Self&); //purposely not implemented
	- };
	-
	-
	-
	-} // end namespace itk
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkVectorImageToFourDImageFilter.cpp b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkVectorImageToFourDImageFilter.cpp
	deleted file mode 100644
	index e03fbe84fb..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkVectorImageToFourDImageFilter.cpp
	+++ /dev/null
	@@ -1,101 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef __itkVectorImageToFourDImageFilter_cpp
	-#define __itkVectorImageToFourDImageFilter_cpp
	-
	-#include "itkVectorImageToFourDImageFilter.h"
	-#include <itkImageRegionConstIterator.h>
	-#include <itkImageRegionConstIteratorWithIndex.h>
	-#include <itkImageRegionIterator.h>
	-#include <vnl/vnl_vector.h>
	-#include <itkOrientationDistributionFunction.h>
	-#include <itkContinuousIndex.h>
	-
	-#include <vtkSmartPointer.h>
	-#include <vtkPolyData.h>
	-#include <vtkCellArray.h>
	-#include <vtkPoints.h>
	-#include <vtkPolyLine.h>
	-
	-#include <boost/math/special_functions.hpp>
	-#include <boost/progress.hpp>
	-
	-
	-using namespace boost::math;
	-
	-namespace itk {
	-
	-template< class PixelType >
	-VectorImageToFourDImageFilter< PixelType>::VectorImageToFourDImageFilter()
	-{
	-
	-}
	-
	-
	-template< class PixelType >
	-void VectorImageToFourDImageFilter< PixelType>
	-::GenerateData()
	-{
	- Vector<float, 4> spacing4;
	- Point<float, 4> origin4;
	- Matrix<double, 4, 4> direction4; direction4.SetIdentity();
	- ImageRegion<4> imageRegion4;
	-
	- Vector<double, 3> spacing3 = m_InputImage->GetSpacing();
	- Point<float, 3> origin3 = m_InputImage->GetOrigin();
	- Matrix<double, 3, 3> direction3 = m_InputImage->GetDirection();
	- ImageRegion<3> imageRegion3 = m_InputImage->GetLargestPossibleRegion();
	-
	- spacing4[0] = spacing3[0]; spacing4[1] = spacing3[1]; spacing4[2] = spacing3[2]; spacing4[3] = 1;
	- origin4[0] = origin3[0]; origin4[1] = origin3[1]; origin4[2] = origin3[2]; origin4[3] = 0;
	- for (int r=0; r<3; r++)
	- for (int c=0; c<3; c++)
	- direction4[r][c] = direction3[r][c];
	-
	- imageRegion4.SetSize(0, imageRegion3.GetSize()[0]);
	- imageRegion4.SetSize(1, imageRegion3.GetSize()[1]);
	- imageRegion4.SetSize(2, imageRegion3.GetSize()[2]);
	- imageRegion4.SetSize(3, m_InputImage->GetVectorLength());
	-
	- m_OutputImage = OutputImageType::New();
	- m_OutputImage->SetSpacing( spacing4 );
	- m_OutputImage->SetOrigin( origin4 );
	- m_OutputImage->SetDirection( direction4 );
	- m_OutputImage->SetRegions( imageRegion4 );
	- m_OutputImage->Allocate();
	- m_OutputImage->FillBuffer(0);
	- ImageRegionIterator< InputImageType > iit(m_InputImage, m_InputImage->GetLargestPossibleRegion() );
	-
	- while( !iit.IsAtEnd() )
	- {
	- auto idx3 = iit.GetIndex();
	-
	- typename InputImageType::PixelType pix = iit.Get();
	-
	- for (unsigned int i=0; i<pix.GetSize(); ++i)
	- {
	- typename OutputImageType::IndexType idx4;
	- idx4[0] = idx3[0]; idx4[1] = idx3[1]; idx4[2] = idx3[2]; idx4[3] = i;
	- m_OutputImage->SetPixel(idx4, pix[i]);
	- }
	-
	- ++iit;
	- }
	-}
	-
	-}
	-
	-#endif // __itkVectorImageToFourDImageFilter_cpp
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkVectorImageToFourDImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkVectorImageToFourDImageFilter.h
	deleted file mode 100644
	index 88856faf34..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkVectorImageToFourDImageFilter.h
	+++ /dev/null
	@@ -1,74 +0,0 @@
	-/*=========================================================================
	-
	- Program: Insight Segmentation & Registration Toolkit
	- Module: $RCSfile: itkDiffusionTensor3DReconstructionImageFilter.h,v $
	- Language: C++
	- Date: $Date: 2006-03-27 17:01:06 $
	- Version: $Revision: 1.12 $
	-
	- Copyright (c) Insight Software Consortium. All rights reserved.
	- See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
	-
	- This software is distributed WITHOUT ANY WARRANTY; without even
	- the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
	- PURPOSE. See the above copyright notices for more information.
	-
	-=========================================================================*/
	-#ifndef __itkVectorImageToFourDImageFilter_h_
	-#define __itkVectorImageToFourDImageFilter_h_
	-
	-#include "itkImageToImageFilter.h"
	-#include <itkImage.h>
	-#include <itkVectorImage.h>
	-
	-namespace itk{
	-
	-/**
	-* \brief Flip peaks along specified axes
	-*/
	-
	-template< class PixelType >
	-class VectorImageToFourDImageFilter : public ProcessObject
	-{
	-
	-public:
	-
	- typedef VectorImageToFourDImageFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ProcessObject Superclass;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(VectorImageToFourDImageFilter, ProcessObject)
	-
	- typedef VectorImage<PixelType, 3> InputImageType;
	- typedef Image<PixelType, 4> OutputImageType;
	- typedef typename OutputImageType::RegionType OutputImageRegionType;
	-
	- itkSetMacro(InputImage, typename InputImageType::Pointer)
	- itkGetMacro(OutputImage, typename OutputImageType::Pointer)
	-
	- void GenerateData();
	-
	-protected:
	- VectorImageToFourDImageFilter();
	- ~VectorImageToFourDImageFilter(){}
	-
	- typename InputImageType::Pointer m_InputImage;
	- typename OutputImageType::Pointer m_OutputImage;
	-
	-private:
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkVectorImageToFourDImageFilter.cpp"
	-#endif
	-
	-#endif //__itkVectorImageToFourDImageFilter_h_
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkVectorImageToImageFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkVectorImageToImageFilter.h
	deleted file mode 100644
	index 026bb2c4ee..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkVectorImageToImageFilter.h
	+++ /dev/null
	@@ -1,77 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-/*===================================================================
	-
	-This file is based heavily on a corresponding ITK filter.
	-
	-===================================================================*/
	-#ifndef __itkVectorImageToImageFilter_h_
	-#define __itkVectorImageToImageFilter_h_
	-
	-#include "itkImageToImageFilter.h"
	-#include "itkVectorImage.h"
	-
	-namespace itk{
	-/** \class VectorImageToImageFilter
	- * \brief This class extracts an image out of a vectorimage
	- *
	- * An image is extracted at a designated index of a vectorimage. If non index is set, it is an index of 0 used.
	- */
	-
	-template< class TPixelType >
	-class VectorImageToImageFilter :
	- public ImageToImageFilter< VectorImage < TPixelType, 3 >, Image < TPixelType, 3 > >
	-{
	-
	-public:
	-
	- typedef VectorImageToImageFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageToImageFilter< VectorImage < TPixelType, 3 >, Image < TPixelType, 3 > > Superclass;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(VectorImageToImageFilter, ImageToImageFilter)
	-
	- typedef typename Superclass::InputImageType InputImageType;
	- typedef typename Superclass::OutputImageType OutputImageType;
	- typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
	-
	- itkSetMacro( Index, unsigned int)
	-
	- protected:
	- VectorImageToImageFilter();
	- ~VectorImageToImageFilter() {}
	- void PrintSelf(std::ostream& os, Indent indent) const override;
	-
	- //void BeforeThreadedGenerateData();
	- virtual void GenerateData() override;
	-
	- unsigned int m_Index;
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkVectorImageToImageFilter.txx"
	-#endif
	-
	-#endif //__itkVectorImageToImageFilter_h_
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkVectorImageToImageFilter.txx b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkVectorImageToImageFilter.txx
	deleted file mode 100644
	index df423bb027..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/itkVectorImageToImageFilter.txx
	+++ /dev/null
	@@ -1,79 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkVectorImageToImageFilter_txx
	-#define __itkVectorImageToImageFilter_txx
	-
	-#include <time.h>
	-#include <stdio.h>
	-#include <stdlib.h>
	-
	-#define _USE_MATH_DEFINES
	-#include <math.h>
	-
	-#include "itkImageRegionIterator.h"
	-
	-
	-namespace itk {
	-
	-
	-template< class TPixelType >
	-VectorImageToImageFilter< TPixelType >
	-::VectorImageToImageFilter()
	- : m_Index(0)
	-{
	- this->SetNumberOfRequiredInputs( 1 );
	-}
	-
	-template< class TPixelType >
	-void
	-VectorImageToImageFilter< TPixelType >
	-::GenerateData()
	-{
	- typename OutputImageType::Pointer outputImage =
	- static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0));
	-
	- outputImage->SetSpacing(this->GetInput()->GetSpacing());
	- outputImage->SetOrigin(this->GetInput()->GetOrigin());
	- outputImage->SetRegions(this->GetInput()->GetLargestPossibleRegion());
	- outputImage->Allocate();
	-
	- ImageRegionIterator< OutputImageType > oit(outputImage, outputImage->GetLargestPossibleRegion());
	- oit.GoToBegin();
	-
	- // InputIteratorType;
	- typename InputImageType::Pointer inputImagePointer = NULL;
	- inputImagePointer = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) );
	-
	- ImageRegionIterator <InputImageType> git( inputImagePointer, inputImagePointer->GetLargestPossibleRegion() );
	- git.GoToBegin();
	- while( !git.IsAtEnd() )
	- {
	- oit.Set(git.Get()[m_Index]);
	- ++oit;
	- ++git;
	- }
	-}
	-
	-template< class TPixelType >
	-void VectorImageToImageFilter< TPixelType >::PrintSelf(std::ostream& os, Indent indent) const
	-{
	- Superclass::PrintSelf(os,indent);
	-}
	-
	-}
	-
	-#endif // __itkVectorImageToImageFilter_txx
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.h
	deleted file mode 100644
	index ed4ac09101..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.h
	+++ /dev/null
	@@ -1,505 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef _MITK_PartialVolumeAnalysisClusteringCalculator_H
	-#define _MITK_PartialVolumeAnalysisClusteringCalculator_H
	-
	-#include <MitkDiffusionCoreExports.h>
	-
	-#include "mitkCommon.h"
	-#include "mitkImage.h"
	-
	-#include <itkObject.h>
	-#include <itkObjectFactory.h>
	-#include <itkImage.h>
	-#include <itkRGBAPixel.h>
	-
	-#include <vnl/vnl_vector.h>
	-
	-namespace mitk
	-{
	-
	- class MITKDIFFUSIONCORE_EXPORT PartialVolumeAnalysisClusteringCalculator : public itk::Object
	- {
	- public:
	-
	- typedef vnl_vector<double> VecType;
	- typedef mitk::Image::HistogramType MitkHistType;
	-
	- class HistType
	- {
	- public:
	-
	- HistType()
	- {
	- }
	-
	- HistType(const HistType& p)
	- {
	- this->xVals = p.xVals;
	- this->hVals = p.hVals;
	- }
	-
	- ~HistType()
	- {
	- }
	-
	- HistType operator= (const HistType& p)
	- {
	- if (this != &p) // protect against invalid self-assignment
	- {
	- this->xVals = p.xVals;
	- this->hVals = p.hVals;
	- }
	- return *this;
	- }
	-
	- void InitByMitkHistogram(const MitkHistType* histogram)
	- {
	- xVals.set_size(histogram->GetSize()[0]);
	- hVals.set_size(histogram->GetSize()[0]);
	- double sum = histogram->GetTotalFrequency();
	- MitkHistType::ConstIterator endIt = histogram->End();
	- MitkHistType::ConstIterator it = histogram->Begin();
	- bool firstNonEmptyBinFound = false;
	- //++it;
	- int i=0;
	- while (it != endIt)
	- {
	- if(it.GetFrequency() \|\| firstNonEmptyBinFound)
	- {
	- firstNonEmptyBinFound = true;
	- xVals(i) = it.GetMeasurementVector().GetElement(0);
	- hVals(i) = it.GetFrequency()/sum;
	- }
	- ++i;
	- ++it;
	- }
	-
	- }
	-
	- void SetXVals(VecType x)
	- {xVals = x;}
	-
	- void SetHVals(VecType h)
	- {hVals = h;}
	-
	- void SetXVals(std::vector<double> x)
	- {
	- int s = x.size();
	- xVals.set_size(s);
	- for(int i=0; i<s; i++)
	- {
	- xVals(i) = x[i];
	- }
	- }
	-
	- void SetHVals(std::vector<double> h)
	- {
	- int s = h.size();
	- hVals.set_size(s);
	- for(int i=0; i<s; i++)
	- {
	- hVals(i) = h[i];
	- }
	- }
	-
	- std::vector<double>* GetXVals()
	- {
	- int s = xVals.size();
	- std::vector<double>* retval = new std::vector<double>(s);
	- for(int i=0; i<s; i++)
	- {
	- (*retval)[i] = xVals(i);
	- }
	- return retval;
	- }
	-
	- std::vector<double>* GetHVals()
	- {
	- int s = hVals.size();
	- std::vector<double>* retval = new std::vector<double>(s);
	- for(int i=0; i<s; i++)
	- {
	- (*retval)[i] = hVals(i);
	- }
	- return retval;
	- }
	-
	- VecType xVals;
	- VecType hVals;
	- };
	-
	- class ClusterResultType
	- {
	- public:
	-
	- // ClusterResultType()
	- // {
	- // vals.push_back(VecType());
	- // vals.push_back(VecType());
	- // mixedVals.push_back(VecType());
	- // }
	-
	- ClusterResultType(int sz)
	- {
	- vals.push_back(VecType(sz));
	- vals.push_back(VecType(sz));
	- mixedVals.push_back(VecType(sz));
	- combiVals.set_size(sz);
	- }
	-
	- ~ClusterResultType()
	- {
	- }
	-
	-// ClusterResultType operator= (const ClusterResultType *p)
	-// {
	-
	-// MITK_DEBUG << "AOJHIFAHFOF";
	-// if (this != &p) // protect against invalid self-assignment
	-// {
	-// MITK_DEBUG << "HRRRHRHRR";
	-// this->vals.clear();
	-// this->mixedVals.clear();
	-
	-// int s = p.vals.size();
	-// for(int i=0; i<s;i++)
	-// {
	-// VecType v = p.vals[i];
	-// this->vals.push_back(v);
	-// }
	-
	-// s = p.mixedVals.size();
	-// for(int i=0; i<s;i++)
	-// {
	-// VecType v = p.mixedVals[i];
	-// this->mixedVals.push_back(v);
	-// }
	-
	-// this->combiVals = p.combiVals;
	-// }
	-// return *this;
	-// }
	-
	- void Initialize (const ClusterResultType *p)
	- {
	- if (this != p) // protect against invalid self-assignment
	- {
	- this->vals.clear();
	- this->mixedVals.clear();
	-
	- int s = p->vals.size();
	- for(int i=0; i<s;i++)
	- {
	- VecType v = p->vals[i];
	- this->vals.push_back(v);
	- }
	-
	- s = p->mixedVals.size();
	- for(int i=0; i<s;i++)
	- {
	- VecType v = p->mixedVals[i];
	- this->mixedVals.push_back(v);
	- }
	-
	- this->combiVals = p->combiVals;
	- }
	- }
	-
	- std::vector<double> GetFiberVals()
	- {
	- if(vals.size()==2 && vals[1].data_block())
	- {
	- int s = vals[1].size();
	- std::vector<double> retval(s);
	- for(int i=0; i<s; i++)
	- {
	- retval[i] = vals[1](i);
	- }
	- return retval;
	- }
	- else
	- {
	- MITK_ERROR << "GetFiberVals() struct not initialized!!";
	- return std::vector<double>(0);
	- }
	- }
	-
	- std::vector<double> GetNonFiberVals()
	- {
	- if(vals.size()==2 && vals[0].data_block())
	- {
	- int s = vals[0].size();
	- std::vector<double> retval(s);
	- for(int i=0; i<s; i++)
	- {
	- retval[i] = vals[0](i);
	- }
	- return retval;
	- }
	- else
	- {
	- MITK_ERROR << "GetNonFiberVals() struct not initialized!!";
	- return std::vector<double>(0);
	- }
	- }
	-
	- std::vector<double> GetMixedVals()
	- {
	- if(mixedVals.size()==1 && mixedVals[0].data_block())
	- {
	- int s = mixedVals[0].size();
	- std::vector<double> retval(s);
	- for(int i=0; i<s; i++)
	- {
	- retval[i] = mixedVals[0](i);
	- }
	- return retval;
	- }
	- else
	- {
	- MITK_ERROR << "GetMixedVals() struct not initialized!!";
	- return std::vector<double>(0);
	- }
	- }
	-
	- std::vector<double> GetCombiVals()
	- {
	- if(combiVals.data_block())
	- {
	- int s = combiVals.size();
	- std::vector<double> retval(s);
	- for(int i=0; i<s; i++)
	- {
	- retval[i] = combiVals(i);
	- }
	- return retval;
	- }
	- else
	- {
	- MITK_ERROR << "GetCombiVals() struct not initialized!!";
	- return std::vector<double>(0);
	- }
	- }
	-
	-
	-// void Print(VecType vec, int nr=10)
	-// {
	-// int sz = vec.size();
	-// int incr = (int)((1.0sz)/(1.0nr));
	-// for(int i=0; i<sz; i = i+incr)
	-// {
	-// std::cout << vec(i) << " ";
	-// }
	-// std::cout << std::endl;
	-// }
	-
	-// void Print(int nr=10)
	-// {
	-// MITK_DEBUG << "CURVES" << std::endl;
	-// MITK_DEBUG << "Fiber Vals: ";
	-// Print(vals[0],nr);
	-// MITK_DEBUG << "Non-Fiber Vals: ";
	-// Print(vals[1],nr);
	-// MITK_DEBUG << "Mixed Vals: ";
	-// Print(mixedVals[0],nr);
	-// MITK_DEBUG << "Combined Vals: ";
	-// Print(combiVals,nr);
	-// }
	-
	- std::vector<VecType> vals;
	- std::vector<VecType> mixedVals;
	- VecType combiVals;
	-
	- };
	-
	- class ParamsType
	- {
	- public:
	- ParamsType()
	- {
	- }
	-
	- ~ParamsType()
	- {
	- }
	-
	- void Initialize(const ParamsType *p)
	- {
	- if (this != p) // protect against invalid self-assignment
	- {
	- means[0] = p->means[0];
	- means[1] = p->means[1];
	- sigmas[0] = p->sigmas[0];
	- sigmas[1] = p->sigmas[1];
	- ps[0] = p->ps[0];
	- ps[1] = p->ps[1];
	- }
	- }
	-
	-// void Print()
	-// {
	-// MITK_DEBUG << "PARAMS" << std::endl;
	-// MITK_DEBUG << "Class 1: " << means[0] << " +- " << sqrt(sigmas[0]) << " (p=" << ps[0] << ")" << std::endl;
	-// MITK_DEBUG << "Class 2: " << means[1] << " +- " << sqrt(sigmas[1]) << " (p=" << ps[1] << ")" << std::endl;
	-// MITK_DEBUG << "Partial V: p=" << 1.0-ps[0]-ps[1] << std::endl;
	-// }
	-
	- double means[2];
	- double sigmas[2];
	- double ps[2];
	- };
	-
	- struct HelperStructClusteringResults
	- {
	- MitkHistType *interestingHist;
	- MitkHistType *totalHist;
	- double p_interesting;
	- };
	-
	- struct HelperStructRGBChannels
	- {
	- mitk::Image::Pointer r;
	- mitk::Image::Pointer g;
	- mitk::Image::Pointer b;
	-
	- ~HelperStructRGBChannels()
	- {
	- r = nullptr;
	- g = nullptr;
	- b = nullptr;
	- }
	- };
	-
	- struct HelperStructPerformRGBClusteringRetval
	- {
	- HelperStructRGBChannels *rgbChannels;
	- mitk::Image::Pointer rgb;
	-
	- ParamsType *params;
	- ClusterResultType *result;
	- HistType *hist;
	-
	- HelperStructPerformRGBClusteringRetval() :
	- rgbChannels(nullptr), params(nullptr), result(nullptr), hist(nullptr)
	- {
	- }
	-
	- ~HelperStructPerformRGBClusteringRetval()
	- {
	- rgb = nullptr;
	- delete rgbChannels;
	- }
	- };
	-
	- struct HelperStructPerformClusteringRetval
	- {
	- mitk::Image::Pointer clusteredImage;
	- mitk::Image::Pointer displayImage;
	-
	- ParamsType *params;
	- ClusterResultType *result;
	- HistType *hist;
	-
	- HelperStructPerformClusteringRetval() :
	- clusteredImage(nullptr), displayImage(nullptr),
	- params(nullptr), result(nullptr), hist(nullptr)
	- {
	- }
	-
	- ~HelperStructPerformClusteringRetval()
	- {
	- clusteredImage = nullptr;
	- displayImage = nullptr;
	- }
	- };
	-
	- mitkClassMacroItkParent( PartialVolumeAnalysisClusteringCalculator, itk::Object )
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- ParamsType *InitialGuess(HistType h) const;
	-
	- ParamsType Cluster(const HistType h, ParamsType initialGuess) const;
	-
	- ClusterResultType CalculateCurves(ParamsType params, VecType xVals) const;
	-
	- void Normalize(ParamsType params, ClusterResultType* curves) const;
	-
	- HelperStructPerformClusteringRetval* PerformClustering(mitk::Image::ConstPointer image, const MitkHistType histogram, int classIdent, HelperStructPerformClusteringRetval precResult = nullptr) const;
	-
	- HelperStructPerformRGBClusteringRetval* PerformRGBClustering(mitk::Image::ConstPointer image, const MitkHistType *histogram) const;
	-
	- HelperStructPerformClusteringRetval* PerformQuantiles(mitk::Image::ConstPointer image, const MitkHistType *histogram, double p1, double p2) const;
	-
	- HelperStructPerformRGBClusteringRetval* PerformRGBQuantiles(mitk::Image::ConstPointer image, const MitkHistType *histogram, double p1, double p2 ) const;
	-
	- double* PerformQuantification(mitk::Image::ConstPointer image, mitk::Image::Pointer clusteredImage, mitk::Image::Pointer mask = nullptr) const;
	-
	- mitk::Image::Pointer CaculateAngularErrorImage(
	- mitk::Image::Pointer comp1, mitk::Image::Pointer comp2, mitk::Image::Pointer probImg) const;
	-
	- template < unsigned int VImageDimension >
	- void InternalGenerateRGB( HelperStructRGBChannels *rgb, mitk::Image::Pointer retval ) const;
	-
	- template < typename TPixel, unsigned int VImageDimension >
	- void InternalGenerateProbabilityImage(
	- const itk::Image< TPixel, VImageDimension > *image,
	- const HelperStructClusteringResults clusterResults,
	- mitk::Image::Pointer outImage1, mitk::Image::Pointer outImage2 ) const;
	-
	- template < typename TPixel, unsigned int VImageDimension >
	- void InternalQuantify(
	- const itk::Image< TPixel, VImageDimension > *image,
	- mitk::Image::Pointer clusteredImage, double* retval, mitk::Image::Pointer mask ) const;
	-
	- template < typename TPixel, unsigned int VImageDimension >
	- void InternalGenerateQuantileImage(
	- const itk::Image< TPixel, VImageDimension > *image,
	- double* q,
	- mitk::Image::Pointer outImage1, mitk::Image::Pointer outImage2 ) const;
	-
	- ParamsType* Cluster(const HistType h) const
	- {return Cluster(h, InitialGuess(h));}
	-
	- void SetMaxIt(unsigned int it)
	- { m_MaxIt = it; }
	-
	- unsigned int GetMaxIt()
	- { return m_MaxIt; }
	-
	- void SetStepsNumIntegration(unsigned int n)
	- { m_StepsNumIntegration = n; }
	-
	- unsigned int GetStepsNumIntegration()
	- { return m_StepsNumIntegration; }
	-
	- protected:
	-
	- PartialVolumeAnalysisClusteringCalculator();
	-
	- ~PartialVolumeAnalysisClusteringCalculator() override;
	-
	- unsigned int m_MaxIt;
	- unsigned int m_StepsNumIntegration;
	-
	- };
	-
	-}
	-
	-#endif // #define _MITK_PartialVolumeAnalysisClusteringCalculator_H
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.h b/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.h
	deleted file mode 100644
	index 3f45fb1bb8..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.h
	+++ /dev/null
	@@ -1,384 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef _MITK_PartialVolumeAnalysisHistogramCalculator_H
	-#define _MITK_PartialVolumeAnalysisHistogramCalculator_H
	-
	-#include "MitkDiffusionCoreExports.h"
	-
	-#include <itkObject.h>
	-#include <itkImage.h>
	-#include <itkTimeStamp.h>
	-
	-
	-#include "mitkImage.h"
	-#include "mitkImageTimeSelector.h"
	-#include "mitkPlanarFigure.h"
	-
	-
	-
	-namespace mitk
	-{
	-
	- /**
	- * \brief Class for calculating statistics and histogram for an (optionally
	- * masked) image.
	- *
	- * Images can be masked by either a (binary) image (of the same dimensions as
	- * the original image) or by a closed mitk::PlanarFigure, e.g. a circle or
	- * polygon. When masking with a planar figure, the slice corresponding to the
	- * plane containing the figure is extracted and then clipped with contour
	- * defined by the figure. Planar figures need to be aligned along the main axes
	- * of the image (axial, sagittal, coronal). Planar figures on arbitrary
	- * rotated planes are not supported.
	- *
	- * For each operating mode (no masking, masking by image, masking by planar
	- * figure), the calculated statistics and histogram are cached so that, when
	- * switching back and forth between operation modes without modifying mask or
	- * image, the information doesn't need to be recalculated.
	- *
	- * Note: currently time-resolved and multi-channel pictures are not properly
	- * supported.
	- */
	- class MITKDIFFUSIONCORE_EXPORT PartialVolumeAnalysisHistogramCalculator : public itk::Object
	- {
	- public:
	-
	- enum
	- {
	- MASKING_MODE_NONE = 0,
	- MASKING_MODE_IMAGE,
	- MASKING_MODE_PLANARFIGURE
	- };
	-
	- typedef mitk::Image::HistogramType HistogramType;
	- typedef mitk::Image::HistogramType::ConstIterator HistogramConstIteratorType;
	-
	- struct Statistics
	- {
	- unsigned int N;
	- double Min;
	- double Max;
	- double Mean;
	- double Median;
	- double Variance;
	- double Sigma;
	- double RMS;
	-
	- void Reset()
	- {
	- N = 0;
	- Min = 0.0;
	- Max = 0.0;
	- Mean = 0.0;
	- Median = 0.0;
	- Variance = 0.0;
	- Sigma = 0.0;
	- RMS = 0.0;
	- }
	- };
	-
	- typedef Statistics StatisticsType;
	-
	- typedef itk::TimeStamp TimeStampType;
	- typedef bool BoolType;
	-
	- typedef itk::Image< unsigned char, 3 > MaskImage3DType;
	- typedef itk::Image< unsigned char, 2 > MaskImage2DType;
	-
	- typedef itk::Image< float, 2 > InternalImage2DType;
	-
	- mitkClassMacroItkParent( PartialVolumeAnalysisHistogramCalculator, itk::Object )
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** \brief Set image from which to compute statistics. */
	- void SetImage( const mitk::Image *image );
	-
	- /** \brief Set binary image for masking. */
	- void SetImageMask( const mitk::Image *imageMask );
	-
	- /** \brief Set planar figure for masking. */
	- void SetPlanarFigure( const mitk::PlanarFigure *planarFigure );
	-
	- /** \brief Set image for which the same resampling will be applied.
	- and available via GetAdditionalResampledImage() */
	- void AddAdditionalResamplingImage( const mitk::Image *image );
	-
	- /** \brief Set/Get operation mode for masking */
	- void SetMaskingMode( unsigned int mode );
	-
	- /** \brief Set/Get operation mode for masking */
	- itkGetMacro( MaskingMode, unsigned int );
	-
	- /** \brief Set/Get operation mode for masking */
	- void SetMaskingModeToNone();
	-
	- /** \brief Set/Get operation mode for masking */
	- void SetMaskingModeToImage();
	-
	- /** \brief Set/Get operation mode for masking */
	- void SetMaskingModeToPlanarFigure();
	-
	- /** \brief Set histogram number of bins. */
	- void SetNumberOfBins( unsigned int number )
	- {
	- if(m_NumberOfBins != number)
	- {
	- m_NumberOfBins = number;
	- SetModified();
	- }
	- }
	-
	- /** \brief Get histogram number of bins. */
	- unsigned int GetNumberOfBins( )
	- { return m_NumberOfBins; }
	-
	- /** \brief Set upsampling factor. */
	- void SetUpsamplingFactor( float number )
	- {
	- if(m_UpsamplingFactor != number)
	- {
	- m_UpsamplingFactor = number;
	- SetModified();
	- }
	- }
	-
	- /** \brief Get upsampling factor. */
	- float GetUpsamplingFactor( )
	- { return m_UpsamplingFactor; }
	-
	- /** \brief Set gaussian sigma. */
	- void SetGaussianSigma( float number )
	- {
	- if(m_GaussianSigma != number)
	- {
	- m_GaussianSigma = number;
	- SetModified();
	- }
	- }
	-
	- /** \brief Get thickness of planar figure. */
	- unsigned int GetPlanarFigureThickness( )
	- { return m_PlanarFigureThickness; }
	-
	-
	- /** \brief Set thickness of planar figure. */
	- void SetPlanarFigureThickness( unsigned int number )
	- {
	- if(m_PlanarFigureThickness != number)
	- {
	- m_PlanarFigureThickness = number;
	- SetModified();
	- }
	- }
	-
	- /** \brief Get histogram number of bins. */
	- float GetGaussianSigma( )
	- { return m_GaussianSigma; }
	-
	- void SetModified();
	-
	- /** \brief Compute statistics (together with histogram) for the current
	- * masking mode.
	- *
	- * Computation is not executed if statistics is already up to date. In this
	- * case, false is returned; otherwise, true.*/
	- virtual bool ComputeStatistics( );
	-
	-
	- /** \brief Retrieve the histogram depending on the current masking mode. */
	- const HistogramType *GetHistogram( ) const;
	-
	- /** \brief Retrieve statistics depending on the current masking mode. */
	- const Statistics &GetStatistics( ) const;
	-
	- const Image::Pointer GetInternalImage()
	- {
	- return m_InternalImage;
	- }
	-
	- const Image::Pointer GetInternalAdditionalResampledImage(unsigned int i)
	- {
	- if(i < m_InternalAdditionalResamplingImages.size())
	- {
	- return m_InternalAdditionalResamplingImages[i];
	- }
	- else
	- {
	- return nullptr;
	- }
	- }
	-
	- void SetForceUpdate(bool b)
	- {
	- m_ForceUpdate = b;
	- }
	-
	- protected:
	-
	- PartialVolumeAnalysisHistogramCalculator();
	-
	- ~PartialVolumeAnalysisHistogramCalculator() override;
	-
	- /** \brief Depending on the masking mode, the image and mask from which to
	- * calculate statistics is extracted from the original input image and mask
	- * data.
	- *
	- * For example, a when using a PlanarFigure as mask, the 2D image slice
	- * corresponding to the PlanarFigure will be extracted from the original
	- * image. If masking is disabled, the original image is simply passed
	- * through. */
	- void ExtractImageAndMask( );
	-
	-
	- /** \brief If the passed vector matches any of the three principal axes
	- * of the passed geometry, the ínteger value corresponding to the axis
	- * is set and true is returned. */
	- bool GetPrincipalAxis( const Geometry3D *geometry, Vector3D vector,
	- unsigned int &axis );
	-
	- template < typename TPixel, unsigned int VImageDimension >
	- void InternalCalculateStatisticsUnmasked(
	- const itk::Image< TPixel, VImageDimension > *image,
	- Statistics &statistics,
	- typename HistogramType::ConstPointer *histogram );
	-
	- template < typename TPixel, unsigned int VImageDimension >
	- void InternalCalculateStatisticsMasked(
	- const itk::Image< TPixel, VImageDimension > *image,
	- itk::Image< unsigned char, VImageDimension > *maskImage,
	- Statistics &statistics,
	- typename HistogramType::ConstPointer *histogram );
	-
	- template < typename TPixel, unsigned int VImageDimension >
	- void InternalCalculateMaskFromPlanarFigure(
	- itk::Image< TPixel, VImageDimension > *image, unsigned int axis );
	-
	- template < typename TPixel, unsigned int VImageDimension >
	- void InternalReorientImagePlane(
	- const itk::Image< TPixel, VImageDimension > image, mitk::BaseGeometry imggeo, mitk::BaseGeometry* planegeo3D, int additionalIndex );
	-
	- template < typename TPixel, unsigned int VImageDimension >
	- void InternalResampleImageFromMask(
	- const itk::Image< TPixel, VImageDimension > *image, int additionalIndex );
	-
	- void InternalResampleImage(
	- const MaskImage3DType image/, mitk::Geometry3D* imggeo*/ );
	-
	- template < typename TPixel, unsigned int VImageDimension >
	- void InternalCropAdditionalImage(
	- itk::Image< TPixel, VImageDimension > *image, int additionalIndex );
	-
	- void InternalMaskImage( mitk::Image *image );
	-
	- /** Connection from ITK to VTK */
	- template <typename ITK_Exporter, typename VTK_Importer>
	- void ConnectPipelines(ITK_Exporter exporter, VTK_Importer* importer)
	- {
	- importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback());
	-
	- importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback());
	- importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback());
	- importer->SetSpacingCallback(exporter->GetSpacingCallback());
	- importer->SetOriginCallback(exporter->GetOriginCallback());
	- importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback());
	-
	- importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback());
	-
	- importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback());
	- importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback());
	- importer->SetDataExtentCallback(exporter->GetDataExtentCallback());
	- importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback());
	- importer->SetCallbackUserData(exporter->GetCallbackUserData());
	- }
	-
	- /** Connection from VTK to ITK */
	- template <typename VTK_Exporter, typename ITK_Importer>
	- void ConnectPipelines(VTK_Exporter* exporter, ITK_Importer importer)
	- {
	- importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback());
	-
	- importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback());
	- importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback());
	- importer->SetSpacingCallback(exporter->GetSpacingCallback());
	- importer->SetOriginCallback(exporter->GetOriginCallback());
	- importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback());
	-
	- importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback());
	-
	- importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback());
	- importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback());
	- importer->SetDataExtentCallback(exporter->GetDataExtentCallback());
	- importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback());
	- importer->SetCallbackUserData(exporter->GetCallbackUserData());
	- }
	-
	- void UnmaskedStatisticsProgressUpdate();
	- void MaskedStatisticsProgressUpdate();
	-
	- mitk::Image::ConstPointer m_Image;
	- mitk::Image::ConstPointer m_ImageMask;
	- mitk::PlanarFigure::ConstPointer m_PlanarFigure;
	-
	- HistogramType::ConstPointer m_ImageHistogram;
	- HistogramType::ConstPointer m_MaskedImageHistogram;
	- HistogramType::ConstPointer m_PlanarFigureHistogram;
	-
	- HistogramType::Pointer m_EmptyHistogram;
	-
	- StatisticsType m_ImageStatistics;
	- StatisticsType m_MaskedImageStatistics;
	- StatisticsType m_PlanarFigureStatistics;
	-
	- Statistics m_EmptyStatistics;
	-
	- unsigned int m_MaskingMode;
	- bool m_MaskingModeChanged;
	-
	- mitk::Image::Pointer m_InternalImage;
	- MaskImage3DType::Pointer m_InternalImageMask3D;
	- MaskImage2DType::Pointer m_InternalImageMask2D;
	- itk::ImageRegion<3> m_InternalMask3D;
	- std::vector<mitk::Image::ConstPointer> m_AdditionalResamplingImages;
	- std::vector<mitk::Image::Pointer> m_InternalAdditionalResamplingImages;
	-
	- TimeStampType m_ImageStatisticsTimeStamp;
	- TimeStampType m_MaskedImageStatisticsTimeStamp;
	- TimeStampType m_PlanarFigureStatisticsTimeStamp;
	-
	- BoolType m_ImageStatisticsCalculationTriggerBool;
	- BoolType m_MaskedImageStatisticsCalculationTriggerBool;
	- BoolType m_PlanarFigureStatisticsCalculationTriggerBool;
	-
	- unsigned int m_NumberOfBins;
	-
	- float m_UpsamplingFactor;
	-
	- float m_GaussianSigma;
	-
	- itk::ImageRegion<3> m_CropRegion;
	-
	- bool m_ForceUpdate;
	-
	- unsigned int m_PlanarFigureThickness;
	-
	- };
	-
	-}
	-
	-#endif // #define _MITK_PartialVolumeAnalysisHistogramCalculator_H
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDicomDiffusionImageHeaderReader.h b/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDicomDiffusionImageHeaderReader.h
	deleted file mode 100644
	index ca61499835..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDicomDiffusionImageHeaderReader.h
	+++ /dev/null
	@@ -1,115 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef __mitkDicomDiffusionImageHeaderReader_h__
	-#define __mitkDicomDiffusionImageHeaderReader_h__
	-
	-#include <MitkDiffusionCoreExports.h>
	-
	-#include <mitkFileReader.h>
	-#include "itkImageSeriesReader.h"
	-#include "itkImageFileReader.h"
	-#include "itkImage.h"
	-#include "itkGDCMImageIO.h"
	-#include "mitkDiffusionImageHeaderInformation.h"
	-
	-namespace mitk
	-{
	- /**
	- @brief Reads the header information from a DICOM series and stores it into an output object of type
	- DiffusionImageHeaderInformation
	- */
	- class MITKDIFFUSIONCORE_EXPORT DicomDiffusionImageHeaderReader : public itk::Object
	- {
	- public:
	-
	- mitkClassMacroItkParent( DicomDiffusionImageHeaderReader, itk::Object );
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** En enum to distinguish in processing between the different vendoors */
	- enum SupportedVendors{
	- SV_SIEMENS,
	- SV_SIEMENS_MOSAIC,
	- SV_PHILIPS,
	- SV_GE,
	- SV_UNKNOWN_VENDOR
	- };
	-
	- typedef std::vector< std::string > FileNamesContainer;
	-
	- typedef short PixelValueType;
	- typedef itk::Image< PixelValueType, 2 > SliceType;
	- typedef itk::Image< PixelValueType, 3 > VolumeType;
	- typedef itk::ImageSeriesReader< VolumeType > VolumeReaderType;
	- typedef itk::ImageFileReader< SliceType > SliceReaderType;
	- typedef itk::GDCMImageIO ImageIOType;
	-
	- /** Set the dicom file names to be considered */
	- void SetSeriesDicomFilenames(FileNamesContainer dicomFilenames)
	- { this->m_DicomFilenames = dicomFilenames; }
	-
	- void SetGdcmIO(ImageIOType::Pointer gdcmIO)
	- { this->m_GdcmIO = gdcmIO; }
	-
	- /** Set the volume reader in case the default volume reader shouldn't be used */
	- void SetVolumeReader(VolumeReaderType::Pointer volumeReader)
	- { this->m_VolumeReader = volumeReader; }
	-
	- /** Set the output object that will contain the read-in information after update */
	- void SetOutputPointer(DiffusionImageHeaderInformation::Pointer output)
	- { this->m_Output = output; }
	-
	- /** do the work */
	- virtual void Update();
	-
	- /** return output */
	- DiffusionImageHeaderInformation::Pointer GetOutput();
	-
	- /** identify vendor */
	- SupportedVendors GetVendorID();
	-
	- protected:
	- /** Default c'tor */
	- DicomDiffusionImageHeaderReader();
	-
	- /** Default d'tor */
	- ~DicomDiffusionImageHeaderReader() override;
	-
	- void ReadPublicTags();
	- void ReadPublicTags2();
	- void TransformGradients();
	-
	- FileNamesContainer m_DicomFilenames;
	- DiffusionImageHeaderInformation::Pointer m_Output;
	-
	- ImageIOType::Pointer m_GdcmIO;
	- VolumeReaderType::Pointer m_VolumeReader;
	-
	- bool m_SliceOrderIS;
	- bool m_SingleSeries;
	- int m_nSlice;
	- std::vector<float> m_sliceLocations;
	-
	- };
	-
	-}
	-
	-#endif
	-
	-
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDicomDiffusionImageReader.cpp b/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDicomDiffusionImageReader.cpp
	deleted file mode 100644
	index 17a1485e07..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDicomDiffusionImageReader.cpp
	+++ /dev/null
	@@ -1,141 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkDicomDiffusionImageReader_cpp
	-#define __mitkDicomDiffusionImageReader_cpp
	-
	-#include "mitkDicomDiffusionImageReader.h"
	-
	-#include "itkImageSeriesReader.h"
	-
	-
	-namespace mitk
	-{
	-
	-template <class TPixelType, const int TDimension>
	-void DicomDiffusionImageReader<TPixelType, TDimension>
	-::PrintSelf(std::ostream& os, itk::Indent indent) const
	-{
	- Superclass::PrintSelf(os, indent);
	-}
	-
	-
	-template <class TPixelType, const int TDimension>
	-void DicomDiffusionImageReader<TPixelType, TDimension>
	-::GenerateOutputInformation(void)
	-{
	- typename OutputImageType::Pointer output = this->GetOutput();
	- typedef itk::ImageSeriesReader<InputImageType> ReaderType;
	-
	- // Read the first (or last) volume and use its size.
	- if (m_Headers.size() > 0)
	- {
	- typename ReaderType::Pointer reader = ReaderType::New();
	-
	- try
	- {
	- // Read the image
	- reader->SetFileNames (m_Headers[0]->m_DicomFilenames);
	- reader->UpdateOutputInformation();
	-
	- output->SetSpacing( reader->GetOutput()->GetSpacing() ); // Set the image spacing
	- output->SetOrigin( reader->GetOutput()->GetOrigin() ); // Set the image origin
	- output->SetDirection( reader->GetOutput()->GetDirection() ); // Set the image direction
	- output->SetLargestPossibleRegion( reader->GetOutput()->GetLargestPossibleRegion() );
	- output->SetVectorLength( m_Headers.size() );
	- }
	- catch (itk::ExceptionObject &e)
	- {
	- throw e;
	- }
	- }
	- else
	- {
	- itkExceptionMacro(<< "At least one filename is required." );
	- }
	-}
	-
	-
	-template <class TPixelType, const int TDimension>
	- void
	- DicomDiffusionImageReader<TPixelType, TDimension>
	- ::EnlargeOutputRequestedRegion(itk::DataObject *output)
	- {
	- typename OutputImageType::Pointer out = dynamic_cast<OutputImageType*>(output);
	- out->SetRequestedRegion( out->GetLargestPossibleRegion() );
	-}
	-
	-
	-template <class TPixelType, const int TDimension>
	-void DicomDiffusionImageReader<TPixelType, TDimension>
	-::GenerateData()
	-{
	- typedef itk::ImageSeriesReader<InputImageType> ReaderType;
	-
	- typename OutputImageType::Pointer output = this->GetOutput();
	-
	- typedef typename OutputImageType::RegionType RegionType;
	- RegionType requestedRegion = output->GetRequestedRegion();
	-
	- // Each file must have the same size.
	- SizeType validSize = requestedRegion.GetSize();
	-
	- int numberOfVolumes = static_cast<int>(m_Headers.size());
	-
	- // Allocate the output buffer
	- output->SetBufferedRegion( requestedRegion );
	- output->Allocate();
	-
	- itk::ProgressReporter progress(this, 0,
	- m_Headers.size(),
	- m_Headers.size());
	-
	- itk::ImageRegionIterator<OutputImageType> ot (output, requestedRegion );
	-
	- typename OutputImageType::PixelType vec;
	-
	- for (int i = 0; i < numberOfVolumes; i ++)
	- {
	-
	- MITK_INFO << "Loading volume " << i+1 << "/" << numberOfVolumes;
	- typename ReaderType::Pointer reader = ReaderType::New();
	- reader->SetFileNames(m_Headers[i]->m_DicomFilenames);
	- reader->UpdateLargestPossibleRegion();
	-
	- if (reader->GetOutput()->GetRequestedRegion().GetSize() != validSize)
	- {
	- itkExceptionMacro(<< "Size mismatch!");
	- }
	-
	- itk::ImageRegionConstIterator<InputImageType> it (reader->GetOutput(),
	- reader->GetOutput()->GetLargestPossibleRegion());
	-
	- while (!it.IsAtEnd())
	- {
	- vec = ot.Get();
	- vec.SetElement(i, it.Get());
	- ot.Set(vec);
	- ++it;
	- ++ot;
	- }
	- ot.GoToBegin();
	- progress.CompletedPixel();
	- }
	-}
	-
	-} //namespace MITK
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDicomDiffusionImageReader.h b/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDicomDiffusionImageReader.h
	deleted file mode 100644
	index b9007f5f1f..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDicomDiffusionImageReader.h
	+++ /dev/null
	@@ -1,102 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkDicomDiffusionImageReader_h
	-#define __mitkDicomDiffusionImageReader_h
	-
	-#include "itkImageSource.h"
	-#include "itkVectorImage.h"
	-#include "mitkDiffusionImageHeaderInformation.h"
	-#include "itkDataObject.h"
	-#include "mitkCommon.h"
	-
	-namespace mitk
	-{
	-
	-/** \brief Reads in the image data stored as DICOM series. The series is specified by a HeaderContainer
	- */
	-
	-template <class TPixelType, const int TDimension>
	-class DicomDiffusionImageReader : public itk::ImageSource< itk::VectorImage< TPixelType, TDimension > >
	-{
	-public:
	-
	- typedef itk::VectorImage< TPixelType, TDimension > OutputImageType;
	- typedef itk::Image<TPixelType, TDimension > InputImageType;
	- typedef itk::ImageSource< OutputImageType > ImageSourceType;
	-
	- mitkClassMacro( DicomDiffusionImageReader, ImageSourceType );
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	-
	- /** The size of the output image. */
	- typedef typename OutputImageType::SizeType SizeType;
	-
	- /** The region of the output image. */
	- typedef typename OutputImageType::RegionType ImageRegionType;
	-
	- typedef std::vector<DiffusionImageHeaderInformation::Pointer> HeaderContainer;
	-
	- /** Set the vector of strings that contains the file names. Files
	- * are processed in sequential order. */
	- void SetHeaders (const HeaderContainer &headers)
	- {
	- if ( m_Headers != headers)
	- {
	- m_Headers = headers;
	- this->Modified();
	- }
	- }
	- const HeaderContainer & GetHeaders() const
	- {
	- return m_Headers;
	- }
	-
	- /** Prepare the allocation of the output image during the first back
	- * propagation of the pipeline. */
	- virtual void GenerateOutputInformation(void);
	-
	- /** Give the reader a chance to indicate that it will produce more
	- * output than it was requested to produce. ImageSeriesReader cannot
	- * currently read a portion of an image (since the ImageIO objects
	- * cannot read a portion of an image), so the ImageSeriesReader must
	- * enlarge the RequestedRegion to the size of the image on disk. */
	- virtual void EnlargeOutputRequestedRegion(itk::DataObject *output);
	-
	-protected:
	- void PrintSelf(std::ostream& os, itk::Indent indent) const;
	-
	- /** Does the real work. */
	- virtual void GenerateData();
	-
	- /** A list of filenames to be processed. */
	- HeaderContainer m_Headers;
	-
	- /** The number of independent variables in the images that comprise
	- * the series. */
	- int m_NumberOfDimensionsInImage;
	-
	-
	-private:
	- void operator=(const Self&); //purposely not implemented
	-};
	-
	-} //namespace MITK
	-
	-#include "mitkDicomDiffusionImageReader.cpp"
	-
	-#endif // __mitkDicomDiffusionImageReader_h
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDiffusionDICOMFileReader.h b/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDiffusionDICOMFileReader.h
	deleted file mode 100644
	index 3a9a4ff708..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDiffusionDICOMFileReader.h
	+++ /dev/null
	@@ -1,92 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef MITKDIFFUSIONDICOMFILEREADER_H
	-#define MITKDIFFUSIONDICOMFILEREADER_H
	-
	-#include "MitkDiffusionCoreExports.h"
	-
	-#include "mitkDICOMITKSeriesGDCMReader.h"
	-#include "mitkDiffusionHeaderDICOMFileReader.h"
	-#include "mitkClassicDICOMSeriesReader.h"
	-
	-namespace mitk
	-{
	-
	-class MITKDIFFUSIONCORE_EXPORT DiffusionDICOMFileReader
	- : public ClassicDICOMSeriesReader
	-{
	-public:
	-
	- mitkClassMacro( DiffusionDICOMFileReader, ClassicDICOMSeriesReader )
	- mitkCloneMacro( DiffusionDICOMFileReader )
	-
	- itkNewMacro( DiffusionDICOMFileReader )
	-
	- void AnalyzeInputFiles() override;
	-
	- bool LoadImages() override;
	-
	- bool CanHandleFile(const std::string &filename) override;
	-
	- void SetResolveMosaic( bool flag )
	- {
	- m_ResolveMosaic = flag;
	- }
	-
	- void SetApplyRotationToGradients( bool apply )
	- {
	- m_ApplyRotationToGradients = apply;
	- }
	-
	- std::string GetStudyName(int i){ return m_Study_names.at(i); }
	- std::string GetSeriesName(int i){ return m_Series_names.at(i); }
	-
	- std::vector<std::string> sop_instance_uids() const;
	- std::vector<std::string> frame_of_reference_uids() const;
	- std::vector<std::string> series_instance_uids() const;
	- std::vector<std::string> study_instance_uids() const;
	- std::vector<std::string> patient_names() const;
	- std::vector<std::string> patient_ids() const;
	-
	-protected:
	- DiffusionDICOMFileReader();
	- ~DiffusionDICOMFileReader() override;
	-
	- bool LoadSingleOutputImage( DiffusionHeaderDICOMFileReader::DICOMHeaderListType, DICOMImageBlockDescriptor&, bool);
	-
	- //mitk::DiffusionHeaderDICOMFileReader::DICOMHeaderListType m_RetrievedHeader;
	-
	- std::vector< mitk::DiffusionHeaderDICOMFileReader::DICOMHeaderListType > m_OutputHeaderContainer;
	- std::vector< mitk::DiffusionHeaderDICOMFileReader::Pointer> m_OutputReaderContainer;
	- std::vector< bool > m_IsMosaicData;
	- std::vector< std::string > m_Study_names;
	- std::vector< std::string > m_Series_names;
	-
	- bool m_ResolveMosaic;
	- bool m_ApplyRotationToGradients;
	-
	- std::vector< std::string > m_sop_instance_uids;
	- std::vector< std::string > m_frame_of_reference_uids;
	- std::vector< std::string > m_series_instance_uids;
	- std::vector< std::string > m_study_instance_uids;
	- std::vector< std::string > m_patient_names;
	- std::vector< std::string > m_patient_ids;
	-};
	-
	-}
	-
	-#endif // MITKDIFFUSIONDICOMFILEREADER_H
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDiffusionDICOMFileReaderHelper.h b/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDiffusionDICOMFileReaderHelper.h
	deleted file mode 100644
	index f7cece2af4..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDiffusionDICOMFileReaderHelper.h
	+++ /dev/null
	@@ -1,281 +0,0 @@
	-#ifndef MITKDIFFUSIONDICOMFILEREADERHELPER_H
	-#define MITKDIFFUSIONDICOMFILEREADERHELPER_H
	-
	-#include "itkImageSeriesReader.h"
	-#include "itkVectorImage.h"
	-
	-#include "itkImageRegionIteratorWithIndex.h"
	-
	-namespace mitk
	-{
	-
	-/**
	- * @brief The MosaicDescriptor struct is a help struct holding the necessary information for
	- * loading a mosaic DICOM file into an MITK file with correct geometry information
	- */
	-struct MosaicDescriptor
	-{
	- unsigned int nimages;
	- bool slicenormalup;
	-
	- itk::ImageBase<3>::SpacingType spacing;
	- itk::ImageBase<3>::DirectionType direction;
	- float origin[3];
	-};
	-
	-class DiffusionDICOMFileReaderHelper
	-{
	-public:
	- typedef std::vector< std::string > StringContainer;
	-
	- typedef std::vector< StringContainer > VolumeFileNamesContainer;
	-
	- std::string GetOutputName(const VolumeFileNamesContainer& filenames)
	- {
	- typedef itk::Image< short, 3> InputImageType;
	- typedef itk::ImageSeriesReader< InputImageType > SeriesReaderType;
	-
	- SeriesReaderType::Pointer probe_reader = SeriesReaderType::New();
	- probe_reader->SetFileNames( filenames.at(0) );
	- probe_reader->GenerateOutputInformation();
	- probe_reader->Update();
	-
	- std::string seriesDescTag, seriesNumberTag, patientName;
	- SeriesReaderType::DictionaryArrayRawPointer inputDict = probe_reader->GetMetaDataDictionaryArray();
	-
	- if( ! itk::ExposeMetaData< std::string > ( (inputDict)[0], "0008\|103e", seriesDescTag ) )
	- seriesDescTag = "UNSeries";
	-
	- if( ! itk::ExposeMetaData< std::string > ( (inputDict)[0], "0020\|0011", seriesNumberTag ) )
	- seriesNumberTag = "00000";
	-
	- if( ! itk::ExposeMetaData< std::string > ( (inputDict)[0], "0010\|0010", patientName ) )
	- patientName = "UnknownName";
	-
	- std::stringstream ss;
	- ss << seriesDescTag << "_" << seriesNumberTag << "_" << patientName;
	-
	- return ss.str();
	-
	- }
	-
	- template< typename PixelType, unsigned int VecImageDimension>
	- typename itk::VectorImage< PixelType, VecImageDimension >::Pointer LoadToVector(
	- const VolumeFileNamesContainer& filenames
	- //const itk::ImageBase<3>::RegionType requestedRegion
	- )
	- {
	- typedef itk::Image< PixelType, 3> InputImageType;
	- typedef itk::ImageSeriesReader< InputImageType > SeriesReaderType;
	-
	- typename SeriesReaderType::Pointer probe_reader = SeriesReaderType::New();
	- probe_reader->SetFileNames( filenames.at(0) );
	- probe_reader->GenerateOutputInformation();
	- const itk::ImageBase<3>::RegionType requestedRegion = probe_reader->GetOutput()->GetLargestPossibleRegion();
	-
	- MITK_INFO << " --- Probe reader : \n" <<
	- " Retrieved LPR " << requestedRegion;
	-
	- typedef itk::VectorImage< PixelType, 3 > VectorImageType;
	-
	- typename VectorImageType::Pointer output_image = VectorImageType::New();
	- output_image->SetNumberOfComponentsPerPixel( filenames.size() );
	- output_image->SetSpacing( probe_reader->GetOutput()->GetSpacing() );
	- output_image->SetOrigin( probe_reader->GetOutput()->GetOrigin() );
	- output_image->SetDirection( probe_reader->GetOutput()->GetDirection() );
	- output_image->SetLargestPossibleRegion( probe_reader->GetOutput()->GetLargestPossibleRegion() );
	- output_image->SetBufferedRegion( requestedRegion );
	- output_image->Allocate();
	-
	- itk::ImageRegionIterator< VectorImageType > vecIter(
	- output_image, requestedRegion );
	-
	- auto volumesFileNamesIter = filenames.begin();
	-
	- // iterate over the given volumes
	- unsigned int component = 0;
	- while( volumesFileNamesIter != filenames.end() )
	- {
	-
	- MITK_INFO << " ======== Loading volume " << component+1 << " of " << filenames.size();
	-
	- typename SeriesReaderType::Pointer volume_reader = SeriesReaderType::New();
	- volume_reader->SetFileNames( *volumesFileNamesIter );
	-
	- try
	- {
	- volume_reader->UpdateLargestPossibleRegion();
	- }
	- catch( const itk::ExceptionObject &e)
	- {
	- mitkThrow() << " ITK Series reader failed : "<< e.what();
	- }
	-
	- itk::ImageRegionConstIterator< InputImageType > iRCIter (
	- volume_reader->GetOutput(),
	- volume_reader->GetOutput()->GetLargestPossibleRegion() );
	-
	- // transfer to vector image
	- iRCIter.GoToBegin();
	- vecIter.GoToBegin();
	-
	-
	-
	- while( !iRCIter.IsAtEnd() )
	- {
	- typename VectorImageType::PixelType vector_pixel = vecIter.Get();
	- vector_pixel.SetElement( component, iRCIter.Get() );
	- vecIter.Set( vector_pixel );
	-
	- ++vecIter;
	- ++iRCIter;
	- }
	-
	- ++volumesFileNamesIter;
	- component++;
	- }
	-
	- return output_image;
	-
	- }
	-
	-
	- /**
	- * Create the vector image for the resulting diffusion image from a mosaic DICOM image set,
	- * The method needs to be provided with the MosaicDescriptor struct to be able to compute the
	- * correct index and to set the geometry information of the image itself.
	- */
	- template< typename PixelType, unsigned int VecImageDimension>
	- typename itk::VectorImage< PixelType, VecImageDimension >::Pointer LoadMosaicToVector(
	- const VolumeFileNamesContainer& filenames,
	- const MosaicDescriptor& mosaicInfo )
	- {
	- typedef itk::Image< PixelType, 3> MosaicImageType;
	- typedef itk::ImageFileReader< MosaicImageType > SingleImageReaderType;
	-
	- // generate output
	- typedef itk::VectorImage< PixelType, 3 > VectorImageType;
	-
	- auto volumesFileNamesIter = filenames.begin();
	-
	- // probe the first file to retrieve the size of the 2d image
	- // we need this information to compute the index relation between mosaic and resulting 3d position
	- // but we need it only once
	- typename SingleImageReaderType::Pointer mosaic_probe = SingleImageReaderType::New();
	- mosaic_probe->SetFileName( (*volumesFileNamesIter).at(0) );
	- try
	- {
	- mosaic_probe->UpdateLargestPossibleRegion();
	- }
	- catch( const itk::ExceptionObject &e)
	- {
	- mitkThrow() << " ITK Image file reader failed : "<< e.what();
	- }
	-
	- typename MosaicImageType::RegionType mosaic_lpr = mosaic_probe->GetOutput()->GetLargestPossibleRegion();
	- MITK_INFO << " == MOSAIC: " << mosaic_lpr;
	-
	- itk::ImageBase<3>::SizeValueType images_per_row = ceil( sqrt( (float) mosaicInfo.nimages ) );
	-
	- itk::ImageBase<3>::RegionType requestedRegion;
	- requestedRegion.SetSize( 0, mosaic_lpr.GetSize()[0]/images_per_row);
	- requestedRegion.SetSize( 1, mosaic_lpr.GetSize()[1]/images_per_row);
	- requestedRegion.SetSize( 2, mosaicInfo.nimages);
	-
	- typename VectorImageType::Pointer output_image = VectorImageType::New();
	- output_image->SetNumberOfComponentsPerPixel( filenames.size() );
	-
	- typename VectorImageType::DirectionType dmatrix;
	- dmatrix.SetIdentity();
	-
	- std::vector<double> dirx = mosaic_probe->GetImageIO()->GetDirection(0);
	- std::vector<double> diry = mosaic_probe->GetImageIO()->GetDirection(1);
	- std::vector<double> dirz = mosaic_probe->GetImageIO()->GetDirection(2);
	-
	- dmatrix.GetVnlMatrix().set_column( 0, &dirx[0] );
	- dmatrix.GetVnlMatrix().set_column( 1, &diry[0] );
	- dmatrix.GetVnlMatrix().set_column( 2, &dirz[0] );
	-
	-
	- /*
	- FIXME!!! The struct currently does not provide the geometry information
	- the loading works as required*/
	- output_image->SetSpacing( mosaicInfo.spacing );
	- output_image->SetOrigin( mosaic_probe->GetOutput()->GetOrigin() );
	- output_image->SetDirection( dmatrix );
	- output_image->SetLargestPossibleRegion( requestedRegion );
	- output_image->SetBufferedRegion( requestedRegion );
	- output_image->Allocate();
	-
	- itk::ImageRegionIteratorWithIndex< VectorImageType > vecIter(
	- output_image, requestedRegion );
	-
	- // hold the image sizes in an extra variable ( used very often )
	- typename MosaicImageType::SizeValueType dx = requestedRegion.GetSize()[0];
	- typename MosaicImageType::SizeValueType dy = requestedRegion.GetSize()[1];
	-
	- // iterate over the given volumes
	- unsigned int component = 0;
	- while( volumesFileNamesIter != filenames.end() )
	- {
	-
	- MITK_INFO << " ======== Loading volume " << component+1 << " of " << filenames.size();
	-
	- typename SingleImageReaderType::Pointer mosaic_reader = SingleImageReaderType::New();
	- mosaic_reader->SetFileName( (*volumesFileNamesIter).at(0) );
	-
	- try
	- {
	- mosaic_reader->UpdateLargestPossibleRegion();
	- }
	- catch( const itk::ExceptionObject &e)
	- {
	- mitkThrow() << " ITK Image file reader failed : "<< e.what();
	- }
	-
	- typename MosaicImageType::Pointer current_mosaic = mosaic_reader->GetOutput();
	-
	- vecIter.GoToBegin();
	- while( !vecIter.IsAtEnd() )
	- {
	- typename VectorImageType::PixelType vector_pixel = vecIter.Get();
	- typename VectorImageType::IndexType threeD_index = vecIter.GetIndex();
	-
	- typename MosaicImageType::IndexType mosaic_index;
	-
	- mosaic_index[2] = 0;
	-
	- // first find the corresponding tile in the mosaic
	- // this is defined by the z-position of the vector (3D) image iterator
	- // in x : z_index % #images_in_grid
	- // in y : z_index / #images_in_grid
	- //
	- // the remaining is just computing the correct position in the mosaic, done by
	- // --------- index of (0,0,z) ----- + --- current 2d position ---
	- mosaic_index[0] = (threeD_index[2] % images_per_row) * dx + threeD_index[0];
	- mosaic_index[1] = (threeD_index[2] / images_per_row) * dy + threeD_index[1];
	-
	- typename MosaicImageType::PixelType mosaic_pixel = current_mosaic->GetPixel( mosaic_index );
	-
	- vector_pixel.SetElement( component, mosaic_pixel );
	-
	- vecIter.Set( vector_pixel );
	-
	- ++vecIter;
	- }
	-
	- ++volumesFileNamesIter;
	- component++;
	-
	- }
	-
	- return output_image;
	-
	- }
	-
	-};
	-
	-
	-}
	-
	-#endif // MITKDIFFUSIONDICOMFILEREADERHELPER_H
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDiffusionHeaderDICOMFileReader.h b/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDiffusionHeaderDICOMFileReader.h
	deleted file mode 100644
	index e647a1dd2f..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDiffusionHeaderDICOMFileReader.h
	+++ /dev/null
	@@ -1,120 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef MITKDIFFUSIONHEADERFILEREADER_H
	-#define MITKDIFFUSIONHEADERFILEREADER_H
	-
	-#include <MitkDiffusionCoreExports.h>
	-#include <mitkCommon.h>
	-
	-#include <itkLightObject.h>
	-#include <itkObjectFactory.h>
	-
	-#include "gdcmScanner.h"
	-#include "gdcmReader.h"
	-#include <vnl/vnl_vector_fixed.h>
	-
	-
	-namespace mitk
	-{
	-
	-/**
	- * @brief The DiffusionImageHeaderInformation struct
	- */
	-struct DiffusionImageDICOMHeaderInformation
	-{
	- DiffusionImageDICOMHeaderInformation()
	- : b_value(0),
	- baseline(false),
	- isotropic(false)
	- {
	- g_vector.fill(0);
	- }
	-
	- void Print()
	- {
	- MITK_INFO << " DiffusionImageHeaderInformation : \n"
	- << " : b value : " << b_value << "\n"
	- << " : gradient : " << g_vector << "\n"
	- << " : isotropic : " << isotropic << "\n --- \n";
	- }
	-
	- unsigned int b_value;
	- vnl_vector_fixed< double, 3> g_vector;
	- bool baseline;
	- bool isotropic;
	-};
	-
	-struct DiffusionImageMosaicDICOMHeaderInformation
	- : public DiffusionImageDICOMHeaderInformation
	-{
	- unsigned long n_images;
	- bool slicenormalup;
	-};
	-
	-
	-
	-/**
	- * @class DiffusionHeaderDICOMFileReader
	- *
	- * @brief Abstract class for all vendor specific diffusion file header reader
	- *
	- * To provide a diffusion header reader for a new vendor, reimplement the \sa ReadDiffusionHeader method.
	- */
	-class MITKDIFFUSIONCORE_EXPORT DiffusionHeaderDICOMFileReader
	- : public itk::LightObject
	-{
	-public:
	-
	- typedef std::vector< DiffusionImageDICOMHeaderInformation > DICOMHeaderListType;
	-
	- mitkClassMacroItkParent( DiffusionHeaderDICOMFileReader, itk::LightObject )
	- itkSimpleNewMacro( Self )
	-
	- /**
	- * @brief IsDiffusionHeader Parse the given dicom file and collect the special diffusion image information
	- * @return
	- */
	- virtual bool ReadDiffusionHeader( std::string ){ return false; }
	-
	- DICOMHeaderListType GetHeaderInformation();
	-
	-protected:
	- DiffusionHeaderDICOMFileReader();
	-
	- ~DiffusionHeaderDICOMFileReader() override;
	-
	- DICOMHeaderListType m_HeaderInformationList;
	-};
	-
	-/**
	- * @brief Retrieve the value of a gdcm tag to the given string
	- *
	- * @param tag the gdcm::Tag to be search for
	- * @param dataset a gdcm::DataSet to look into
	- * @param target a string to store the value of the given tag if found
	- * @param verbose make some output
	- *
	- * @return true if a string was found, false otherwise
	- */
	-bool RevealBinaryTag(const gdcm::Tag tag, const gdcm::DataSet& dataset, std::string& target);
	-
	-bool RevealBinaryTagC(const gdcm::Tag tag, const gdcm::DataSet& dataset, char* target_array );
	-
	-
	-} // end namespace mitk
	-
	-#endif // MITKDIFFUSIONHEADERFILEREADER_H
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDiffusionHeaderGEDICOMFileReader.h b/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDiffusionHeaderGEDICOMFileReader.h
	deleted file mode 100644
	index e57f9947f2..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDiffusionHeaderGEDICOMFileReader.h
	+++ /dev/null
	@@ -1,28 +0,0 @@
	-#ifndef MITKDIFFUSIONHEADERGEDICOMFILEREADER_H
	-#define MITKDIFFUSIONHEADERGEDICOMFILEREADER_H
	-
	-#include "MitkDiffusionCoreExports.h"
	-#include "mitkDiffusionHeaderDICOMFileReader.h"
	-
	-namespace mitk
	-{
	-
	-class MITKDIFFUSIONCORE_EXPORT DiffusionHeaderGEDICOMFileReader
	- : public DiffusionHeaderDICOMFileReader
	-{
	-public:
	-
	- mitkClassMacro( DiffusionHeaderGEDICOMFileReader, DiffusionHeaderDICOMFileReader )
	- itkNewMacro( Self )
	-
	- bool ReadDiffusionHeader(std::string filename) override;
	-
	-protected:
	- DiffusionHeaderGEDICOMFileReader();
	-
	- ~DiffusionHeaderGEDICOMFileReader() override;
	-};
	-
	-}
	-
	-#endif // MITKDIFFUSIONHEADERGEDICOMFILEREADER_H
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDiffusionHeaderPhilipsDICOMFileReader.h b/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDiffusionHeaderPhilipsDICOMFileReader.h
	deleted file mode 100644
	index 28584ff5a6..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDiffusionHeaderPhilipsDICOMFileReader.h
	+++ /dev/null
	@@ -1,45 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef MITKDIFFUSIONHEADERPHILIPSDICOMREADER_H
	-#define MITKDIFFUSIONHEADERPHILIPSDICOMREADER_H
	-
	-
	-#include <MitkDiffusionCoreExports.h>
	-#include "mitkDiffusionHeaderDICOMFileReader.h"
	-
	-namespace mitk
	-{
	-
	-class MITKDIFFUSIONCORE_EXPORT DiffusionHeaderPhilipsDICOMFileReader
	- : public DiffusionHeaderDICOMFileReader
	-{
	-public:
	-
	- mitkClassMacro( DiffusionHeaderPhilipsDICOMFileReader, DiffusionHeaderDICOMFileReader )
	- itkNewMacro( Self )
	-
	- bool ReadDiffusionHeader(std::string filename) override;
	-
	-protected:
	- DiffusionHeaderPhilipsDICOMFileReader();
	-
	- ~DiffusionHeaderPhilipsDICOMFileReader() override;
	-};
	-
	-}
	-
	-#endif // MITKDIFFUSIONHEADERPHILIPSDICOMREADER_H
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDiffusionHeaderSiemensDICOMFileHelper.h b/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDiffusionHeaderSiemensDICOMFileHelper.h
	deleted file mode 100644
	index 26abbfab51..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDiffusionHeaderSiemensDICOMFileHelper.h
	+++ /dev/null
	@@ -1,45 +0,0 @@
	-#ifndef MITKDIFFUSIONHEADERSIEMENSDICOMFILEHELPER_H
	-#define MITKDIFFUSIONHEADERSIEMENSDICOMFILEHELPER_H
	-
	-#include <string>
	-#include <vector>
	-
	-namespace mitk
	-{
	-
	-enum SiemensDiffusionHeaderType {
	- SIEMENS_CSA1 = 0,
	- SIEMENS_CSA2
	-};
	-
	-SiemensDiffusionHeaderType GetHeaderType( std::string header );
	-
	-struct Siemens_Header_Format
	-{
	- Siemens_Header_Format( size_t nlen,
	- size_t vm,
	- size_t vr,
	- size_t syngodt,
	- size_t nitems )
	- : NameLength( nlen ),
	- Delimiter( "\0" ),
	- VM( vm ),
	- VR( vr ),
	- Syngodt( syngodt ),
	- NumItems( nitems )
	- {
	-
	- }
	-
	- size_t NameLength;
	- std::string Delimiter;
	- size_t VM;
	- size_t VR;
	- size_t Syngodt;
	- size_t NumItems;
	-};
	-
	-bool ParseInputString( std::string input, std::vector<double>& values, Siemens_Header_Format format_specs );
	-
	-} //end namespace
	-#endif // MITKDIFFUSIONHEADERSIEMENSDICOMFILEHELPER_H
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDiffusionHeaderSiemensDICOMFileReader.h b/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDiffusionHeaderSiemensDICOMFileReader.h
	deleted file mode 100644
	index 0968c608fe..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDiffusionHeaderSiemensDICOMFileReader.h
	+++ /dev/null
	@@ -1,49 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef MITKDIFFUSIONHEADERSIEMENSDICOMFILEREADER_H
	-#define MITKDIFFUSIONHEADERSIEMENSDICOMFILEREADER_H
	-
	-#include "MitkDiffusionCoreExports.h"
	-
	-#include "mitkDiffusionHeaderDICOMFileReader.h"
	-#include "mitkDiffusionHeaderSiemensDICOMFileHelper.h"
	-
	-namespace mitk
	-{
	-
	-class MITKDIFFUSIONCORE_EXPORT DiffusionHeaderSiemensDICOMFileReader
	- : public DiffusionHeaderDICOMFileReader
	-{
	-public:
	-
	- mitkClassMacro( DiffusionHeaderSiemensDICOMFileReader, DiffusionHeaderDICOMFileReader )
	- itkNewMacro( Self )
	-
	- bool ReadDiffusionHeader(std::string filename) override;
	-
	-protected:
	- DiffusionHeaderSiemensDICOMFileReader();
	-
	- ~DiffusionHeaderSiemensDICOMFileReader() override;
	-
	- bool ExtractSiemensDiffusionTagInformation( std::string tag_value, mitk::DiffusionImageDICOMHeaderInformation& values );
	-
	- std::vector< Siemens_Header_Format > m_SiemensFormatsCollection;
	-};
	-
	-}
	-#endif // MITKDIFFUSIONHEADERSIEMENSDICOMFILEREADER_H
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDiffusionHeaderSiemensMosaicDICOMFileReader.h b/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDiffusionHeaderSiemensMosaicDICOMFileReader.h
	deleted file mode 100644
	index 0f0b0ab883..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkDiffusionHeaderSiemensMosaicDICOMFileReader.h
	+++ /dev/null
	@@ -1,53 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef MITKDIFFUSIONHEADERSIEMENSMOSAICDICOMFILEREADER_H
	-#define MITKDIFFUSIONHEADERSIEMENSMOSAICDICOMFILEREADER_H
	-
	-#include "mitkDiffusionHeaderSiemensDICOMFileReader.h"
	-#include "mitkDiffusionDICOMFileReaderHelper.h"
	-
	-namespace mitk
	-{
	-
	-class MITKDIFFUSIONCORE_EXPORT DiffusionHeaderSiemensMosaicDICOMFileReader
	- : public DiffusionHeaderSiemensDICOMFileReader
	-{
	-public:
	- mitkClassMacro( DiffusionHeaderSiemensMosaicDICOMFileReader,
	- DiffusionHeaderSiemensDICOMFileReader )
	- itkNewMacro( Self )
	-
	- bool ReadDiffusionHeader(std::string filename) override;
	-
	- mitk::MosaicDescriptor GetMosaicDescriptor()
	- {
	- return m_MosaicDescriptor;
	- }
	-
	- void RetrieveMosaicInformation(std::string filename);
	-
	-protected:
	- DiffusionHeaderSiemensMosaicDICOMFileReader();
	-
	- ~DiffusionHeaderSiemensMosaicDICOMFileReader() override;
	-
	- mitk::MosaicDescriptor m_MosaicDescriptor;
	-};
	-
	-}
	-
	-#endif // MITKDIFFUSIONHEADERSIEMENSMOSAICDICOMFILEREADER_H
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkGEDicomDiffusionImageHeaderReader.h b/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkGEDicomDiffusionImageHeaderReader.h
	deleted file mode 100644
	index a3f800e2d8..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkGEDicomDiffusionImageHeaderReader.h
	+++ /dev/null
	@@ -1,48 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef __mitkGEDicomDiffusionImageHeaderReader_h__
	-#define __mitkGEDicomDiffusionImageHeaderReader_h__
	-
	-#include "mitkDicomDiffusionImageHeaderReader.h"
	-
	-namespace mitk
	-{
	-
	- class GEDicomDiffusionImageHeaderReader : public DicomDiffusionImageHeaderReader
	- {
	- public:
	-
	- mitkClassMacro( GEDicomDiffusionImageHeaderReader, DicomDiffusionImageHeaderReader );
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- void Update() override;
	-
	- protected:
	-
	- GEDicomDiffusionImageHeaderReader();
	- ~GEDicomDiffusionImageHeaderReader() override;
	-
	- };
	-
	-}
	-
	-#endif
	-
	-
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkGroupDiffusionHeadersFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkGroupDiffusionHeadersFilter.h
	deleted file mode 100644
	index a01d62dc0a..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkGroupDiffusionHeadersFilter.h
	+++ /dev/null
	@@ -1,110 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef _mitkGroupDiffusionHeadersFilter_h
	-#define _mitkGroupDiffusionHeadersFilter_h
	-
	-#include <MitkDiffusionCoreExports.h>
	-
	-#include "mitkBaseProcess.h"
	-#include "mitkDiffusionImageHeaderInformation.h"
	-
	-namespace mitk
	-{
	- /**
	- * @brief Groups Headers containing Diffusion Information
	- * @ingroup Process
	- */
	- class MITKDIFFUSIONCORE_EXPORT GroupDiffusionHeadersFilter : public BaseProcess
	- {
	- public:
	- mitkClassMacro( GroupDiffusionHeadersFilter, BaseProcess );
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- typedef mitk::DiffusionImageHeaderInformation HeaderType;
	- typedef HeaderType::Pointer HeaderPointer;
	- typedef std::vector<HeaderPointer> InputType;
	-
	- typedef std::vector<InputType> OutputType;
	-
	- /**
	- * Sets the input of this process object
	- * @param input the input
	- */
	- virtual void SetInput( InputType input );
	-
	- /**
	- * Sets the input n'th of this process object
	- * @param idx the number associated with the given input
	- */
	- virtual void SetInput( const unsigned int& idx, InputType input );
	-
	- /**
	- * Sets the input n'th of this process object
	- * @param idx the number associated with the given input
	- */
	- virtual void SetNthOutput( const unsigned int& idx, InputType output );
	-
	- /**
	- * @returns the input tree of the process object
	- */
	- InputType GetInput( void );
	-
	- /**
	- * @param idx the index of the input to return
	- * @returns the input object with the given index
	- */
	- InputType GetInput( const unsigned int& idx );
	-
	- OutputType GetOutput();
	-
	- virtual DataObjectPointer MakeOutput ( DataObjectPointerArraySizeType ){}
	-
	- virtual DataObjectPointer MakeOutput(const DataObjectIdentifierType& ) {}
	-
	- virtual void GenerateOutputInformation();
	-
	- virtual void Update();
	-
	- protected:
	-
	- /**
	- * A default constructor
	- */
	- GroupDiffusionHeadersFilter();
	-
	- /**
	- * The destructor
	- */
	- virtual ~GroupDiffusionHeadersFilter();
	-
	- OutputType m_Output;
	- InputType m_Input;
	-
	- private:
	-
	- void operator=( const Self& ); //purposely not implemented
	- }
	- ;
	-
	-} //end of namespace mitk
	-
	-#endif
	-
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkPhilipsDicomDiffusionImageHeaderReader.h b/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkPhilipsDicomDiffusionImageHeaderReader.h
	deleted file mode 100644
	index 8ff911c372..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkPhilipsDicomDiffusionImageHeaderReader.h
	+++ /dev/null
	@@ -1,53 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef __mitkPhilipsDicomDiffusionImageHeaderReader_h__
	-#define __mitkPhilipsDicomDiffusionImageHeaderReader_h__
	-
	-#include "mitkDicomDiffusionImageHeaderReader.h"
	-
	-namespace mitk
	-{
	- /**
	- @brief The PhilipsDicomDiffusionImageHeaderReader class reads in the image header information for the Philips DICOM Format */
	- class PhilipsDicomDiffusionImageHeaderReader : public DicomDiffusionImageHeaderReader
	- {
	- public:
	-
	- mitkClassMacro( PhilipsDicomDiffusionImageHeaderReader, DicomDiffusionImageHeaderReader );
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** read in the data */
	- void Update() override;
	-
	- protected:
	-
	- /** Default c'tor */
	- PhilipsDicomDiffusionImageHeaderReader();
	-
	- /** Default d'tor */
	- ~PhilipsDicomDiffusionImageHeaderReader() override;
	-
	- };
	-
	-}
	-
	-#endif
	-
	-
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkSiemensDicomDiffusionImageHeaderReader.h b/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkSiemensDicomDiffusionImageHeaderReader.h
	deleted file mode 100644
	index eafffc783a..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkSiemensDicomDiffusionImageHeaderReader.h
	+++ /dev/null
	@@ -1,59 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef __mitkSiemensDicomDiffusionImageHeaderReader_h__
	-#define __mitkSiemensDicomDiffusionImageHeaderReader_h__
	-
	-#include "mitkDicomDiffusionImageHeaderReader.h"
	-
	-namespace mitk
	-{
	- /**
	- @brief The SiemensDicomDiffusionImageHeaderReader class reads in the header information for the standard Siemens DICOM format
	- */
	- class SiemensDicomDiffusionImageHeaderReader : public DicomDiffusionImageHeaderReader
	- {
	- public:
	-
	- mitkClassMacro( SiemensDicomDiffusionImageHeaderReader, DicomDiffusionImageHeaderReader );
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Extract the key value for the key nameString from the tagString */
	- int ExtractSiemensDiffusionInformation( std::string tagString, std::string nameString, std::vector<double>& valueArray, int startPos = 0 );
	-
	- /** Extracts the diffusion gradient information from the tagString and stores it into the valueArray vector */
	- int ExtractSiemensDiffusionGradientInformation( std::string tagString, std::string nameString, std::vector<double>& valueArray);
	-
	- /** Read the data */
	- void Update() override;
	-
	- protected:
	- /** Default c'tor */
	- SiemensDicomDiffusionImageHeaderReader();
	-
	- /** Default d'tor */
	- ~SiemensDicomDiffusionImageHeaderReader() override;
	-
	- };
	-
	-}
	-
	-#endif
	-
	-
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkSiemensMosaicDicomDiffusionImageHeaderReader.h b/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkSiemensMosaicDicomDiffusionImageHeaderReader.h
	deleted file mode 100644
	index a5ac1878bf..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/DicomImport/mitkSiemensMosaicDicomDiffusionImageHeaderReader.h
	+++ /dev/null
	@@ -1,55 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef __mitkSiemensMosaicDicomDiffusionImageHeaderReader_h__
	-#define __mitkSiemensMosaicDicomDiffusionImageHeaderReader_h__
	-
	-#include "mitkDicomDiffusionImageHeaderReader.h"
	-
	-namespace mitk
	-{
	- /**
	- @brief The SiemensMosaicDicomDiffusionImageHeaderReader class reads the image header for diffusion MR data stored in
	- Siemens MOSAIC Format
	- */
	- class SiemensMosaicDicomDiffusionImageHeaderReader : public DicomDiffusionImageHeaderReader
	- {
	- public:
	- mitkClassMacro( SiemensMosaicDicomDiffusionImageHeaderReader, DicomDiffusionImageHeaderReader );
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Extracts the information stored under the key nameString in the tagString */
	- int ExtractSiemensDiffusionInformation( std::string tagString, std::string nameString, std::vector<double>& valueArray );
	-
	- /** Read the data */
	- void Update() override;
	-
	- protected:
	- /** Default c'tor */
	- SiemensMosaicDicomDiffusionImageHeaderReader();
	-
	- /** Default class d'tor */
	- ~SiemensMosaicDicomDiffusionImageHeaderReader() override;
	- };
	-
	-}
	-
	-#endif
	-
	-
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCorrectionFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCorrectionFilter.h
	deleted file mode 100644
	index 93596f0d78..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCorrectionFilter.h
	+++ /dev/null
	@@ -1,94 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef MITKDIFFUSIONIMAGECORRECTIONFILTER_H
	-#define MITKDIFFUSIONIMAGECORRECTIONFILTER_H
	-
	-#include "mitkImageSource.h"
	-#include <MitkDiffusionCoreExports.h>
	-
	-namespace mitk
	-{
	-/**
	- * @class DiffusionImageCorrectionFilter
	- */
	-class MITKDIFFUSIONCORE_EXPORT DiffusionImageCorrectionFilter
	- : public ImageSource
	-{
	-public:
	- /** class macros */
	- mitkClassMacro( DiffusionImageCorrectionFilter,
	- ImageSource )
	-
	- itkSimpleNewMacro(Self)
	-
	- typedef short DiffusionPixelType;
	- typedef vnl_matrix_fixed< double, 3, 3 > TransformMatrixType;
	-
	- typedef std::vector< TransformMatrixType > TransformsVectorType;
	-
	- typedef Superclass::OutputType DiffusionImageType;
	- typedef DiffusionImageType::Pointer DiffusionImageTypePointer;
	- typedef itk::VectorImage<DiffusionPixelType,3> ImageType;
	-
	- /**
	- * @brief Set the mitk image ( a 3d+t image ) which is to be reinterpreted as dw image
	- * @param mitkImage
	- */
	- void SetImage( DiffusionImageTypePointer input )
	- {
	- m_SourceImage = input;
	- }
	-
	- /**
	- * @brief Correct each gradient direction according to the given transform
	- *
	- * The size of the input is expected to correspond to the count of gradient images in the image.
	- */
	- void CorrectDirections( const TransformsVectorType& );
	-
	- /**
	- * @brief Correct all gradient directions according to the given transform
	- *
	- * This will apply the same rotation to all directions.
	- */
	- void CorrectDirections( const TransformMatrixType& );
	-
	- void GenerateOutputInformation() override {}
	-
	-
	-protected:
	- DiffusionImageCorrectionFilter();
	- ~DiffusionImageCorrectionFilter() override {}
	-
	- /**
	- * @brief Get the rotation component following the Finite Strain
	- *
	- * For a given transformation \f$A\f$ its rotation component is defined as \f$ (AA^{T})^{-1/2}\f$.
	- *
	- * The computation first computes \f$ B = AA^T \f$ and then estimates the square root. Square root of
	- * diagonal matrices is defined as
	- * \f$ S = Q * \sqrt{C} * Q^{-1} \f$ with \f$ C \f$ having the eigenvalues on the diagonal.
	- *
	- */
	- TransformMatrixType GetRotationComponent( const TransformMatrixType& );
	-
	- DiffusionImageTypePointer m_SourceImage;
	-};
	-
	-}
	-
	-#endif // MITKDIFFUSIONIMAGECORRECTIONFILTER_H
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCreationFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCreationFilter.h
	deleted file mode 100644
	index e113c124f0..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCreationFilter.h
	+++ /dev/null
	@@ -1,106 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef DIFFUSIONIMAGECREATIONFILTER_H
	-#define DIFFUSIONIMAGECREATIONFILTER_H
	-
	-#include "mitkImageToImageFilter.h"
	-#include "mitkDiffusionPropertyHelper.h"
	-#include <MitkDiffusionCoreExports.h>
	-
	-namespace mitk
	-{
	-
	-/**
	- * @brief The DiffusionImageHeaderDescriptor struct bundles the necessary diffusion-weighted image header meta information.
	- */
	-struct MITKDIFFUSIONCORE_EXPORT DiffusionImageHeaderDescriptor
	-{
	- DiffusionImageHeaderDescriptor()
	- : m_GradientDirections(nullptr)
	- {
	- m_BValue = -1;
	- }
	-
	- float m_BValue;
	- mitk::DiffusionPropertyHelper::BValueMapType m_BValueMapType;
	- mitk::DiffusionPropertyHelper::MeasurementFrameType m_MeasurementFrame;
	- mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer m_GradientDirections;
	-};
	-
	-/**
	- * @brief The DiffusionImageCreationFilter class creates a diffusion-weighted image out of a
	- * given 3D+t regular image and sufficient additional information about gradient directions and b values
	- *
	- * For easier use, the filter supports the usage of reference images. Here a diffusion-weighted (dw) image is expected and the meta
	- * information of this image will be used for the output dw image. The diffusion information can also be specified by setting the HeaderDescriptor
	- * directly (SetHeaderDescriptor).
	- *
	- * At least one of reference image or descriptor must be used, otherwise an exception is thrown.
	- */
	-class MITKDIFFUSIONCORE_EXPORT DiffusionImageCreationFilter
	- : public ImageToImageFilter
	-{
	-public:
	- /** class macros */
	- mitkClassMacro( DiffusionImageCreationFilter,
	- ImageToImageFilter )
	-
	- itkNewMacro(Self)
	-
	- typedef short DiffusionPixelType;
	- typedef mitk::DiffusionPropertyHelper DPH;
	-
	- typedef mitk::Image OutputType;
	- typedef mitk::DiffusionPropertyHelper::ImageType VectorImageType;
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionType GradientDirectionType;
	- typedef mitk::DiffusionPropertyHelper::MeasurementFrameType MeasurementFrameType;
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionsContainerType GradientDirectionContainerType;
	-
	- /**
	- * @brief SetReferenceImage Set a diffusion image as reference, i.e. the header information will be extracted from it
	- * @param reference_image A reference diffusion-weigted image - will throw exception of the input is not DW image
	- */
	- void SetReferenceImage( mitk::Image::Pointer reference_image );
	-
	- /**
	- * @brief SetHeaderDescriptor set the information to be used with the dw image
	- * @param header_descriptor
	- *
	- * \sa DiffusionImageHeaderDescriptor
	- */
	- void SetHeaderDescriptor( DiffusionImageHeaderDescriptor header_descriptor );
	-
	- void GenerateData() override;
	-protected:
	- DiffusionImageCreationFilter();
	- ~DiffusionImageCreationFilter() override;
	-
	- GradientDirectionContainerType::Pointer InternalGetGradientDirections( );
	- MeasurementFrameType InternalGetMeasurementFrame();
	- float InternalGetBValue();
	-
	- VectorImageType::Pointer RemapIntoVectorImage( mitk::Image::Pointer input);
	-
	- mitk::Image::Pointer m_ReferenceImage;
	-
	- DiffusionImageHeaderDescriptor m_HeaderDescriptor;
	- bool m_HeaderDescriptorSet;
	-};
	-
	-} //end namespace mitk
	-
	-#endif // DIFFUSIONIMAGECREATIONFILTER_H
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageHeaderInformation.h b/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageHeaderInformation.h
	deleted file mode 100644
	index 3478904ede..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageHeaderInformation.h
	+++ /dev/null
	@@ -1,123 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef MITK_DiffusionImageHeaderInformation_H
	-#define MITK_DiffusionImageHeaderInformation_H
	-
	-#include <itkObject.h>
	-#include "vnl/vnl_vector_fixed.h"
	-#include "mitkCommon.h"
	-#include "itkObjectFactory.h"
	-
	-namespace mitk
	-{
	-
	- enum DiffusionHeaderGroup{
	- DHG_NotYetGrouped,
	- DHG_ZeroDiffusionWeighted,
	- DHG_NonZeroDiffusionWeighted,
	- DHG_Other,
	- };
	-
	- class DiffusionImageHeaderInformation : public itk::Object
	- {
	-
	- public:
	-
	- mitkClassMacroItkParent( DiffusionImageHeaderInformation, itk::Object );
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- typedef std::vector< std::string > FileNamesContainer;
	-
	- //DiffusionImageHeaderInformation(int nRows, int nCols, float xRes, float yRes, float xOrigin,
	- // float yOrigin, float zOrigin, float sliceThickness, float sliceSpacing,
	- // int nSliceInVolume, float xRow, float yRow, float zRow, float xCol,
	- // float yCol, float zCol, float xSlice, float ySlice, float zSlice,
	- // float bValue, vnl_vector_fixed<double, 3> DiffusionVector,
	- // std::string vendor, bool mosaic, DiffusionHeaderGroup headerGroup = DHG_NotYetGrouped):
	- // nRows(nRows), nCols(nCols),xRes(xRes),
	- // yRes(yRes),xOrigin(xOrigin),yOrigin(yOrigin),zOrigin(zOrigin),
	- // sliceThickness(sliceThickness),sliceSpacing(sliceSpacing),
	- // nSliceInVolume(nSliceInVolume), xRow(xRow), yRow(yRow), zRow(zRow),
	- // xCol(xCol),yCol(yCol),zCol(zCol),xSlice(xSlice),ySlice(ySlice),zSlice(zSlice),
	- // bValue(bValue), DiffusionVector(DiffusionVector), vendor(vendor),mosaic(mosaic),
	- // headerGroup(headerGroup) {}
	-
	- std::string seriesDescription;
	- int seriesNumber;
	- std::string patientName;
	- int nRows;
	- int nCols;
	- float xRes;
	- float yRes;
	- float xOrigin;
	- float yOrigin;
	- float zOrigin;
	- float sliceThickness;
	- float sliceSpacing;
	- int nSliceInVolume;
	- float xRow;
	- float yRow;
	- float zRow;
	- float xCol;
	- float yCol;
	- float zCol;
	- float xSlice;
	- float ySlice;
	- float zSlice;
	- float bValue;
	- vnl_vector_fixed<double, 3> DiffusionVector;
	- std::string vendor;
	- bool mosaic;
	- DiffusionHeaderGroup headerGroup;
	-
	- FileNamesContainer m_DicomFilenames;
	-
	- inline bool isIdentical(const DiffusionImageHeaderInformation::Pointer other) const {
	- return nRows == other->nRows &&
	- nCols == other->nCols &&
	- xRes == other->xRes &&
	- yRes == other->yRes &&
	- xOrigin == other->xOrigin &&
	- yOrigin == other->yOrigin &&
	- zOrigin == other->zOrigin &&
	- sliceThickness == other->sliceThickness &&
	- sliceSpacing == other->sliceSpacing &&
	- nSliceInVolume == other->nSliceInVolume &&
	- xRow == other->xRow &&
	- yRow == other->yRow &&
	- zRow == other->zRow &&
	- xCol == other->xCol &&
	- yCol == other->yCol &&
	- zCol == other->zCol &&
	- xSlice == other->xSlice &&
	- ySlice == other->ySlice &&
	- zSlice == other->zSlice;
	- }
	-
	- protected:
	-
	- DiffusionImageHeaderInformation();
	- ~DiffusionImageHeaderInformation() override;
	-
	- };
	-
	-} // namespace
	-
	-#endif // MITK_DiffusionImageHeaderInformation_H
	-
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageTransformedCreationFilter.cxx b/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageTransformedCreationFilter.cxx
	deleted file mode 100644
	index a04f4b6885..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageTransformedCreationFilter.cxx
	+++ /dev/null
	@@ -1,268 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef DIFFUSIONIMAGETRANSFORMEDCREATIONFILTER_CXX
	-#define DIFFUSIONIMAGETRANSFORMEDCREATIONFILTER_CXX
	-
	-#include "mitkDiffusionImageTransformedCreationFilter.h"
	-#include "mitkDiffusionImageCorrectionFilter.h"
	-
	-#include "mitkImageCast.h"
	-#include "mitkImageWriteAccessor.h"
	-#include "mitkImageTimeSelector.h"
	-#include "mitkProperties.h"
	-#include "mitkIOUtil.h"
	-
	-
	-#include <itkResampleImageFilter.h>
	-#include <itkNearestNeighborInterpolateImageFunction.h>
	-#include <itkWindowedSincInterpolateImageFunction.h>
	-#include <itkBSplineInterpolateImageFunction.h>
	-#include <itkLinearInterpolateImageFunction.h>
	-
	-
	-template <typename TTransformType, typename ItkImageType>
	-static void ResampleImage( typename ItkImageType::Pointer itk_reference,
	- mitk::Image::Pointer mitk_input,
	- typename TTransformType::Pointer transform,
	- unsigned int interpolator,
	- mitk::Image::Pointer output_target, unsigned int position )
	-{
	-
	-
	- typedef itk::LinearInterpolateImageFunction< ItkImageType, double > InterpolatorType;
	- typename InterpolatorType::Pointer linear_interpolator = InterpolatorType::New();
	-
	- typedef itk::NearestNeighborInterpolateImageFunction< ItkImageType, double > NearestNeighborInterpolatorType;
	- typename NearestNeighborInterpolatorType::Pointer nn_interpolator = NearestNeighborInterpolatorType::New();
	-
	- typedef itk::WindowedSincInterpolateImageFunction< ItkImageType, 7> WindowedSincInterpolatorType;
	- typename WindowedSincInterpolatorType::Pointer sinc_interpolator = WindowedSincInterpolatorType::New();
	-
	- typedef itk::BSplineInterpolateImageFunction< ItkImageType, double, double> BSplineInterpolatorType;
	- typename BSplineInterpolatorType::Pointer bicubic_interpolator = BSplineInterpolatorType::New();
	- bicubic_interpolator->SetSplineOrder(3);
	-
	- typedef typename itk::ResampleImageFilter< ItkImageType, ItkImageType, double> ResampleImageFilterType;
	- typename ResampleImageFilterType::Pointer resampler = ResampleImageFilterType::New();
	-
	- // Create interpolator pool
	- typedef itk::InterpolateImageFunction< ItkImageType, double> InterpolateFunctionBaseType;
	- std::vector< InterpolateFunctionBaseType* > InterpolateFunctionsPool;
	-
	- InterpolateFunctionsPool.push_back( nn_interpolator.GetPointer() );
	- InterpolateFunctionsPool.push_back( linear_interpolator.GetPointer() );
	- InterpolateFunctionsPool.push_back( bicubic_interpolator.GetPointer() );
	- InterpolateFunctionsPool.push_back( sinc_interpolator.GetPointer() );
	-
	- // select interpolator by the selection flag
	- resampler->SetInterpolator( InterpolateFunctionsPool.at( interpolator ) );
	-
	- typename ItkImageType::Pointer itk_input;
	- mitk::CastToItkImage< ItkImageType >( mitk_input, itk_input );
	-
	- resampler->SetInput( itk_input );
	- resampler->SetTransform( transform );
	- resampler->SetReferenceImage( itk_reference );
	- resampler->UseReferenceImageOn();
	- resampler->Update();
	-
	- mitk::Image::Pointer current_resampled = mitk::Image::New();
	- current_resampled->InitializeByItk( resampler->GetOutput() );
	- current_resampled->SetImportChannel( resampler->GetOutput()->GetBufferPointer(),
	- mitk::Image::CopyMemory );
	-
	- mitk::ImageWriteAccessor imac( current_resampled );
	- output_target->SetImportVolume( imac.GetData(),
	- position, 0, mitk::Image::CopyMemory );
	-
	-}
	-/*
	-template< typename TTransformType >
	-static mitk::DiffusionPropertyHelper::GradientDirectionType
	-TransformGradientDirection( mitk::DiffusionPropertyHelper::GradientDirectionType vec_in,
	- typename TTransformType::Pointer transform )
	-{
	- mitk::DiffusionPropertyHelper::GradientDirectionType vec_out;
	- vec_out.fill(1.0);
	-
	- typedef typename TTransformType::MatrixType TMatrixType;
	-
	- return vec_out;
	-}
	-*/
	-template< typename TTransformType>
	-mitk::DiffusionImageTransformedCreationFilter<TTransformType>
	-::DiffusionImageTransformedCreationFilter()
	-{
	- this->m_OutputPrefix = "/tmp/";
	-}
	-
	-template< typename TTransformType>
	-mitk::DiffusionImageTransformedCreationFilter<TTransformType>
	-::~DiffusionImageTransformedCreationFilter()
	-{
	-
	-}
	-
	-template< typename TTransformType>
	-mitk::DiffusionImageHeaderDescriptor
	-mitk::DiffusionImageTransformedCreationFilter<TTransformType>
	-::GetTransformedHeaderInformation()
	-{
	- typedef mitk::DiffusionPropertyHelper DPH;
	-
	- DiffusionImageHeaderDescriptor dwhdesc;
	- dwhdesc.m_BValue = DPH::GetReferenceBValue( this->m_DiffusionReferenceImage );
	- // TODO : here comes transformation of the gradients
	- dwhdesc.m_GradientDirections = DPH::GetGradientContainer( this->m_DiffusionReferenceImage );
	- dwhdesc.m_MeasurementFrame = DPH::GetMeasurementFrame( this->m_DiffusionReferenceImage );
	- dwhdesc.m_BValueMapType = DPH::GetBValueMap( this->m_DiffusionReferenceImage );
	-
	- return dwhdesc;
	-}
	-
	-template< typename TTransformType>
	-void mitk::DiffusionImageTransformedCreationFilter< TTransformType >
	-::GenerateOutputInformation()
	-{
	- MITK_INFO << "Debug info";
	-}
	-
	-
	-template< typename TTransformType>
	-void mitk::DiffusionImageTransformedCreationFilter<TTransformType>
	-::GenerateData()
	-{
	-
	- mitk::Image::Pointer input = this->GetInput();
	-
	- // validity checks
	- if( m_InternalTransforms.size() != input->GetTimeSteps() )
	- {
	- mitkThrow() << "Number of transforms" << m_InternalTransforms.size() << "differ from number of timesteps" << input->GetTimeSteps();
	- }
	-
	- typedef itk::Image< DiffusionPropertyHelper::DiffusionPixelType, 3> ImageType;
	-
	- // create intermediate output
	- mitk::Image::Pointer resampled_output = mitk::Image::New();
	- resampled_output->Initialize( input );
	-
	- ImageType::Pointer current_itk_reference = ImageType::New();
	- CastToItkImage( this->m_ResamplingReferenceImage, current_itk_reference );
	-
	- unsigned int time_dim = input->GetDimension(3);
	- for( unsigned int time_idx = 0; time_idx < time_dim; time_idx++ )
	- {
	-
	- mitk::ImageTimeSelector::Pointer t_sel = mitk::ImageTimeSelector::New();
	- t_sel->SetInput( input );
	- t_sel->SetTimeNr( time_idx );
	- t_sel->Update();
	- ResampleImage< TTransformType, ImageType>( current_itk_reference,
	- t_sel->GetOutput(),
	- this->m_InternalTransforms.at(time_idx),
	- this->m_InterpolationLevel,
	- resampled_output, time_idx);
	- }
	-
	- // call here creation filter
	- mitk::DiffusionImageCreationFilter::Pointer creator =
	- mitk::DiffusionImageCreationFilter::New();
	-
	- creator->SetInput( resampled_output );
	- creator->SetHeaderDescriptor( this->GetTransformedHeaderInformation() );
	- creator->Update();
	-
	- mitk::Image::Pointer output = creator->GetOutput();
	- mitk::DiffusionPropertyHelper::CopyProperties(resampled_output, output, true);
	-
	- typedef mitk::DiffusionPropertyHelper DPH;
	- float BValue = mitk::DiffusionPropertyHelper::GetReferenceBValue( creator->GetOutput() );
	-
	- mitk::BValueMapProperty::BValueMap BValueMap = mitk::BValueMapProperty::CreateBValueMap( mitk::DiffusionPropertyHelper::GetGradientContainer( creator->GetOutput() ), BValue );
	- output->GetPropertyList()->ReplaceProperty( DPH::GRADIENTCONTAINERPROPERTYNAME.c_str(), mitk::GradientDirectionsProperty::New( mitk::DiffusionPropertyHelper::GetGradientContainer( creator->GetOutput() )) );
	- output->GetPropertyList()->ReplaceProperty( DPH::MEASUREMENTFRAMEPROPERTYNAME.c_str(), mitk::MeasurementFrameProperty::New( mitk::DiffusionPropertyHelper::GetMeasurementFrame( creator->GetOutput() ) ) );
	- output->GetPropertyList()->ReplaceProperty( DPH::BVALUEMAPPROPERTYNAME.c_str(), mitk::BValueMapProperty::New( BValueMap ) );
	- output->GetPropertyList()->ReplaceProperty( DPH::REFERENCEBVALUEPROPERTYNAME.c_str(), mitk::FloatProperty::New( BValue ) );
	-
	- // correct gradients
	- mitk::DiffusionImageCorrectionFilter::Pointer corrector = mitk::DiffusionImageCorrectionFilter::New();
	- corrector->SetImage( output) ;
	- corrector->CorrectDirections( this->m_RotationMatrices );
	-
	- DPH pHelper( output );
	- pHelper.InitializeImage();
	-
	- m_OutputCache = output;
	- this->SetPrimaryOutput( m_OutputCache );
	- m_OutputCache->Modified();
	-}
	-
	-template< typename TTransformType>
	-void mitk::DiffusionImageTransformedCreationFilter<TTransformType>
	-::SetTransformParameters(const TransformParametersContainerType &params)
	-{
	- if( params.empty() )
	- {
	- MITK_ERROR << "Empty parameter list given.";
	- return;
	- }
	-
	- TransformContainerType transforms;
	-
	- auto iter = std::begin( params );
	- while( iter != std::end( params ) )
	- {
	- typename TTransformType::Pointer transform = TTransformType::New();
	- transform->SetParameters( (*iter) );
	-
	- transforms.push_back( transform );
	-
	- ++iter;
	- }
	-
	- this->SetTransforms( transforms );
	-}
	-
	-template< typename TTransformType>
	-void mitk::DiffusionImageTransformedCreationFilter<TTransformType>
	-::SetTransforms(const TransformContainerType &transforms)
	-{
	- if( transforms.empty() )
	- {
	- MITK_ERROR << "Empty transform list given.";
	- return;
	- }
	-
	- this->m_InternalTransforms.reserve( transforms.size() );
	- std::copy( transforms.begin(), transforms.end(),
	- std::back_inserter(this->m_InternalTransforms ) );
	-
	- MatrixType E;
	- E.set_identity();
	-
	- for( auto iter = std::begin(this->m_InternalTransforms); iter != std::end( this->m_InternalTransforms); ++iter)
	- {
	- MatrixType A = E * (*iter)->GetMatrix().GetVnlMatrix();
	- this->m_RotationMatrices.push_back( A );
	- }
	-}
	-
	-
	-
	-#endif // DIFFUSIONIMAGETRANSFORMEDCREATIONFILTER_CXX
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageTransformedCreationFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageTransformedCreationFilter.h
	deleted file mode 100644
	index 5039c443ce..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageTransformedCreationFilter.h
	+++ /dev/null
	@@ -1,116 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef DIFFUSIONIMAGETRANSFORMEDCREATIONFILTER_H
	-#define DIFFUSIONIMAGETRANSFORMEDCREATIONFILTER_H
	-
	-#include "mitkDiffusionPropertyHelper.h"
	-#include "mitkDiffusionImageCreationFilter.h"
	-#include "mitkDiffusionImageCorrectionFilter.h"
	-
	-#include <MitkDiffusionCoreExports.h>
	-
	-
	-namespace mitk
	-{
	-
	-
	-/**
	- * @brief DiffusionImageTransformedCreationFilter extends its superclass ( DiffusionImageCreationFilter ) by providing the possibility
	- * to specify a list of transforms to be applied to the separate volumes before
	- */
	-template <typename TTransformType >
	-class MITKDIFFUSIONCORE_EXPORT DiffusionImageTransformedCreationFilter
	- : public ImageToImageFilter
	-{
	-public:
	- /** class macros */
	- mitkClassMacro( DiffusionImageTransformedCreationFilter,
	- ImageToImageFilter )
	-
	- itkNewMacro(Self)
	-
	- enum InterpolatorLevel
	- {
	- NearestNeighbor = 0,
	- Trilinear,
	- BSpline_Bicubic,
	- WindowedSinc
	- };
	-
	- typedef std::vector< typename TTransformType::Pointer > TransformContainerType;
	- typedef std::vector< typename TTransformType::ParametersType > TransformParametersContainerType;
	-
	- /** Set a transform container to be used, one transform per volume */
	- void SetTransforms( const TransformContainerType& );
	-
	- /** Set a container of transform parameters to be used to create transforms for transforming the input */
	- void SetTransformParameters( const TransformParametersContainerType& );
	-
	- /** Set interpolation type for resampling */
	- void SetInterpolationLevel( InterpolatorLevel lvl)
	- {
	- m_InterpolationLevel = lvl;
	- }
	-
	- void GenerateData() override;
	-
	- void SetResamplingReferenceImage( mitk::Image::Pointer image )
	- {
	- this->m_ResamplingReferenceImage = image;
	- }
	-
	- void SetReferenceDiffusionImage( mitk::Image::Pointer dwimage )
	- {
	- this->m_DiffusionReferenceImage = dwimage;
	- }
	-
	- void SetOutputPrefix( std::string prefix )
	-{
	- this->m_OutputPrefix = prefix;
	-}
	-
	- virtual void GenerateOutputInformation() override;
	-
	-protected:
	- DiffusionImageTransformedCreationFilter();
	- ~DiffusionImageTransformedCreationFilter();
	-
	- DiffusionImageHeaderDescriptor GetTransformedHeaderInformation();
	-
	- TransformContainerType m_InternalTransforms;
	-
	- mitk::Image::Pointer m_ResamplingReferenceImage;
	-
	- mitk::Image::Pointer m_DiffusionReferenceImage;
	-
	- InterpolatorLevel m_InterpolationLevel;
	-
	- typedef DiffusionImageCorrectionFilter::TransformMatrixType MatrixType;
	- std::vector< MatrixType > m_RotationMatrices;
	-
	- std::string m_OutputPrefix;
	-
	- mitk::Image::Pointer m_OutputCache;
	-};
	-
	-} // end namespace mitk
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	- #include "mitkDiffusionImageTransformedCreationFilter.cxx"
	-#endif
	-
	-#endif // DIFFUSIONIMAGETRANSFORMEDCREATIONFILTER_H
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/OdfImages/mitkOdfImage.h b/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/OdfImages/mitkOdfImage.h
	deleted file mode 100644
	index 2d93081570..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/OdfImages/mitkOdfImage.h
	+++ /dev/null
	@@ -1,77 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef __mitkOdfImage__h
	-#define __mitkOdfImage__h
	-
	-#include "mitkImage.h"
	-#include "itkVectorImage.h"
	-#include "mitkImageVtkAccessor.h"
	-
	-#include <MitkDiffusionCoreExports.h>
	-
	-// generate by n-fold subdivisions of an icosahedron
	-// 1 - 12
	-// 2 - 42
	-// 3 - 92
	-// 4 - 162
	-// 5 - 252
	-// 6 - 362
	-// 7 - 492
	-// 8 - 642
	-// 9 - 812
	-// 10 - 1002
	-#define ODF_SAMPLING_SIZE 252
	-
	-namespace mitk
	-{
	-
	- /**
	- * \brief this class encapsulates orientation distribution images
	- */
	- class MITKDIFFUSIONCORE_EXPORT OdfImage : public Image
	- {
	-
	- public:
	-
	- typedef float ScalarPixelType;
	- typedef itk::Vector< ScalarPixelType, ODF_SAMPLING_SIZE > PixelType;
	- typedef itk::Image< itk::Vector< ScalarPixelType, ODF_SAMPLING_SIZE >, 3 > ItkOdfImageType;
	-
	- mitkClassMacro( OdfImage, Image )
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- virtual const vtkImageData* GetNonRgbVtkImageData(int t = 0, int n = 0) const;
	- virtual vtkImageData* GetNonRgbVtkImageData(int t = 0, int n = 0);
	-
	- const vtkImageData* GetVtkImageData(int t = 0, int n = 0) const override;
	- vtkImageData* GetVtkImageData(int t = 0, int n = 0) override;
	-
	- virtual void ConstructRgbImage() const;
	-
	- protected:
	- OdfImage();
	- ~OdfImage() override;
	-
	- mutable mitk::Image::Pointer m_RgbImage;
	-
	- };
	-
	-} // namespace mitk
	-
	-#endif /* __mitkOdfImage__h */
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/OdfImages/mitkOdfImageSource.h b/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/OdfImages/mitkOdfImageSource.h
	deleted file mode 100644
	index 072bc57aad..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/OdfImages/mitkOdfImageSource.h
	+++ /dev/null
	@@ -1,64 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef OdfImageSource_H_HEADER_INCLUDED_C1E7D6EC
	-#define OdfImageSource_H_HEADER_INCLUDED_C1E7D6EC
	-
	-#include "mitkImageSource.h"
	-#include "mitkOdfImage.h"
	-#include <MitkDiffusionCoreExports.h>
	-
	-namespace mitk {
	-
	-class MITKDIFFUSIONCORE_EXPORT OdfImageSource : public ImageSource
	-{
	-public:
	-
	- typedef mitk::OdfImage OutputImageType;
	- typedef OutputImageType::Pointer OutputImagePointer;
	- typedef SlicedData::RegionType OutputImageRegionType;
	- typedef itk::DataObject::Pointer DataObjectPointer;
	-
	- mitkClassMacro(OdfImageSource,ImageSource);
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /**
	- * Allocates a new output object and returns it. Currently the
	- * index idx is not evaluated.
	- * @param idx the index of the output for which an object should be created
	- * @returns the new object
	- */
	- itk::DataObject::Pointer MakeOutput ( DataObjectPointerArraySizeType idx ) override;
	-
	- /**
	- * This is a default implementation to make sure we have something.
	- * Once all the subclasses of ProcessObject provide an appopriate
	- * MakeOutput(), then ProcessObject::MakeOutput() can be made pure
	- * virtual.
	- */
	- itk::DataObject::Pointer MakeOutput(const DataObjectIdentifierType &name) override;
	-
	-protected:
	- OdfImageSource();
	- ~OdfImageSource() override {}
	-
	-};
	-
	-} // namespace mitk
	-
	-#endif /* OdfImageSource_H_HEADER_INCLUDED_C1E7D6EC */
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/Properties/mitkBValueMapProperty.h b/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/Properties/mitkBValueMapProperty.h
	deleted file mode 100644
	index c7af5e239c..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/Properties/mitkBValueMapProperty.h
	+++ /dev/null
	@@ -1,74 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef MITKBVALUEMAPPROPERTY_H
	-#define MITKBVALUEMAPPROPERTY_H
	-
	-#include "mitkBaseProperty.h"
	-#include <map>
	-#include <vector>
	-
	-#include <MitkDiffusionCoreExports.h>
	-#include <itkVectorContainer.h>
	-#include <vnl/vnl_vector_fixed.h>
	-namespace mitk
	-{
	-
	- /** This property will store the b value map */
	-
	- class MITKDIFFUSIONCORE_EXPORT BValueMapProperty : public mitk::BaseProperty
	- {
	- public:
	- /**
	- * \brief The BValueMap contains seperated IndicesVectors for each b value (index for GradientDirectionContainer)
	- * key := b value
	- * value := indicesVector
	- */
	- typedef std::map< unsigned int , std::vector< unsigned int > > BValueMap;
	- typedef unsigned int IndexType;
	- typedef vnl_vector_fixed< double, 3 > ValueType;
	- typedef ValueType GradientDirectionType;
	- typedef itk::VectorContainer< IndexType, GradientDirectionType > GradientDirectionsContainerType;
	- mitkClassMacro(BValueMapProperty, BaseProperty)
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- mitkNewMacro1Param(BValueMapProperty, const BValueMapProperty&)
	- mitkNewMacro1Param(BValueMapProperty, const BValueMap&)
	-
	- const BValueMap & GetBValueMap() const;
	- void SetBValueMap(const BValueMap & map);
	-
	- static BValueMap CreateBValueMap(const GradientDirectionsContainerType * gdc, float referenceBValue);
	- static float GetBValueOfGradientDirection(unsigned int i, float referenceBValue, const GradientDirectionsContainerType *gdc);
	- protected:
	-
	- BValueMapProperty();
	- ~BValueMapProperty() override;
	-
	- BValueMapProperty(const BValueMapProperty& other);
	- BValueMapProperty(const BValueMap& bValueMap);
	-
	- bool IsEqual(const BaseProperty& property) const override;
	- bool Assign(const BaseProperty & property) override;
	-
	- BValueMap m_BValueMap;
	-
	- itk::LightObject::Pointer InternalClone() const override;
	- };
	-}
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/Properties/mitkDiffusionPropertyHelper.h b/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/Properties/mitkDiffusionPropertyHelper.h
	deleted file mode 100644
	index a97b07f5a8..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/Properties/mitkDiffusionPropertyHelper.h
	+++ /dev/null
	@@ -1,126 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef MITKDIFFUSIONPROPERTYHELPER_H
	-#define MITKDIFFUSIONPROPERTYHELPER_H
	-
	-#include <MitkDiffusionCoreExports.h>
	-
	-#include <mitkImage.h>
	-#include <mitkBValueMapProperty.h>
	-#include <mitkGradientDirectionsProperty.h>
	-#include <mitkMeasurementFrameProperty.h>
	-#include <mitkDataNode.h>
	-#include <usModuleActivator.h>
	-
	-namespace mitk
	-{
	- /** \brief Helper class for mitk::Images containing diffusion weighted data
	- *
	- * This class takes a pointer to a mitk::Image containing diffusion weighted information and provides
	- * functions to manipulate the diffusion meta-data. Will log an error if required information is
	- * missing.
	- */
	-
	- class MITKDIFFUSIONCORE_EXPORT DiffusionPropertyHelper
	- {
	- public:
	-
	- typedef short DiffusionPixelType;
	- typedef mitk::BValueMapProperty::BValueMap BValueMapType;
	- typedef GradientDirectionsProperty::GradientDirectionType GradientDirectionType;
	- typedef GradientDirectionsProperty::GradientDirectionsContainerType GradientDirectionsContainerType;
	- typedef mitk::MeasurementFrameProperty::MeasurementFrameType MeasurementFrameType;
	- typedef itk::VectorImage< DiffusionPixelType, 3> ImageType;
	-
	- static bool IsDiffusionWeightedImage(const mitk::Image *);
	- static bool IsDiffusionWeightedImage(const mitk::DataNode* node);
	-
	- static void CopyProperties(mitk::Image* source, mitk::Image* target, bool ignore_original_gradients=false);
	-
	- static ImageType::Pointer GetItkVectorImage(Image *image);
	- static const BValueMapType & GetBValueMap(const mitk::Image *);
	- static float GetReferenceBValue(const mitk::Image *);
	- static std::vector< int > GetBValueVector(const mitk::Image *);
	- static const MeasurementFrameType & GetMeasurementFrame(const mitk::Image *);
	- static GradientDirectionsContainerType::Pointer GetOriginalGradientContainer(const mitk::Image *);
	- static GradientDirectionsContainerType::Pointer GetGradientContainer(const mitk::Image *);
	-
	- static void SetApplyMatrixToGradients(mitk::Image* image, bool apply);
	- static void SetApplyMfToGradients(mitk::Image* image, bool apply);
	- static void SetMeasurementFrame(mitk::Image* image, MeasurementFrameType mf);
	- static void SetReferenceBValue(mitk::Image* image, float b_value);
	- static void SetBValueMap(mitk::Image* image, BValueMapType map);
	- static void SetOriginalGradientContainer(mitk::Image* image, GradientDirectionsContainerType::Pointer g_cont);
	- static void SetGradientContainer(mitk::Image* image, GradientDirectionsContainerType::Pointer g_cont);
	- static void RotateGradients(mitk::Image* image, vnl_matrix_fixed<double, 3, 3> rotation_matrix, bool normalize_columns);
	- static void RotateOriginalGradients(mitk::Image* image, vnl_matrix_fixed<double, 3, 3> rotation_matrix, bool normalize_columns);
	-
	- static void AverageRedundantGradients(mitk::Image* image, double precision);
	- static void InitializeImage(mitk::Image* image);
	-
	- static GradientDirectionsContainerType::Pointer CalcAveragedDirectionSet(double precision, GradientDirectionsContainerType::Pointer directions);
	-
	- static void SetupProperties(); // called in DiffusionCoreIOActivator
	-
	- static const std::string GetBvaluePropertyName() { return BVALUEMAPPROPERTYNAME; }
	- static const std::string GetGradientContainerPropertyName() { return GRADIENTCONTAINERPROPERTYNAME; }
	- static const std::string GetMeasurementFramePropertyName() { return MEASUREMENTFRAMEPROPERTYNAME; }
	-
	- protected:
	-
	- DiffusionPropertyHelper();
	- ~DiffusionPropertyHelper();
	-
	- static const std::string GRADIENTCONTAINERPROPERTYNAME;
	- static const std::string ORIGINALGRADIENTCONTAINERPROPERTYNAME;
	- static const std::string MEASUREMENTFRAMEPROPERTYNAME;
	- static const std::string REFERENCEBVALUEPROPERTYNAME;
	- static const std::string BVALUEMAPPROPERTYNAME;
	- static const std::string MODALITY;
	- static const std::string APPLY_MATRIX_TO_GRADIENTS;
	- static const std::string APPLY_MF_TO_GRADIENTS;
	-
	- /**
	- * \brief Apply the previously set MeasurementFrame and the image rotation matrix to all gradients
	- *
	- * \warning first set the MeasurementFrame
	- */
	- static void ApplyMeasurementFrameAndRotationMatrix(mitk::Image* image);
	-
	- /**
	- * \brief Apply the inverse of the previously set MeasurementFrame and the image rotation matrix to all gradients
	- *
	- * \warning first set the MeasurementFrame
	- */
	- static void UnApplyMeasurementFrameAndRotationMatrix(mitk::Image* image);
	-
	- /**
	- * \brief Update the BValueMap (m_B_ValueMap) using the current gradient directions (m_Directions)
	- *
	- * \warning Have to be called after each manipulation on the GradientDirectionContainer
	- * !especially after manipulation of the m_Directions (GetDirections()) container via pointer access!
	- */
	- static void UpdateBValueMap(mitk::Image* image);
	-
	- /// Determines whether gradients can be considered to be equal
	- static bool AreAlike(GradientDirectionType g1, GradientDirectionType g2, double precision);
	-
	- /// Get the b value belonging to an index
	- static float GetB_Value(const mitk::Image* image, unsigned int i);
	- };
	-}
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/Properties/mitkGradientDirectionsProperty.h b/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/Properties/mitkGradientDirectionsProperty.h
	deleted file mode 100644
	index 11c188b54c..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/Properties/mitkGradientDirectionsProperty.h
	+++ /dev/null
	@@ -1,68 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef MITKGRADIENTDIRECTIONSPROPERTY_H
	-#define MITKGRADIENTDIRECTIONSPROPERTY_H
	-
	-#include "mitkBaseProperty.h"
	-#include <vnl/vnl_vector_fixed.h>
	-#include <itkVectorContainer.h>
	-#include <itkVector.h>
	-
	-#include <MitkDiffusionCoreExports.h>
	-
	-namespace mitk
	-{
	-
	- /** This property will store the gradients directions and the original gradient directions */
	- class MITKDIFFUSIONCORE_EXPORT GradientDirectionsProperty : public mitk::BaseProperty
	- {
	- public:
	- typedef unsigned int IndexType;
	- typedef vnl_vector_fixed< double, 3 > ValueType;
	- typedef ValueType GradientDirectionType;
	- typedef itk::VectorContainer< IndexType, GradientDirectionType > GradientDirectionsContainerType;
	- typedef std::vector< itk::Vector<double,3> > AlternativeGradientDirectionsContainerType;
	-
	- mitkClassMacro(GradientDirectionsProperty, BaseProperty)
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- mitkNewMacro1Param(GradientDirectionsProperty, const GradientDirectionsProperty&);
	- mitkNewMacro1Param(GradientDirectionsProperty, const GradientDirectionsContainerType::Pointer);
	- mitkNewMacro1Param(GradientDirectionsProperty, const AlternativeGradientDirectionsContainerType );
	-
	- const GradientDirectionsContainerType::Pointer GetGradientDirectionsContainer() const;
	-
	- protected:
	-
	- GradientDirectionsProperty();
	- ~GradientDirectionsProperty() override;
	-
	- GradientDirectionsProperty(const GradientDirectionsProperty& other);
	- GradientDirectionsProperty(const GradientDirectionsContainerType::Pointer gradientDirectionsContainer);
	- GradientDirectionsProperty(const AlternativeGradientDirectionsContainerType gradientDirectionsContainer);
	-
	- bool IsEqual(const BaseProperty& property) const override;
	- bool Assign(const BaseProperty & property) override;
	-
	- GradientDirectionsContainerType::Pointer m_GradientDirectionsContainer;
	-
	- itk::LightObject::Pointer InternalClone() const override;
	- };
	-}
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/Properties/mitkMeasurementFrameProperty.h b/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/Properties/mitkMeasurementFrameProperty.h
	deleted file mode 100644
	index a2e5a8fcd5..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/Properties/mitkMeasurementFrameProperty.h
	+++ /dev/null
	@@ -1,60 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef MITKMEASUREMENTFRAMEPROPERTY_H
	-#define MITKMEASUREMENTFRAMEPROPERTY_H
	-
	-#include "mitkBaseProperty.h"
	-#include <vnl/vnl_matrix_fixed.h>
	-
	-#include <MitkDiffusionCoreExports.h>
	-
	-namespace mitk
	-{
	-
	- /** This property will store the measurement frame */
	- class MITKDIFFUSIONCORE_EXPORT MeasurementFrameProperty : public mitk::BaseProperty
	- {
	- public:
	- typedef vnl_matrix_fixed< double, 3, 3 > MeasurementFrameType;
	- mitkClassMacro(MeasurementFrameProperty, BaseProperty)
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- mitkNewMacro1Param(MeasurementFrameProperty, const MeasurementFrameProperty&);
	- mitkNewMacro1Param(MeasurementFrameProperty, const MeasurementFrameType&);
	-
	- const MeasurementFrameType &GetMeasurementFrame() const;
	- void SetMeasurementFrame(const MeasurementFrameType & frame);
	-
	- protected:
	-
	- MeasurementFrameProperty();
	- ~MeasurementFrameProperty() override;
	-
	- MeasurementFrameProperty(const MeasurementFrameProperty& other);
	- MeasurementFrameProperty(const MeasurementFrameType& measurementFrame);
	-
	- bool IsEqual(const BaseProperty& property) const override;
	- bool Assign(const BaseProperty & property) override;
	-
	- MeasurementFrameType m_MeasurementFrame;
	-
	- itk::LightObject::Pointer InternalClone() const override;
	- };
	-}
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/Properties/mitkNodePredicateIsDWI.h b/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/Properties/mitkNodePredicateIsDWI.h
	deleted file mode 100644
	index 2e6c06c8b7..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/Properties/mitkNodePredicateIsDWI.h
	+++ /dev/null
	@@ -1,56 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef MITKNODEPREDICATEISDWI_H_HEADER_INCLUDED_
	-#define MITKNODEPREDICATEISDWI_H_HEADER_INCLUDED_
	-
	-#include <MitkDiffusionCoreExports.h>
	-
	-#include "mitkNodePredicateBase.h"
	-#include "mitkBaseProperty.h"
	-#include "mitkBaseData.h"
	-
	-namespace mitk {
	-
	- /**Documentation
	- * @brief Predicate that evaluates whether a given node contains a diffusion weighted image
	- * @ingroup DataStorage
	- */
	-
	- class MITKDIFFUSIONCORE_EXPORT NodePredicateIsDWI : public NodePredicateBase
	- {
	- public:
	- mitkClassMacro(NodePredicateIsDWI, NodePredicateBase);
	- itkFactorylessNewMacro(NodePredicateIsDWI)
	-
	- //##Documentation
	- //## @brief Standard Destructor
	- ~NodePredicateIsDWI() override;
	-
	- //##Documentation
	- //## @brief Checks, if the node's data contains a property that is equal to m_ValidProperty
	- bool CheckNode(const mitk::DataNode* node) const override;
	-
	- protected:
	- //##Documentation
	- //## @brief Constructor to check for a named property
	- NodePredicateIsDWI();
	- };
	-
	-} // namespace mitk
	-
	-#endif /* MITKNODEPREDICATEISDWI_H_HEADER_INCLUDED_ */
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/TensorImages/mitkTensorImage.h b/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/TensorImages/mitkTensorImage.h
	deleted file mode 100644
	index 0f25732df3..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/TensorImages/mitkTensorImage.h
	+++ /dev/null
	@@ -1,65 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef __mitkTensorImage__h
	-#define __mitkTensorImage__h
	-
	-#include "mitkImage.h"
	-#include "itkVectorImage.h"
	-
	-#include <MitkDiffusionCoreExports.h>
	-
	-
	-#define TENSOR_NUM_ELEMENTS 6
	-
	-namespace mitk
	-{
	-
	- /**
	- * \brief this class encapsulates tensor images
	- */
	- class MITKDIFFUSIONCORE_EXPORT TensorImage : public Image
	- {
	-
	- public:
	-
	- typedef float ScalarPixelType;
	- typedef itk::DiffusionTensor3D<ScalarPixelType> PixelType;
	- typedef itk::Image<PixelType,3> ItkTensorImageType;
	-
	- mitkClassMacro( TensorImage, Image )
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- virtual vtkImageData* GetNonRgbVtkImageData(int t = 0, int n = 0);
	-
	- vtkImageData* GetVtkImageData(int t = 0, int n = 0) override;
	- const vtkImageData* GetVtkImageData(int t = 0, int n = 0) const override;
	-
	- virtual void ConstructRgbImage() const;
	-
	- protected:
	- TensorImage();
	- ~TensorImage() override;
	-
	- mutable mitk::Image::Pointer m_RgbImage;
	-
	- };
	-
	-} // namespace mitk
	-
	-#endif /* __mitkTensorImage__h */
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/mitkPeakImage.h b/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/mitkPeakImage.h
	deleted file mode 100644
	index a30d5f188e..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/mitkPeakImage.h
	+++ /dev/null
	@@ -1,66 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef __mitkPeakImage__h
	-#define __mitkPeakImage__h
	-
	-#include "mitkImage.h"
	-#include <vtkPolyData.h>
	-#include <vtkSmartPointer.h>
	-
	-#include <MitkDiffusionCoreExports.h>
	-
	-namespace mitk
	-{
	-
	- /**
	- * \brief this class encapsulates tensor images
	- */
	- class MITKDIFFUSIONCORE_EXPORT PeakImage : public Image
	- {
	-
	- public:
	- typedef float PixelType;
	- typedef itk::Image<PixelType, 4> ItkPeakImageType;
	-
	- mitkClassMacro( PeakImage, Image )
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- void ConstructPolydata();
	-
	- vtkSmartPointer< vtkPolyData > GetPolyData()
	- {
	- if (m_PolyData==nullptr)
	- this->ConstructPolydata();
	- return m_PolyData;
	- }
	-
	- void SetCustomColor(float r, float g, float b);
	- void ColorByOrientation();
	-
	- protected:
	- PeakImage();
	- ~PeakImage() override;
	-
	- mutable vtkSmartPointer< vtkPolyData > m_PolyData;
	-
	- };
	-
	-} // namespace mitk
	-
	-#endif /* __mitkPeakImage__h */
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/mitkRegistrationObject.h b/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/mitkRegistrationObject.h
	deleted file mode 100644
	index 6e541a204e..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/mitkRegistrationObject.h
	+++ /dev/null
	@@ -1,74 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef MITKREGISTRATIONOBJECT_H
	-#define MITKREGISTRATIONOBJECT_H
	-
	-#include <MitkDiffusionCoreExports.h>
	-
	-#include "mitkBaseData.h"
	-#include "mitkGeometry3D.h"
	-
	-#include "mitkImage.h"
	-
	-namespace mitk
	-{
	-/**
	- * @brief The RegistrationObject class stores all necessary information for image registration.
	- *
	- *
	- */
	-
	-class MITKDIFFUSIONCORE_EXPORT RegistrationObject : public BaseData
	-{
	-public:
	-
	- mitkClassMacro( RegistrationObject, BaseData );
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- void SetReferenceGeometry( mitk::Geometry3D::Pointer );
	-
	- void SetReferenceImage( mitk::Image::Pointer );
	-
	- void SetTransformation( mitk::AffineGeometryFrame3D::Pointer );
	-
	- mitk::Geometry3D::Pointer GetReferenceGeometry() const
	- {
	- return m_ReferenceGeometry;
	- }
	-
	- mitk::AffineGeometryFrame3D::Pointer GetTransformation() const
	- {
	- return m_Transformation;
	- }
	-
	-protected:
	- RegistrationObject();
	- virtual ~RegistrationObject(){}
	-
	- /**
	- * @brief Reference geometry of the fixed image used for registration computation
	- */
	- mitk::Geometry3D::Pointer m_ReferenceGeometry;
	-
	- mitk::AffineGeometryFrame3D::Pointer m_Transformation;
	-
	-
	-};
	-
	-}
	-#endif // MITKREGISTRATIONOBJECT_H
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/mitkShImage.h b/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/mitkShImage.h
	deleted file mode 100644
	index 9aed1448e1..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/mitkShImage.h
	+++ /dev/null
	@@ -1,71 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef __mitkShImage__h
	-#define __mitkShImage__h
	-
	-#include "mitkImage.h"
	-#include "itkVectorImage.h"
	-#include "mitkImageVtkAccessor.h"
	-
	-#include <MitkDiffusionCoreExports.h>
	-
	-namespace mitk
	-{
	-
	- /**
	- * \brief this class encapsulates spherical harmonics coefficients
	- */
	- class MITKDIFFUSIONCORE_EXPORT ShImage : public Image
	- {
	-
	- public:
	-
	- typedef itk::Image<float,4 > ShOnDiskType; // we store the sh images in MRtrix 4D float format and convert on load to 3D multi-component images
	-
	- mitkClassMacro( ShImage, Image )
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- virtual const vtkImageData* GetNonRgbVtkImageData(int t = 0, int n = 0) const;
	- virtual vtkImageData* GetNonRgbVtkImageData(int t = 0, int n = 0);
	-
	- const vtkImageData* GetVtkImageData(int t = 0, int n = 0) const override;
	- vtkImageData* GetVtkImageData(int t = 0, int n = 0) override;
	-
	- virtual void ConstructRgbImage() const;
	-
	- unsigned int ShOrder();
	- unsigned int NumCoefficients();
	-
	- protected:
	- ShImage();
	- ~ShImage() override;
	-
	- template<int num_components>
	- void Construct() const;
	-
	- void PrintSelf(std::ostream &os, itk::Indent indent) const override;
	-
	- mutable mitk::Image::Pointer m_RgbImage;
	- unsigned int m_ShOrder;
	- unsigned int m_NumCoefficients;
	- };
	-
	-} // namespace mitk
	-
	-#endif /* __mitkShImage__h */
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/mitkShImageSource.h b/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/mitkShImageSource.h
	deleted file mode 100644
	index 2db7ea84a7..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/IODataStructures/mitkShImageSource.h
	+++ /dev/null
	@@ -1,64 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef ShImageSource_H_HEADER_INCLUDED_C1E7D6EC
	-#define ShImageSource_H_HEADER_INCLUDED_C1E7D6EC
	-
	-#include "mitkImageSource.h"
	-#include "mitkShImage.h"
	-#include <MitkDiffusionCoreExports.h>
	-
	-namespace mitk {
	-
	-class MITKDIFFUSIONCORE_EXPORT ShImageSource : public ImageSource
	-{
	-public:
	-
	- typedef mitk::ShImage OutputImageType;
	- typedef OutputImageType::Pointer OutputImagePointer;
	- typedef SlicedData::RegionType OutputImageRegionType;
	- typedef itk::DataObject::Pointer DataObjectPointer;
	-
	- mitkClassMacro(ShImageSource,ImageSource);
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /**
	- * Allocates a new output object and returns it. Currently the
	- * index idx is not evaluated.
	- * @param idx the index of the output for which an object should be created
	- * @returns the new object
	- */
	- itk::DataObject::Pointer MakeOutput ( DataObjectPointerArraySizeType idx ) override;
	-
	- /**
	- * This is a default implementation to make sure we have something.
	- * Once all the subclasses of ProcessObject provide an appopriate
	- * MakeOutput(), then ProcessObject::MakeOutput() can be made pure
	- * virtual.
	- */
	- itk::DataObject::Pointer MakeOutput(const DataObjectIdentifierType &name) override;
	-
	-protected:
	- ShImageSource();
	- ~ShImageSource() override {}
	-
	-};
	-
	-} // namespace mitk
	-
	-#endif /* ShImageSource_H_HEADER_INCLUDED_C1E7D6EC */
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Rendering/mitkOdfNormalizationMethodProperty.h b/Modules/DiffusionImaging/DiffusionCore/include/Rendering/mitkOdfNormalizationMethodProperty.h
	deleted file mode 100644
	index 38fca53e1b..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Rendering/mitkOdfNormalizationMethodProperty.h
	+++ /dev/null
	@@ -1,137 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_OdfNormalizationMethodProperty__H_
	-#define _MITK_OdfNormalizationMethodProperty__H_
	-
	-#include "mitkEnumerationProperty.h"
	-#include "mitkEnumerationPropertySerializer.h"
	-#include <MitkDiffusionCoreExports.h>
	-
	-#include "mitkSerializerMacros.h"
	-
	-namespace mitk
	-{
	-
	- enum OdfNormalizationMethod
	- {
	- ODFN_MINMAX,
	- ODFN_MAX,
	- ODFN_NONE,
	- ODFN_GLOBAL_MAX
	- };
	-
	-/**
	- * Encapsulates the enumeration for ODF normalization. Valid values are
	- * ODFN_MINMAX, ODFN_MAX, ODFN_NONE ODFN_GLOBAL_MAX
	- * Default is ODFN_MINMAX
	- */
	-class MITKDIFFUSIONCORE_EXPORT OdfNormalizationMethodProperty : public EnumerationProperty
	-{
	-public:
	-
	- mitkClassMacro( OdfNormalizationMethodProperty, EnumerationProperty );
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- mitkNewMacro1Param(OdfNormalizationMethodProperty, const IdType&);
	-
	- mitkNewMacro1Param(OdfNormalizationMethodProperty, const std::string&);
	-
	- /**
	- * Returns the current interpolation value as defined by VTK constants.
	- */
	- virtual int GetNormalization();
	-
	- /**
	- * Sets the interpolation type to ODFN_MINMAX.
	- */
	- virtual void SetNormalizationToMinMax();
	-
	- /**
	- * Sets the interpolation type to ODFN_MAX.
	- */
	- virtual void SetNormalizationToMax();
	-
	- /**
	- * Sets the interpolation type to ODFN_NONE.
	- */
	- virtual void SetNormalizationToNone();
	-
	- /**
	- * Sets the interpolation type to ODFN_GLOBAL_MAX.
	- */
	- virtual void SetNormalizationToGlobalMax();
	-
	-protected:
	-
	- /** Sets reslice interpolation mode to default (VTK_RESLICE_NEAREST).
	- */
	- OdfNormalizationMethodProperty( );
	-
	- /**
	- * Constructor. Sets reslice interpolation to the given value.
	- */
	- OdfNormalizationMethodProperty( const IdType& value );
	-
	- /**
	- * Constructor. Sets reslice interpolation to the given value.
	- */
	- OdfNormalizationMethodProperty( const std::string& value );
	-
	- /**
	- * this function is overridden as protected, so that the user may not add
	- * additional invalid interpolation types.
	- */
	- bool AddEnum( const std::string& name, const IdType& id ) override;
	-
	- /**
	- * Adds the enumeration types as defined by vtk to the list of known
	- * enumeration values.
	- */
	- virtual void AddInterpolationTypes();
	-};
	-
	-class MITKDIFFUSIONCORE_EXPORT OdfNormalizationMethodPropertySerializer : public EnumerationPropertySerializer
	-{
	- public:
	-
	- mitkClassMacro( OdfNormalizationMethodPropertySerializer, EnumerationPropertySerializer );
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- BaseProperty::Pointer Deserialize(TiXmlElement* element) override
	- {
	- if (!element) return nullptr;
	- const char* sa( element->Attribute("value") );
	- std::string s(sa?sa:"");
	- OdfNormalizationMethodProperty::Pointer property = OdfNormalizationMethodProperty::New();
	- property->SetValue( s );
	- return property.GetPointer();
	- }
	-
	- protected:
	-
	- OdfNormalizationMethodPropertySerializer () {}
	- ~OdfNormalizationMethodPropertySerializer () override {}
	-};
	-
	-
	-} // end of namespace mitk
	-
	-#endif
	-
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Rendering/mitkOdfScaleByProperty.h b/Modules/DiffusionImaging/DiffusionCore/include/Rendering/mitkOdfScaleByProperty.h
	deleted file mode 100644
	index 434835edc1..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Rendering/mitkOdfScaleByProperty.h
	+++ /dev/null
	@@ -1,117 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_OdfScaleByProperty__H_
	-#define _MITK_OdfScaleByProperty__H_
	-
	-#include <MitkDiffusionCoreExports.h>
	-#include "mitkEnumerationProperty.h"
	-#include "mitkEnumerationPropertySerializer.h"
	-
	-namespace mitk
	-{
	-
	- enum OdfScaleBy
	- {
	- ODFSB_NONE,
	- ODFSB_GFA,
	- ODFSB_PC
	- };
	-
	-/**
	- * Encapsulates the enumeration for ODF normalization. Valid values are
	- * ODFSB_NONE, ODFSB_GFA, ODFSB_PC
	- * Default is ODFSB_NONE
	- */
	-class MITKDIFFUSIONCORE_EXPORT OdfScaleByProperty : public EnumerationProperty
	-{
	-public:
	-
	- mitkClassMacro( OdfScaleByProperty, EnumerationProperty );
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- mitkNewMacro1Param(OdfScaleByProperty, const IdType&);
	-
	- mitkNewMacro1Param(OdfScaleByProperty, const std::string&);
	-
	- /**
	- * Returns the current interpolation value as defined by VTK constants.
	- */
	- virtual int GetScaleBy();
	-
	- virtual void SetScaleByNothing();
	- virtual void SetScaleByGFA();
	- virtual void SetScaleByPrincipalCurvature();
	-
	-protected:
	-
	- /** Sets reslice interpolation mode to default (ODFSB_NONE).
	- */
	- OdfScaleByProperty( );
	-
	- /**
	- * Constructor. Sets reslice interpolation to the given value.
	- */
	- OdfScaleByProperty( const IdType& value );
	-
	- /**
	- * Constructor. Sets reslice interpolation to the given value.
	- */
	- OdfScaleByProperty( const std::string& value );
	-
	- /**
	- * this function is overridden as protected, so that the user may not add
	- * additional invalid interpolation types.
	- */
	- bool AddEnum( const std::string& name, const IdType& id ) override;
	-
	- /**
	- * Adds the enumeration types as defined by vtk to the list of known
	- * enumeration values.
	- */
	- virtual void AddInterpolationTypes();
	-};
	-
	-class MITKDIFFUSIONCORE_EXPORT OdfScaleByPropertySerializer : public EnumerationPropertySerializer
	-{
	- public:
	-
	- mitkClassMacro( OdfScaleByPropertySerializer, EnumerationPropertySerializer );
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- BaseProperty::Pointer Deserialize(TiXmlElement* element) override
	- {
	- if (!element) return nullptr;
	- const char* sa( element->Attribute("value") );
	- std::string s(sa?sa:"");
	- OdfScaleByProperty::Pointer property = OdfScaleByProperty::New();
	- property->SetValue( s );
	- return property.GetPointer();
	- }
	-
	- protected:
	-
	- OdfScaleByPropertySerializer () {}
	- ~OdfScaleByPropertySerializer () override {}
	-};
	-
	-} // end of namespace mitk
	-
	-#endif
	-
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Rendering/mitkOdfVtkMapper2D.h b/Modules/DiffusionImaging/DiffusionCore/include/Rendering/mitkOdfVtkMapper2D.h
	deleted file mode 100644
	index 241998c6d6..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Rendering/mitkOdfVtkMapper2D.h
	+++ /dev/null
	@@ -1,161 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef ODFVTKMAPPER2D_H_HEADER_INCLUDED
	-#define ODFVTKMAPPER2D_H_HEADER_INCLUDED
	-
	-#include "mitkVtkMapper.h"
	-#include "vtkPropAssembly.h"
	-#include "vtkAppendPolyData.h"
	-#include "vtkActor.h"
	-#include "vtkPolyDataMapper.h"
	-#include "vtkPlane.h"
	-#include "vtkCutter.h"
	-#include "vtkClipPolyData.h"
	-#include "vtkTransform.h"
	-#include "vtkDataArrayTemplate.h"
	-#include "vtkSmartPointer.h"
	-#include "vtkOdfSource.h"
	-#include "vtkThickPlane.h"
	-#include <mitkDiffusionFunctionCollection.h>
	-
	-namespace mitk {
	-
	-//##Documentation
	-//## @brief Mapper for spherical object densitiy function representations
	-//##
	-template<class TPixelType, int NrOdfDirections>
	-class OdfVtkMapper2D : public VtkMapper
	-{
	- struct OdfDisplayGeometry {
	- double vp[ 3 ], vnormal[ 3 ];
	- Vector3D normal;
	- double d, d1, d2;
	- mitk::Point3D M3D, L3D, O3D;
	-
	- double vp_original[ 3 ], vnormal_original[ 3 ];
	- mitk::Vector2D size, origin;
	-
	- bool Equals(OdfDisplayGeometry other)
	- {
	- return other.vp_original[0] == vp[0] &&
	- other.vp_original[1] == vp[1] &&
	- other.vp_original[2] == vp[2] &&
	- other.vnormal_original[0] == vnormal[0] &&
	- other.vnormal_original[1] == vnormal[1] &&
	- other.vnormal_original[2] == vnormal[2] &&
	- other.size[0] == size[0] &&
	- other.size[1] == size[1] &&
	- other.origin[0] == origin[0] &&
	- other.origin[1] == origin[1];
	- }
	- };
	-
	-public:
	-
	- mitkClassMacro(OdfVtkMapper2D,VtkMapper)
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- vtkProp* GetVtkProp(mitk::BaseRenderer* renderer) override;
	- bool IsVisibleOdfs(mitk::BaseRenderer* renderer);
	- void MitkRenderOverlay(mitk::BaseRenderer* renderer) override;
	- void MitkRenderOpaqueGeometry(mitk::BaseRenderer* renderer) override;
	- void MitkRenderTranslucentGeometry(mitk::BaseRenderer* renderer) override;
	- void MitkRenderVolumetricGeometry(mitk::BaseRenderer* /renderer/) override{}
	-
	- OdfDisplayGeometry MeasureDisplayedGeometry(mitk::BaseRenderer* renderer);
	- double GetMinImageSpacing( int index );
	- void ApplyPropertySettings();
	- virtual void Slice(mitk::BaseRenderer* renderer, OdfDisplayGeometry dispGeo);
	- virtual int GetIndex(mitk::BaseRenderer* renderer);
	- static void SetDefaultProperties(DataNode* node, BaseRenderer* renderer = nullptr, bool overwrite = false);
	- void Update(mitk::BaseRenderer * renderer) override;
	- void GenerateDataForRenderer(mitk::BaseRenderer* renderer) override;
	- bool IsLODEnabled( BaseRenderer * /renderer/ ) const override { return true; }
	-
	- class LocalStorage : public mitk::Mapper::BaseLocalStorage
	- {
	- public:
	-
	- std::vector< vtkSmartPointer<vtkPropAssembly> > m_PropAssemblies;
	- std::vector< vtkSmartPointer<vtkAppendPolyData> > m_OdfsPlanes;
	- std::vector< vtkSmartPointer<vtkActor> > m_OdfsActors;
	- std::vector< vtkSmartPointer<vtkPolyDataMapper> > m_OdfsMappers;
	- vtkSmartPointer< vtkPolyData > m_TemplateOdf;
	-
	- itk::TimeStamp m_LastUpdateTime;
	-
	- /** \brief Default constructor of the local storage. */
	- LocalStorage();
	- /** \brief Default deconstructor of the local storage. */
	- ~LocalStorage() override
	- {
	- }
	- };
	-
	-protected:
	-
	- OdfVtkMapper2D();
	- ~OdfVtkMapper2D() override;
	-
	- static void GlyphMethod(void *arg);
	- bool IsPlaneRotated(mitk::BaseRenderer* renderer);
	- static bool m_ToggleTensorEllipsoidView;
	- static bool m_ToggleColourisationMode;
	- static bool m_ToggleGlyphPlacementMode;
	-
	-
	- typedef vnl_matrix_fixed<double, 3, 3> DirectionsType;
	-
	-
	-private:
	-
	- mitk::Image* GetInput();
	-
	- static vtkSmartPointer<vtkTransform> m_OdfTransform;
	- static vtkSmartPointer<vtkOdfSource> m_OdfSource;
	- static float m_Scaling;
	- static int m_Normalization;
	- static int m_ScaleBy;
	- static float m_IndexParam1;
	- static float m_IndexParam2;
	- static vtkSmartPointer<vtkDoubleArray> m_ColourScalars;
	- int m_ShowMaxNumber;
	- std::vector< vtkSmartPointer<vtkPlane> > m_Planes;
	- std::vector< vtkSmartPointer<vtkCutter> > m_Cutters;
	- std::vector< vtkSmartPointer<vtkThickPlane> > m_ThickPlanes1;
	- std::vector< vtkSmartPointer<vtkClipPolyData> > m_Clippers1;
	- std::vector< vtkSmartPointer<vtkThickPlane> > m_ThickPlanes2;
	- std::vector< vtkSmartPointer<vtkClipPolyData> > m_Clippers2;
	- vtkImageData* m_VtkImage ;
	- std::vector< OdfDisplayGeometry > m_LastDisplayGeometry;
	- mitk::LocalStorageHandler<LocalStorage> m_LSH;
	-
	- static vnl_matrix<float> m_Sh2Basis;
	- static vnl_matrix<float> m_Sh4Basis;
	- static vnl_matrix<float> m_Sh6Basis;
	- static vnl_matrix<float> m_Sh8Basis;
	- static vnl_matrix<float> m_Sh10Basis;
	- static vnl_matrix<float> m_Sh12Basis;
	-};
	-
	-} // namespace mitk
	-
	-#include "mitkOdfVtkMapper2D.txx"
	-
	-#endif /* ODFVTKMAPPER2D_H_HEADER_INCLUDED */
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Rendering/mitkOdfVtkMapper2D.txx b/Modules/DiffusionImaging/DiffusionCore/include/Rendering/mitkOdfVtkMapper2D.txx
	deleted file mode 100644
	index 8c4ce97730..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Rendering/mitkOdfVtkMapper2D.txx
	+++ /dev/null
	@@ -1,984 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef __mitkOdfVtkMapper2D_txx__
	-#define __mitkOdfVtkMapper2D_txx__
	-
	-#include "mitkOdfVtkMapper2D.h"
	-#include "mitkDataNode.h"
	-#include "mitkBaseRenderer.h"
	-#include "mitkMatrixConvert.h"
	-#include "mitkGeometry3D.h"
	-#include "mitkTimeGeometry.h"
	-#include "mitkOdfNormalizationMethodProperty.h"
	-#include "mitkOdfScaleByProperty.h"
	-#include "mitkProperties.h"
	-#include "mitkTensorImage.h"
	-#include "mitkShImage.h"
	-
	-#include "vtkSphereSource.h"
	-#include "vtkPropCollection.h"
	-#include "vtkMaskedGlyph3D.h"
	-#include "vtkGlyph2D.h"
	-#include "vtkGlyph3D.h"
	-#include "vtkMaskedProgrammableGlyphFilter.h"
	-#include "vtkImageData.h"
	-#include "vtkLinearTransform.h"
	-#include "vtkCamera.h"
	-#include "vtkPointData.h"
	-#include "vtkTransformPolyDataFilter.h"
	-#include "vtkTransform.h"
	-#include "vtkOdfSource.h"
	-#include "vtkDoubleArray.h"
	-#include "vtkLookupTable.h"
	-#include "vtkProperty.h"
	-#include "vtkPolyDataNormals.h"
	-#include "vtkLight.h"
	-#include "vtkLightCollection.h"
	-#include "vtkMath.h"
	-#include "vtkFloatArray.h"
	-#include "vtkDelaunay2D.h"
	-#include "vtkMapper.h"
	-#include <vtkInformationVector.h>
	-#include <vtkInformation.h>
	-#include "vtkRenderer.h"
	-
	-#include "itkOrientationDistributionFunction.h"
	-
	-#include "itkFixedArray.h"
	-
	-#include <mitkGL.h>
	-#include "vtkOpenGLRenderer.h"
	-
	-#define _USE_MATH_DEFINES
	-#include <cmath>
	-
	-#include <ciso646>
	-
	-
	-template<class T, int N>
	-vtkSmartPointer<vtkTransform> mitk::OdfVtkMapper2D<T,N>::m_OdfTransform = vtkSmartPointer<vtkTransform>::New();
	-
	-template<class T, int N>
	-vtkSmartPointer<vtkOdfSource> mitk::OdfVtkMapper2D<T,N>::m_OdfSource = vtkSmartPointer<vtkOdfSource>::New();
	-
	-template<class T, int N>
	-float mitk::OdfVtkMapper2D<T,N>::m_Scaling;
	-
	-template<class T, int N>
	-int mitk::OdfVtkMapper2D<T,N>::m_Normalization;
	-
	-template<class T, int N>
	-int mitk::OdfVtkMapper2D<T,N>::m_ScaleBy;
	-
	-template<class T, int N>
	-float mitk::OdfVtkMapper2D<T,N>::m_IndexParam1;
	-
	-template<class T, int N>
	-float mitk::OdfVtkMapper2D<T,N>::m_IndexParam2;
	-
	-template<class T, int N>
	-bool mitk::OdfVtkMapper2D<T, N>::m_ToggleTensorEllipsoidView = false;
	-
	-template<class T, int N>
	-bool mitk::OdfVtkMapper2D<T, N>::m_ToggleColourisationMode = false;
	-
	-template<class T, int N>
	-bool mitk::OdfVtkMapper2D<T, N>::m_ToggleGlyphPlacementMode = true;
	-
	-template<class T, int N>
	-vtkSmartPointer<vtkDoubleArray> mitk::OdfVtkMapper2D<T, N>::m_ColourScalars = nullptr;
	-
	-
	-template<class T, int N>
	-vnl_matrix<float> mitk::OdfVtkMapper2D<T, N>::m_Sh2Basis = mitk::sh::CalcShBasisForDirections(2, itk::PointShell<N, vnl_matrix_fixed<double, 3, N> >::DistributePointShell()->as_matrix());
	-template<class T, int N>
	-vnl_matrix<float> mitk::OdfVtkMapper2D<T, N>::m_Sh4Basis = mitk::sh::CalcShBasisForDirections(4, itk::PointShell<N, vnl_matrix_fixed<double, 3, N> >::DistributePointShell()->as_matrix());
	-template<class T, int N>
	-vnl_matrix<float> mitk::OdfVtkMapper2D<T, N>::m_Sh6Basis = mitk::sh::CalcShBasisForDirections(6, itk::PointShell<N, vnl_matrix_fixed<double, 3, N> >::DistributePointShell()->as_matrix());
	-template<class T, int N>
	-vnl_matrix<float> mitk::OdfVtkMapper2D<T, N>::m_Sh8Basis = mitk::sh::CalcShBasisForDirections(8, itk::PointShell<N, vnl_matrix_fixed<double, 3, N> >::DistributePointShell()->as_matrix());
	-template<class T, int N>
	-vnl_matrix<float> mitk::OdfVtkMapper2D<T, N>::m_Sh10Basis = mitk::sh::CalcShBasisForDirections(10, itk::PointShell<N, vnl_matrix_fixed<double, 3, N> >::DistributePointShell()->as_matrix());
	-template<class T, int N>
	-vnl_matrix<float> mitk::OdfVtkMapper2D<T, N>::m_Sh12Basis = mitk::sh::CalcShBasisForDirections(12, itk::PointShell<N, vnl_matrix_fixed<double, 3, N> >::DistributePointShell()->as_matrix());
	-
	-
	-template<class T, int N>
	-mitk::OdfVtkMapper2D<T,N>::LocalStorage::LocalStorage()
	-{
	- m_PropAssemblies.push_back(vtkSmartPointer<vtkPropAssembly>::New());
	- m_PropAssemblies.push_back(vtkSmartPointer<vtkPropAssembly>::New());
	- m_PropAssemblies.push_back(vtkSmartPointer<vtkPropAssembly>::New());
	-
	- m_OdfsPlanes.push_back(vtkSmartPointer<vtkAppendPolyData>::New());
	- m_OdfsPlanes.push_back(vtkSmartPointer<vtkAppendPolyData>::New());
	- m_OdfsPlanes.push_back(vtkSmartPointer<vtkAppendPolyData>::New());
	-
	- m_OdfsPlanes[0]->AddInputData(vtkSmartPointer<vtkPolyData>::New());
	- m_OdfsPlanes[1]->AddInputData(vtkSmartPointer<vtkPolyData>::New());
	- m_OdfsPlanes[2]->AddInputData(vtkSmartPointer<vtkPolyData>::New());
	-
	- m_OdfsActors.push_back(vtkSmartPointer<vtkActor>::New());
	- m_OdfsActors.push_back(vtkSmartPointer<vtkActor>::New());
	- m_OdfsActors.push_back(vtkSmartPointer<vtkActor>::New());
	-
	- m_OdfsActors[0]->GetProperty()->SetInterpolationToGouraud();
	- m_OdfsActors[1]->GetProperty()->SetInterpolationToGouraud();
	- m_OdfsActors[2]->GetProperty()->SetInterpolationToGouraud();
	-
	- m_OdfsMappers.push_back(vtkSmartPointer<vtkPolyDataMapper>::New());
	- m_OdfsMappers.push_back(vtkSmartPointer<vtkPolyDataMapper>::New());
	- m_OdfsMappers.push_back(vtkSmartPointer<vtkPolyDataMapper>::New());
	-
	- vtkSmartPointer<vtkLookupTable> lut = vtkSmartPointer<vtkLookupTable>::New();
	-
	- m_OdfsMappers[0]->SetLookupTable(lut);
	- m_OdfsMappers[1]->SetLookupTable(lut);
	- m_OdfsMappers[2]->SetLookupTable(lut);
	-
	- m_OdfsActors[0]->SetMapper(m_OdfsMappers[0]);
	- m_OdfsActors[1]->SetMapper(m_OdfsMappers[1]);
	- m_OdfsActors[2]->SetMapper(m_OdfsMappers[2]);
	-}
	-
	-template<class T, int N>
	-mitk::OdfVtkMapper2D<T,N>
	-::OdfVtkMapper2D()
	-{
	- m_LastDisplayGeometry.push_back(OdfDisplayGeometry());
	- m_LastDisplayGeometry.push_back(OdfDisplayGeometry());
	- m_LastDisplayGeometry.push_back(OdfDisplayGeometry());
	-
	- m_Planes.push_back(vtkSmartPointer<vtkPlane>::New());
	- m_Planes.push_back(vtkSmartPointer<vtkPlane>::New());
	- m_Planes.push_back(vtkSmartPointer<vtkPlane>::New());
	-
	- m_Cutters.push_back(vtkSmartPointer<vtkCutter>::New());
	- m_Cutters.push_back(vtkSmartPointer<vtkCutter>::New());
	- m_Cutters.push_back(vtkSmartPointer<vtkCutter>::New());
	-
	- m_Cutters[0]->SetCutFunction( m_Planes[0] );
	- m_Cutters[0]->GenerateValues( 1, 0, 1 );
	-
	- m_Cutters[1]->SetCutFunction( m_Planes[1] );
	- m_Cutters[1]->GenerateValues( 1, 0, 1 );
	-
	- m_Cutters[2]->SetCutFunction( m_Planes[2] );
	- m_Cutters[2]->GenerateValues( 1, 0, 1 );
	-
	- // Windowing the cutted planes in direction 1
	- m_ThickPlanes1.push_back(vtkSmartPointer<vtkThickPlane>::New());
	- m_ThickPlanes1.push_back(vtkSmartPointer<vtkThickPlane>::New());
	- m_ThickPlanes1.push_back(vtkSmartPointer<vtkThickPlane>::New());
	-
	- m_Clippers1.push_back(vtkSmartPointer<vtkClipPolyData>::New());
	- m_Clippers1.push_back(vtkSmartPointer<vtkClipPolyData>::New());
	- m_Clippers1.push_back(vtkSmartPointer<vtkClipPolyData>::New());
	-
	- m_Clippers1[0]->SetClipFunction( m_ThickPlanes1[0] );
	- m_Clippers1[1]->SetClipFunction( m_ThickPlanes1[1] );
	- m_Clippers1[2]->SetClipFunction( m_ThickPlanes1[2] );
	-
	- // Windowing the cutted planes in direction 2
	- m_ThickPlanes2.push_back(vtkSmartPointer<vtkThickPlane>::New());
	- m_ThickPlanes2.push_back(vtkSmartPointer<vtkThickPlane>::New());
	- m_ThickPlanes2.push_back(vtkSmartPointer<vtkThickPlane>::New());
	-
	- m_Clippers2.push_back(vtkSmartPointer<vtkClipPolyData>::New());
	- m_Clippers2.push_back(vtkSmartPointer<vtkClipPolyData>::New());
	- m_Clippers2.push_back(vtkSmartPointer<vtkClipPolyData>::New());
	-
	- m_Clippers2[0]->SetClipFunction( m_ThickPlanes2[0] );
	- m_Clippers2[1]->SetClipFunction( m_ThickPlanes2[1] );
	- m_Clippers2[2]->SetClipFunction( m_ThickPlanes2[2] );
	-
	- m_ShowMaxNumber = 500;
	-}
	-
	-template<class T, int N>
	-mitk::OdfVtkMapper2D<T,N>
	-::~OdfVtkMapper2D()
	-{
	-
	-}
	-
	-template<class T, int N>
	-mitk::Image* mitk::OdfVtkMapper2D<T,N>
	-::GetInput()
	-{
	- return static_cast<mitk::Image * > ( m_DataNode->GetData() );
	-}
	-
	-template<class T, int N>
	-vtkProp* mitk::OdfVtkMapper2D<T,N>
	-::GetVtkProp(mitk::BaseRenderer* renderer)
	-{
	- LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer);
	- return localStorage->m_PropAssemblies[GetIndex(renderer)];
	-}
	-
	-template<class T, int N>
	-int mitk::OdfVtkMapper2D<T,N>
	-::GetIndex(mitk::BaseRenderer* renderer)
	-{
	- if(!strcmp(renderer->GetName(),"stdmulti.widget1"))
	- return 0;
	-
	- if(!strcmp(renderer->GetName(),"stdmulti.widget2"))
	- return 1;
	-
	- if(!strcmp(renderer->GetName(),"stdmulti.widget3"))
	- return 2;
	-
	- return 0;
	-}
	-
	-template<class T, int N>
	-void mitk::OdfVtkMapper2D<T,N>
	-::GlyphMethod(void *arg)
	-{
	- vtkMaskedProgrammableGlyphFilter* pfilter=(vtkMaskedProgrammableGlyphFilter*)arg;
	-
	- double point[3];
	- double debugpoint[3];
	- pfilter->GetPoint(point);
	- pfilter->GetPoint(debugpoint);
	-
	- itk::Point<double,3> p(point);
	- Vector3D spacing = pfilter->GetGeometry()->GetSpacing();
	- p[0] /= spacing[0];
	- p[1] /= spacing[1];
	- p[2] /= spacing[2];
	-
	- mitk::Point3D p2;
	- pfilter->GetGeometry()->IndexToWorld( p, p2 );
	- point[0] = p2[0];
	- point[1] = p2[1];
	- point[2] = p2[2];
	-
	- vtkPointData* data = pfilter->GetPointData();
	- vtkDataArray* image_vals = data->GetArray("vector");
	- vtkIdType id = pfilter->GetPointId();
	- m_OdfTransform->Identity();
	- m_OdfTransform->Translate(point[0],point[1],point[2]);
	-
	- typedef itk::OrientationDistributionFunction<float,N> OdfType;
	- OdfType odf;
	-
	- if( image_vals->GetNumberOfComponents()==6 && !m_ToggleTensorEllipsoidView )
	- {
	- float tensorelems[6] = {
	- (float)image_vals->GetComponent(id,0),
	- (float)image_vals->GetComponent(id,1),
	- (float)image_vals->GetComponent(id,2),
	- (float)image_vals->GetComponent(id,3),
	- (float)image_vals->GetComponent(id,4),
	- (float)image_vals->GetComponent(id,5),
	- };
	- itk::DiffusionTensor3D<float> tensor(tensorelems);
	- odf.InitFromTensor(tensor);
	- }
	- else if( image_vals->GetNumberOfComponents()==6 && m_ToggleTensorEllipsoidView )
	- {
	- float tensorelems[6] = {
	- (float)image_vals->GetComponent(id,0),
	- (float)image_vals->GetComponent(id,1),
	- (float)image_vals->GetComponent(id,2),
	- (float)image_vals->GetComponent(id,3),
	- (float)image_vals->GetComponent(id,4),
	- (float)image_vals->GetComponent(id,5),
	- };
	- itk::DiffusionTensor3D<float> tensor( tensorelems );
	- odf.InitFromEllipsoid( tensor );
	- }
	- else if (image_vals->GetNumberOfComponents() == ODF_SAMPLING_SIZE)
	- {
	- for(int i=0; i<N; i++)
	- odf[i] = (double)image_vals->GetComponent(id,i);
	- }
	- else
	- {
	- int nrCoeffs = image_vals->GetNumberOfComponents();
	- Vector< float, N > odf_vals;
	- vnl_vector< float > coeffs(nrCoeffs);
	- for(int i=0; i<nrCoeffs; i++)
	- coeffs[i] = (float)image_vals->GetComponent(id,i);
	-
	- switch (nrCoeffs)
	- {
	- case 6:
	- odf_vals = ( m_Sh2Basis * coeffs ).data_block();
	- break;
	- case 15:
	- odf_vals = ( m_Sh4Basis * coeffs ).data_block();
	- break;
	- case 28:
	- odf_vals = ( m_Sh6Basis * coeffs ).data_block();
	- break;
	- case 45:
	- odf_vals = ( m_Sh8Basis * coeffs ).data_block();
	- break;
	- case 66:
	- odf_vals = ( m_Sh10Basis * coeffs ).data_block();
	- break;
	- case 91:
	- odf_vals = ( m_Sh12Basis * coeffs ).data_block();
	- break;
	- default :
	- mitkThrow() << "SH order larger 12 not supported in current ODF mapper version";
	- }
	-
	- for(int i=0; i<N; i++)
	- odf[i] = odf_vals[i];
	- }
	-
	- if (m_ToggleColourisationMode)
	- {
	- m_OdfSource->SetUseCustomColor(true);
	- vnl_vector_fixed<double,3> d = odf.GetPrincipalDiffusionDirection();
	- m_OdfSource->SetColor(fabs(d[0])255,fabs(d[1])255,fabs(d[2])*255);
	- }
	- else
	- {
	- m_OdfSource->SetUseCustomColor(false);
	- }
	-
	- switch(m_ScaleBy)
	- {
	- case ODFSB_NONE:
	- m_OdfSource->SetScale(m_Scaling);
	- break;
	- case ODFSB_GFA:
	- m_OdfSource->SetScale(m_Scaling*odf.GetGeneralizedFractionalAnisotropy());
	- break;
	- case ODFSB_PC:
	- m_OdfSource->SetScale(m_Scaling*odf.GetPrincipleCurvature(m_IndexParam1, m_IndexParam2, 0));
	- break;
	- }
	-
	- m_OdfSource->SetNormalization(m_Normalization);
	- m_OdfSource->SetOdf(odf);
	- m_OdfSource->Modified();
	-}
	-
	-template<class T, int N>
	-typename mitk::OdfVtkMapper2D<T,N>::OdfDisplayGeometry mitk::OdfVtkMapper2D<T,N>
	-::MeasureDisplayedGeometry(mitk::BaseRenderer* renderer)
	-{
	- PlaneGeometry::ConstPointer worldPlaneGeometry = renderer->GetCurrentWorldPlaneGeometry();
	-
	- // set up the cutter orientation according to the current geometry of
	- // the renderers plane
	- double vp[ 3 ], vnormal[ 3 ];
	- Point3D point = worldPlaneGeometry->GetOrigin();
	- Vector3D normal = worldPlaneGeometry->GetNormal(); normal.Normalize();
	- vnl2vtk( point.GetVnlVector(), vp );
	- vnl2vtk( normal.GetVnlVector(), vnormal );
	-
	- Point2D dispSizeInMM = renderer->GetViewportSizeInMM();
	-
	- Point2D displayGeometryOriginInMM = renderer->GetOriginInMM();
	-
	- mitk::Vector2D size = dispSizeInMM.GetVectorFromOrigin();
	- mitk::Vector2D origin = displayGeometryOriginInMM.GetVectorFromOrigin();
	-
	- //
	- // \|------O------\|
	- // \| d2 \|
	- // L d1 M \|
	- // \| \|
	- // \|-------------\|
	- //
	-
	- mitk::Vector2D M;
	- mitk::Vector2D L;
	- mitk::Vector2D O;
	-
	- M[0] = origin[0] + size[0]/2;
	- M[1] = origin[1] + size[1]/2;
	-
	- L[0] = origin[0];
	- L[1] = origin[1] + size[1]/2;
	-
	- O[0] = origin[0] + size[0]/2;
	- O[1] = origin[1] + size[1];
	-
	- mitk::Point2D point1;
	- point1[0] = M[0]; point1[1] = M[1];
	- mitk::Point3D M3D;
	- renderer->GetCurrentWorldPlaneGeometry()->Map(point1, M3D);
	-
	- point1[0] = L[0]; point1[1] = L[1];
	- mitk::Point3D L3D;
	- renderer->GetCurrentWorldPlaneGeometry()->Map(point1, L3D);
	-
	- point1[0] = O[0]; point1[1] = O[1];
	- mitk::Point3D O3D;
	- renderer->GetCurrentWorldPlaneGeometry()->Map(point1, O3D);
	-
	- double d1 = sqrt((M3D[0]-L3D[0])*(M3D[0]-L3D[0])
	- + (M3D[1]-L3D[1])*(M3D[1]-L3D[1])
	- + (M3D[2]-L3D[2])*(M3D[2]-L3D[2]));
	- double d2 = sqrt((M3D[0]-O3D[0])*(M3D[0]-O3D[0])
	- + (M3D[1]-O3D[1])*(M3D[1]-O3D[1])
	- + (M3D[2]-O3D[2])*(M3D[2]-O3D[2]));
	- double d = d1>d2 ? d1 : d2;
	- d = d2;
	-
	- OdfDisplayGeometry retval;
	- retval.vp[0] = vp[0];
	- retval.vp[1] = vp[1];
	- retval.vp[2] = vp[2];
	- retval.vnormal[0] = vnormal[0];
	- retval.vnormal[1] = vnormal[1];
	- retval.vnormal[2] = vnormal[2];
	- retval.normal[0] = normal[0];
	- retval.normal[1] = normal[1];
	- retval.normal[2] = normal[2];
	- retval.d = d;
	- retval.d1 = d1;
	- retval.d2 = d2;
	- retval.M3D[0] = M3D[0];
	- retval.M3D[1] = M3D[1];
	- retval.M3D[2] = M3D[2];
	- retval.L3D[0] = L3D[0];
	- retval.L3D[1] = L3D[1];
	- retval.L3D[2] = L3D[2];
	- retval.O3D[0] = O3D[0];
	- retval.O3D[1] = O3D[1];
	- retval.O3D[2] = O3D[2];
	-
	- retval.vp_original[0] = vp[0];
	- retval.vp_original[1] = vp[1];
	- retval.vp_original[2] = vp[2];
	- retval.vnormal_original[0] = vnormal[0];
	- retval.vnormal_original[1] = vnormal[1];
	- retval.vnormal_original[2] = vnormal[2];
	- retval.size[0] = size[0];
	- retval.size[1] = size[1];
	- retval.origin[0] = origin[0];
	- retval.origin[1] = origin[1];
	-
	- return retval;
	-}
	-
	-template<class T, int N>
	-void mitk::OdfVtkMapper2D<T,N>
	-::Slice(mitk::BaseRenderer* renderer, OdfDisplayGeometry dispGeo)
	-{
	- LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer);
	-
	- vtkLinearTransform * vtktransform =
	- this->GetDataNode()->GetVtkTransform(this->GetTimestep());
	-
	- int index = GetIndex(renderer);
	-
	- vtkSmartPointer<vtkTransform> inversetransform = vtkSmartPointer<vtkTransform>::New();
	- inversetransform->Identity();
	- inversetransform->Concatenate(vtktransform->GetLinearInverse());
	- double myscale[3];
	- ((vtkTransform*)vtktransform)->GetScale(myscale);
	- myscale[0] = fabs(myscale[0]);
	- myscale[1] = fabs(myscale[1]);
	- myscale[2] = fabs(myscale[2]);
	- inversetransform->PostMultiply();
	- inversetransform->Scale(myscale[0],myscale[1],myscale[2]);
	- inversetransform->TransformPoint( dispGeo.vp, dispGeo.vp );
	- inversetransform->TransformNormalAtPoint( dispGeo.vp, dispGeo.vnormal, dispGeo.vnormal );
	-
	- // vtk works in axis align coords
	- // thus the normal also must be axis align, since
	- // we do not allow arbitrary cutting through volume
	- //
	- // vnormal should already be axis align, but in order
	- // to get rid of precision effects, we set the two smaller
	- // components to zero here
	- int dims[3];
	- m_VtkImage->GetDimensions(dims);
	- double spac[3];
	- m_VtkImage->GetSpacing(spac);
	- if(fabs(dispGeo.vnormal[0]) > fabs(dispGeo.vnormal[1])
	- && fabs(dispGeo.vnormal[0]) > fabs(dispGeo.vnormal[2]) )
	- {
	- if(fabs(dispGeo.vp[0]/spac[0]) < 0.4)
	- dispGeo.vp[0] = 0.4*spac[0];
	- if(fabs(dispGeo.vp[0]/spac[0]) > (dims[0]-1)-0.4)
	- dispGeo.vp[0] = ((dims[0]-1)-0.4)*spac[0];
	- dispGeo.vnormal[1] = 0;
	- dispGeo.vnormal[2] = 0;
	- }
	-
	- if(fabs(dispGeo.vnormal[1]) > fabs(dispGeo.vnormal[0]) && fabs(dispGeo.vnormal[1]) > fabs(dispGeo.vnormal[2]) )
	- {
	- if(fabs(dispGeo.vp[1]/spac[1]) < 0.4)
	- dispGeo.vp[1] = 0.4*spac[1];
	- if(fabs(dispGeo.vp[1]/spac[1]) > (dims[1]-1)-0.4)
	- dispGeo.vp[1] = ((dims[1]-1)-0.4)*spac[1];
	- dispGeo.vnormal[0] = 0;
	- dispGeo.vnormal[2] = 0;
	- }
	-
	- if(fabs(dispGeo.vnormal[2]) > fabs(dispGeo.vnormal[1]) && fabs(dispGeo.vnormal[2]) > fabs(dispGeo.vnormal[0]) )
	- {
	- if(fabs(dispGeo.vp[2]/spac[2]) < 0.4)
	- dispGeo.vp[2] = 0.4*spac[2];
	- if(fabs(dispGeo.vp[2]/spac[2]) > (dims[2]-1)-0.4)
	- dispGeo.vp[2] = ((dims[2]-1)-0.4)*spac[2];
	- dispGeo.vnormal[0] = 0;
	- dispGeo.vnormal[1] = 0;
	- }
	-
	-
	- m_Planes[index]->SetTransform( (vtkAbstractTransform*)nullptr );
	- m_Planes[index]->SetOrigin( dispGeo.vp );
	- m_Planes[index]->SetNormal( dispGeo.vnormal );
	-
	- vtkSmartPointer<vtkPoints> points;
	- vtkSmartPointer<vtkPoints> tmppoints;
	- vtkSmartPointer<vtkPolyData> polydata;
	- vtkSmartPointer<vtkFloatArray> pointdata;
	- vtkSmartPointer<vtkDelaunay2D> delaunay;
	- vtkSmartPointer<vtkPolyData> cuttedPlane;
	-
	- // the cutter only works if we do not have a 2D-image
	- // or if we have a 2D-image and want to see the whole image.
	- //
	- // for side views of 2D-images, we need some special treatment
	- if(!( (dims[0] == 1 && dispGeo.vnormal[0] != 0) \|\|
	- (dims[1] == 1 && dispGeo.vnormal[1] != 0) \|\|
	- (dims[2] == 1 && dispGeo.vnormal[2] != 0) ))
	- {
	- m_Cutters[index]->SetCutFunction( m_Planes[index] );
	- m_Cutters[index]->SetInputData( m_VtkImage );
	- m_Cutters[index]->Update();
	- cuttedPlane = m_Cutters[index]->GetOutput();
	- }
	- else
	- {
	- // cutting of a 2D-Volume does not work,
	- // so we have to build up our own polydata object
	- cuttedPlane = vtkSmartPointer<vtkPolyData>::New();
	- points = vtkSmartPointer<vtkPoints>::New();
	- points->SetNumberOfPoints(m_VtkImage->GetNumberOfPoints());
	- for(int i=0; i<m_VtkImage->GetNumberOfPoints(); i++)
	- {
	- points->SetPoint(i, m_VtkImage->GetPoint(i));
	- }
	- cuttedPlane->SetPoints(points);
	-
	- int nZero1, nZero2;
	- if(dims[0]==1)
	- {
	- nZero1 = 1; nZero2 = 2;
	- }
	- else if(dims[1]==1)
	- {
	- nZero1 = 0; nZero2 = 2;
	- }
	- else
	- {
	- nZero1 = 0; nZero2 = 1;
	- }
	-
	- tmppoints = vtkSmartPointer<vtkPoints>::New();
	- for(int j=0; j<m_VtkImage->GetNumberOfPoints(); j++){
	- double pt[3];
	- m_VtkImage->GetPoint(j,pt);
	- tmppoints->InsertNextPoint(pt[nZero1],pt[nZero2],0);
	- }
	-
	- polydata = vtkSmartPointer<vtkPolyData>::New();
	- polydata->SetPoints( tmppoints );
	- delaunay = vtkSmartPointer<vtkDelaunay2D>::New();
	- delaunay->SetInputData( polydata );
	- delaunay->Update();
	- vtkCellArray* polys = delaunay->GetOutput()->GetPolys();
	- cuttedPlane->SetPolys(polys);
	- }
	-
	- if(cuttedPlane->GetNumberOfPoints())
	- {
	- // WINDOWING HERE
	- dispGeo.vnormal[0] = dispGeo.M3D[0]-dispGeo.O3D[0];
	- dispGeo.vnormal[1] = dispGeo.M3D[1]-dispGeo.O3D[1];
	- dispGeo.vnormal[2] = dispGeo.M3D[2]-dispGeo.O3D[2];
	- vtkMath::Normalize(dispGeo.vnormal);
	- dispGeo.vp[0] = dispGeo.M3D[0];
	- dispGeo.vp[1] = dispGeo.M3D[1];
	- dispGeo.vp[2] = dispGeo.M3D[2];
	-
	- inversetransform->TransformPoint( dispGeo.vp, dispGeo.vp );
	- inversetransform->TransformNormalAtPoint( dispGeo.vp, dispGeo.vnormal, dispGeo.vnormal );
	-
	- m_ThickPlanes1[index]->count = 0;
	- m_ThickPlanes1[index]->SetTransform((vtkAbstractTransform*)nullptr );
	- m_ThickPlanes1[index]->SetPose( dispGeo.vnormal, dispGeo.vp );
	- m_ThickPlanes1[index]->SetThickness(dispGeo.d2);
	- m_Clippers1[index]->SetClipFunction( m_ThickPlanes1[index] );
	- m_Clippers1[index]->SetInputData( cuttedPlane );
	- m_Clippers1[index]->SetInsideOut(1);
	- m_Clippers1[index]->Update();
	-
	- dispGeo.vnormal[0] = dispGeo.M3D[0]-dispGeo.L3D[0];
	- dispGeo.vnormal[1] = dispGeo.M3D[1]-dispGeo.L3D[1];
	- dispGeo.vnormal[2] = dispGeo.M3D[2]-dispGeo.L3D[2];
	- vtkMath::Normalize(dispGeo.vnormal);
	- dispGeo.vp[0] = dispGeo.M3D[0];
	- dispGeo.vp[1] = dispGeo.M3D[1];
	- dispGeo.vp[2] = dispGeo.M3D[2];
	-
	- inversetransform->TransformPoint( dispGeo.vp, dispGeo.vp );
	- inversetransform->TransformNormalAtPoint( dispGeo.vp, dispGeo.vnormal, dispGeo.vnormal );
	-
	- m_ThickPlanes2[index]->count = 0;
	- m_ThickPlanes2[index]->SetTransform((vtkAbstractTransform*)nullptr );
	- m_ThickPlanes2[index]->SetPose( dispGeo.vnormal, dispGeo.vp );
	- m_ThickPlanes2[index]->SetThickness(dispGeo.d1);
	- m_Clippers2[index]->SetClipFunction( m_ThickPlanes2[index] );
	- m_Clippers2[index]->SetInputData( m_Clippers1[index]->GetOutput() );
	- m_Clippers2[index]->SetInsideOut(1);
	- m_Clippers2[index]->Update();
	-
	- cuttedPlane = m_Clippers2[index]->GetOutput ();
	-
	- if(cuttedPlane->GetNumberOfPoints())
	- {
	- localStorage->m_OdfsPlanes[index]->RemoveAllInputs();
	-
	- vtkSmartPointer<vtkPolyDataNormals> normals = vtkSmartPointer<vtkPolyDataNormals>::New();
	- normals->SetInputConnection( m_OdfSource->GetOutputPort() );
	- normals->SplittingOff();
	- normals->ConsistencyOff();
	- normals->AutoOrientNormalsOff();
	- normals->ComputePointNormalsOn();
	- normals->ComputeCellNormalsOff();
	- normals->FlipNormalsOff();
	- normals->NonManifoldTraversalOff();
	-
	- vtkSmartPointer<vtkTransformPolyDataFilter> trans = vtkSmartPointer<vtkTransformPolyDataFilter>::New();
	- trans->SetInputConnection( normals->GetOutputPort() );
	- trans->SetTransform(m_OdfTransform);
	-
	- vtkSmartPointer<vtkMaskedProgrammableGlyphFilter> glyphGenerator = vtkSmartPointer<vtkMaskedProgrammableGlyphFilter>::New();
	- glyphGenerator->SetMaximumNumberOfPoints(std::min(m_ShowMaxNumber,(int)cuttedPlane->GetNumberOfPoints()));
	- glyphGenerator->SetRandomMode( m_ToggleGlyphPlacementMode );
	- glyphGenerator->SetUseMaskPoints(1);
	- glyphGenerator->SetSourceConnection(trans->GetOutputPort() );
	- glyphGenerator->SetInput(cuttedPlane);
	- glyphGenerator->SetColorModeToColorBySource();
	- glyphGenerator->SetGeometry(this->GetDataNode()->GetData()->GetGeometry());
	- glyphGenerator->SetGlyphMethod(&(GlyphMethod),(void *)glyphGenerator);
	-
	- try
	- {
	- glyphGenerator->Update();
	- }
	- catch( itk::ExceptionObject& err )
	- {
	- std::cout << err << std::endl;
	- }
	-
	- localStorage->m_OdfsPlanes[index]->AddInputConnection(glyphGenerator->GetOutputPort());
	- localStorage->m_OdfsPlanes[index]->Update();
	- }
	- }
	- localStorage->m_OdfsMappers[index]->ScalarVisibilityOn();
	- localStorage->m_OdfsMappers[index]->SetScalarModeToUsePointFieldData();
	- localStorage->m_OdfsMappers[index]->SelectColorArray("ODF_COLORS");
	-
	- localStorage->m_PropAssemblies[index]->VisibilityOn();
	- if(localStorage->m_PropAssemblies[index]->GetParts()->IsItemPresent(localStorage->m_OdfsActors[index]))
	- {
	- localStorage->m_PropAssemblies[index]->RemovePart(localStorage->m_OdfsActors[index]);
	- }
	- localStorage->m_OdfsMappers[index]->SetInputData(localStorage->m_OdfsPlanes[index]->GetOutput());
	- localStorage->m_PropAssemblies[index]->AddPart(localStorage->m_OdfsActors[index]);
	-}
	-
	-template<class T, int N>
	-bool mitk::OdfVtkMapper2D<T,N>
	-::IsVisibleOdfs(mitk::BaseRenderer* renderer)
	-{
	- mitk::Image::Pointer input = const_cast<mitk::Image*>(this->GetInput());
	- const TimeGeometry *inputTimeGeometry = input->GetTimeGeometry();
	- if(inputTimeGeometry==nullptr \|\| inputTimeGeometry->CountTimeSteps()==0 \|\| !inputTimeGeometry->IsValidTimeStep(this->GetTimestep()))
	- return false;
	-
	- if(this->IsPlaneRotated(renderer))
	- return false;
	-
	- bool retval = false;
	- switch(GetIndex(renderer))
	- {
	- case 0:
	- GetDataNode()->GetVisibility(retval, renderer, "VisibleOdfs_T");
	- break;
	- case 1:
	- GetDataNode()->GetVisibility(retval, renderer, "VisibleOdfs_S");
	- break;
	- case 2:
	- GetDataNode()->GetVisibility(retval, renderer, "VisibleOdfs_C");
	- break;
	- }
	-
	- return retval;
	-}
	-
	-template<class T, int N>
	-void mitk::OdfVtkMapper2D<T,N>
	-::MitkRenderOverlay(mitk::BaseRenderer* renderer)
	-{
	- if ( this->IsVisibleOdfs(renderer)==false )
	- return;
	-
	- if ( this->GetVtkProp(renderer)->GetVisibility() )
	- this->GetVtkProp(renderer)->RenderOverlay(renderer->GetVtkRenderer());
	-}
	-
	-template<class T, int N>
	-void mitk::OdfVtkMapper2D<T,N>
	-::MitkRenderOpaqueGeometry(mitk::BaseRenderer* renderer)
	-{
	- if ( this->IsVisibleOdfs( renderer )==false )
	- return;
	-
	- if ( this->GetVtkProp(renderer)->GetVisibility() )
	- {
	- // adapt cam pos
	- this->GetVtkProp(renderer)->RenderOpaqueGeometry( renderer->GetVtkRenderer() );
	- }
	-}
	-
	-template<class T, int N>
	-void mitk::OdfVtkMapper2D<T,N>
	-::MitkRenderTranslucentGeometry(mitk::BaseRenderer* renderer)
	-{
	- if ( this->IsVisibleOdfs(renderer)==false )
	- return;
	-
	- if ( this->GetVtkProp(renderer)->GetVisibility() )
	- this->GetVtkProp(renderer)->RenderTranslucentPolygonalGeometry(renderer->GetVtkRenderer());
	-
	-}
	-
	-template<class T, int N>
	-void mitk::OdfVtkMapper2D<T,N>
	-::Update(mitk::BaseRenderer* renderer)
	-{
	- bool visible = true;
	- GetDataNode()->GetVisibility(visible, renderer, "visible");
	-
	- if ( !visible ) return;
	-
	- mitk::Image::Pointer input = const_cast<mitk::Image*>( this->GetInput() );
	- if ( input.IsNull() ) return ;
	-
	- std::string classname("TensorImage");
	- if(classname.compare(input->GetNameOfClass())==0)
	- m_VtkImage = dynamic_cast<mitk::TensorImage*>( this->GetInput() )->GetNonRgbVtkImageData();
	-
	- std::string qclassname("OdfImage");
	- if(qclassname.compare(input->GetNameOfClass())==0)
	- m_VtkImage = dynamic_cast<mitk::OdfImage*>( this->GetInput() )->GetNonRgbVtkImageData();
	-
	- std::string shclassname("ShImage");
	- if(shclassname.compare(input->GetNameOfClass())==0)
	- m_VtkImage = dynamic_cast<mitk::ShImage*>( this->GetInput() )->GetNonRgbVtkImageData();
	-
	- if( m_VtkImage )
	- {
	- // make sure, that we have point data with more than 1 component (as vectors)
	- vtkPointData* pointData = m_VtkImage->GetPointData();
	- if ( pointData == nullptr )
	- {
	- itkWarningMacro( << "m_VtkImage->GetPointData() returns NULL!" );
	- return ;
	- }
	- if ( pointData->GetNumberOfArrays() == 0 )
	- {
	- itkWarningMacro( << "m_VtkImage->GetPointData()->GetNumberOfArrays() is 0!" );
	- return ;
	- }
	- else if ( pointData->GetArrayName( 0 ) == nullptr )
	- {
	- m_VtkImage->GetPointData()->GetArray(0)->SetName("vector");
	- }
	-
	- GenerateDataForRenderer(renderer);
	- }
	- else
	- {
	- itkWarningMacro( << "m_VtkImage is NULL!" );
	- return ;
	- }
	-}
	-
	-template<class T, int N>
	-void mitk::OdfVtkMapper2D<T,N>
	-::GenerateDataForRenderer( mitk::BaseRenderer *renderer )
	-{
	- LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer);
	-
	- OdfDisplayGeometry dispGeo = MeasureDisplayedGeometry( renderer);
	-
	- if ((localStorage->m_LastUpdateTime >= m_DataNode->GetMTime()) //was the node modified?
	- && (localStorage->m_LastUpdateTime >= m_DataNode->GetPropertyList()->GetMTime()) //was a property modified?
	- && (localStorage->m_LastUpdateTime >= m_DataNode->GetPropertyList(renderer)->GetMTime())
	- && dispGeo.Equals(m_LastDisplayGeometry.at(GetIndex(renderer))))
	- {
	- return;
	- }
	-
	- localStorage->m_LastUpdateTime.Modified();
	-
	- if(!IsVisibleOdfs(renderer))
	- {
	- localStorage->m_OdfsActors[0]->VisibilityOff();
	- localStorage->m_OdfsActors[1]->VisibilityOff();
	- localStorage->m_OdfsActors[2]->VisibilityOff();
	- }
	- else
	- {
	- localStorage->m_OdfsActors[0]->VisibilityOn();
	- localStorage->m_OdfsActors[1]->VisibilityOn();
	- localStorage->m_OdfsActors[2]->VisibilityOn();
	-
	- m_OdfSource->SetAdditionalScale(GetMinImageSpacing(GetIndex(renderer)));
	- ApplyPropertySettings();
	- Slice(renderer, dispGeo);
	- m_LastDisplayGeometry[GetIndex(renderer)] = dispGeo;
	- }
	-}
	-
	-template<class T, int N>
	-double mitk::OdfVtkMapper2D<T,N>::GetMinImageSpacing( int index )
	-{
	- // Spacing adapted scaling
	- double spacing[3];
	- m_VtkImage->GetSpacing(spacing);
	- double min = spacing[0];
	- if(index==0)
	- {
	- min = spacing[0];
	- min = min > spacing[1] ? spacing[1] : min;
	- }
	- if(index==1)
	- {
	- min = spacing[1];
	- min = min > spacing[2] ? spacing[2] : min;
	- }
	- if(index==2)
	- {
	- min = spacing[0];
	- min = min > spacing[2] ? spacing[2] : min;
	- }
	- return min;
	-}
	-
	-template<class T, int N>
	-void mitk::OdfVtkMapper2D<T,N>
	-::ApplyPropertySettings()
	-{
	- this->GetDataNode()->GetFloatProperty( "Scaling", m_Scaling );
	- this->GetDataNode()->GetIntProperty( "ShowMaxNumber", m_ShowMaxNumber );
	-
	- OdfNormalizationMethodProperty* nmp = dynamic_cast<OdfNormalizationMethodProperty*>(this->GetDataNode()->GetProperty( "Normalization" ));
	- if(nmp)
	- m_Normalization = nmp->GetNormalization();
	-
	- OdfScaleByProperty* sbp = dynamic_cast<OdfScaleByProperty*>(this->GetDataNode()->GetProperty( "ScaleBy" ));
	- if(sbp)
	- m_ScaleBy = sbp->GetScaleBy();
	-
	- this->GetDataNode()->GetFloatProperty( "IndexParam1", m_IndexParam1);
	- this->GetDataNode()->GetFloatProperty( "IndexParam2", m_IndexParam2);
	-
	- this->GetDataNode()->GetBoolProperty( "DiffusionCore.Rendering.OdfVtkMapper.SwitchTensorView", m_ToggleTensorEllipsoidView );
	- this->GetDataNode()->GetBoolProperty( "DiffusionCore.Rendering.OdfVtkMapper.ColourisationModeBit", m_ToggleColourisationMode );
	- this->GetDataNode()->GetBoolProperty( "DiffusionCore.Rendering.OdfVtkMapper.RandomModeBit", m_ToggleGlyphPlacementMode);
	-}
	-
	-template <class T, int N>
	-bool mitk::OdfVtkMapper2D<T,N>
	-::IsPlaneRotated(mitk::BaseRenderer* renderer)
	-{
	- PlaneGeometry::ConstPointer worldPlaneGeometry = renderer->GetCurrentWorldPlaneGeometry();
	-
	- double vnormal[ 3 ];
	- Vector3D normal = worldPlaneGeometry->GetNormal(); normal.Normalize();
	- vnl2vtk( normal.GetVnlVector(), vnormal );
	-
	- mitk::Image* currentImage = dynamic_cast<mitk::Image* >( this->GetDataNode()->GetData() );
	- if( currentImage == nullptr )
	- return false;
	- mitk::Vector3D imageNormal0 = currentImage->GetSlicedGeometry()->GetAxisVector(0);
	- mitk::Vector3D imageNormal1 = currentImage->GetSlicedGeometry()->GetAxisVector(1);
	- mitk::Vector3D imageNormal2 = currentImage->GetSlicedGeometry()->GetAxisVector(2);
	- imageNormal0.Normalize();
	- imageNormal1.Normalize();
	- imageNormal2.Normalize();
	-
	- double eps = 0.000001; // Did you mean: std::numeric_limits<T>::epsilon(); ?
	- int test = 0;
	- if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal0.GetVnlVector()))-1) > eps )
	- test++;
	- if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal1.GetVnlVector()))-1) > eps )
	- test++;
	- if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal2.GetVnlVector()))-1) > eps )
	- test++;
	- if (test==3)
	- return true;
	- return false;
	-}
	-
	-template<class T, int N>
	-void mitk::OdfVtkMapper2D<T,N>
	-::SetDefaultProperties(mitk::DataNode* node, mitk::BaseRenderer* /renderer/, bool /overwrite/)
	-{
	- node->SetProperty( "ShowMaxNumber", mitk::IntProperty::New( 500 ) );
	- node->SetProperty( "Normalization", mitk::OdfNormalizationMethodProperty::New());
	-
	- mitk::OdfScaleByProperty::Pointer prop = mitk::OdfScaleByProperty::New();
	- prop->SetScaleByGFA();
	- node->SetProperty( "ScaleBy", prop);
	-
	- if (dynamic_cast<mitk::TensorImage*>(node->GetData()))
	- {
	- node->AddProperty( "DiffusionCore.Rendering.OdfVtkMapper.ColourisationModeBit", mitk::BoolProperty::New( true ) );
	- node->SetProperty( "Scaling", mitk::FloatProperty::New( 3.0 ) );
	- }
	- else
	- {
	- node->AddProperty( "DiffusionCore.Rendering.OdfVtkMapper.ColourisationModeBit", mitk::BoolProperty::New( false ) );
	- node->SetProperty( "Scaling", mitk::FloatProperty::New( 1.5 ) );
	- }
	-
	- node->SetProperty( "IndexParam1", mitk::FloatProperty::New(2));
	- node->SetProperty( "IndexParam2", mitk::FloatProperty::New(1));
	- node->SetProperty( "visible", mitk::BoolProperty::New( true ) );
	- node->SetProperty( "VisibleOdfs_T", mitk::BoolProperty::New( false ) );
	- node->SetProperty( "VisibleOdfs_C", mitk::BoolProperty::New( false ) );
	- node->SetProperty( "VisibleOdfs_S", mitk::BoolProperty::New( false ) );
	- node->SetProperty( "layer", mitk::IntProperty::New(100));
	- node->SetProperty( "DoRefresh", mitk::BoolProperty::New( true ) );
	- node->AddProperty( "DiffusionCore.Rendering.OdfVtkMapper.SwitchTensorView", mitk::BoolProperty::New( true) );
	- node->AddProperty( "DiffusionCore.Rendering.OdfVtkMapper.RandomModeBit", mitk::BoolProperty::New( true ) );
	-}
	-
	-#endif // __mitkOdfVtkMapper2D_txx__
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Rendering/mitkVectorImageVtkGlyphMapper3D.h b/Modules/DiffusionImaging/DiffusionCore/include/Rendering/mitkVectorImageVtkGlyphMapper3D.h
	deleted file mode 100644
	index 737b3b9619..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Rendering/mitkVectorImageVtkGlyphMapper3D.h
	+++ /dev/null
	@@ -1,99 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_VECTOR_IMAGE_VTK_MAPPER_3D__H
	-#define _MITK_VECTOR_IMAGE_VTK_MAPPER_3D__H
	-
	-#include <MitkDiffusionCoreExports.h>
	-
	-#include "mitkVtkMapper.h"
	-#include "mitkImage.h"
	-
	-class vtkMaskedGlyph3D;
	-class vtkActor;
	-class vtkPolyDataMapper;
	-class vtkMaskPoints;
	-
	-
	-namespace mitk
	-{
	-
	-class MITKDIFFUSIONCORE_EXPORT VectorImageVtkGlyphMapper3D : public VtkMapper
	-{
	-public:
	- mitkClassMacro( VectorImageVtkGlyphMapper3D, VtkMapper );
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- enum GlyphType {LineGlyph, ArrowGlyph};
	-
	- itkSetMacro(MaximumNumberOfPoints, unsigned int);
	- itkGetMacro(MaximumNumberOfPoints, unsigned int);
	-
	- itkSetMacro(UseMaskPoints, bool);
	- itkGetMacro(UseMaskPoints, bool);
	- itkBooleanMacro(UseMaskPoints);
	-
	- itkSetMacro(RandomMode, bool);
	- itkGetMacro(RandomMode, bool);
	- itkBooleanMacro(RandomMode);
	-
	- vtkProp* GetVtkProp(mitk::BaseRenderer* renderer) override;
	-
	- LocalStorageHandler<BaseLocalStorage> m_LSH;
	-
	-protected:
	- /**
	- * Constructor. Doesn't do anything...
	- */
	- VectorImageVtkGlyphMapper3D();
	-
	- /**
	- * Destructor
	- */
	- ~VectorImageVtkGlyphMapper3D() override;
	-
	- /**
	- * Generate a vtkPolyData by creating vectors as glyphs
	- * This method is called, each time a specific renderer is updated.
	- */
	- void GenerateDataForRenderer( mitk::BaseRenderer* renderer ) override;
	-
	- /**
	- * Returns the input data object of the given filter. In this
	- * case, a mitk::Image is returned.
	- */
	- Image* GetInput();
	-
	- vtkMaskedGlyph3D* m_Glyph3DGenerator;
	- vtkActor* m_Glyph3DActor;
	- vtkPolyDataMapper* m_Glyph3DMapper;
	-
	- GlyphType m_GlyphType;
	- unsigned int m_MaximumNumberOfPoints;
	- bool m_UseMaskPoints;
	- bool m_RandomMode;
	-
	-};
	-
	-
	-} //end of namespace mitk
	-
	-#endif
	-
	-
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Rendering/vtkMaskedProgrammableGlyphFilter.h b/Modules/DiffusionImaging/DiffusionCore/include/Rendering/vtkMaskedProgrammableGlyphFilter.h
	deleted file mode 100644
	index 371a0fc84d..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Rendering/vtkMaskedProgrammableGlyphFilter.h
	+++ /dev/null
	@@ -1,114 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __vtkMaskedProgrammableGlyphFilter_h
	-#define __vtkMaskedProgrammableGlyphFilter_h
	-
	-#include <MitkDiffusionCoreExports.h>
	-
	-#include "vtkProgrammableGlyphFilter.h"
	-#include "mitkBaseGeometry.h"
	-
	-class vtkMaskPoints;
	-/**
	- * This class masked points of the input data set and glyphs
	- * only the selected poitns. Points may be selected either by
	- * random or by ratio.
	- * Additionally, this class allows to set the InputScalars,
	- * InputVectors and InputNormals by their field name in the
	- * input dataset.
	- */
	-class MITKDIFFUSIONCORE_EXPORT vtkMaskedProgrammableGlyphFilter : public vtkProgrammableGlyphFilter
	-{
	-public:
	- vtkTypeMacro(vtkMaskedProgrammableGlyphFilter,vtkProgrammableGlyphFilter);
	- void PrintSelf(ostream& os, vtkIndent indent) override;
	-
	- /**
	- * Constructor
	- */
	- static vtkMaskedProgrammableGlyphFilter *New();
	-
	- /**
	- * Limit the number of points to glyph
	- */
	- vtkSetMacro(MaximumNumberOfPoints, int);
	- vtkGetMacro(MaximumNumberOfPoints, int);
	-
	- /**
	- * Set the input to this filter.
	- */
	- virtual void SetInput(vtkDataSet *input);
	-
	- /**
	- * Set/get whether to mask points
	- */
	- vtkSetMacro(UseMaskPoints, int);
	- vtkGetMacro(UseMaskPoints, int);
	-
	- /**
	- * Set/get flag to cause randomization of which points to mask.
	- */
	- void SetRandomMode(int mode);
	- int GetRandomMode();
	-
	- ///**
	- // * If you want to use an arbitrary scalars array, then set its name here.
	- // * By default this in nullptr and the filter will use the active scalar array.
	- // */
	- //vtkGetStringMacro(InputScalarsSelection);
	- //void SelectInputScalars(const char *fieldName)
	- // {this->SetInputScalarsSelection(fieldName);}
	-
	- ///**
	- // * If you want to use an arbitrary vectors array, then set its name here.
	- // * By default this in nullptr and the filter will use the active vector array.
	- // */
	- //vtkGetStringMacro(InputVectorsSelection);
	- //void SelectInputVectors(const char *fieldName)
	- // {this->SetInputVectorsSelection(fieldName);}
	-
	- ///**
	- // * If you want to use an arbitrary normals array, then set its name here.
	- // * By default this in nullptr and the filter will use the active normal array.
	- // */
	- //vtkGetStringMacro(InputNormalsSelection);
	- //void SelectInputNormals(const char *fieldName)
	- // {this->SetInputNormalsSelection(fieldName);}
	-
	- void SetGeometry(mitk::BaseGeometry::Pointer geo)
	- { this->m_Geometry = geo; }
	- mitk::BaseGeometry::Pointer GetGeometry()
	- { return this->m_Geometry; }
	-
	-protected:
	- vtkMaskedProgrammableGlyphFilter();
	- ~vtkMaskedProgrammableGlyphFilter() override;
	-
	- int RequestData(vtkInformation , vtkInformationVector , vtkInformationVector ) override;
	-
	- vtkMaskPoints *MaskPoints;
	- int MaximumNumberOfPoints;
	- int UseMaskPoints;
	-
	- mitk::BaseGeometry::Pointer m_Geometry;
	-
	-private:
	- vtkMaskedProgrammableGlyphFilter(const vtkMaskedProgrammableGlyphFilter&); // Not implemented.
	- void operator=(const vtkMaskedProgrammableGlyphFilter&); // Not implemented.
	-};
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Rendering/vtkOdfSource.h b/Modules/DiffusionImaging/DiffusionCore/include/Rendering/vtkOdfSource.h
	deleted file mode 100644
	index 805b328ce1..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Rendering/vtkOdfSource.h
	+++ /dev/null
	@@ -1,85 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __vtkOdfSource_h
	-#define __vtkOdfSource_h
	-
	-#include <MitkDiffusionCoreExports.h>
	-
	-#include "vtkPolyDataAlgorithm.h"
	-#include "mitkCommon.h"
	-#include <vtkFloatArray.h>
	-#include <itkOrientationDistributionFunction.h>
	-#include <mitkOdfNormalizationMethodProperty.h>
	-
	-class MITKDIFFUSIONCORE_EXPORT vtkOdfSource : public vtkPolyDataAlgorithm
	-{
	-public:
	-
	- vtkTypeMacro(vtkOdfSource,vtkPolyDataAlgorithm);
	- void PrintSelf(ostream& os, vtkIndent indent) override;
	-
	- typedef itk::OrientationDistributionFunction<float, ODF_SAMPLING_SIZE> OdfType;
	- // Description:
	- // Construct sphere with radius=0.5 and default resolution 8 in both Phi
	- // and Theta directions. Theta ranges from (0,360) and phi (0,180) degrees.
	- static vtkOdfSource *New();
	-
	- vtkSetMacro(Scale,double)
	- vtkGetMacro(Scale,double)
	-
	- vtkSetMacro(AdditionalScale,double)
	- vtkGetMacro(AdditionalScale,double)
	-
	- vtkSetMacro(Normalization,int)
	- vtkGetMacro(Normalization,int)
	-
	- vtkSetMacro(Odf,OdfType)
	- vtkGetMacro(Odf,OdfType)
	-
	- vtkSetMacro(UseCustomColor,bool)
	- vtkGetMacro(UseCustomColor,bool)
	-
	- void SetColor(int r, int g, int b)
	- {
	- this->r = r;
	- this->g = g;
	- this->b = b;
	- }
	-
	-protected:
	- vtkOdfSource();
	- ~vtkOdfSource() override;
	-
	- int RequestData(vtkInformation , vtkInformationVector , vtkInformationVector ) override;
	- int RequestInformation(vtkInformation , vtkInformationVector , vtkInformationVector ) override;
	-
	- OdfType Odf;
	- double Scale;
	- double AdditionalScale;
	- int Normalization;
	- int r;
	- int g;
	- int b;
	- bool UseCustomColor;
	- vtkSmartPointer<vtkLookupTable> lut;
	-
	-private:
	- vtkOdfSource(const vtkOdfSource&); // Not implemented.
	- void operator=(const vtkOdfSource&); // Not implemented.
	-};
	-
	-#endif //__vtkOdfSource_h
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/Rendering/vtkThickPlane.h b/Modules/DiffusionImaging/DiffusionCore/include/Rendering/vtkThickPlane.h
	deleted file mode 100644
	index 5087858ccf..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/Rendering/vtkThickPlane.h
	+++ /dev/null
	@@ -1,96 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-// .NAME vtkPlane - perform various plane computations
	-// .SECTION Description
	-// vtkPlane provides methods for various plane computations. These include
	-// projecting points onto a plane, evaluating the plane equation, and
	-// returning plane normal. vtkPlane is a concrete implementation of the
	-// abstract class vtkImplicitFunction.
	-
	-#ifndef __vtkThickPlane_h
	-#define __vtkThickPlane_h
	-
	-#include <MitkDiffusionCoreExports.h>
	-
	-#include "vtkImplicitFunction.h"
	-#include "mitkCommon.h"
	-
	-class MITKDIFFUSIONCORE_EXPORT vtkThickPlane : public vtkImplicitFunction
	-{
	-public:
	- // Description
	- // Construct plane passing through origin and normal to z-axis.
	- static vtkThickPlane *New();
	-
	- vtkTypeMacro(vtkThickPlane,vtkImplicitFunction);
	- void PrintSelf(ostream& os, vtkIndent indent) override;
	-
	- // Description
	- // Evaluate plane equation for point x[3].
	- double EvaluateFunction(double x[3]) override;
	- void EvaluateFunction(vtkDataArray* input, vtkDataArray* output) override;
	- double EvaluateFunction(double x, double y, double z) override;
	-
	- // Description
	- // Evaluate function gradient at point x[3].
	- void EvaluateGradient(double x[3], double g[3]) override;
	-
	- // Description:
	- // Set/get plane normal. Plane is defined by point and normal.
	- virtual void SetPose (double _n1, double _n2, double _n3, double _o1, double _o2, double _o3);
	- virtual void SetPose (double _n[3], double _o[3]);
	-
	- vtkGetVectorMacro(Normal,double,3);
	- vtkGetVectorMacro(Origin,double,3);
	-
	- // Description:
	- // Set/get point through which plane passes. Plane is defined by point
	- // and normal.
	- virtual void SetThickness (double _arg);
	- vtkGetMacro(Thickness,double);
	-
	- int count;
	-
	-protected:
	- vtkThickPlane();
	- ~vtkThickPlane() override {};
	-
	- // Description:
	- // Set/get plane normal. Plane is defined by point and normal.
	- virtual void SetNormal (double _arg1, double _arg2, double _arg3);
	- virtual void SetNormal (double _arg[3]);
	-
	- // Description:
	- // Set/get point through which plane passes. Plane is defined by point
	- // and normal.
	- virtual void SetOrigin (double _arg1, double _arg2, double _arg3);
	- virtual void SetOrigin (double _arg[3]);
	-
	- double Normal[3];
	- double Origin[3];
	- double Thickness;
	- double Distance;
	-
	-private:
	- vtkThickPlane(const vtkThickPlane&); // Not implemented.
	- void operator=(const vtkThickPlane&); // Not implemented.
	-};
	-
	-#endif
	-
	-
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/include/mitkDiffusionFunctionCollection.h b/Modules/DiffusionImaging/DiffusionCore/include/mitkDiffusionFunctionCollection.h
	deleted file mode 100644
	index 37935c9174..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/include/mitkDiffusionFunctionCollection.h
	+++ /dev/null
	@@ -1,259 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkDiffusionFunctionCollection_h_
	-#define __mitkDiffusionFunctionCollection_h_
	-
	-
	-#include <MitkDiffusionCoreExports.h>
	-#include <vnl/vnl_vector.h>
	-#include <vnl/vnl_vector_fixed.h>
	-#include <itkVectorContainer.h>
	-#include <itkImage.h>
	-#include <itkLinearInterpolateImageFunction.h>
	-#include <mitkImage.h>
	-#include <mitkShImage.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <mitkOdfImage.h>
	-#include <mitkTensorImage.h>
	-#include <mitkPeakImage.h>
	-#include <itkOrientationDistributionFunction.h>
	-#include <mitkImageCast.h>
	-#include <mitkImageToItk.h>
	-
	-namespace mitk{
	-
	-class MITKDIFFUSIONCORE_EXPORT imv
	-{
	-public:
	-
	- static std::vector< std::pair< itk::Index<3>, double > > IntersectImage(const itk::Vector<double,3>& spacing, itk::Index<3>& si, itk::Index<3>& ei, itk::ContinuousIndex<float, 3>& sf, itk::ContinuousIndex<float, 3>& ef);
	-
	- static itk::Point<float, 3> GetItkPoint(double point[3])
	- {
	- itk::Point<float, 3> itkPoint;
	- itkPoint[0] = static_cast<float>(point[0]);
	- itkPoint[1] = static_cast<float>(point[1]);
	- itkPoint[2] = static_cast<float>(point[2]);
	- return itkPoint;
	- }
	-
	- template< class TType >
	- static itk::Point<float, 3> GetItkPoint(double point[3])
	- {
	- itk::Point<TType, 3> itkPoint;
	- itkPoint[0] = static_cast<TType>(point[0]);
	- itkPoint[1] = static_cast<TType>(point[1]);
	- itkPoint[2] = static_cast<TType>(point[2]);
	- return itkPoint;
	- }
	-
	- template< class TType >
	- static itk::Vector<float, 3> GetItkVector(double point[3])
	- {
	- itk::Vector<TType, 3> itkVector;
	- itkVector[0] = static_cast<TType>(point[0]);
	- itkVector[1] = static_cast<TType>(point[1]);
	- itkVector[2] = static_cast<TType>(point[2]);
	- return itkVector;
	- }
	-
	- template< class TPixelType, class TOutPixelType=TPixelType >
	- static TOutPixelType GetImageValue(const itk::Point<float, 3>& itkP, bool interpolate, typename itk::LinearInterpolateImageFunction< itk::Image< TPixelType, 3 >, float >::Pointer interpolator)
	- {
	- if (interpolator==nullptr)
	- return 0.0;
	-
	- itk::ContinuousIndex< float, 3> cIdx;
	- interpolator->ConvertPointToContinuousIndex(itkP, cIdx);
	-
	- if (interpolator->IsInsideBuffer(cIdx))
	- {
	- if (interpolate)
	- return interpolator->EvaluateAtContinuousIndex(cIdx);
	- else
	- {
	- itk::Index<3> idx;
	- interpolator->ConvertContinuousIndexToNearestIndex(cIdx, idx);
	- return interpolator->EvaluateAtIndex(idx);
	- }
	- }
	- else
	- return 0.0;
	- }
	-
	- template< class TPixelType=unsigned char >
	- static bool IsInsideMask(const itk::Point<float, 3>& itkP, bool interpolate, typename itk::LinearInterpolateImageFunction< itk::Image< TPixelType, 3 >, float >::Pointer interpolator, float threshold=0.5)
	- {
	- if (interpolator==nullptr)
	- return false;
	-
	- itk::ContinuousIndex< float, 3> cIdx;
	- interpolator->ConvertPointToContinuousIndex(itkP, cIdx);
	-
	- if (interpolator->IsInsideBuffer(cIdx))
	- {
	- float value = 0.0;
	- if (interpolate)
	- value = interpolator->EvaluateAtContinuousIndex(cIdx);
	- else
	- {
	- itk::Index<3> idx;
	- interpolator->ConvertContinuousIndexToNearestIndex(cIdx, idx);
	- value = interpolator->EvaluateAtIndex(idx);
	- }
	-
	- if (value>=threshold)
	- return true;
	- }
	- return false;
	- }
	-
	- template< class TType=float >
	- static vnl_matrix_fixed< TType, 3, 3 > GetRotationMatrixVnl(TType rx, TType ry, TType rz)
	- {
	- rx = rx*itk::Math::pi/180;
	- ry = ry*itk::Math::pi/180;
	- rz = rz*itk::Math::pi/180;
	-
	- vnl_matrix_fixed< TType, 3, 3 > rotX; rotX.set_identity();
	- rotX[1][1] = cos(rx);
	- rotX[2][2] = rotX[1][1];
	- rotX[1][2] = -sin(rx);
	- rotX[2][1] = -rotX[1][2];
	-
	- vnl_matrix_fixed< TType, 3, 3 > rotY; rotY.set_identity();
	- rotY[0][0] = cos(ry);
	- rotY[2][2] = rotY[0][0];
	- rotY[0][2] = sin(ry);
	- rotY[2][0] = -rotY[0][2];
	-
	- vnl_matrix_fixed< TType, 3, 3 > rotZ; rotZ.set_identity();
	- rotZ[0][0] = cos(rz);
	- rotZ[1][1] = rotZ[0][0];
	- rotZ[0][1] = -sin(rz);
	- rotZ[1][0] = -rotZ[0][1];
	-
	- vnl_matrix_fixed< TType, 3, 3 > rot = rotZrotYrotX;
	- return rot;
	- }
	-
	- template< class TType=float >
	- static itk::Matrix< TType, 3, 3 > GetRotationMatrixItk(TType rx, TType ry, TType rz)
	- {
	- rx = rx*itk::Math::pi/180;
	- ry = ry*itk::Math::pi/180;
	- rz = rz*itk::Math::pi/180;
	-
	- itk::Matrix< TType, 3, 3 > rotX; rotX.SetIdentity();
	- rotX[1][1] = cos(rx);
	- rotX[2][2] = rotX[1][1];
	- rotX[1][2] = -sin(rx);
	- rotX[2][1] = -rotX[1][2];
	-
	- itk::Matrix< TType, 3, 3 > rotY; rotY.SetIdentity();
	- rotY[0][0] = cos(ry);
	- rotY[2][2] = rotY[0][0];
	- rotY[0][2] = sin(ry);
	- rotY[2][0] = -rotY[0][2];
	-
	- itk::Matrix< TType, 3, 3 > rotZ; rotZ.SetIdentity();
	- rotZ[0][0] = cos(rz);
	- rotZ[1][1] = rotZ[0][0];
	- rotZ[0][1] = -sin(rz);
	- rotZ[1][0] = -rotZ[0][1];
	-
	- itk::Matrix< TType, 3, 3 > rot = rotZrotYrotX;
	- return rot;
	- }
	-};
	-
	-class MITKDIFFUSIONCORE_EXPORT convert
	-{
	-public:
	- static mitk::OdfImage::ItkOdfImageType::Pointer GetItkOdfFromTensorImage(mitk::Image::Pointer mitkImage);
	- static mitk::OdfImage::Pointer GetOdfFromTensorImage(mitk::Image::Pointer mitkImage);
	- static mitk::TensorImage::ItkTensorImageType::Pointer GetItkTensorFromTensorImage(mitk::Image::Pointer mitkImage);
	- static mitk::PeakImage::ItkPeakImageType::Pointer GetItkPeakFromPeakImage(mitk::Image::Pointer mitkImage);
	-
	- template<unsigned int NUM_COEFFS>
	- static typename itk::Image< itk::Vector<float, NUM_COEFFS>, 3>::Pointer GetItkShFromShImage(mitk::Image::Pointer mitkImage)
	- {
	- mitk::ShImage::Pointer mitkShImage = dynamic_cast<mitk::ShImage*>(mitkImage.GetPointer());
	- if (mitkShImage.IsNull())
	- mitkThrow() << "Input image is not a SH image!";
	-
	- typename itk::Image< itk::Vector<float, NUM_COEFFS>, 3>::Pointer itkvol;
	- mitk::CastToItkImage(mitkImage, itkvol);
	-
	- return itkvol;
	- }
	-
	- static mitk::OdfImage::ItkOdfImageType::Pointer GetItkOdfFromShImage(mitk::Image::Pointer mitkImage);
	- static mitk::OdfImage::Pointer GetOdfFromShImage(mitk::Image::Pointer mitkImage);
	- static mitk::OdfImage::ItkOdfImageType::Pointer GetItkOdfFromOdfImage(mitk::Image::Pointer mitkImage);
	-};
	-
	-class MITKDIFFUSIONCORE_EXPORT sh
	-{
	-public:
	- static double factorial(int number);
	- static void Cart2Sph(double x, double y, double z, double* spherical);
	- static vnl_vector_fixed<double, 3> Sph2Cart(const double& theta, const double& phi, const double& rad);
	- static double legendre0(int l);
	- static double spherical_harmonic(int m,int l,double theta,double phi, bool complexPart);
	- static double Yj(int m, int k, float theta, float phi, bool mrtrix=true);
	- static vnl_matrix<float> CalcShBasisForDirections(unsigned int sh_order, vnl_matrix<double> U, bool mrtrix=true);
	- static float GetValue(const vnl_vector<float>& coefficients, const int& sh_order, const vnl_vector_fixed<double, 3>& dir, const bool mrtrix);
	- static float GetValue(const vnl_vector<float> &coefficients, const int &sh_order, const double theta, const double phi, const bool mrtrix);
	- static unsigned int ShOrder(int num_coeffs);
	-
	- template <unsigned int N, typename TComponent=float>
	- static void SampleOdf(const vnl_vector<float>& coefficients, itk::OrientationDistributionFunction<TComponent, N>& odf)
	- {
	- auto dirs = odf.GetDirections();
	- auto basis = CalcShBasisForDirections(ShOrder(coefficients.size()), *dirs);
	- auto odf_vals = basis * coefficients;
	- for (unsigned int i=0; i<odf_vals.size(); ++i)
	- odf[i] = odf_vals[i];
	- }
	-};
	-
	-class MITKDIFFUSIONCORE_EXPORT gradients
	-{
	-private:
	- typedef std::vector<unsigned int> IndiciesVector;
	- typedef mitk::BValueMapProperty::BValueMap BValueMap;
	-
	- typedef DiffusionPropertyHelper::GradientDirectionsContainerType GradientDirectionContainerType;
	- typedef DiffusionPropertyHelper::GradientDirectionType GradientDirectionType;
	-
	-public:
	-
	- static GradientDirectionContainerType::Pointer ReadBvalsBvecs(std::string bvals_file, std::string bvecs_file, double& reference_bval);
	- static void WriteBvalsBvecs(std::string bvals_file, std::string bvecs_file, GradientDirectionContainerType::Pointer gradients, double reference_bval);
	- static std::vector<unsigned int> GetAllUniqueDirections(const BValueMap &bValueMap, GradientDirectionContainerType *refGradientsContainer );
	-
	- static bool CheckForDifferingShellDirections(const BValueMap &bValueMap, GradientDirectionContainerType::ConstPointer refGradientsContainer);
	- static vnl_matrix<double> ComputeSphericalHarmonicsBasis(const vnl_matrix<double> & QBallReference, const unsigned int & LOrder);
	- static vnl_matrix<double> ComputeSphericalFromCartesian(const IndiciesVector & refShell, const GradientDirectionContainerType * refGradientsContainer);
	- static GradientDirectionContainerType::Pointer CreateNormalizedUniqueGradientDirectionContainer(const BValueMap &bValueMap, const GradientDirectionContainerType * origninalGradentcontainer);
	-};
	-
	-}
	-
	-#endif //__mitkDiffusionFunctionCollection_h_
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/Reconstruction/MultishellProcessing/itkADCAverageFunctor.cpp b/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/Reconstruction/MultishellProcessing/itkADCAverageFunctor.cpp
	deleted file mode 100644
	index 0e3c0b2800..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/Reconstruction/MultishellProcessing/itkADCAverageFunctor.cpp
	+++ /dev/null
	@@ -1,56 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "itkADCAverageFunctor.h"
	-#include <cmath>
	-#include <iostream>
	-#include <iomanip>
	-
	-void itk::ADCAverageFunctor::operator()(vnl_matrix<double> & newSignal, const vnl_matrix<double> & SignalMatrix, const double & S0)
	-{
	-
	- vnl_matrix<double> ADCMatrix(SignalMatrix.rows(),SignalMatrix.cols());
	-
	- // Calculate ADC for each measurement
	- for(unsigned int i = 0 ; i < SignalMatrix.rows(); ++i)
	- for(unsigned int j = 0; j < SignalMatrix.cols(); ++j)
	- ADCMatrix(i,j) = std::log(SignalMatrix(i,j) / S0) / (-m_BValueList[j]);// D = ln(S/S0)/-b
	-
	-
	- // Calculate new Signal using Average ADC
	- for(unsigned int i = 0 ; i < SignalMatrix.rows(); ++i){
	- double averageADC = ADCMatrix.get_row(i).mean();
	- newSignal.put(i,0, S0 * std::exp(-m_TargetBvalue * averageADC) ); // S = S0exp(-bD)
	-
	- //OUTPUT FOR EVALUATION
	- // Root Mean Squares Error
	- double error = 0;
	- for(unsigned int j = 0 ; j < SignalMatrix.cols(); ++j)
	- error += std::pow(SignalMatrix(i,j) - S0 * std::exp(-m_BValueList[j] * averageADC),2); // sum of squres
	- error /= (double)SignalMatrix.cols(); // mean
	- error = std::sqrt(error);
	-
	- newSignal.put(i, 1, error ); // RMS Error
	-
	- /*std::cout << std::scientific << std::setprecision(5)
	- << averageADC << "," // AverageADC
	- << S0 << "," // S0 value
	- << error << ","; // End error
	- for(unsigned int j = 0; j < SignalMatrix.get_row(i).size(); j++ )
	- std::cout << std::scientific << std::setprecision(5) << SignalMatrix.get_row(i)[j] << ","; // S_n Values corresponding to shell 1 to shell n
	- std::cout << std::endl;*/
	- }
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/Reconstruction/MultishellProcessing/itkADCFitFunctor.cpp b/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/Reconstruction/MultishellProcessing/itkADCFitFunctor.cpp
	deleted file mode 100644
	index 695663fbf2..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/Reconstruction/MultishellProcessing/itkADCFitFunctor.cpp
	+++ /dev/null
	@@ -1,64 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "itkADCFitFunctor.h"
	-#include <cmath>
	-#include <iostream>
	-#include <iomanip>
	-#include "vnl/algo/vnl_levenberg_marquardt.h"
	-void itk::ADCFitFunctor::operator()(vnl_matrix<double> & newSignal,const vnl_matrix<double> & SignalMatrix, const double & S0)
	-{
	-
	- vnl_vector<double> initalGuess(1);
	- // initialize Least Squres Function
	- // SignalMatrix.cols() defines the number of shells points
	- lestSquaresFunction model(SignalMatrix.cols());
	- model.set_bvalues(m_BValueList);// set BValue Vector e.g.: [1000, 2000, 3000] <- shell b Values
	-
	- // initialize Levenberg Marquardt
	- vnl_levenberg_marquardt minimizer(model);
	- minimizer.set_max_function_evals(1000); // Iterations
	- minimizer.set_f_tolerance(1e-10); // Function tolerance
	-
	- // for each Direction calculate LSF Coeffs ADC & AKC
	- for(unsigned int i = 0 ; i < SignalMatrix.rows(); i++)
	- {
	- model.set_measurements(SignalMatrix.get_row(i));
	- model.set_reference_measurement(S0);
	-
	- initalGuess.put(0, 0.f); // ADC_slow
	-
	- // start Levenberg-Marquardt
	- minimizer.minimize_without_gradient(initalGuess);
	-
	- const double & ADC = initalGuess.get(0);
	-
	- newSignal.put(i, 0, S0 * std::exp(-m_TargetBvalue * ADC) );
	- newSignal.put(i, 1, minimizer.get_end_error()); // RMS Error
	-
	- //OUTPUT FOR EVALUATION
	- std::cout << std::scientific << std::setprecision(5)
	- << ADC << "," // lambda
	- << S0 << "," // S0 value
	- << minimizer.get_end_error() << ","; // End error
	- for(unsigned int j = 0; j < SignalMatrix.get_row(i).size(); j++ ){
	- std::cout << std::scientific << std::setprecision(5) << SignalMatrix.get_row(i)[j]; // S_n Values corresponding to shell 1 to shell n
	- if(j != SignalMatrix.get_row(i).size()-1) std::cout << ",";
	- }
	- std::cout << std::endl;
	- }
	-
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/Reconstruction/MultishellProcessing/itkBiExpFitFunctor.cpp b/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/Reconstruction/MultishellProcessing/itkBiExpFitFunctor.cpp
	deleted file mode 100644
	index 0d06ca33d6..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/Reconstruction/MultishellProcessing/itkBiExpFitFunctor.cpp
	+++ /dev/null
	@@ -1,70 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "itkBiExpFitFunctor.h"
	-#include <cmath>
	-#include <iostream>
	-#include <iomanip>
	-
	-void itk::BiExpFitFunctor::operator()(vnl_matrix<double> & newSignal,const vnl_matrix<double> & SignalMatrix, const double & S0)
	-{
	-
	- vnl_vector<double> initalGuess(3);
	- // initialize Least Squres Function
	- // SignalMatrix.cols() defines the number of shells points
	- lestSquaresFunction model(SignalMatrix.cols());
	- model.set_bvalues(m_BValueList);// set BValue Vector e.g.: [1000, 2000, 3000] <- shell b Values
	-
	- // initialize Levenberg Marquardt
	- vnl_levenberg_marquardt minimizer(model);
	- minimizer.set_max_function_evals(1000); // Iterations
	- minimizer.set_f_tolerance(1e-10); // Function tolerance
	-
	- // for each Direction calculate LSF Coeffs ADC & AKC
	- for(unsigned int i = 0 ; i < SignalMatrix.rows(); i++)
	- {
	- model.set_measurements(SignalMatrix.get_row(i));
	- model.set_reference_measurement(S0);
	-
	- initalGuess.put(0, 0.f); // ADC_slow
	- initalGuess.put(1, 0.009f); // ADC_fast
	- initalGuess.put(2, 0.7f); // lambda
	-
	- // start Levenberg-Marquardt
	- minimizer.minimize_without_gradient(initalGuess);
	-
	- const double & ADC_slow = initalGuess.get(0);
	- const double & ADC_fast = initalGuess.get(1);
	- const double & lambda = initalGuess(2);
	-
	- newSignal.put(i, 0, S0 * (lambda * std::exp(-m_TargetBvalue * ADC_slow) + (1-lambda)* std::exp(-m_TargetBvalue * ADC_fast)));
	- newSignal.put(i, 1, minimizer.get_end_error()); // RMS Error
	-
	- //OUTPUT FOR EVALUATION
	- /*std::cout << std::scientific << std::setprecision(5)
	- << ADC_slow << "," // lambda
	- << ADC_fast << "," // alpha
	- << lambda << "," // lambda
	- << S0 << "," // S0 value
	- << minimizer.get_end_error() << ","; // End error
	- for(unsigned int j = 0; j < SignalMatrix.get_row(i).size(); j++ ){
	- std::cout << std::scientific << std::setprecision(5) << SignalMatrix.get_row(i)[j]; // S_n Values corresponding to shell 1 to shell n
	- if(j != SignalMatrix.get_row(i).size()-1) std::cout << ",";
	- }
	- std::cout << std::endl;*/
	- }
	-
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/Reconstruction/MultishellProcessing/itkKurtosisFitFunctor.cpp b/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/Reconstruction/MultishellProcessing/itkKurtosisFitFunctor.cpp
	deleted file mode 100644
	index d6680f23f0..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/Reconstruction/MultishellProcessing/itkKurtosisFitFunctor.cpp
	+++ /dev/null
	@@ -1,66 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "itkKurtosisFitFunctor.h"
	-#include <iostream>
	-#include <iomanip>
	-
	-void itk::KurtosisFitFunctor::operator()(vnl_matrix<double> & newSignal, const vnl_matrix<double> & SignalMatrix, const double & S0)
	-{
	-
	- vnl_vector<double> initalGuess(2);
	- // initialize Least Squres Function
	- // SignalMatrix.cols() defines the number of shells points
	- lestSquaresFunction model(SignalMatrix.cols());
	- model.set_bvalues(m_BValueList);// set BValue Vector e.g.: [1000, 2000, 3000] <- shell b Values
	-
	- // initialize Levenberg Marquardt
	- vnl_levenberg_marquardt minimizer(model);
	- minimizer.set_max_function_evals(1000); // Iterations
	- minimizer.set_f_tolerance(1e-10); // Function tolerance
	-
	- // for each Direction calculate LSF Coeffs ADC & AKC
	- for(unsigned int i = 0 ; i < SignalMatrix.rows(); i++)
	- {
	- model.set_measurements(SignalMatrix.get_row(i));
	- model.set_reference_measurement(S0);
	-
	- initalGuess.put(0, 0.f); // ADC
	- initalGuess.put(1, 0.8f); // AKC
	-
	- // start Levenberg-Marquardt
	- minimizer.minimize_without_gradient(initalGuess);
	-
	- const double & ADC = initalGuess.get(0);
	- const double & AKC = initalGuess.get(1);
	-
	- newSignal.put(i, 0, S0 * std::exp(-m_TargetBvalue * ADC + 1./6. * m_TargetBvalue* m_TargetBvalue * ADC * ADC * AKC));
	- newSignal.put(i, 1, minimizer.get_end_error()); // RMS Error
	-
	- //OUTPUT FOR EVALUATION
	-
	- /*std::cout << std::scientific << std::setprecision(5)
	- << initalGuess[0] << "," // fitted ADC
	- << initalGuess[1] << "," // fitted AKC
	- << S0 << "," // S0 value
	- << minimizer.get_end_error() << ","; // End error
	- for(unsigned int j = 0; j < SignalMatrix.get_row(i).size(); j++ ){
	- std::cout << std::scientific << std::setprecision(5) << SignalMatrix.get_row(i)[j]; // S_n Values corresponding to shell 1 to shell n
	- if(j != SignalMatrix.get_row(i).size()-1) std::cout << ",";
	- }
	- std::cout << std::endl;*/
	- }
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/Registration/mitkDWIHeadMotionCorrectionFilter.cpp b/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/Registration/mitkDWIHeadMotionCorrectionFilter.cpp
	deleted file mode 100644
	index 4ef6f130fa..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/Registration/mitkDWIHeadMotionCorrectionFilter.cpp
	+++ /dev/null
	@@ -1,149 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef MITKDWIHEADMOTIONCORRECTIONFILTER_CPP
	-#define MITKDWIHEADMOTIONCORRECTIONFILTER_CPP
	-
	-#include "mitkDWIHeadMotionCorrectionFilter.h"
	-
	-#include "itkSplitDWImageFilter.h"
	-#include "itkB0ImageExtractionToSeparateImageFilter.h"
	-
	-#include "mitkImageTimeSelector.h"
	-
	-#include <itkExtractDwiChannelFilter.h>
	-#include <mitkMultiModalAffineDefaultRegistrationAlgorithm.h>
	-#include <mitkAlgorithmHelper.h>
	-#include <mitkMaskedAlgorithmHelper.h>
	-#include <mitkImageMappingHelper.h>
	-#include <mitkRegistrationHelper.h>
	-#include <mitkRegistrationWrapper.h>
	-#include <mitkRegistrationWrapperMapper3D.h>
	-
	-#include <itkComposeImageFilter.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <mitkImageCast.h>
	-#include <mitkDiffusionImageCorrectionFilter.h>
	-#include <mitkImageWriteAccessor.h>
	-#include <mitkProperties.h>
	-#include <mitkBValueMapProperty.h>
	-
	-#include <vector>
	-
	-#include "mitkIOUtil.h"
	-#include <itkImage.h>
	-
	-typedef mitk::DiffusionPropertyHelper DPH;
	-typedef itk::ExtractDwiChannelFilter< short > ExtractorType;
	-
	-mitk::DWIHeadMotionCorrectionFilter::DWIHeadMotionCorrectionFilter()
	-{
	-
	-}
	-
	-mitk::Image::Pointer mitk::DWIHeadMotionCorrectionFilter::GetCorrectedImage() const
	-{
	- return m_CorrectedImage;
	-}
	-
	-void mitk::DWIHeadMotionCorrectionFilter::UpdateOutputInformation()
	- {
	- Superclass::UpdateOutputInformation();
	- }
	-
	-void mitk::DWIHeadMotionCorrectionFilter::GenerateData()
	- {
	- InputImageType::Pointer input = const_cast<InputImageType*>(this->GetInput(0));
	-
	- if (!DPH::IsDiffusionWeightedImage(input))
	- mitkThrow() << "Input is not a diffusion-weighted image!";
	-
	- ITKDiffusionImageType::Pointer itkVectorImagePointer = DPH::GetItkVectorImage(input);
	- int num_gradients = itkVectorImagePointer->GetVectorLength();
	-
	- typedef itk::ComposeImageFilter < ITKDiffusionVolumeType > ComposeFilterType;
	- ComposeFilterType::Pointer composer = ComposeFilterType::New();
	-
	- // Extract unweighted volumes
	- mitk::BValueMapProperty::BValueMap bval_map = DPH::GetBValueMap(input);
	-
	- int first_unweighted_index = bval_map.begin()->second.front();
	- MITK_INFO << "Reference b-value: " << bval_map.begin()->first << " (volume " << first_unweighted_index << ")";
	-
	- ExtractorType::Pointer filter = ExtractorType::New();
	- filter->SetInput( itkVectorImagePointer);
	- filter->SetChannelIndex(first_unweighted_index);
	- filter->Update();
	-
	- mitk::Image::Pointer fixedImage = mitk::Image::New();
	- fixedImage->InitializeByItk( filter->GetOutput() );
	- fixedImage->SetImportChannel( filter->GetOutput()->GetBufferPointer() );
	- composer->SetInput(0, filter->GetOutput());
	-
	- mitk::MultiModalAffineDefaultRegistrationAlgorithm< ITKDiffusionVolumeType >::Pointer algo = mitk::MultiModalAffineDefaultRegistrationAlgorithm< ITKDiffusionVolumeType >::New();
	- mitk::MITKAlgorithmHelper helper(algo);
	-
	- typedef vnl_matrix_fixed< double, 3, 3> TransformMatrixType;
	- std::vector< TransformMatrixType > estimated_transforms;
	- std::vector< ITKDiffusionVolumeType::Pointer > registered_itk_images;
	- for (int i=0; i<num_gradients; ++i)
	- {
	- if (i==first_unweighted_index)
	- continue;
	-
	- MITK_INFO << "Correcting volume " << i;
	-
	- ExtractorType::Pointer filter = ExtractorType::New();
	- filter->SetInput( itkVectorImagePointer);
	- filter->SetChannelIndex(i);
	- filter->Update();
	-
	- mitk::Image::Pointer movingImage = mitk::Image::New();
	- movingImage->InitializeByItk( filter->GetOutput() );
	- movingImage->SetImportChannel( filter->GetOutput()->GetBufferPointer() );
	-
	- helper.SetData(movingImage, fixedImage);
	- mitk::MAPRegistrationWrapper::Pointer reg = helper.GetMITKRegistrationWrapper();
	- mitk::MITKRegistrationHelper::Affine3DTransformType::Pointer affine = mitk::MITKRegistrationHelper::getAffineMatrix(reg, false);
	- estimated_transforms.push_back(affine->GetMatrix().GetVnlMatrix());
	-
	- mitk::Image::Pointer registered_mitk_image = mitk::ImageMappingHelper::map(movingImage, reg, false, 0, nullptr, false, 0, mitk::ImageMappingInterpolator::BSpline_3);
	- ITKDiffusionVolumeType::Pointer registered_itk_image = ITKDiffusionVolumeType::New();
	- mitk::CastToItkImage(registered_mitk_image, registered_itk_image);
	- registered_itk_images.push_back(registered_itk_image);
	- }
	-
	- int i=1;
	- for (auto image : registered_itk_images)
	- {
	- composer->SetInput(i, image);
	- ++i;
	- }
	- composer->Update();
	-
	- m_CorrectedImage = mitk::GrabItkImageMemory( composer->GetOutput() );
	- DPH::CopyProperties(input, m_CorrectedImage, true);
	-
	- typedef mitk::DiffusionImageCorrectionFilter CorrectionFilterType;
	- CorrectionFilterType::Pointer corrector = CorrectionFilterType::New();
	- corrector->SetImage( m_CorrectedImage );
	- corrector->CorrectDirections( estimated_transforms );
	-
	- DPH::InitializeImage(m_CorrectedImage);
	-}
	-
	-#endif // MITKDWIHEADMOTIONCORRECTIONFILTER_CPP
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/Registration/mitkPyramidImageRegistrationMethod.cpp b/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/Registration/mitkPyramidImageRegistrationMethod.cpp
	deleted file mode 100644
	index 286290d192..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/Registration/mitkPyramidImageRegistrationMethod.cpp
	+++ /dev/null
	@@ -1,597 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkPyramidImageRegistrationMethod.h"
	-
	-#include "mitkException.h"
	-#include "mitkImageAccessByItk.h"
	-
	-mitk::PyramidImageRegistrationMethod::PyramidImageRegistrationMethod()
	- : m_FixedImage(nullptr),
	- m_MovingImage(nullptr),
	- m_CrossModalityRegistration(true),
	- m_UseAffineTransform(true),
	- m_UseWindowedSincInterpolator(false),
	- m_UseNearestNeighborInterpolator(false),
	- m_UseMask(false),
	- m_EstimatedParameters(nullptr),
	- m_InitialParameters(0),
	- m_Verbose(false)
	-{
	-
	-}
	-
	-mitk::PyramidImageRegistrationMethod::~PyramidImageRegistrationMethod()
	-{
	- if( m_EstimatedParameters != nullptr)
	- {
	- delete [] m_EstimatedParameters;
	- }
	-
	-}
	-
	-void mitk::PyramidImageRegistrationMethod::SetFixedImage(mitk::Image::Pointer fixed)
	-{
	- if( fixed.IsNotNull() )
	- {
	- m_FixedImage = fixed;
	- }
	-}
	-
	-void mitk::PyramidImageRegistrationMethod::SetMovingImage(mitk::Image::Pointer moving)
	-{
	- if( moving.IsNotNull() )
	- {
	- m_MovingImage = moving;
	- }
	-}
	-
	-
	-void mitk::PyramidImageRegistrationMethod::SetFixedImageMask(mitk::Image::Pointer mask)
	-{
	- m_FixedImageMask = mask;
	-}
	-
	-void mitk::PyramidImageRegistrationMethod::Update()
	-{
	- if( m_MovingImage.IsNull() )
	- {
	- mitkThrow() << " Moving image is null";
	- }
	-
	- if( m_FixedImage.IsNull() )
	- {
	- mitkThrow() << " Moving image is null";
	- }
	-
	- unsigned int allowedDimension = 3;
	-
	- if( m_FixedImage->GetDimension() != allowedDimension \|\|
	- m_MovingImage->GetDimension() != allowedDimension )
	- {
	- mitkThrow() << " Only 3D Images supported.";
	- }
	-
	- //
	- // One possibility: use the FixedDimesnionByItk, but this instantiates ALL possible
	- // pixel type combinations!
	- // AccessTwoImagesFixedDimensionByItk( m_FixedImage, m_MovingImage, RegisterTwoImages, 3);
	- // in helper: TypeSubset : short, float
	- AccessTwoImagesFixedDimensionTypeSubsetByItk( m_FixedImage, m_MovingImage, RegisterTwoImagesV4, 3);
	-
	-}
	-
	-mitk::PyramidImageRegistrationMethod::TransformMatrixType mitk::PyramidImageRegistrationMethod
	-::GetLastRotationMatrix()
	-{
	- TransformMatrixType output;
	- if( m_EstimatedParameters == nullptr )
	- {
	- output.set_identity();
	- return output;
	- }
	-
	- typedef itk::MatrixOffsetTransformBase< double, 3, 3> BaseTransformType;
	- BaseTransformType::Pointer base_transform = BaseTransformType::New();
	-
	- if( this->m_UseAffineTransform )
	- {
	- typedef itk::AffineTransform< double > TransformType;
	- TransformType::Pointer transform = TransformType::New();
	-
	- TransformType::ParametersType affine_params( TransformType::ParametersDimension );
	- this->GetParameters( &affine_params[0] );
	-
	- transform->SetParameters( affine_params );
	- base_transform = transform;
	- }
	- else
	- {
	- typedef itk::Euler3DTransform< double > RigidTransformType;
	- RigidTransformType::Pointer rtransform = RigidTransformType::New();
	-
	- RigidTransformType::ParametersType rigid_params( RigidTransformType::ParametersDimension );
	- this->GetParameters( &rigid_params[0] );
	-
	- rtransform->SetParameters( rigid_params );
	-
	- base_transform = rtransform;
	- }
	-
	- return base_transform->GetMatrix().GetVnlMatrix();
	-
	-}
	-
	-mitk::Image::Pointer mitk::PyramidImageRegistrationMethod
	-::GetResampledMovingImage()
	-{
	-
	- mitk::Image::Pointer output = mitk::Image::New();
	- //output->Initialize( this->m_FixedImage );
	-
	- AccessFixedDimensionByItk_1( this->m_MovingImage, ResampleMitkImage, 3, output );
	-
	- return output;
	-
	-}
	-
	-mitk::Image::Pointer mitk::PyramidImageRegistrationMethod::GetResampledMovingImage(mitk::Image::Pointer movingImage, double* transform)
	-{
	- mitk::Image::Pointer output = mitk::Image::New();
	-
	-
	- unsigned int dim = 12;
	- if( !m_UseAffineTransform )
	- dim = 6;
	-
	- if (m_EstimatedParameters == nullptr)
	- m_EstimatedParameters = new double[dim];
	-
	- double tmpParams[12];
	- // save and set temporal transformation values
	- for( unsigned int i=0; i<dim; i++)
	- {
	- tmpParams[i] = m_EstimatedParameters[i];
	- m_EstimatedParameters[i] = transform[i];
	- }
	-
	- AccessFixedDimensionByItk_1( movingImage, ResampleMitkImage, 3, output );
	-
	- // Restore old values
	- for( unsigned int i=0; i<dim; i++)
	- {
	- m_EstimatedParameters[i] = tmpParams[i];
	- }
	-
	- return output;
	-
	-}
	-
	-// ITK 4 Includes
	-#include <itkImageRegistrationMethodv4.h>
	-#include <itkGradientDescentLineSearchOptimizerv4.h>
	-#include <itkMattesMutualInformationImageToImageMetricv4.h>
	-#include <itkJointHistogramMutualInformationImageToImageMetricv4.h>
	-#include <itkCorrelationImageToImageMetricv4.h>
	-#include <itkOptimizerParameterScalesEstimator.h>
	-#include <itkRegistrationParameterScalesFromPhysicalShift.h>
	-
	-template <typename TPixel1, unsigned int VImageDimension1, typename TPixel2, unsigned int VImageDimension2>
	-void mitk::PyramidImageRegistrationMethod::
	-RegisterTwoImagesV4(itk::Image<TPixel1, VImageDimension1>* itkImage1, itk::Image<TPixel2, VImageDimension2>* itkImage2)
	-{
	- // Basic typedefs needed
	- typedef typename itk::Image<TPixel1, VImageDimension1> ItkImageTypeFixed;
	- typedef typename itk::Image<TPixel2, VImageDimension1> ItkImageTypeMoving;
	-
	- typedef itk::MatrixOffsetTransformBase< double, VImageDimension1, VImageDimension2 > BaseTransformType;
	-
	- typedef itk::Image< double, 3> ItkRegistrationImageType;
	- typedef itk::CastImageFilter< ItkImageTypeFixed, ItkRegistrationImageType> FixedCastFilterType;
	- typedef itk::CastImageFilter< ItkImageTypeMoving, ItkRegistrationImageType> MovingCastFilterType;
	-
	- typedef typename itk::ImageRegistrationMethodv4< ItkRegistrationImageType, ItkRegistrationImageType, AffineTransformType> RegistrationType;
	- typedef typename itk::MattesMutualInformationImageToImageMetricv4< ItkRegistrationImageType, ItkRegistrationImageType> MIMetricType;
	- typedef typename itk::CorrelationImageToImageMetricv4< ItkRegistrationImageType, ItkRegistrationImageType > NCMetricType;
	- typedef typename itk::ImageToImageMetricv4< ItkRegistrationImageType, ItkRegistrationImageType > BaseMetricType;
	-
	- typedef typename itk::ImageRegistrationMethodv4< ItkRegistrationImageType, ItkRegistrationImageType, RigidTransformType> RigidRegistrationType;
	-
	- typedef itk::GradientDescentLineSearchOptimizerv4 OptimizerType;
	-
	- typename ItkImageTypeFixed::Pointer referenceImage = itkImage1;
	- typename ItkImageTypeMoving::Pointer movingImage = itkImage2;
	-
	- // initial parameter dimension ( affine = default )
	- unsigned int paramDim = 12;
	- typename BaseTransformType::Pointer transform;
	- if( m_UseAffineTransform )
	- {
	- transform = AffineTransformType::New();
	- }
	- else
	- {
	- transform = RigidTransformType::New();
	- paramDim = 6;
	- }
	-
	- typename BaseTransformType::ParametersType initialParams(paramDim);
	-
	- initialParams.Fill(0);
	- if( m_UseAffineTransform )
	- {
	- initialParams[0] = initialParams[4] = initialParams[8] = 1;
	- }
	-
	-
	- // [Prepare registration]
	- // The ITKv4 Methods ( the MI Metric ) require double-type images so we need to perform cast first
	- typename FixedCastFilterType::Pointer caster_f = FixedCastFilterType::New();
	- typename MovingCastFilterType::Pointer caster_m = MovingCastFilterType::New();
	-
	- try
	- {
	- caster_f->SetInput(0, referenceImage );
	- caster_m->SetInput(0, movingImage );
	-
	- caster_f->Update();
	- caster_m->Update();
	-
	- }
	- catch( const itk::ExceptionObject &/e/ )
	- {
	- return ;
	- }
	-
	- // [Prepare Registration]
	- // Estimate the size of the pyramid based on image dimension
	- // here the image size on the topmost level must remain higher than the threshold
	- unsigned int max_pyramid_lvl = 4;
	- unsigned int max_schedule_val = 8;
	- const unsigned int min_required_image_size = 12;
	- typename ItkImageTypeFixed::RegionType::SizeType image_size = referenceImage->GetLargestPossibleRegion().GetSize();
	- unsigned int min_value = std::min( image_size[0], std::min( image_size[1], image_size[2]));
	-
	- // Adapt also the optimizer settings to the number of levels
	- float optmaxstep = 10;
	- float optminstep = 0.1f;
	- unsigned int iterations = 40;
	- unsigned int convergence_win_size = 8;
	- double convergence_tolerance = 1e-5;
	- while( max_schedule_val > 1.0 && (min_value / max_schedule_val < min_required_image_size) )
	- {
	- max_schedule_val /= 2;
	- max_pyramid_lvl--;
	- optmaxstep -= 2;
	- optminstep *= 0.5f;
	- convergence_win_size += 4;
	- convergence_tolerance *= 0.5;
	- }
	-
	- typename RegistrationType::ShrinkFactorsArrayType shrink_factors(max_pyramid_lvl);
	- shrink_factors.Fill(1);
	-
	- shrink_factors[0] = max_schedule_val;
	- for( unsigned int i=1; i<max_pyramid_lvl; i++)
	- {
	- shrink_factors[i] = std::max(shrink_factors[i - 1] / 2, itk::SizeValueType(1));
	- }
	-
	- if(m_Verbose)
	- {
	- MITK_INFO("dw.pyramid.reg") << " : Pyramid size set to : " << max_pyramid_lvl;
	- }
	-
	- // [Prepare Registration]
	- // Initialize the optimizer
	- // (i) Use the scales estimator ( depends on metric )
	- typename OptimizerType::Pointer optimizer = OptimizerType::New();
	- typename BaseMetricType::Pointer base_metric;
	- if( m_CrossModalityRegistration )
	- {
	- typename MIMetricType::Pointer metric = MIMetricType::New();
	-
	- typename itk::RegistrationParameterScalesFromPhysicalShift< MIMetricType >::Pointer mi_estimator =
	- itk::RegistrationParameterScalesFromPhysicalShift< MIMetricType >::New();
	- mi_estimator->SetMetric( metric );
	-
	- optimizer->SetScalesEstimator( mi_estimator );
	-
	- base_metric = metric;
	- }
	- else
	- {
	- typename NCMetricType::Pointer metric = NCMetricType::New();
	-
	- typename itk::RegistrationParameterScalesFromPhysicalShift< NCMetricType >::Pointer nc_estimator =
	- itk::RegistrationParameterScalesFromPhysicalShift< NCMetricType >::New();
	-
	- nc_estimator->SetMetric( metric );
	-
	- optimizer->SetScalesEstimator( nc_estimator );
	-
	- base_metric = metric;
	- }
	-
	- optimizer->SetDoEstimateLearningRateOnce( false );
	- optimizer->SetDoEstimateLearningRateAtEachIteration( true );
	- optimizer->SetNumberOfIterations( iterations );
	- optimizer->SetConvergenceWindowSize( convergence_win_size );
	- optimizer->SetMaximumStepSizeInPhysicalUnits( optmaxstep );
	- optimizer->SetMinimumConvergenceValue( convergence_tolerance );
	-
	- // line search options
	- optimizer->SetEpsilon( 1e-3 );
	- optimizer->SetLowerLimit( 0.3 );
	- optimizer->SetUpperLimit( 1.7 );
	- optimizer->SetMaximumLineSearchIterations( 20 );
	-
	- // add observer tag if verbose
	- unsigned long vopt_tag = 0;
	- if(m_Verbose)
	- {
	- MITK_INFO << " :: Starting at " << initialParams;
	-
	- OptimizerIterationCommandv4< OptimizerType >::Pointer iterationObserver =
	- OptimizerIterationCommandv4<OptimizerType>::New();
	-
	- vopt_tag = optimizer->AddObserver( itk::IterationEvent(), iterationObserver );
	- }
	-
	-
	- // Initializing by Geometry
	- if( !m_UseAffineTransform && m_InitializeByGeometry )
	- {
	- typedef itk::CenteredVersorTransformInitializer< ItkImageTypeFixed, ItkImageTypeMoving> TransformInitializerType;
	- typename TransformInitializerType::TransformType::Pointer rigidTransform = TransformInitializerType::TransformType::New() ;
	- MITK_INFO << "Initializer starting at : " << rigidTransform->GetParameters();
	-
	- typename TransformInitializerType::Pointer initializer = TransformInitializerType::New();
	- initializer->SetTransform( rigidTransform);
	- initializer->SetFixedImage( referenceImage.GetPointer() );
	- initializer->SetMovingImage( movingImage.GetPointer() );
	- initializer->MomentsOn();
	- initializer->InitializeTransform();
	-
	- MITK_INFO << "Initialized Rigid position : " << rigidTransform->GetParameters();
	- initialParams[3] = rigidTransform->GetParameters()[3];
	- initialParams[4] = rigidTransform->GetParameters()[4];
	- initialParams[5] = rigidTransform->GetParameters()[5];
	- }
	-
	- // [Prepare Registration]
	- // Masking (Optional)
	- if( m_UseMask )
	- {
	- typedef itk::Image<unsigned char, 3> BinaryImageType;
	- BinaryImageType::Pointer itkFixedImageMask = BinaryImageType::New();
	- itk::ImageMaskSpatialObject< 3 >::Pointer fixedMaskSpatialObject = itk::ImageMaskSpatialObject< 3 >::New();
	-
	- CastToItkImage( m_FixedImageMask, itkFixedImageMask);
	- itk::NotImageFilter<BinaryImageType, BinaryImageType>::Pointer notFilter = itk::NotImageFilter<BinaryImageType, BinaryImageType>::New();
	- notFilter->SetInput(itkFixedImageMask);
	- notFilter->Update();
	- fixedMaskSpatialObject->SetImage( notFilter->GetOutput() );
	- base_metric->SetFixedImageMask( fixedMaskSpatialObject );
	- }
	-
	-
	- if( m_EstimatedParameters != nullptr)
	- {
	- delete [] m_EstimatedParameters;
	- }
	-
	- m_EstimatedParameters = new double[paramDim];
	-
	- //-----------------
	- //-----------------
	-
	- // [Prepare Registration]
	- // combine all components to set-up registration
	- if( m_UseAffineTransform )
	- {
	-
	- typename RegistrationType::Pointer registration = RegistrationType::New();
	-
	- registration->SetFixedImage( 0, caster_f->GetOutput() );
	- registration->SetMovingImage( 0, caster_m->GetOutput() );
	- registration->SetMetric( base_metric );
	- registration->SetOptimizer( optimizer );
	- registration->SetMovingInitialTransform( transform.GetPointer() );
	- registration->SetNumberOfLevels(max_pyramid_lvl);
	- registration->SetShrinkFactorsPerLevel( shrink_factors );
	-
	- // observe the pyramid level change in order to adapt parameters
	- typename PyramidOptControlCommandv4<RegistrationType>::Pointer pyramid_observer =
	- PyramidOptControlCommandv4<RegistrationType>::New();
	- unsigned int pyramid_tag = registration->AddObserver( itk::InitializeEvent(), pyramid_observer );
	-
	-
	- try
	- {
	- registration->Update();
	- }
	- catch( const itk::ExceptionObject &e)
	- {
	- registration->Print( std::cout );
	-
	- MITK_ERROR << "[Registration Update] Caught ITK exception: ";
	- MITK_ERROR("itk.exception") << e.what();
	-
	- mitkThrow() << "Registration failed with exception: " << e.what();
	- }
	-
	- // [Post Registration]
	- // Retrieve the last transformation parameters from the performed registration task
	- typename BaseTransformType::ParametersType finalParameters = registration->GetOptimizer()->GetCurrentPosition();
	- for( unsigned int i=0; i<paramDim; i++)
	- {
	- m_EstimatedParameters[i] = finalParameters[i];
	- }
	-
	- if( m_Verbose )
	- {
	- MITK_INFO("Params") << optimizer->GetValue() << " :: " << finalParameters;
	- }
	-
	- if( pyramid_tag )
	- {
	- registration->RemoveObserver( pyramid_tag );
	- }
	-
	- }
	- //-----------
	- //-----------
	- else
	- {
	-
	- typename RigidRegistrationType::Pointer registration = RigidRegistrationType::New();
	-
	- registration->SetFixedImage( 0, caster_f->GetOutput() );
	- registration->SetMovingImage( 0, caster_m->GetOutput() );
	- registration->SetMetric( base_metric );
	- registration->SetOptimizer( optimizer );
	- registration->SetMovingInitialTransform( transform.GetPointer() );
	- registration->SetNumberOfLevels(max_pyramid_lvl);
	- registration->SetShrinkFactorsPerLevel( shrink_factors );
	-
	- // observe the pyramid level change in order to adapt parameters
	- typename PyramidOptControlCommandv4<RigidRegistrationType>::Pointer pyramid_observer =
	- PyramidOptControlCommandv4<RigidRegistrationType>::New();
	- unsigned int pyramid_tag = registration->AddObserver( itk::InitializeEvent(), pyramid_observer );
	-
	-
	- try
	- {
	- registration->Update();
	- }
	- catch( const itk::ExceptionObject &e)
	- {
	- registration->Print( std::cout );
	-
	- MITK_ERROR << "[Registration Update] Caught ITK exception: ";
	- MITK_ERROR("itk.exception") << e.what();
	-
	- mitkThrow() << "Registration failed with exception: " << e.what();
	- }
	-
	- // [Post Registration]
	- // Retrieve the last transformation parameters from the performed registration task
	- typename BaseTransformType::ParametersType finalParameters = registration->GetOptimizer()->GetCurrentPosition();
	- for( unsigned int i=0; i<paramDim; i++)
	- {
	- m_EstimatedParameters[i] = finalParameters[i];
	- }
	-
	- if( m_Verbose )
	- {
	- MITK_INFO("Params") << optimizer->GetValue() << " :: " << finalParameters;
	- }
	-
	- if( pyramid_tag )
	- {
	- registration->RemoveObserver( pyramid_tag );
	- }
	-
	- }
	-
	- if( m_Verbose )
	- {
	- MITK_INFO("Termination") << optimizer->GetStopConditionDescription();
	- }
	-
	- // remove optimizer tag if used
	- if( vopt_tag )
	- {
	- optimizer->RemoveObserver( vopt_tag );
	- }
	-
	-
	-
	-
	-
	-}
	-
	-template< typename TPixel, unsigned int VDimension>
	-void mitk::PyramidImageRegistrationMethod::
	-ResampleMitkImage( itk::Image<TPixel, VDimension>* itkImage,
	- mitk::Image::Pointer& outputImage )
	-{
	- typedef typename itk::Image< TPixel, VDimension> ImageType;
	- typedef typename itk::ResampleImageFilter< ImageType, ImageType, double> ResampleImageFilterType;
	-
	- typedef itk::LinearInterpolateImageFunction< ImageType, double > InterpolatorType;
	- typename InterpolatorType::Pointer linear_interpolator = InterpolatorType::New();
	-
	-
	- typedef itk::NearestNeighborInterpolateImageFunction< ImageType, double > NearestNeighborInterpolatorType;
	- typename NearestNeighborInterpolatorType::Pointer nn_interpolator = NearestNeighborInterpolatorType::New();
	-
	-
	- typedef itk::WindowedSincInterpolateImageFunction< ImageType, 7> WindowedSincInterpolatorType;
	- typename WindowedSincInterpolatorType::Pointer sinc_interpolator = WindowedSincInterpolatorType::New();
	-
	- typename ImageType::Pointer reference_image = ImageType::New();
	- CastToItkImage(m_FixedImage,reference_image);
	-
	- typedef itk::MatrixOffsetTransformBase< double, 3, 3> BaseTransformType;
	- BaseTransformType::Pointer base_transform = BaseTransformType::New();
	-
	- if( this->m_UseAffineTransform )
	- {
	- typedef itk::AffineTransform< double > TransformType;
	- TransformType::Pointer transform = TransformType::New();
	-
	- TransformType::ParametersType affine_params( TransformType::ParametersDimension );
	- this->GetParameters( &affine_params[0] );
	-
	- transform->SetParameters( affine_params );
	-
	- base_transform = transform;
	- }
	- // Rigid
	- else
	- {
	- typedef itk::Euler3DTransform< double > RigidTransformType;
	- RigidTransformType::Pointer rtransform = RigidTransformType::New();
	-
	- RigidTransformType::ParametersType rigid_params( RigidTransformType::ParametersDimension );
	- this->GetParameters( &rigid_params[0] );
	-
	- rtransform->SetParameters( rigid_params );
	-
	- base_transform = rtransform;
	- }
	-
	- typename ResampleImageFilterType::Pointer resampler = ResampleImageFilterType::New();
	-
	- resampler->SetInterpolator( linear_interpolator );
	- if( m_UseWindowedSincInterpolator )
	- resampler->SetInterpolator( sinc_interpolator );
	- if ( m_UseNearestNeighborInterpolator)
	- resampler->SetInterpolator ( nn_interpolator );
	-
	- //resampler->SetNumberOfThreads(1);
	-
	- resampler->SetInput( itkImage );
	- resampler->SetTransform( base_transform );
	- resampler->SetReferenceImage( reference_image );
	- resampler->UseReferenceImageOn();
	-
	- resampler->Update();
	-
	- mitk::GrabItkImageMemory( resampler->GetOutput(), outputImage);
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/Registration/mitkRegistrationWrapper.cpp b/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/Registration/mitkRegistrationWrapper.cpp
	deleted file mode 100644
	index 23d8c6504e..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/Registration/mitkRegistrationWrapper.cpp
	+++ /dev/null
	@@ -1,244 +0,0 @@
	-#include "mitkRegistrationWrapper.h"
	-
	-#include "mitkPyramidImageRegistrationMethod.h"
	-#include "mitkImage.h"
	-#include <mitkDiffusionImageCorrectionFilter.h>
	-#include "itkB0ImageExtractionImageFilter.h"
	-#include <itkResampleImageFilter.h>
	-#include <itkWindowedSincInterpolateImageFunction.h>
	-#include <itkLinearInterpolateImageFunction.h>
	-#include <itkNearestNeighborExtrapolateImageFunction.h>
	-#include <itkBSplineInterpolateImageFunction.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <mitkProperties.h>
	-#include <mitkFloatPropertyExtension.h>
	-#include <itkImageDuplicator.h>
	-
	-#include <vnl/vnl_inverse.h>
	-
	-void mitk::RegistrationWrapper::ApplyTransformationToImage(mitk::Image::Pointer img, const mitk::RegistrationWrapper::RidgidTransformType &transformation,double* offset, mitk::Image* resampleReference, bool binary)
	-{
	-
	- if (!mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( img ) )
	- {
	-
	- ItkImageType::Pointer itkImage = ItkImageType::New();
	-
	- CastToItkImage(img, itkImage);
	-
	- typedef itk::Euler3DTransform< double > RigidTransformType;
	- RigidTransformType::Pointer rtransform = RigidTransformType::New();
	- RigidTransformType::ParametersType parameters(RigidTransformType::ParametersDimension);
	-
	- for (int i = 0; i<6;++i)
	- parameters[i] = transformation[i];
	-
	- rtransform->SetParameters( parameters );
	-
	- mitk::Point3D origin = img->GetGeometry()->GetOrigin();
	- // overwrite origin only if an offset was supplied
	- if (offset[0] != 0 \|\| offset[1] != 0 \|\| offset[2] != 0)
	- {
	- origin[0]=offset[0];
	- origin[1]=offset[1];
	- origin[2]=offset[2];
	- }
	-
	- mitk::Point3D newOrigin = rtransform->GetInverseTransform()->TransformPoint(origin);
	-
	- itk::Matrix<double,3,3> dir = itkImage->GetDirection();
	- itk::Matrix<double,3,3> transM ( vnl_inverse(rtransform->GetMatrix().GetVnlMatrix()));
	- itk::Matrix<double,3,3> newDirection = transM * dir;
	-
	- itkImage->SetOrigin(newOrigin);
	- itkImage->SetDirection(newDirection);
	-
	- // Perform Resampling if reference image is provided
	- if (resampleReference != nullptr)
	- {
	- typedef itk::ResampleImageFilter<ItkImageType, ItkImageType> ResampleFilterType;
	-
	- ItkImageType::Pointer itkReference = ItkImageType::New();
	- CastToItkImage(resampleReference,itkReference);
	-
	- typedef itk::Function::WelchWindowFunction<4> WelchWindowFunction;
	- typedef itk::WindowedSincInterpolateImageFunction< ItkImageType, 4,WelchWindowFunction> WindowedSincInterpolatorType;
	- WindowedSincInterpolatorType::Pointer sinc_interpolator = WindowedSincInterpolatorType::New();
	-
	-
	- typedef itk::LinearInterpolateImageFunction< ItkImageType> LinearInterpolatorType;
	- LinearInterpolatorType::Pointer lin_interpolator = LinearInterpolatorType::New();
	-
	- typedef itk::NearestNeighborInterpolateImageFunction< ItkImageType, double > NearestNeighborInterpolatorType;
	- NearestNeighborInterpolatorType::Pointer nn_interpolator = NearestNeighborInterpolatorType::New();
	-
	- typedef itk::BSplineInterpolateImageFunction< ItkImageType, double > BSplineInterpolatorType;
	- BSplineInterpolatorType::Pointer bSpline_interpolator = BSplineInterpolatorType::New();
	-
	-
	- ResampleFilterType::Pointer resampler = ResampleFilterType::New();
	- resampler->SetInput(itkImage);
	- resampler->SetReferenceImage( itkReference );
	- resampler->UseReferenceImageOn();
	- if (binary)
	- resampler->SetInterpolator(nn_interpolator);
	- else
	- resampler->SetInterpolator(lin_interpolator);
	-
	- resampler->Update();
	-
	- GrabItkImageMemory(resampler->GetOutput(), img);
	- }
	- else
	- {
	- // !! CastToItk behaves very differently depending on the original data type
	- // if the target type is the same as the original, only a pointer to the data is set
	- // and an additional GrabItkImageMemory will cause a segfault when the image is destroyed
	- // GrabItkImageMemory - is not necessary in this case since we worked on the original data
	- // See Bug 17538 - this is why we duplicate the itkImage first and then create a new mitk::Image from it.
	- itk::ImageDuplicator<ItkImageType>::Pointer duplicator = itk::ImageDuplicator<ItkImageType>::New();
	- duplicator->SetInputImage(itkImage);
	- duplicator->Update();
	- GrabItkImageMemory(duplicator->GetOutput(), img);
	- }
	-
	- }
	- else
	- {
	- mitk::Image::Pointer diffImages = dynamic_cast<mitk::Image*>(img.GetPointer());
	-
	-// mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer gradientDirections =
	-// static_cast<mitk::GradientDirectionsProperty*>( img->GetProperty(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() )->GetGradientDirectionsContainer();
	- typedef itk::Euler3DTransform< double > RigidTransformType;
	- RigidTransformType::Pointer rtransform = RigidTransformType::New();
	- RigidTransformType::ParametersType parameters(RigidTransformType::ParametersDimension);
	-
	- for (int i = 0; i<6;++i)
	- {
	- parameters[i] = transformation[i];
	- }
	-
	- rtransform->SetParameters( parameters );
	-
	- typedef itk::VectorImage<short, 3> ITKDiffusionImageType;
	- ITKDiffusionImageType::Pointer itkVectorImagePointer = ITKDiffusionImageType::New();
	- mitk::CastToItkImage(diffImages, itkVectorImagePointer);
	-
	- mitk::Point3D b0origin = itkVectorImagePointer->GetOrigin();
	- // overwrite origin only if an offset was supplied
	- if (offset[0] != 0 \|\| offset[1] != 0 \|\| offset[2] != 0)
	- {
	- b0origin[0]=offset[0];
	- b0origin[1]=offset[1];
	- b0origin[2]=offset[2];
	- }
	-
	- mitk::Point3D newOrigin = rtransform->GetInverseTransform()->TransformPoint(b0origin);
	-
	- itk::Matrix<double,3,3> dir = itkVectorImagePointer->GetDirection();
	- itk::Matrix<double,3,3> transM ( vnl_inverse(rtransform->GetMatrix().GetVnlMatrix()));
	- itk::Matrix<double,3,3> newDirection = transM * dir;
	-
	- itkVectorImagePointer->SetOrigin(newOrigin);
	- itkVectorImagePointer->SetDirection(newDirection);
	-
	- // !! CastToItk behaves very differently depending on the original data type
	- // if the target type is the same as the original, only a pointer to the data is set
	- // and an additional GrabItkImageMemory will cause a segfault when the image is destroyed
	- // GrabItkImageMemory - is not necessary in this case since we worked on the original data
	- // See Bug 17538 - this is why we duplicate the itkImage first and then create a new mitk::Image from it.
	- itk::ImageDuplicator<ITKDiffusionImageType>::Pointer duplicator = itk::ImageDuplicator<ITKDiffusionImageType>::New();
	- duplicator->SetInputImage(itkVectorImagePointer);
	- duplicator->Update();
	- GrabItkImageMemory(duplicator->GetOutput(), img);
	-
	- mitk::DiffusionPropertyHelper::CopyProperties(diffImages, img, false);
	- mitk::DiffusionPropertyHelper::InitializeImage(img);
	-
	- mitk::DiffusionImageCorrectionFilter::Pointer correctionFilter = mitk::DiffusionImageCorrectionFilter::New();
	-
	- // For Diff. Images: Need to rotate the gradients (works in-place)
	- correctionFilter->SetImage(img);
	- correctionFilter->CorrectDirections(transM.GetVnlMatrix());
	- }
	-}
	-
	-void mitk::RegistrationWrapper::GetTransformation(mitk::Image::Pointer fixedImage, mitk::Image::Pointer movingImage, RidgidTransformType transformation,double* offset, bool useSameOrigin, mitk::Image* mask)
	-{
	- // Handle the case that fixed/moving image is a DWI image
	- mitk::Image* fixedDwi = dynamic_cast<mitk::Image*> (fixedImage.GetPointer());
	- mitk::Image* movingDwi = dynamic_cast<mitk::Image*> (movingImage.GetPointer());
	- itk::B0ImageExtractionImageFilter<short,short >::Pointer b0Extraction = itk::B0ImageExtractionImageFilter<short,short>::New();
	- offset[0]=offset[1]=offset[2]=0;
	-
	- if ( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( fixedDwi ) )
	- { // Set b0 extraction as fixed image
	- auto fixedGradientDirections = mitk::DiffusionPropertyHelper::GetGradientContainer(fixedDwi);
	- auto itkFixedDwiPointer = mitk::DiffusionPropertyHelper::GetItkVectorImage(fixedDwi);
	- b0Extraction->SetInput( itkFixedDwiPointer );
	- b0Extraction->SetDirections(fixedGradientDirections);
	- b0Extraction->Update();
	- mitk::Image::Pointer tmp = mitk::Image::New();
	- tmp->InitializeByItk(b0Extraction->GetOutput());
	- tmp->SetVolume(b0Extraction->GetOutput()->GetBufferPointer());
	- fixedImage = tmp;
	- }
	- if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( movingDwi ))
	- { // Set b0 extraction as moving image
	- auto movingGradientDirections = mitk::DiffusionPropertyHelper::GetGradientContainer(movingDwi);
	- auto itkMovingDwiPointer = mitk::DiffusionPropertyHelper::GetItkVectorImage(movingDwi);
	-
	- b0Extraction->SetInput( itkMovingDwiPointer );
	- b0Extraction->SetDirections(movingGradientDirections);
	- b0Extraction->Update();
	- mitk::Image::Pointer tmp = mitk::Image::New();
	- tmp->InitializeByItk(b0Extraction->GetOutput());
	- tmp->SetVolume(b0Extraction->GetOutput()->GetBufferPointer());
	- movingImage = tmp;
	- }
	-
	- // align the offsets of the two images. this is done to avoid non-overlapping initialization
	- // Point3D origin = fixedImage->GetGeometry()->GetOrigin();
	-
	-
	- Point3D center = fixedImage->GetGeometry()->GetCenter();
	- Point3D centerMoving = movingImage->GetGeometry()->GetCenter();
	- Point3D originMoving = movingImage->GetGeometry()->GetOrigin();
	-
	-
	- mitk::Image::Pointer tmpImage = movingImage->Clone();
	- if (useSameOrigin)
	- {
	-
	- offset[0] = (originMoving[0]-centerMoving[0])+center[0];
	- offset[1] = (originMoving[1]-centerMoving[1])+center[1];
	- offset[2] = (originMoving[2]-centerMoving[2])+center[2];
	- Point3D translatedOrigin;
	- translatedOrigin[0]= offset[0];
	- translatedOrigin[1]= offset[1];
	- translatedOrigin[2]= offset[2];
	- tmpImage->GetGeometry()->SetOrigin(translatedOrigin);
	- }
	- // Start registration
	- mitk::PyramidImageRegistrationMethod::Pointer registrationMethod = mitk::PyramidImageRegistrationMethod::New();
	- registrationMethod->SetFixedImage( fixedImage );
	-
	- if (mask != nullptr)
	- {
	- registrationMethod->SetFixedImageMask(mask);
	- registrationMethod->SetUseFixedImageMask(true);
	- }
	- else
	- {
	- registrationMethod->SetUseFixedImageMask(false);
	- }
	-
	- registrationMethod->SetTransformToRigid();
	- registrationMethod->SetCrossModalityOn();
	- registrationMethod->SetVerboseOn();
	-
	-
	- registrationMethod->SetMovingImage(tmpImage);
	- registrationMethod->Update();
	- registrationMethod->GetParameters(transformation); // first three: euler angles, last three translation
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/itkDiffusionOdfPrepareVisualizationImageFilter.cpp b/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/itkDiffusionOdfPrepareVisualizationImageFilter.cpp
	deleted file mode 100644
	index a75c90d1f4..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/itkDiffusionOdfPrepareVisualizationImageFilter.cpp
	+++ /dev/null
	@@ -1,181 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkDiffusionOdfPrepareVisualizationImageFilter_cpp
	-#define __itkDiffusionOdfPrepareVisualizationImageFilter_cpp
	-
	-#include <time.h>
	-#include <stdio.h>
	-#include <stdlib.h>
	-
	-#include "itkDiffusionOdfPrepareVisualizationImageFilter.h"
	-#include "itkImageRegionConstIterator.h"
	-#include "itkImageRegionConstIteratorWithIndex.h"
	-#include "itkImageRegionIterator.h"
	-#include "itkArray.h"
	-#include "vnl/vnl_vector.h"
	-#include "itkOrientationDistributionFunction.h"
	-
	-namespace itk {
	-
	- template< class TOdfPixelType, int NrOdfDirections>
	- DiffusionOdfPrepareVisualizationImageFilter< TOdfPixelType, NrOdfDirections>
	- ::DiffusionOdfPrepareVisualizationImageFilter() :
	- m_Threshold(0),
	- m_ScaleByGfaType(GfaFilterType::GFA_STANDARD),
	- m_DoScaleGfa(false),
	- m_GfaParam1(2),
	- m_GfaParam2(1)
	- {
	- // At least 1 inputs is necessary for a vector image.
	- // For images added one at a time we need at least six
	- this->SetNumberOfRequiredInputs( 1 );
	- }
	-
	- template< class TOdfPixelType,
	- int NrOdfDirections>
	- void DiffusionOdfPrepareVisualizationImageFilter< TOdfPixelType,
	- NrOdfDirections>
	- ::BeforeThreadedGenerateData()
	- {
	- if( m_NormalizationMethod == PV_GLOBAL_MAX )
	- {
	- typename InputImageType::Pointer inputImagePointer = nullptr;
	- inputImagePointer = static_cast< InputImageType * >(
	- this->ProcessObject::GetInput(0) );
	-
	- typename GfaFilterType::Pointer filter = GfaFilterType::New();
	- filter->SetInput(inputImagePointer);
	- filter->SetNumberOfThreads(4);
	- filter->SetComputationMethod(GfaFilterType::GFA_MAX_ODF_VALUE);
	- filter->Update();
	-
	- typedef typename itk::MinimumMaximumImageCalculator< typename GfaFilterType::OutputImageType >
	- MaxFilterType;
	- typename MaxFilterType::Pointer maxFilter = MaxFilterType::New();
	- maxFilter->SetImage(filter->GetOutput());
	- maxFilter->ComputeMaximum();
	-
	- m_GlobalInputMaximum = maxFilter->GetMaximum();
	- }
	-
	- //if(m_DoScaleGfa)
	- {
	- typename InputImageType::Pointer inputImagePointer = nullptr;
	- inputImagePointer = static_cast< InputImageType * >(
	- this->ProcessObject::GetInput(0) );
	-
	- typename GfaFilterType::Pointer filter = GfaFilterType::New();
	- filter->SetInput(inputImagePointer);
	- filter->SetNumberOfThreads(4);
	- filter->SetComputationMethod(m_ScaleByGfaType);
	- filter->SetParam1(m_GfaParam1);
	- filter->SetParam2(m_GfaParam2);
	- filter->Update();
	- m_GfaImage = filter->GetOutput();
	- }
	- }
	-
	- template< class TOdfPixelType,
	- int NrOdfDirections>
	- void DiffusionOdfPrepareVisualizationImageFilter< TOdfPixelType,
	- NrOdfDirections>
	- ::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread,
	- ThreadIdType )
	- {
	- typename OutputImageType::Pointer outputImage =
	- static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0));
	- ImageRegionIterator< OutputImageType > oit(outputImage, outputRegionForThread);
	- oit.GoToBegin();
	-
	- typedef itk::OrientationDistributionFunction<TOdfPixelType,NrOdfDirections> OdfType;
	- typedef ImageRegionConstIterator< InputImageType > InputIteratorType;
	- typedef typename InputImageType::PixelType OdfVectorType;
	- typename InputImageType::Pointer inputImagePointer = nullptr;
	- inputImagePointer = static_cast< InputImageType * >(
	- this->ProcessObject::GetInput(0) );
	- InputIteratorType git(inputImagePointer, outputRegionForThread );
	- git.GoToBegin();
	-
	- typedef ImageRegionConstIterator< GfaImageType > GfaIteratorType;
	- GfaIteratorType gfaIt(m_GfaImage, outputRegionForThread);
	-
	- while( !git.IsAtEnd() )
	- {
	- OdfVectorType b = git.Get();
	- OdfType odf = b.GetDataPointer();
	-
	- switch( m_NormalizationMethod )
	- {
	- case PV_NONE:
	- {
	- break;
	- }
	- case PV_MAX:
	- {
	- odf = odf.MaxNormalize();
	- break;
	- }
	- case PV_MIN_MAX:
	- {
	- odf = odf.MinMaxNormalize();
	- break;
	- }
	- case PV_GLOBAL_MAX:
	- {
	- odf *= 1.0/m_GlobalInputMaximum;
	- break;
	- }
	- case PV_MIN_MAX_INVERT:
	- {
	- odf = odf.MinMaxNormalize();
	- for(int i=0; i<NrOdfDirections; i++)
	- {
	- odf[i] = 1.0 - odf[i];
	- }
	- break;
	- }
	- }
	-
	- if(m_DoScaleGfa)
	- {
	- odf *= gfaIt.Get();
	- ++gfaIt;
	- }
	-
	- odf *= 0.5;
	- oit.Set( odf.GetDataPointer() );
	- ++oit;
	- ++git; // Gradient image iterator
	- }
	-
	- std::cout << "One Thread finished extraction" << std::endl;
	- }
	-
	- template< class TOdfPixelType,
	- int NrOdfDirections>
	- void DiffusionOdfPrepareVisualizationImageFilter< TOdfPixelType,
	- NrOdfDirections>
	- ::PrintSelf(std::ostream& os, Indent indent) const
	- {
	- Superclass::PrintSelf(os,indent);
	- os << indent << "m_Threshold: " <<
	- m_Threshold << std::endl;
	- }
	-
	-}
	-
	-#endif // __itkDiffusionOdfPrepareVisualizationImageFilter_cpp
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/itkDwiGradientLengthCorrectionFilter.cpp b/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/itkDwiGradientLengthCorrectionFilter.cpp
	deleted file mode 100644
	index d32184a330..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/itkDwiGradientLengthCorrectionFilter.cpp
	+++ /dev/null
	@@ -1,86 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-/*=========================================================================
	-
	-Program: Tensor ToolKit - TTK
	-Module: $URL: svn://scm.gforge.inria.fr/svn/ttk/trunk/Algorithms/itkElectrostaticRepulsionDiffusionGradientReductionFilter.txx $
	-Language: C++
	-Date: $Date: 2010-06-07 13:39:13 +0200 (Mo, 07 Jun 2010) $
	-Version: $Revision: 68 $
	-
	-Copyright (c) INRIA 2010. All rights reserved.
	-See LICENSE.txt for details.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without even
	-the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
	-PURPOSE. See the above copyright notices for more information.
	-
	-=========================================================================*/
	-
	-#include "itkDwiGradientLengthCorrectionFilter.h"
	-
	-itk::DwiGradientLengthCorrectionFilter::DwiGradientLengthCorrectionFilter()
	- : m_ReferenceBValue(0)
	- , m_RoundingValue(0)
	- , m_ReferenceGradientDirectionContainer(nullptr)
	- , m_OutputGradientDirectionContainer(nullptr)
	-{
	-}
	-
	-itk::DwiGradientLengthCorrectionFilter::~DwiGradientLengthCorrectionFilter()
	-{
	-}
	-
	-void itk::DwiGradientLengthCorrectionFilter::GenerateData()
	-{
	-
	- if(m_ReferenceBValue == 0 \|\| m_RoundingValue == 0 \|\| m_ReferenceGradientDirectionContainer.IsNull())
	- itkExceptionMacro("Wrong initialization");
	-
	- m_OutputGradientDirectionContainer = GradientDirectionContainerType::New();
	-
	- m_NewBValue = itk::NumericTraits<double>::max();
	- GradientDirectionContainerType::ConstIterator it = m_ReferenceGradientDirectionContainer->Begin();
	- for(; it != m_ReferenceGradientDirectionContainer->End(); ++it)
	- {
	- const double twonorm = it.Value().two_norm();
	- const double currentBValue = m_ReferenceBValuetwonormtwonorm ;
	- const double roundedBValue = int((currentBValue + 0.5 * m_RoundingValue)/m_RoundingValue)*m_RoundingValue;
	-
	- if (roundedBValue<m_NewBValue && roundedBValue>1)
	- m_NewBValue = roundedBValue;
	- }
	-
	- it = m_ReferenceGradientDirectionContainer->Begin();
	- for(; it != m_ReferenceGradientDirectionContainer->End(); ++it)
	- {
	- const double twonorm = it.Value().two_norm();
	- const double currentBValue = m_ReferenceBValuetwonormtwonorm ;
	- const double roundedBValue = int((currentBValue + 0.5 * m_RoundingValue)/m_RoundingValue)*m_RoundingValue;
	-
	- if (roundedBValue>1)
	- {
	- const double f = std::sqrt(roundedBValue/m_NewBValue);
	- GradientDirectionType grad = it.Value();
	- m_OutputGradientDirectionContainer->push_back( grad.normalize() * f );
	- }
	- else
	- {
	- GradientDirectionType grad; grad.fill(0.0);
	- m_OutputGradientDirectionContainer->push_back( grad );
	- }
	- }
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.cpp b/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.cpp
	deleted file mode 100644
	index 72ad985147..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.cpp
	+++ /dev/null
	@@ -1,987 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#include "mitkPartialVolumeAnalysisClusteringCalculator.h"
	-
	-#include "mitkImageAccessByItk.h"
	-#include "mitkImageToItk.h"
	-#include "itkScalarImageToHistogramGenerator.h"
	-#include "itkListSample.h"
	-
	-namespace mitk
	-{
	-
	- PartialVolumeAnalysisClusteringCalculator::PartialVolumeAnalysisClusteringCalculator()
	- : m_MaxIt(100), m_StepsNumIntegration(100)
	- {
	- }
	-
	-
	- PartialVolumeAnalysisClusteringCalculator::~PartialVolumeAnalysisClusteringCalculator()
	- {
	- }
	-
	- PartialVolumeAnalysisClusteringCalculator::ParamsType*
	- PartialVolumeAnalysisClusteringCalculator::InitialGuess(HistType h) const
	- {
	- int s = h.xVals.size();
	- int s30 = 0.3 * s;
	- int s70 = 0.7 * s;
	- auto params = new ParamsType();
	- params->means[0] = h.xVals(s30);
	- params->means[1] = h.xVals(s70);
	- params->sigmas[0] = (h.xVals(s-1) - h.xVals(0)) / 5.0;
	- params->sigmas[1] = (h.xVals(s-1) - h.xVals(0)) / 5.0;
	- params->ps[0] = 0.4;
	- params->ps[1] = 0.4;
	-
	- return params;
	- }
	-
	- PartialVolumeAnalysisClusteringCalculator::ParamsType*
	- PartialVolumeAnalysisClusteringCalculator::Cluster(HistType h, ParamsType *initialGuess) const
	- {
	- auto params = new ParamsType();
	- params->Initialize(initialGuess);
	-
	- double ll = 9999999999999999999.9;
	- double oll;
	- double sml = (h.xVals[1] - h.xVals[0]) / 1000;
	-
	- int arraysz = h.xVals.size();
	-
	- for (unsigned int it = 0; it < m_MaxIt; it++)
	- {
	- // wie sehen basisfunktionen zu aktuellen params aus?
	- ClusterResultType curves = CalculateCurves(*params,h.xVals);
	-
	- // summe der basisfunktionen
	- for(int i=0; i<arraysz; i++)
	- {
	- if(curves.combiVals(i) == 0)
	- {
	- curves.combiVals(i) = 0.00000000000000000001;
	- }
	- }
	-
	- // alte log likelihood
	- oll = ll;
	- ll = 0;
	-
	- // neue likelihood
	- for(int i=0; i<arraysz; i++)
	- {
	- ll -= h.hVals(i) * log(curves.combiVals(i));
	- }
	-
	- if( it>2 && oll-ll < arraysz/2*1e-15 )
	- {
	- break;
	- }
	-
	- for(int j=0; j<2; j++)
	- {
	- VecType array, p(arraysz);
	- array = curves.vals[j];
	-
	- for(int i=0; i<arraysz; i++)
	- {
	- p(i) = h.hVals(i)*array(i)/curves.combiVals(i);
	- }
	-
	- params->ps[j] = 0;
	- params->means[j] = 0;
	- for(int i=0; i<arraysz; i++)
	- {
	- params->ps[j] += p(i);
	- params->means[j] += h.xVals(i)*p(i);
	- }
	- params->means[j] /= params->ps[j];
	-
	- VecType vr = h.xVals;
	- for(int i=0; i<arraysz; i++)
	- {
	- vr(i) -= params->means[j];
	- }
	-
	- params->sigmas[j] = 0;
	- for(int i=0; i<arraysz; i++)
	- {
	- params->sigmas[j] += vr(i)vr(i)p(i);
	- }
	- params->sigmas[j] /= params->ps[j];
	- params->sigmas[j] += sml;
	-
	- }
	-
	- double p3 = 0;
	- for(int i=0; i<arraysz; i++)
	- {
	- p3 += h.hVals(i)*curves.mixedVals[0](i)/curves.combiVals(i);
	- }
	- p3 += 1e-3;
	-
	- double sum = 0;
	- for(int j=0; j<2; j++)
	- {
	- params->ps[j] = params->ps[j] + 1e-3;
	- sum += params->ps[j];
	- }
	- sum += p3;
	-
	- for(int j=0; j<2; j++)
	- {
	- params->ps[j] = params->ps[j] / sum;
	- }
	- p3 /= sum;
	-
	- }
	-
	- return params;
	-
	- }
	-
	- void PartialVolumeAnalysisClusteringCalculator::Normalize(ParamsType params, ClusterResultType* curves) const
	- {
	- double sum1=0, sum2=0, sum3=0;
	- int arraysz = curves->vals[0].size();
	-
	- for(int i=0; i<arraysz; i++)
	- {
	- sum1 += curves->vals[0](i);
	- sum2 += curves->vals[1](i);
	- sum3 += curves->mixedVals[0](i);
	- }
	-
	- sum1 /= params.ps[0];
	- sum2 /= params.ps[1];
	- sum3 /= 1.0 -params.ps[0] -params.ps[1];
	-
	- for(int i=0; i<arraysz; i++)
	- {
	- curves->vals[0](i) /= sum1;
	- curves->vals[1](i) /= sum2;
	- curves->mixedVals[0](i) /= sum3;
	- }
	-
	- for(int i=0; i<arraysz; i++)
	- {
	- curves->combiVals(i) = curves->mixedVals[0](i) + curves->vals[0](i) + curves->vals[1](i);
	- }
	- }
	-
	- PartialVolumeAnalysisClusteringCalculator::ClusterResultType
	- PartialVolumeAnalysisClusteringCalculator::CalculateCurves(ParamsType params, VecType xVals) const
	- {
	-
	- int arraysz = xVals.size();
	- ClusterResultType result(arraysz);
	-
	- for( int j=0; j<2; j++)
	- {
	- for(int i=0; i<arraysz; i++)
	- {
	- double d = xVals(i)-params.means[j];
	- double amp = params.ps[j]/sqrt(2itk::Math::piparams.sigmas[j]);
	-
	- result.vals[j](i) = ampexp(-0.5 (d*d)/params.sigmas[j]);
	- }
	- }
	-
	- for(int i=0; i<arraysz; i++)
	- {
	- result.mixedVals[0](i) = 0;
	- }
	-
	- for(double t=0; t<=1; t = t + 1.0/(m_StepsNumIntegration-1.0))
	- {
	- for(int i=0; i<arraysz; i++)
	- {
	- double d = xVals(i)-(tparams.means[0]+(1-t)params.means[1]);
	- double v = tparams.sigmas[0]+(1-t)params.sigmas[1];
	- double p = 1.0 - params.ps[0] - params.ps[1];
	- double amp = (1.0/m_StepsNumIntegration) * p / sqrt(2.0itk::Math::piv);
	-
	- result.mixedVals[0](i) = result.mixedVals[0](i) + ampexp(-0.5 (d*d)/v);
	-
	- // MITK_INFO << "d=" << d << "v=" <<v << "p=" << p << "amp=" << amp << "result=" << ampexp(-0.5 (d*d)/v) << std::endl;
	- }
	- // MITK_INFO << "t=" << t << std::endl;
	- // params.Print();
	- // result.Print();
	- }
	-
	- for(int i=0; i<arraysz; i++)
	- {
	- result.combiVals(i) = result.mixedVals[0](i) + result.vals[0](i) + result.vals[1](i);
	- }
	-
	- return result;
	- }
	-
	- PartialVolumeAnalysisClusteringCalculator::HelperStructPerformRGBClusteringRetval*
	- PartialVolumeAnalysisClusteringCalculator::PerformRGBClustering(mitk::Image::ConstPointer image, const MitkHistType *histogram) const
	- {
	-
	- auto rgbChannels = new HelperStructRGBChannels();
	-
	- HelperStructPerformClusteringRetval *resultr = PerformClustering(image, histogram, 2);
	- rgbChannels->r = resultr->clusteredImage;
	-
	- HelperStructPerformClusteringRetval *resultg = PerformClustering(image, histogram, 0, resultr);
	- rgbChannels->g = resultg->clusteredImage;
	-
	- HelperStructPerformClusteringRetval *resultb = PerformClustering(image, histogram, 1, resultr);
	- rgbChannels->b = resultb->clusteredImage;
	-
	- mitk::Image::Pointer outImage = mitk::Image::New();
	-
	- switch(rgbChannels->r->GetDimension())
	- {
	- case 2:
	- InternalGenerateRGB<2>(rgbChannels, outImage);
	- break;
	- case 3:
	- InternalGenerateRGB<3>(rgbChannels, outImage);
	- break;
	- case 4:
	- InternalGenerateRGB<4>(rgbChannels, outImage);
	- break;
	- default:
	- InternalGenerateRGB<3>(rgbChannels, outImage);
	- }
	-
	- auto retval
	- = new HelperStructPerformRGBClusteringRetval();
	- retval->rgbChannels = rgbChannels;
	- retval->rgb = outImage;
	- retval->params = resultr->params;
	- retval->result = resultr->result;
	- retval->hist = resultr->hist;
	-
	- delete resultr;
	- delete resultg;
	-
	- return retval;
	-
	- }
	-
	- template < unsigned int VImageDimension >
	- void PartialVolumeAnalysisClusteringCalculator::InternalGenerateRGB( HelperStructRGBChannels *rgbin, mitk::Image::Pointer retval ) const
	- {
	- typedef itk::Image< float, VImageDimension > ProbImageType;
	- typedef itk::Image< typename itk::RGBAPixel<unsigned char>, VImageDimension > RGBImageType;
	-
	- typedef mitk::ImageToItk<ProbImageType> CastFilterType;
	- typename CastFilterType::Pointer castFilter = CastFilterType::New();
	- castFilter->SetInput( rgbin->r );
	- castFilter->Update();
	-
	- typename ProbImageType::Pointer r = castFilter->GetOutput();
	-
	- castFilter = CastFilterType::New();
	- castFilter->SetInput( rgbin->g );
	- castFilter->Update();
	- typename ProbImageType::Pointer g = castFilter->GetOutput();
	-
	- typename RGBImageType::Pointer rgb = RGBImageType::New();
	- rgb->SetSpacing( g->GetSpacing() ); // Set the image spacing
	- rgb->SetOrigin( g->GetOrigin() ); // Set the image origin
	- rgb->SetDirection( g->GetDirection() ); // Set the image direction
	- rgb->SetRegions( g->GetLargestPossibleRegion() );
	- rgb->Allocate();
	-
	- itk::ImageRegionConstIterator<ProbImageType>
	- itr(r, r->GetLargestPossibleRegion());
	- itk::ImageRegionConstIterator<ProbImageType>
	- itg(g, g->GetLargestPossibleRegion());
	-
	- itk::ImageRegionIterator<RGBImageType>
	- itrgb(rgb, rgb->GetLargestPossibleRegion());
	-
	- itr.GoToBegin();
	- itg.GoToBegin();
	-
	- float maxr = 0;
	- float maxg = 0;
	-
	- while( !itr.IsAtEnd() )
	- {
	- typename ProbImageType::PixelType pr = itr.Get();
	- typename ProbImageType::PixelType pg = itg.Get();
	-
	- if(pr > maxr)
	- {
	- maxr = pr;
	- }
	-
	- if(pg > maxg)
	- {
	- maxg = pg;
	- }
	-
	- ++itr;
	- ++itg;
	- }
	-
	- itr.GoToBegin();
	- itg.GoToBegin();
	- itrgb.GoToBegin();
	-
	- while( !itr.IsAtEnd() )
	- {
	- typename ProbImageType::PixelType pr = itr.Get();
	- typename ProbImageType::PixelType pg = itg.Get();
	-
	- typename RGBImageType::PixelType prgb;
	-
	- float valr = (pr/maxr)*255.0f;
	- float valg = (pg/maxg)*255.0f;
	- float alpha = valr>valg ? valr : valg;
	- prgb.Set(valr, valg, 0.0f, alpha);
	-
	- itrgb.Set(prgb);
	-
	- ++itr;
	- ++itg;
	- ++itrgb;
	- }
	-
	- retval->InitializeByItk(rgb.GetPointer());
	- retval->SetVolume(rgb->GetBufferPointer());
	-
	- }
	-
	-
	- PartialVolumeAnalysisClusteringCalculator::HelperStructPerformClusteringRetval*
	- PartialVolumeAnalysisClusteringCalculator::PerformClustering(mitk::Image::ConstPointer image, const MitkHistType histogram, int classIdent, HelperStructPerformClusteringRetval precResult) const
	- {
	-
	- auto retval =
	- new HelperStructPerformClusteringRetval();
	-
	- if(precResult == nullptr)
	- {
	- retval->hist = new HistType();
	- retval->hist->InitByMitkHistogram(histogram);
	-
	- ParamsType params;
	- params.Initialize( Cluster(*(retval->hist)) );
	- ClusterResultType result = CalculateCurves(params,retval->hist->xVals);
	- Normalize(params, &result);
	-
	- retval->params = new ParamsType();
	- retval->params->Initialize(&params);
	- retval->result = new ClusterResultType(10);
	- retval->result->Initialize(&result);
	- }
	- else
	- {
	- retval->params = new ParamsType();
	- retval->params->Initialize(precResult->params);
	- retval->result = new ClusterResultType(10);
	- retval->result->Initialize(precResult->result);
	- }
	-
	- VecType totalProbs = retval->result->combiVals;
	- VecType pvProbs = retval->result->mixedVals[0];
	- VecType fiberProbs;
	- VecType nonFiberProbs;
	- VecType interestingProbs;
	- double p_fiber;
	- double p_nonFiber;
	- double p_interesting;
	-// if(retval->params->means[0]<retval->params->means[1])
	-// {
	- fiberProbs = retval->result->vals[1];
	- nonFiberProbs = retval->result->vals[0];
	- p_fiber = retval->params->ps[1];
	- p_nonFiber = retval->params->ps[0];
	-// }
	-// else
	-// {
	-// fiberProbs = retval->result->vals[0];
	-// nonFiberProbs = retval->result->vals[1];
	-// p_fiber = retval->params->ps[0];
	-// p_nonFiber = retval->params->ps[1];
	-// }
	-
	- switch(classIdent)
	- {
	- case 0:
	- interestingProbs = nonFiberProbs;
	- p_interesting = p_nonFiber;
	- break;
	- case 1:
	- interestingProbs = pvProbs;
	- p_interesting = 1 - p_fiber - p_nonFiber;
	- break;
	- case 2:
	- default:
	- interestingProbs = fiberProbs;
	- p_interesting = p_fiber;
	- break;
	- }
	-
	- double sum = histogram->GetTotalFrequency();
	-
	- // initialize two histograms for class and total probabilities
	- MitkHistType::MeasurementVectorType min(1);
	- MitkHistType::MeasurementVectorType max(1);
	- min.Fill(histogram->GetDimensionMins(0)[0]);
	- max.Fill(histogram->GetDimensionMaxs(0)[histogram->GetDimensionMaxs(0).size()-1]);
	-
	- MitkHistType::Pointer interestingHist = MitkHistType::New();
	- interestingHist->SetMeasurementVectorSize(1);
	- interestingHist->Initialize(histogram->GetSize(),min,max);
	- MitkHistType::Iterator newIt = interestingHist->Begin();
	- MitkHistType::Iterator newEnd = interestingHist->End();
	-
	- MitkHistType::Pointer totalHist = MitkHistType::New();
	- totalHist->SetMeasurementVectorSize(1);
	- totalHist->Initialize(histogram->GetSize(),min,max);
	- MitkHistType::Iterator totalIt = totalHist->Begin();
	-
	- int i=0;
	- while (newIt != newEnd)
	- {
	- newIt.SetFrequency(interestingProbs(i)*sum);
	- totalIt.SetFrequency(totalProbs(i)*sum);
	- ++newIt;
	- ++totalIt;
	- ++i;
	- }
	-
	- mitk::Image::Pointer outImage1 = mitk::Image::New();
	- mitk::Image::Pointer outImage2 = mitk::Image::New();
	-
	- HelperStructClusteringResults clusterResults;
	- clusterResults.interestingHist = interestingHist;
	- clusterResults.totalHist = totalHist;
	- clusterResults.p_interesting = p_interesting;
	-
	- AccessFixedDimensionByItk_3(
	- image.GetPointer(),
	- InternalGenerateProbabilityImage,
	- 3,
	- clusterResults,
	- outImage1, outImage2);
	-
	- retval->clusteredImage = outImage1;
	- retval->displayImage = outImage2;
	-
	- return retval;
	-
	- }
	-
	- template < typename TPixel, unsigned int VImageDimension >
	- void PartialVolumeAnalysisClusteringCalculator::InternalGenerateProbabilityImage(
	- const itk::Image< TPixel, VImageDimension > *image,
	- const HelperStructClusteringResults clusterResults,
	- mitk::Image::Pointer outImage1, mitk::Image::Pointer outImage2 ) const
	- {
	-
	- typedef itk::Image< TPixel, VImageDimension > ImageType;
	- typedef itk::Image< itk::RGBAPixel<unsigned char>, VImageDimension > DisplayImageType;
	- typedef itk::Image< float, VImageDimension > ProbImageType;
	-
	- typename ProbImageType::Pointer probimage = ProbImageType::New();
	- probimage->SetSpacing( image->GetSpacing() ); // Set the image spacing
	- probimage->SetOrigin( image->GetOrigin() ); // Set the image origin
	- probimage->SetDirection( image->GetDirection() ); // Set the image direction
	- probimage->SetRegions( image->GetLargestPossibleRegion() );
	- probimage->Allocate();
	- probimage->FillBuffer(0);
	-
	- typename DisplayImageType::Pointer displayimage = DisplayImageType::New();
	- displayimage->SetSpacing( image->GetSpacing() ); // Set the image spacing
	- displayimage->SetOrigin( image->GetOrigin() ); // Set the image origin
	- displayimage->SetDirection( image->GetDirection() ); // Set the image direction
	- displayimage->SetRegions( image->GetLargestPossibleRegion() );
	- displayimage->Allocate();
	-
	- typename DisplayImageType::PixelType rgba;
	- rgba.Set(0.0f, 0.0f, 0.0f, 0.0f);
	- displayimage->FillBuffer(rgba);
	-
	- itk::ImageRegionConstIterator<ImageType>
	- itimage(image, image->GetLargestPossibleRegion());
	-
	- itk::ImageRegionIterator<ProbImageType>
	- itprob(probimage, probimage->GetLargestPossibleRegion());
	-
	- itk::ImageRegionIterator<DisplayImageType>
	- itdisp(displayimage, displayimage->GetLargestPossibleRegion());
	-
	- itimage.GoToBegin();
	- itprob.GoToBegin();
	-
	- MitkHistType::IndexType index(1);
	- float maxp = 0;
	- while( !itimage.IsAtEnd() )
	- {
	- if(itimage.Get())
	- {
	- MitkHistType::MeasurementVectorType meas(1);
	- meas.Fill(itimage.Get());
	- double aposteriori = 0;
	- bool success = clusterResults.interestingHist->GetIndex(meas, index );
	- if(success)
	- {
	- double aprioriProb = clusterResults.interestingHist->GetFrequency(index);
	- double intensityProb = clusterResults.totalHist->GetFrequency(index);
	- double p_interesting = clusterResults.p_interesting;
	- aposteriori = p_interesting * aprioriProb / intensityProb;
	- }
	- else
	- {
	- MITK_ERROR << "index not found in histogram";
	- }
	-
	- if(aposteriori > 0.0000000000000001)
	- {
	- itprob.Set( aposteriori );
	- maxp = aposteriori > maxp ? aposteriori : maxp;
	- }
	- else
	- {
	- itprob.Set(0.0f);
	- }
	- }
	-
	- ++itimage;
	- ++itprob;
	- }
	-
	- itprob.GoToBegin();
	- itdisp.GoToBegin();
	-
	- while( !itprob.IsAtEnd() )
	- {
	- if(itprob.Get())
	- {
	- typename DisplayImageType::PixelType rgba;
	- rgba.Set(255.0f, 0.0f, 0.0f, 255.0f*(itprob.Get()/maxp));
	- itdisp.Set( rgba );
	- }
	- ++itprob;
	- ++itdisp;
	- }
	-
	- outImage1->InitializeByItk(probimage.GetPointer());
	- outImage1->SetVolume(probimage->GetBufferPointer());
	-
	- outImage2->InitializeByItk(displayimage.GetPointer());
	- outImage2->SetVolume(displayimage->GetBufferPointer());
	-
	- }
	-
	-
	- double* PartialVolumeAnalysisClusteringCalculator::PerformQuantification(
	- mitk::Image::ConstPointer image, mitk::Image::Pointer clusteredImage, mitk::Image::Pointer mask) const
	- {
	-
	- auto retval = new double[2];
	-
	- AccessFixedDimensionByItk_3(
	- image.GetPointer(),
	- InternalQuantify,
	- 3,
	- clusteredImage.GetPointer(),
	- retval, mask );
	-
	- return retval;
	-
	- }
	-
	- template < typename TPixel, unsigned int VImageDimension >
	- void PartialVolumeAnalysisClusteringCalculator::InternalQuantify(
	- const itk::Image< TPixel, VImageDimension > *image,
	- mitk::Image::Pointer clusteredImage, double* retval, mitk::Image::Pointer mask ) const
	- {
	- typedef itk::Image< TPixel, VImageDimension > ImageType;
	- typedef itk::Image< float, VImageDimension > ProbImageType;
	- typedef itk::Image< unsigned char, VImageDimension > MaskImageType;
	-
	- typedef mitk::ImageToItk<ProbImageType> CastFilterType;
	- typename CastFilterType::Pointer castFilter = CastFilterType::New();
	- castFilter->SetInput( clusteredImage );
	- castFilter->Update();
	- typename ProbImageType::Pointer clusterImage = castFilter->GetOutput();
	-
	- typename MaskImageType::Pointer itkmask = nullptr;
	- if(mask.IsNotNull())
	- {
	- typedef mitk::ImageToItk<MaskImageType> CastFilterType2;
	- typename CastFilterType2::Pointer castFilter2 = CastFilterType2::New();
	- castFilter2->SetInput( mask );
	- castFilter2->Update();
	- itkmask = castFilter2->GetOutput();
	- }
	- else
	- {
	- itkmask = MaskImageType::New();
	- itkmask->SetSpacing( clusterImage->GetSpacing() ); // Set the image spacing
	- itkmask->SetOrigin( clusterImage->GetOrigin() ); // Set the image origin
	- itkmask->SetDirection( clusterImage->GetDirection() ); // Set the image direction
	- itkmask->SetRegions( clusterImage->GetLargestPossibleRegion() );
	- itkmask->Allocate();
	- itkmask->FillBuffer(1);
	- }
	-
	- itk::ImageRegionConstIterator<ImageType>
	- itimage(image, image->GetLargestPossibleRegion());
	-
	- itk::ImageRegionConstIterator<ProbImageType>
	- itprob(clusterImage, clusterImage->GetLargestPossibleRegion());
	-
	- itk::ImageRegionConstIterator<MaskImageType>
	- itmask(itkmask, itkmask->GetLargestPossibleRegion());
	-
	- itimage.GoToBegin();
	- itprob.GoToBegin();
	- itmask.GoToBegin();
	-
	- double totalProb = 0;
	- double measurement = 0;
	- double error = 0;
	-
	- while( !itimage.IsAtEnd() && !itprob.IsAtEnd() && !itmask.IsAtEnd() )
	- {
	- double valImag = itimage.Get();
	- double valProb = itprob.Get();
	- double valMask = itmask.Get();
	-
	- typename ProbImageType::PixelType prop = valProb * valMask;
	-
	- totalProb += prop;
	- measurement += valImag * prop;
	- error += valImag * valImag * prop;
	-
	- ++itimage;
	- ++itprob;
	- ++itmask;
	- }
	-
	- measurement = measurement / totalProb;
	- error = error / totalProb;
	- retval[0] = measurement;
	- retval[1] = sqrt( error - measurement*measurement );
	-
	- }
	-
	-
	- mitk::Image::Pointer PartialVolumeAnalysisClusteringCalculator::CaculateAngularErrorImage(
	- mitk::Image::Pointer comp1, mitk::Image::Pointer comp2, mitk::Image::Pointer probImg) const
	- {
	-
	- // cast input images to itk
	- typedef itk::Image<float, 3> ImageType;
	- typedef mitk::ImageToItk<ImageType> CastType;
	- CastType::Pointer caster = CastType::New();
	- caster->SetInput(comp1);
	- caster->Update();
	- ImageType::Pointer comp1Image = caster->GetOutput();
	-
	- caster = CastType::New();
	- caster->SetInput(comp2);
	- caster->Update();
	- ImageType::Pointer comp2Image = caster->GetOutput();
	-
	- caster = CastType::New();
	- caster->SetInput(probImg);
	- caster->Update();
	- ImageType::Pointer probImage = caster->GetOutput();
	-
	- // figure out maximum probability for fiber class
	- float maxProb = 0;
	- itk::ImageRegionConstIterator<ImageType>
	- itprob(probImage, probImage->GetLargestPossibleRegion());
	- itprob.GoToBegin();
	- while( !itprob.IsAtEnd() )
	- {
	- maxProb = itprob.Get() > maxProb ? itprob.Get() : maxProb;
	- ++itprob;
	- }
	-
	- // generate a list sample of angles at positions
	- // where the fiber-prob is higher than .2*maxprob
	- typedef float MeasurementType;
	- const unsigned int MeasurementVectorLength = 2;
	- typedef itk::Vector< MeasurementType , MeasurementVectorLength >
	- MeasurementVectorType;
	- typedef itk::Statistics::ListSample< MeasurementVectorType > ListSampleType;
	- ListSampleType::Pointer listSample = ListSampleType::New();
	- listSample->SetMeasurementVectorSize( MeasurementVectorLength );
	-
	- itk::ImageRegionIterator<ImageType>
	- it1(comp1Image, comp1Image->GetLargestPossibleRegion());
	- itk::ImageRegionIterator<ImageType>
	- it2(comp2Image, comp2Image->GetLargestPossibleRegion());
	-
	- it1.GoToBegin();
	- it2.GoToBegin();
	- itprob.GoToBegin();
	-
	- while( !itprob.IsAtEnd() )
	- {
	- if(itprob.Get() > 0.2 * maxProb)
	- {
	- MeasurementVectorType mv;
	- mv[0] = ( MeasurementType ) it1.Get();
	- mv[1] = ( MeasurementType ) it2.Get();
	- listSample->PushBack(mv);
	- }
	- ++it1;
	- ++it2;
	- ++itprob;
	- }
	-
	- // generate a histogram from the list sample
	- typedef float HistogramMeasurementType;
	- typedef itk::Statistics::Histogram< HistogramMeasurementType, itk::Statistics::DenseFrequencyContainer2 > HistogramType;
	- typedef itk::Statistics::SampleToHistogramFilter< ListSampleType, HistogramType > GeneratorType;
	- GeneratorType::Pointer generator = GeneratorType::New();
	-
	- GeneratorType::HistogramType::SizeType size(2);
	- size.Fill(30);
	- generator->SetHistogramSize( size );
	-
	- generator->SetInput( listSample );
	- generator->SetMarginalScale( 10.0 );
	-
	- generator->Update();
	-
	- // look for frequency mode in the histogram
	- GeneratorType::HistogramType::ConstPointer histogram = generator->GetOutput();
	- GeneratorType::HistogramType::ConstIterator iter = histogram->Begin();
	- float maxFreq = 0;
	- MeasurementVectorType maxValue;
	- maxValue.Fill(0);
	- while ( iter != histogram->End() )
	- {
	- if(iter.GetFrequency() > maxFreq)
	- {
	- maxFreq = iter.GetFrequency();
	- maxValue[0] = iter.GetMeasurementVector()[0];
	- maxValue[1] = iter.GetMeasurementVector()[1];
	- }
	- ++iter;
	- }
	-
	- // generate return image that contains the angular
	- // error of the voxels to the histogram max measurement
	- ImageType::Pointer returnImage = ImageType::New();
	- returnImage->SetSpacing( comp1Image->GetSpacing() ); // Set the image spacing
	- returnImage->SetOrigin( comp1Image->GetOrigin() ); // Set the image origin
	- returnImage->SetDirection( comp1Image->GetDirection() ); // Set the image direction
	- returnImage->SetRegions( comp1Image->GetLargestPossibleRegion() );
	- returnImage->Allocate();
	-
	- itk::ImageRegionConstIterator<ImageType>
	- cit1(comp1Image, comp1Image->GetLargestPossibleRegion());
	-
	- itk::ImageRegionConstIterator<ImageType>
	- cit2(comp2Image, comp2Image->GetLargestPossibleRegion());
	-
	- itk::ImageRegionIterator<ImageType>
	- itout(returnImage, returnImage->GetLargestPossibleRegion());
	-
	- cit1.GoToBegin();
	- cit2.GoToBegin();
	- itout.GoToBegin();
	-
	- vnl_vector<float> v(3);
	- v[0] = cos( maxValue[0] ) * sin( maxValue[1] );
	- v[1] = sin( maxValue[0] ) * sin( maxValue[1] );
	- v[2] = cos( maxValue[1] );
	-// MITK_INFO << "max vector: " << v;
	- while( !cit1.IsAtEnd() )
	- {
	- vnl_vector<float> v1(3);
	- v1[0] = cos( cit1.Get() ) * sin( cit2.Get() );
	- v1[1] = sin( cit1.Get() ) * sin( cit2.Get() );
	- v1[2] = cos( cit2.Get() );
	-
	- itout.Set(fabs(angle(v,v1)));
	-// MITK_INFO << "ang_error " << v1 << ": " << fabs(angle(v,v1));
	-
	- ++cit1;
	- ++cit2;
	- ++itout;
	- }
	-
	- mitk::Image::Pointer retval = mitk::Image::New();
	- retval->InitializeByItk(returnImage.GetPointer());
	- retval->SetVolume(returnImage->GetBufferPointer());
	- return retval;
	- }
	-
	- PartialVolumeAnalysisClusteringCalculator::HelperStructPerformRGBClusteringRetval*
	- PartialVolumeAnalysisClusteringCalculator::PerformRGBQuantiles(mitk::Image::ConstPointer image, const MitkHistType *histogram, double p1, double p2) const
	- {
	-
	- auto rgbChannels = new HelperStructRGBChannels();
	-
	- HelperStructPerformClusteringRetval *resultr = PerformQuantiles(image, histogram, p2, 999999999.0 );
	- rgbChannels->r = resultr->clusteredImage;
	-
	- HelperStructPerformClusteringRetval *resultg = PerformQuantiles(image, histogram, -999999999.0, p1 );
	- rgbChannels->g = resultg->clusteredImage;
	-
	- HelperStructPerformClusteringRetval *resultb = PerformQuantiles(image, histogram, p1, p2 );
	- rgbChannels->b = resultb->clusteredImage;
	-
	- mitk::Image::Pointer outImage = mitk::Image::New();
	-
	- switch(rgbChannels->r->GetDimension())
	- {
	- case 2:
	- InternalGenerateRGB<2>(rgbChannels, outImage);
	- break;
	- case 3:
	- InternalGenerateRGB<3>(rgbChannels, outImage);
	- break;
	- case 4:
	- InternalGenerateRGB<4>(rgbChannels, outImage);
	- break;
	- default:
	- InternalGenerateRGB<3>(rgbChannels, outImage);
	- }
	-
	- auto retval
	- = new HelperStructPerformRGBClusteringRetval();
	- retval->rgbChannels = rgbChannels;
	- retval->rgb = outImage;
	- retval->params = resultr->params;
	- retval->result = resultr->result;
	- retval->hist = resultr->hist;
	-
	- delete resultr;
	- delete resultg;
	-
	- return retval;
	-
	- }
	-
	- PartialVolumeAnalysisClusteringCalculator::HelperStructPerformClusteringRetval*
	- PartialVolumeAnalysisClusteringCalculator::PerformQuantiles(mitk::Image::ConstPointer image, const MitkHistType *histogram, double p1, double p2 ) const
	- {
	-
	- auto retval =
	- new HelperStructPerformClusteringRetval();
	-
	- retval->hist = new HistType();
	- retval->hist->InitByMitkHistogram(histogram);
	-
	- auto q = new double[2];
	- q[0] = histogram->Quantile(0, p1);
	- q[1] = histogram->Quantile(0, p2);
	-
	- mitk::Image::Pointer outImage1 = mitk::Image::New();
	- mitk::Image::Pointer outImage2 = mitk::Image::New();
	-
	- AccessFixedDimensionByItk_3(
	- image.GetPointer(),
	- InternalGenerateQuantileImage,
	- 3, q,
	- outImage1, outImage2);
	-
	- retval->clusteredImage = outImage1;
	- retval->displayImage = outImage2;
	-
	- delete[] q;
	- return retval;
	-
	- }
	-
	- template < typename TPixel, unsigned int VImageDimension >
	- void PartialVolumeAnalysisClusteringCalculator::InternalGenerateQuantileImage(
	- const itk::Image< TPixel, VImageDimension > image, double q,
	- mitk::Image::Pointer outImage1, mitk::Image::Pointer outImage2 ) const
	- {
	-
	- typedef itk::Image< TPixel, VImageDimension > ImageType;
	- typedef itk::Image< itk::RGBAPixel<unsigned char>, VImageDimension > DisplayImageType;
	- typedef itk::Image< float, VImageDimension > ProbImageType;
	-
	- typename ProbImageType::Pointer probimage = ProbImageType::New();
	- probimage->SetSpacing( image->GetSpacing() ); // Set the image spacing
	- probimage->SetOrigin( image->GetOrigin() ); // Set the image origin
	- probimage->SetDirection( image->GetDirection() ); // Set the image direction
	- probimage->SetRegions( image->GetLargestPossibleRegion() );
	- probimage->Allocate();
	- probimage->FillBuffer(0);
	-
	- typename DisplayImageType::Pointer displayimage = DisplayImageType::New();
	- displayimage->SetSpacing( image->GetSpacing() ); // Set the image spacing
	- displayimage->SetOrigin( image->GetOrigin() ); // Set the image origin
	- displayimage->SetDirection( image->GetDirection() ); // Set the image direction
	- displayimage->SetRegions( image->GetLargestPossibleRegion() );
	- displayimage->Allocate();
	-
	- typename DisplayImageType::PixelType rgba;
	- rgba.Set(0.0f, 0.0f, 0.0f, 0.0f);
	- displayimage->FillBuffer(rgba);
	-
	- itk::ImageRegionConstIterator<ImageType>
	- itimage(image, image->GetLargestPossibleRegion());
	-
	- itk::ImageRegionIterator<ProbImageType>
	- itprob(probimage, probimage->GetLargestPossibleRegion());
	-
	- itk::ImageRegionIterator<DisplayImageType>
	- itdisp(displayimage, displayimage->GetLargestPossibleRegion());
	-
	- itimage.GoToBegin();
	- itprob.GoToBegin();
	-
	- while( !itimage.IsAtEnd() )
	- {
	- if(itimage.Get() > q[0] && itimage.Get() < q[1])
	- {
	- itprob.Set(1.0f);
	- }
	-
	- ++itimage;
	- ++itprob;
	- }
	-
	- itprob.GoToBegin();
	- itdisp.GoToBegin();
	-
	- while( !itprob.IsAtEnd() )
	- {
	- if(itprob.Get())
	- {
	- typename DisplayImageType::PixelType rgba;
	- rgba.Set(255.0f, 0.0f, 0.0f, 255.0f);
	- itdisp.Set( rgba );
	- }
	- ++itprob;
	- ++itdisp;
	- }
	-
	- outImage1->InitializeByItk(probimage.GetPointer());
	- outImage1->SetVolume(probimage->GetBufferPointer());
	-
	- outImage2->InitializeByItk(displayimage.GetPointer());
	- outImage2->SetVolume(displayimage->GetBufferPointer());
	-
	- }
	-
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.cpp b/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.cpp
	deleted file mode 100644
	index 1c4de5612d..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.cpp
	+++ /dev/null
	@@ -1,1270 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#include "mitkPartialVolumeAnalysisHistogramCalculator.h"
	-#include "mitkImageAccessByItk.h"
	-#include "mitkExtractImageFilter.h"
	-
	-#include <itkScalarImageToHistogramGenerator.h>
	-
	-#include <itkStatisticsImageFilter.h>
	-#include <itkLabelStatisticsImageFilter.h>
	-#include <itkBSplineUpsampleImageFilter.h>
	-#include <itkBSplineResampleImageFilterBase.h>
	-#include "itkResampleImageFilter.h"
	-#include "itkGaussianInterpolateImageFunction.h"
	-
	-#include <itkCastImageFilter.h>
	-#include <itkImageFileWriter.h>
	-#include <itkVTKImageImport.h>
	-#include <itkVTKImageExport.h>
	-
	-
	-#include <vtkPoints.h>
	-#include <vtkCellArray.h>
	-#include <vtkPolyData.h>
	-#include <vtkLinearExtrusionFilter.h>
	-#include <vtkPolyDataToImageStencil.h>
	-#include <vtkImageStencil.h>
	-#include <vtkImageImport.h>
	-#include <vtkImageExport.h>
	-#include <vtkImageData.h>
	-
	-#include <vtkMetaImageWriter.h>
	-
	-#include <exception>
	-
	-#include "itkGaussianInterpolateImageFunction.h"
	-#include "itkBSplineInterpolateImageFunction.h"
	-#include "itkNearestNeighborInterpolateImageFunction.h"
	-
	-#include "itkImageMaskSpatialObject.h"
	-#include "itkRegionOfInterestImageFilter.h"
	-#include "itkListSample.h"
	-
	-#include "mitkAbstractTransformGeometry.h"
	-
	-#include <iostream>
	-#include <sstream>
	-
	-namespace mitk
	-{
	-
	- PartialVolumeAnalysisHistogramCalculator::PartialVolumeAnalysisHistogramCalculator()
	- : m_MaskingMode( MASKING_MODE_NONE ),
	- m_MaskingModeChanged( false ),
	- m_NumberOfBins(256),
	- m_UpsamplingFactor(1),
	- m_GaussianSigma(0),
	- m_ForceUpdate(false),
	- m_PlanarFigureThickness(0)
	- {
	- m_EmptyHistogram = HistogramType::New();
	- m_EmptyHistogram->SetMeasurementVectorSize(1);
	- HistogramType::SizeType histogramSize(1);
	- histogramSize.Fill( 256 );
	- m_EmptyHistogram->Initialize( histogramSize );
	-
	- m_EmptyStatistics.Reset();
	- }
	-
	-
	- PartialVolumeAnalysisHistogramCalculator::~PartialVolumeAnalysisHistogramCalculator()
	- {
	- }
	-
	-
	- void PartialVolumeAnalysisHistogramCalculator::SetImage( const mitk::Image *image )
	- {
	- if ( m_Image != image )
	- {
	- m_Image = image;
	- this->Modified();
	-
	- m_ImageStatisticsTimeStamp.Modified();
	- m_ImageStatisticsCalculationTriggerBool = true;
	- }
	- }
	-
	- void PartialVolumeAnalysisHistogramCalculator::AddAdditionalResamplingImage( const mitk::Image *image )
	- {
	- m_AdditionalResamplingImages.push_back(image);
	- this->Modified();
	- m_ImageStatisticsTimeStamp.Modified();
	- m_ImageStatisticsCalculationTriggerBool = true;
	- }
	-
	- void PartialVolumeAnalysisHistogramCalculator::SetModified( )
	- {
	- this->Modified();
	- m_ImageStatisticsTimeStamp.Modified();
	- m_ImageStatisticsCalculationTriggerBool = true;
	- m_MaskedImageStatisticsTimeStamp.Modified();
	- m_MaskedImageStatisticsCalculationTriggerBool = true;
	- m_PlanarFigureStatisticsTimeStamp.Modified();
	- m_PlanarFigureStatisticsCalculationTriggerBool = true;
	- }
	-
	- void PartialVolumeAnalysisHistogramCalculator::SetImageMask( const mitk::Image *imageMask )
	- {
	- if ( m_Image.IsNull() )
	- {
	- itkExceptionMacro( << "Image needs to be set first!" );
	- }
	-
	- if ( m_Image->GetTimeSteps() != imageMask->GetTimeSteps() )
	- {
	- itkExceptionMacro( << "Image and image mask need to have equal number of time steps!" );
	- }
	-
	- if ( m_ImageMask != imageMask )
	- {
	- m_ImageMask = imageMask;
	- this->Modified();
	-
	- m_MaskedImageStatisticsTimeStamp.Modified();
	- m_MaskedImageStatisticsCalculationTriggerBool = true;
	- }
	- }
	-
	-
	- void PartialVolumeAnalysisHistogramCalculator::SetPlanarFigure( const mitk::PlanarFigure *planarFigure )
	- {
	- if ( m_Image.IsNull() )
	- {
	- itkExceptionMacro( << "Image needs to be set first!" );
	- }
	-
	- if ( m_PlanarFigure != planarFigure )
	- {
	- m_PlanarFigure = planarFigure;
	- this->Modified();
	-
	- m_PlanarFigureStatisticsTimeStamp.Modified();
	- m_PlanarFigureStatisticsCalculationTriggerBool = true;
	- }
	- }
	-
	-
	- void PartialVolumeAnalysisHistogramCalculator::SetMaskingMode( unsigned int mode )
	- {
	- if ( m_MaskingMode != mode )
	- {
	- m_MaskingMode = mode;
	- m_MaskingModeChanged = true;
	- this->Modified();
	- }
	- }
	-
	-
	- void PartialVolumeAnalysisHistogramCalculator::SetMaskingModeToNone()
	- {
	- if ( m_MaskingMode != MASKING_MODE_NONE )
	- {
	- m_MaskingMode = MASKING_MODE_NONE;
	- m_MaskingModeChanged = true;
	- this->Modified();
	- }
	- }
	-
	-
	- void PartialVolumeAnalysisHistogramCalculator::SetMaskingModeToImage()
	- {
	- if ( m_MaskingMode != MASKING_MODE_IMAGE )
	- {
	- m_MaskingMode = MASKING_MODE_IMAGE;
	- m_MaskingModeChanged = true;
	- this->Modified();
	- }
	- }
	-
	-
	- void PartialVolumeAnalysisHistogramCalculator::SetMaskingModeToPlanarFigure()
	- {
	- if ( m_MaskingMode != MASKING_MODE_PLANARFIGURE )
	- {
	- m_MaskingMode = MASKING_MODE_PLANARFIGURE;
	- m_MaskingModeChanged = true;
	- this->Modified();
	- }
	- }
	-
	-
	-
	- bool PartialVolumeAnalysisHistogramCalculator::ComputeStatistics()
	- {
	-
	- MITK_DEBUG << "ComputeStatistics() start";
	-
	- if ( m_Image.IsNull() )
	- {
	- itkExceptionMacro( << "Image not set!" );
	- }
	-
	- if ( m_Image->GetReferenceCount() == 1 )
	- {
	- MITK_DEBUG << "No Stats calculated; no one else holds a reference on it";
	- return false;
	- }
	-
	- // If a mask was set but we are the only ones to still hold a reference on
	- // it, delete it.
	- if ( m_ImageMask.IsNotNull() && (m_ImageMask->GetReferenceCount() == 1) )
	- {
	- m_ImageMask = nullptr;
	- }
	-
	-
	- // Check if statistics is already up-to-date
	- unsigned long imageMTime = m_ImageStatisticsTimeStamp.GetMTime();
	- unsigned long maskedImageMTime = m_MaskedImageStatisticsTimeStamp.GetMTime();
	- unsigned long planarFigureMTime = m_PlanarFigureStatisticsTimeStamp.GetMTime();
	-
	- bool imageStatisticsCalculationTrigger = m_ImageStatisticsCalculationTriggerBool;
	- bool maskedImageStatisticsCalculationTrigger = m_MaskedImageStatisticsCalculationTriggerBool;
	- bool planarFigureStatisticsCalculationTrigger = m_PlanarFigureStatisticsCalculationTriggerBool;
	-
	- if ( /prevent calculation without mask/!m_ForceUpdate &&( m_MaskingMode == MASKING_MODE_NONE \|\| (
	- ((m_MaskingMode != MASKING_MODE_NONE) \|\| (imageMTime > m_Image->GetMTime() && !imageStatisticsCalculationTrigger))
	- && ((m_MaskingMode != MASKING_MODE_IMAGE) \|\| (m_ImageMask.IsNotNull() && maskedImageMTime > m_ImageMask->GetMTime() && !maskedImageStatisticsCalculationTrigger))
	- && ((m_MaskingMode != MASKING_MODE_PLANARFIGURE) \|\| (m_PlanarFigure.IsNotNull() && planarFigureMTime > m_PlanarFigure->GetMTime() && !planarFigureStatisticsCalculationTrigger)) ) ) )
	- {
	- MITK_DEBUG << "Returning, statistics already up to date!";
	- if ( m_MaskingModeChanged )
	- {
	- m_MaskingModeChanged = false;
	- return true;
	- }
	- else
	- {
	- return false;
	- }
	- }
	-
	- // Reset state changed flag
	- m_MaskingModeChanged = false;
	-
	-
	- // Depending on masking mode, extract and/or generate the required image
	- // and mask data from the user input
	- this->ExtractImageAndMask( );
	-
	-
	- Statistics *statistics;
	- HistogramType::ConstPointer *histogram;
	- switch ( m_MaskingMode )
	- {
	- case MASKING_MODE_NONE:
	- default:
	- statistics = &m_ImageStatistics;
	- histogram = &m_ImageHistogram;
	-
	- m_ImageStatisticsTimeStamp.Modified();
	- m_ImageStatisticsCalculationTriggerBool = false;
	- break;
	-
	- case MASKING_MODE_IMAGE:
	- statistics = &m_MaskedImageStatistics;
	- histogram = &m_MaskedImageHistogram;
	-
	- m_MaskedImageStatisticsTimeStamp.Modified();
	- m_MaskedImageStatisticsCalculationTriggerBool = false;
	- break;
	-
	- case MASKING_MODE_PLANARFIGURE:
	- statistics = &m_PlanarFigureStatistics;
	- histogram = &m_PlanarFigureHistogram;
	-
	- m_PlanarFigureStatisticsTimeStamp.Modified();
	- m_PlanarFigureStatisticsCalculationTriggerBool = false;
	- break;
	- }
	-
	- // Calculate statistics and histogram(s)
	- if ( m_InternalImage->GetDimension() == 3 )
	- {
	- if ( m_MaskingMode == MASKING_MODE_NONE )
	- {
	- // Reset state changed flag
	- AccessFixedDimensionByItk_2(
	- m_InternalImage,
	- InternalCalculateStatisticsUnmasked,
	- 3,
	- *statistics,
	- histogram );
	- }
	- else
	- {
	- AccessFixedDimensionByItk_3(
	- m_InternalImage,
	- InternalCalculateStatisticsMasked,
	- 3,
	- m_InternalImageMask3D.GetPointer(),
	- *statistics,
	- histogram );
	- }
	- }
	- else if ( m_InternalImage->GetDimension() == 2 )
	- {
	- if ( m_MaskingMode == MASKING_MODE_NONE )
	- {
	- AccessFixedDimensionByItk_2(
	- m_InternalImage,
	- InternalCalculateStatisticsUnmasked,
	- 2,
	- *statistics,
	- histogram );
	- }
	- else
	- {
	- AccessFixedDimensionByItk_3(
	- m_InternalImage,
	- InternalCalculateStatisticsMasked,
	- 2,
	- m_InternalImageMask2D.GetPointer(),
	- *statistics,
	- histogram );
	- }
	- }
	- else
	- {
	- MITK_ERROR << "ImageStatistics: Image dimension not supported!";
	- }
	-
	- // Release unused image smart pointers to free memory
	- // m_InternalImage = mitk::Image::Pointer();
	- m_InternalImageMask3D = MaskImage3DType::Pointer();
	- m_InternalImageMask2D = MaskImage2DType::Pointer();
	- return true;
	- }
	-
	-
	- const PartialVolumeAnalysisHistogramCalculator::HistogramType *
	- PartialVolumeAnalysisHistogramCalculator::GetHistogram( ) const
	- {
	- if ( m_Image.IsNull() )
	- {
	- return nullptr;
	- }
	-
	- switch ( m_MaskingMode )
	- {
	- case MASKING_MODE_NONE:
	- default:
	- return m_ImageHistogram;
	-
	- case MASKING_MODE_IMAGE:
	- return m_MaskedImageHistogram;
	-
	- case MASKING_MODE_PLANARFIGURE:
	- return m_PlanarFigureHistogram;
	- }
	- }
	-
	-
	- const PartialVolumeAnalysisHistogramCalculator::Statistics &
	- PartialVolumeAnalysisHistogramCalculator::GetStatistics( ) const
	- {
	- if ( m_Image.IsNull() )
	- {
	- return m_EmptyStatistics;
	- }
	-
	- switch ( m_MaskingMode )
	- {
	- case MASKING_MODE_NONE:
	- default:
	- return m_ImageStatistics;
	-
	- case MASKING_MODE_IMAGE:
	- return m_MaskedImageStatistics;
	-
	- case MASKING_MODE_PLANARFIGURE:
	- return m_PlanarFigureStatistics;
	- }
	- }
	-
	-
	- void PartialVolumeAnalysisHistogramCalculator::ExtractImageAndMask( )
	- {
	-
	- MITK_DEBUG << "ExtractImageAndMask( ) start";
	-
	- if ( m_Image.IsNull() )
	- {
	- throw std::runtime_error( "Error: image empty!" );
	- }
	-
	- mitk::Image timeSliceImage = const_cast<mitk::Image>(m_Image.GetPointer());//imageTimeSelector->GetOutput();
	-
	- switch ( m_MaskingMode )
	- {
	- case MASKING_MODE_NONE:
	- {
	- m_InternalImage = timeSliceImage;
	- int s = m_AdditionalResamplingImages.size();
	- m_InternalAdditionalResamplingImages.resize(s);
	- for(int i=0; i<s; i++)
	- {
	- m_InternalAdditionalResamplingImages[i] = const_cast<mitk::Image*>(m_AdditionalResamplingImages[i].GetPointer());
	- }
	- m_InternalImageMask2D = nullptr;
	- m_InternalImageMask3D = nullptr;
	- break;
	- }
	-
	- case MASKING_MODE_IMAGE:
	- {
	- if ( m_ImageMask.IsNotNull() && (m_ImageMask->GetReferenceCount() > 1) )
	- {
	- ImageTimeSelector::Pointer maskedImageTimeSelector = ImageTimeSelector::New();
	- maskedImageTimeSelector->SetInput( m_ImageMask );
	- maskedImageTimeSelector->SetTimeNr( 0 );
	- maskedImageTimeSelector->UpdateLargestPossibleRegion();
	- mitk::Image *timeSliceMaskedImage = maskedImageTimeSelector->GetOutput();
	-
	- InternalMaskImage(timeSliceMaskedImage);
	-
	- if(m_UpsamplingFactor != 1)
	- {
	- InternalResampleImage(m_InternalImageMask3D);
	- }
	-
	- AccessFixedDimensionByItk_1(
	- timeSliceImage,
	- InternalResampleImageFromMask, 3, -1 );
	-
	- int s = m_AdditionalResamplingImages.size();
	- m_InternalAdditionalResamplingImages.resize(s);
	- for(int i=0; i<s; i++)
	- {
	- AccessFixedDimensionByItk_1(
	- m_AdditionalResamplingImages[i],
	- InternalResampleImageFromMask, 3, i );
	- }
	-
	- }
	- else
	- {
	- throw std::runtime_error( "Error: image mask empty!" );
	- }
	- break;
	- }
	-
	- case MASKING_MODE_PLANARFIGURE:
	- {
	- m_InternalImageMask2D = nullptr;
	-
	- if ( m_PlanarFigure.IsNull() )
	- {
	- throw std::runtime_error( "Error: planar figure empty!" );
	- }
	- if ( !m_PlanarFigure->IsClosed() )
	- {
	- throw std::runtime_error( "Masking not possible for non-closed figures" );
	- }
	-
	- const BaseGeometry *imageGeometry = timeSliceImage->GetUpdatedGeometry();
	- if ( imageGeometry == nullptr )
	- {
	- throw std::runtime_error( "Image geometry invalid!" );
	- }
	-
	- const PlaneGeometry *planarFigureGeometry2D = m_PlanarFigure->GetPlaneGeometry();
	- if ( planarFigureGeometry2D == nullptr )
	- {
	- throw std::runtime_error( "Planar-Figure not yet initialized!" );
	- }
	-
	- const PlaneGeometry *planarFigureGeometry =
	- dynamic_cast< const PlaneGeometry * >( planarFigureGeometry2D );
	- const AbstractTransformGeometry *abstrTransfGeometry =
	- dynamic_cast< const AbstractTransformGeometry * >( planarFigureGeometry2D );
	-
	- if ( !planarFigureGeometry \|\| abstrTransfGeometry )
	- {
	- throw std::runtime_error( "Only PlaneGeometry supported." );
	- }
	-
	-
	-// unsigned int axis = 2;
	-// unsigned int slice = 0;
	-
	- AccessFixedDimensionByItk_3(
	- timeSliceImage,
	- InternalReorientImagePlane, 3,
	- timeSliceImage->GetGeometry(),
	- m_PlanarFigure->GetGeometry(), -1 );
	-
	- AccessFixedDimensionByItk_1(
	- m_InternalImage,
	- InternalCalculateMaskFromPlanarFigure,
	- 3, 2 );
	-
	- int s = m_AdditionalResamplingImages.size();
	- for(int i=0; i<s; i++)
	- {
	- AccessFixedDimensionByItk_3(
	- m_AdditionalResamplingImages[i],
	- InternalReorientImagePlane, 3,
	- timeSliceImage->GetGeometry(),
	- m_PlanarFigure->GetGeometry(), i );
	-
	- AccessFixedDimensionByItk_1(
	- m_InternalAdditionalResamplingImages[i],
	- InternalCropAdditionalImage, 3, i );
	- }
	- }
	- }
	-
	- }
	-
	-
	- bool PartialVolumeAnalysisHistogramCalculator::GetPrincipalAxis(
	- const Geometry3D *geometry, Vector3D vector,
	- unsigned int &axis )
	- {
	- vector.Normalize();
	- for ( unsigned int i = 0; i < 3; ++i )
	- {
	- Vector3D axisVector = geometry->GetAxisVector( i );
	- axisVector.Normalize();
	-
	- if ( fabs( fabs( axisVector * vector ) - 1.0) < mitk::eps )
	- {
	- axis = i;
	- return true;
	- }
	- }
	-
	- return false;
	- }
	-
	- void PartialVolumeAnalysisHistogramCalculator::InternalMaskImage(
	- mitk::Image *image )
	- {
	-
	- typedef itk::ImageMaskSpatialObject<3> ImageMaskSpatialObject;
	- typedef itk::Image< unsigned char, 3 > ImageType;
	-
	- typedef mitk::ImageToItk<ImageType> CastType;
	- CastType::Pointer caster = CastType::New();
	- caster->SetInput(image);
	- caster->Update();
	-
	- ImageMaskSpatialObject::Pointer maskSO = ImageMaskSpatialObject::New();
	- maskSO->SetImage ( caster->GetOutput() );
	- m_InternalMask3D =
	- maskSO->GetAxisAlignedBoundingBoxRegion();
	-
	- // check if bounding box is empty, if so set it to 1,1,1
	- // to prevent empty mask image
	- if (m_InternalMask3D.GetSize()[0] == 0 )
	- {
	- m_InternalMask3D.SetSize(0,1);
	- m_InternalMask3D.SetSize(1,1);
	- m_InternalMask3D.SetSize(2,1);
	- }
	- MITK_DEBUG << "Bounding Box Region: " << m_InternalMask3D;
	-
	- // crop the mask image to the BoundingBoxRegion extracted via the spatial masking object
	- typedef itk::RegionOfInterestImageFilter< ImageType, MaskImage3DType > ROIFilterType;
	- ROIFilterType::Pointer roi = ROIFilterType::New();
	- roi->SetRegionOfInterest(m_InternalMask3D);
	- roi->SetInput(caster->GetOutput());
	- roi->Update();
	-
	- m_InternalImageMask3D = roi->GetOutput();
	-
	- MITK_DEBUG << "Created m_InternalImageMask3D";
	-
	- }
	-
	-
	- template < typename TPixel, unsigned int VImageDimension >
	- void PartialVolumeAnalysisHistogramCalculator::InternalReorientImagePlane(
	- const itk::Image< TPixel, VImageDimension > *image,
	- mitk::BaseGeometry* , mitk::BaseGeometry* planegeo3D, int additionalIndex )
	- {
	-
	- MITK_DEBUG << "InternalReorientImagePlane() start";
	-
	- typedef itk::Image< TPixel, VImageDimension > ImageType;
	- typedef itk::Image< float, VImageDimension > FloatImageType;
	-
	- typedef itk::ResampleImageFilter<ImageType, FloatImageType, double> ResamplerType;
	- typename ResamplerType::Pointer resampler = ResamplerType::New();
	-
	- mitk::PlaneGeometry* planegeo = dynamic_cast<mitk::PlaneGeometry*>(planegeo3D);
	- if ( !planegeo )
	- {
	- throw std::runtime_error( "Unexpected null pointer returned for pointer to PlaneGeometry." );
	- }
	- else
	- {
	- mitk::AbstractTransformGeometry* abstrGeo = dynamic_cast<mitk::AbstractTransformGeometry*>(planegeo3D);
	- if ( abstrGeo )
	- {
	- throw std::runtime_error( "Unexpected pointer to AbstractTransformGeometry returned." );
	- }
	- }
	-
	- float upsamp = m_UpsamplingFactor;
	- float gausssigma = m_GaussianSigma;
	-
	- // Spacing
	- typename ResamplerType::SpacingType spacing = planegeo->GetSpacing();
	- spacing[0] = image->GetSpacing()[0] / upsamp;
	- spacing[1] = image->GetSpacing()[1] / upsamp;
	- spacing[2] = image->GetSpacing()[2];
	- if(m_PlanarFigureThickness)
	- {
	- spacing[2] = image->GetSpacing()[2] / upsamp;
	- }
	- resampler->SetOutputSpacing( spacing );
	-
	- // Size
	- typename ResamplerType::SizeType size;
	- size[0] = planegeo->GetExtentInMM(0) / spacing[0];
	- size[1] = planegeo->GetExtentInMM(1) / spacing[1];
	- size[2] = 1+2m_PlanarFigureThickness; // klaus add +2m_PlanarFigureThickness
	- MITK_DEBUG << "setting size2:="<<size[2] << " (before " << 1 << ")";
	- resampler->SetSize( size );
	-
	- // Origin
	- typename mitk::Point3D orig = planegeo->GetOrigin();
	- typename mitk::Point3D corrorig;
	- planegeo3D->WorldToIndex(orig,corrorig);
	- corrorig[0] += 0.5/upsamp;
	- corrorig[1] += 0.5/upsamp;
	- if(m_PlanarFigureThickness)
	- {
	- float thickyyy = m_PlanarFigureThickness;
	- thickyyy/=upsamp;
	- corrorig[2] -= thickyyy; // klaus add -= (float)m_PlanarFigureThickness/upsamp statt += 0
	- }
	- planegeo3D->IndexToWorld(corrorig,corrorig);
	- resampler->SetOutputOrigin(corrorig );
	-
	- // Direction
	- typename ResamplerType::DirectionType direction;
	- typename mitk::AffineTransform3D::MatrixType matrix = planegeo->GetIndexToWorldTransform()->GetMatrix();
	- for(unsigned int c = 0; c < matrix.ColumnDimensions; ++c)
	- {
	- double sum = 0;
	- for(unsigned int r = 0 ; r<matrix.RowDimensions; r++)
	- {
	- sum += matrix(r,c)*matrix(r,c);
	- }
	- for(unsigned int r = 0 ; r<matrix.RowDimensions; ++r)
	- {
	- direction(r,c) = matrix(r,c)/sqrt(sum);
	- }
	- }
	- resampler->SetOutputDirection( direction );
	-
	- // Gaussian interpolation
	- if(gausssigma != 0)
	- {
	- double sigma[3];
	- for( unsigned int d = 0; d < 3; d++ )
	- {
	- sigma[d] = gausssigma * image->GetSpacing()[d];
	- }
	- double alpha = 2.0;
	-
	- typedef itk::GaussianInterpolateImageFunction<ImageType, double>
	- GaussianInterpolatorType;
	-
	- typename GaussianInterpolatorType::Pointer interpolator
	- = GaussianInterpolatorType::New();
	-
	- interpolator->SetInputImage( image );
	- interpolator->SetParameters( sigma, alpha );
	-
	- resampler->SetInterpolator( interpolator );
	- }
	- else
	- {
	- // typedef typename itk::BSplineInterpolateImageFunction<ImageType, double>
	- // InterpolatorType;
	- typedef typename itk::LinearInterpolateImageFunction<ImageType, double> InterpolatorType;
	-
	- typename InterpolatorType::Pointer interpolator
	- = InterpolatorType::New();
	-
	- interpolator->SetInputImage( image );
	-
	- resampler->SetInterpolator( interpolator );
	-
	- }
	-
	- // Other resampling options
	- resampler->SetInput( image );
	- resampler->SetDefaultPixelValue(0);
	-
	- MITK_DEBUG << "Resampling requested image plane ... ";
	- resampler->Update();
	- MITK_DEBUG << " ... done";
	-
	- if(additionalIndex < 0)
	- {
	- this->m_InternalImage = mitk::Image::New();
	- this->m_InternalImage->InitializeByItk( resampler->GetOutput() );
	- this->m_InternalImage->SetVolume( resampler->GetOutput()->GetBufferPointer() );
	- }
	- else
	- {
	- unsigned int myIndex = additionalIndex;
	- this->m_InternalAdditionalResamplingImages.push_back(mitk::Image::New());
	- this->m_InternalAdditionalResamplingImages[myIndex]->InitializeByItk( resampler->GetOutput() );
	- this->m_InternalAdditionalResamplingImages[myIndex]->SetVolume( resampler->GetOutput()->GetBufferPointer() );
	- }
	-
	- }
	-
	- template < typename TPixel, unsigned int VImageDimension >
	- void PartialVolumeAnalysisHistogramCalculator::InternalResampleImageFromMask(
	- const itk::Image< TPixel, VImageDimension > *image, int additionalIndex )
	- {
	- typedef itk::Image< TPixel, VImageDimension > ImageType;
	-
	- typename ImageType::Pointer outImage = ImageType::New();
	- outImage->SetSpacing( m_InternalImageMask3D->GetSpacing() ); // Set the image spacing
	- outImage->SetOrigin( m_InternalImageMask3D->GetOrigin() ); // Set the image origin
	- outImage->SetDirection( m_InternalImageMask3D->GetDirection() ); // Set the image direction
	- outImage->SetRegions( m_InternalImageMask3D->GetLargestPossibleRegion() );
	- outImage->Allocate();
	- outImage->FillBuffer(0);
	-
	- typedef itk::InterpolateImageFunction<ImageType, double>
	- BaseInterpType;
	- typedef itk::GaussianInterpolateImageFunction<ImageType, double>
	- GaussianInterpolatorType;
	- typedef itk::LinearInterpolateImageFunction<ImageType, double>
	- LinearInterpolatorType;
	-
	- typename BaseInterpType::Pointer interpolator;
	-
	- if(m_GaussianSigma != 0)
	- {
	- double sigma[3];
	- for( unsigned int d = 0; d < 3; d++ )
	- {
	- sigma[d] = m_GaussianSigma * image->GetSpacing()[d];
	- }
	- double alpha = 2.0;
	-
	- interpolator = GaussianInterpolatorType::New();
	- dynamic_cast<GaussianInterpolatorType*>(interpolator.GetPointer())->SetParameters( sigma, alpha );
	-
	- }
	- else
	- {
	- interpolator = LinearInterpolatorType::New();
	- }
	-
	- interpolator->SetInputImage( image );
	-
	- itk::ImageRegionConstIterator<MaskImage3DType>
	- itmask(m_InternalImageMask3D, m_InternalImageMask3D->GetLargestPossibleRegion());
	- itk::ImageRegionIterator<ImageType>
	- itimage(outImage, outImage->GetLargestPossibleRegion());
	-
	- itmask.GoToBegin();
	- itimage.GoToBegin();
	-
	- itk::Point< double, 3 > point;
	- itk::ContinuousIndex< double, 3 > index;
	- while( !itmask.IsAtEnd() )
	- {
	- if(itmask.Get() != 0)
	- {
	- outImage->TransformIndexToPhysicalPoint (itimage.GetIndex(), point);
	- image->TransformPhysicalPointToContinuousIndex(point, index);
	- itimage.Set(interpolator->EvaluateAtContinuousIndex(index));
	- }
	-
	- ++itmask;
	- ++itimage;
	- }
	-
	- if(additionalIndex < 0)
	- {
	- this->m_InternalImage = mitk::Image::New();
	- this->m_InternalImage->InitializeByItk( outImage.GetPointer() );
	- this->m_InternalImage->SetVolume( outImage->GetBufferPointer() );
	- }
	- else
	- {
	- this->m_InternalAdditionalResamplingImages[additionalIndex] = mitk::Image::New();
	- this->m_InternalAdditionalResamplingImages[additionalIndex]->InitializeByItk( outImage.GetPointer() );
	- this->m_InternalAdditionalResamplingImages[additionalIndex]->SetVolume( outImage->GetBufferPointer() );
	- }
	-
	- }
	-
	- void PartialVolumeAnalysisHistogramCalculator::InternalResampleImage(
	- const MaskImage3DType *image )
	- {
	- typedef itk::ResampleImageFilter<MaskImage3DType, MaskImage3DType, double> ResamplerType;
	- ResamplerType::Pointer resampler = ResamplerType::New();
	-
	- // Size
	- ResamplerType::SizeType size;
	- size[0] = m_UpsamplingFactor * image->GetLargestPossibleRegion().GetSize()[0];
	- size[1] = m_UpsamplingFactor * image->GetLargestPossibleRegion().GetSize()[1];
	- size[2] = m_UpsamplingFactor * image->GetLargestPossibleRegion().GetSize()[2];;
	- resampler->SetSize( size );
	-
	- // Origin
	- mitk::Point3D orig = image->GetOrigin();
	- resampler->SetOutputOrigin(orig );
	-
	- // Spacing
	- ResamplerType::SpacingType spacing;
	- spacing[0] = image->GetSpacing()[0] / m_UpsamplingFactor;
	- spacing[1] = image->GetSpacing()[1] / m_UpsamplingFactor;
	- spacing[2] = image->GetSpacing()[2] / m_UpsamplingFactor;
	- resampler->SetOutputSpacing( spacing );
	-
	- resampler->SetOutputDirection( image->GetDirection() );
	-
	- typedef itk::NearestNeighborInterpolateImageFunction<MaskImage3DType, double>
	- InterpolatorType;
	-
	- InterpolatorType::Pointer interpolator
	- = InterpolatorType::New();
	-
	- interpolator->SetInputImage( image );
	-
	- resampler->SetInterpolator( interpolator );
	-
	- // Other resampling options
	- resampler->SetInput( image );
	- resampler->SetDefaultPixelValue(0);
	- resampler->Update();
	-
	- m_InternalImageMask3D = resampler->GetOutput();
	-
	- }
	-
	-
	-
	- template < typename TPixel, unsigned int VImageDimension >
	- void PartialVolumeAnalysisHistogramCalculator::InternalCalculateStatisticsUnmasked(
	- const itk::Image< TPixel, VImageDimension > *image,
	- Statistics &statistics,
	- typename HistogramType::ConstPointer *histogram )
	- {
	- MITK_DEBUG << "InternalCalculateStatisticsUnmasked()";
	-
	- typedef itk::Image< TPixel, VImageDimension > ImageType;
	-
	- // Progress listening...
	- typedef itk::SimpleMemberCommand< PartialVolumeAnalysisHistogramCalculator > ITKCommandType;
	- ITKCommandType::Pointer progressListener;
	- progressListener = ITKCommandType::New();
	- progressListener->SetCallbackFunction( this,
	- &PartialVolumeAnalysisHistogramCalculator::UnmaskedStatisticsProgressUpdate );
	-
	- // Issue 100 artificial progress events since ScalarIMageToHistogramGenerator
	- // does not (yet?) support progress reporting
	- this->InvokeEvent( itk::StartEvent() );
	- for ( unsigned int i = 0; i < 100; ++i )
	- {
	- this->UnmaskedStatisticsProgressUpdate();
	- }
	-
	- // Calculate statistics (separate filter)
	- typedef itk::StatisticsImageFilter< ImageType > StatisticsFilterType;
	- typename StatisticsFilterType::Pointer statisticsFilter = StatisticsFilterType::New();
	- statisticsFilter->SetInput( image );
	- unsigned long observerTag = statisticsFilter->AddObserver(
	- itk::ProgressEvent(), progressListener );
	-
	- statisticsFilter->Update();
	-
	- statisticsFilter->RemoveObserver( observerTag );
	-
	-
	- this->InvokeEvent( itk::EndEvent() );
	-
	- statistics.N = image->GetBufferedRegion().GetNumberOfPixels();
	- statistics.Min = statisticsFilter->GetMinimum();
	- statistics.Max = statisticsFilter->GetMaximum();
	- statistics.Mean = statisticsFilter->GetMean();
	- statistics.Median = 0.0;
	- statistics.Sigma = statisticsFilter->GetSigma();
	- statistics.RMS = sqrt( statistics.Mean * statistics.Mean
	- + statistics.Sigma * statistics.Sigma );
	-
	- typename ImageType::Pointer inImage = const_cast<ImageType*>(image);
	-
	- // Calculate histogram
	- typedef itk::Statistics::ScalarImageToHistogramGenerator< ImageType >
	- HistogramGeneratorType;
	- typename HistogramGeneratorType::Pointer histogramGenerator = HistogramGeneratorType::New();
	- histogramGenerator->SetInput( inImage );
	- histogramGenerator->SetMarginalScale( 10 ); // Defines y-margin width of histogram
	- histogramGenerator->SetNumberOfBins( m_NumberOfBins ); // CT range [-1024, +2048] --> bin size 4 values
	- histogramGenerator->SetHistogramMin( statistics.Min );
	- histogramGenerator->SetHistogramMax( statistics.Max );
	- histogramGenerator->Compute();
	- *histogram = histogramGenerator->GetOutput();
	- }
	-
	-
	- template < typename TPixel, unsigned int VImageDimension >
	- void PartialVolumeAnalysisHistogramCalculator::InternalCalculateStatisticsMasked(
	- const itk::Image< TPixel, VImageDimension > *image,
	- itk::Image< unsigned char, VImageDimension > *maskImage,
	- Statistics &,
	- typename HistogramType::ConstPointer *histogram )
	- {
	- MITK_DEBUG << "InternalCalculateStatisticsMasked() start";
	-
	- typedef itk::Image< TPixel, VImageDimension > ImageType;
	- typedef itk::Image< unsigned char, VImageDimension > MaskImageType;
	-
	- // generate a list sample of angles at positions
	- // where the fiber-prob is higher than .2*maxprob
	- typedef TPixel MeasurementType;
	- const unsigned int MeasurementVectorLength = 1;
	- typedef itk::Vector< MeasurementType , MeasurementVectorLength >
	- MeasurementVectorType;
	- typedef itk::Statistics::ListSample< MeasurementVectorType > ListSampleType;
	- typename ListSampleType::Pointer listSample = ListSampleType::New();
	- listSample->SetMeasurementVectorSize( MeasurementVectorLength );
	-
	- itk::ImageRegionConstIterator<MaskImageType>
	- itmask(maskImage, maskImage->GetLargestPossibleRegion());
	- itk::ImageRegionConstIterator<ImageType>
	- itimage(image, image->GetLargestPossibleRegion());
	-
	- itmask.GoToBegin();
	- itimage.GoToBegin();
	-
	- while( !itmask.IsAtEnd() )
	- {
	- if(itmask.Get() != 0)
	- {
	- // apend to list
	- MeasurementVectorType mv;
	- mv[0] = ( MeasurementType ) itimage.Get();
	- listSample->PushBack(mv);
	- }
	- ++itmask;
	- ++itimage;
	- }
	-
	- // generate a histogram from the list sample
	- typedef double HistogramMeasurementType;
	- typedef itk::Statistics::Histogram< HistogramMeasurementType, itk::Statistics::DenseFrequencyContainer2 > HistogramType;
	- typedef itk::Statistics::SampleToHistogramFilter< ListSampleType, HistogramType > GeneratorType;
	- typename GeneratorType::Pointer generator = GeneratorType::New();
	- typename GeneratorType::HistogramType::SizeType size(MeasurementVectorLength);
	- size.Fill(m_NumberOfBins);
	- generator->SetHistogramSize( size );
	- generator->SetInput( listSample );
	- generator->SetMarginalScale( 10.0 );
	- generator->Update();
	- *histogram = generator->GetOutput();
	-
	- }
	-
	-
	- template < typename TPixel, unsigned int VImageDimension >
	- void PartialVolumeAnalysisHistogramCalculator::InternalCropAdditionalImage(
	- itk::Image< TPixel, VImageDimension > *image, int additionalIndex )
	- {
	- typedef itk::Image< TPixel, VImageDimension > ImageType;
	- typedef itk::RegionOfInterestImageFilter< ImageType, ImageType > ROIFilterType;
	- typename ROIFilterType::Pointer roi = ROIFilterType::New();
	- roi->SetRegionOfInterest(m_CropRegion);
	- roi->SetInput(image);
	- roi->Update();
	-
	- m_InternalAdditionalResamplingImages[additionalIndex] = mitk::Image::New();
	- m_InternalAdditionalResamplingImages[additionalIndex]->InitializeByItk(roi->GetOutput());
	- m_InternalAdditionalResamplingImages[additionalIndex]->SetVolume(roi->GetOutput()->GetBufferPointer());
	- }
	-
	- template < typename TPixel, unsigned int VImageDimension >
	- void PartialVolumeAnalysisHistogramCalculator::InternalCalculateMaskFromPlanarFigure(
	- itk::Image< TPixel, VImageDimension > *image, unsigned int axis )
	- {
	-
	- MITK_DEBUG << "InternalCalculateMaskFromPlanarFigure() start";
	-
	- typedef itk::Image< TPixel, VImageDimension > ImageType;
	-
	- // Generate mask image as new image with same header as input image and
	- // initialize with "1".
	- MaskImage3DType::Pointer newMaskImage = MaskImage3DType::New();
	- newMaskImage->SetSpacing( image->GetSpacing() ); // Set the image spacing
	- newMaskImage->SetOrigin( image->GetOrigin() ); // Set the image origin
	- newMaskImage->SetDirection( image->GetDirection() ); // Set the image direction
	- newMaskImage->SetRegions( image->GetLargestPossibleRegion() );
	- newMaskImage->Allocate();
	- newMaskImage->FillBuffer( 1 );
	-
	- // Generate VTK polygon from (closed) PlanarFigure polyline
	- // (The polyline points are shifted by -0.5 in z-direction to make sure
	- // that the extrusion filter, which afterwards elevates all points by +0.5
	- // in z-direction, creates a 3D object which is cut by the the plane z=0)
	- const mitk::PlaneGeometry *planarFigureGeometry2D = m_PlanarFigure->GetPlaneGeometry();
	- const typename PlanarFigure::PolyLineType planarFigurePolyline = m_PlanarFigure->GetPolyLine( 0 );
	- const mitk::BaseGeometry *imageGeometry3D = m_InternalImage->GetGeometry( 0 );
	-
	- vtkPolyData *polyline = vtkPolyData::New();
	- polyline->Allocate( 1, 1 );
	-
	- // Determine x- and y-dimensions depending on principal axis
	- int i0, i1;
	- switch ( axis )
	- {
	- case 0:
	- i0 = 1;
	- i1 = 2;
	- break;
	-
	- case 1:
	- i0 = 0;
	- i1 = 2;
	- break;
	-
	- case 2:
	- default:
	- i0 = 0;
	- i1 = 1;
	- break;
	- }
	-
	- // Create VTK polydata object of polyline contour
	- bool outOfBounds = false;
	- vtkPoints *points = vtkPoints::New();
	- typename PlanarFigure::PolyLineType::const_iterator it;
	- for ( it = planarFigurePolyline.begin();
	- it != planarFigurePolyline.end();
	- ++it )
	- {
	- Point3D point3D;
	-
	- // Convert 2D point back to the local index coordinates of the selected
	- // image
	- mitk::Point2D point2D = *it;
	- planarFigureGeometry2D->WorldToIndex(point2D, point2D);
	- point2D[0] -= 0.5/m_UpsamplingFactor;
	- point2D[1] -= 0.5/m_UpsamplingFactor;
	- planarFigureGeometry2D->IndexToWorld(point2D, point2D);
	- planarFigureGeometry2D->Map( point2D, point3D );
	-
	- // Polygons (partially) outside of the image bounds can not be processed
	- // further due to a bug in vtkPolyDataToImageStencil
	- if ( !imageGeometry3D->IsInside( point3D ) )
	- {
	- outOfBounds = true;
	- }
	-
	- imageGeometry3D->WorldToIndex( point3D, point3D );
	- point3D[i0] += 0.5;
	- point3D[i1] += 0.5;
	-
	- // Add point to polyline array
	- points->InsertNextPoint( point3D[i0], point3D[i1], -0.5 );
	- }
	- polyline->SetPoints( points );
	- points->Delete();
	-
	- if ( outOfBounds )
	- {
	- polyline->Delete();
	- throw std::runtime_error( "Figure at least partially outside of image bounds!" );
	- }
	-
	- std::size_t numberOfPoints = planarFigurePolyline.size();
	- auto ptIds = new vtkIdType[numberOfPoints];
	- for ( std::size_t i = 0; i < numberOfPoints; ++i )
	- {
	- ptIds[i] = i;
	- }
	- polyline->InsertNextCell( VTK_POLY_LINE, numberOfPoints, ptIds );
	-
	-
	- // Extrude the generated contour polygon
	- vtkLinearExtrusionFilter *extrudeFilter = vtkLinearExtrusionFilter::New();
	- extrudeFilter->SetInputData( polyline );
	- extrudeFilter->SetScaleFactor( 1 );
	- extrudeFilter->SetExtrusionTypeToNormalExtrusion();
	- extrudeFilter->SetVector( 0.0, 0.0, 1.0 );
	-
	- // Make a stencil from the extruded polygon
	- vtkPolyDataToImageStencil *polyDataToImageStencil = vtkPolyDataToImageStencil::New();
	- polyDataToImageStencil->SetInputConnection( extrudeFilter->GetOutputPort() );
	-
	-
	-
	- // Export from ITK to VTK (to use a VTK filter)
	- typedef itk::VTKImageImport< MaskImage3DType > ImageImportType;
	- typedef itk::VTKImageExport< MaskImage3DType > ImageExportType;
	-
	- typename ImageExportType::Pointer itkExporter = ImageExportType::New();
	- itkExporter->SetInput( newMaskImage );
	-
	- vtkImageImport *vtkImporter = vtkImageImport::New();
	- this->ConnectPipelines( itkExporter, vtkImporter );
	- vtkImporter->Update();
	-
	-
	- // Apply the generated image stencil to the input image
	- vtkImageStencil *imageStencilFilter = vtkImageStencil::New();
	- imageStencilFilter->SetInputData( vtkImporter->GetOutput() );
	- imageStencilFilter->SetStencilConnection(polyDataToImageStencil->GetOutputPort() );
	- imageStencilFilter->ReverseStencilOff();
	- imageStencilFilter->SetBackgroundValue( 0 );
	- imageStencilFilter->Update();
	-
	-
	- // Export from VTK back to ITK
	- vtkImageExport *vtkExporter = vtkImageExport::New();
	- vtkExporter->SetInputData( imageStencilFilter->GetOutput() );
	- vtkExporter->Update();
	-
	- typename ImageImportType::Pointer itkImporter = ImageImportType::New();
	- this->ConnectPipelines( vtkExporter, itkImporter );
	- itkImporter->Update();
	-
	- // calculate cropping bounding box
	- m_InternalImageMask3D = itkImporter->GetOutput();
	- m_InternalImageMask3D->SetDirection(image->GetDirection());
	-
	- itk::ImageRegionIterator<MaskImage3DType>
	- itmask(m_InternalImageMask3D, m_InternalImageMask3D->GetLargestPossibleRegion());
	- itmask.GoToBegin();
	- while( !itmask.IsAtEnd() )
	- {
	- if(itmask.Get() != 0)
	- {
	- typename ImageType::IndexType index = itmask.GetIndex();
	- for(unsigned int thick=0; thick<2*m_PlanarFigureThickness+1; thick++)
	- {
	- index[axis] = thick;
	- m_InternalImageMask3D->SetPixel(index, itmask.Get());
	- }
	- }
	- ++itmask;
	- }
	-
	- itmask.GoToBegin();
	- itk::ImageRegionIterator<ImageType>
	- itimage(image, image->GetLargestPossibleRegion());
	- itimage.GoToBegin();
	-
	- typename ImageType::SizeType lowersize;
	- lowersize.Fill(std::numeric_limits<typename ImageType::SizeValueType>::max());
	- typename ImageType::SizeType uppersize;
	- uppersize.Fill(std::numeric_limits<typename ImageType::SizeValueType>::min());
	- while( !itmask.IsAtEnd() )
	- {
	- if(itmask.Get() == 0)
	- {
	- itimage.Set(0);
	- }
	- else
	- {
	- typename ImageType::IndexType index = itimage.GetIndex();
	- typename ImageType::SizeType signedindex;
	- signedindex[0] = index[0];
	- signedindex[1] = index[1];
	- signedindex[2] = index[2];
	-
	- lowersize[0] = signedindex[0] < lowersize[0] ? signedindex[0] : lowersize[0];
	- lowersize[1] = signedindex[1] < lowersize[1] ? signedindex[1] : lowersize[1];
	- lowersize[2] = signedindex[2] < lowersize[2] ? signedindex[2] : lowersize[2];
	-
	- uppersize[0] = signedindex[0] > uppersize[0] ? signedindex[0] : uppersize[0];
	- uppersize[1] = signedindex[1] > uppersize[1] ? signedindex[1] : uppersize[1];
	- uppersize[2] = signedindex[2] > uppersize[2] ? signedindex[2] : uppersize[2];
	- }
	-
	- ++itmask;
	- ++itimage;
	- }
	-
	- typename ImageType::IndexType index;
	- index[0] = lowersize[0];
	- index[1] = lowersize[1];
	- index[2] = lowersize[2];
	-
	- typename ImageType::SizeType size;
	- size[0] = uppersize[0] - lowersize[0] + 1;
	- size[1] = uppersize[1] - lowersize[1] + 1;
	- size[2] = uppersize[2] - lowersize[2] + 1;
	-
	- m_CropRegion = itk::ImageRegion<3>(index, size);
	-
	- // crop internal image
	- typedef itk::RegionOfInterestImageFilter< ImageType, ImageType > ROIFilterType;
	- typename ROIFilterType::Pointer roi = ROIFilterType::New();
	- roi->SetRegionOfInterest(m_CropRegion);
	- roi->SetInput(image);
	- roi->Update();
	-
	- m_InternalImage = mitk::Image::New();
	- m_InternalImage->InitializeByItk(roi->GetOutput());
	- m_InternalImage->SetVolume(roi->GetOutput()->GetBufferPointer());
	-
	- // crop internal mask
	- typedef itk::RegionOfInterestImageFilter< MaskImage3DType, MaskImage3DType > ROIMaskFilterType;
	- typename ROIMaskFilterType::Pointer roi2 = ROIMaskFilterType::New();
	- roi2->SetRegionOfInterest(m_CropRegion);
	- roi2->SetInput(m_InternalImageMask3D);
	- roi2->Update();
	- m_InternalImageMask3D = roi2->GetOutput();
	-
	- // Clean up VTK objects
	- polyline->Delete();
	- extrudeFilter->Delete();
	- polyDataToImageStencil->Delete();
	- vtkImporter->Delete();
	- imageStencilFilter->Delete();
	- //vtkExporter->Delete(); // TODO: crashes when outcommented; memory leak??
	- delete[] ptIds;
	-
	- }
	-
	-
	- void PartialVolumeAnalysisHistogramCalculator::UnmaskedStatisticsProgressUpdate()
	- {
	- // Need to throw away every second progress event to reach a final count of
	- // 100 since two consecutive filters are used in this case
	- static int updateCounter = 0;
	- if ( updateCounter++ % 2 == 0 )
	- {
	- this->InvokeEvent( itk::ProgressEvent() );
	- }
	- }
	-
	-
	- void PartialVolumeAnalysisHistogramCalculator::MaskedStatisticsProgressUpdate()
	- {
	- this->InvokeEvent( itk::ProgressEvent() );
	- }
	-
	-
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkDicomDiffusionImageHeaderReader.cpp b/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkDicomDiffusionImageHeaderReader.cpp
	deleted file mode 100644
	index fbe24d0c63..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkDicomDiffusionImageHeaderReader.cpp
	+++ /dev/null
	@@ -1,328 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkDicomDiffusionImageHeaderReader.h"
	-
	-#include <mitkLocaleSwitch.h>
	-
	-#include "mitkGEDicomDiffusionImageHeaderReader.h"
	-#include "mitkPhilipsDicomDiffusionImageHeaderReader.h"
	-#include "mitkSiemensDicomDiffusionImageHeaderReader.h"
	-#include "mitkSiemensMosaicDicomDiffusionImageHeaderReader.h"
	-
	-void InsertUnique( std::vector<float> & vec, float value )
	-{
	- int n = vec.size();
	- if (n == 0)
	- {
	- vec.push_back( value );
	- return;
	- }
	-
	- for (int k = 0; k < n ; k++)
	- {
	- if (vec[k] == value)
	- {
	- return;
	- }
	- }
	-
	- // if we get here, it means value is not in vec.
	- vec.push_back( value );
	- return;
	-
	-}
	-
	-mitk::DicomDiffusionImageHeaderReader::DicomDiffusionImageHeaderReader()
	-{
	- m_SliceOrderIS = true;
	- m_SingleSeries = true;
	-}
	-
	-mitk::DicomDiffusionImageHeaderReader::~DicomDiffusionImageHeaderReader()
	-{
	-}
	-
	-mitk::DicomDiffusionImageHeaderReader::SupportedVendors
	-mitk::DicomDiffusionImageHeaderReader::GetVendorID()
	-{
	- // adapted from namic-sandbox
	- // DicomToNrrdConverter.cxx
	-
	- m_GdcmIO = ImageIOType::New();
	- m_GdcmIO->LoadPrivateTagsOn();
	- m_GdcmIO->SetMaxSizeLoadEntry( 65536 );
	-
	- m_VolumeReader = VolumeReaderType::New();
	- m_VolumeReader->SetImageIO( m_GdcmIO );
	- m_VolumeReader->SetFileNames( m_DicomFilenames );
	-
	- try
	- {
	- m_VolumeReader->Update();
	- }
	- catch (itk::ExceptionObject &excp)
	- {
	- std::cerr << "Exception thrown while reading slice" << std::endl;
	- std::cerr << excp << std::endl;
	- return SV_UNKNOWN_VENDOR;
	- }
	-
	- VolumeReaderType::DictionaryArrayRawPointer inputDict
	- = m_VolumeReader->GetMetaDataDictionaryArray();
	-
	- std::string vendor;
	- itk::ExposeMetaData<std::string> ( (inputDict)[0], "0008\|0070", vendor );
	- // std::cout << vendor << std::endl;
	-
	- std::string ImageType;
	- itk::ExposeMetaData<std::string> ( (inputDict)[0], "0008\|0008", ImageType );
	- //std::cout << ImageType << std::endl;
	-
	- if ( vendor.find("GE") != std::string::npos )
	- {
	- // for GE data
	- return SV_GE;
	- }
	- else if( vendor.find("SIEMENS") != std::string::npos )
	- {
	- if ( ImageType.find("MOSAIC") != std::string::npos )
	- {
	- // for Siemens MOSAIC
	- return SV_SIEMENS_MOSAIC;
	- }
	- else
	- {
	- // for Siemens SPLIT
	- return SV_SIEMENS;
	- }
	- }
	- else if( vendor.find("PHILIPS") != std::string::npos )
	- {
	- // for philips data
	- return SV_PHILIPS;
	- }
	- else
	- {
	- // for unrecognized vendors
	- return SV_UNKNOWN_VENDOR;
	- }
	-}
	-
	-// do the work
	-void mitk::DicomDiffusionImageHeaderReader::Update()
	-{
	-
	- // check if there are filenames
	- if(m_DicomFilenames.size())
	- {
	-
	- m_Output = mitk::DiffusionImageHeaderInformation::New();
	- m_Output->m_DicomFilenames = m_DicomFilenames;
	-
	- // create correct reader
	- switch(GetVendorID())
	- {
	- case(SV_GE):
	- {
	- GEDicomDiffusionImageHeaderReader::Pointer reader
	- = GEDicomDiffusionImageHeaderReader::New();
	- reader->SetSeriesDicomFilenames(this->m_DicomFilenames);
	- reader->SetGdcmIO(this->m_GdcmIO);
	- reader->SetVolumeReader(this->m_VolumeReader);
	- reader->SetOutputPointer(this->m_Output);
	- reader->Update();
	- this->m_Output = reader->GetOutput();
	- break;
	- }
	- case(SV_SIEMENS):
	- {
	- SiemensDicomDiffusionImageHeaderReader::Pointer reader
	- = SiemensDicomDiffusionImageHeaderReader::New();
	- reader->SetSeriesDicomFilenames(this->m_DicomFilenames);
	- reader->SetGdcmIO(this->m_GdcmIO);
	- reader->SetVolumeReader(this->m_VolumeReader);
	- reader->SetOutputPointer(this->m_Output);
	- reader->Update();
	- this->m_Output = reader->GetOutput();
	- break;
	- }
	- case(SV_SIEMENS_MOSAIC):
	- {
	-
	- SiemensMosaicDicomDiffusionImageHeaderReader::Pointer reader
	- = SiemensMosaicDicomDiffusionImageHeaderReader::New();
	- reader->SetSeriesDicomFilenames(this->m_DicomFilenames);
	- reader->SetGdcmIO(this->m_GdcmIO);
	- reader->SetVolumeReader(this->m_VolumeReader);
	- reader->SetOutputPointer(this->m_Output);
	- reader->Update();
	- this->m_Output = reader->GetOutput();
	- break;
	- }
	- case(SV_PHILIPS):
	- {
	-
	- PhilipsDicomDiffusionImageHeaderReader::Pointer reader
	- = PhilipsDicomDiffusionImageHeaderReader::New();
	- reader->SetSeriesDicomFilenames(this->m_DicomFilenames);
	- reader->SetGdcmIO(this->m_GdcmIO);
	- reader->SetVolumeReader(this->m_VolumeReader);
	- reader->SetOutputPointer(this->m_Output);
	- reader->Update();
	- this->m_Output = reader->GetOutput();
	- break;
	- }
	- case(SV_UNKNOWN_VENDOR):
	- {
	- std::cerr << "diffusion header reader: unknown vendor" << std::endl;
	- break;
	- }
	- }
	- }
	-}
	-
	-// return output
	-mitk::DiffusionImageHeaderInformation::Pointer
	-mitk::DicomDiffusionImageHeaderReader::GetOutput()
	-{
	- return m_Output;
	-}
	-
	-void mitk::DicomDiffusionImageHeaderReader::ReadPublicTags()
	-{
	- mitk::LocaleSwitch localeSwitch("C");
	-
	- VolumeReaderType::DictionaryArrayRawPointer inputDict
	- = m_VolumeReader->GetMetaDataDictionaryArray();
	-
	- // load in all public tags
	- m_nSlice = inputDict->size();
	- std::string tag;
	-
	- tag.clear();
	- itk::ExposeMetaData<std::string> ( (inputDict)[0], "0008\|103e", tag );
	- this->m_Output->seriesDescription = tag.c_str();
	-
	- tag.clear();
	- itk::ExposeMetaData<std::string> ( (inputDict)[0], "0020\|0011", tag );
	- this->m_Output->seriesNumber = atoi(tag.c_str());
	-
	- tag.clear();
	- itk::ExposeMetaData<std::string> ( (inputDict)[0], "0010\|0010", tag );
	- this->m_Output->patientName = tag.c_str();
	-
	- tag.clear();
	- itk::ExposeMetaData<std::string> ( (inputDict)[0], "0028\|0010", tag );
	- this->m_Output->nRows = atoi( tag.c_str() );
	-
	- tag.clear();
	- itk::ExposeMetaData<std::string> ( (inputDict)[0], "0028\|0011", tag );
	- this->m_Output->nCols = atoi( tag.c_str() );
	-
	- tag.clear();
	- itk::ExposeMetaData<std::string> ( (inputDict)[0], "0028\|0030", tag );
	- sscanf( tag.c_str(), "%f\\%f", &this->m_Output->xRes, &this->m_Output->yRes );
	-
	- tag.clear();
	- itk::ExposeMetaData<std::string> ( (inputDict)[0], "0020\|0032", tag );
	- sscanf( tag.c_str(), "%f\\%f\\%f", &this->m_Output->xOrigin, &this->m_Output->yOrigin, &this->m_Output->zOrigin );
	-
	- tag.clear();
	- itk::ExposeMetaData<std::string> ( (inputDict)[0], "0018\|0050", tag );
	- this->m_Output->sliceThickness = atof( tag.c_str() );
	-
	- tag.clear();
	- itk::ExposeMetaData<std::string> ( (inputDict)[0], "0018\|0088", tag );
	- this->m_Output->sliceSpacing = atof( tag.c_str() );
	-
	- // figure out how many slices are there in a volume, each unique
	- // SliceLocation represent one slice
	- for (int k = 0; k < m_nSlice; k++)
	- {
	- tag.clear();
	- itk::ExposeMetaData<std::string> ( (inputDict)[k], "0020\|1041", tag);
	- float sliceLocation = atof( tag.c_str() );
	- InsertUnique( m_sliceLocations, sliceLocation );
	- }
	-
	- // check ImageOrientationPatient and figure out slice direction in
	- // L-P-I (right-handed) system.
	- // In Dicom, the coordinate frame is L-P by default. Look at
	- // http://medical.nema.org/dicom/2007/07_03pu.pdf , page 301
	- tag.clear();
	- itk::ExposeMetaData<std::string> ( (inputDict)[0], "0020\|0037", tag );
	- float xRow, yRow, zRow, xCol, yCol, zCol, xSlice, ySlice, zSlice /, orthoSliceSpacing/;
	- sscanf( tag.c_str(), "%f\\%f\\%f\\%f\\%f\\%f", &xRow, &yRow, &zRow, &xCol, &yCol, &zCol );
	-
	- // In Dicom, the measurement frame is L-P by default. Look at
	- // http://medical.nema.org/dicom/2007/07_03pu.pdf , page 301, in
	- // order to make this compatible with Slicer's RAS frame, we
	- // multiply the direction cosines by the negatives of the resolution
	- // (resolution is required by nrrd format). Direction cosine is not
	- // affacted since the resulting frame is still a right-handed frame.
	- xRow = -xRow;
	- yRow = -yRow;
	-
	- xCol = -xCol;
	- yCol = -yCol;
	-
	- // Cross product, this gives I-axis direction
	- xSlice = (yRowzCol-zRowyCol)*this->m_Output->sliceSpacing;
	- ySlice = (zRowxCol-xRowzCol)*this->m_Output->sliceSpacing;
	- zSlice = (xRowyCol-yRowxCol)*this->m_Output->sliceSpacing;
	-
	- xRow *= this->m_Output->xRes;
	- yRow *= this->m_Output->xRes;
	- zRow *= this->m_Output->xRes;
	-
	- xCol *= this->m_Output->yRes;
	- yCol *= this->m_Output->yRes;
	- zCol *= this->m_Output->yRes;
	-
	- this->m_Output->xRow = xRow;
	- this->m_Output->yRow = yRow;
	- this->m_Output->zRow = zRow;
	- this->m_Output->xCol = xCol;
	- this->m_Output->yCol = yCol;
	- this->m_Output->zCol = zCol;
	- this->m_Output->xSlice = xSlice;
	- this->m_Output->ySlice = ySlice;
	- this->m_Output->zSlice = zSlice;
	-}
	-
	-
	-void mitk::DicomDiffusionImageHeaderReader::ReadPublicTags2()
	-{
	-
	- if (!m_SliceOrderIS)
	- {
	- this->m_Output->xSlice = -this->m_Output->xSlice;
	- this->m_Output->ySlice = -this->m_Output->ySlice;
	- this->m_Output->zSlice = -this->m_Output->zSlice;
	- }
	-
	-}
	-
	-void mitk::DicomDiffusionImageHeaderReader::TransformGradients()
	-{
	- // transform gradient directions into RAS frame
	- if ( !m_SliceOrderIS )
	- {
	- this->m_Output->DiffusionVector[2] = -this->m_Output->DiffusionVector[2]; // I -> S
	- }
	-}
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkDiffusionDICOMFileReader.cpp b/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkDiffusionDICOMFileReader.cpp
	deleted file mode 100644
	index c5bed76809..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkDiffusionDICOMFileReader.cpp
	+++ /dev/null
	@@ -1,437 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkDiffusionDICOMFileReader.h"
	-
	-#include "mitkDiffusionDICOMFileReaderHelper.h"
	-
	-#include "mitkDiffusionHeaderSiemensDICOMFileReader.h"
	-#include "mitkDiffusionHeaderSiemensMosaicDICOMFileReader.h"
	-#include "mitkDiffusionHeaderGEDICOMFileReader.h"
	-#include "mitkDiffusionHeaderPhilipsDICOMFileReader.h"
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <mitkITKImageImport.h>
	-
	-#include "mitkStringProperty.h"
	-#include <mitkImageCast.h>
	-
	-static void PerformHeaderAnalysis( mitk::DiffusionHeaderDICOMFileReader::DICOMHeaderListType headers )
	-{
	- unsigned int images = headers.size();
	-
	- unsigned int unweighted_images = 0;
	- unsigned int weighted_images = 0;
	-
	- mitk::DiffusionHeaderDICOMFileReader::DICOMHeaderListType::const_iterator c_iter = headers.begin();
	- while( c_iter != headers.end() )
	- {
	- const mitk::DiffusionImageDICOMHeaderInformation h = *c_iter;
	- if( h.baseline ) unweighted_images++;
	- if( h.b_value > 0 ) weighted_images++;
	-
	- ++c_iter;
	- }
	-
	- MITK_INFO << " :: Analyzed volumes " << images << "\n"
	- << " :: \t"<< unweighted_images << " b = 0" << "\n"
	- << " :: \t"<< weighted_images << " b > 0";
	-}
	-
	-mitk::DiffusionDICOMFileReader::DiffusionDICOMFileReader()
	-{
	- m_ApplyRotationToGradients = true;
	- m_ResolveMosaic = true;
	-}
	-
	-mitk::DiffusionDICOMFileReader::~DiffusionDICOMFileReader()
	-{
	-
	-}
	-
	-bool mitk::DiffusionDICOMFileReader
	-::LoadImages()
	-{
	- unsigned int numberOfOutputs = this->GetNumberOfOutputs();
	- bool success = true;
	-
	- for(unsigned int o = 0; o < numberOfOutputs; ++o)
	- {
	- success &= this->LoadSingleOutputImage( this->m_OutputHeaderContainer.at(o),
	- this->InternalGetOutput(o), this->m_IsMosaicData.at(o) );
	- }
	-
	- return success;
	-}
	-
	-bool mitk::DiffusionDICOMFileReader
	-::LoadSingleOutputImage( DiffusionHeaderDICOMFileReader::DICOMHeaderListType retrievedHeader,
	- DICOMImageBlockDescriptor& block, bool is_mosaic)
	-{
	- // prepare data reading
	- DiffusionDICOMFileReaderHelper helper;
	- DiffusionDICOMFileReaderHelper::VolumeFileNamesContainer filenames;
	-
	- const DICOMImageFrameList& frames = block.GetImageFrameList();
	- int numberOfDWImages = block.GetIntProperty("timesteps", 1);
	-
	- int numberOfFramesPerDWImage = frames.size() / numberOfDWImages;
	-
	- assert( int( double((double) frames.size() / (double) numberOfDWImages)) == numberOfFramesPerDWImage );
	- for( int idx = 0; idx < numberOfDWImages; idx++ )
	- {
	- std::vector< std::string > FileNamesPerVolume;
	-
	- auto timeStepStart = frames.begin() + idx * numberOfFramesPerDWImage;
	- auto timeStepEnd = frames.begin() + (idx+1) * numberOfFramesPerDWImage;
	- for (auto frameIter = timeStepStart;
	- frameIter != timeStepEnd;
	- ++frameIter)
	- {
	- FileNamesPerVolume.push_back( (*frameIter)->Filename );
	- }
	-
	- filenames.push_back( FileNamesPerVolume );
	- }
	-
	- // TODO : only prototyping to test loading of diffusion images
	- // we need some solution for the different types
	- mitk::Image::Pointer output_image = mitk::Image::New();
	-
	- mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer directions =
	- mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::New();
	-
	-
	- double max_bvalue = 0;
	- for( int idx = 0; idx < numberOfDWImages; idx++ )
	- {
	- DiffusionImageDICOMHeaderInformation header = retrievedHeader.at(idx);
	-
	- if( max_bvalue < header.b_value )
	- max_bvalue = header.b_value;
	- }
	-
	- // normalize the retrieved gradient directions according to the set b-value (maximal one)
	- for( int idx = 0; idx < numberOfDWImages; idx++ )
	- {
	- DiffusionImageDICOMHeaderInformation header = retrievedHeader.at(idx);
	- mitk::DiffusionPropertyHelper::GradientDirectionType grad = header.g_vector;
	-
	- grad.normalize();
	- grad *= sqrt( header.b_value / max_bvalue );
	-
	- directions->push_back( grad );
	- }
	-
	- // initialize the output image
	- mitk::DiffusionPropertyHelper::SetOriginalGradientContainer(output_image, directions);
	- mitk::DiffusionPropertyHelper::SetReferenceBValue(output_image, max_bvalue);
	-
	- if( is_mosaic && this->m_ResolveMosaic )
	- {
	- mitk::DiffusionHeaderSiemensMosaicDICOMFileReader::Pointer mosaic_reader =
	- mitk::DiffusionHeaderSiemensMosaicDICOMFileReader::New();
	-
	- // retrieve the remaining meta-information needed for mosaic reconstruction
	- // it suffices to get it exemplatory from the first file in the file list
	- mosaic_reader->RetrieveMosaicInformation( filenames.at(0).at(0) );
	-
	- mitk::MosaicDescriptor mdesc = mosaic_reader->GetMosaicDescriptor();
	- mitk::CastToMitkImage( helper.LoadMosaicToVector<short, 3>( filenames, mdesc ), output_image );
	-
	- }
	- else
	- {
	- mitk::CastToMitkImage( helper.LoadToVector<short, 3>( filenames ), output_image );
	- }
	-
	- mitk::DiffusionPropertyHelper::SetApplyMatrixToGradients(output_image, m_ApplyRotationToGradients);
	- mitk::DiffusionPropertyHelper::InitializeImage(output_image);
	- output_image->SetProperty("diffusion.dicom.importname", mitk::StringProperty::New( helper.GetOutputName(filenames) ) );
	-
	- block.SetMitkImage( (mitk::Image::Pointer) output_image );
	-
	- return block.GetMitkImage().IsNotNull();
	-
	-}
	-
	-std::vector<std::string> mitk::DiffusionDICOMFileReader::patient_ids() const
	-{
	- return m_patient_ids;
	-}
	-
	-std::vector<std::string> mitk::DiffusionDICOMFileReader::patient_names() const
	-{
	- return m_patient_names;
	-}
	-
	-std::vector<std::string> mitk::DiffusionDICOMFileReader::study_instance_uids() const
	-{
	- return m_study_instance_uids;
	-}
	-
	-std::vector<std::string> mitk::DiffusionDICOMFileReader::series_instance_uids() const
	-{
	- return m_series_instance_uids;
	-}
	-
	-std::vector<std::string> mitk::DiffusionDICOMFileReader::frame_of_reference_uids() const
	-{
	- return m_frame_of_reference_uids;
	-}
	-
	-std::vector<std::string> mitk::DiffusionDICOMFileReader::sop_instance_uids() const
	-{
	- return m_sop_instance_uids;
	-}
	-
	-void mitk::DiffusionDICOMFileReader
	-::AnalyzeInputFiles()
	-{
	- m_Study_names.clear();
	- m_Series_names.clear();
	- this->SetGroup3DandT(true);
	-
	- Superclass::AnalyzeInputFiles();
	-
	- // collect output from superclass
	- size_t number_of_outputs = this->GetNumberOfOutputs();
	-
	- if(number_of_outputs == 0)
	- {
	- MITK_ERROR << "Failed to parse input, retrieved 0 outputs from SeriesGDCMReader ";
	- }
	-
	- MITK_INFO("diffusion.dicomreader") << "Retrieved " << number_of_outputs << " outputs.";
	- std::vector< bool > valid_input_list;
	-
	- for( unsigned int outputidx = 0; outputidx < this->GetNumberOfOutputs(); outputidx++ )
	- {
	- DICOMImageBlockDescriptor block_0 = this->GetOutput(outputidx);
	-
	- // collect vendor ID from the first output, first image
	- StringList inputFilename;
	- DICOMImageFrameInfo::Pointer frame_0 = block_0.GetImageFrameList().at(0);
	- inputFilename.push_back( frame_0->Filename );
	-
	-
	- mitk::DiffusionHeaderDICOMFileReader::Pointer headerReader;
	-
	- bool isMosaic = false;
	- gdcm::Scanner gdcmScanner;
	-
	- gdcm::Tag t_sop_instance_uid(0x0008, 0x0018);
	- gdcm::Tag t_frame_of_reference_uid(0x0020, 0x0052);
	- gdcm::Tag t_series_instance_uid(0x0020, 0x000E);
	- gdcm::Tag t_study_instance_uid(0x0020, 0x000D);
	- gdcm::Tag t_patient_name(0x0010, 0x0010);
	- gdcm::Tag t_patient_id(0x0010, 0x0020);
	-
	- gdcm::Tag t_vendor(0x008, 0x0070);
	- gdcm::Tag t_imagetype(0x0008, 0x0008);
	- gdcm::Tag t_StudyDescription(0x0008, 0x1030);
	- gdcm::Tag t_SeriesDescription(0x0008, 0x103E);
	-
	- // add DICOM Tag for vendor
	- gdcmScanner.AddTag( t_vendor );
	- // add DICOM Tag for image type
	- gdcmScanner.AddTag( t_imagetype );
	- gdcmScanner.AddTag( t_StudyDescription );
	- gdcmScanner.AddTag( t_SeriesDescription );
	-
	- gdcmScanner.AddTag( t_sop_instance_uid );
	- gdcmScanner.AddTag( t_frame_of_reference_uid );
	- gdcmScanner.AddTag( t_series_instance_uid );
	- gdcmScanner.AddTag( t_study_instance_uid );
	- gdcmScanner.AddTag( t_patient_name );
	- gdcmScanner.AddTag( t_patient_id );
	-
	- if( gdcmScanner.Scan( inputFilename ) )
	- {
	-
	- // retrieve both vendor and image type
	- const char* ch_vendor = gdcmScanner.GetValue( frame_0->Filename.c_str(), t_vendor );
	- const char* ch_image_type = gdcmScanner.GetValue( frame_0->Filename.c_str(), t_imagetype );
	-
	- const char* temp = gdcmScanner.GetValue( frame_0->Filename.c_str(), t_sop_instance_uid );
	- if (temp!=nullptr)
	- m_sop_instance_uids.push_back(std::string(temp));
	- else
	- m_sop_instance_uids.push_back("-");
	-
	- temp = nullptr; temp = gdcmScanner.GetValue( frame_0->Filename.c_str(), t_frame_of_reference_uid );
	- if (temp!=nullptr)
	- m_frame_of_reference_uids.push_back(std::string(temp));
	- else
	- m_frame_of_reference_uids.push_back("-");
	-
	- temp = nullptr; temp = gdcmScanner.GetValue( frame_0->Filename.c_str(), t_series_instance_uid );
	- if (temp!=nullptr)
	- m_series_instance_uids.push_back(std::string(temp));
	- else
	- m_series_instance_uids.push_back("-");
	-
	- temp = nullptr; temp = gdcmScanner.GetValue( frame_0->Filename.c_str(), t_study_instance_uid );
	- if (temp!=nullptr)
	- m_study_instance_uids.push_back(std::string(temp));
	- else
	- m_study_instance_uids.push_back("-");
	-
	- temp = nullptr; temp = gdcmScanner.GetValue( frame_0->Filename.c_str(), t_patient_name );
	- if (temp!=nullptr)
	- m_patient_names.push_back(std::string(temp));
	- else
	- m_patient_names.push_back("-");
	-
	- temp = nullptr; temp = gdcmScanner.GetValue( frame_0->Filename.c_str(), t_patient_id );
	- if (temp!=nullptr)
	- m_patient_ids.push_back(std::string(temp));
	- else
	- m_patient_ids.push_back("-");
	-
	- if( ch_vendor == nullptr \|\| ch_image_type == nullptr )
	- {
	- MITK_WARN << "Unable to retrieve vendor/image information from " << frame_0->Filename.c_str() << "\n" <<
	- "Output " << outputidx+1 << " is not valid, skipping analysis.";
	- valid_input_list.push_back(false);
	- continue;
	-
	- }
	-
	- std::string vendor = std::string( ch_vendor );
	- std::string image_type = std::string( ch_image_type );
	- MITK_INFO("diffusion.dicomreader") << "Output " << outputidx+1 << " Got vendor: " << vendor << " image type " << image_type;
	-
	- // parse vendor tag
	- if( vendor.find("SIEMENS") != std::string::npos \|\| vendor.find("Siemens HealthCare GmbH") != std::string::npos )
	- {
	- if( image_type.find("MOSAIC") != std::string::npos )
	- {
	- headerReader = mitk::DiffusionHeaderSiemensMosaicDICOMFileReader::New();
	- isMosaic = true;
	- }
	- else
	- {
	- headerReader = mitk::DiffusionHeaderSiemensDICOMFileReader::New();
	- }
	-
	- }
	- else if( vendor.find("GE") != std::string::npos )
	- {
	- headerReader = mitk::DiffusionHeaderGEDICOMFileReader::New();
	- }
	- else if( vendor.find("Philips") != std::string::npos )
	- {
	- headerReader = mitk::DiffusionHeaderPhilipsDICOMFileReader::New();
	- }
	- else
	- {
	- // unknown vendor
	- }
	-
	- if( headerReader.IsNull() )
	- {
	- MITK_ERROR << "No header reader for given vendor. ";
	- valid_input_list.push_back(false);
	- continue;
	- }
	-
	- }
	- else
	- {
	- valid_input_list.push_back(false);
	- continue;
	- }
	-
	- bool canread = false;
	- // iterate over the threeD+t block
	-
	- int numberOfTimesteps = block_0.GetIntProperty("timesteps", 1);
	- int framesPerTimestep = block_0.GetImageFrameList().size() / numberOfTimesteps;
	-
	- for( int idx = 0; idx < numberOfTimesteps; idx++ )
	- {
	- int access_idx = idx * framesPerTimestep;
	- DICOMImageFrameInfo::Pointer frame = this->GetOutput( outputidx ).GetImageFrameList().at( access_idx );
	- canread = headerReader->ReadDiffusionHeader( frame->Filename );
	- }
	-
	- if( canread )
	- {
	- // collect the information
	- mitk::DiffusionHeaderDICOMFileReader::DICOMHeaderListType retrievedHeader = headerReader->GetHeaderInformation();
	-
	- m_IsMosaicData.push_back(isMosaic);
	- m_OutputHeaderContainer.push_back( retrievedHeader );
	- m_OutputReaderContainer.push_back( headerReader );
	- valid_input_list.push_back(true);
	-
	- const char* ch_StudyDescription = gdcmScanner.GetValue( frame_0->Filename.c_str(), t_StudyDescription );
	- const char* ch_SeriesDescription = gdcmScanner.GetValue( frame_0->Filename.c_str(), t_SeriesDescription );
	- if( ch_StudyDescription != nullptr )
	- m_Study_names.push_back(ch_StudyDescription);
	- else
	- m_Study_names.push_back("-");
	-
	- if( ch_SeriesDescription != nullptr )
	- m_Series_names.push_back(ch_SeriesDescription);
	- else
	- m_Series_names.push_back("-");
	- }
	- }
	-
	- // check status of the outputs and remove the non-valid
	- std::vector< DICOMImageBlockDescriptor > valid_outputs;
	- for ( unsigned int outputidx = 0; outputidx < this->GetNumberOfOutputs(); ++outputidx )
	- {
	- if( valid_input_list.at(outputidx) )
	- {
	- valid_outputs.push_back( this->InternalGetOutput( outputidx ) );
	- }
	- }
	-
	- // clear complete list
	- this->ClearOutputs();
	- this->SetNumberOfOutputs( valid_outputs.size() );
	-
	- // insert only the valid ones
	- for ( unsigned int outputidx = 0; valid_outputs.size(); ++outputidx )
	- this->SetOutput( outputidx, valid_outputs.at( outputidx ) );
	-
	- for( unsigned int outputidx = 0; outputidx < this->GetNumberOfOutputs(); outputidx++ )
	- {
	- // TODO : Analyze outputs + header information, i.e. for the loading confidence
	- MITK_INFO("diffusion.dicomreader") << "---- DICOM Analysis Report ---- :: Output " << outputidx+1 << " of " << this->GetNumberOfOutputs();
	-
	- try{
	- PerformHeaderAnalysis( this->m_OutputHeaderContainer.at( outputidx) );
	- }
	- catch( const std::exception& se)
	- {
	- MITK_ERROR << "STD Exception " << se.what();
	- }
	-
	- MITK_INFO("diffusion.dicomreader") << "===========================================";
	- }
	-}
	-
	-
	-bool mitk::DiffusionDICOMFileReader
	-::CanHandleFile(const std::string & /* filename */)
	-{
	- //FIXME :
	- return true;
	-}
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkDiffusionHeaderDICOMFileReader.cpp b/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkDiffusionHeaderDICOMFileReader.cpp
	deleted file mode 100644
	index 967816360a..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkDiffusionHeaderDICOMFileReader.cpp
	+++ /dev/null
	@@ -1,82 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkDiffusionHeaderDICOMFileReader.h"
	-
	-mitk::DiffusionHeaderDICOMFileReader
	-::DiffusionHeaderDICOMFileReader()
	-{
	-
	-}
	-
	-mitk::DiffusionHeaderDICOMFileReader
	-::~DiffusionHeaderDICOMFileReader()
	-{
	-
	-}
	-
	-mitk::DiffusionHeaderDICOMFileReader::DICOMHeaderListType
	-mitk::DiffusionHeaderDICOMFileReader
	-::GetHeaderInformation()
	-{
	- if( m_HeaderInformationList.size() < 1 )
	- {
	- MITK_WARN << "No information retrieved yet. Call AnalyzeInputFiles first!";
	- }
	-
	- return m_HeaderInformationList;
	-}
	-
	-bool mitk::RevealBinaryTag(const gdcm::Tag tag, const gdcm::DataSet& dataset, std::string& target)
	-{
	- if( dataset.FindDataElement( tag ) )
	- {
	- MITK_DEBUG << "Found tag " << tag.PrintAsPipeSeparatedString();
	-
	- const gdcm::DataElement& de = dataset.GetDataElement( tag );
	- target = std::string( de.GetByteValue()->GetPointer(),
	- de.GetByteValue()->GetLength() );
	- return true;
	-
	- }
	- else
	- {
	- MITK_DEBUG << "Could not find tag " << tag.PrintAsPipeSeparatedString();
	- return false;
	- }
	-}
	-
	-bool mitk::RevealBinaryTagC(const gdcm::Tag tag, const gdcm::DataSet& dataset, char * target_array )
	-{
	- if( dataset.FindDataElement( tag ) )
	- {
	- MITK_DEBUG << "Found tag " << tag.PrintAsPipeSeparatedString();
	-
	- const gdcm::DataElement& de = dataset.GetDataElement( tag );
	-
	- size_t bytesize = de.GetValue().GetLength(); // GetLength();
	- //target_array = new char[bytesize];
	- memcpy( target_array, de.GetByteValue()->GetPointer(), bytesize);
	-
	- return true;
	-
	- }
	- else
	- {
	- MITK_DEBUG << "Could not find tag " << tag.PrintAsPipeSeparatedString();
	- return false;
	- }
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkDiffusionHeaderGEDICOMFileReader.cpp b/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkDiffusionHeaderGEDICOMFileReader.cpp
	deleted file mode 100644
	index e90e9b77a4..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkDiffusionHeaderGEDICOMFileReader.cpp
	+++ /dev/null
	@@ -1,102 +0,0 @@
	-#include "mitkDiffusionHeaderGEDICOMFileReader.h"
	-#include <vnl/vnl_math.h>
	-
	-mitk::DiffusionHeaderGEDICOMFileReader
	-::DiffusionHeaderGEDICOMFileReader()
	-{
	-
	-}
	-
	-mitk::DiffusionHeaderGEDICOMFileReader
	-::~DiffusionHeaderGEDICOMFileReader()
	-{
	-
	-}
	-
	-bool mitk::DiffusionHeaderGEDICOMFileReader
	-::ReadDiffusionHeader(std::string filename)
	-{
	-
	- gdcm::Reader gdcmReader;
	- gdcmReader.SetFileName( filename.c_str() );
	-
	- gdcmReader.Read();
	-
	- gdcm::Tag ge_bvalue_tag( 0x0043, 0x1039 );
	- gdcm::Tag ge_gradient_x( 0x0019, 0x10bb );
	- gdcm::Tag ge_gradient_y( 0x0019, 0x10bc );
	- gdcm::Tag ge_gradient_z( 0x0019, 0x10bd );
	-
	- bool success = true;
	- DiffusionImageDICOMHeaderInformation header_info;
	-
	- std::string ge_tagvalue_string;
	- char* pEnd;
	-
	- // start with b-value
	- success = RevealBinaryTag( ge_bvalue_tag, gdcmReader.GetFile().GetDataSet(), ge_tagvalue_string );
	- // b value stored in the first bytes
	- // typical example: "1000\8\0\0" for bvalue=1000
	- // "40\8\0\0" for bvalue=40
	- // so we need to cut off the last 6 elements
	- const char* bval_string = ge_tagvalue_string.substr(0,ge_tagvalue_string.length()-6).c_str();
	- header_info.b_value = static_cast<unsigned int>(strtod( bval_string, &pEnd ));
	-
	- // now retrieve the gradient direction
	- if(success &&
	- RevealBinaryTag( ge_gradient_x, gdcmReader.GetFile().GetDataSet(), ge_tagvalue_string ) )
	- {
	- header_info.g_vector[0] = strtod( ge_tagvalue_string.c_str(), &pEnd );
	- }
	- else
	- {
	- success = false;
	- }
	-
	- if( success &&
	- RevealBinaryTag( ge_gradient_y, gdcmReader.GetFile().GetDataSet(), ge_tagvalue_string ) )
	- {
	- header_info.g_vector[1] = strtod( ge_tagvalue_string.c_str(), &pEnd );
	- }
	- else
	- {
	- success = false;
	- }
	-
	- if( success &&
	- RevealBinaryTag( ge_gradient_z, gdcmReader.GetFile().GetDataSet(), ge_tagvalue_string ) )
	- {
	- header_info.g_vector[2] = strtod( ge_tagvalue_string.c_str(), &pEnd );
	- }
	- else
	- {
	- success = false;
	- }
	-
	- if( success )
	- {
	- // Fix for (0,0,0) direction in IVIM datasets
	- if( header_info.b_value > 0 &&
	- header_info.g_vector.two_norm() < vnl_math::eps )
	- {
	- header_info.g_vector.fill(1);
	- header_info.g_vector.normalize();
	- header_info.isotropic = true;
	- }
	-
	- // mark baseline
	- if( header_info.b_value == 0 )
	- header_info.baseline = true;
	-
	- this->m_HeaderInformationList.push_back( header_info );
	-
	- header_info.Print();
	- }
	-
	- return success;
	-
	-
	-
	-}
	-
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkDiffusionHeaderPhilipsDICOMFileReader.cpp b/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkDiffusionHeaderPhilipsDICOMFileReader.cpp
	deleted file mode 100644
	index a9c8710521..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkDiffusionHeaderPhilipsDICOMFileReader.cpp
	+++ /dev/null
	@@ -1,97 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkDiffusionHeaderPhilipsDICOMFileReader.h"
	-
	-#include <sstream>
	-
	-#include <vnl/vnl_math.h>
	-
	-mitk::DiffusionHeaderPhilipsDICOMFileReader::DiffusionHeaderPhilipsDICOMFileReader()
	-{
	-}
	-
	-mitk::DiffusionHeaderPhilipsDICOMFileReader::~DiffusionHeaderPhilipsDICOMFileReader()
	-{
	-
	-}
	-
	-bool mitk::DiffusionHeaderPhilipsDICOMFileReader::ReadDiffusionHeader(std::string filename)
	-{
	- gdcm::Reader gdcmReader;
	- gdcmReader.SetFileName( filename.c_str() );
	-
	- gdcmReader.Read();
	-
	- gdcm::Tag philips_bvalue_tag( 0x2001, 0x1003 );
	- //gdcm::Tag philips_gradient_direction( 0x2001, 0x1004 );
	-
	- DiffusionImageDICOMHeaderInformation header_info;
	- //std::string tagvalue_string;
	- //char* pEnd;
	-
	- // reveal b-value
	- float bvalue = 0;
	- if( RevealBinaryTagC( philips_bvalue_tag, gdcmReader.GetFile().GetDataSet(), (char*) &bvalue) )
	- {
	-
	- header_info.b_value = std::ceil( bvalue );
	-
	- if( header_info.b_value == 0)
	- header_info.baseline = true;
	- }
	- else
	- {
	- MITK_WARN("diffusion.dicomreader.philips") << "No b-value found. Most probably no diffusion-weighted image.";
	- return false;
	- }
	-
	- gdcm::Tag philips_new_bvalue_tag( 0x0018,0x9087 );
	- double dbvalue = 0;
	- if( RevealBinaryTagC( philips_new_bvalue_tag, gdcmReader.GetFile().GetDataSet(), (char*) &dbvalue) )
	- {
	- MITK_INFO("philips.dicom.diffusion.bvalue") << dbvalue;
	- }
	-
	- if( header_info.baseline )
	- {
	- // no direction in unweighted images
	- header_info.g_vector.fill(0);
	- }
	- else
	- {
	- MITK_INFO("philips.dicom.diffusion.gradientdir") << "Parsing gradient direction.";
	-
	- gdcm::Tag philips_gradient_direction_new( 0x0018, 0x9089 );
	- double gr_dir_arr[3] = {1,0,-1};
	-
	- if( RevealBinaryTagC( philips_gradient_direction_new, gdcmReader.GetFile().GetDataSet(), (char*) &gr_dir_arr ) )
	- {
	- MITK_INFO("philips.dicom.diffusion.gradient") << "(" << gr_dir_arr[0] <<"," << gr_dir_arr[1] <<"," <<gr_dir_arr[2] <<")";
	- }
	-
	- header_info.g_vector.copy_in( &gr_dir_arr[0] );
	- if( header_info.g_vector.two_norm() < vnl_math::eps )
	- {
	- header_info.g_vector.fill(1);
	- header_info.isotropic = true;
	- }
	- }
	-
	- this->m_HeaderInformationList.push_back( header_info );
	-
	- return true;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkDiffusionHeaderSiemensDICOMFileHelper.cpp b/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkDiffusionHeaderSiemensDICOMFileHelper.cpp
	deleted file mode 100644
	index d5e17f2e14..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkDiffusionHeaderSiemensDICOMFileHelper.cpp
	+++ /dev/null
	@@ -1,42 +0,0 @@
	-#include "mitkDiffusionHeaderSiemensDICOMFileHelper.h"
	-
	-#include <cstdlib>
	-#include <cmath>
	-
	-mitk::SiemensDiffusionHeaderType mitk::GetHeaderType( std::string header )
	-{
	- // The CSA2 format begins with the string ‘SV10’, the CSA1 format does not.
	- if( header.find("SV10") != std::string::npos )
	- {
	- return mitk::SIEMENS_CSA2;
	- }
	- else
	- {
	- return mitk::SIEMENS_CSA1;
	- }
	-}
	-
	-bool mitk::ParseInputString( std::string input, std::vector<double>& values, Siemens_Header_Format format_specs )
	-{
	- // TODO : Compute offset based on the format_specs, where does the 84 come from???
	- int offset = 84;
	- int vm = *(input.c_str() + format_specs.NameLength );
	-
	- for (int k = 0; k < vm; k++)
	- {
	- int itemLength = *(input.c_str() + offset + 4);
	-
	- int strideSize = static_cast<int> (ceil(static_cast<double>(itemLength)/4) * 4);
	- std::string valueString = input.substr( offset+16, itemLength );
	-
	- double value = atof( valueString.c_str() );
	- values.push_back( value );
	-
	- offset += 16+strideSize;
	- }
	-
	- // If there are no values it is invalid
	- return (values.size() > 0 );
	-}
	-
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkDiffusionHeaderSiemensDICOMFileReader.cpp b/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkDiffusionHeaderSiemensDICOMFileReader.cpp
	deleted file mode 100644
	index 1c9386429b..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkDiffusionHeaderSiemensDICOMFileReader.cpp
	+++ /dev/null
	@@ -1,250 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkDiffusionHeaderSiemensDICOMFileReader.h"
	-#include "mitkDiffusionHeaderSiemensDICOMFileHelper.h"
	-#include "mitkDiffusionHeaderDICOMFileReader.h"
	-
	-#include "gdcmScanner.h"
	-#include "gdcmReader.h"
	-
	-#include <vnl/vnl_math.h>
	-
	-static bool GetTagFromHierarchy( std::vector< gdcm::Tag > hierarchy, const gdcm::Tag& t_tag, const gdcm::DataSet& dataset, gdcm::DataSet& target)
	-{
	- if( hierarchy.empty() )
	- return false;
	-
	- const gdcm::DataElement& de = dataset.GetDataElement( hierarchy.at(0) );
	- const auto seq = de.GetValueAsSQ();
	-
	- if (seq==nullptr)
	- return false;
	-
	- // last level of hierarchy, retrieve the first apperance
	- if( hierarchy.size() == 1 )
	- {
	- gdcm::Item& item2 = seq->GetItem(1);
	- gdcm::DataSet& nestedds2 = item2.GetNestedDataSet();
	-
	- const gdcm::DataElement& nde2 = nestedds2.GetDataElement( t_tag );
	-
	- if( !nde2.IsEmpty() )
	- {
	- target = nestedds2;
	- return true;
	- }
	- else
	- {
	- return false;
	- }
	- }
	- else
	- {
	- if( seq->FindDataElement( hierarchy.at(1) ) )
	- {
	- for( gdcm::SequenceOfItems::SizeType i=1; i< seq->GetNumberOfItems(); i++ )
	- {
	- gdcm::Item& item = seq->GetItem(i);
	- gdcm::DataSet &nestedds = item.GetNestedDataSet();
	-
	- // recursive call
	- return GetTagFromHierarchy( std::vector< gdcm::Tag >( hierarchy.begin() + 1, hierarchy.end() ), t_tag, nestedds, target);
	- }
	- }
	-
	- return false;
	- }
	-
	-}
	-
	-/**
	- * @brief Extract b value from the siemens diffusion tag
	- */
	-bool mitk::DiffusionHeaderSiemensDICOMFileReader
	-::ExtractSiemensDiffusionTagInformation( std::string tag_value, mitk::DiffusionImageDICOMHeaderInformation& values)
	-{
	- SiemensDiffusionHeaderType hformat = mitk::GetHeaderType( tag_value );
	- Siemens_Header_Format specs = this->m_SiemensFormatsCollection.at( hformat );
	-
	- MITK_DEBUG << " Header format: " << hformat;
	- MITK_DEBUG << " :: Retrieving b value. ";
	-
	- std::string::size_type tag_position =
	- tag_value.find( "B_value", 0 );
	-
	- if( tag_position == std::string::npos )
	- {
	- MITK_ERROR << "No b value information found. ";
	- return false;
	- }
	-
	- std::string value_string = tag_value.substr( tag_position, tag_value.size() - tag_position + 1 );
	-
	- std::vector<double> value_array;
	- if( ParseInputString(value_string, value_array, specs) )
	- {
	- values.b_value = value_array.at(0);
	- }
	- else
	- {
	- MITK_INFO("diffusion.dicomreader.siemens") << "No b-value tag found. ";
	- return false;
	- }
	-
	- // search for GradientDirectionInformation if the bvalue is not null
	- if( values.b_value > 0 )
	- {
	- std::string::size_type tag_position = tag_value.find( "DiffusionGradientDirection", 0 );
	- // Possibly it is a IVIM dataset, i.e. the gradient direction is not relevant
	- // and possibly either not set or set to zero
	- if( tag_position == std::string::npos )
	- {
	- MITK_WARN << "No gradient direction information, but non-zero b-value. Possibly an IVIM dataset. " << "\n"
	- << "Setting gradient to (1,1,1).";
	-
	- values.isotropic = true;
	- values.g_vector.fill(1);
	- return false;
	- }
	-
	- value_array.clear();
	- std::string gradient_direction_str = tag_value.substr( tag_position, tag_value.size() - tag_position + 1 );
	-
	- if( ParseInputString(gradient_direction_str, value_array, specs) )
	- {
	- if( value_array.size() != 3 )
	- {
	- MITK_ERROR << " Retrieved gradient information of length " << value_array.size();
	- return false;
	- }
	-
	- for( unsigned int i=0; i<value_array.size(); i++)
	- {
	- values.g_vector[i] = value_array.at(i);
	- }
	-
	- // Test for isotropic data (i.e. IVIM)
	- if( values.g_vector.two_norm() < vnl_math::eps )
	- {
	- values.g_vector.fill(1);
	- values.isotropic = true;
	- }
	- }
	-
	- }
	- else
	- {
	- values.baseline = true;
	- }
	-
	- return true;
	-}
	-
	-mitk::DiffusionHeaderSiemensDICOMFileReader
	-::DiffusionHeaderSiemensDICOMFileReader()
	-{
	- Siemens_Header_Format Siemens_CSA1_Format( 64, sizeof(int32_t), 4, sizeof(int32_t), sizeof(int32_t) );
	- Siemens_Header_Format Siemens_CSA2_Format( 64, sizeof(int32_t), 4, sizeof(int32_t), sizeof(int32_t) );
	-
	- m_SiemensFormatsCollection.push_back( Siemens_CSA1_Format );
	- m_SiemensFormatsCollection.push_back( Siemens_CSA2_Format );
	-}
	-
	-mitk::DiffusionHeaderSiemensDICOMFileReader
	-::~DiffusionHeaderSiemensDICOMFileReader()
	-{
	-
	-}
	-
	-bool mitk::DiffusionHeaderSiemensDICOMFileReader
	-::ReadDiffusionHeader(std::string filename)
	-{
	- gdcm::Reader gdcmReader;
	- gdcmReader.SetFileName( filename.c_str() );
	-
	- gdcmReader.Read();
	-
	- MITK_INFO << " -- Analyzing: " << filename;
	-
	- bool retVal = false;
	-
	- const gdcm::DataSet& dataset = gdcmReader.GetFile().GetDataSet();
	-
	- const gdcm::Tag t_sie_diffusion( 0x0029,0x1010 );
	- //const gdcm::Tag t_sie_diffusion_vec( 0x0029,0x100e );
	- //const gdcm::Tag t_sie_diffusion2( 0x0029,0x100c );
	-
	- std::string siemens_diffusionheader_str;
	- if( RevealBinaryTag( t_sie_diffusion, dataset, siemens_diffusionheader_str ) )
	- {
	- DiffusionImageDICOMHeaderInformation values;
	- this->ExtractSiemensDiffusionTagInformation( siemens_diffusionheader_str, values );
	-
	- m_HeaderInformationList.push_back( values );
	- retVal = true;
	- }
	- else
	- {
	- const gdcm::Tag t_sie_bvalue( 0x0018, 0x9087);
	- const gdcm::Tag t_sie_gradient( 0x0021, 0x1146);
	-
	- std::vector< gdcm::Tag > bv_hierarchy;
	- bv_hierarchy.push_back( gdcm::Tag(0x5200,0x9230) );
	- bv_hierarchy.push_back( gdcm::Tag(0x0018,0x9117) );
	-
	- gdcm::DataSet bvalueset;
	- GetTagFromHierarchy( bv_hierarchy, t_sie_bvalue, dataset, bvalueset );
	-
	- DiffusionImageDICOMHeaderInformation values;
	- double dbvalue = 0;
	- if( mitk::RevealBinaryTagC( t_sie_bvalue, bvalueset, (char*) &dbvalue) )
	- {
	- MITK_INFO("siemens.dicom.diffusion.bvalue") << dbvalue;
	- values.b_value = std::ceil( dbvalue );
	-
	- if( values.b_value == 0)
	- values.baseline = true;
	- }
	-
	- if( !values.baseline )
	- {
	- std::vector< gdcm::Tag > g_hierarchy;
	- g_hierarchy.push_back( gdcm::Tag(0x5200,0x9230) );
	- g_hierarchy.push_back( gdcm::Tag(0x0021,0x11fe) );
	-
	- GetTagFromHierarchy( g_hierarchy, t_sie_gradient, dataset, bvalueset );
	-
	- double gr_dir_arr[3] = {1,0,-1};
	- if( mitk::RevealBinaryTagC( t_sie_gradient, bvalueset, (char*) &gr_dir_arr ) )
	- {
	- MITK_INFO("siemens.dicom.diffusion.gradient") << "(" << gr_dir_arr[0] <<"," << gr_dir_arr[1] <<"," <<gr_dir_arr[2] <<")";
	- }
	-
	- values.g_vector.copy_in( &gr_dir_arr[0] );
	- }
	-
	- if( true )
	- {
	- m_HeaderInformationList.push_back( values );
	- retVal = true;
	- }
	- }
	-
	- return retVal;
	-
	-
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkDiffusionHeaderSiemensMosaicDICOMFileReader.cpp b/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkDiffusionHeaderSiemensMosaicDICOMFileReader.cpp
	deleted file mode 100644
	index cda9e35bd3..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkDiffusionHeaderSiemensMosaicDICOMFileReader.cpp
	+++ /dev/null
	@@ -1,143 +0,0 @@
	-#include "mitkDiffusionHeaderSiemensDICOMFileHelper.h"
	-#include "mitkDiffusionHeaderSiemensMosaicDICOMFileReader.h"
	-
	-#include <sstream>
	-
	-mitk::DiffusionHeaderSiemensMosaicDICOMFileReader::DiffusionHeaderSiemensMosaicDICOMFileReader()
	- : DiffusionHeaderSiemensDICOMFileReader()
	-{
	-
	-}
	-
	-mitk::DiffusionHeaderSiemensMosaicDICOMFileReader
	-::~DiffusionHeaderSiemensMosaicDICOMFileReader()
	-{
	-
	-}
	-
	-void mitk::DiffusionHeaderSiemensMosaicDICOMFileReader
	-::RetrieveMosaicInformation(std::string filename)
	-{
	- // retrieve also mosaic information
	- if( !this->ReadDiffusionHeader( filename ) )
	- {
	- MITK_ERROR << "Using MOSAIC Reader for non-mosaic files ";
	- }
	-
	- gdcm::Reader gdcmReader;
	- gdcmReader.SetFileName( filename.c_str() );
	-
	- gdcmReader.Read();
	- const gdcm::DataSet& dataset = gdcmReader.GetFile().GetDataSet();
	-
	- // (0018,0088) DS [2.5] # 4, 1 SpacingBetweenSlices
	- // important for mosaic data
	- std::string spacing_between_slices;
	- if( RevealBinaryTag( gdcm::Tag(0x0018, 0x0088 ), dataset, spacing_between_slices ) )
	- {
	- std::istringstream ifs_spacing(spacing_between_slices );
	- ifs_spacing >> this->m_MosaicDescriptor.spacing[2];
	- }
	-
	- //(0028,0030) DS [2.5\2.5] # 8, 2 PixelSpacing
	- std::string inplace_spacing;
	- if( RevealBinaryTag( gdcm::Tag(0x0028, 0x0030 ), dataset, inplace_spacing ) )
	- {
	- std::stringstream iplss( inplace_spacing );
	- std::string buffer;
	- unsigned int idx=0;
	- while( std::getline( iplss, buffer, '\\' ) )
	- {
	- std::istringstream substream(buffer);
	- substream >> this->m_MosaicDescriptor.spacing[idx++];
	- }
	- }
	-
	- // (0020,0032) DS [-802.51815986633\-801.18644070625\-30.680992126465] # 50, 3 ImagePositionPatient
	- std::string position_patient;
	- if( RevealBinaryTag( gdcm::Tag( 0x0028, 0x0032), dataset, position_patient) )
	- {
	- std::stringstream ppass( inplace_spacing );
	- std::string buffer;
	- unsigned int idx=0;
	- while( std::getline( ppass, buffer, '\\' ) )
	- {
	- std::istringstream substream(buffer);
	- substream >> this->m_MosaicDescriptor.origin[idx++];
	- }
	- }
	-
	-}
	-
	-bool mitk::DiffusionHeaderSiemensMosaicDICOMFileReader
	-::ReadDiffusionHeader(std::string filename)
	-{
	- gdcm::Reader gdcmReader;
	- gdcmReader.SetFileName( filename.c_str() );
	-
	- gdcmReader.Read();
	-
	- MITK_INFO << " -- Analyzing: " << filename;
	-
	- const gdcm::DataSet& dataset = gdcmReader.GetFile().GetDataSet();
	-
	- const gdcm::Tag t_sie_diffusion( 0x0029,0x1010 );
	- const gdcm::Tag t_sie_diffusion_alt( 0x0029,0x1110 );
	- std::string siemens_diffusionheader_str;
	-
	- if( RevealBinaryTag( t_sie_diffusion, dataset, siemens_diffusionheader_str )
	- \|\| RevealBinaryTag( t_sie_diffusion_alt, dataset, siemens_diffusionheader_str) )
	- {
	- mitk::DiffusionImageMosaicDICOMHeaderInformation header_values;
	- // wait for success
	- if( !this->ExtractSiemensDiffusionTagInformation( siemens_diffusionheader_str, header_values ))
	- return false;
	-
	- mitk::SiemensDiffusionHeaderType hformat = GetHeaderType( siemens_diffusionheader_str );
	- Siemens_Header_Format specs = this->m_SiemensFormatsCollection.at( hformat );
	-
	- std::string::size_type tag_position = siemens_diffusionheader_str.find( "NumberOfImagesInMosaic", 0 );
	- if( tag_position != std::string::npos )
	- {
	- std::vector<double> value_array;
	- ParseInputString( siemens_diffusionheader_str.substr( tag_position, siemens_diffusionheader_str.size() - tag_position + 1 ),
	- value_array,
	- specs
	- );
	-
	- header_values.n_images = value_array[0];
	- this->m_MosaicDescriptor.nimages = value_array[0];
	- }
	-
	- tag_position = siemens_diffusionheader_str.find("SliceNormalVector", 0);
	- if( tag_position != std::string::npos )
	- {
	- std::vector<double> value_array;
	- ParseInputString( siemens_diffusionheader_str.substr( tag_position, siemens_diffusionheader_str.size() - tag_position + 1 ),
	- value_array,
	- specs
	- );
	-
	- MITK_DEBUG << "SliceNormal";
	- for( unsigned int i=0; i<value_array.size(); i++)
	- {
	- MITK_DEBUG << value_array.at(i);
	- }
	-
	- if( value_array.size() > 2 )
	- {
	- header_values.slicenormalup = (value_array[2] > 0);
	- this->m_MosaicDescriptor.slicenormalup = ( value_array[2] > 0);
	- }
	-
	- }
	-
	-
	-
	- m_HeaderInformationList.push_back( header_values );
	-
	- }
	-
	- return (m_HeaderInformationList.size() > 0);
	-
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkGEDicomDiffusionImageHeaderReader.cpp b/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkGEDicomDiffusionImageHeaderReader.cpp
	deleted file mode 100644
	index ec4b280d0e..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkGEDicomDiffusionImageHeaderReader.cpp
	+++ /dev/null
	@@ -1,127 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkGEDicomDiffusionImageHeaderReader.h"
	-
	-#include <mitkLocaleSwitch.h>
	-
	-
	-#include "gdcmGlobal.h"
	-#include "gdcmDict.h"
	-#include "gdcmDicts.h"
	-#include "gdcmDictEntry.h"
	-#include "gdcmDictEntry.h"
	-#include "gdcmDict.h"
	-#include "gdcmFile.h"
	-#include "gdcmSerieHelper.h"
	-
	-
	-mitk::GEDicomDiffusionImageHeaderReader::GEDicomDiffusionImageHeaderReader()
	-{
	-}
	-
	-mitk::GEDicomDiffusionImageHeaderReader::~GEDicomDiffusionImageHeaderReader()
	-{
	-}
	-
	-// do the work
	-void mitk::GEDicomDiffusionImageHeaderReader::Update()
	-{
	-
	- // check if there are filenames
	- if(m_DicomFilenames.size())
	- {
	- mitk::LocaleSwitch localeSwitch("C");
	-
	- // adapted from namic-sandbox
	- // DicomToNrrdConverter.cxx
	-
	- VolumeReaderType::DictionaryArrayRawPointer inputDict
	- = m_VolumeReader->GetMetaDataDictionaryArray();
	-
	- ReadPublicTags();
	-
	- float x0, y0, z0;
	- float x1, y1, z1;
	- std::string tag;
	- tag.clear();
	- itk::ExposeMetaData<std::string> ( (inputDict)[0], "0020\|0032", tag );
	- sscanf( tag.c_str(), "%f\\%f\\%f", &x0, &y0, &z0 );
	- std::cout << "Slice 0: " << tag << std::endl;
	- tag.clear();
	-
	- // assume volume interleaving, i.e. the second dicom file stores
	- // the second slice in the same volume as the first dicom file
	- itk::ExposeMetaData<std::string> ( (inputDict)[1], "0020\|0032", tag );
	- sscanf( tag.c_str(), "%f\\%f\\%f", &x1, &y1, &z1 );
	- std::cout << "Slice 1: " << tag << std::endl;
	- x1 -= x0; y1 -= y0; z1 -= z0;
	- x0 = x1this->m_Output->xSlice + y1this->m_Output->ySlice + z1*this->m_Output->zSlice;
	- if (x0 < 0)
	- {
	- m_SliceOrderIS = false;
	- }
	-
	- ReadPublicTags2();
	-
	- int nSliceInVolume;
	- int nVolume;
	-
	- nSliceInVolume = m_sliceLocations.size();
	- nVolume = m_nSlice/nSliceInVolume;
	-
	- // assume volume interleaving
	- std::cout << "Number of Slices: " << m_nSlice << std::endl;
	- std::cout << "Number of Volume: " << nVolume << std::endl;
	- std::cout << "Number of Slices in each volume: " << nSliceInVolume << std::endl;
	-
	- for (int k = 0; k < m_nSlice; k += nSliceInVolume)
	- {
	- tag.clear();
	- bool exist = itk::ExposeMetaData<std::string> ( (inputDict)[k], "0043\|1039", tag);
	- float b = atof( tag.c_str() );
	- this->m_Output->bValue = b;
	-
	- vnl_vector_fixed<double, 3> vect3d;
	- if (!exist \|\| b == 0)
	- {
	- vect3d.fill( 0 );
	- this->m_Output->DiffusionVector = vect3d;
	- continue;
	- }
	-
	- vect3d.fill( 0 );
	- tag.clear();
	- itk::ExposeMetaData<std::string> ( (inputDict)[k], "0019\|10bb", tag);
	- vect3d[0] = atof( tag.c_str() );
	-
	- tag.clear();
	- itk::ExposeMetaData<std::string> ( (inputDict)[k], "0019\|10bc", tag);
	- vect3d[1] = atof( tag.c_str() );
	-
	- tag.clear();
	- itk::ExposeMetaData<std::string> ( (inputDict)[k], "0019\|10bd", tag);
	- vect3d[2] = atof( tag.c_str() );
	-
	- vect3d.normalize();
	- this->m_Output->DiffusionVector = vect3d;
	- }
	-
	- TransformGradients();
	- }
	-}
	-
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkGroupDiffusionHeadersFilter.cpp b/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkGroupDiffusionHeadersFilter.cpp
	deleted file mode 100644
	index 19f16aff96..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkGroupDiffusionHeadersFilter.cpp
	+++ /dev/null
	@@ -1,157 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#include "mitkGroupDiffusionHeadersFilter.h"
	-
	-
	-mitk::GroupDiffusionHeadersFilter::GroupDiffusionHeadersFilter()
	-{
	- // Modify superclass default values, may be overridden by subclasses
	- this->SetNumberOfRequiredInputs( 1 );
	- this->SetNumberOfRequiredOutputs( 4 );
	-}
	-
	-
	-mitk::GroupDiffusionHeadersFilter::~GroupDiffusionHeadersFilter()
	-{}
	-
	-void mitk::GroupDiffusionHeadersFilter::GenerateOutputInformation()
	-{
	-}
	-
	-void mitk::GroupDiffusionHeadersFilter::Update()
	-{
	- InputType input = static_cast<InputType>( this->GetInput( ) );
	- this->SetNthOutput(0, input);
	-
	- InputType dwi;
	- InputType zerodwi;
	- InputType other;
	-
	- bool foundDWI = false;
	-
	- // check each series' first image
	- unsigned int size = input.size();
	- HeaderPointer header;
	- HeaderPointer dwiHeader;
	- for ( unsigned int i = 0 ; i < size ; ++i )
	- {
	- header = input[i];
	-
	- // list of files
	- if( header->bValue > 0)
	- {
	- header->headerGroup = DHG_NonZeroDiffusionWeighted;
	- if(!foundDWI)
	- dwiHeader = header;
	- foundDWI = true;
	- }
	- else
	- {
	- header->headerGroup = DHG_ZeroDiffusionWeighted;
	- }
	- }
	-
	- if(foundDWI)
	- {
	- for ( unsigned int i = 0 ; i < size ; ++i )
	- {
	- header = input[i];
	-
	- // list of files
	- if( !header->isIdentical(dwiHeader))
	- {
	- header->headerGroup = DHG_Other;
	- }
	- }
	- }
	- else
	- {
	- for ( unsigned int i = 0 ; i < size ; ++i )
	- {
	- header = input[i];
	- header->headerGroup = DHG_Other;
	- }
	- }
	-
	- for ( unsigned int i = 0 ; i < size ; ++i )
	- {
	- header = input[i];
	-
	- switch (header->headerGroup)
	- {
	- case DHG_Other:
	- other.push_back(header);
	- break;
	- case DHG_ZeroDiffusionWeighted:
	- zerodwi.push_back(header);
	- break;
	- case DHG_NonZeroDiffusionWeighted:
	- dwi.push_back(header);
	- break;
	- case DHG_NotYetGrouped:
	- break;
	- }
	- }
	-
	- this->SetNthOutput(1, dwi);
	- this->SetNthOutput(2, zerodwi);
	- this->SetNthOutput(3, other);
	-
	-}
	-
	-void mitk::GroupDiffusionHeadersFilter::SetInput( mitk::GroupDiffusionHeadersFilter::InputType input )
	-{
	- // Process object is not const-correct so the const_cast is required here
	- m_Input = input;
	-}
	-
	-
	-void mitk::GroupDiffusionHeadersFilter::SetInput( const unsigned int& /idx/, mitk::GroupDiffusionHeadersFilter::InputType input )
	-{
	- this->SetInput( input );
	-}
	-
	-
	-mitk::GroupDiffusionHeadersFilter::InputType mitk::GroupDiffusionHeadersFilter::GetInput( void )
	-{
	- return m_Input;
	-}
	-
	-
	-mitk::GroupDiffusionHeadersFilter::InputType mitk::GroupDiffusionHeadersFilter::GetInput( const unsigned int& /idx/ )
	-{
	- return this->GetInput();
	-}
	-
	-mitk::GroupDiffusionHeadersFilter::OutputType
	-mitk::GroupDiffusionHeadersFilter::GetOutput()
	-{
	- return m_Output;
	-}
	-
	-void mitk::GroupDiffusionHeadersFilter::SetNthOutput( const unsigned int& idx, InputType output )
	-{
	- if(idx >= m_Output.size())
	- m_Output.resize(idx+1);
	- m_Output[idx] = output;
	-}
	-
	-void mitk::GroupDiffusionHeadersFilter::operator=( const mitk::GroupDiffusionHeadersFilter::Self& )
	-{}
	-
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkPhilipsDicomDiffusionImageHeaderReader.cpp b/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkPhilipsDicomDiffusionImageHeaderReader.cpp
	deleted file mode 100644
	index 9ab48da865..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkPhilipsDicomDiffusionImageHeaderReader.cpp
	+++ /dev/null
	@@ -1,42 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#include "mitkPhilipsDicomDiffusionImageHeaderReader.h"
	-
	-mitk::PhilipsDicomDiffusionImageHeaderReader::PhilipsDicomDiffusionImageHeaderReader()
	-{
	-}
	-
	-mitk::PhilipsDicomDiffusionImageHeaderReader::~PhilipsDicomDiffusionImageHeaderReader()
	-{
	-}
	-
	-// do the work
	-void mitk::PhilipsDicomDiffusionImageHeaderReader::Update()
	-{
	-
	- // check if there are filenames
	- if(m_DicomFilenames.size())
	- {
	- ReadPublicTags();
	-
	- ReadPublicTags2();
	-
	- TransformGradients();
	-
	- }
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkSiemensDicomDiffusionImageHeaderReader.cpp b/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkSiemensDicomDiffusionImageHeaderReader.cpp
	deleted file mode 100644
	index 951716f314..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkSiemensDicomDiffusionImageHeaderReader.cpp
	+++ /dev/null
	@@ -1,246 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkSiemensDicomDiffusionImageHeaderReader.h"
	-
	-#include <mitkLocaleSwitch.h>
	-
	-
	-#include "gdcmGlobal.h"
	-//#include <gdcmVersion.h>
	-
	-#include "gdcmFile.h"
	-#include "gdcmImageReader.h"
	-#include "gdcmDictEntry.h"
	-#include "gdcmDicts.h"
	-#include "gdcmTag.h"
	-
	-mitk::SiemensDicomDiffusionImageHeaderReader::SiemensDicomDiffusionImageHeaderReader()
	-{
	-}
	-
	-mitk::SiemensDicomDiffusionImageHeaderReader::~SiemensDicomDiffusionImageHeaderReader()
	-{
	-}
	-
	-int mitk::SiemensDicomDiffusionImageHeaderReader::ExtractSiemensDiffusionInformation( std::string tagString, std::string nameString, std::vector<double>& valueArray, int startPos )
	-{
	- std::string::size_type atPosition = tagString.find( nameString, startPos );
	- if ( atPosition == std::string::npos)
	- {
	- return 0;
	- }
	- else
	- {
	- std::string infoAsString = tagString.substr( atPosition, tagString.size()-atPosition+1 );
	- const char * infoAsCharPtr = infoAsString.c_str();
	-
	- int vm = *(infoAsCharPtr+64);
	-
	- int offset = 84;
	- for (int k = 0; k < vm; k++)
	- {
	- int itemLength = *(infoAsCharPtr+offset+4);
	- int strideSize = static_cast<int> (ceil(static_cast<double>(itemLength)/4) * 4);
	- std::string valueString = infoAsString.substr( offset+16, itemLength );
	- valueArray.push_back( atof(valueString.c_str()) );
	- offset += 16+strideSize;
	- }
	- return vm;
	- }
	-}
	-
	-int mitk::SiemensDicomDiffusionImageHeaderReader::ExtractSiemensDiffusionGradientInformation( std::string tagString, std::string nameString, std::vector<double>& valueArray )
	-{
	- int nItems = 0;
	- std::string::size_type pos = -1;
	- while(nItems != 3)
	- {
	- nItems = ExtractSiemensDiffusionInformation( tagString, nameString, valueArray, pos+1 );
	- pos = tagString.find( nameString, pos+1 );
	- if ( pos == std::string::npos )
	- {
	- break;
	- }
	- }
	- return nItems;
	-}
	-
	-// do the work
	-void mitk::SiemensDicomDiffusionImageHeaderReader::Update()
	-{
	-
	- // check if there are filenames
	- if(m_DicomFilenames.size())
	- {
	- mitk::LocaleSwitch localeSwitch("C");
	-
	- // adapted from slicer
	- // DicomToNrrdConverter.cxx
	-
	- VolumeReaderType::DictionaryArrayRawPointer
	- inputDict = m_VolumeReader->GetMetaDataDictionaryArray();
	-
	- ReadPublicTags();
	-
	- float x0, y0, z0;
	- float x1, y1, z1;
	- std::string tag;
	- tag.clear();
	- itk::ExposeMetaData<std::string> ( (inputDict)[0], "0020\|0032", tag );
	- sscanf( tag.c_str(), "%f\\%f\\%f", &x0, &y0, &z0 );
	- //MITK_INFO << "Slice 0: " << tag << std::endl;
	- tag.clear();
	-
	- // assume volume interleaving, i.e. the second dicom file stores
	- // the second slice in the same volume as the first dicom file
	- if((*inputDict).size() > 1)
	- {
	- itk::ExposeMetaData<std::string> ( (inputDict)[1], "0020\|0032", tag );
	- sscanf( tag.c_str(), "%f\\%f\\%f", &x1, &y1, &z1 );
	- //MITK_INFO << "Slice 1: " << tag << std::endl;
	- x1 -= x0; y1 -= y0; z1 -= z0;
	- x0 = x1this->m_Output->xSlice + y1this->m_Output->ySlice + z1*this->m_Output->zSlice;
	- if (x0 < 0)
	- {
	- m_SliceOrderIS = false;
	- }
	- }
	-
	- ReadPublicTags2();
	-
	- int nStride = 1;
	- this->m_Output->nSliceInVolume = m_sliceLocations.size();
	-
	- nStride = this->m_Output->nSliceInVolume;
	-
	- MITK_INFO << m_DicomFilenames[0] << std::endl;
	- MITK_INFO << "Dims " << this->m_Output->nRows << "x"
	- << this->m_Output->nCols << "x" << this->m_Output->nSliceInVolume << " " << std::endl;
	-
	- for (int k = 0; k < m_nSlice; k += nStride )
	- {
	-
	- gdcm::ImageReader reader;
	- reader.SetFileName( m_DicomFilenames[k].c_str() );
	- if( !reader.Read() )
	- {
	- itkExceptionMacro(<< "Cannot read requested file");
	- }
	- const gdcm::File &f = reader.GetFile();
	- const gdcm::DataSet &ds = f.GetDataSet();
	-
	- // gdcm::DataSet ds = header0->GetDataSet();
	- auto it = ds.Begin();
	-
	- // Copy of the header->content
	- // copy information stored in 0029,1010 into a string for parsing
	- for(; it != ds.End(); ++it)
	- {
	- const gdcm::DataElement &ref = *it;
	- if (ref.GetTag() == gdcm::Tag(0x0029,0x1010)) {
	- tag = std::string(ref.GetByteValue()->GetPointer(),ref.GetByteValue()->GetLength());
	- }
	- }
	-
	- // parse B_value from 0029,1010 tag
	- std::vector<double> valueArray(0);
	- vnl_vector_fixed<double, 3> vect3d;
	- int nItems = ExtractSiemensDiffusionInformation(tag, "B_value", valueArray);
	- if (nItems != 1 \|\| valueArray[0] == 0) // did not find enough information
	- {
	- tag.clear();
	- MITK_INFO << "Reading diffusion info from 0019\|100c and 0019\|100e tags" << std::endl;
	- bool success = false;
	-
	- for(it = ds.Begin(); it != ds.End(); ++it)
	- {
	- const gdcm::DataElement &ref = *it;
	- if (ref.GetTag() == gdcm::Tag(0x0019,0x100c)) {
	- tag = std::string(ref.GetByteValue()->GetPointer(),ref.GetByteValue()->GetLength());
	- this->m_Output->bValue = atof( tag.c_str() );
	- success = true;
	- }
	- }
	-
	- tag.clear();
	- if(success)
	- {
	- if(this->m_Output->bValue == 0)
	- {
	- MITK_INFO << "BV: 0 (Baseline image)";
	- continue;
	- }
	-
	- success = false;
	- for(it = ds.Begin(); it != ds.End(); ++it)
	- {
	- const gdcm::DataElement &ref = *it;
	- if (ref.GetTag() == gdcm::Tag(0x0019,0x100e)) {
	- tag = std::string(ref.GetByteValue()->GetPointer(),ref.GetByteValue()->GetLength());
	- success = true;
	- }
	- }
	-
	- if(success)
	- {
	- memcpy( &vect3d[0], tag.c_str()+0, 8 );
	- memcpy( &vect3d[1], tag.c_str()+8, 8 );
	- memcpy( &vect3d[2], tag.c_str()+16, 8 );
	- vect3d.normalize();
	- this->m_Output->DiffusionVector = vect3d;
	- TransformGradients();
	- MITK_INFO << "BV: " << this->m_Output->bValue;
	- MITK_INFO << " GD: " << this->m_Output->DiffusionVector;
	- continue;
	- }
	- }
	- }
	- else
	- {
	- MITK_INFO << "Reading diffusion info from 0029,1010 tag" << std::endl;
	- this->m_Output->bValue = valueArray[0];
	-
	- if(this->m_Output->bValue == 0)
	- {
	- MITK_INFO << "BV: 0 (Baseline image)";
	- continue;
	- }
	-
	- valueArray.resize(0);
	- nItems = ExtractSiemensDiffusionGradientInformation(tag, "DiffusionGradientDirection", valueArray);
	- if (nItems == 3)
	- {
	- vect3d[0] = valueArray[0];
	- vect3d[1] = valueArray[1];
	- vect3d[2] = valueArray[2];
	- vect3d.normalize();
	- this->m_Output->DiffusionVector = vect3d;
	- TransformGradients();
	- MITK_INFO << "BV: " << this->m_Output->bValue;
	- MITK_INFO << " GD: " << this->m_Output->DiffusionVector;
	- continue;
	- }
	- }
	-
	- MITK_ERROR << "No diffusion info found, forcing to BASELINE image." << std::endl;
	- this->m_Output->bValue = 0.0;
	- vect3d.fill( 0.0 );
	- this->m_Output->DiffusionVector = vect3d;
	-
	- }
	- }
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkSiemensMosaicDicomDiffusionImageHeaderReader.cpp b/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkSiemensMosaicDicomDiffusionImageHeaderReader.cpp
	deleted file mode 100644
	index 34b444d29b..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/DicomImport/mitkSiemensMosaicDicomDiffusionImageHeaderReader.cpp
	+++ /dev/null
	@@ -1,251 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#include "mitkSiemensMosaicDicomDiffusionImageHeaderReader.h"
	-
	-#include "gdcmGlobal.h"
	-//#include "gdcmVersion.h"
	-
	-#include "gdcmFile.h"
	-#include "gdcmImageReader.h"
	-#include "gdcmDict.h"
	-#include "gdcmDicts.h"
	-#include "gdcmDictEntry.h"
	-#include "gdcmDictEntry.h"
	-#include "gdcmDict.h"
	-#include "gdcmFile.h"
	-#include "gdcmSerieHelper.h"
	-
	-
	-mitk::SiemensMosaicDicomDiffusionImageHeaderReader::SiemensMosaicDicomDiffusionImageHeaderReader()
	-{
	-}
	-
	-mitk::SiemensMosaicDicomDiffusionImageHeaderReader::~SiemensMosaicDicomDiffusionImageHeaderReader()
	-{
	-}
	-
	-int mitk::SiemensMosaicDicomDiffusionImageHeaderReader::ExtractSiemensDiffusionInformation( std::string tagString, std::string nameString, std::vector<double>& valueArray )
	-{
	- std::string::size_type atPosition = tagString.find( nameString );
	- if ( atPosition == std::string::npos)
	- {
	- return 0;
	- }
	- else
	- {
	- std::string infoAsString = tagString.substr( atPosition, tagString.size()-atPosition+1 );
	- const char * infoAsCharPtr = infoAsString.c_str();
	-
	- int vm = *(infoAsCharPtr+64);
	- std::string vr = infoAsString.substr( 68, 4 );
	- //int syngodt = *(infoAsCharPtr+72);
	- //int nItems = *(infoAsCharPtr+76);
	- //int localDummy = *(infoAsCharPtr+80);
	-
	- int offset = 84;
	- for (int k = 0; k < vm; k++)
	- {
	- int itemLength = *(infoAsCharPtr+offset+4);
	- int strideSize = static_cast<int> (ceil(static_cast<double>(itemLength)/4) * 4);
	- std::string valueString = infoAsString.substr( offset+16, itemLength );
	- valueArray.push_back( atof(valueString.c_str()) );
	- offset += 16+strideSize;
	- }
	- return vm;
	- }
	-}
	-
	-// do the work
	-void mitk::SiemensMosaicDicomDiffusionImageHeaderReader::Update()
	-{
	-
	- // check if there are filenames
	- if(m_DicomFilenames.size())
	- {
	- // adapted from namic-sandbox
	- // DicomToNrrdConverter.cxx
	-
	- VolumeReaderType::DictionaryArrayRawPointer inputDict
	- = m_VolumeReader->GetMetaDataDictionaryArray();
	-
	- ReadPublicTags();
	-
	- int mMosaic = 0; // number of raws in each mosaic block;
	- int nMosaic = 0; // number of columns in each mosaic block
	-
	- std::cout << "Siemens SliceMosaic......" << std::endl;
	-
	- m_SliceOrderIS = false;
	-
	- // for siemens mosaic image, figure out mosaic slice order from 0029\|1010
	- std::string tag;
	- tag.clear();
	-
	- gdcm::ImageReader reader;
	- reader.SetFileName( m_DicomFilenames[0].c_str() );
	- if( !reader.Read() )
	- {
	- itkExceptionMacro(<< "Cannot read requested file");
	- }
	- const gdcm::File &f = reader.GetFile();
	- const gdcm::DataSet &ds = f.GetDataSet();
	-
	- // gdcm::DataSet ds = header0->GetDataSet();
	- auto it = ds.Begin();
	-
	- // Copy of the header->content
	- // copy information stored in 0029,1010 into a string for parsing
	- for(; it != ds.End(); ++it)
	- {
	- const gdcm::DataElement &ref = *it;
	- if (ref.GetTag() == gdcm::Tag(0x0029,0x1010)) {
	- tag = std::string(ref.GetByteValue()->GetPointer(),ref.GetByteValue()->GetLength());
	- }
	- }
	-
	- // parse SliceNormalVector from 0029,1010 tag
	- std::vector<double> valueArray(0);
	- int nItems = ExtractSiemensDiffusionInformation(tag, "SliceNormalVector", valueArray);
	- if (nItems != 3) // did not find enough information
	- {
	- std::cout << "Warning: Cannot find complete information on SliceNormalVector in 0029\|1010\n";
	- std::cout << " Slice order may be wrong.\n";
	- }
	- else if (valueArray[2] > 0)
	- {
	- m_SliceOrderIS = true;
	- }
	-
	- // parse NumberOfImagesInMosaic from 0029,1010 tag
	- valueArray.resize(0);
	- nItems = ExtractSiemensDiffusionInformation(tag, "NumberOfImagesInMosaic", valueArray);
	-
	- // Hot-Fix for Bug 14459, no valid Tag (0029,1010)
	- if (valueArray.size() < 1) // NO data was found
	- {
	- MITK_ERROR << "MOSAIC Image has no valid tag (0029,1010). ABORTING" << std::endl;
	- mitkThrow() << "MOSAIC Image has no valid tag (0029,1010). ABORTING";
	- return;
	- }
	- if (nItems == 0) // did not find enough information
	- {
	- std::cout << "Warning: Cannot find complete information on NumberOfImagesInMosaic in 0029\|1010\n";
	- std::cout << " Resulting image may contain empty slices.\n";
	- }
	- else
	- {
	- this->m_Output->nSliceInVolume = static_cast<int>(valueArray[0]);
	- mMosaic = static_cast<int> (ceil(sqrt(valueArray[0])));
	- nMosaic = mMosaic;
	- }
	- std::cout << "Mosaic in " << mMosaic << " X " << nMosaic << " blocks (total number of blocks = " << valueArray[0] << ").\n";
	-
	-
	- ReadPublicTags2();
	-
	- int nStride = 1;
	-
	- std::cout << "Data in Siemens Mosaic Format\n";
	- //nVolume = nSlice;
	- //std::cout << "Number of Volume: " << nVolume << std::endl;
	- std::cout << "Number of Slices in each volume: " << this->m_Output->nSliceInVolume << std::endl;
	- nStride = 1;
	-
	- for (int k = 0; k < m_nSlice; k += nStride )
	- {
	- gdcm::ImageReader reader;
	- reader.SetFileName( m_DicomFilenames[0].c_str() );
	- if( !reader.Read() )
	- {
	- itkExceptionMacro(<< "Cannot read requested file");
	- }
	- const gdcm::File &f = reader.GetFile();
	- const gdcm::DataSet &ds = f.GetDataSet();
	-
	- // gdcm::DataSet ds = header0->GetDataSet();
	- auto it = ds.Begin();
	-
	- // Copy of the header->content
	- // copy information stored in 0029,1010 into a string for parsing
	- for(; it != ds.End(); ++it)
	- {
	- const gdcm::DataElement &ref = *it;
	- if (ref.GetTag() == gdcm::Tag(0x0029,0x1010)) {
	- tag = std::string(ref.GetByteValue()->GetPointer(),ref.GetByteValue()->GetLength());
	- }
	- }
	-
	- // parse B_value from 0029,1010 tag
	- std::vector<double> valueArray(0);
	- vnl_vector_fixed<double, 3> vect3d;
	- int nItems = ExtractSiemensDiffusionInformation(tag, "B_value", valueArray);
	- if (nItems != 1 \|\| valueArray[0] == 0) // did not find enough information
	- {
	- MITK_INFO << "Reading diffusion info from 0019\|100c and 0019\|100e tags";
	- tag.clear();
	- bool success = itk::ExposeMetaData<std::string> ( (inputDict)[0], "0019\|100c", tag );
	- if(success)
	- {
	- this->m_Output->bValue = atof( tag.c_str() );
	- tag.clear();
	- success = itk::ExposeMetaData<std::string> ( (inputDict)[k], "0019\|100e", tag);
	- if(success)
	- {
	- memcpy( &vect3d[0], tag.c_str()+0, 8 );
	- memcpy( &vect3d[1], tag.c_str()+8, 8 );
	- memcpy( &vect3d[2], tag.c_str()+16, 8 );
	- vect3d.normalize();
	- this->m_Output->DiffusionVector = vect3d;
	- TransformGradients();
	- MITK_INFO << "BV: " << this->m_Output->bValue;
	- MITK_INFO << " GD: " << this->m_Output->DiffusionVector << std::endl;
	- continue;
	- }
	- }
	- }
	- else
	- {
	- MITK_INFO << "Reading diffusion info from 0029\|1010 tags";
	- this->m_Output->bValue = valueArray[0];
	-
	- // parse DiffusionGradientDirection from 0029,1010 tag
	- valueArray.resize(0);
	- nItems = ExtractSiemensDiffusionInformation(tag, "DiffusionGradientDirection", valueArray);
	- if (nItems == 3)
	- {
	- vect3d[0] = valueArray[0];
	- vect3d[1] = valueArray[1];
	- vect3d[2] = valueArray[2];
	- vect3d.normalize();
	- this->m_Output->DiffusionVector = vect3d;
	- TransformGradients();
	- MITK_INFO << "BV: " << this->m_Output->bValue;
	- MITK_INFO << " GD: " << this->m_Output->DiffusionVector;
	- continue;
	- }
	- }
	-
	- MITK_ERROR << "No diffusion info found, assuming BASELINE" << std::endl;
	- this->m_Output->bValue = 0.0;
	- vect3d.fill( 0.0 );
	- this->m_Output->DiffusionVector = vect3d;
	-
	- }
	-
	- }
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCorrectionFilter.cpp b/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCorrectionFilter.cpp
	deleted file mode 100644
	index 148a29ea18..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCorrectionFilter.cpp
	+++ /dev/null
	@@ -1,117 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef MITKDIFFUSIONIMAGECORRECTIONFILTER_CPP
	-#define MITKDIFFUSIONIMAGECORRECTIONFILTER_CPP
	-
	-#include "mitkDiffusionImageCorrectionFilter.h"
	-
	-#include <vnl/algo/vnl_symmetric_eigensystem.h>
	-#include <vnl/vnl_inverse.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-
	-typedef mitk::DiffusionPropertyHelper DPH;
	-
	-mitk::DiffusionImageCorrectionFilter::DiffusionImageCorrectionFilter()
	-{
	-
	-}
	-
	-
	-mitk::DiffusionImageCorrectionFilter::TransformMatrixType
	-mitk::DiffusionImageCorrectionFilter
	-::GetRotationComponent(const TransformMatrixType &A)
	-{
	- TransformMatrixType B;
	-
	- B = A * A.transpose();
	-
	- // get the eigenvalues and eigenvectors
	- typedef double MType;
	- vnl_vector< MType > eigvals;
	- vnl_matrix< MType > eigvecs;
	- vnl_symmetric_eigensystem_compute< MType > ( B, eigvecs, eigvals );
	-
	- vnl_matrix_fixed< MType, 3, 3 > eigvecs_fixed;
	- eigvecs_fixed.set_columns(0, eigvecs );
	-
	- TransformMatrixType C;
	- C.set_identity();
	-
	- vnl_vector_fixed< MType, 3 > eigvals_sqrt;
	- for(unsigned int i=0; i<3; i++)
	- {
	- C(i,i) = std::sqrt( eigvals[i] );
	- }
	-
	- TransformMatrixType S = vnl_inverse( eigvecs_fixed * C * vnl_inverse( eigvecs_fixed )) * A;
	-
	- return S;
	-}
	-
	-
	-void mitk::DiffusionImageCorrectionFilter
	-::CorrectDirections( const TransformsVectorType& transformations)
	-{
	- if( m_SourceImage.IsNull() )
	- {
	- mitkThrow() << " No diffusion image given! ";
	- }
	-
	- DPH::GradientDirectionsContainerType::Pointer directions = DPH::GetGradientContainer(m_SourceImage);
	- DPH::GradientDirectionsContainerType::Pointer corrected_directions = DPH::GradientDirectionsContainerType::New();
	-
	- mitk::BValueMapProperty::BValueMap bval_map = DPH::GetBValueMap(m_SourceImage);
	- size_t first_unweighted_index = bval_map.begin()->second.front();
	-
	- unsigned int transformed = 0;
	- for(size_t i=0; i< directions->Size(); i++ )
	- {
	-
	- // skip b-zero images
	- if(i==first_unweighted_index)
	- {
	- corrected_directions->push_back(directions->ElementAt(i));
	- continue;
	- }
	-
	- auto corrected = GetRotationComponent(transformations.at(transformed)) * directions->ElementAt(i);
	- // store the corrected direction
	- corrected_directions->push_back(corrected);
	- transformed++;
	- }
	-
	- // replace the old directions with the corrected ones
	- DPH::SetGradientContainer(m_SourceImage, corrected_directions);
	-}
	-
	-
	-void mitk::DiffusionImageCorrectionFilter::CorrectDirections( const TransformMatrixType& transformation)
	-{
	- if( m_SourceImage.IsNull() )
	- {
	- mitkThrow() << " No diffusion image given! ";
	- }
	- TransformsVectorType transfVec;
	- for (unsigned int i=0; i< DPH::GetGradientContainer(m_SourceImage)->Size();i++)
	- {
	- transfVec.push_back(transformation);
	- }
	- this->CorrectDirections(transfVec);
	-}
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCreationFilter.cpp b/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCreationFilter.cpp
	deleted file mode 100644
	index ab097d9ef1..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageCreationFilter.cpp
	+++ /dev/null
	@@ -1,218 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkDiffusionImageCreationFilter.h"
	-#include "mitkProperties.h"
	-#include "mitkImageTimeSelector.h"
	-
	-#include "mitkImageCast.h"
	-#include "mitkImageToItk.h"
	-#include "mitkImageAccessByItk.h"
	-#include "mitkITKImageImport.h"
	-
	-#include "mitkIOUtil.h"
	-#include <itkComposeImageFilter.h>
	-
	-
	-/**
	- * @brief RemapIntoVectorImage Take a 3d+t image and reinterpret it as vector image
	- * @return vectoriamge
	- */
	-mitk::DiffusionImageCreationFilter::VectorImageType::Pointer
	-mitk::DiffusionImageCreationFilter::RemapIntoVectorImage( mitk::Image::Pointer input)
	-{
	- typedef itk::Image<mitk::DiffusionPropertyHelper::DiffusionPixelType, 3> ImageVolumeType;
	- typedef itk::ComposeImageFilter< ImageVolumeType > ComposeFilterType;
	-
	- ComposeFilterType::Pointer vec_composer = ComposeFilterType::New();
	- mitk::ImageTimeSelector::Pointer t_selector = mitk::ImageTimeSelector::New();
	- t_selector->SetInput( input );
	-
	- for( unsigned int i=0; i< input->GetTimeSteps(); i++)
	- {
	- t_selector->SetTimeNr(i);
	- t_selector->Update();
	-
	- ImageVolumeType::Pointer singleImageItk;
	- mitk::CastToItkImage( t_selector->GetOutput(), singleImageItk );
	-
	- vec_composer->SetInput( i, singleImageItk );
	- }
	-
	- try
	- {
	- vec_composer->Update();
	- }
	- catch( const itk::ExceptionObject& e)
	- {
	- MITK_ERROR << "Caught exception while updating compose filter: " << e.what();
	- }
	-
	- mitk::DiffusionImageCreationFilter::VectorImageType::Pointer vector_image = vec_composer->GetOutput();
	- vector_image->GetPixelContainer()->ContainerManageMemoryOff();
	-
	- return vector_image;
	-}
	-
	-mitk::DiffusionImageCreationFilter::DiffusionImageCreationFilter()
	- : m_ReferenceImage( nullptr )
	-{
	- m_HeaderDescriptorSet = false;
	-
	- this->SetNumberOfRequiredInputs(1);
	- this->SetNumberOfRequiredOutputs(1);
	-}
	-
	-mitk::DiffusionImageCreationFilter::~DiffusionImageCreationFilter()
	-{
	-
	-}
	-
	-void mitk::DiffusionImageCreationFilter::SetReferenceImage( mitk::Image::Pointer reference_image )
	-{
	- if( reference_image.IsNull() )
	- {
	- mitkThrow() << "Null-pointer image provided as reference. ";
	- }
	-
	- if( ! DPH::IsDiffusionWeightedImage(reference_image) )
	- {
	- mitkThrow() << "The image provided as reference is not a diffusion-weighted image. Cannot proceed. ";
	- }
	-
	- this->m_ReferenceImage = reference_image;
	-}
	-
	-void mitk::DiffusionImageCreationFilter::GenerateData()
	-{
	- const mitk::Image::Pointer input_image = this->GetInput(0);
	- if( input_image.IsNull() )
	- {
	- mitkThrow() << "No input specified. Cannot proceed ";
	- }
	-
	- if( !( m_HeaderDescriptorSet ^ m_ReferenceImage.IsNotNull() ) )
	- {
	- mitkThrow() << "Either a header descriptor or a reference diffusion-weighted image have to be provided. Terminating.";
	- }
	-
	- mitk::Image::Pointer outputForCache = this->GetOutput();
	-
	- if( input_image->GetTimeSteps() > 1 )
	- {
	- mitk::Image::Pointer mitkvectorimage = mitk::GrabItkImageMemory<DPH::ImageType>( RemapIntoVectorImage( input_image ));
	- outputForCache->Initialize( mitkvectorimage );
	- }
	- // no need to remap, we expect to have a vector image directly
	- else
	- {
	- outputForCache->Initialize( input_image );
	- }
	-
	- // header information
	- GradientDirectionContainerType::Pointer DiffusionVectors = this->InternalGetGradientDirections( );
	- MeasurementFrameType MeasurementFrame = this->InternalGetMeasurementFrame();
	- float BValue = this->InternalGetBValue();
	-
	- // create BValueMap
	- mitk::BValueMapProperty::BValueMap BValueMap = mitk::BValueMapProperty::CreateBValueMap( DiffusionVectors, BValue );
	- DPH::SetGradientContainer(outputForCache, DiffusionVectors);
	- DPH::SetMeasurementFrame(outputForCache, MeasurementFrame);
	- DPH::SetBValueMap(outputForCache, BValueMap);
	- DPH::SetReferenceBValue(outputForCache, BValue);
	-
	- outputForCache->Modified();
	-}
	-
	-void mitk::DiffusionImageCreationFilter::SetHeaderDescriptor(DiffusionImageHeaderDescriptor header_descriptor)
	-{
	- this->m_HeaderDescriptor = header_descriptor;
	- this->m_HeaderDescriptorSet = true;
	-}
	-
	-mitk::DiffusionImageCreationFilter::MeasurementFrameType
	-mitk::DiffusionImageCreationFilter::InternalGetMeasurementFrame()
	-{
	- MeasurementFrameType MeasurementFrame;
	-
	- if( m_ReferenceImage.IsNotNull() )
	- {
	- MeasurementFrame = DPH::GetMeasurementFrame( m_ReferenceImage );
	- }
	- else if ( m_HeaderDescriptorSet )
	- {
	- MeasurementFrame = m_HeaderDescriptor.m_MeasurementFrame;
	- }
	- else
	- {
	- MeasurementFrame(0,0) = 1;
	- MeasurementFrame(0,1) = 0;
	- MeasurementFrame(0,2) = 0;
	- MeasurementFrame(1,0) = 0;
	- MeasurementFrame(1,1) = 1;
	- MeasurementFrame(1,2) = 0;
	- MeasurementFrame(2,0) = 0;
	- MeasurementFrame(2,1) = 0;
	- MeasurementFrame(2,2) = 1;
	-
	- MITK_WARN << "Created default measurement frame as non provided ( no reference image or header information provided)";
	- }
	-
	- return MeasurementFrame;
	-}
	-
	-mitk::DiffusionImageCreationFilter::GradientDirectionContainerType::Pointer
	-mitk::DiffusionImageCreationFilter::InternalGetGradientDirections()
	-{
	- GradientDirectionContainerType::Pointer DiffusionVectors = GradientDirectionContainerType::New();
	-
	- if( this->m_ReferenceImage )
	- {
	- DiffusionVectors = DPH::GetGradientContainer( this->m_ReferenceImage );
	- }
	- else if ( m_HeaderDescriptorSet )
	- {
	- DiffusionVectors = m_HeaderDescriptor.m_GradientDirections;
	- }
	-
	- return DiffusionVectors;
	-
	-}
	-
	-float mitk::DiffusionImageCreationFilter::InternalGetBValue()
	-{
	- float bvalue = -1;
	-
	- if( m_ReferenceImage.IsNotNull() )
	- {
	- bvalue = DPH::GetReferenceBValue( m_ReferenceImage );
	- }
	- else if ( m_HeaderDescriptorSet )
	- {
	- bvalue = m_HeaderDescriptor.m_BValue;
	- }
	- else
	- {
	- MITK_ERROR << "No reference image and no header descriptor provided.";
	- }
	-
	- return bvalue;
	-}
	-
	-
	-
	-
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageHeaderInformation.cpp b/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageHeaderInformation.cpp
	deleted file mode 100644
	index 7b3897166d..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/DiffusionWeightedImages/mitkDiffusionImageHeaderInformation.cpp
	+++ /dev/null
	@@ -1,28 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkDiffusionImageHeaderInformation.h"
	-
	-mitk::DiffusionImageHeaderInformation::DiffusionImageHeaderInformation()
	-{
	-
	-}
	-
	-mitk::DiffusionImageHeaderInformation::~DiffusionImageHeaderInformation()
	-{
	-
	-}
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/OdfImages/mitkOdfImage.cpp b/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/OdfImages/mitkOdfImage.cpp
	deleted file mode 100644
	index e647906565..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/OdfImages/mitkOdfImage.cpp
	+++ /dev/null
	@@ -1,88 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkOdfImage.h"
	-#include "mitkImageCast.h"
	-#include "itkImage.h"
	-#include "mitkImageVtkAccessor.h"
	-#include "itkOdfToRgbImageFilter.h"
	-#include <mitkProperties.h>
	-
	-mitk::OdfImage::OdfImage() : Image()
	-{
	- m_RgbImage = nullptr;
	- // not needed anymore as soon as all diffusion images are identified via properties anyway
	- this->SetProperty("IsOdfImage", mitk::BoolProperty::New(true));
	-}
	-
	-mitk::OdfImage::~OdfImage()
	-{
	-
	-}
	-
	-const vtkImageData* mitk::OdfImage::GetVtkImageData(int t, int n) const
	-{
	- if(m_RgbImage.IsNull())
	- ConstructRgbImage();
	- return m_RgbImage->GetVtkImageData(t,n);
	-}
	-
	-vtkImageData*mitk::OdfImage::GetVtkImageData(int t, int n)
	-{
	- if(m_RgbImage.IsNull())
	- ConstructRgbImage();
	- return m_RgbImage->GetVtkImageData(t,n);
	-}
	-
	-void mitk::OdfImage::ConstructRgbImage() const
	-{
	- typedef itk::Image<itk::Vector<float,ODF_SAMPLING_SIZE>,3> ImageType;
	- typedef itk::OdfToRgbImageFilter<ImageType> FilterType;
	- FilterType::Pointer filter = FilterType::New();
	-
	- ImageType::Pointer itkvol = ImageType::New();
	- mitk::CastToItkImage(this, itkvol);
	- filter->SetInput(itkvol);
	- filter->Update();
	-
	- m_RgbImage = mitk::Image::New();
	- m_RgbImage->InitializeByItk( filter->GetOutput() );
	- m_RgbImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
	-}
	-
	-const vtkImageData* mitk::OdfImage::GetNonRgbVtkImageData(int t, int n) const
	-{
	- return Superclass::GetVtkImageData(t,n);
	-}
	-
	-vtkImageData* mitk::OdfImage::GetNonRgbVtkImageData(int t, int n)
	-{
	- return Superclass::GetVtkImageData(t,n);
	-}
	-
	-//
	-//void mitk::OdfImage::CopyConstruct(mitk::Image::Pointer img)
	-//{
	-// m_LargestPossibleRegion = img->GetLargestPossibleRegion();
	-// m_RequestedRegion = img->GetRequestedRegion();
	-// m_Channels.push_back(img->GetChannelData(0).GetPointer());
	-// m_Volumes.push_back(img->GetVolumeData(0).GetPointer());
	-// m_Slices.push_back(img->GetSliceData(0).GetPointer());
	-// m_Dimension = img->GetDimension();
	-// m_Dimensions = img->GetDimensions();
	-// m_PixelType = img->GetPixelType();
	-//}
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/OdfImages/mitkOdfImageSource.cpp b/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/OdfImages/mitkOdfImageSource.cpp
	deleted file mode 100644
	index e34cd738ab..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/OdfImages/mitkOdfImageSource.cpp
	+++ /dev/null
	@@ -1,45 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#include "mitkOdfImageSource.h"
	-
	-
	-mitk::OdfImageSource::OdfImageSource()
	-{
	- // Create the output. We use static_cast<> here because we know the default
	- // output must be of type TOutputImage
	- OutputImageType::Pointer output
	- = static_cast<OutputImageType*>(this->MakeOutput(0).GetPointer());
	- Superclass::SetNumberOfRequiredOutputs(1);
	- Superclass::SetNthOutput(0, output.GetPointer());
	-}
	-
	-itk::DataObject::Pointer mitk::OdfImageSource::MakeOutput ( DataObjectPointerArraySizeType /idx/ )
	-{
	- return OutputImageType::New().GetPointer();
	-}
	-
	-
	-itk::DataObject::Pointer mitk::OdfImageSource::MakeOutput( const DataObjectIdentifierType & name )
	-{
	- itkDebugMacro("MakeOutput(" << name << ")");
	- if( this->IsIndexedOutputName(name) )
	- {
	- return this->MakeOutput( this->MakeIndexFromOutputName(name) );
	- }
	- return static_cast<itk::DataObject *>(OutputImageType::New().GetPointer());
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/Properties/mitkBValueMapProperty.cpp b/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/Properties/mitkBValueMapProperty.cpp
	deleted file mode 100644
	index 3e364ab6e7..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/Properties/mitkBValueMapProperty.cpp
	+++ /dev/null
	@@ -1,103 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkBValueMapProperty.h"
	-
	-mitk::BValueMapProperty::BValueMapProperty()
	- : m_BValueMap()
	-{
	-}
	-
	-mitk::BValueMapProperty::BValueMapProperty(const BValueMapProperty& other)
	- : mitk::BaseProperty(other)
	-{
	- m_BValueMap = other.GetBValueMap();
	-}
	-
	-mitk::BValueMapProperty::BValueMapProperty(const BValueMap& bValueMap)
	-{
	- m_BValueMap = bValueMap;
	-}
	-
	-mitk::BValueMapProperty::~BValueMapProperty()
	-{
	-}
	-
	-const mitk::BValueMapProperty::BValueMap & mitk::BValueMapProperty::GetBValueMap() const
	-{
	- return m_BValueMap;
	-}
	-
	-void mitk::BValueMapProperty::SetBValueMap(const BValueMap & map)
	-{
	- this->m_BValueMap = map;
	-}
	-
	-bool mitk::BValueMapProperty::IsEqual(const BaseProperty& property) const
	-{
	- return this->m_BValueMap == static_cast<const Self&>(property).m_BValueMap;
	-}
	-
	-bool mitk::BValueMapProperty::Assign(const BaseProperty& property)
	-{
	- this->m_BValueMap = static_cast<const Self&>(property).m_BValueMap;
	- return true;
	-}
	-
	-mitk::BValueMapProperty::BValueMap mitk::BValueMapProperty::CreateBValueMap(const mitk::BValueMapProperty::GradientDirectionsContainerType * gdc, float referenceBValue)
	-{
	- mitk::BValueMapProperty::BValueMap map;
	-
	- mitk::BValueMapProperty::GradientDirectionsContainerType::ConstIterator gdcit;
	- for( gdcit = gdc->Begin(); gdcit != gdc->End(); ++gdcit)
	- {
	- float keyBValue = mitk::BValueMapProperty::GetBValueOfGradientDirection(gdcit.Index(),referenceBValue, gdc);
	- map[keyBValue].push_back(gdcit.Index());
	- }
	-
	- return map;
	-}
	-
	-
	-float mitk::BValueMapProperty::GetBValueOfGradientDirection(unsigned int i, float referenceBValue, const mitk::BValueMapProperty::GradientDirectionsContainerType * gdc)
	-{
	- if(i > gdc->Size()-1)
	- return -1;
	-
	- if(gdc->ElementAt(i).one_norm() <= 0.0)
	- {
	- return 0;
	- }
	- else
	- {
	- double twonorm = gdc->ElementAt(i).two_norm();
	- double bval = referenceBValuetwonormtwonorm;
	-
	- if (bval<0)
	- bval = ceil(bval - 0.5);
	- else
	- bval = floor(bval + 0.5);
	-
	- return bval;
	- }
	-}
	-
	-itk::LightObject::Pointer mitk::BValueMapProperty::InternalClone() const
	-{
	- itk::LightObject::Pointer result(new Self(*this));
	- result->UnRegister();
	- return result;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/Properties/mitkBValueMapPropertySerializer.cpp b/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/Properties/mitkBValueMapPropertySerializer.cpp
	deleted file mode 100644
	index fe9d8dd741..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/Properties/mitkBValueMapPropertySerializer.cpp
	+++ /dev/null
	@@ -1,131 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef mitkBValueMapPropertySerializer_h_included
	-#define mitkBValueMapPropertySerializer_h_included
	-
	-#include "mitkBasePropertySerializer.h"
	-
	-#include "mitkBValueMapProperty.h"
	-
	-#include <MitkDiffusionCoreExports.h>
	-
	-namespace mitk
	-{
	-
	-class MITKDIFFUSIONCORE_EXPORT BValueMapPropertySerializer : public BasePropertySerializer
	-{
	-
	-protected:
	-
	-
	- void split(const std::string &s, char delim, std::vector<unsigned int> &elems) {
	- std::stringstream ss(s);
	- std::string item;
	- while (std::getline(ss, item, delim)) {
	- elems.push_back(std::atoi(item.c_str()));
	- }
	- }
	-
	- std::vector<unsigned int> split(const std::string &s, char delim) {
	- std::vector<unsigned int> elems;
	- split(s, delim, elems);
	- return elems;
	- }
	-
	-public:
	-
	- mitkClassMacro( BValueMapPropertySerializer, BasePropertySerializer )
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- TiXmlElement* Serialize() override
	- {
	- if (const BValueMapProperty* prop = dynamic_cast<const BValueMapProperty*>(m_Property.GetPointer()))
	- {
	-
	- BValueMapProperty::BValueMap map = prop->GetBValueMap();
	-
	- if(map.empty()) return nullptr;
	-
	- BValueMapProperty::BValueMap::const_iterator it = map.begin();
	- BValueMapProperty::BValueMap::const_iterator end = map.end();
	-
	- auto element = new TiXmlElement("bvaluemap");
	-
	-
	-
	- while (it != end) {
	- auto child = new TiXmlElement("entry");
	- {
	- std::stringstream ss;
	- ss << it->first;
	- child->SetAttribute("key", ss.str());
	- }
	-
	- {
	- std::stringstream ss;
	- for(unsigned int i = 0 ; i < it->second.size(); i++)
	- {
	-
	- ss << it->second[i] << ",";
	- }
	- child->SetAttribute("value", ss.str());
	- }
	- element->InsertEndChild(*child);
	- ++it;
	- }
	-
	- return element;
	- }
	- else return nullptr;
	- }
	-
	-
	- BaseProperty::Pointer Deserialize(TiXmlElement* element) override
	- {
	- if (!element) return nullptr;
	-
	- BValueMapProperty::BValueMap map;
	-
	- TiXmlElement* entry = element->FirstChildElement( "entry" )->ToElement();
	- while(entry != nullptr){
	-
	- std::string key, value;
	- entry->QueryStringAttribute("key",&key);
	- entry->QueryStringAttribute("value",&value);
	-
	- std::vector<unsigned int> indices = split(value.c_str(), ',');
	-
	- map[std::atoi(key.c_str())] = indices;
	- entry = entry->NextSiblingElement( "entry" );
	- }
	-
	- return BValueMapProperty::New(map).GetPointer();
	- }
	-
	-protected:
	-
	- BValueMapPropertySerializer(){}
	- ~BValueMapPropertySerializer() override {}
	-};
	-
	-} // namespace
	-
	-// important to put this into the GLOBAL namespace (because it starts with 'namespace mitk')
	-MITK_REGISTER_SERIALIZER(BValueMapPropertySerializer)
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/Properties/mitkDiffusionPropertyHelper.cpp b/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/Properties/mitkDiffusionPropertyHelper.cpp
	deleted file mode 100644
	index 882f377814..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/Properties/mitkDiffusionPropertyHelper.cpp
	+++ /dev/null
	@@ -1,615 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkDiffusionPropertyHelper.h"
	-#include <mitkITKImageImport.h>
	-#include <mitkImageCast.h>
	-#include <itkImageRegionIterator.h>
	-#include <mitkProperties.h>
	-#include <vnl/algo/vnl_matrix_inverse.h>
	-
	-#include <mitkCoreServices.h>
	-#include <mitkPropertyPersistenceInfo.h>
	-#include <mitkIPropertyDescriptions.h>
	-#include <mitkIPropertyPersistence.h>
	-
	-const std::string mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME = "DWMRI.GradientDirections";
	-const std::string mitk::DiffusionPropertyHelper::ORIGINALGRADIENTCONTAINERPROPERTYNAME = "DWMRI.OriginalGradientDirections";
	-const std::string mitk::DiffusionPropertyHelper::MEASUREMENTFRAMEPROPERTYNAME = "DWMRI.MeasurementFrame";
	-const std::string mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME = "DWMRI.ReferenceBValue";
	-const std::string mitk::DiffusionPropertyHelper::BVALUEMAPPROPERTYNAME = "DWMRI.BValueMap";
	-const std::string mitk::DiffusionPropertyHelper::MODALITY = "DWMRI.Modality";
	-const std::string mitk::DiffusionPropertyHelper::APPLY_MATRIX_TO_GRADIENTS = "DWMRI.ApplyMatrixToGradients";
	-const std::string mitk::DiffusionPropertyHelper::APPLY_MF_TO_GRADIENTS = "DWMRI.ApplyMfToGradients";
	-
	-mitk::DiffusionPropertyHelper::DiffusionPropertyHelper()
	-{
	-}
	-
	-mitk::DiffusionPropertyHelper::~DiffusionPropertyHelper()
	-{
	-}
	-
	-
	-mitk::DiffusionPropertyHelper::ImageType::Pointer mitk::DiffusionPropertyHelper::GetItkVectorImage(mitk::Image* image)
	-{
	- ImageType::Pointer vectorImage = ImageType::New();
	- mitk::CastToItkImage(image, vectorImage);
	- return vectorImage;
	-}
	-
	-mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer
	-mitk::DiffusionPropertyHelper::CalcAveragedDirectionSet(double precision, GradientDirectionsContainerType::Pointer directions)
	-{
	- // save old and construct new direction container
	- GradientDirectionsContainerType::Pointer newDirections = GradientDirectionsContainerType::New();
	-
	- // fill new direction container
	- for(GradientDirectionsContainerType::ConstIterator gdcitOld = directions->Begin();
	- gdcitOld != directions->End(); ++gdcitOld)
	- {
	- // already exists?
	- bool found = false;
	- for(GradientDirectionsContainerType::ConstIterator gdcitNew = newDirections->Begin();
	- gdcitNew != newDirections->End(); ++gdcitNew)
	- {
	- if(AreAlike(gdcitNew.Value(), gdcitOld.Value(), precision))
	- {
	- found = true;
	- break;
	- }
	- }
	-
	- // if not found, add it to new container
	- if(!found)
	- {
	- newDirections->push_back(gdcitOld.Value());
	- }
	- }
	-
	- return newDirections;
	-}
	-
	-void mitk::DiffusionPropertyHelper::AverageRedundantGradients(mitk::Image* image, double precision)
	-{
	- GradientDirectionsContainerType::Pointer oldDirs = GetOriginalGradientContainer(image);
	- GradientDirectionsContainerType::Pointer newDirs = CalcAveragedDirectionSet(precision, oldDirs);
	-
	- // if sizes equal, we do not need to do anything in this function
	- if(oldDirs->size() == newDirs->size())
	- return;
	-
	- // new image
	- ImageType::Pointer oldImage = ImageType::New();
	- mitk::CastToItkImage( image, oldImage);
	- ImageType::Pointer newITKImage = ImageType::New();
	- newITKImage->SetSpacing( oldImage->GetSpacing() ); // Set the image spacing
	- newITKImage->SetOrigin( oldImage->GetOrigin() ); // Set the image origin
	- newITKImage->SetDirection( oldImage->GetDirection() ); // Set the image direction
	- newITKImage->SetLargestPossibleRegion( oldImage->GetLargestPossibleRegion() );
	- newITKImage->SetVectorLength( newDirs->size() );
	- newITKImage->SetBufferedRegion( oldImage->GetLargestPossibleRegion() );
	- newITKImage->Allocate();
	-
	- // average image data that corresponds to identical directions
	- itk::ImageRegionIterator< ImageType > newIt(newITKImage, newITKImage->GetLargestPossibleRegion());
	- newIt.GoToBegin();
	- itk::ImageRegionIterator< ImageType > oldIt(oldImage, oldImage->GetLargestPossibleRegion());
	- oldIt.GoToBegin();
	-
	- // initial new value of voxel
	- ImageType::PixelType newVec;
	- newVec.SetSize(newDirs->size());
	- newVec.AllocateElements(newDirs->size());
	-
	- // find which gradients should be averaged
	- GradientDirectionsContainerType::Pointer oldDirections = oldDirs;
	- std::vector<std::vector<int> > dirIndices;
	- for(GradientDirectionsContainerType::ConstIterator gdcitNew = newDirs->Begin();
	- gdcitNew != newDirs->End(); ++gdcitNew)
	- {
	- dirIndices.push_back(std::vector<int>(0));
	- for(GradientDirectionsContainerType::ConstIterator gdcitOld = oldDirs->Begin();
	- gdcitOld != oldDirections->End(); ++gdcitOld)
	- {
	- if(AreAlike(gdcitNew.Value(), gdcitOld.Value(), precision))
	- {
	- //MITK_INFO << gdcitNew.Value() << " " << gdcitOld.Value();
	- dirIndices[gdcitNew.Index()].push_back(gdcitOld.Index());
	- }
	- }
	- }
	-
	- //int ind1 = -1;
	- while(!newIt.IsAtEnd())
	- {
	- // init new vector with zeros
	- newVec.Fill(0.0);
	-
	- // the old voxel value with duplicates
	- ImageType::PixelType oldVec = oldIt.Get();
	-
	- for(unsigned int i=0; i<dirIndices.size(); i++)
	- {
	- // do the averaging
	- const unsigned int numavg = dirIndices[i].size();
	- unsigned int sum = 0;
	- for(unsigned int j=0; j<numavg; j++)
	- {
	- //MITK_INFO << newVec[i] << " << " << oldVec[dirIndices[i].at(j)];
	- sum += oldVec[dirIndices[i].at(j)];
	- }
	- if(numavg == 0)
	- {
	- MITK_ERROR << "VectorImage: Error on averaging. Possibly due to corrupted data";
	- return;
	- }
	- newVec[i] = sum / numavg;
	- }
	-
	- newIt.Set(newVec);
	-
	- ++newIt;
	- ++oldIt;
	- }
	-
	- mitk::GrabItkImageMemory( newITKImage, image );
	-
	- SetOriginalGradientContainer(image, newDirs);
	- InitializeImage(image);
	- std::cout << std::endl;
	-}
	-
	-void mitk::DiffusionPropertyHelper::ApplyMeasurementFrameAndRotationMatrix(mitk::Image* image)
	-{
	-
	- if( image->GetProperty(mitk::DiffusionPropertyHelper::ORIGINALGRADIENTCONTAINERPROPERTYNAME.c_str()).IsNull() )
	- {
	- return;
	- }
	-
	- GradientDirectionsContainerType::Pointer originalDirections = GetOriginalGradientContainer(image);
	-
	- MeasurementFrameType measurementFrame = GetMeasurementFrame(image);
	-
	- mitk::Vector3D s = image->GetGeometry()->GetSpacing();
	- mitk::VnlVector c0 = image->GetGeometry()->GetMatrixColumn(0)/s[0];
	- mitk::VnlVector c1 = image->GetGeometry()->GetMatrixColumn(1)/s[1];
	- mitk::VnlVector c2 = image->GetGeometry()->GetMatrixColumn(2)/s[2];
	- MeasurementFrameType imageRotationMatrix;
	- imageRotationMatrix[0][0] = c0[0];
	- imageRotationMatrix[1][0] = c0[1];
	- imageRotationMatrix[2][0] = c0[2];
	- imageRotationMatrix[0][1] = c1[0];
	- imageRotationMatrix[1][1] = c1[1];
	- imageRotationMatrix[2][1] = c1[2];
	- imageRotationMatrix[0][2] = c2[0];
	- imageRotationMatrix[1][2] = c2[1];
	- imageRotationMatrix[2][2] = c2[2];
	-
	- GradientDirectionsContainerType::Pointer directions = GradientDirectionsContainerType::New();
	-
	- if( originalDirections.IsNull() \|\| ( originalDirections->size() == 0 ) )
	- {
	- // original direction container was not set
	- return;
	- }
	-
	- bool apply_matrix = true;
	- image->GetPropertyList()->GetBoolProperty(mitk::DiffusionPropertyHelper::APPLY_MATRIX_TO_GRADIENTS.c_str(), apply_matrix);
	- bool apply_mf = true;
	- image->GetPropertyList()->GetBoolProperty(mitk::DiffusionPropertyHelper::APPLY_MF_TO_GRADIENTS.c_str(), apply_mf);
	-
	- if (apply_matrix)
	- {
	- MITK_INFO << "Applying image rotation to diffusion-gradient directions:";
	- std::cout << imageRotationMatrix << std::endl;
	- }
	- if (apply_mf)
	- {
	- MITK_INFO << "Applying measurement frame to diffusion-gradient directions:";
	- std::cout << measurementFrame << std::endl;
	- }
	-
	- int c = 0;
	- for(GradientDirectionsContainerType::ConstIterator gdcit = originalDirections->Begin();
	- gdcit != originalDirections->End(); ++gdcit)
	- {
	- vnl_vector<double> vec = gdcit.Value();
	- if (apply_matrix)
	- vec = vec.pre_multiply(measurementFrame);
	- if (apply_mf)
	- vec = vec.pre_multiply(imageRotationMatrix);
	- directions->InsertElement(c, vec);
	- c++;
	- }
	-
	- SetGradientContainer(image, directions);
	-}
	-
	-void mitk::DiffusionPropertyHelper::UnApplyMeasurementFrameAndRotationMatrix(mitk::Image* image)
	-{
	-
	- if( image->GetProperty(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).IsNull() )
	- {
	- return;
	- }
	-
	- GradientDirectionsContainerType::Pointer modifiedDirections = GetGradientContainer(image);
	-
	- MeasurementFrameType measurementFrame = GetMeasurementFrame(image);
	- measurementFrame = vnl_matrix_inverse<double>(measurementFrame).pinverse();
	-
	- mitk::Vector3D s = image->GetGeometry()->GetSpacing();
	- mitk::VnlVector c0 = image->GetGeometry()->GetMatrixColumn(0)/s[0];
	- mitk::VnlVector c1 = image->GetGeometry()->GetMatrixColumn(1)/s[1];
	- mitk::VnlVector c2 = image->GetGeometry()->GetMatrixColumn(2)/s[2];
	- MeasurementFrameType imageRotationMatrix;
	- imageRotationMatrix[0][0] = c0[0];
	- imageRotationMatrix[1][0] = c0[1];
	- imageRotationMatrix[2][0] = c0[2];
	- imageRotationMatrix[0][1] = c1[0];
	- imageRotationMatrix[1][1] = c1[1];
	- imageRotationMatrix[2][1] = c1[2];
	- imageRotationMatrix[0][2] = c2[0];
	- imageRotationMatrix[1][2] = c2[1];
	- imageRotationMatrix[2][2] = c2[2];
	- imageRotationMatrix = vnl_matrix_inverse<double>(imageRotationMatrix).pinverse();
	-
	- GradientDirectionsContainerType::Pointer directions = GradientDirectionsContainerType::New();
	-
	- if( modifiedDirections.IsNull() \|\| ( modifiedDirections->size() == 0 ) )
	- {
	- // original direction container was not set
	- return;
	- }
	-
	- bool apply_matrix = true;
	- image->GetPropertyList()->GetBoolProperty(mitk::DiffusionPropertyHelper::APPLY_MATRIX_TO_GRADIENTS.c_str(), apply_matrix);
	- bool apply_mf = true;
	- image->GetPropertyList()->GetBoolProperty(mitk::DiffusionPropertyHelper::APPLY_MF_TO_GRADIENTS.c_str(), apply_mf);
	-
	- if (apply_matrix)
	- {
	- MITK_INFO << "Reverting image rotation to diffusion-gradient directions:";
	- std::cout << imageRotationMatrix << std::endl;
	- }
	- if (apply_mf)
	- {
	- MITK_INFO << "Reverting measurement frame to diffusion-gradient directions:";
	- std::cout << measurementFrame << std::endl;
	- }
	-
	- int c = 0;
	- for(GradientDirectionsContainerType::ConstIterator gdcit = modifiedDirections->Begin();
	- gdcit != modifiedDirections->End(); ++gdcit)
	- {
	- vnl_vector<double> vec = gdcit.Value();
	- if (apply_matrix)
	- vec = vec.pre_multiply(imageRotationMatrix);
	- if (apply_mf)
	- vec = vec.pre_multiply(measurementFrame);
	- directions->InsertElement(c, vec);
	- c++;
	- }
	-
	- SetOriginalGradientContainer(image, directions);
	-}
	-
	-void mitk::DiffusionPropertyHelper::SetApplyMatrixToGradients(mitk::Image* image, bool apply)
	-{
	- image->GetPropertyList()->SetProperty( mitk::DiffusionPropertyHelper::APPLY_MATRIX_TO_GRADIENTS.c_str(), mitk::BoolProperty::New(apply) );
	-}
	-
	-void mitk::DiffusionPropertyHelper::SetApplyMfToGradients(mitk::Image* image, bool apply)
	-{
	- image->GetPropertyList()->SetProperty( mitk::DiffusionPropertyHelper::APPLY_MF_TO_GRADIENTS.c_str(), mitk::BoolProperty::New(apply) );
	-}
	-
	-void mitk::DiffusionPropertyHelper::UpdateBValueMap(mitk::Image* image)
	-{
	- BValueMapType b_ValueMap;
	-
	- if(image->GetProperty(mitk::DiffusionPropertyHelper::BVALUEMAPPROPERTYNAME.c_str()).IsNotNull())
	- b_ValueMap = GetBValueMap(image);
	-
	- if(!b_ValueMap.empty())
	- b_ValueMap.clear();
	-
	- if(GetGradientContainer(image).IsNotNull())
	- {
	- GradientDirectionsContainerType::Pointer directions = GetGradientContainer(image);
	-
	- for(auto gdcit = directions->Begin(); gdcit!=directions->End(); ++gdcit)
	- {
	- b_ValueMap[GetB_Value(image, gdcit.Index())].push_back(gdcit.Index());
	- }
	- }
	-
	- SetBValueMap(image, b_ValueMap);
	-}
	-
	-bool mitk::DiffusionPropertyHelper::AreAlike(GradientDirectionType g1, GradientDirectionType g2, double precision)
	-{
	- GradientDirectionType diff = g1 - g2;
	- GradientDirectionType diff2 = g1 + g2;
	- return diff.two_norm() < precision \|\| diff2.two_norm() < precision;
	-}
	-
	-float mitk::DiffusionPropertyHelper::GetB_Value(const mitk::Image* image, unsigned int i)
	-{
	- GradientDirectionsContainerType::Pointer directions = GetGradientContainer(image);
	- float b_value = GetReferenceBValue(image);
	-
	- if(i > directions->Size()-1)
	- return -1;
	-
	- if(directions->ElementAt(i).one_norm() <= 0.0)
	- {
	- return 0;
	- }
	- else
	- {
	- double twonorm = directions->ElementAt(i).two_norm();
	- double bval = b_valuetwonormtwonorm;
	-
	- if (bval<0)
	- bval = ceil(bval - 0.5);
	- else
	- bval = floor(bval + 0.5);
	-
	- return bval;
	- }
	-}
	-
	-void mitk::DiffusionPropertyHelper::CopyProperties(mitk::Image* source, mitk::Image* target, bool ignore_original_gradients)
	-{
	- mitk::PropertyList::Pointer props = source->GetPropertyList()->Clone();
	- if (ignore_original_gradients)
	- props->RemoveProperty(mitk::DiffusionPropertyHelper::ORIGINALGRADIENTCONTAINERPROPERTYNAME);
	- target->SetPropertyList(props);
	-}
	-
	-void mitk::DiffusionPropertyHelper::InitializeImage(mitk::Image* image)
	-{
	- if ( image->GetProperty(mitk::DiffusionPropertyHelper::APPLY_MATRIX_TO_GRADIENTS.c_str()).IsNull() )
	- image->SetProperty( mitk::DiffusionPropertyHelper::APPLY_MATRIX_TO_GRADIENTS.c_str(), mitk::BoolProperty::New(true) );
	-
	- if ( image->GetProperty(mitk::DiffusionPropertyHelper::APPLY_MF_TO_GRADIENTS.c_str()).IsNull() )
	- image->SetProperty( mitk::DiffusionPropertyHelper::APPLY_MF_TO_GRADIENTS.c_str(), mitk::BoolProperty::New(true) );
	-
	- if( image->GetProperty(mitk::DiffusionPropertyHelper::ORIGINALGRADIENTCONTAINERPROPERTYNAME.c_str()).IsNull() )
	- {
	- // we don't have the original gradient directions. Therefore use the modified directions and rotate them back.
	- UnApplyMeasurementFrameAndRotationMatrix(image);
	- }
	- else
	- ApplyMeasurementFrameAndRotationMatrix(image);
	- UpdateBValueMap(image);
	-
	- // initialize missing properties
	- mitk::MeasurementFrameProperty::Pointer mf = dynamic_cast<mitk::MeasurementFrameProperty *>( image->GetProperty(MEASUREMENTFRAMEPROPERTYNAME.c_str()).GetPointer());
	- if( mf.IsNull() )
	- {
	- //no measurement frame present, identity is assumed
	- MeasurementFrameType identity;
	- identity.set_identity();
	- image->GetPropertyList()->ReplaceProperty( mitk::DiffusionPropertyHelper::MEASUREMENTFRAMEPROPERTYNAME.c_str(), mitk::MeasurementFrameProperty::New( identity ));
	- }
	-}
	-
	-bool mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(const mitk::DataNode* node)
	-{
	- if ( node==nullptr )
	- return false;
	- if ( node->GetData()==nullptr )
	- return false;
	- return IsDiffusionWeightedImage(dynamic_cast<mitk::Image *>(node->GetData()));
	-}
	-
	-
	-bool mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(const mitk::Image * image)
	-{
	- bool isDiffusionWeightedImage( true );
	-
	- if( image == nullptr )
	- {
	- isDiffusionWeightedImage = false;
	- }
	-
	- if( isDiffusionWeightedImage )
	- {
	- mitk::FloatProperty::Pointer referenceBValue = dynamic_cast<mitk::FloatProperty *>(image->GetProperty(REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer());
	-
	- if( referenceBValue.IsNull() )
	- {
	- isDiffusionWeightedImage = false;
	- }
	-
	- }
	-
	- unsigned int gradientDirections( 0 );
	- if( isDiffusionWeightedImage )
	- {
	- mitk::GradientDirectionsProperty::Pointer gradientDirectionsProperty = dynamic_cast<mitk::GradientDirectionsProperty *>(image->GetProperty(GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer());
	-
	- if( gradientDirectionsProperty.IsNull() )
	- {
	- isDiffusionWeightedImage = false;
	- }
	- else
	- {
	- gradientDirections = gradientDirectionsProperty->GetGradientDirectionsContainer()->size();
	- }
	- }
	-
	- if( isDiffusionWeightedImage )
	- {
	- unsigned int components = image->GetPixelType().GetNumberOfComponents();
	-
	- if( components != gradientDirections )
	- {
	- isDiffusionWeightedImage = false;
	- }
	- }
	-
	- return isDiffusionWeightedImage;
	-}
	-
	-const mitk::DiffusionPropertyHelper::BValueMapType & mitk::DiffusionPropertyHelper::GetBValueMap(const mitk::Image *image)
	-{
	- return dynamic_cast<mitk::BValueMapProperty *>(image->GetProperty(BVALUEMAPPROPERTYNAME.c_str()).GetPointer())->GetBValueMap();
	-}
	-
	-
	-
	-std::vector< int > mitk::DiffusionPropertyHelper::GetBValueVector(const mitk::Image* image)
	-{
	- auto gcon = mitk::DiffusionPropertyHelper::GetGradientContainer(image);
	- float b_value = mitk::DiffusionPropertyHelper::GetReferenceBValue(image);
	- std::vector< int > bvalues;
	-
	- for (unsigned int i=0; i<gcon->Size(); ++i)
	- {
	- double twonorm = gcon->ElementAt(i).two_norm();
	- double bval = b_valuetwonormtwonorm;
	-
	- if (bval<0)
	- bval = ceil(bval - 0.5);
	- else
	- bval = floor(bval + 0.5);
	-
	- bvalues.push_back(bval);
	- }
	- return bvalues;
	-}
	-
	-float mitk::DiffusionPropertyHelper::GetReferenceBValue(const mitk::Image *image)
	-{
	- return dynamic_cast<mitk::FloatProperty *>(image->GetProperty(REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer())->GetValue();
	-}
	-
	-const mitk::DiffusionPropertyHelper::MeasurementFrameType & mitk::DiffusionPropertyHelper::GetMeasurementFrame(const mitk::Image *image)
	-{
	- mitk::MeasurementFrameProperty::Pointer mf = dynamic_cast<mitk::MeasurementFrameProperty *>( image->GetProperty(MEASUREMENTFRAMEPROPERTYNAME.c_str()).GetPointer());
	- if( mf.IsNull() )
	- {
	- //no measurement frame present, identity is assumed
	- MeasurementFrameType identity;
	- identity.set_identity();
	- mf = mitk::MeasurementFrameProperty::New( identity );
	- }
	-
	- return mf->GetMeasurementFrame();
	-}
	-
	-mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer mitk::DiffusionPropertyHelper::GetOriginalGradientContainer(const mitk::Image *image)
	-{
	- return dynamic_cast<mitk::GradientDirectionsProperty *>(image->GetProperty(ORIGINALGRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer())->GetGradientDirectionsContainer();
	-}
	-
	-mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer mitk::DiffusionPropertyHelper::GetGradientContainer(const mitk::Image *image)
	-{
	- return dynamic_cast<mitk::GradientDirectionsProperty *>(image->GetProperty(GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer())->GetGradientDirectionsContainer();
	-}
	-
	-void mitk::DiffusionPropertyHelper::SetReferenceBValue(mitk::Image* image, float b_value)
	-{
	- image->GetPropertyList()->ReplaceProperty(REFERENCEBVALUEPROPERTYNAME.c_str(), mitk::FloatProperty::New(b_value));
	-}
	-
	-void mitk::DiffusionPropertyHelper::SetBValueMap(mitk::Image* image, BValueMapType map)
	-{
	- image->GetPropertyList()->ReplaceProperty( mitk::DiffusionPropertyHelper::BVALUEMAPPROPERTYNAME.c_str(), mitk::BValueMapProperty::New(map));
	-}
	-
	-void mitk::DiffusionPropertyHelper::SetOriginalGradientContainer(mitk::Image* image, GradientDirectionsContainerType::Pointer g_cont)
	-{
	- image->GetPropertyList()->ReplaceProperty(ORIGINALGRADIENTCONTAINERPROPERTYNAME.c_str(), mitk::GradientDirectionsProperty::New(g_cont));
	-}
	-
	-void mitk::DiffusionPropertyHelper::SetGradientContainer(mitk::Image* image, GradientDirectionsContainerType::Pointer g_cont)
	-{
	- image->GetPropertyList()->ReplaceProperty(GRADIENTCONTAINERPROPERTYNAME.c_str(), mitk::GradientDirectionsProperty::New(g_cont));
	-}
	-
	-void mitk::DiffusionPropertyHelper::SetMeasurementFrame(mitk::Image* image, MeasurementFrameType mf)
	-{
	- image->GetPropertyList()->ReplaceProperty( MEASUREMENTFRAMEPROPERTYNAME.c_str(), mitk::MeasurementFrameProperty::New( mf ) );
	-}
	-
	-void mitk::DiffusionPropertyHelper::RotateGradients(mitk::Image* image, vnl_matrix_fixed<double, 3, 3> rotation_matrix, bool normalize_columns)
	-{
	- if (normalize_columns)
	- rotation_matrix = rotation_matrix.normalize_columns();
	-
	- int c = 0;
	- auto new_gradients = GradientDirectionsContainerType::New();
	- auto old_gradients = GetGradientContainer(image);
	- for(auto gdcit = old_gradients->Begin(); gdcit != old_gradients->End(); ++gdcit)
	- {
	- vnl_vector<double> vec = gdcit.Value();
	- vec = vec.pre_multiply(rotation_matrix);
	- new_gradients->InsertElement(c, vec);
	- c++;
	- }
	- SetGradientContainer(image, new_gradients);
	-}
	-
	-void mitk::DiffusionPropertyHelper::RotateOriginalGradients(mitk::Image* image, vnl_matrix_fixed<double, 3, 3> rotation_matrix, bool normalize_columns)
	-{
	- if (normalize_columns)
	- rotation_matrix = rotation_matrix.normalize_columns();
	-
	- int c = 0;
	- auto new_gradients = GradientDirectionsContainerType::New();
	- auto old_gradients = GetOriginalGradientContainer(image);
	- for(auto gdcit = old_gradients->Begin(); gdcit != old_gradients->End(); ++gdcit)
	- {
	- vnl_vector<double> vec = gdcit.Value();
	- vec = vec.pre_multiply(rotation_matrix);
	- new_gradients->InsertElement(c, vec);
	- c++;
	- }
	- SetOriginalGradientContainer(image, new_gradients);
	-}
	-
	-void mitk::DiffusionPropertyHelper::SetupProperties()
	-{
	- //register relevant properties
	- //non-persistent properties
	- mitk::CoreServices::GetPropertyDescriptions()->AddDescription(mitk::DiffusionPropertyHelper::BVALUEMAPPROPERTYNAME, "This map stores which b values belong to which gradients.");
	- mitk::CoreServices::GetPropertyDescriptions()->AddDescription(mitk::DiffusionPropertyHelper::ORIGINALGRADIENTCONTAINERPROPERTYNAME, "The original gradients used during acquisition. This property may be empty.");
	- //persistent properties
	- mitk::CoreServices::GetPropertyDescriptions()->AddDescription(mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME, "The reference b value the gradients are normalized to.");
	- mitk::CoreServices::GetPropertyDescriptions()->AddDescription(mitk::DiffusionPropertyHelper::MEASUREMENTFRAMEPROPERTYNAME, "The measurment frame used during acquisition.");
	- mitk::CoreServices::GetPropertyDescriptions()->AddDescription(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME, "The gradients after applying measurement frame and image matrix.");
	- mitk::CoreServices::GetPropertyDescriptions()->AddDescription(mitk::DiffusionPropertyHelper::MODALITY, "Defines the modality used for acquisition. DWMRI signifies diffusion weighted images.");
	-
	- mitk::PropertyPersistenceInfo::Pointer PPI_referenceBValue = mitk::PropertyPersistenceInfo::New();
	- PPI_referenceBValue->SetNameAndKey(mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME, "DWMRI_b-value");
	- mitk::PropertyPersistenceInfo::Pointer PPI_measurementFrame = mitk::PropertyPersistenceInfo::New();
	- PPI_measurementFrame->SetNameAndKey(mitk::DiffusionPropertyHelper::MEASUREMENTFRAMEPROPERTYNAME, "measurement frame");
	- mitk::PropertyPersistenceInfo::Pointer PPI_gradientContainer = mitk::PropertyPersistenceInfo::New();
	- PPI_gradientContainer->SetNameAndKey(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME, "DWMRI_gradient");
	- mitk::PropertyPersistenceInfo::Pointer PPI_modality = mitk::PropertyPersistenceInfo::New();
	- PPI_modality->SetNameAndKey(mitk::DiffusionPropertyHelper::MODALITY, "modality");
	-
	- mitk::CoreServices::GetPropertyPersistence()->AddInfo(PPI_referenceBValue.GetPointer() , true);
	- mitk::CoreServices::GetPropertyPersistence()->AddInfo(PPI_measurementFrame.GetPointer(), true);
	- mitk::CoreServices::GetPropertyPersistence()->AddInfo(PPI_gradientContainer.GetPointer(), true);
	- mitk::CoreServices::GetPropertyPersistence()->AddInfo(PPI_modality.GetPointer(), true);
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/Properties/mitkGradientDirectionsProperty.cpp b/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/Properties/mitkGradientDirectionsProperty.cpp
	deleted file mode 100644
	index 1ef0d3e495..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/Properties/mitkGradientDirectionsProperty.cpp
	+++ /dev/null
	@@ -1,83 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkGradientDirectionsProperty.h"
	-
	-mitk::GradientDirectionsProperty::GradientDirectionsProperty()
	-{
	- m_GradientDirectionsContainer = mitk::GradientDirectionsProperty::GradientDirectionsContainerType::New();
	-}
	-
	-mitk::GradientDirectionsProperty::GradientDirectionsProperty(const GradientDirectionsProperty& other)
	- : mitk::BaseProperty(other)
	-{
	- m_GradientDirectionsContainer = other.GetGradientDirectionsContainer();
	-}
	-
	-mitk::GradientDirectionsProperty::GradientDirectionsProperty(const GradientDirectionsContainerType::Pointer gradientDirectionsContainer)
	-{
	- m_GradientDirectionsContainer = gradientDirectionsContainer;
	-}
	-
	-mitk::GradientDirectionsProperty::GradientDirectionsProperty(const AlternativeGradientDirectionsContainerType gradientDirectionsContainer)
	-{
	- m_GradientDirectionsContainer = mitk::GradientDirectionsProperty::GradientDirectionsContainerType::New();
	- for(unsigned int index(0); index < gradientDirectionsContainer.size(); index++)
	- {
	- GradientDirectionType newDirection = gradientDirectionsContainer.at(index).GetVnlVector();
	- m_GradientDirectionsContainer->InsertElement( index, newDirection);
	- }
	-}
	-
	-mitk::GradientDirectionsProperty::~GradientDirectionsProperty()
	-{
	-}
	-
	-const mitk::GradientDirectionsProperty::GradientDirectionsContainerType::Pointer mitk::GradientDirectionsProperty::GetGradientDirectionsContainer() const
	-{
	- return m_GradientDirectionsContainer;
	-}
	-
	-bool mitk::GradientDirectionsProperty::IsEqual(const BaseProperty& property) const
	-{
	-
	- GradientDirectionsContainerType::Pointer lhs = this->m_GradientDirectionsContainer;
	- GradientDirectionsContainerType::Pointer rhs = static_cast<const Self&>(property).m_GradientDirectionsContainer;
	-
	- if(lhs->Size() != rhs->Size()) return false;
	-
	- GradientDirectionsContainerType::Iterator lhsit = lhs->Begin();
	- GradientDirectionsContainerType::Iterator rhsit = rhs->Begin();
	-
	- bool equal = true;
	- for(unsigned int i = 0 ; i < lhs->Size(); i++, ++lhsit, ++rhsit)
	- equal \|= lhsit.Value() == rhsit.Value();
	-
	- return equal;
	-}
	-
	-bool mitk::GradientDirectionsProperty::Assign(const BaseProperty& property)
	-{
	- this->m_GradientDirectionsContainer = static_cast<const Self&>(property).m_GradientDirectionsContainer;
	- return true;
	-}
	-
	-itk::LightObject::Pointer mitk::GradientDirectionsProperty::InternalClone() const
	-{
	- itk::LightObject::Pointer result(new Self(*this));
	- result->UnRegister();
	- return result;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/Properties/mitkGradientDirectionsPropertySerializer.cpp b/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/Properties/mitkGradientDirectionsPropertySerializer.cpp
	deleted file mode 100644
	index 320b76cd4f..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/Properties/mitkGradientDirectionsPropertySerializer.cpp
	+++ /dev/null
	@@ -1,106 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef mitkGradientDirectionPropertySerializer_h_included
	-#define mitkGradientDirectionPropertySerializer_h_included
	-
	-#include "mitkBasePropertySerializer.h"
	-
	-#include "mitkGradientDirectionsProperty.h"
	-
	-#include "MitkDiffusionCoreExports.h"
	-
	-namespace mitk
	-{
	-
	-class MITKDIFFUSIONCORE_EXPORT GradientDirectionsPropertySerializer : public BasePropertySerializer
	-{
	- public:
	-
	- mitkClassMacro( GradientDirectionsPropertySerializer, BasePropertySerializer )
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- TiXmlElement* Serialize() override
	- {
	- if (const GradientDirectionsProperty* prop = dynamic_cast<const GradientDirectionsProperty*>(m_Property.GetPointer()))
	- {
	-
	- typedef mitk::GradientDirectionsProperty::GradientDirectionsContainerType GradientDirectionsContainerType;
	- GradientDirectionsContainerType::Pointer gdc = prop->GetGradientDirectionsContainer().GetPointer();
	-
	- if(gdc.IsNull() \|\| gdc->Size() == 0) return nullptr;
	-
	-
	- GradientDirectionsContainerType::Iterator it = gdc->Begin();
	- GradientDirectionsContainerType::Iterator end = gdc->End();
	-
	- auto element = new TiXmlElement("gradientdirections");
	-
	- while (it != end) {
	- auto child = new TiXmlElement("entry");
	- std::stringstream ss;
	- ss << it.Value();
	- child->SetAttribute("value", ss.str());
	- element->InsertEndChild(*child);
	-
	- ++it;
	- }
	-
	- return element;
	- }
	- else return nullptr;
	- }
	-
	- BaseProperty::Pointer Deserialize(TiXmlElement* element) override
	- {
	- if (!element) return nullptr;
	-
	- mitk::GradientDirectionsProperty::GradientDirectionsContainerType::Pointer gdc;
	- gdc = mitk::GradientDirectionsProperty::GradientDirectionsContainerType::New();
	-
	- TiXmlElement* entry = element->FirstChildElement( "entry" )->ToElement();
	- while(entry != nullptr){
	-
	- std::stringstream ss;
	- std::string value;
	-
	- entry->QueryStringAttribute("value",&value);
	- ss << value;
	-
	- vnl_vector_fixed<double, 3> vector;
	- vector.read_ascii(ss);
	-
	- gdc->push_back(vector);
	-
	- entry = entry->NextSiblingElement( "entry" );
	- }
	-
	- return GradientDirectionsProperty::New(gdc).GetPointer();
	- }
	-
	- protected:
	-
	- GradientDirectionsPropertySerializer() {}
	- ~GradientDirectionsPropertySerializer() override {}
	-};
	-
	-} // namespace
	-
	-// important to put this into the GLOBAL namespace (because it starts with 'namespace mitk')
	-MITK_REGISTER_SERIALIZER(GradientDirectionsPropertySerializer)
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/Properties/mitkMeasurementFrameProperty.cpp b/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/Properties/mitkMeasurementFrameProperty.cpp
	deleted file mode 100644
	index dea5153be0..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/Properties/mitkMeasurementFrameProperty.cpp
	+++ /dev/null
	@@ -1,65 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkMeasurementFrameProperty.h"
	-
	-mitk::MeasurementFrameProperty::MeasurementFrameProperty()
	- : m_MeasurementFrame()
	-{
	-}
	-
	-mitk::MeasurementFrameProperty::MeasurementFrameProperty(const MeasurementFrameProperty& other)
	- : mitk::BaseProperty(other)
	-{
	- m_MeasurementFrame = other.GetMeasurementFrame();
	-}
	-
	-mitk::MeasurementFrameProperty::MeasurementFrameProperty(const MeasurementFrameType& measurementFrame)
	-{
	- m_MeasurementFrame = measurementFrame;
	-}
	-
	-mitk::MeasurementFrameProperty::~MeasurementFrameProperty()
	-{
	-}
	-
	-const mitk::MeasurementFrameProperty::MeasurementFrameType & mitk::MeasurementFrameProperty::GetMeasurementFrame() const
	-{
	- return m_MeasurementFrame;
	-}
	-
	-void mitk::MeasurementFrameProperty::SetMeasurementFrame(const MeasurementFrameType & frame)
	-{
	- m_MeasurementFrame = frame;
	-}
	-
	-bool mitk::MeasurementFrameProperty::IsEqual(const BaseProperty& property) const
	-{
	- return this->m_MeasurementFrame == static_cast<const Self&>(property).m_MeasurementFrame;
	-}
	-
	-bool mitk::MeasurementFrameProperty::Assign(const BaseProperty& property)
	-{
	- this->m_MeasurementFrame = static_cast<const Self&>(property).m_MeasurementFrame;
	- return true;
	-}
	-
	-itk::LightObject::Pointer mitk::MeasurementFrameProperty::InternalClone() const
	-{
	- itk::LightObject::Pointer result(new Self(*this));
	- result->UnRegister();
	- return result;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/Properties/mitkMeasurementFramePropertySerializer.cpp b/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/Properties/mitkMeasurementFramePropertySerializer.cpp
	deleted file mode 100644
	index 937ba5013c..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/Properties/mitkMeasurementFramePropertySerializer.cpp
	+++ /dev/null
	@@ -1,89 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef mitkMeasurementFramePropertySerializer_h_included
	-#define mitkMeasurementFramePropertySerializer_h_included
	-
	-#include "mitkBasePropertySerializer.h"
	-
	-#include "mitkMeasurementFrameProperty.h"
	-
	-#include <MitkDiffusionCoreExports.h>
	-
	-namespace mitk
	-{
	-
	-class MITKDIFFUSIONCORE_EXPORT MeasurementFramePropertySerializer : public BasePropertySerializer
	-{
	- public:
	-
	- mitkClassMacro( MeasurementFramePropertySerializer, BasePropertySerializer )
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- TiXmlElement* Serialize() override
	- {
	- if (const MeasurementFrameProperty* prop = dynamic_cast<const MeasurementFrameProperty*>(m_Property.GetPointer()))
	- {
	-
	- typedef mitk::MeasurementFrameProperty::MeasurementFrameType MeasurementFrameType;
	- const MeasurementFrameType & mft = prop->GetMeasurementFrame();
	-
	- if(mft.is_zero()) return nullptr;
	-
	- auto element = new TiXmlElement("measurementframe");
	-
	- auto child = new TiXmlElement("entry");
	- std::stringstream ss;
	- ss << mft;
	- child->SetAttribute("value", ss.str());
	- element->InsertEndChild(*child);
	-
	- return element;
	- }
	- else return nullptr;
	- }
	-
	- BaseProperty::Pointer Deserialize(TiXmlElement* element) override
	- {
	- if (!element) return nullptr;
	-
	- TiXmlElement* entry = element->FirstChildElement( "entry" )->ToElement();
	-
	- std::stringstream ss;
	- std::string value;
	-
	- entry->QueryStringAttribute("value",&value);
	- ss << value;
	-
	- MeasurementFrameProperty::MeasurementFrameType matrix;
	- matrix.read_ascii(ss);
	-
	- return MeasurementFrameProperty::New(matrix).GetPointer();
	- }
	-
	- protected:
	-
	- MeasurementFramePropertySerializer() {}
	- ~MeasurementFramePropertySerializer() override {}
	-};
	-
	-} // namespace
	-
	-// important to put this into the GLOBAL namespace (because it starts with 'namespace mitk')
	-MITK_REGISTER_SERIALIZER(MeasurementFramePropertySerializer)
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/Properties/mitkNodePredicateIsDWI.cpp b/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/Properties/mitkNodePredicateIsDWI.cpp
	deleted file mode 100644
	index 93eeadfadb..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/Properties/mitkNodePredicateIsDWI.cpp
	+++ /dev/null
	@@ -1,39 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkNodePredicateIsDWI.h"
	-#include "mitkDataNode.h"
	-#include <mitkDiffusionPropertyHelper.h>
	-
	-mitk::NodePredicateIsDWI::NodePredicateIsDWI()
	-: NodePredicateBase()
	-{
	-}
	-
	-mitk::NodePredicateIsDWI::~NodePredicateIsDWI()
	-{
	-}
	-
	-
	-bool mitk::NodePredicateIsDWI::CheckNode(const mitk::DataNode* node) const
	-{
	- if (node == nullptr)
	- throw std::invalid_argument("NodePredicateIsDWI: invalid node");
	-
	- mitk::Image* image = dynamic_cast<mitk::Image*>(node->GetData());
	-
	- return mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( image );
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/TensorImages/mitkTensorImage.cpp b/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/TensorImages/mitkTensorImage.cpp
	deleted file mode 100644
	index d6e527832f..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/TensorImages/mitkTensorImage.cpp
	+++ /dev/null
	@@ -1,77 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkTensorImage.h"
	-#include "mitkImageDataItem.h"
	-#include "mitkImageCast.h"
	-
	-#include "itkDiffusionTensor3D.h"
	-#include "itkTensorToRgbImageFilter.h"
	-
	-#include "vtkImageData.h"
	-
	-// #ifdef _OPENMP
	-// #include "omp.h"
	-// #endif
	-
	-mitk::TensorImage::TensorImage() : Image()
	-{
	- m_RgbImage = nullptr;
	-}
	-
	-mitk::TensorImage::~TensorImage()
	-{
	-
	-}
	-
	-vtkImageData* mitk::TensorImage::GetVtkImageData(int t, int n)
	-{
	- if(m_RgbImage.IsNull())
	- {
	- ConstructRgbImage();
	- }
	- return m_RgbImage->GetVtkImageData(t,n);
	-}
	-
	-const vtkImageData*mitk::TensorImage::GetVtkImageData(int t, int n) const
	-{
	- if(m_RgbImage.IsNull())
	- {
	- ConstructRgbImage();
	- }
	- return m_RgbImage->GetVtkImageData(t,n);
	-}
	-
	-void mitk::TensorImage::ConstructRgbImage() const
	-{
	- typedef itk::TensorToRgbImageFilter<ItkTensorImageType> FilterType;
	- FilterType::Pointer filter = FilterType::New();
	-
	- ItkTensorImageType::Pointer itkvol = ItkTensorImageType::New();
	- mitk::CastToItkImage(this, itkvol);
	- filter->SetInput(itkvol);
	- filter->Update();
	-
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk( filter->GetOutput() );
	- image->SetVolume( filter->GetOutput()->GetBufferPointer() );
	- m_RgbImage = image;
	-}
	-
	-vtkImageData* mitk::TensorImage::GetNonRgbVtkImageData(int t, int n)
	-{
	- return Superclass::GetVtkImageData(t,n);
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/mitkPeakImage.cpp b/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/mitkPeakImage.cpp
	deleted file mode 100644
	index fcedbcda2d..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/mitkPeakImage.cpp
	+++ /dev/null
	@@ -1,221 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkPeakImage.h"
	-#include "mitkImageDataItem.h"
	-#include "mitkImageCast.h"
	-#include <mitkImageToItk.h>
	-#include <vtkPolyLine.h>
	-#include <vtkPointData.h>
	-#include <mitkImagePixelWriteAccessor.h>
	-#include <mitkImagePixelReadAccessor.h>
	-
	-mitk::PeakImage::PeakImage() : Image()
	-{
	- m_PolyData = nullptr;
	-}
	-
	-mitk::PeakImage::~PeakImage()
	-{
	-
	-}
	-
	-void mitk::PeakImage::ConstructPolydata()
	-{
	- MITK_INFO << "PeakImage constructing polydata";
	- if (this->GetDimensions()[3]%3!=0)
	- mitkThrow() << "Fourth dimension needs to be a multiple of 3";
	-
	- typedef mitk::ImageToItk< ItkPeakImageType > CasterType;
	- CasterType::Pointer caster = CasterType::New();
	- caster->SetInput(this);
	- caster->Update();
	- ItkPeakImageType::ConstPointer itkImg = caster->GetOutput();
	-
	- int sz_x = static_cast<int>(this->GetDimensions()[0]);
	- int sz_y = static_cast<int>(this->GetDimensions()[1]);
	- int sz_z = static_cast<int>(this->GetDimensions()[2]);
	- unsigned int num_dirs = this->GetDimensions()[3]/3;
	-
	- double minSpacing = 1;
	- ItkPeakImageType::SpacingType spacing = itkImg->GetSpacing();
	- if(spacing[0]<spacing[1] && spacing[0]<spacing[2])
	- minSpacing = spacing[0];
	- else if (spacing[1] < spacing[2])
	- minSpacing = spacing[1];
	- else
	- minSpacing = spacing[2];
	-
	- vtkSmartPointer<vtkCellArray> m_VtkCellArray = vtkSmartPointer<vtkCellArray>::New();
	- vtkSmartPointer<vtkPoints> m_VtkPoints = vtkSmartPointer<vtkPoints>::New();
	-
	-#ifdef WIN32
	-#pragma omp parallel for
	-#else
	-#pragma omp parallel for collapse(3)
	-#endif
	- for (int x=0; x<sz_x; ++x)
	- for (int y=0; y<sz_y; ++y)
	- for (int z=0; z<sz_z; ++z)
	- {
	- itk::Index<4> idx4; idx4[0] = x; idx4[1] = y; idx4[2] = z;
	-
	- for (unsigned int i=0; i<num_dirs; i++)
	- {
	- itk::ContinuousIndex<double, 4> center;
	- center[0] = idx4[0];
	- center[1] = idx4[1];
	- center[2] = idx4[2];
	- center[3] = 0;
	-
	- itk::Point<double, 4> worldCenter;
	- itkImg->TransformContinuousIndexToPhysicalPoint( center, worldCenter );
	-
	- idx4[3] = 0;
	- vnl_vector_fixed< float, 3 > dir;
	- idx4[3] = i*3;
	- dir[0] = itkImg->GetPixel(idx4);
	- idx4[3] += 1;
	- dir[1] = itkImg->GetPixel(idx4);
	- idx4[3] += 1;
	- dir[2] = itkImg->GetPixel(idx4);
	-
	- if (dir.magnitude()<0.001f)
	- continue;
	-
	-#pragma omp critical
	- {
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	- // add direction to vector field (with spacing compensation)
	- itk::Point<double> worldStart;
	- worldStart[0] = worldCenter[0]-static_cast<double>(dir[0])/2*minSpacing;
	- worldStart[1] = worldCenter[1]-static_cast<double>(dir[1])/2*minSpacing;
	- worldStart[2] = worldCenter[2]-static_cast<double>(dir[2])/2*minSpacing;
	- vtkIdType id = m_VtkPoints->InsertNextPoint(worldStart.GetDataPointer());
	- container->GetPointIds()->InsertNextId(id);
	- itk::Point<double> worldEnd;
	- worldEnd[0] = worldCenter[0]+static_cast<double>(dir[0])/2*minSpacing;
	- worldEnd[1] = worldCenter[1]+static_cast<double>(dir[1])/2*minSpacing;
	- worldEnd[2] = worldCenter[2]+static_cast<double>(dir[2])/2*minSpacing;
	- id = m_VtkPoints->InsertNextPoint(worldEnd.GetDataPointer());
	- container->GetPointIds()->InsertNextId(id);
	- m_VtkCellArray->InsertNextCell(container);
	- }
	- }
	- }
	-
	- m_PolyData = vtkSmartPointer<vtkPolyData>::New();
	- m_PolyData->SetPoints(m_VtkPoints);
	- m_PolyData->SetLines(m_VtkCellArray);
	- MITK_INFO << "PeakImage finished constructing polydata";
	-
	- ColorByOrientation();
	-
	- this->Modified();
	-}
	-
	-void mitk::PeakImage::SetCustomColor(float r, float g, float b)
	-{
	- vtkPoints* extrPoints = nullptr;
	- extrPoints = m_PolyData->GetPoints();
	- int numOfPoints = 0;
	- if (extrPoints!=nullptr)
	- numOfPoints = static_cast<int>(extrPoints->GetNumberOfPoints());
	-
	- int componentSize = 4;
	-
	- vtkSmartPointer<vtkUnsignedCharArray> colors = vtkSmartPointer<vtkUnsignedCharArray>::New();
	- colors->Allocate(numOfPoints * componentSize);
	- colors->SetNumberOfComponents(componentSize);
	- colors->SetName("FIBER_COLORS");
	-
	- unsigned char rgba[4] = {0,0,0,0};
	- for(long i=0; i<m_PolyData->GetNumberOfPoints(); ++i)
	- {
	- rgba[0] = static_cast<unsigned char>(r);
	- rgba[1] = static_cast<unsigned char>(g);
	- rgba[2] = static_cast<unsigned char>(b);
	- rgba[3] = 255;
	- colors->InsertTypedTuple(i, rgba);
	- }
	-
	- m_PolyData->GetPointData()->AddArray(colors);
	- this->Modified();
	-}
	-
	-void mitk::PeakImage::ColorByOrientation()
	-{
	- //===== FOR WRITING A TEST ========================
	- // colorT size == tupelComponents * tupelElements
	- // compare color results
	- // to cover this code 100% also PolyData needed, where colorarray already exists
	- // + one fiber with exactly 1 point
	- // + one fiber with 0 points
	- //=================================================
	-
	- vtkPoints* extrPoints = nullptr;
	- extrPoints = m_PolyData->GetPoints();
	- int numOfPoints = 0;
	- if (extrPoints!=nullptr)
	- numOfPoints = static_cast<int>(extrPoints->GetNumberOfPoints());
	-
	- //colors and alpha value for each single point, RGBA = 4 components
	- unsigned char rgba[4] = {0,0,0,0};
	- int componentSize = 4;
	-
	- vtkSmartPointer<vtkUnsignedCharArray> colors = vtkSmartPointer<vtkUnsignedCharArray>::New();
	- colors->Allocate(numOfPoints * componentSize);
	- colors->SetNumberOfComponents(componentSize);
	- colors->SetName("FIBER_COLORS");
	-
	- int num_peaks = static_cast<int>(m_PolyData->GetNumberOfLines());
	- if (num_peaks < 1)
	- return;
	-
	- vtkCellArray* fiberList = m_PolyData->GetLines();
	- fiberList->InitTraversal();
	- for (int fi=0; fi<num_peaks; ++fi)
	- {
	- vtkIdType* idList; // contains the point id's of the line
	- vtkIdType num_points; // number of points for current line
	- fiberList->GetNextCell(num_points, idList);
	-
	- if (num_points == 2)
	- {
	- vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[0])[0], extrPoints->GetPoint(idList[0])[1],extrPoints->GetPoint(idList[0])[2]);
	- vnl_vector_fixed< double, 3 > nextPntvtk(extrPoints->GetPoint(idList[1])[0], extrPoints->GetPoint(idList[1])[1], extrPoints->GetPoint(idList[1])[2]);
	-
	- vnl_vector_fixed< double, 3 > diff1;
	- diff1 = currentPntvtk - nextPntvtk;
	- diff1.normalize();
	-
	- rgba[0] = static_cast<unsigned char>(255.0 * std::fabs(diff1[0]));
	- rgba[1] = static_cast<unsigned char>(255.0 * std::fabs(diff1[1]));
	- rgba[2] = static_cast<unsigned char>(255.0 * std::fabs(diff1[2]));
	- rgba[3] = 255;
	- colors->InsertTypedTuple(idList[0], rgba);
	- colors->InsertTypedTuple(idList[1], rgba);
	- }
	- else
	- {
	- MITK_INFO << "Peak with point number!=2 detected!" ;
	- continue;
	- }
	- }
	-
	- m_PolyData->GetPointData()->AddArray(colors);
	- this->Modified();
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/mitkRegistrationObject.cpp b/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/mitkRegistrationObject.cpp
	deleted file mode 100644
	index f349fa6cba..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/mitkRegistrationObject.cpp
	+++ /dev/null
	@@ -1,45 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkRegistrationObject.h"
	-
	-mitk::RegistrationObject::RegistrationObject()
	- : m_ReferenceGeometry(0),
	- m_Transformation(0)
	-{
	-
	-}
	-
	-void mitk::RegistrationObject::SetReferenceGeometry(mitk::Geometry3D::Pointer geom)
	-{
	- if( m_ReferenceGeometry.IsNull() )
	- m_ReferenceGeometry = mitk::Geometry3D::New();
	-
	- m_ReferenceGeometry = geom->Clone();
	-}
	-
	-void mitk::RegistrationObject::SetReferenceImage(mitk::Image::Pointer image)
	-{
	- this->SetReferenceGeometry( image->GetTimeGeometry()->GetGeometryForTimeStep() );
	-}
	-
	-void mitk::RegistrationObject::SetTransformation(itk::AffineGeometryFrame::Pointer transform)
	-{
	- if( m_Transformation.IsNull() )
	- m_Transformation = mitk::AffineGeometryFrame3D::New();
	-
	- m_Transformation = transform;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/mitkShImage.cpp b/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/mitkShImage.cpp
	deleted file mode 100644
	index 90d273e9a8..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/mitkShImage.cpp
	+++ /dev/null
	@@ -1,144 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkShImage.h"
	-#include "mitkImageCast.h"
	-#include "itkImage.h"
	-#include "mitkImageVtkAccessor.h"
	-#include <mitkProperties.h>
	-#include "itkShToRgbImageFilter.h"
	-
	-mitk::ShImage::ShImage() : Image()
	- , m_ShOrder(0)
	- , m_NumCoefficients(0)
	-{
	- m_RgbImage = nullptr;
	- // not needed anymore as soon as all diffusion images are identified via properties anyway
	- this->SetProperty("IsShImage", mitk::BoolProperty::New(true));
	-}
	-
	-mitk::ShImage::~ShImage()
	-{
	-
	-}
	-
	-unsigned int mitk::ShImage::NumCoefficients()
	-{
	- if (m_NumCoefficients==0 \|\| m_ShOrder==0)
	- {
	- m_NumCoefficients = static_cast<unsigned int>(this->m_ImageDescriptor->GetChannelTypeById(0).GetNumberOfComponents());
	- int c=3, d=2-2*static_cast<int>(m_NumCoefficients);
	- int D = cc-4d;
	- if (D>0)
	- {
	- int s = (-c+static_cast<int>(sqrt(D)))/2;
	- if (s<0)
	- s = (-c-static_cast<int>(sqrt(D)))/2;
	- m_ShOrder = static_cast<unsigned int>(s);
	- }
	- else if (D==0)
	- m_ShOrder = static_cast<unsigned int>(-c/2);
	- }
	- return m_NumCoefficients;
	-}
	-
	-unsigned int mitk::ShImage::ShOrder()
	-{
	- NumCoefficients();
	- return m_ShOrder;
	-}
	-
	-vtkImageData* mitk::ShImage::GetVtkImageData(int t, int n)
	-{
	- if(m_RgbImage.IsNull())
	- {
	- ShOrder();
	- NumCoefficients();
	- ConstructRgbImage();
	- }
	- return m_RgbImage->GetVtkImageData(t,n);
	-}
	-
	-const vtkImageData*mitk::ShImage::GetVtkImageData(int t, int n) const
	-{
	- if(m_RgbImage.IsNull())
	- {
	- ConstructRgbImage();
	- }
	- return m_RgbImage->GetVtkImageData(t,n);
	-}
	-
	-template<int nShOrder>
	-void mitk::ShImage::Construct() const
	-{
	- typedef itk::Image<itk::Vector<float, ( nShOrder * nShOrder + nShOrder + 2)/2 + nShOrder >,3> ImageType;
	- typedef itk::ShToRgbImageFilter<ImageType, nShOrder> FilterType;
	- typename FilterType::Pointer filter = FilterType::New();
	-
	- typename ImageType::Pointer itkvol = ImageType::New();
	- mitk::CastToItkImage(this, itkvol);
	- filter->SetInput(itkvol);
	- filter->Update();
	-
	- itk::Image<itk::RGBAPixel<unsigned char>,3>::Pointer tmp = filter->GetOutput();
	- m_RgbImage = mitk::Image::New();
	- m_RgbImage->InitializeByItk( tmp.GetPointer() );
	- m_RgbImage->SetVolume( tmp->GetBufferPointer() );
	-}
	-
	-void mitk::ShImage::ConstructRgbImage() const
	-{
	- switch (this->m_ImageDescriptor->GetChannelTypeById(0).GetNumberOfComponents())
	- {
	- case 6:
	- Construct<2>();
	- break;
	- case 15:
	- Construct<4>();
	- break;
	- case 28:
	- Construct<6>();
	- break;
	- case 45:
	- Construct<8>();
	- break;
	- case 66:
	- Construct<10>();
	- break;
	- case 91:
	- Construct<12>();
	- break;
	- default :
	- mitkThrow() << "SH order larger 12 not supported";
	- }
	-}
	-
	-const vtkImageData* mitk::ShImage::GetNonRgbVtkImageData(int t, int n) const
	-{
	- return Superclass::GetVtkImageData(t,n);
	-}
	-
	-vtkImageData* mitk::ShImage::GetNonRgbVtkImageData(int t, int n)
	-{
	- return Superclass::GetVtkImageData(t,n);
	-}
	-
	-void mitk::ShImage::PrintSelf(std::ostream &os, itk::Indent indent) const
	-{
	- os << indent << "Spherical harmonics order: " << m_ShOrder << std::endl;
	- os << indent << "Number of coefficients: " << m_NumCoefficients << std::endl;
	- Superclass::PrintSelf(os, indent);
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/mitkShImageSource.cpp b/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/mitkShImageSource.cpp
	deleted file mode 100644
	index c3bc718496..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/mitkShImageSource.cpp
	+++ /dev/null
	@@ -1,45 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#include "mitkShImageSource.h"
	-
	-
	-mitk::ShImageSource::ShImageSource()
	-{
	- // Create the output. We use static_cast<> here because we know the default
	- // output must be of type TOutputImage
	- OutputImageType::Pointer output
	- = static_cast<OutputImageType*>(this->MakeOutput(0).GetPointer());
	- Superclass::SetNumberOfRequiredOutputs(1);
	- Superclass::SetNthOutput(0, output.GetPointer());
	-}
	-
	-itk::DataObject::Pointer mitk::ShImageSource::MakeOutput ( DataObjectPointerArraySizeType /idx/ )
	-{
	- return OutputImageType::New().GetPointer();
	-}
	-
	-
	-itk::DataObject::Pointer mitk::ShImageSource::MakeOutput( const DataObjectIdentifierType & name )
	-{
	- itkDebugMacro("MakeOutput(" << name << ")");
	- if( this->IsIndexedOutputName(name) )
	- {
	- return this->MakeOutput( this->MakeIndexFromOutputName(name) );
	- }
	- return static_cast<itk::DataObject *>(OutputImageType::New().GetPointer());
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/Rendering/mitkOdfNormalizationMethodProperty.cpp b/Modules/DiffusionImaging/DiffusionCore/src/Rendering/mitkOdfNormalizationMethodProperty.cpp
	deleted file mode 100644
	index e200f71cb6..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/Rendering/mitkOdfNormalizationMethodProperty.cpp
	+++ /dev/null
	@@ -1,99 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkOdfNormalizationMethodProperty.h"
	-
	-// ODFN_MINMAX, ODFN_MAX, ODFN_NONE ODFN_GLOBAL_MAX
	-
	-mitk::OdfNormalizationMethodProperty::OdfNormalizationMethodProperty( )
	-{
	- this->AddInterpolationTypes();
	- this->SetValue( static_cast<IdType>( ODFN_MAX ) );
	-}
	-
	-
	-mitk::OdfNormalizationMethodProperty::OdfNormalizationMethodProperty( const IdType& value )
	-{
	- this->AddInterpolationTypes();
	- if ( IsValidEnumerationValue( value ) )
	- {
	- this->SetValue( value ) ;
	- }
	- else
	- {
	- this->SetValue( static_cast<IdType>( ODFN_MINMAX ) );
	- }
	-}
	-
	-mitk::OdfNormalizationMethodProperty::OdfNormalizationMethodProperty( const std::string& value )
	-{
	- this->AddInterpolationTypes();
	- if ( IsValidEnumerationValue( value ) )
	- {
	- this->SetValue( value );
	- }
	- else
	- {
	- this->SetValue( static_cast<IdType>( ODFN_MINMAX ) );
	- }
	-}
	-
	-
	-int mitk::OdfNormalizationMethodProperty::GetNormalization()
	-{
	- return static_cast<int>( this->GetValueAsId() );
	-}
	-
	-
	-void mitk::OdfNormalizationMethodProperty::SetNormalizationToMinMax()
	-{
	- this->SetValue( static_cast<IdType>( ODFN_MINMAX ) );
	-}
	-
	-
	-void mitk::OdfNormalizationMethodProperty::SetNormalizationToMax()
	-{
	- this->SetValue( static_cast<IdType>( ODFN_MAX ) );
	-}
	-
	-
	-void mitk::OdfNormalizationMethodProperty::SetNormalizationToNone()
	-{
	- this->SetValue( static_cast<IdType>( ODFN_NONE ) );
	-}
	-
	-
	-void mitk::OdfNormalizationMethodProperty::SetNormalizationToGlobalMax()
	-{
	- this->SetValue( static_cast<IdType>( ODFN_GLOBAL_MAX ) );
	-}
	-
	-
	-void mitk::OdfNormalizationMethodProperty::AddInterpolationTypes()
	-{
	- AddEnum( "Min-Max", static_cast<IdType>( ODFN_MINMAX ) );
	- AddEnum( "Maximum", static_cast<IdType>( ODFN_MAX ) );
	- AddEnum( "None", static_cast<IdType>( ODFN_NONE ) );
	- AddEnum( "Global Maximum", static_cast<IdType>( ODFN_GLOBAL_MAX ) );
	-}
	-
	-
	-bool mitk::OdfNormalizationMethodProperty::AddEnum( const std::string& name, const IdType& id )
	-{
	- return Superclass::AddEnum( name, id );
	-}
	-
	-MITK_REGISTER_SERIALIZER( OdfNormalizationMethodPropertySerializer )
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/Rendering/mitkOdfScaleByProperty.cpp b/Modules/DiffusionImaging/DiffusionCore/src/Rendering/mitkOdfScaleByProperty.cpp
	deleted file mode 100644
	index aff7ab28ad..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/Rendering/mitkOdfScaleByProperty.cpp
	+++ /dev/null
	@@ -1,87 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkOdfScaleByProperty.h"
	-
	-// ODFN_NONE, ODFN_GFA, ODFN_PC
	-
	-mitk::OdfScaleByProperty::OdfScaleByProperty( )
	-{
	- this->AddInterpolationTypes();
	- this->SetValue( static_cast<IdType>( ODFSB_NONE ) );
	-}
	-
	-
	-mitk::OdfScaleByProperty::OdfScaleByProperty( const IdType& value )
	-{
	- this->AddInterpolationTypes();
	- if ( IsValidEnumerationValue( value ) )
	- {
	- this->SetValue( value ) ;
	- }
	- else
	- {
	- this->SetValue( static_cast<IdType>( ODFSB_NONE ) );
	- }
	-}
	-
	-mitk::OdfScaleByProperty::OdfScaleByProperty( const std::string& value )
	-{
	- this->AddInterpolationTypes();
	- if ( IsValidEnumerationValue( value ) )
	- {
	- this->SetValue( value );
	- }
	- else
	- {
	- this->SetValue( static_cast<IdType>( ODFSB_NONE ) );
	- }
	-}
	-
	-
	-int mitk::OdfScaleByProperty::GetScaleBy()
	-{
	- return static_cast<int>( this->GetValueAsId() );
	-}
	-
	-void mitk::OdfScaleByProperty::AddInterpolationTypes()
	-{
	- AddEnum( "None", static_cast<IdType>( ODFSB_NONE ) );
	- AddEnum( "GFA", static_cast<IdType>( ODFSB_GFA ) );
	- AddEnum( "Principal Curvature", static_cast<IdType>( ODFSB_PC ) );
	-}
	-
	-void mitk::OdfScaleByProperty::SetScaleByNothing()
	-{
	- SetValue(ODFSB_NONE);
	-}
	-
	-void mitk::OdfScaleByProperty::SetScaleByGFA()
	-{
	- SetValue(ODFSB_GFA);
	-}
	-
	-void mitk::OdfScaleByProperty::SetScaleByPrincipalCurvature()
	-{
	- SetValue(ODFSB_PC);
	-}
	-
	-bool mitk::OdfScaleByProperty::AddEnum( const std::string& name, const IdType& id )
	-{
	- return Superclass::AddEnum( name, id );
	-}
	-
	-MITK_REGISTER_SERIALIZER( OdfScaleByPropertySerializer )
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/Rendering/mitkVectorImageVtkGlyphMapper3D.cpp b/Modules/DiffusionImaging/DiffusionCore/src/Rendering/mitkVectorImageVtkGlyphMapper3D.cpp
	deleted file mode 100644
	index 17f4dc8ac8..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/Rendering/mitkVectorImageVtkGlyphMapper3D.cpp
	+++ /dev/null
	@@ -1,219 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkVectorImageVtkGlyphMapper3D.h"
	-
	-#include <vtkMaskedGlyph3D.h>
	-#include <vtkActor.h>
	-#include <vtkPolyDataMapper.h>
	-#include <vtkArrowSource.h>
	-#include <vtkLineSource.h>
	-#include <vtkImageData.h>
	-#include <vtkPolyData.h>
	-#include <vtkPointData.h>
	-#include <vtkLookupTable.h>
	-#include <mitkLookupTable.h>
	-#include <mitkLookupTableProperty.h>
	-
	-
	-/*
	-* Constructor. Doesn't do anything...
	-*/
	-mitk::VectorImageVtkGlyphMapper3D::VectorImageVtkGlyphMapper3D()
	-{
	- m_RandomMode = true;
	- m_UseMaskPoints = true;
	- m_MaximumNumberOfPoints = 5000;
	- m_GlyphType = ArrowGlyph;
	- m_Glyph3DGenerator = vtkMaskedGlyph3D::New();
	- m_Glyph3DMapper = vtkPolyDataMapper::New();
	- m_Glyph3DActor = vtkActor::New();
	-}
	-
	-vtkProp* mitk::VectorImageVtkGlyphMapper3D::GetVtkProp(mitk::BaseRenderer* /renderer/)
	-{
	- return m_Glyph3DActor;
	-}
	-
	-/*
	-* Destructor
	-*/
	-mitk::VectorImageVtkGlyphMapper3D::~VectorImageVtkGlyphMapper3D()
	-{
	- if ( m_Glyph3DMapper != nullptr )
	- m_Glyph3DMapper->Delete();
	- if ( m_Glyph3DGenerator != nullptr )
	- m_Glyph3DGenerator->Delete();
	-}
	-
	-/*
	-* Generate a vtkPolyData by creating vectors as glyphs
	-* This method is called, each time a specific renderer is updated.
	-*/
	-void mitk::VectorImageVtkGlyphMapper3D::GenerateDataForRenderer( mitk::BaseRenderer* renderer )
	-{
	-
	- bool visible = true;
	- GetDataNode()->GetVisibility(visible, renderer, "visible");
	-
	- if ( !visible )
	- {
	- if ( m_Glyph3DActor != nullptr )
	- m_Glyph3DActor->VisibilityOff();
	- return ;
	- }
	- else
	- {
	- if ( m_Glyph3DActor != nullptr )
	- m_Glyph3DActor->VisibilityOn();
	- }
	-
	- BaseLocalStorage *ls = m_LSH.GetLocalStorage(renderer);
	- bool needGenerateData = ls->IsGenerateDataRequired( renderer, this, GetDataNode() );
	-
	- if(!needGenerateData)
	- {
	- return;
	- }
	-
	- ls->UpdateGenerateDataTime();
	-
	- //
	- // get the input image...
	- //
	- mitk::Image::Pointer mitkImage = this->GetInput();
	- if ( mitkImage.GetPointer() == nullptr )
	- {
	- itkWarningMacro( << "VectorImage is null !" );
	- return;
	- }
	-
	- //
	- // make sure, that the input image is an vector image
	- //
	- if ( mitkImage->GetPixelType().GetNumberOfComponents() <= 1 )
	- {
	- itkWarningMacro( << "VectorImage has only one scalar component!" );
	- return ;
	- }
	-
	- vtkImageData* vtkImage = mitkImage->GetVtkImageData();
	-
	- //
	- // make sure, that we have point data with more than 1 component (as vectors)
	- //
	- vtkPointData* pointData = vtkImage->GetPointData();
	- if ( pointData == nullptr )
	- {
	- itkWarningMacro( << "vtkImage->GetPointData() returns nullptr!" );
	- return ;
	- }
	- if ( pointData->GetNumberOfArrays() == 0 )
	- {
	- itkWarningMacro( << "vtkImage->GetPointData()->GetNumberOfArrays() is 0!" );
	- return ;
	- }
	- else if ( pointData->GetArrayName( 0 ) == nullptr )
	- {
	- vtkImage->GetPointData() ->GetArray( 0 ) ->SetName( "vector" );
	- }
	-
	- if ( vtkImage->GetNumberOfPoints() != 0 )
	- {
	-
	- //
	- // create the glyph, which has to be shown at each point
	- // of the masked image
	- //
	- vtkPolyData* glyph;
	- if ( m_GlyphType == LineGlyph )
	- {
	- vtkLineSource * lineSource = vtkLineSource::New();
	- lineSource->Update();
	- glyph = lineSource->GetOutput();
	- }
	- else if ( m_GlyphType == ArrowGlyph )
	- {
	- vtkArrowSource * arrowSource = vtkArrowSource::New();
	- arrowSource->Update();
	- glyph = arrowSource->GetOutput();
	- }
	- else
	- {
	- // Use a vtkLineSource as default, if the GlyphType is
	- // unknown
	- itkWarningMacro( << "unknown glyph type!" );
	- vtkLineSource * lineSource = vtkLineSource::New();
	- lineSource->Update();
	- glyph = lineSource->GetOutput();
	- }
	-m_RandomMode = false;
	-m_UseMaskPoints = false;
	-m_MaximumNumberOfPoints = 808080;
	- //
	- // set up the actual glyphing filter
	- //
	- m_Glyph3DGenerator->SetSourceData( glyph );
	- m_Glyph3DGenerator->SetInput( vtkImage );
	- //m_Glyph3DGenerator->SetInputConnection(m_Cutter->GetOutputPort());
	- m_Glyph3DGenerator->SetInputArrayToProcess (1, 0,0, vtkDataObject::FIELD_ASSOCIATION_POINTS , "vector");
	-
	- //m_Glyph3DGenerator->SelectInputVectors( vtkImage->GetPointData() ->GetArray( 0 ) ->GetName() );
	- m_Glyph3DGenerator->OrientOn();
	- m_Glyph3DGenerator->SetVectorModeToUseVector();
	- m_Glyph3DGenerator->SetScaleFactor( 0.00392156862745 );
	- m_Glyph3DGenerator->SetScaleModeToScaleByVector();
	- m_Glyph3DGenerator->SetUseMaskPoints( m_UseMaskPoints );
	- m_Glyph3DGenerator->SetRandomMode( m_RandomMode );
	- m_Glyph3DGenerator->SetMaximumNumberOfPoints( m_MaximumNumberOfPoints );
	- m_Glyph3DGenerator->Update();
	- m_Glyph3DMapper->SetInputConnection( m_Glyph3DGenerator->GetOutputPort() );
	- m_Glyph3DActor->SetMapper( m_Glyph3DMapper );
	-
	- if (GetDataNode()->GetProperty("LookupTable"))
	- {
	- mitk::LookupTable::Pointer mitkLookupTable = mitk::LookupTable::New();
	- m_Glyph3DMapper->Update();
	- mitkLookupTable->SetVtkLookupTable(dynamic_cast<vtkLookupTable*>(m_Glyph3DMapper->GetLookupTable()));
	- mitk::LookupTableProperty::Pointer LookupTableProp = mitk::LookupTableProperty::New( mitkLookupTable );
	- GetDataNode()->SetProperty( "LookupTable", LookupTableProp );
	- }
	- else
	- {
	- mitk::LookupTableProperty::Pointer mitkLutProp = dynamic_cast<mitk::LookupTableProperty*>(GetDataNode()->GetProperty("LookupTable"));
	- if (mitkLutProp.IsNotNull())
	- m_Glyph3DMapper->SetLookupTable( mitkLutProp->GetLookupTable()->GetVtkLookupTable() );
	-
	- }
	-
	- //vtkDataSetWriter* writer = vtkDataSetWriter::New();
	- //writer->SetInput( vtkImage );
	- //writer->SetFileName( "out.vtk" );
	- //writer->Update();
	- }
	-
	-}
	-
	-
	-/*
	-* Returns the input data object of the given filter. In this
	-* case, a mitk::Image is returned.
	-*/
	-mitk::Image* mitk::VectorImageVtkGlyphMapper3D::GetInput()
	-{
	- return dynamic_cast<mitk::Image*>( GetDataNode()->GetData() );
	-}
	-
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/Rendering/vtkMaskedProgrammableGlyphFilter.cpp b/Modules/DiffusionImaging/DiffusionCore/src/Rendering/vtkMaskedProgrammableGlyphFilter.cpp
	deleted file mode 100644
	index 9911fc6dc4..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/Rendering/vtkMaskedProgrammableGlyphFilter.cpp
	+++ /dev/null
	@@ -1,100 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "vtkMaskedProgrammableGlyphFilter.h"
	-
	-#include "vtkMaskPoints.h"
	-#include "vtkObjectFactory.h"
	-#include "vtkPolyData.h"
	-
	-vtkStandardNewMacro(vtkMaskedProgrammableGlyphFilter);
	-
	-vtkMaskedProgrammableGlyphFilter::vtkMaskedProgrammableGlyphFilter()
	-{
	- //this->SetColorModeToColorByScalar();
	- //this->SetScaleModeToScaleByVector();
	- this->MaskPoints = vtkMaskPoints::New();
	- this->MaximumNumberOfPoints = 5000;
	- this->UseMaskPoints = 1;
	-}
	-
	-vtkMaskedProgrammableGlyphFilter::~vtkMaskedProgrammableGlyphFilter()
	-{
	- if(this->MaskPoints)
	- {
	- this->MaskPoints->Delete();
	- }
	-}
	-
	-void vtkMaskedProgrammableGlyphFilter::SetInput(vtkDataSet *input)
	-{
	- this->MaskPoints->SetInputData(input);
	- this->Superclass::SetInputData(this->MaskPoints->GetOutput());
	-}
	-
	-void vtkMaskedProgrammableGlyphFilter::SetRandomMode(int mode)
	-{
	- this->MaskPoints->SetRandomMode(mode);
	-}
	-
	-int vtkMaskedProgrammableGlyphFilter::GetRandomMode()
	-{
	- return this->MaskPoints->GetRandomMode();
	-}
	-
	-int vtkMaskedProgrammableGlyphFilter::RequestData(
	- vtkInformation *request,
	- vtkInformationVector **inputVector,
	- vtkInformationVector *outputVector)
	-{
	- if (this->UseMaskPoints)
	- {
	- vtkIdType numPts = this->MaskPoints->GetPolyDataInput(0)->GetNumberOfPoints();
	- this->MaskPoints->SetMaximumNumberOfPoints(MaximumNumberOfPoints);
	- this->MaskPoints->SetOnRatio(numPts / MaximumNumberOfPoints);
	- this->Superclass::SetInputConnection(this->MaskPoints->GetOutputPort());
	- this->MaskPoints->Update();
	- }
	- else
	- {
	- this->Superclass::SetInputData(this->MaskPoints->GetInput());
	- }
	-
	- return this->Superclass::RequestData(
	- request,inputVector,outputVector);
	-}
	-
	-
	-void vtkMaskedProgrammableGlyphFilter::PrintSelf(ostream& os, vtkIndent indent)
	-{
	- this->Superclass::PrintSelf(os,indent);
	- //os << indent << "InputScalarsSelection: "
	- // << (this->InputScalarsSelection ? this->InputScalarsSelection : "(none)")
	- // << endl;
	-
	- //os << indent << "InputVectorsSelection: "
	- // << (this->InputVectorsSelection ? this->InputVectorsSelection : "(none)")
	- // << endl;
	-
	- //os << indent << "InputNormalsSelection: "
	- // << (this->InputNormalsSelection ? this->InputNormalsSelection : "(none)")
	- // << endl;
	-
	- os << indent << "MaximumNumberOfPoints: " << this->GetMaximumNumberOfPoints()
	- << endl;
	-
	- os << indent << "UseMaskPoints: " << (this->UseMaskPoints?"on":"off") << endl;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/Rendering/vtkOdfSource.cxx b/Modules/DiffusionImaging/DiffusionCore/src/Rendering/vtkOdfSource.cxx
	deleted file mode 100644
	index 60a63733b5..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/Rendering/vtkOdfSource.cxx
	+++ /dev/null
	@@ -1,130 +0,0 @@
	-#include "vtkOdfSource.h"
	-
	-#include "vtkCellArray.h"
	-#include "vtkInformation.h"
	-#include "vtkInformationVector.h"
	-#include "vtkPoints.h"
	-#include "vtkStreamingDemandDrivenPipeline.h"
	-#include "vtkObjectFactory.h"
	-#include "vtkDoubleArray.h"
	-#include "vtkCellData.h"
	-#include <vtkLookupTable.h>
	-#include <limits>
	-#include <vtkPointData.h>
	-
	-vtkStandardNewMacro(vtkOdfSource);
	-
	-vtkOdfSource::vtkOdfSource()
	- : r(0)
	- , g(0)
	- , b(0)
	- , UseCustomColor(false)
	-{
	- Scale = 1;
	- lut = vtkSmartPointer<vtkLookupTable>::New();
	- lut->SetRange(0,1);
	- lut->Build();
	- this->SetNumberOfInputPorts(0);
	-}
	-
	-vtkOdfSource::~vtkOdfSource()
	-{
	-
	-}
	-
	-//----------------------------------------------------------------------------
	-int vtkOdfSource::RequestData(
	- vtkInformation *vtkNotUsed(request),
	- vtkInformationVector **vtkNotUsed(inputVector),
	- vtkInformationVector *outputVector)
	-{
	- vtkPolyData* TemplateOdf = OdfType::GetBaseMesh();
	- // get the info object
	- vtkInformation *outInfo = outputVector->GetInformationObject(0);
	- // get the ouptut
	- vtkPolyData *output = vtkPolyData::SafeDownCast(outInfo->Get(vtkDataObject::DATA_OBJECT()));
	-
	- OdfType colorOdf;
	- switch(Normalization)
	- {
	- case mitk::ODFN_MINMAX:
	- Odf = Odf.MinMaxNormalize();
	- colorOdf = Odf;
	- break;
	- case mitk::ODFN_MAX:
	- Odf = Odf.MaxNormalize();
	- colorOdf = Odf;
	- break;
	- case mitk::ODFN_NONE:
	- colorOdf = Odf.MaxNormalize();
	- break;
	- default:
	- Odf = Odf.MaxNormalize();
	- colorOdf = Odf;
	- }
	-
	- vtkCellArray* polys = TemplateOdf->GetPolys();
	- output->SetPolys(polys);
	- polys->InitTraversal();
	- vtkSmartPointer<vtkPoints> newPoints = vtkSmartPointer<vtkPoints>::New();
	- int numPoints = TemplateOdf->GetPoints()->GetNumberOfPoints();
	- newPoints->Allocate(numPoints);
	-
	- vtkSmartPointer<vtkUnsignedCharArray> point_colors = vtkSmartPointer<vtkUnsignedCharArray>::New();
	- point_colors->Allocate(output->GetNumberOfPoints() * 4);
	- point_colors->SetNumberOfComponents(4);
	- point_colors->SetName("ODF_COLORS");
	- unsigned char rgba[4];
	- double rgb[3];
	-
	- for(int j=0; j<numPoints; j++)
	- {
	- double p[3];
	- TemplateOdf->GetPoints()->GetPoint(j,p);
	- double val = Odf.GetElement(j);
	- p[0] = valScaleAdditionalScale0.5;
	- p[1] = valScaleAdditionalScale0.5;
	- p[2] = valScaleAdditionalScale0.5;
	- newPoints->InsertNextPoint(p);
	-
	- if (UseCustomColor)
	- {
	- rgba[0] = (unsigned char)r;
	- rgba[1] = (unsigned char)g;
	- rgba[2] = (unsigned char)b;
	- }
	- else
	- {
	- double color_val = colorOdf.GetElement(j);
	- lut->GetColor(1-color_val, rgb);
	- rgba[0] = (unsigned char)(255.0*rgb[0]);
	- rgba[1] = (unsigned char)(255.0*rgb[1]);
	- rgba[2] = (unsigned char)(255.0*rgb[2]);
	- }
	- rgba[3] = 255;
	- point_colors->InsertTypedTuple(j, rgba);
	- }
	- output->SetPoints(newPoints);
	- output->GetPointData()->AddArray(point_colors);
	- return 1;
	-}
	-
	-//----------------------------------------------------------------------------
	-void vtkOdfSource::PrintSelf(ostream& os, vtkIndent indent)
	-{
	- this->Superclass::PrintSelf(os,indent);
	-}
	-
	-//----------------------------------------------------------------------------
	-int vtkOdfSource::RequestInformation(
	- vtkInformation *vtkNotUsed(request),
	- vtkInformationVector **vtkNotUsed(inputVector),
	- vtkInformationVector *outputVector)
	-{
	- // get the info object
	- vtkInformation *outInfo = outputVector->GetInformationObject(0);
	-
	- outInfo->Set(vtkAlgorithm::CAN_HANDLE_PIECE_REQUEST(),0);
	-
	- return 1;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/Rendering/vtkThickPlane.cxx b/Modules/DiffusionImaging/DiffusionCore/src/Rendering/vtkThickPlane.cxx
	deleted file mode 100644
	index 02edd0a0c2..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/Rendering/vtkThickPlane.cxx
	+++ /dev/null
	@@ -1,144 +0,0 @@
	-/*=========================================================================
	-
	-Program: Visualization Toolkit
	-
	-Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
	-All rights reserved.
	-See Copyright.txt or http://www.kitware.com/Copyright.htm for details.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without even
	-the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
	-PURPOSE. See the above copyright notice for more information.
	-
	-=========================================================================*/
	-#include "vtkThickPlane.h"
	-#include "vtkMath.h"
	-#include "vtkObjectFactory.h"
	-
	-vtkStandardNewMacro(vtkThickPlane);
	-
	-// Construct plane passing through origin and normal to z-axis.
	-vtkThickPlane::vtkThickPlane()
	-{
	- this->Normal[0] = 0.0;
	- this->Normal[1] = 0.0;
	- this->Normal[2] = 1.0;
	-
	- this->Origin[0] = 0.0;
	- this->Origin[1] = 0.0;
	- this->Origin[2] = 0.0;
	-}
	-
	-// Evaluate plane equation for point x[3].
	-double vtkThickPlane::EvaluateFunction(double x[3])
	-{
	- return this->EvaluateFunction(x[0],x[1],x[2]);
	-}
	-
	-void vtkThickPlane::EvaluateFunction(vtkDataArray* input, vtkDataArray* output)
	-{
	- vtkImplicitFunction::EvaluateFunction(input, output);
	-}
	-
	-// Evaluate plane equation for point x,y,z.
	-double vtkThickPlane::EvaluateFunction(double x,double y,double z)
	-{
	- // PointPlaneDistance = Distance - Normal*Point
	- double ppd = Distance - ( this->Normal[0]*x +
	- this->Normal[1]*y +
	- this->Normal[2]*z );
	-
	- if( std::abs(ppd) <= Thickness )
	- {
	- count++;
	- return 0;
	- }
	-
	- if( ppd >= 0 )
	- return ppd - Thickness;
	-
	- return std::abs(ppd + Thickness);
	-}
	-
	-// Evaluate function gradient at point x[3].
	-void vtkThickPlane::EvaluateGradient(double vtkNotUsed(x)[3], double n[3])
	-{
	- for (int i=0; i<3; i++)
	- {
	- n[i] = this->Normal[i];
	- }
	-}
	-
	-void vtkThickPlane::SetPose (double _n1, double _n2, double _n3, double _o1, double _o2, double _o3)
	-{
	- SetNormal(_n1,_n2,_n3);
	- SetOrigin(_o1,_o2,_o3);
	- Distance = Normal[0]Origin[0]+Normal[1]Origin[1]+Normal[2]*Origin[2];
	- if(Distance < 0.0)
	- {
	- Distance = -Distance;
	- Normal[0] = -Normal[0];
	- Normal[1] = -Normal[1];
	- Normal[2] = -Normal[2];
	- }
	-}
	-
	-void vtkThickPlane::SetPose (double _n[3], double _o[3])
	-{
	- SetPose(_n[0],_n[1],_n[2],_o[0],_o[1],_o[2]);
	-}
	-
	-void vtkThickPlane::SetNormal (double _arg1, double _arg2, double _arg3)
	-{
	- vtkDebugMacro(<< this->GetClassName() << " (" << this << "): setting " << Normal << " to (" << _arg1 << "," << _arg2 << "," << _arg3 << ")");
	- if ((this->Normal[0] != _arg1)\|\|(this->Normal[1] != _arg2)\|\|(this->Normal[2] != _arg3))
	- {
	- double length = sqrt(_arg1_arg1+_arg2_arg2+_arg3*_arg3);
	- this->Normal[0] = _arg1/length;
	- this->Normal[1] = _arg2/length;
	- this->Normal[2] = _arg3/length;
	- this->Modified();
	- }
	-};
	-
	-void vtkThickPlane::SetNormal (double _arg[3])
	-{
	- this->SetNormal (_arg[0], _arg[1], _arg[2]);
	-}
	-
	-void vtkThickPlane::SetOrigin (double _arg1, double _arg2, double _arg3)
	-{
	- vtkDebugMacro(<< this->GetClassName() << " (" << this << "): setting " << Origin << " to (" << _arg1 << "," << _arg2 << "," << _arg3 << ")");
	- if ((this->Normal[0] != _arg1)\|\|(this->Normal[1] != _arg2)\|\|(this->Normal[2] != _arg3))
	- {
	- this->Origin[0] = _arg1;
	- this->Origin[1] = _arg2;
	- this->Origin[2] = _arg3;
	- this->Modified();
	- }
	-};
	-
	-void vtkThickPlane::SetOrigin (double _arg[3])
	-{
	- this->SetOrigin (_arg[0], _arg[1], _arg[2]);
	-}
	-
	-void vtkThickPlane::SetThickness (double _arg)
	-{
	- Thickness = std::abs(_arg);
	-}
	-
	-#define VTK_PLANE_TOL 1.0e-06
	-
	-void vtkThickPlane::PrintSelf(ostream& os, vtkIndent indent)
	-{
	- this->Superclass::PrintSelf(os,indent);
	-
	- os << indent << "Normal: (" << this->Normal[0] << ", "
	- << this->Normal[1] << ", " << this->Normal[2] << ")\n";
	-
	- os << indent << "Origin: (" << this->Origin[0] << ", "
	- << this->Origin[1] << ", " << this->Origin[2] << ")\n";
	-
	- os << indent << "Thickness: " << this->Thickness << "\n";
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionCore/src/mitkDiffusionFunctionCollection.cpp b/Modules/DiffusionImaging/DiffusionCore/src/mitkDiffusionFunctionCollection.cpp
	deleted file mode 100644
	index eaa009d443..0000000000
	--- a/Modules/DiffusionImaging/DiffusionCore/src/mitkDiffusionFunctionCollection.cpp
	+++ /dev/null
	@@ -1,707 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkDiffusionFunctionCollection.h"
	-#include "mitkNumericTypes.h"
	-
	-#include <boost/math/special_functions/legendre.hpp>
	-#include <boost/math/special_functions/spherical_harmonic.hpp>
	-#include <boost/version.hpp>
	-#include <itkPointShell.h>
	-#include "itkVectorContainer.h"
	-#include "vnl/vnl_vector.h"
	-#include <vtkBox.h>
	-#include <vtkMath.h>
	-#include <itksys/SystemTools.hxx>
	-#include <boost/algorithm/string.hpp>
	-#include <itkShToOdfImageFilter.h>
	-#include <itkTensorImageToOdfImageFilter.h>
	-
	-// Intersect a finite line (with end points p0 and p1) with all of the
	-// cells of a vtkImageData
	-std::vector< std::pair< itk::Index<3>, double > > mitk::imv::IntersectImage(const itk::Vector<double,3>& spacing, itk::Index<3>& si, itk::Index<3>& ei, itk::ContinuousIndex<float, 3>& sf, itk::ContinuousIndex<float, 3>& ef)
	-{
	- std::vector< std::pair< itk::Index<3>, double > > out;
	- if (si == ei)
	- {
	- double d[3];
	- for (int i=0; i<3; ++i)
	- d[i] = static_cast<double>(sf[i]-ef[i])*spacing[i];
	- double len = std::sqrt( d[0]d[0] + d[1]d[1] + d[2]*d[2] );
	- out.push_back( std::pair< itk::Index<3>, double >(si, len) );
	- return out;
	- }
	-
	- double bounds[6];
	-
	- double entrancePoint[3];
	- double exitPoint[3];
	-
	- double startPoint[3];
	- double endPoint[3];
	-
	- double t0, t1;
	- for (unsigned int i=0; i<3; ++i)
	- {
	- startPoint[i] = static_cast<double>(sf[i]);
	- endPoint[i] = static_cast<double>(ef[i]);
	-
	- if (si[i]>ei[i])
	- {
	- auto t = si[i];
	- si[i] = ei[i];
	- ei[i] = t;
	- }
	- }
	-
	- for (auto x = si[0]; x<=ei[0]; ++x)
	- for (auto y = si[1]; y<=ei[1]; ++y)
	- for (auto z = si[2]; z<=ei[2]; ++z)
	- {
	- bounds[0] = static_cast<double>(x) - 0.5;
	- bounds[1] = static_cast<double>(x) + 0.5;
	- bounds[2] = static_cast<double>(y) - 0.5;
	- bounds[3] = static_cast<double>(y) + 0.5;
	- bounds[4] = static_cast<double>(z) - 0.5;
	- bounds[5] = static_cast<double>(z) + 0.5;
	-
	- int entryPlane;
	- int exitPlane;
	- int hit = vtkBox::IntersectWithLine(bounds,
	- startPoint,
	- endPoint,
	- t0,
	- t1,
	- entrancePoint,
	- exitPoint,
	- entryPlane,
	- exitPlane);
	- if (hit)
	- {
	- if (entryPlane>=0 && exitPlane>=0)
	- {
	- double d[3];
	- for (int i=0; i<3; ++i)
	- d[i] = (exitPoint[i] - entrancePoint[i])*spacing[i];
	- double len = std::sqrt( d[0]d[0] + d[1]d[1] + d[2]*d[2] );
	-
	- itk::Index<3> idx; idx[0] = x; idx[1] = y; idx[2] = z;
	- out.push_back( std::pair< itk::Index<3>, double >(idx, len) );
	- }
	- else if (entryPlane>=0)
	- {
	- double d[3];
	- for (int i=0; i<3; ++i)
	- d[i] = (static_cast<double>(ef[i]) - entrancePoint[i])*spacing[i];
	- double len = std::sqrt( d[0]d[0] + d[1]d[1] + d[2]*d[2] );
	-
	- itk::Index<3> idx; idx[0] = x; idx[1] = y; idx[2] = z;
	- out.push_back( std::pair< itk::Index<3>, double >(idx, len) );
	- }
	- else if (exitPlane>=0)
	- {
	- double d[3];
	- for (int i=0; i<3; ++i)
	- d[i] = (exitPoint[i]-static_cast<double>(sf[i]))*spacing[i];
	- double len = std::sqrt( d[0]d[0] + d[1]d[1] + d[2]*d[2] );
	-
	- itk::Index<3> idx; idx[0] = x; idx[1] = y; idx[2] = z;
	- out.push_back( std::pair< itk::Index<3>, double >(idx, len) );
	- }
	- }
	- }
	- return out;
	-}
	-
	-//------------------------- SH-function ------------------------------------
	-
	-double mitk::sh::factorial(int number) {
	- if(number <= 1) return 1;
	- double result = 1.0;
	- for(int i=1; i<=number; i++)
	- result *= i;
	- return result;
	-}
	-
	-void mitk::sh::Cart2Sph(double x, double y, double z, double *spherical)
	-{
	- double phi, th, rad;
	- rad = sqrt(xx+yy+z*z);
	- if( rad < mitk::eps )
	- {
	- th = itk::Math::pi/2;
	- phi = itk::Math::pi/2;
	- }
	- else
	- {
	- th = acos(z/rad);
	- phi = atan2(y, x);
	- }
	- spherical[0] = phi;
	- spherical[1] = th;
	- spherical[2] = rad;
	-}
	-
	-vnl_vector_fixed<double, 3> mitk::sh::Sph2Cart(const double& theta, const double& phi, const double& rad)
	-{
	- vnl_vector_fixed<double, 3> dir;
	- dir[0] = rad * sin(theta) * cos(phi);
	- dir[1] = rad * sin(theta) * sin(phi);
	- dir[2] = rad * cos(theta);
	- return dir;
	-}
	-
	-double mitk::sh::legendre0(int l)
	-{
	- if( l%2 != 0 )
	- {
	- return 0;
	- }
	- else
	- {
	- double prod1 = 1.0;
	- for(int i=1;i<l;i+=2) prod1 *= i;
	- double prod2 = 1.0;
	- for(int i=2;i<=l;i+=2) prod2 *= i;
	- return pow(-1.0,l/2.0)*(prod1/prod2);
	- }
	-}
	-
	-double mitk::sh::Yj(int m, int k, float theta, float phi, bool mrtrix)
	-{
	- if (!mrtrix)
	- {
	- if (m<0)
	- return sqrt(2.0)*static_cast<double>(::boost::math::spherical_harmonic_r(static_cast<unsigned int>(k), -m, theta, phi));
	- else if (m==0)
	- return static_cast<double>(::boost::math::spherical_harmonic_r(static_cast<unsigned int>(k), m, theta, phi));
	- else
	- return pow(-1.0,m)sqrt(2.0)static_cast<double>(::boost::math::spherical_harmonic_i(static_cast<unsigned int>(k), m, theta, phi));
	- }
	- else
	- {
	- double plm = static_cast<double>(::boost::math::legendre_p<float>(k,abs(m),-cos(theta)));
	- double mag = sqrt((2.0k+1.0)/(4.0itk::Math::pi)::boost::math::factorial<double>(k-abs(m))/::boost::math::factorial<double>(k+abs(m)))plm;
	- if (m>0)
	- return magstatic_cast<double>(cos(mphi));
	- else if (m==0)
	- return mag;
	- else
	- return magstatic_cast<double>(sin(-mphi));
	- }
	-
	- return 0;
	-}
	-
	-mitk::OdfImage::ItkOdfImageType::Pointer mitk::convert::GetItkOdfFromShImage(mitk::Image::Pointer mitkImage)
	-{
	- mitk::ShImage::Pointer mitkShImage = dynamic_cast<mitk::ShImage*>(mitkImage.GetPointer());
	- if (mitkShImage.IsNull())
	- mitkThrow() << "Input image is not a SH image!";
	- mitk::OdfImage::ItkOdfImageType::Pointer output;
	- switch (mitkShImage->ShOrder())
	- {
	- case 2:
	- {
	- typedef itk::ShToOdfImageFilter< float, 2 > ShConverterType;
	- typename ShConverterType::InputImageType::Pointer itkvol = ShConverterType::InputImageType::New();
	- mitk::CastToItkImage(mitkImage, itkvol);
	- typename ShConverterType::Pointer converter = ShConverterType::New();
	- converter->SetInput(itkvol);
	- converter->Update();
	- output = converter->GetOutput();
	- break;
	- }
	- case 4:
	- {
	- typedef itk::ShToOdfImageFilter< float, 4 > ShConverterType;
	- typename ShConverterType::InputImageType::Pointer itkvol = ShConverterType::InputImageType::New();
	- mitk::CastToItkImage(mitkImage, itkvol);
	- typename ShConverterType::Pointer converter = ShConverterType::New();
	- converter->SetInput(itkvol);
	- converter->Update();
	- output = converter->GetOutput();
	- break;
	- }
	- case 6:
	- {
	- typedef itk::ShToOdfImageFilter< float, 6 > ShConverterType;
	- typename ShConverterType::InputImageType::Pointer itkvol = ShConverterType::InputImageType::New();
	- mitk::CastToItkImage(mitkImage, itkvol);
	- typename ShConverterType::Pointer converter = ShConverterType::New();
	- converter->SetInput(itkvol);
	- converter->Update();
	- output = converter->GetOutput();
	- break;
	- }
	- case 8:
	- {
	- typedef itk::ShToOdfImageFilter< float, 8 > ShConverterType;
	- typename ShConverterType::InputImageType::Pointer itkvol = ShConverterType::InputImageType::New();
	- mitk::CastToItkImage(mitkImage, itkvol);
	- typename ShConverterType::Pointer converter = ShConverterType::New();
	- converter->SetInput(itkvol);
	- converter->Update();
	- output = converter->GetOutput();
	- break;
	- }
	- case 10:
	- {
	- typedef itk::ShToOdfImageFilter< float, 10 > ShConverterType;
	- typename ShConverterType::InputImageType::Pointer itkvol = ShConverterType::InputImageType::New();
	- mitk::CastToItkImage(mitkImage, itkvol);
	- typename ShConverterType::Pointer converter = ShConverterType::New();
	- converter->SetInput(itkvol);
	- converter->Update();
	- output = converter->GetOutput();
	- break;
	- }
	- case 12:
	- {
	- typedef itk::ShToOdfImageFilter< float, 12 > ShConverterType;
	- typename ShConverterType::InputImageType::Pointer itkvol = ShConverterType::InputImageType::New();
	- mitk::CastToItkImage(mitkImage, itkvol);
	- typename ShConverterType::Pointer converter = ShConverterType::New();
	- converter->SetInput(itkvol);
	- converter->Update();
	- output = converter->GetOutput();
	- break;
	- }
	- default:
	- mitkThrow() << "SH orders higher than 12 are not supported!";
	- }
	-
	- return output;
	-}
	-
	-mitk::OdfImage::Pointer mitk::convert::GetOdfFromShImage(mitk::Image::Pointer mitkImage)
	-{
	- mitk::OdfImage::Pointer image = mitk::OdfImage::New();
	- auto img = GetItkOdfFromShImage(mitkImage);
	- image->InitializeByItk( img.GetPointer() );
	- image->SetVolume( img->GetBufferPointer() );
	- return image;
	-}
	-
	-mitk::OdfImage::ItkOdfImageType::Pointer mitk::convert::GetItkOdfFromTensorImage(mitk::Image::Pointer mitkImage)
	-{
	- typedef itk::TensorImageToOdfImageFilter< float, float > FilterType;
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetInput( GetItkTensorFromTensorImage(mitkImage) );
	- filter->Update();
	- return filter->GetOutput();
	-}
	-
	-mitk::TensorImage::ItkTensorImageType::Pointer mitk::convert::GetItkTensorFromTensorImage(mitk::Image::Pointer mitkImage)
	-{
	- typedef mitk::ImageToItk< mitk::TensorImage::ItkTensorImageType > CasterType;
	- CasterType::Pointer caster = CasterType::New();
	- caster->SetInput(mitkImage);
	- caster->Update();
	- return caster->GetOutput();
	-}
	-
	-mitk::PeakImage::ItkPeakImageType::Pointer mitk::convert::GetItkPeakFromPeakImage(mitk::Image::Pointer mitkImage)
	-{
	- typedef mitk::ImageToItk< mitk::PeakImage::ItkPeakImageType > CasterType;
	- CasterType::Pointer caster = CasterType::New();
	- caster->SetInput(mitkImage);
	- caster->SetCopyMemFlag(true);
	- caster->Update();
	- return caster->GetOutput();
	-}
	-
	-mitk::OdfImage::Pointer mitk::convert::GetOdfFromTensorImage(mitk::Image::Pointer mitkImage)
	-{
	- mitk::OdfImage::Pointer image = mitk::OdfImage::New();
	- auto img = GetItkOdfFromTensorImage(mitkImage);
	- image->InitializeByItk( img.GetPointer() );
	- image->SetVolume( img->GetBufferPointer() );
	- return image;
	-}
	-
	-mitk::OdfImage::ItkOdfImageType::Pointer mitk::convert::GetItkOdfFromOdfImage(mitk::Image::Pointer mitkImage)
	-{
	- typedef mitk::ImageToItk< mitk::OdfImage::ItkOdfImageType > CasterType;
	- CasterType::Pointer caster = CasterType::New();
	- caster->SetInput(mitkImage);
	- caster->Update();
	- return caster->GetOutput();
	-}
	-
	-vnl_matrix<float> mitk::sh::CalcShBasisForDirections(unsigned int sh_order, vnl_matrix<double> U, bool mrtrix)
	-{
	- vnl_matrix<float> sh_basis = vnl_matrix<float>(U.cols(), (sh_order*sh_order + sh_order + 2)/2 + sh_order );
	- for(unsigned int i=0; i<U.cols(); i++)
	- {
	- double x = U(0,i);
	- double y = U(1,i);
	- double z = U(2,i);
	- double spherical[3];
	- mitk::sh::Cart2Sph(x,y,z,spherical);
	- U(0,i) = spherical[0];
	- U(1,i) = spherical[1];
	- U(2,i) = spherical[2];
	- }
	-
	- for(unsigned int i=0; i<U.cols(); i++)
	- {
	- for(int k=0; k<=static_cast<int>(sh_order); k+=2)
	- {
	- for(int m=-k; m<=k; m++)
	- {
	- int j = (k*k + k + 2)/2 + m - 1;
	- double phi = U(0,i);
	- double th = U(1,i);
	- sh_basis(i,j) = mitk::sh::Yj(m,k,th,phi, mrtrix);
	- }
	- }
	- }
	-
	- return sh_basis;
	-}
	-
	-unsigned int mitk::sh::ShOrder(int num_coeffs)
	-{
	- int c=3, d=2-2*num_coeffs;
	- int D = cc-4d;
	- if (D>0)
	- {
	- int s = (-c+static_cast<int>(sqrt(D)))/2;
	- if (s<0)
	- s = (-c-static_cast<int>(sqrt(D)))/2;
	- return static_cast<unsigned int>(s);
	- }
	- else if (D==0)
	- return static_cast<unsigned int>(-c/2);
	- return 0;
	-}
	-
	-float mitk::sh::GetValue(const vnl_vector<float> &coefficients, const int &sh_order, const double theta, const double phi, const bool mrtrix)
	-{
	- float val = 0;
	- for(int k=0; k<=sh_order; k+=2)
	- {
	- for(int m=-k; m<=k; m++)
	- {
	- unsigned int j = static_cast<unsigned int>((k*k + k + 2)/2 + m - 1);
	- val += coefficients[j] * mitk::sh::Yj(m, k, theta, phi, mrtrix);
	- }
	- }
	-
	- return val;
	-}
	-
	-float mitk::sh::GetValue(const vnl_vector<float> &coefficients, const int &sh_order, const vnl_vector_fixed<double, 3> &dir, const bool mrtrix)
	-{
	- double spherical[3];
	- mitk::sh::Cart2Sph(dir[0], dir[1], dir[2], spherical);
	-
	- float val = 0;
	- for(int k=0; k<=sh_order; k+=2)
	- {
	- for(int m=-k; m<=k; m++)
	- {
	- int j = (k*k + k + 2)/2 + m - 1;
	- val += coefficients[j] * mitk::sh::Yj(m, k, spherical[1], spherical[0], mrtrix);
	- }
	- }
	-
	- return val;
	-}
	-
	-//------------------------- gradients-function ------------------------------------
	-
	-
	-mitk::gradients::GradientDirectionContainerType::Pointer mitk::gradients::ReadBvalsBvecs(std::string bvals_file, std::string bvecs_file, double& reference_bval)
	-{
	- mitk::gradients::GradientDirectionContainerType::Pointer directioncontainer = mitk::gradients::GradientDirectionContainerType::New();
	-
	- std::vector<float> bvec_entries;
	- if (!itksys::SystemTools::FileExists(bvecs_file))
	- mitkThrow() << "bvecs file not existing: " << bvecs_file;
	- else
	- {
	- std::string line;
	- std::ifstream myfile (bvecs_file.c_str());
	- if (myfile.is_open())
	- {
	- while (std::getline(myfile, line))
	- {
	- std::vector<std::string> strs;
	- boost::split(strs,line,boost::is_any_of("\t \n"));
	- for (auto token : strs)
	- {
	- if (!token.empty())
	- {
	- try
	- {
	- bvec_entries.push_back(boost::lexical_cast<float>(token));
	- }
	- catch(...)
	- {
	- mitkThrow() << "Encountered invalid bvecs file entry >" << token << "<";
	- }
	- }
	- }
	- }
	- myfile.close();
	- }
	- else
	- {
	- mitkThrow() << "bvecs file could not be opened: " << bvals_file;
	- }
	- }
	-
	- reference_bval = -1;
	- std::vector<float> bval_entries;
	- if (!itksys::SystemTools::FileExists(bvals_file))
	- mitkThrow() << "bvals file not existing: " << bvals_file;
	- else
	- {
	- std::string line;
	- std::ifstream myfile (bvals_file.c_str());
	- if (myfile.is_open())
	- {
	- while (std::getline(myfile, line))
	- {
	- std::vector<std::string> strs;
	- boost::split(strs,line,boost::is_any_of("\t \n"));
	- for (auto token : strs)
	- {
	- if (!token.empty())
	- {
	- try {
	- bval_entries.push_back(boost::lexical_cast<float>(token));
	- if (bval_entries.back()>reference_bval)
	- reference_bval = bval_entries.back();
	- }
	- catch(...)
	- {
	- mitkThrow() << "Encountered invalid bvals file entry >" << token << "<";
	- }
	- }
	- }
	- }
	- myfile.close();
	- }
	- else
	- {
	- mitkThrow() << "bvals file could not be opened: " << bvals_file;
	- }
	- }
	-
	- for(unsigned int i=0; i<bval_entries.size(); i++)
	- {
	- double b_val = bval_entries.at(i);
	-
	- mitk::gradients::GradientDirectionType vec;
	- vec[0] = bvec_entries.at(i);
	- vec[1] = bvec_entries.at(i+bval_entries.size());
	- vec[2] = bvec_entries.at(i+2*bval_entries.size());
	-
	- // Adjust the vector length to encode gradient strength
	- if (reference_bval>0)
	- {
	- double factor = b_val/reference_bval;
	- if(vec.magnitude() > 0)
	- {
	- vec.normalize();
	- vec[0] = sqrt(factor)*vec[0];
	- vec[1] = sqrt(factor)*vec[1];
	- vec[2] = sqrt(factor)*vec[2];
	- }
	- }
	-
	- directioncontainer->InsertElement(i,vec);
	- }
	-
	- return directioncontainer;
	-}
	-
	-void mitk::gradients::WriteBvalsBvecs(std::string bvals_file, std::string bvecs_file, GradientDirectionContainerType::Pointer gradients, double reference_bval)
	-{
	- std::ofstream myfile;
	- myfile.open (bvals_file.c_str());
	- for(unsigned int i=0; i<gradients->Size(); i++)
	- {
	- double twonorm = gradients->ElementAt(i).two_norm();
	- myfile << std::round(reference_bvaltwonormtwonorm) << " ";
	- }
	- myfile.close();
	-
	- std::ofstream myfile2;
	- myfile2.open (bvecs_file.c_str());
	- for(int j=0; j<3; j++)
	- {
	- for(unsigned int i=0; i<gradients->Size(); i++)
	- {
	- GradientDirectionType direction = gradients->ElementAt(i);
	- direction.normalize();
	- myfile2 << direction.get(j) << " ";
	- }
	- myfile2 << std::endl;
	- }
	-}
	-
	-std::vector<unsigned int> mitk::gradients::GetAllUniqueDirections(const BValueMap & refBValueMap, GradientDirectionContainerType *refGradientsContainer )
	-{
	-
	- IndiciesVector directioncontainer;
	- auto mapIterator = refBValueMap.begin();
	-
	- if(refBValueMap.find(0) != refBValueMap.end() && refBValueMap.size() > 1)
	- mapIterator++; //skip bzero Values
	-
	- for( ; mapIterator != refBValueMap.end(); mapIterator++){
	-
	- IndiciesVector currentShell = mapIterator->second;
	-
	- while(currentShell.size()>0)
	- {
	- unsigned int wntIndex = currentShell.back();
	- currentShell.pop_back();
	-
	- auto containerIt = directioncontainer.begin();
	- bool directionExist = false;
	- while(containerIt != directioncontainer.end())
	- {
	- if (fabs(dot_product(refGradientsContainer->ElementAt(*containerIt), refGradientsContainer->ElementAt(wntIndex))) > 0.9998)
	- {
	- directionExist = true;
	- break;
	- }
	- containerIt++;
	- }
	- if(!directionExist)
	- {
	- directioncontainer.push_back(wntIndex);
	- }
	- }
	- }
	-
	- return directioncontainer;
	-}
	-
	-
	-bool mitk::gradients::CheckForDifferingShellDirections(const BValueMap & refBValueMap, GradientDirectionContainerType::ConstPointer refGradientsContainer)
	-{
	- auto mapIterator = refBValueMap.begin();
	-
	- if(refBValueMap.find(0) != refBValueMap.end() && refBValueMap.size() > 1)
	- mapIterator++; //skip bzero Values
	-
	- for( ; mapIterator != refBValueMap.end(); mapIterator++){
	-
	- auto mapIterator_2 = refBValueMap.begin();
	- if(refBValueMap.find(0) != refBValueMap.end() && refBValueMap.size() > 1)
	- mapIterator_2++; //skip bzero Values
	-
	- for( ; mapIterator_2 != refBValueMap.end(); mapIterator_2++){
	-
	- if(mapIterator_2 == mapIterator) continue;
	-
	- IndiciesVector currentShell = mapIterator->second;
	- IndiciesVector testShell = mapIterator_2->second;
	- for (unsigned int i = 0; i< currentShell.size(); i++)
	- if (fabs(dot_product(refGradientsContainer->ElementAt(currentShell[i]), refGradientsContainer->ElementAt(testShell[i]))) <= 0.9998) { return true; }
	-
	- }
	- }
	- return false;
	-}
	-
	-vnl_matrix<double> mitk::gradients::ComputeSphericalFromCartesian(const IndiciesVector & refShell, const GradientDirectionContainerType * refGradientsContainer)
	-{
	-
	- vnl_matrix<double> Q(3, refShell.size());
	- Q.fill(0.0);
	-
	- for(unsigned int i = 0; i < refShell.size(); i++)
	- {
	- GradientDirectionType dir = refGradientsContainer->ElementAt(refShell[i]);
	- double x = dir.normalize().get(0);
	- double y = dir.normalize().get(1);
	- double z = dir.normalize().get(2);
	- double cart[3];
	- mitk::sh::Cart2Sph(x,y,z,cart);
	- Q(0,i) = cart[0];
	- Q(1,i) = cart[1];
	- Q(2,i) = cart[2];
	- }
	- return Q;
	-}
	-
	-vnl_matrix<double> mitk::gradients::ComputeSphericalHarmonicsBasis(const vnl_matrix<double> & QBallReference, const unsigned int & LOrder)
	-{
	- vnl_matrix<double> SHBasisOutput(QBallReference.cols(), (LOrder+1)(LOrder+2)0.5);
	- SHBasisOutput.fill(0.0);
	- for(unsigned int i=0; i<SHBasisOutput.rows(); i++)
	- for(int k = 0; k <= (int)LOrder; k += 2)
	- for(int m =- k; m <= k; m++)
	- {
	- int j = ( k * k + k + 2 ) / 2.0 + m - 1;
	- double phi = QBallReference(0,i);
	- double th = QBallReference(1,i);
	- double val = mitk::sh::Yj(m,k,th,phi);
	- SHBasisOutput(i,j) = val;
	- }
	- return SHBasisOutput;
	-}
	-
	-mitk::gradients::GradientDirectionContainerType::Pointer mitk::gradients::CreateNormalizedUniqueGradientDirectionContainer(const mitk::gradients::BValueMap & bValueMap,
	- const GradientDirectionContainerType *origninalGradentcontainer)
	-{
	- mitk::gradients::GradientDirectionContainerType::Pointer directioncontainer = mitk::gradients::GradientDirectionContainerType::New();
	- auto mapIterator = bValueMap.begin();
	-
	- if(bValueMap.find(0) != bValueMap.end() && bValueMap.size() > 1){
	- mapIterator++; //skip bzero Values
	- vnl_vector_fixed<double, 3> vec;
	- vec.fill(0.0);
	- directioncontainer->push_back(vec);
	- }
	-
	- for( ; mapIterator != bValueMap.end(); mapIterator++){
	-
	- IndiciesVector currentShell = mapIterator->second;
	-
	- while(currentShell.size()>0)
	- {
	- unsigned int wntIndex = currentShell.back();
	- currentShell.pop_back();
	-
	- mitk::gradients::GradientDirectionContainerType::Iterator containerIt = directioncontainer->Begin();
	- bool directionExist = false;
	- while(containerIt != directioncontainer->End())
	- {
	- if (fabs(dot_product(containerIt.Value(), origninalGradentcontainer->ElementAt(wntIndex))) > 0.9998)
	- {
	- directionExist = true;
	- break;
	- }
	- containerIt++;
	- }
	- if(!directionExist)
	- {
	- GradientDirectionType dir(origninalGradentcontainer->ElementAt(wntIndex));
	- directioncontainer->push_back(dir.normalize());
	- }
	- }
	- }
	-
	- return directioncontainer;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionIO/CMakeLists.txt b/Modules/DiffusionImaging/DiffusionIO/CMakeLists.txt
	deleted file mode 100644
	index fbe023567b..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/CMakeLists.txt
	+++ /dev/null
	@@ -1,8 +0,0 @@
	-MITK_CREATE_MODULE(
	- SUBPROJECTS MITK-DTI
	- INCLUDE_DIRS ${CMAKE_CURRENT_BINARY_DIR}
	- DEPENDS MitkConnectomics MitkQuantification MitkFiberTracking
	- AUTOLOAD_WITH MitkCore
	- PACKAGE_DEPENDS PUBLIC DCMTK
	-)
	-
	diff --git a/Modules/DiffusionImaging/DiffusionIO/files.cmake b/Modules/DiffusionImaging/DiffusionIO/files.cmake
	deleted file mode 100644
	index 7af682f8bc..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/files.cmake
	+++ /dev/null
	@@ -1,42 +0,0 @@
	-set(CPP_FILES
	- mitkDiffusionModuleActivator.cpp
	- mitkNrrdTbssImageWriterFactory.cpp
	- #mitkFiberBundleIOFactory.cpp
	- mitkConnectomicsNetworkReader.cpp
	- mitkConnectomicsNetworkWriter.cpp
	- mitkConnectomicsNetworkCSVWriter.cpp
	- mitkConnectomicsNetworkMatrixWriter.cpp
	- mitkConnectomicsNetworkSerializer.cpp
	- mitkConnectomicsNetworkDefinitions.cpp
	- mitkNrrdTbssRoiImageIOFactory.cpp
	- #mitkFiberBundleWriterFactory.cpp
	- mitkNrrdTbssRoiImageWriterFactory.cpp
	- mitkFiberTrackingObjectFactory.cpp
	- mitkConnectomicsObjectFactory.cpp
	- mitkQuantificationObjectFactory.cpp
	- mitkNrrdTbssImageIOFactory.cpp
	-
	- mitkDiffusionIOMimeTypes.cpp
	-
	- mitkFiberBundleDicomReader.cpp
	- mitkFiberBundleDicomWriter.cpp
	- mitkFiberBundleTckReader.cpp
	- mitkFiberBundleTrackVisReader.cpp
	- mitkFiberBundleTrackVisWriter.cpp
	- mitkFiberBundleVtkReader.cpp
	- mitkFiberBundleVtkWriter.cpp
	- mitkFiberBundleSerializer.cpp
	- mitkFiberBundleMapper2D.cpp
	- mitkFiberBundleMapper3D.cpp
	- mitkPeakImageMapper2D.cpp
	- mitkPeakImageMapper3D.cpp
	-
	- mitkTractographyForestReader.cpp
	- mitkTractographyForestWriter.cpp
	- mitkTractographyForestSerializer.cpp
	-
	- mitkPlanarFigureCompositeWriter.cpp
	- mitkPlanarFigureCompositeReader.cpp
	- mitkPlanarFigureCompositeSerializer.cpp
	-)
	-
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkCSVWriter.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkCSVWriter.cpp
	deleted file mode 100644
	index c9b0a3badf..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkCSVWriter.cpp
	+++ /dev/null
	@@ -1,141 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkConnectomicsNetworkCSVWriter.h"
	-#include "mitkConnectomicsNetworkDefinitions.h"
	-#include "mitkDiffusionIOMimeTypes.h"
	-#include <mitkConnectomicsNetworkProperties.h>
	-#include <mitkStringProperty.h>
	-#include <boost/algorithm/string.hpp>
	-
	-mitk::ConnectomicsNetworkCSVWriter::ConnectomicsNetworkCSVWriter()
	- : AbstractFileWriter(mitk::ConnectomicsNetwork::GetStaticNameOfClass(), CustomMimeType( mitk::DiffusionIOMimeTypes::CONNECTOMICS_LIST_MIMETYPE() ), "Write only CSV Connectomics Networks" )
	-{
	- RegisterService();
	-}
	-
	-mitk::ConnectomicsNetworkCSVWriter::ConnectomicsNetworkCSVWriter(const mitk::ConnectomicsNetworkCSVWriter& other)
	- : AbstractFileWriter(other)
	-{
	-}
	-
	-
	-mitk::ConnectomicsNetworkCSVWriter::~ConnectomicsNetworkCSVWriter()
	-{}
	-
	-mitk::ConnectomicsNetworkCSVWriter* mitk::ConnectomicsNetworkCSVWriter::Clone() const
	-{
	- return new ConnectomicsNetworkCSVWriter(*this);
	-}
	-
	-void mitk::ConnectomicsNetworkCSVWriter::Write()
	-{
	- MITK_INFO << "Writing connectomics network";
	- InputType::ConstPointer input = dynamic_cast<const InputType*>(this->GetInput());
	- if (input.IsNull() )
	- {
	- MITK_ERROR <<"Sorry, input to ConnectomicsNetworkMatrixWriter is nullptr!";
	- return;
	- }
	-
	- this->ValidateOutputLocation();
	-
	- std::ostream* out;
	- std::ofstream outStream;
	-
	- if( this->GetOutputStream() )
	- {
	- out = this->GetOutputStream();
	- }
	- else
	- {
	- outStream.open( this->GetOutputLocation().c_str() );
	- out = &outStream;
	- }
	-
	- if ( !out->good() )
	- {
	- mitkThrow() << "Could not open stream.";
	- }
	-
	- try
	- {
	- const std::string& locale = "C";
	- const std::string& currLocale = setlocale( LC_ALL, nullptr );
	- setlocale(LC_ALL, locale.c_str());
	-
	- std::locale previousLocale(out->getloc());
	- std::locale I("C");
	- out->imbue(I);
	-
	- // construct header
	- std::stringstream header;
	-
	- mitk::StringProperty::Pointer addHeaderInfoProperty = dynamic_cast<mitk::StringProperty*>(input->GetProperty(connectomicsDataAdditionalHeaderInformation.c_str()).GetPointer());
	- if(addHeaderInfoProperty.IsNotNull())
	- {
	- std::string additionalHeaderInfo = addHeaderInfoProperty->GetValue();
	- // if the additional header info contains newlines we need to add #
	- // in front of the new lines
	- std::vector<std::string> strings;
	- boost::split(strings, additionalHeaderInfo, boost::is_any_of("\n"));
	- for( unsigned int index(0); index < strings.size(); ++index)
	- {
	- header << "#" << strings[index] << "\n";
	- }
	- }
	-
	- // construct body
	- std::stringstream body;
	-
	- std::vector< InputType::VertexDescriptorType > nodes = input->GetVectorOfAllVertexDescriptors();
	- for(unsigned int i(0); i < nodes.size(); ++i)
	- {
	- for(unsigned int j(0); j < i; ++j)
	- {
	- double weight(0);
	- if( input->EdgeExists(nodes[i], nodes[j]) )
	- {
	- weight = (input->GetEdge(nodes[i], nodes[j])).edge_weight;
	- }
	- body << (input->GetNode(nodes[i])).label << " "
	- << (input->GetNode(nodes[j])).label << " "
	- << weight << "\n";
	- }
	- }
	-
	- (*out)<< header.str() << body.str();
	-
	- setlocale(LC_ALL, currLocale.c_str());
	- MITK_INFO << "Connectomics network connection list written";
	- }
	- catch(...)
	- {
	- mitkThrow() << "Error while writing to stream.";
	- }
	-}
	-
	-mitk::IFileIO::ConfidenceLevel mitk::ConnectomicsNetworkCSVWriter::GetConfidenceLevel() const
	-{
	- if (AbstractFileWriter::GetConfidenceLevel() == Unsupported)
	- {
	- return Unsupported;
	- }
	-
	- // exporting is supported but will result in loss of data
	- // which prevents re-import
	- return PartiallySupported;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkCSVWriter.h b/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkCSVWriter.h
	deleted file mode 100644
	index 1f37d2382f..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkCSVWriter.h
	+++ /dev/null
	@@ -1,61 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkConnectomicsNetworkCSVWriter_h
	-#define __mitkConnectomicsNetworkCSVWriter_h
	-
	-#include <mitkAbstractFileWriter.h>
	-#include "mitkConnectomicsNetwork.h"
	-#include <vtkPolyDataWriter.h>
	-
	-
	-namespace mitk
	-{
	-
	- /**
	- * Writes connectomics networks to a file
	- *
	- * This export is write only, information is lost.
	- * @ingroup Process
	- */
	- class ConnectomicsNetworkCSVWriter : public mitk::AbstractFileWriter
	- {
	- public:
	- typedef mitk::ConnectomicsNetwork InputType;
	- typedef std::vector< std::pair< std::pair<
	- mitk::ConnectomicsNetwork::NetworkNode, mitk::ConnectomicsNetwork::NetworkNode >
	- , mitk::ConnectomicsNetwork::NetworkEdge > > EdgeVectorType;
	- typedef std::vector< mitk::ConnectomicsNetwork::NetworkNode > VertexVectorType;
	-
	- ConnectomicsNetworkCSVWriter();
	- ~ConnectomicsNetworkCSVWriter() override;
	-
	- using AbstractFileWriter::Write;
	- void Write() override;
	-
	- mitk::IFileIO::ConfidenceLevel GetConfidenceLevel() const override;
	-
	- protected:
	-
	- ConnectomicsNetworkCSVWriter(const ConnectomicsNetworkCSVWriter& other);
	- mitk::ConnectomicsNetworkCSVWriter* Clone() const override;
	-
	- };
	-
	-
	-} // end of namespace mitk
	-
	-#endif //__mitkConnectomicsNetworkCSVWriter_h
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkDefinitions.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkDefinitions.cpp
	deleted file mode 100644
	index 9b42fac5ee..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkDefinitions.cpp
	+++ /dev/null
	@@ -1,65 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkConnectomicsNetworkDefinitions.h"
	-
	-//============== XML const chars ===================
	-
	-//==== Header information ====
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_CONNECTOMICS_FILE = "connectomics_network_file" ;
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_FILE_VERSION = "file_version" ;
	-const char* mitk::ConnectomicsNetworkDefinitions::VERSION_STRING = "0.2" ;
	-const char* mitk::ConnectomicsNetworkDefinitions::ASCII_FILE = "ascii_file" ;
	-const char* mitk::ConnectomicsNetworkDefinitions::FILE_NAME = "file_name" ;
	-
	-//==== Geometry details ====
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_GEOMETRY = "geometry";
	-
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_XX = "xx";
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_XY = "xy";
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_XZ = "xz";
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_YX = "yx";
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_YY = "yy";
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_YZ = "yz";
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_ZX = "zx";
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_ZY = "zy";
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_ZZ = "zz";
	-
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_ORIGIN_X = "origin_x";
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_ORIGIN_Y = "origin_y";
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_ORIGIN_Z = "origin_z";
	-
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_SPACING_X = "spacing_x";
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_SPACING_Y = "spacing_y";
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_SPACING_Z = "spacing_z";
	-
	-//==== Connectomics structures ====
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_VERTICES = "vertices";
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_EDGES = "edges";
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_VERTEX = "vertex";
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_EDGE = "edge";
	-
	-//==== Connectomics properties ====
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_VERTEX_ID = "v_id";
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_VERTEX_LABEL = "v_label";
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_VERTEX_X = "v_x";
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_VERTEX_Y = "v_y";
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_VERTEX_Z = "v_z";
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_EDGE_ID = "e_id";
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_EDGE_SOURCE_ID = "e_s_id";
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_EDGE_TARGET_ID = "e_t_id";
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_EDGE_FIBERCOUNT_ID = "e_weight";
	-const char* mitk::ConnectomicsNetworkDefinitions::XML_EDGE_DOUBLE_WEIGHT_ID = "e_double_weight";
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkDefinitions.h b/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkDefinitions.h
	deleted file mode 100644
	index 053c08fd76..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkDefinitions.h
	+++ /dev/null
	@@ -1,86 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkConnectomicsNetworkDefinitions_h
	-#define __mitkConnectomicsNetworkDefinitions_h
	-
	-namespace mitk
	-{
	-
	- /** \brief The XML consts for reading and writing
	- */
	-
	- class ConnectomicsNetworkDefinitions
	- {
	- public:
	-
	- //============== XML const chars ===================
	-
	- //==== Header information ====
	- static const char* XML_CONNECTOMICS_FILE;
	- static const char* XML_FILE_VERSION;
	- static const char* VERSION_STRING;
	- static const char* ASCII_FILE;
	- static const char* FILE_NAME;
	-
	- //==== Geometry details ====
	- static const char* XML_GEOMETRY;
	-
	- static const char* XML_MATRIX_XX;
	- static const char* XML_MATRIX_XY;
	- static const char* XML_MATRIX_XZ;
	- static const char* XML_MATRIX_YX;
	- static const char* XML_MATRIX_YY;
	- static const char* XML_MATRIX_YZ;
	- static const char* XML_MATRIX_ZX;
	- static const char* XML_MATRIX_ZY;
	- static const char* XML_MATRIX_ZZ;
	-
	- static const char* XML_ORIGIN_X;
	- static const char* XML_ORIGIN_Y;
	- static const char* XML_ORIGIN_Z;
	-
	- static const char* XML_SPACING_X;
	- static const char* XML_SPACING_Y;
	- static const char* XML_SPACING_Z;
	-
	- //==== Connectomics structures ====
	- static const char* XML_VERTICES;
	- static const char* XML_EDGES;
	- static const char* XML_VERTEX;
	- static const char* XML_EDGE;
	-
	- //==== Connectomics properties ====
	- static const char* XML_VERTEX_ID;
	- static const char* XML_VERTEX_LABEL;
	- static const char* XML_VERTEX_X;
	- static const char* XML_VERTEX_Y;
	- static const char* XML_VERTEX_Z;
	- static const char* XML_EDGE_ID;
	- static const char* XML_EDGE_SOURCE_ID;
	- static const char* XML_EDGE_TARGET_ID;
	- static const char* XML_EDGE_FIBERCOUNT_ID;
	- static const char* XML_EDGE_DOUBLE_WEIGHT_ID;
	-
	- private:
	- ConnectomicsNetworkDefinitions();
	- ~ConnectomicsNetworkDefinitions();
	-
	- };
	-
	-} //namespace MITK
	-
	-#endif // __mitkConnectomicsNetworkDefinitions_h
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkMatrixWriter.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkMatrixWriter.cpp
	deleted file mode 100644
	index 1748e4032a..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkMatrixWriter.cpp
	+++ /dev/null
	@@ -1,151 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkConnectomicsNetworkMatrixWriter.h"
	-#include "mitkConnectomicsNetworkDefinitions.h"
	-#include "mitkDiffusionIOMimeTypes.h"
	-#include <mitkConnectomicsNetworkProperties.h>
	-#include <boost/algorithm/string.hpp>
	-
	-mitk::ConnectomicsNetworkMatrixWriter::ConnectomicsNetworkMatrixWriter()
	- : AbstractFileWriter(mitk::ConnectomicsNetwork::GetStaticNameOfClass(), CustomMimeType( mitk::DiffusionIOMimeTypes::CONNECTOMICS_MATRIX_MIMETYPE() ), "Write only Matrix Connectomics Networks" )
	-{
	- RegisterService();
	-}
	-
	-mitk::ConnectomicsNetworkMatrixWriter::ConnectomicsNetworkMatrixWriter(const mitk::ConnectomicsNetworkMatrixWriter& other)
	- : AbstractFileWriter(other)
	-{
	-}
	-
	-
	-mitk::ConnectomicsNetworkMatrixWriter::~ConnectomicsNetworkMatrixWriter()
	-{}
	-
	-mitk::ConnectomicsNetworkMatrixWriter* mitk::ConnectomicsNetworkMatrixWriter::Clone() const
	-{
	- return new ConnectomicsNetworkMatrixWriter(*this);
	-}
	-
	-void mitk::ConnectomicsNetworkMatrixWriter::Write()
	-{
	- MITK_INFO << "Writing connectomics network";
	- InputType::ConstPointer input = dynamic_cast<const InputType*>(this->GetInput());
	- if (input.IsNull() )
	- {
	- MITK_ERROR <<"Sorry, input to ConnectomicsNetworkMatrixWriter is nullptr!";
	- return;
	- }
	-
	- this->ValidateOutputLocation();
	-
	- std::ostream* out;
	- std::ofstream outStream;
	-
	- if( this->GetOutputStream() )
	- {
	- out = this->GetOutputStream();
	- }
	- else
	- {
	- outStream.open( this->GetOutputLocation().c_str() );
	- out = &outStream;
	- }
	-
	- if ( !out->good() )
	- {
	- mitkThrow() << "Could not open stream.";
	- }
	-
	- try
	- {
	- const std::string& locale = "C";
	- const std::string& currLocale = setlocale( LC_ALL, nullptr );
	- setlocale(LC_ALL, locale.c_str());
	-
	- std::locale previousLocale(out->getloc());
	- std::locale I("C");
	- out->imbue(I);
	-
	- // construct header
	- std::stringstream header;
	-
	- mitk::StringProperty::Pointer addHeaderInfoProperty = dynamic_cast<mitk::StringProperty*>(input->GetProperty(connectomicsDataAdditionalHeaderInformation.c_str()).GetPointer());
	- if(addHeaderInfoProperty.IsNotNull())
	- {
	- std::string additionalHeaderInfo = addHeaderInfoProperty->GetValue();
	- // if the additional header info contains newlines we need to add #
	- // in front of the new lines
	- std::vector<std::string> strings;
	- boost::split(strings, additionalHeaderInfo, boost::is_any_of("\n"));
	- for( unsigned int index(0); index < strings.size(); ++index)
	- {
	- header << "#" << strings[index] << "\n";
	- }
	- }
	-
	- // add the order of labels to the header
	- std::vector< InputType::VertexDescriptorType > nodes = input->GetVectorOfAllVertexDescriptors();
	- header << "#";
	- for(unsigned int index(0); index < nodes.size(); ++index)
	- {
	- header << " " << (input->GetNode(nodes[index])).label;
	- }
	-
	- // construct body
	- std::stringstream body;
	-
	- for(unsigned int i(0); i < nodes.size(); ++i)
	- {
	- for(unsigned int j(0); j < nodes.size(); ++j)
	- {
	- if( input->EdgeExists(nodes[i], nodes[j]))
	- {
	- body << (input->GetEdge(nodes[i], nodes[j])).fiber_count;
	- }
	- else
	- {
	- body << 0;
	- }
	- if(j < nodes.size() - 1)
	- {
	- body << " ";
	- }
	- }
	- body << "\n";
	- }
	-
	- (*out)<< header.str() << "\n" << body.str();
	- setlocale(LC_ALL, currLocale.c_str());
	- MITK_INFO << "Connectomics network connection list written";
	- }
	- catch(...)
	- {
	- mitkThrow() << "Error while writing to stream.";
	- }
	-}
	-
	-mitk::IFileIO::ConfidenceLevel mitk::ConnectomicsNetworkMatrixWriter::GetConfidenceLevel() const
	-{
	- if (AbstractFileWriter::GetConfidenceLevel() == Unsupported)
	- {
	- return Unsupported;
	- }
	-
	- // exporting is supported but will result in loss of data
	- // which prevents re-import
	- return PartiallySupported;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkMatrixWriter.h b/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkMatrixWriter.h
	deleted file mode 100644
	index 0351d049c4..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkMatrixWriter.h
	+++ /dev/null
	@@ -1,62 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkConnectomicsNetworkMatrixWriter_h
	-#define __mitkConnectomicsNetworkMatrixWriter_h
	-
	-#include <mitkAbstractFileWriter.h>
	-#include "mitkConnectomicsNetwork.h"
	-#include <vtkPolyDataWriter.h>
	-
	-
	-namespace mitk
	-{
	-
	- /**
	- * Writes connectomics networks to a file
	- *
	- *
	- * This export is write only, information is lost.
	- * @ingroup Process
	- */
	- class ConnectomicsNetworkMatrixWriter : public mitk::AbstractFileWriter
	- {
	- public:
	- typedef mitk::ConnectomicsNetwork InputType;
	- typedef std::vector< std::pair< std::pair<
	- mitk::ConnectomicsNetwork::NetworkNode, mitk::ConnectomicsNetwork::NetworkNode >
	- , mitk::ConnectomicsNetwork::NetworkEdge > > EdgeVectorType;
	- typedef std::vector< mitk::ConnectomicsNetwork::NetworkNode > VertexVectorType;
	-
	- ConnectomicsNetworkMatrixWriter();
	- ~ConnectomicsNetworkMatrixWriter() override;
	-
	- using AbstractFileWriter::Write;
	- void Write() override;
	-
	- mitk::IFileIO::ConfidenceLevel GetConfidenceLevel() const override;
	-
	- protected:
	-
	- ConnectomicsNetworkMatrixWriter(const ConnectomicsNetworkMatrixWriter& other);
	- mitk::ConnectomicsNetworkMatrixWriter* Clone() const override;
	-
	- };
	-
	-
	-} // end of namespace mitk
	-
	-#endif //__mitkConnectomicsNetworkMatrixWriter_h
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkReader.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkReader.cpp
	deleted file mode 100644
	index 33c74281da..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkReader.cpp
	+++ /dev/null
	@@ -1,228 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkConnectomicsNetworkReader.h"
	-#include "mitkConnectomicsNetworkDefinitions.h"
	-#include <tinyxml.h>
	-#include "itksys/SystemTools.hxx"
	-#include <vtkMatrix4x4.h>
	-#include "mitkGeometry3D.h"
	-#include <mitkCustomMimeType.h>
	-#include "mitkDiffusionIOMimeTypes.h"
	-
	-namespace mitk
	-{
	-
	- ConnectomicsNetworkReader::ConnectomicsNetworkReader(const ConnectomicsNetworkReader& other)
	- : mitk::AbstractFileReader(other)
	- {
	- }
	-
	- ConnectomicsNetworkReader::ConnectomicsNetworkReader()
	- : mitk::AbstractFileReader( CustomMimeType( mitk::DiffusionIOMimeTypes::CONNECTOMICS_MIMETYPE() ), mitk::DiffusionIOMimeTypes::CONNECTOMICS_MIMETYPE_DESCRIPTION() )
	- {
	- m_ServiceReg = this->RegisterService();
	- }
	-
	- ConnectomicsNetworkReader::~ConnectomicsNetworkReader()
	- {
	- }
	-
	- std::vector<itk::SmartPointer<BaseData> > ConnectomicsNetworkReader::Read()
	- {
	- std::vector<itk::SmartPointer<mitk::BaseData> > result;
	- std::string location = GetInputLocation();
	-
	- std::string ext = itksys::SystemTools::GetFilenameLastExtension(location);
	- ext = itksys::SystemTools::LowerCase(ext);
	-
	- if ( location == "")
	- {
	- MITK_ERROR << "No file name specified.";
	- }
	- else if (ext == ".cnf")
	- {
	- try
	- {
	- mitk::ConnectomicsNetwork::Pointer outputNetwork = mitk::ConnectomicsNetwork::New();
	-
	- TiXmlDocument doc( location );
	- bool loadOkay = doc.LoadFile();
	- if(!loadOkay)
	- {
	- mitkThrow() << "Could not open file " << location << " for reading.";
	- }
	-
	- TiXmlHandle hDoc(&doc);
	- TiXmlElement* pElem;
	- TiXmlHandle hRoot(nullptr);
	-
	- pElem = hDoc.FirstChildElement().Element();
	-
	- // save this for later
	- hRoot = TiXmlHandle(pElem);
	-
	- //get file version
	- std::string version("");
	- hRoot.Element()->QueryStringAttribute(mitk::ConnectomicsNetworkDefinitions::XML_FILE_VERSION, &version);
	-
	- // read geometry
	- pElem = hRoot.FirstChildElement(mitk::ConnectomicsNetworkDefinitions::XML_GEOMETRY).Element();
	-
	- mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New();
	-
	- // read origin
	- mitk::Point3D origin;
	- double temp = 0;
	- pElem->Attribute(mitk::ConnectomicsNetworkDefinitions::XML_ORIGIN_X, &temp);
	- origin[0] = temp;
	- pElem->Attribute(mitk::ConnectomicsNetworkDefinitions::XML_ORIGIN_Y, &temp);
	- origin[1] = temp;
	- pElem->Attribute(mitk::ConnectomicsNetworkDefinitions::XML_ORIGIN_Z, &temp);
	- origin[2] = temp;
	- geometry->SetOrigin(origin);
	-
	- // read spacing
	- ScalarType spacing[3];
	- pElem->Attribute(mitk::ConnectomicsNetworkDefinitions::XML_SPACING_X, &temp);
	- spacing[0] = temp;
	- pElem->Attribute(mitk::ConnectomicsNetworkDefinitions::XML_SPACING_Y, &temp);
	- spacing[1] = temp;
	- pElem->Attribute(mitk::ConnectomicsNetworkDefinitions::XML_SPACING_Z, &temp);
	- spacing[2] = temp;
	- geometry->SetSpacing(spacing);
	-
	- // read transform
	- vtkMatrix4x4* m = vtkMatrix4x4::New();
	- pElem->Attribute(mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_XX, &temp);
	- m->SetElement(0,0,temp);
	- pElem->Attribute(mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_XY, &temp);
	- m->SetElement(1,0,temp);
	- pElem->Attribute(mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_XZ, &temp);
	- m->SetElement(2,0,temp);
	- pElem->Attribute(mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_YX, &temp);
	- m->SetElement(0,1,temp);
	- pElem->Attribute(mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_YY, &temp);
	- m->SetElement(1,1,temp);
	- pElem->Attribute(mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_YZ, &temp);
	- m->SetElement(2,1,temp);
	- pElem->Attribute(mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_ZX, &temp);
	- m->SetElement(0,2,temp);
	- pElem->Attribute(mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_ZY, &temp);
	- m->SetElement(1,2,temp);
	- pElem->Attribute(mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_ZZ, &temp);
	- m->SetElement(2,2,temp);
	-
	- m->SetElement(0,3,origin[0]);
	- m->SetElement(1,3,origin[1]);
	- m->SetElement(2,3,origin[2]);
	- m->SetElement(3,3,1);
	- geometry->SetIndexToWorldTransformByVtkMatrix(m);
	-
	- geometry->SetImageGeometry(true);
	- outputNetwork->SetGeometry(geometry);
	-
	- // read network
	- std::map< int, mitk::ConnectomicsNetwork::VertexDescriptorType > idToVertexMap;
	- // read vertices
	- pElem = hRoot.FirstChildElement(mitk::ConnectomicsNetworkDefinitions::XML_VERTICES).Element();
	- {
	- // walk through the vertices
	- TiXmlElement* vertexElement = pElem->FirstChildElement();
	-
	- for( ; vertexElement; vertexElement=vertexElement->NextSiblingElement())
	- {
	- std::vector< float > pos;
	- std::string label;
	- int vertexID(0);
	-
	- vertexElement->Attribute(mitk::ConnectomicsNetworkDefinitions::XML_VERTEX_X, &temp);
	- pos.push_back(temp);
	- vertexElement->Attribute(mitk::ConnectomicsNetworkDefinitions::XML_VERTEX_Y, &temp);
	- pos.push_back(temp);
	- vertexElement->Attribute(mitk::ConnectomicsNetworkDefinitions::XML_VERTEX_Z, &temp);
	- pos.push_back(temp);
	- vertexElement->Attribute(mitk::ConnectomicsNetworkDefinitions::XML_VERTEX_ID, &vertexID);
	- vertexElement->QueryStringAttribute(mitk::ConnectomicsNetworkDefinitions::XML_VERTEX_LABEL, &label);
	-
	- mitk::ConnectomicsNetwork::VertexDescriptorType newVertex = outputNetwork->AddVertex( vertexID );
	- outputNetwork->SetLabel( newVertex, label );
	- outputNetwork->SetCoordinates( newVertex, pos );
	-
	- if ( idToVertexMap.count( vertexID ) > 0 )
	- {
	- MITK_ERROR << "Aborting network creation, duplicate vertex ID in file.";
	- return result;
	- }
	- idToVertexMap.insert( std::pair< int, mitk::ConnectomicsNetwork::VertexDescriptorType >( vertexID, newVertex) );
	- }
	- }
	-
	- // read edges
	- pElem = hRoot.FirstChildElement(mitk::ConnectomicsNetworkDefinitions::XML_EDGES).Element();
	- {
	- // walk through the edges
	- TiXmlElement* edgeElement = pElem->FirstChildElement();
	-
	- for( ; edgeElement; edgeElement=edgeElement->NextSiblingElement())
	- {
	- int edgeID(0), edgeSourceID(0), edgeTargetID(0), edgeWeight(0);
	- double edgeDoubleWeight(0.0);
	-
	- edgeElement->Attribute(mitk::ConnectomicsNetworkDefinitions::XML_EDGE_ID, &edgeID);
	- edgeElement->Attribute(mitk::ConnectomicsNetworkDefinitions::XML_EDGE_SOURCE_ID, &edgeSourceID);
	- edgeElement->Attribute(mitk::ConnectomicsNetworkDefinitions::XML_EDGE_TARGET_ID, &edgeTargetID);
	- edgeElement->Attribute(mitk::ConnectomicsNetworkDefinitions::XML_EDGE_FIBERCOUNT_ID, &edgeWeight);
	- if(version == "0.1")
	- {
	- // in version 0.1 only the int weight was saved, assume double weight to be one by default
	- edgeDoubleWeight = 1.0;
	- }
	- else
	- {
	- edgeElement->QueryDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_EDGE_DOUBLE_WEIGHT_ID, &edgeDoubleWeight);
	- }
	-
	- mitk::ConnectomicsNetwork::VertexDescriptorType source = idToVertexMap.find( edgeSourceID )->second;
	- mitk::ConnectomicsNetwork::VertexDescriptorType target = idToVertexMap.find( edgeTargetID )->second;
	- outputNetwork->AddEdge( source, target, edgeSourceID, edgeTargetID, edgeWeight, edgeDoubleWeight);
	- }
	- }
	-
	- outputNetwork->UpdateBounds();
	- result.push_back(outputNetwork.GetPointer());
	- MITK_INFO << "Network read";
	- }
	- catch (mitk::Exception e)
	- {
	- MITK_ERROR << e.GetDescription();
	- }
	- catch(...)
	- {
	- MITK_ERROR << "Unknown error occured while trying to read file.";
	- }
	- }
	-
	- return result;
	- }
	-
	-
	-} //namespace MITK
	-
	-mitk::ConnectomicsNetworkReader* mitk::ConnectomicsNetworkReader::Clone() const
	-{
	- return new ConnectomicsNetworkReader(*this);
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkReader.h b/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkReader.h
	deleted file mode 100644
	index 1ec45714a1..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkReader.h
	+++ /dev/null
	@@ -1,53 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkConnectomicsNetworkReader_h
	-#define __mitkConnectomicsNetworkReader_h
	-
	-#include "mitkCommon.h"
	-#include <mitkAbstractFileReader.h>
	-#include <mitkBaseData.h>
	-#include <mitkMimeType.h>
	-#include "mitkConnectomicsNetwork.h"
	-
	-namespace mitk
	-{
	-
	- /** \brief The reader for connectomics network files (.cnf)
	- */
	-
	- class ConnectomicsNetworkReader : public mitk::AbstractFileReader
	- {
	- public:
	-
	- typedef mitk::ConnectomicsNetwork OutputType;
	-
	- ConnectomicsNetworkReader(const ConnectomicsNetworkReader& other);
	- ConnectomicsNetworkReader();
	- ~ConnectomicsNetworkReader() override;
	-
	- using AbstractFileReader::Read;
	- std::vector<itk::SmartPointer<BaseData> > Read() override;
	-
	- private:
	- ConnectomicsNetworkReader* Clone() const override;
	-
	- us::ServiceRegistration<mitk::IFileReader> m_ServiceReg;
	- };
	-
	-} //namespace MITK
	-
	-#endif // __mitkConnectomicsNetworkReader_h
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkSerializer.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkSerializer.cpp
	deleted file mode 100644
	index eaf0d92801..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkSerializer.cpp
	+++ /dev/null
	@@ -1,74 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkConnectomicsNetworkSerializer.h"
	-#include "mitkConnectomicsNetwork.h"
	-#include "mitkConnectomicsNetworkWriter.h"
	-
	-#include <itksys/SystemTools.hxx>
	-
	-
	-MITK_REGISTER_SERIALIZER(ConnectomicsNetworkSerializer)
	-
	-
	-mitk::ConnectomicsNetworkSerializer::ConnectomicsNetworkSerializer()
	-{
	-}
	-
	-
	-mitk::ConnectomicsNetworkSerializer::~ConnectomicsNetworkSerializer()
	-{
	-}
	-
	-
	-std::string mitk::ConnectomicsNetworkSerializer::Serialize()
	-{
	- const ConnectomicsNetwork* conNet = dynamic_cast<const ConnectomicsNetwork*>( m_Data.GetPointer() );
	- if (conNet == nullptr)
	- {
	- MITK_ERROR << " Object at " << (const void*) this->m_Data
	- << " is not an mitk::ConnectomicsNetwork. Cannot serialize as ConnectomicsNetwork.";
	- return "";
	- }
	-
	- std::string filename( this->GetUniqueFilenameInWorkingDirectory() );
	- filename += "_";
	- filename += m_FilenameHint;
	- filename += ".cnf";
	-
	- std::string fullname(m_WorkingDirectory);
	- fullname += "/";
	- fullname += itksys::SystemTools::ConvertToOutputPath(filename.c_str());
	-
	- try
	- {
	- ConnectomicsNetworkWriter writer;
	- writer.SetOutputLocation(fullname);
	- writer.SetInput(const_cast<ConnectomicsNetwork*>(conNet));
	- writer.Write();
	- }
	- catch (std::exception& e)
	- {
	- MITK_ERROR << " Error serializing object at " << (const void*) this->m_Data
	- << " to "
	- << fullname
	- << ": "
	- << e.what();
	- return "";
	- }
	- return filename;
	-}
	-
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkSerializer.h b/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkSerializer.h
	deleted file mode 100644
	index ccaa186ccd..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkSerializer.h
	+++ /dev/null
	@@ -1,39 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef mitkConnectomicsNetworkSerializer_h_included
	-#define mitkConnectomicsNetworkSerializer_h_included
	-
	-#include "mitkBaseDataSerializer.h"
	-
	-namespace mitk
	-{
	-/**
	- \brief Serializes mitk::ConnectomicsNetwork for mitk::SceneIO
	-*/
	-class ConnectomicsNetworkSerializer : public BaseDataSerializer
	-{
	- public:
	- mitkClassMacro( ConnectomicsNetworkSerializer, BaseDataSerializer );
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- std::string Serialize() override;
	- protected:
	- ConnectomicsNetworkSerializer();
	- ~ConnectomicsNetworkSerializer() override;
	-};
	-} // namespace
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkWriter.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkWriter.cpp
	deleted file mode 100644
	index 34fe5a0f09..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkWriter.cpp
	+++ /dev/null
	@@ -1,144 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkConnectomicsNetworkWriter.h"
	-#include "mitkConnectomicsNetworkDefinitions.h"
	-#include <tinyxml.h>
	-#include "itksys/SystemTools.hxx"
	-#include "mitkDiffusionIOMimeTypes.h"
	-
	-mitk::ConnectomicsNetworkWriter::ConnectomicsNetworkWriter()
	- : AbstractFileWriter(mitk::ConnectomicsNetwork::GetStaticNameOfClass(), CustomMimeType( mitk::DiffusionIOMimeTypes::CONNECTOMICS_MIMETYPE() ), mitk::DiffusionIOMimeTypes::CONNECTOMICS_MIMETYPE_DESCRIPTION() )
	-{
	- RegisterService();
	-}
	-
	-mitk::ConnectomicsNetworkWriter::ConnectomicsNetworkWriter(const mitk::ConnectomicsNetworkWriter& other)
	- : AbstractFileWriter(other)
	-{
	-}
	-
	-
	-mitk::ConnectomicsNetworkWriter::~ConnectomicsNetworkWriter()
	-{}
	-
	-mitk::ConnectomicsNetworkWriter* mitk::ConnectomicsNetworkWriter::Clone() const
	-{
	- return new ConnectomicsNetworkWriter(*this);
	-}
	-
	-void mitk::ConnectomicsNetworkWriter::Write()
	-{
	- MITK_INFO << "Writing connectomics network";
	- InputType::ConstPointer input = dynamic_cast<const InputType*>(this->GetInput());
	- if (input.IsNull() )
	- {
	- MITK_ERROR <<"Sorry, input to ConnectomicsNetworkWriter is nullptr!";
	- return;
	- }
	- if ( this->GetOutputLocation().empty() )
	- {
	- MITK_ERROR << "Sorry, filename has not been set!" ;
	- return ;
	- }
	-
	- std::string ext = itksys::SystemTools::GetFilenameLastExtension(this->GetOutputLocation());
	- ext = itksys::SystemTools::LowerCase(ext);
	-
	- // default extension is .cnf
	- if(ext == "")
	- {
	- ext = ".cnf";
	- this->SetOutputLocation(this->GetOutputLocation() + ext);
	- }
	-
	- if (ext == ".cnf")
	- {
	- // Get geometry of the network
	- mitk::BaseGeometry* geometry = input->GetGeometry();
	-
	- // Create XML document
	- TiXmlDocument documentXML;
	- { // begin document
	- TiXmlDeclaration* declXML = new TiXmlDeclaration( "1.0", "", "" ); // TODO what to write here? encoding? etc....
	- documentXML.LinkEndChild( declXML );
	-
	- TiXmlElement* mainXML = new TiXmlElement(mitk::ConnectomicsNetworkDefinitions::XML_CONNECTOMICS_FILE);
	- mainXML->SetAttribute(mitk::ConnectomicsNetworkDefinitions::XML_FILE_VERSION, mitk::ConnectomicsNetworkDefinitions::VERSION_STRING);
	- documentXML.LinkEndChild(mainXML);
	-
	- TiXmlElement* geometryXML = new TiXmlElement(mitk::ConnectomicsNetworkDefinitions::XML_GEOMETRY);
	- { // begin geometry
	- geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_XX, geometry->GetMatrixColumn(0)[0]);
	- geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_XY, geometry->GetMatrixColumn(0)[1]);
	- geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_XZ, geometry->GetMatrixColumn(0)[2]);
	- geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_YX, geometry->GetMatrixColumn(1)[0]);
	- geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_YY, geometry->GetMatrixColumn(1)[1]);
	- geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_YZ, geometry->GetMatrixColumn(1)[2]);
	- geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_ZX, geometry->GetMatrixColumn(2)[0]);
	- geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_ZY, geometry->GetMatrixColumn(2)[1]);
	- geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_MATRIX_ZZ, geometry->GetMatrixColumn(2)[2]);
	-
	- geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_ORIGIN_X, geometry->GetOrigin()[0]);
	- geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_ORIGIN_Y, geometry->GetOrigin()[1]);
	- geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_ORIGIN_Z, geometry->GetOrigin()[2]);
	-
	- geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_SPACING_X, geometry->GetSpacing()[0]);
	- geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_SPACING_Y, geometry->GetSpacing()[1]);
	- geometryXML->SetDoubleAttribute(mitk::ConnectomicsNetworkDefinitions::XML_SPACING_Z, geometry->GetSpacing()[2]);
	-
	- } // end geometry
	- mainXML->LinkEndChild(geometryXML);
	-
	- TiXmlElement* verticesXML = new TiXmlElement(mitk::ConnectomicsNetworkDefinitions::XML_VERTICES);
	- { // begin vertices section
	- VertexVectorType vertexVector = dynamic_cast<const InputType*>(this->GetInput())->GetVectorOfAllNodes();
	- for( unsigned int index = 0; index < vertexVector.size(); index++ )
	- {
	- // not localized as of yet TODO
	- TiXmlElement* vertexXML = new TiXmlElement(mitk::ConnectomicsNetworkDefinitions::XML_VERTEX );
	- vertexXML->SetAttribute( mitk::ConnectomicsNetworkDefinitions::XML_VERTEX_ID , vertexVector[ index ].id );
	- vertexXML->SetAttribute( mitk::ConnectomicsNetworkDefinitions::XML_VERTEX_LABEL , vertexVector[ index ].label );
	- vertexXML->SetDoubleAttribute( mitk::ConnectomicsNetworkDefinitions::XML_VERTEX_X , vertexVector[ index ].coordinates[0] );
	- vertexXML->SetDoubleAttribute( mitk::ConnectomicsNetworkDefinitions::XML_VERTEX_Y , vertexVector[ index ].coordinates[1] );
	- vertexXML->SetDoubleAttribute( mitk::ConnectomicsNetworkDefinitions::XML_VERTEX_Z , vertexVector[ index ].coordinates[2] );
	- verticesXML->LinkEndChild(vertexXML);
	- }
	- } // end vertices section
	- mainXML->LinkEndChild(verticesXML);
	-
	- TiXmlElement* edgesXML = new TiXmlElement(mitk::ConnectomicsNetworkDefinitions::XML_EDGES);
	- { // begin edges section
	- EdgeVectorType edgeVector = dynamic_cast<const InputType*>(this->GetInput())->GetVectorOfAllEdges();
	- for(unsigned int index = 0; index < edgeVector.size(); index++ )
	- {
	- TiXmlElement* edgeXML = new TiXmlElement(mitk::ConnectomicsNetworkDefinitions::XML_EDGE );
	- edgeXML->SetAttribute( mitk::ConnectomicsNetworkDefinitions::XML_EDGE_ID , index );
	- edgeXML->SetAttribute( mitk::ConnectomicsNetworkDefinitions::XML_EDGE_SOURCE_ID , edgeVector[ index ].second.sourceId );
	- edgeXML->SetAttribute( mitk::ConnectomicsNetworkDefinitions::XML_EDGE_TARGET_ID , edgeVector[ index ].second.targetId );
	- edgeXML->SetAttribute( mitk::ConnectomicsNetworkDefinitions::XML_EDGE_FIBERCOUNT_ID , edgeVector[ index ].second.fiber_count );
	- edgeXML->SetDoubleAttribute( mitk::ConnectomicsNetworkDefinitions::XML_EDGE_DOUBLE_WEIGHT_ID , edgeVector[ index ].second.edge_weight );
	- edgesXML->LinkEndChild(edgeXML);
	- }
	- } // end edges section
	- mainXML->LinkEndChild(edgesXML);
	-
	- } // end document
	- documentXML.SaveFile( this->GetOutputLocation().c_str() );
	- MITK_INFO << "Connectomics network written";
	-
	- }
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkWriter.h b/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkWriter.h
	deleted file mode 100644
	index 3e11bf287f..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsNetworkWriter.h
	+++ /dev/null
	@@ -1,57 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkConnectomicsNetworkWriter_h
	-#define __mitkConnectomicsNetworkWriter_h
	-
	-#include <mitkAbstractFileWriter.h>
	-#include "mitkConnectomicsNetwork.h"
	-#include <vtkPolyDataWriter.h>
	-
	-
	-namespace mitk
	-{
	-
	- /**
	- * Writes connectomics networks to a file
	- * @ingroup Process
	- */
	- class ConnectomicsNetworkWriter : public mitk::AbstractFileWriter
	- {
	- public:
	- typedef mitk::ConnectomicsNetwork InputType;
	- typedef std::vector< std::pair< std::pair<
	- mitk::ConnectomicsNetwork::NetworkNode, mitk::ConnectomicsNetwork::NetworkNode >
	- , mitk::ConnectomicsNetwork::NetworkEdge > > EdgeVectorType;
	- typedef std::vector< mitk::ConnectomicsNetwork::NetworkNode > VertexVectorType;
	-
	- ConnectomicsNetworkWriter();
	- ~ConnectomicsNetworkWriter() override;
	-
	- using AbstractFileWriter::Write;
	- void Write() override;
	-
	- protected:
	-
	- ConnectomicsNetworkWriter(const ConnectomicsNetworkWriter& other);
	- mitk::ConnectomicsNetworkWriter* Clone() const override;
	-
	- };
	-
	-
	-} // end of namespace mitk
	-
	-#endif //__mitkConnectomicsNetworkWriter_h
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsObjectFactory.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsObjectFactory.cpp
	deleted file mode 100644
	index 84cb3ebf26..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsObjectFactory.cpp
	+++ /dev/null
	@@ -1,110 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#include "mitkConnectomicsObjectFactory.h"
	-
	-#include "mitkConnectomicsNetwork.h"
	-#include "mitkConnectomicsNetworkMapper3D.h"
	-
	-mitk::ConnectomicsObjectFactory::ConnectomicsObjectFactory()
	- : CoreObjectFactoryBase()
	-{
	- static bool alreadyDone = false;
	- if (!alreadyDone)
	- {
	- MITK_DEBUG << "ConnectomicsObjectFactory c'tor" << std::endl;
	-
	- alreadyDone = true;
	- }
	-
	-}
	-
	-mitk::ConnectomicsObjectFactory::~ConnectomicsObjectFactory()
	-{
	-}
	-
	-mitk::Mapper::Pointer mitk::ConnectomicsObjectFactory::CreateMapper(mitk::DataNode* node, MapperSlotId id)
	-{
	- mitk::Mapper::Pointer newMapper=nullptr;
	-
	- if ( id == mitk::BaseRenderer::Standard3D )
	- {
	- std::string classname("ConnectomicsNetwork");
	- if (node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0)
	- {
	- newMapper = mitk::ConnectomicsNetworkMapper3D::New();
	- newMapper->SetDataNode(node);
	- }
	-
	- }
	-
	- return newMapper;
	-}
	-
	-void mitk::ConnectomicsObjectFactory::SetDefaultProperties(mitk::DataNode* node)
	-{
	- std::string classname("ConnectomicsNetwork");
	- if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0)
	- {
	- mitk::ConnectomicsNetworkMapper3D::SetDefaultProperties(node);
	- }
	-}
	-
	-const char* mitk::ConnectomicsObjectFactory::GetFileExtensions()
	-{
	- std::string fileExtension;
	- this->CreateFileExtensions(m_FileExtensionsMap, fileExtension);
	- return fileExtension.c_str();
	-};
	-
	-mitk::CoreObjectFactoryBase::MultimapType mitk::ConnectomicsObjectFactory::GetFileExtensionsMap()
	-{
	- return m_FileExtensionsMap;
	-}
	-
	-const char* mitk::ConnectomicsObjectFactory::GetSaveFileExtensions()
	-{
	- std::string fileExtension;
	- this->CreateFileExtensions(m_SaveFileExtensionsMap, fileExtension);
	- return fileExtension.c_str();
	-};
	-
	-mitk::CoreObjectFactoryBase::MultimapType mitk::ConnectomicsObjectFactory::GetSaveFileExtensionsMap()
	-{
	- return m_SaveFileExtensionsMap;
	-}
	-
	-void mitk::ConnectomicsObjectFactory::CreateFileExtensionsMap()
	-{
	-}
	-
	-struct RegisterConnectomicsObjectFactory{
	- RegisterConnectomicsObjectFactory()
	- : m_Factory( mitk::ConnectomicsObjectFactory::New() )
	- {
	- mitk::CoreObjectFactory::GetInstance()->RegisterExtraFactory( m_Factory );
	- }
	-
	- ~RegisterConnectomicsObjectFactory()
	- {
	- mitk::CoreObjectFactory::GetInstance()->UnRegisterExtraFactory( m_Factory );
	- }
	-
	- mitk::ConnectomicsObjectFactory::Pointer m_Factory;
	-};
	-
	-static RegisterConnectomicsObjectFactory registerDiffusionCoreObjectFactory;
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsObjectFactory.h b/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsObjectFactory.h
	deleted file mode 100644
	index 809b8fab39..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkConnectomicsObjectFactory.h
	+++ /dev/null
	@@ -1,62 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef MITKCONNECTOMICSOBJECTFACTORY_H
	-#define MITKCONNECTOMICSOBJECTFACTORY_H
	-
	-#include "mitkCoreObjectFactory.h"
	-
	-namespace mitk {
	-
	-class ConnectomicsObjectFactory : public CoreObjectFactoryBase
	-{
	- public:
	- mitkClassMacro(ConnectomicsObjectFactory,CoreObjectFactoryBase)
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- ~ConnectomicsObjectFactory() override;
	-
	- Mapper::Pointer CreateMapper(mitk::DataNode* node, MapperSlotId slotId) override;
	-
	- void SetDefaultProperties(mitk::DataNode* node) override;
	-
	- const char* GetFileExtensions() override;
	-
	- mitk::CoreObjectFactoryBase::MultimapType GetFileExtensionsMap() override;
	-
	- const char* GetSaveFileExtensions() override;
	-
	- mitk::CoreObjectFactoryBase::MultimapType GetSaveFileExtensionsMap() override;
	-
	- protected:
	- ConnectomicsObjectFactory();
	- private:
	- void CreateFileExtensionsMap();
	- std::string m_ExternalFileExtensions;
	- std::string m_InternalFileExtensions;
	- std::string m_SaveFileExtensions;
	- MultimapType m_FileExtensionsMap;
	- MultimapType m_SaveFileExtensionsMap;
	-
	- itk::ObjectFactoryBase::Pointer m_ConnectomicsNetworkIOFactory;
	- itk::ObjectFactoryBase::Pointer m_ConnectomicsNetworkWriterFactory;
	-};
	-
	-}
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkDiffusionIOMimeTypes.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkDiffusionIOMimeTypes.cpp
	deleted file mode 100644
	index f3f367b586..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkDiffusionIOMimeTypes.cpp
	+++ /dev/null
	@@ -1,291 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkDiffusionIOMimeTypes.h"
	-#include "mitkIOMimeTypes.h"
	-#include <itksys/SystemTools.hxx>
	-#include <itkNrrdImageIO.h>
	-#include <itkMetaDataDictionary.h>
	-#include <itkMetaDataObject.h>
	-#include <mitkLogMacros.h>
	-#include <dcmtk/dcmtract/trctractographyresults.h>
	-#include <mitkDICOMDCMTKTagScanner.h>
	-#include <itkGDCMImageIO.h>
	-
	-namespace mitk
	-{
	-
	-std::vector<CustomMimeType*> DiffusionIOMimeTypes::Get()
	-{
	- std::vector<CustomMimeType*> mimeTypes;
	-
	- // order matters here (descending rank for mime types)
	-
	- mimeTypes.push_back(FIBERBUNDLE_VTK_MIMETYPE().Clone());
	- mimeTypes.push_back(FIBERBUNDLE_TRK_MIMETYPE().Clone());
	- mimeTypes.push_back(FIBERBUNDLE_TCK_MIMETYPE().Clone());
	- mimeTypes.push_back(FIBERBUNDLE_DICOM_MIMETYPE().Clone());
	-
	- mimeTypes.push_back(CONNECTOMICS_MIMETYPE().Clone());
	- mimeTypes.push_back(TRACTOGRAPHYFOREST_MIMETYPE().Clone());
	-
	- mimeTypes.push_back(PLANARFIGURECOMPOSITE_MIMETYPE().Clone());
	-
	- return mimeTypes;
	-}
	-
	-// Mime Types
	-CustomMimeType DiffusionIOMimeTypes::PLANARFIGURECOMPOSITE_MIMETYPE()
	-{
	- CustomMimeType mimeType(PLANARFIGURECOMPOSITE_MIMETYPE_NAME());
	- std::string category = "Planar Figure Composite";
	- mimeType.SetComment("Planar Figure Composite");
	- mimeType.SetCategory(category);
	- mimeType.AddExtension("pfc");
	- return mimeType;
	-}
	-
	-
	-CustomMimeType DiffusionIOMimeTypes::TRACTOGRAPHYFOREST_MIMETYPE()
	-{
	- CustomMimeType mimeType(TRACTOGRAPHYFOREST_MIMETYPE_NAME());
	- std::string category = "Tractography Forest";
	- mimeType.SetComment("Tractography Forest");
	- mimeType.SetCategory(category);
	- mimeType.AddExtension("rf");
	- return mimeType;
	-}
	-
	-CustomMimeType DiffusionIOMimeTypes::FIBERBUNDLE_VTK_MIMETYPE()
	-{
	- CustomMimeType mimeType(FIBERBUNDLE_VTK_MIMETYPE_NAME());
	- std::string category = "VTK Fibers";
	- mimeType.SetComment("VTK Fibers");
	- mimeType.SetCategory(category);
	- mimeType.AddExtension("fib");
	- mimeType.AddExtension("vtk");
	- return mimeType;
	-}
	-
	-CustomMimeType DiffusionIOMimeTypes::FIBERBUNDLE_TCK_MIMETYPE()
	-{
	- CustomMimeType mimeType(FIBERBUNDLE_TCK_MIMETYPE_NAME());
	- std::string category = "MRtrix Fibers";
	- mimeType.SetComment("MRtrix Fibers");
	- mimeType.SetCategory(category);
	- mimeType.AddExtension("tck");
	- return mimeType;
	-}
	-
	-CustomMimeType DiffusionIOMimeTypes::FIBERBUNDLE_TRK_MIMETYPE()
	-{
	- CustomMimeType mimeType(FIBERBUNDLE_TRK_MIMETYPE_NAME());
	- std::string category = "TrackVis Fibers";
	- mimeType.SetComment("TrackVis Fibers");
	- mimeType.SetCategory(category);
	- mimeType.AddExtension("trk");
	- return mimeType;
	-}
	-
	-DiffusionIOMimeTypes::FiberBundleDicomMimeType::FiberBundleDicomMimeType()
	- : CustomMimeType(FIBERBUNDLE_DICOM_MIMETYPE_NAME())
	-{
	- std::string category = "DICOM Fibers";
	- this->SetCategory(category);
	- this->SetComment("DICOM Fibers");
	-
	- this->AddExtension("dcm");
	- this->AddExtension("DCM");
	- this->AddExtension("gdcm");
	- this->AddExtension("dc3");
	- this->AddExtension("DC3");
	- this->AddExtension("ima");
	- this->AddExtension("img");
	-}
	-
	-bool DiffusionIOMimeTypes::FiberBundleDicomMimeType::AppliesTo(const std::string &path) const
	-{
	- try
	- {
	- std::ifstream myfile;
	- myfile.open (path, std::ios::binary);
	-// myfile.seekg (128);
	- char *buffer = new char [128];
	- myfile.read (buffer,128);
	- myfile.read (buffer,4);
	- if (std::string(buffer).compare("DICM")!=0)
	- {
	- delete[] buffer;
	- return false;
	- }
	- delete[] buffer;
	-
	- mitk::DICOMDCMTKTagScanner::Pointer scanner = mitk::DICOMDCMTKTagScanner::New();
	- mitk::DICOMTag SOPInstanceUID(0x0008, 0x0016);
	-
	- mitk::StringList relevantFiles;
	- relevantFiles.push_back(path);
	-
	- scanner->AddTag(SOPInstanceUID);
	- scanner->SetInputFiles(relevantFiles);
	- scanner->Scan();
	- mitk::DICOMTagCache::Pointer tagCache = scanner->GetScanCache();
	-
	- mitk::DICOMImageFrameList imageFrameList = mitk::ConvertToDICOMImageFrameList(tagCache->GetFrameInfoList());
	- if (imageFrameList.empty())
	- return false;
	-
	- mitk::DICOMImageFrameInfo *firstFrame = imageFrameList.begin()->GetPointer();
	-
	- std::string tag_value = tagCache->GetTagValue(firstFrame, SOPInstanceUID).value;
	- if (tag_value.empty()) {
	- return false;
	- }
	-
	- if (tag_value.compare(UID_TractographyResultsStorage)!=0)
	- return false;
	-
	- return true;
	- }
	- catch (std::exception& e)
	- {
	- MITK_INFO << e.what();
	- }
	- return false;
	-}
	-
	-DiffusionIOMimeTypes::FiberBundleDicomMimeType* DiffusionIOMimeTypes::FiberBundleDicomMimeType::Clone() const
	-{
	- return new FiberBundleDicomMimeType(*this);
	-}
	-
	-
	-DiffusionIOMimeTypes::FiberBundleDicomMimeType DiffusionIOMimeTypes::FIBERBUNDLE_DICOM_MIMETYPE()
	-{
	- return FiberBundleDicomMimeType();
	-}
	-
	-CustomMimeType DiffusionIOMimeTypes::CONNECTOMICS_MIMETYPE()
	-{
	- CustomMimeType mimeType(CONNECTOMICS_MIMETYPE_NAME());
	- std::string category = "Connectomics Networks";
	- mimeType.SetComment("Connectomics Networks Files");
	- mimeType.SetCategory(category);
	- mimeType.AddExtension("cnf");
	- return mimeType;
	-}
	-
	-CustomMimeType DiffusionIOMimeTypes::CONNECTOMICS_MATRIX_MIMETYPE()
	-{
	- CustomMimeType mimeType(CONNECTOMICS_MATRIX_MIMETYPE_NAME());
	- std::string category = "Connectomics Networks export";
	- mimeType.SetComment("Connectomics Matrix Files");
	- mimeType.SetCategory(category);
	- mimeType.AddExtension("mat");
	- return mimeType;
	-}
	-
	-CustomMimeType DiffusionIOMimeTypes::CONNECTOMICS_LIST_MIMETYPE()
	-{
	- CustomMimeType mimeType(CONNECTOMICS_LIST_MIMETYPE_NAME());
	- std::string category = "Connectomics Networks export";
	- mimeType.SetComment("Connectomics Connection Lists");
	- mimeType.SetCategory(category);
	- mimeType.AddExtension("txt");
	- return mimeType;
	-}
	-
	-// Names
	-std::string DiffusionIOMimeTypes::FIBERBUNDLE_VTK_MIMETYPE_NAME()
	-{
	- static std::string name = IOMimeTypes::DEFAULT_BASE_NAME() + ".FiberBundle.vtk";
	- return name;
	-}
	-
	-std::string DiffusionIOMimeTypes::FIBERBUNDLE_TCK_MIMETYPE_NAME()
	-{
	- static std::string name = IOMimeTypes::DEFAULT_BASE_NAME() + ".FiberBundle.tck";
	- return name;
	-}
	-
	-std::string DiffusionIOMimeTypes::FIBERBUNDLE_TRK_MIMETYPE_NAME()
	-{
	- static std::string name = IOMimeTypes::DEFAULT_BASE_NAME() + ".FiberBundle.trk";
	- return name;
	-}
	-
	-std::string DiffusionIOMimeTypes::FIBERBUNDLE_DICOM_MIMETYPE_NAME()
	-{
	- static std::string name = IOMimeTypes::DEFAULT_BASE_NAME() + ".FiberBundle.dcm";
	- return name;
	-}
	-
	-std::string DiffusionIOMimeTypes::CONNECTOMICS_MIMETYPE_NAME()
	-{
	- static std::string name = IOMimeTypes::DEFAULT_BASE_NAME() + ".cnf";
	- return name;
	-}
	-
	-std::string DiffusionIOMimeTypes::CONNECTOMICS_MATRIX_MIMETYPE_NAME()
	-{
	- static std::string name = IOMimeTypes::DEFAULT_BASE_NAME() + ".mat";
	- return name;
	-}
	-
	-std::string DiffusionIOMimeTypes::CONNECTOMICS_LIST_MIMETYPE_NAME()
	-{
	- static std::string name = IOMimeTypes::DEFAULT_BASE_NAME() + ".txt";
	- return name;
	-}
	-
	-std::string DiffusionIOMimeTypes::PLANARFIGURECOMPOSITE_MIMETYPE_NAME()
	-{
	- static std::string name = IOMimeTypes::DEFAULT_BASE_NAME() + ".pfc";
	- return name;
	-}
	-
	-std::string DiffusionIOMimeTypes::TRACTOGRAPHYFOREST_MIMETYPE_NAME()
	-{
	- static std::string name = IOMimeTypes::DEFAULT_BASE_NAME() + ".rf";
	- return name;
	-}
	-
	-// Descriptions
	-std::string DiffusionIOMimeTypes::FIBERBUNDLE_MIMETYPE_DESCRIPTION()
	-{
	- static std::string description = "Fiberbundles";
	- return description;
	-}
	-
	-std::string DiffusionIOMimeTypes::CONNECTOMICS_MIMETYPE_DESCRIPTION()
	-{
	- static std::string description = "Connectomics Networks";
	- return description;
	-}
	-
	-std::string DiffusionIOMimeTypes::PLANARFIGURECOMPOSITE_MIMETYPE_DESCRIPTION()
	-{
	- static std::string description = "Planar Figure Composite";
	- return description;
	-}
	-
	-std::string DiffusionIOMimeTypes::TRACTOGRAPHYFOREST_MIMETYPE_DESCRIPTION()
	-{
	- static std::string description = "Tractography Forest";
	- return description;
	-}
	-
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkDiffusionIOMimeTypes.h b/Modules/DiffusionImaging/DiffusionIO/mitkDiffusionIOMimeTypes.h
	deleted file mode 100644
	index 4868e62690..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkDiffusionIOMimeTypes.h
	+++ /dev/null
	@@ -1,124 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef MITKDIFFUSIONIOMIMETYPES_H
	-#define MITKDIFFUSIONIOMIMETYPES_H
	-
	-#include "mitkCustomMimeType.h"
	-
	-#include <string>
	-
	-namespace mitk {
	-
	-class DiffusionIOMimeTypes
	-{
	-public:
	-
	- class DiffusionImageNrrdMimeType : public CustomMimeType
	- {
	- public:
	- DiffusionImageNrrdMimeType();
	- bool AppliesTo(const std::string &path) const override;
	- DiffusionImageNrrdMimeType* Clone() const override;
	- };
	-
	- class DiffusionImageNiftiMimeType : public CustomMimeType
	- {
	- public:
	- DiffusionImageNiftiMimeType();
	- bool AppliesTo(const std::string &path) const override;
	- DiffusionImageNiftiMimeType* Clone() const override;
	- };
	- // Get all Diffusion Mime Types
	- static std::vector<CustomMimeType*> Get();
	-
	- // ------------------------------ VTK formats ----------------------------------
	-
	- static CustomMimeType FIBERBUNDLE_VTK_MIMETYPE();
	- static std::string FIBERBUNDLE_VTK_MIMETYPE_NAME();
	-
	- static std::string FIBERBUNDLE_MIMETYPE_DESCRIPTION();
	-
	- // ------------------------------ MRtrix formats ----------------------------------
	-
	- static CustomMimeType FIBERBUNDLE_TCK_MIMETYPE();
	- static std::string FIBERBUNDLE_TCK_MIMETYPE_NAME();
	-
	- // ------------------------------ TrackVis formats ----------------------------------
	-
	- static CustomMimeType FIBERBUNDLE_TRK_MIMETYPE();
	- static std::string FIBERBUNDLE_TRK_MIMETYPE_NAME();
	-
	- // ------------------------------ DICOM formats ----------------------------------
	-
	- class FiberBundleDicomMimeType : public CustomMimeType
	- {
	- public:
	- FiberBundleDicomMimeType();
	- bool AppliesTo(const std::string &path) const override;
	- FiberBundleDicomMimeType* Clone() const override;
	- };
	-
	- static FiberBundleDicomMimeType FIBERBUNDLE_DICOM_MIMETYPE();
	- static std::string FIBERBUNDLE_DICOM_MIMETYPE_NAME();
	-
	- // ------------------------- Image formats (ITK based) --------------------------
	-
	- static DiffusionImageNrrdMimeType DWI_NRRD_MIMETYPE();
	- static DiffusionImageNiftiMimeType DWI_NIFTI_MIMETYPE();
	- static CustomMimeType DTI_MIMETYPE(); // dti
	- static CustomMimeType ODF_MIMETYPE(); // qbi, odf
	-
	- static std::string DWI_NRRD_MIMETYPE_NAME();
	- static std::string DWI_NIFTI_MIMETYPE_NAME();
	- static std::string DTI_MIMETYPE_NAME();
	- static std::string ODF_MIMETYPE_NAME();
	-
	- static std::string DWI_NRRD_MIMETYPE_DESCRIPTION();
	- static std::string DWI_NIFTI_MIMETYPE_DESCRIPTION();
	- static std::string DTI_MIMETYPE_DESCRIPTION();
	- static std::string ODF_MIMETYPE_DESCRIPTION();
	-
	- // ------------------------------ MITK formats ----------------------------------
	-
	- static CustomMimeType CONNECTOMICS_MIMETYPE(); // cnf
	- static CustomMimeType CONNECTOMICS_MATRIX_MIMETYPE(); // mat
	- static CustomMimeType CONNECTOMICS_LIST_MIMETYPE(); // txt
	-
	- static std::string CONNECTOMICS_MIMETYPE_NAME();
	- static std::string CONNECTOMICS_MATRIX_MIMETYPE_NAME();
	- static std::string CONNECTOMICS_LIST_MIMETYPE_NAME();
	-
	- static std::string CONNECTOMICS_MIMETYPE_DESCRIPTION();
	-
	- static CustomMimeType PLANARFIGURECOMPOSITE_MIMETYPE();
	- static std::string PLANARFIGURECOMPOSITE_MIMETYPE_NAME();
	- static std::string PLANARFIGURECOMPOSITE_MIMETYPE_DESCRIPTION();
	-
	- static CustomMimeType TRACTOGRAPHYFOREST_MIMETYPE();
	- static std::string TRACTOGRAPHYFOREST_MIMETYPE_NAME();
	- static std::string TRACTOGRAPHYFOREST_MIMETYPE_DESCRIPTION();
	-
	-private:
	-
	- // purposely not implemented
	- DiffusionIOMimeTypes();
	- DiffusionIOMimeTypes(const DiffusionIOMimeTypes&);
	-};
	-
	-}
	-
	-#endif // MITKDIFFUSIONIOMIMETYPES_H
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkDiffusionModuleActivator.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkDiffusionModuleActivator.cpp
	deleted file mode 100644
	index fac6fb12cc..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkDiffusionModuleActivator.cpp
	+++ /dev/null
	@@ -1,140 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#include <usModuleActivator.h>
	-#include <usModuleContext.h>
	-
	-#include <mitkFiberBundleVtkReader.h>
	-#include <mitkFiberBundleTckReader.h>
	-#include <mitkFiberBundleTrackVisReader.h>
	-#include <mitkConnectomicsNetworkReader.h>
	-#include <mitkPlanarFigureCompositeReader.h>
	-#include <mitkTractographyForestReader.h>
	-#include <mitkFiberBundleDicomReader.h>
	-
	-#include <mitkFiberBundleVtkWriter.h>
	-#include <mitkFiberBundleTrackVisWriter.h>
	-#include <mitkFiberBundleDicomWriter.h>
	-#include <mitkConnectomicsNetworkWriter.h>
	-#include <mitkConnectomicsNetworkCSVWriter.h>
	-#include <mitkConnectomicsNetworkMatrixWriter.h>
	-#include <mitkPlanarFigureCompositeWriter.h>
	-#include <mitkTractographyForestWriter.h>
	-
	-#include <mitkCoreServices.h>
	-#include <mitkIPropertyDescriptions.h>
	-#include <mitkIPropertyPersistence.h>
	-
	-#include "mitkDiffusionIOMimeTypes.h"
	-
	-namespace mitk
	-{
	- /**
	- \brief Registers services for segmentation module.
	- */
	- class DiffusionModuleActivator : public us::ModuleActivator
	- {
	- public:
	-
	- void Load(us::ModuleContext* context) override
	- {
	- m_MimeTypes = mitk::DiffusionIOMimeTypes::Get();
	- for (std::vector<mitk::CustomMimeType*>::const_iterator mimeTypeIter = m_MimeTypes.begin(),
	- iterEnd = m_MimeTypes.end(); mimeTypeIter != iterEnd; ++mimeTypeIter)
	- {
	- us::ServiceProperties props;
	- mitk::CustomMimeType* mt = *mimeTypeIter;
	- if (mt->GetName()==mitk::DiffusionIOMimeTypes::FIBERBUNDLE_VTK_MIMETYPE_NAME())
	- props[ us::ServiceConstants::SERVICE_RANKING() ] = -1;
	- else if (mt->GetName()==mitk::DiffusionIOMimeTypes::FIBERBUNDLE_TRK_MIMETYPE_NAME())
	- props[ us::ServiceConstants::SERVICE_RANKING() ] = -2;
	- else if (mt->GetName()==mitk::DiffusionIOMimeTypes::FIBERBUNDLE_TCK_MIMETYPE_NAME())
	- props[ us::ServiceConstants::SERVICE_RANKING() ] = -3;
	- else if (mt->GetName()==mitk::DiffusionIOMimeTypes::FIBERBUNDLE_DICOM_MIMETYPE_NAME())
	- props[ us::ServiceConstants::SERVICE_RANKING() ] = -4;
	- else
	- props[ us::ServiceConstants::SERVICE_RANKING() ] = 10;
	-
	- context->RegisterService(*mimeTypeIter, props);
	- }
	-
	- m_FiberBundleVtkReader = new FiberBundleVtkReader();
	- m_FiberBundleTrackVisReader = new FiberBundleTrackVisReader();
	- m_FiberBundleTckReader = new FiberBundleTckReader();
	- m_FiberBundleDicomReader = new FiberBundleDicomReader();
	- m_ConnectomicsNetworkReader = new ConnectomicsNetworkReader();
	- m_PlanarFigureCompositeReader = new PlanarFigureCompositeReader();
	- m_TractographyForestReader = new TractographyForestReader();
	-
	- m_FiberBundleVtkWriter = new FiberBundleVtkWriter();
	- m_FiberBundleTrackVisWriter = new FiberBundleTrackVisWriter();
	- m_FiberBundleDicomWriter = new FiberBundleDicomWriter();
	- m_ConnectomicsNetworkWriter = new ConnectomicsNetworkWriter();
	- m_ConnectomicsNetworkCSVWriter = new ConnectomicsNetworkCSVWriter();
	- m_ConnectomicsNetworkMatrixWriter = new ConnectomicsNetworkMatrixWriter();
	- m_PlanarFigureCompositeWriter = new PlanarFigureCompositeWriter();
	- m_TractographyForestWriter = new TractographyForestWriter();
	- }
	-
	- void Unload(us::ModuleContext*) override
	- {
	- for (unsigned int loop(0); loop < m_MimeTypes.size(); ++loop)
	- {
	- delete m_MimeTypes.at(loop);
	- }
	-
	- delete m_FiberBundleVtkReader;
	- delete m_FiberBundleTckReader;
	- delete m_FiberBundleTrackVisReader;
	- delete m_ConnectomicsNetworkReader;
	- delete m_PlanarFigureCompositeReader;
	- delete m_TractographyForestReader;
	- delete m_FiberBundleDicomReader;
	-
	- delete m_FiberBundleDicomWriter;
	- delete m_FiberBundleVtkWriter;
	- delete m_FiberBundleTrackVisWriter;
	- delete m_ConnectomicsNetworkWriter;
	- delete m_ConnectomicsNetworkCSVWriter;
	- delete m_ConnectomicsNetworkMatrixWriter;
	- delete m_PlanarFigureCompositeWriter;
	- delete m_TractographyForestWriter;
	- }
	-
	- private:
	-
	- FiberBundleVtkReader * m_FiberBundleVtkReader;
	- FiberBundleTckReader * m_FiberBundleTckReader;
	- FiberBundleTrackVisReader * m_FiberBundleTrackVisReader;
	- FiberBundleDicomReader * m_FiberBundleDicomReader;
	- ConnectomicsNetworkReader * m_ConnectomicsNetworkReader;
	- PlanarFigureCompositeReader* m_PlanarFigureCompositeReader;
	- TractographyForestReader* m_TractographyForestReader;
	-
	- FiberBundleDicomWriter * m_FiberBundleDicomWriter;
	- FiberBundleVtkWriter * m_FiberBundleVtkWriter;
	- FiberBundleTrackVisWriter * m_FiberBundleTrackVisWriter;
	- ConnectomicsNetworkWriter * m_ConnectomicsNetworkWriter;
	- ConnectomicsNetworkCSVWriter * m_ConnectomicsNetworkCSVWriter;
	- ConnectomicsNetworkMatrixWriter * m_ConnectomicsNetworkMatrixWriter;
	- PlanarFigureCompositeWriter* m_PlanarFigureCompositeWriter;
	- TractographyForestWriter* m_TractographyForestWriter;
	-
	- std::vector<mitk::CustomMimeType*> m_MimeTypes;
	-
	- };
	-}
	-
	-US_EXPORT_MODULE_ACTIVATOR(mitk::DiffusionModuleActivator)
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleDicomReader.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleDicomReader.cpp
	deleted file mode 100644
	index 07d33c1ca0..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleDicomReader.cpp
	+++ /dev/null
	@@ -1,180 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkFiberBundleDicomReader.h"
	-#include <itkMetaDataObject.h>
	-#include <vtkPolyData.h>
	-#include <vtkDataReader.h>
	-#include <vtkPolyDataReader.h>
	-#include <vtkMatrix4x4.h>
	-#include <vtkPolyLine.h>
	-#include <vtkCellArray.h>
	-#include <vtkDataArray.h>
	-#include <vtkFloatArray.h>
	-#include <vtkCellData.h>
	-#include <vtkPointData.h>
	-#include <itksys/SystemTools.hxx>
	-#include <tinyxml.h>
	-#include <vtkCleanPolyData.h>
	-#include <mitkTrackvis.h>
	-#include <mitkCustomMimeType.h>
	-#include "mitkDiffusionIOMimeTypes.h"
	-#include <vtkTransformPolyDataFilter.h>
	-#include <mitkLexicalCast.h>
	-
	-#include "dcmtk/config/osconfig.h" /* make sure OS specific configuration is included first */
	-#include "dcmtk/dcmtract/trctractographyresults.h"
	-#include "dcmtk/dcmtract/trctrack.h"
	-
	-mitk::FiberBundleDicomReader::FiberBundleDicomReader()
	- : mitk::AbstractFileReader( mitk::DiffusionIOMimeTypes::FIBERBUNDLE_DICOM_MIMETYPE_NAME(), "DICOM Fiber Bundle Reader" )
	-{
	- m_ServiceReg = this->RegisterService();
	-}
	-
	-mitk::FiberBundleDicomReader::FiberBundleDicomReader(const FiberBundleDicomReader &other)
	- :mitk::AbstractFileReader(other)
	-{
	-}
	-
	-mitk::FiberBundleDicomReader * mitk::FiberBundleDicomReader::Clone() const
	-{
	- return new FiberBundleDicomReader(*this);
	-}
	-
	-std::vector<itk::SmartPointer<mitk::BaseData> > mitk::FiberBundleDicomReader::Read()
	-{
	-
	- std::vector<itk::SmartPointer<mitk::BaseData> > output_fibs;
	- try
	- {
	- const std::string& locale = "C";
	- const std::string& currLocale = setlocale( LC_ALL, nullptr );
	- setlocale(LC_ALL, locale.c_str());
	-
	- std::string filename = this->GetInputLocation();
	-
	- OFCondition result;
	- TrcTractographyResults *trc = nullptr;
	- result = TrcTractographyResults::loadFile(filename.c_str(), trc);
	- if (result.bad())
	- mitkThrow() << "Unable to load tractography dicom file: " << result.text();
	-
	- OFString val = "-";
	- trc->getPatient().getPatientName(val);
	- MITK_INFO << "Patient Name: " << val; val = "-";
	- trc->getStudy().getStudyInstanceUID(val);
	- MITK_INFO << "Study : " << val; val = "-";
	- trc->getSeries().getSeriesInstanceUID(val);
	- MITK_INFO << "Series : " << val; val = "-";
	- trc->getSOPCommon().getSOPInstanceUID(val);
	- MITK_INFO << "Instance : " << val; val = "-";
	- MITK_INFO << "-------------------------------------------------------------------------";
	- size_t numTrackSets = trc->getNumberOfTrackSets();
	- OFVector<TrcTrackSet*>& sets = trc->getTrackSets();
	- for (size_t ts = 0; ts < numTrackSets; ts++)
	- {
	- size_t numTracks = sets[ts]->getNumberOfTracks();
	- MITK_INFO << " Track Set #" << ts << ": " << numTracks << " Tracks, "
	- << sets[ts]->getNumberOfTrackSetStatistics() << " Track Set Statistics, "
	- << sets[ts]->getNumberOfTrackStatistics() << " Track Statistics, "
	- << sets[ts]->getNumberOfMeasurements() << " Measurements ";
	-
	- vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
	- vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
	-
	- for (size_t t = 0; t < numTracks; t++)
	- {
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	- TrcTrack* track = sets[ts]->getTracks()[t];
	- const Float32* vals = nullptr;
	- size_t numPoints = track->getTrackData(vals);
	-
	- for (size_t v = 0; v < numPoints; ++v)
	- {
	- vtkIdType id = vtkNewPoints->InsertNextPoint(vals[v3],vals[v3+1],vals[v*3+2]);
	- container->GetPointIds()->InsertNextId(id);
	- }
	-
	- vtkNewCells->InsertNextCell(container);
	- }
	-
	- vtkSmartPointer<vtkPolyData> fiberPolyData = vtkSmartPointer<vtkPolyData>::New();
	- fiberPolyData->SetPoints(vtkNewPoints);
	- fiberPolyData->SetLines(vtkNewCells);
	-
	-// // transform polydata from RAS (MRtrix) to LPS (MITK)
	-// mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New();
	-// vtkSmartPointer< vtkMatrix4x4 > matrix = vtkSmartPointer< vtkMatrix4x4 >::New();
	-// matrix->Identity();
	-// matrix->SetElement(0,0,-matrix->GetElement(0,0));
	-// matrix->SetElement(1,1,-matrix->GetElement(1,1));
	-// geometry->SetIndexToWorldTransformByVtkMatrix(matrix);
	-
	-// vtkSmartPointer<vtkTransformPolyDataFilter> transformFilter = vtkSmartPointer<vtkTransformPolyDataFilter>::New();
	-// transformFilter->SetInputData(fiberPolyData);
	-// transformFilter->SetTransform(geometry->GetVtkTransform());
	-// transformFilter->Update();
	-
	- FiberBundle::Pointer fib = FiberBundle::New(fiberPolyData);
	-
	- CodeSequenceMacro* algoCode = sets[ts]->getTrackingAlgorithmIdentification().at(0);
	- val = "-"; algoCode->getCodeValue(val);
	- fib->GetPropertyList()->SetStringProperty("DICOM.algo_code.value",val.c_str());
	- val = "-"; algoCode->getCodeMeaning(val);
	- fib->GetPropertyList()->SetStringProperty("DICOM.algo_code.meaning",val.c_str());
	-
	- CodeSequenceMacro modelCode = sets[ts]->getDiffusionModelCode();
	- val = "-"; modelCode.getCodeValue(val);
	- fib->GetPropertyList()->SetStringProperty("DICOM.model_code.value",val.c_str());
	- val = "-"; modelCode.getCodeMeaning(val);
	- fib->GetPropertyList()->SetStringProperty("DICOM.model_code.meaning",val.c_str());
	-
	- CodeWithModifiers anatomy = sets[ts]->getTrackSetAnatomy();
	- val = "-"; anatomy.getCodeValue(val);
	- fib->GetPropertyList()->SetStringProperty("DICOM.anatomy.value",val.c_str());
	- val = "-"; anatomy.getCodeMeaning(val);
	- fib->GetPropertyList()->SetStringProperty("DICOM.anatomy.meaning",val.c_str());
	-
	- val = "-"; trc->getPatient().getPatientID(val);
	- fib->GetPropertyList()->SetStringProperty("DICOM.patient_id",val.c_str());
	- val = "-"; trc->getPatient().getPatientName(val);
	- fib->GetPropertyList()->SetStringProperty("DICOM.patient_name",val.c_str());
	- val = "-"; trc->getStudy().getStudyInstanceUID(val);
	- fib->GetPropertyList()->SetStringProperty("DICOM.study_instance_uid",val.c_str());
	- val = "-"; trc->getSeries().getSeriesInstanceUID(val);
	- fib->GetPropertyList()->SetStringProperty("DICOM.series_instance_uid",val.c_str());
	- val = "-"; trc->getSOPCommon().getSOPInstanceUID(val);
	- fib->GetPropertyList()->SetStringProperty("DICOM.sop_instance_uid",val.c_str());
	- val = "-"; trc->getSOPCommon().getSOPClassUID(val);
	- fib->GetPropertyList()->SetStringProperty("DICOM.sop_class_uid",val.c_str());
	- val = "-"; trc->getFrameOfReference().getFrameOfReferenceUID(val);
	- fib->GetPropertyList()->SetStringProperty("DICOM.frame_of_reference_uid",val.c_str());
	-
	- output_fibs.push_back(fib.GetPointer());
	- MITK_INFO << "Fiber bundle read";
	- }
	- delete trc;
	-
	- setlocale(LC_ALL, currLocale.c_str());
	- return output_fibs;
	- }
	- catch(...)
	- {
	- throw;
	- }
	- return output_fibs;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleDicomReader.h b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleDicomReader.h
	deleted file mode 100644
	index e4393beb61..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleDicomReader.h
	+++ /dev/null
	@@ -1,52 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkFiberBundleDicomReader_h
	-#define __mitkFiberBundleDicomReader_h
	-
	-#include <mitkCommon.h>
	-#include <mitkFileReader.h>
	-#include <mitkFiberBundle.h>
	-#include <vtkSmartPointer.h>
	-
	-#include <mitkAbstractFileReader.h>
	-
	-namespace mitk
	-{
	-
	- /** \brief
	- */
	-
	- class FiberBundleDicomReader : public AbstractFileReader
	- {
	- public:
	-
	- FiberBundleDicomReader();
	- ~FiberBundleDicomReader() override{}
	- FiberBundleDicomReader(const FiberBundleDicomReader& other);
	- FiberBundleDicomReader * Clone() const override;
	-
	- using mitk::AbstractFileReader::Read;
	- std::vector<itk::SmartPointer<BaseData> > Read() override;
	-
	- private:
	-
	- us::ServiceRegistration<mitk::IFileReader> m_ServiceReg;
	- };
	-
	-} //namespace MITK
	-
	-#endif // __mitkFiberBundleReader_h
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleDicomWriter.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleDicomWriter.cpp
	deleted file mode 100644
	index 30bf0711bd..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleDicomWriter.cpp
	+++ /dev/null
	@@ -1,187 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkFiberBundleDicomWriter.h"
	-#include <vtkSmartPointer.h>
	-#include <itksys/SystemTools.hxx>
	-#include <itkSize.h>
	-#include <vtkFloatArray.h>
	-#include <vtkCellData.h>
	-#include <vtkPointData.h>
	-#include <mitkAbstractFileWriter.h>
	-#include <mitkCustomMimeType.h>
	-#include "mitkDiffusionIOMimeTypes.h"
	-#include "dcmtk/config/osconfig.h" /* make sure OS specific configuration is included first */
	-#include "dcmtk/dcmtract/trctractographyresults.h"
	-
	-mitk::FiberBundleDicomWriter::FiberBundleDicomWriter()
	- : mitk::AbstractFileWriter(mitk::FiberBundle::GetStaticNameOfClass(), mitk::DiffusionIOMimeTypes::FIBERBUNDLE_DICOM_MIMETYPE_NAME(), "DICOM Fiber Bundle Writer")
	-{
	- RegisterService();
	-}
	-
	-mitk::FiberBundleDicomWriter::FiberBundleDicomWriter(const mitk::FiberBundleDicomWriter & other)
	- :mitk::AbstractFileWriter(other)
	-{}
	-
	-mitk::FiberBundleDicomWriter::~FiberBundleDicomWriter()
	-{}
	-
	-mitk::FiberBundleDicomWriter * mitk::FiberBundleDicomWriter::Clone() const
	-{
	- return new mitk::FiberBundleDicomWriter(*this);
	-}
	-
	-void mitk::FiberBundleDicomWriter::Write()
	-{
	- try
	- {
	- mitk::FiberBundle::ConstPointer fib = dynamic_cast<const mitk::FiberBundle*>(this->GetInput());
	- vtkPolyData* poly = fib->GetFiberPolyData();
	- mitk::PropertyList* p_list = fib->GetPropertyList();
	-
	- std::string patient_id = "";
	- if (!p_list->GetStringProperty("DICOM.patient_id", patient_id))
	- patient_id = "-";
	- std::string patient_name = "";
	- if (!p_list->GetStringProperty("DICOM.patient_name", patient_name))
	- patient_name = "-";
	- std::string study_instance_uid = "";
	- if (!p_list->GetStringProperty("DICOM.study_instance_uid", study_instance_uid))
	- study_instance_uid = "-";
	- std::string series_instance_uid = "";
	- if (!p_list->GetStringProperty("DICOM.series_instance_uid", series_instance_uid))
	- series_instance_uid = "-";
	- std::string sop_instance_uid = "";
	- if (!p_list->GetStringProperty("DICOM.sop_instance_uid", sop_instance_uid))
	- sop_instance_uid = "-";
	- std::string frame_of_reference_uid = "";
	- if (!p_list->GetStringProperty("DICOM.frame_of_reference_uid", frame_of_reference_uid))
	- frame_of_reference_uid = "-";
	- std::string algo_code_value = "";
	- if (!p_list->GetStringProperty("DICOM.algo_code.value", algo_code_value))
	- algo_code_value = "-";
	- std::string algo_code_meaning = "";
	- if (!p_list->GetStringProperty("DICOM.algo_code.meaning", algo_code_meaning))
	- algo_code_meaning = "-";
	- std::string model_code_value = "";
	- if (!p_list->GetStringProperty("DICOM.model_code.value", model_code_value))
	- model_code_value = "-";
	- std::string model_code_meaning = "";
	- if (!p_list->GetStringProperty("DICOM.model_code.meaning", model_code_meaning))
	- model_code_meaning = "-";
	- std::string anatomy_value = "";
	- if (!p_list->GetStringProperty("DICOM.anatomy.value", anatomy_value))
	- anatomy_value = "-";
	- std::string anatomy_meaning = "";
	- if (!p_list->GetStringProperty("DICOM.anatomy.meaning", anatomy_meaning))
	- anatomy_meaning = "-";
	-
	- const std::string& locale = "C";
	- const std::string& currLocale = setlocale( LC_ALL, nullptr );
	- setlocale(LC_ALL, locale.c_str());
	-
	- // Instance Number, Label, Description, Creator's Name
	- ContentIdentificationMacro id("1", "TRACTOGRAM", "Tractogram processed with MITK Diffusion", "MIC@DKFZ");
	-
	- // Manufacturer, model name, serial number, software version(s)
	- IODEnhGeneralEquipmentModule::EquipmentInfo equipment("MIC@DKFZ", "dcmtract library", "0815", OFFIS_DCMTK_VERSION_STRING);
	- IODReferences refs;
	-
	- // We need at least one image reference this Tractography Results object is based on.
	- // We provide: Patient ID, Study Instance UID, Series Instance UID, SOP Instance UID, SOP Class UID
	- IODImageReference* ref = new IODImageReference(patient_id.c_str(), study_instance_uid.c_str(), series_instance_uid.c_str(), sop_instance_uid.c_str(), UID_MRImageStorage);
	- refs.add(ref);
	-
	- std::time_t t = std::time(nullptr);
	- char date_buffer[20];
	- std::strftime(date_buffer, sizeof(date_buffer), "%Y%m%d", std::gmtime(&t));
	- char time_buffer[20];
	- std::strftime(time_buffer, sizeof(time_buffer), "%H%M%S", std::gmtime(&t));
	- OFString contentDate(date_buffer);
	- OFString contentTime(time_buffer);
	-
	- OFString val = "-";
	- TrcTractographyResults *trc = nullptr;
	- TrcTractographyResults::create(id, contentDate, contentTime, equipment, refs, trc);
	- trc->getStudy().setStudyInstanceUID(study_instance_uid.c_str());
	- trc->getSeries().setSeriesInstanceUID(series_instance_uid.c_str());
	- trc->getSOPCommon().setSOPInstanceUID(sop_instance_uid.c_str());
	- trc->getSeries().getSeriesInstanceUID(val);
	-
	- // Create track set
	- CodeWithModifiers anatomy("");
	- anatomy.set(anatomy_value.c_str(), "SRT", anatomy_meaning.c_str());
	-
	- // Every CodeSequenceMacro has: Code Value, Coding Scheme Designator, Code Meaning
	- CodeSequenceMacro diffusionModel(model_code_value.c_str(), "DCM", model_code_meaning.c_str());
	- CodeSequenceMacro algorithmId(algo_code_value.c_str(), "DCM", algo_code_meaning.c_str());
	- TrcTrackSet *set = nullptr;
	- trc->addTrackSet("TRACTOGRAM", "Tractogram processed with MITK Diffusion", anatomy, diffusionModel, algorithmId, set);
	-
	- // Create trackset
	- Uint16 cieLabColor[3]; // color the whole track with this color; we use some blue
	- cieLabColor[0] = 30000; // L
	- cieLabColor[1] = 0 ; // a
	- cieLabColor[2] = 0 ; // b
	- std::vector< Float32* > tracts;
	-
	- for (unsigned int i=0; i<fib->GetNumFibers(); i++)
	- {
	- vtkCell* cell = poly->GetCell(i);
	- int numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- Float32* pointData = new Float32[numPoints*3];
	- for(int i=0; i<numPoints ;i++)
	- {
	- double* p = points->GetPoint(i);
	-
	- pointData[i*3] = p[0];
	- pointData[i*3+1] = p[1];
	- pointData[i*3+2] = p[2];
	- }
	- tracts.push_back(pointData);
	-
	- TrcTrack* track = nullptr;
	- set->addTrack(pointData, numPoints, cieLabColor, 1 /* numColors */, track);
	- }
	-
	- // Frame of Reference is required; could be the same as from related MR series
	- trc->getFrameOfReference().setFrameOfReferenceUID(frame_of_reference_uid.c_str());
	-
	- // Set some optional data
	- trc->getPatient().setPatientID(patient_id.c_str());
	- trc->getPatient().setPatientName(patient_name.c_str());
	- trc->getSeries().setSeriesDescription("Tractogram processed with MITK Diffusion");
	-
	- // Save file
	- OFCondition result = trc->saveFile(this->GetOutputLocation().c_str());
	- delete trc;
	- if (result.bad())
	- mitkThrow() << "Unable to save tractography as DICOM file: " << result.text();
	-
	- for (Float32* tract : tracts)
	- delete [] tract;
	-
	- setlocale(LC_ALL, currLocale.c_str());
	- MITK_INFO << "DICOM Fiber bundle written to " << this->GetOutputLocation();
	- }
	- catch(...)
	- {
	- throw;
	- }
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleDicomWriter.h b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleDicomWriter.h
	deleted file mode 100644
	index 3ae28e3443..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleDicomWriter.h
	+++ /dev/null
	@@ -1,47 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkFiberBundleDicomWriter_h
	-#define __mitkFiberBundleDicomWriter_h
	-
	-#include <mitkAbstractFileWriter.h>
	-#include "mitkFiberBundle.h"
	-
	-namespace mitk
	-{
	-
	-/**
	- * Writes fiber bundles to a DICOM file
	- * @ingroup Process
	- */
	-class FiberBundleDicomWriter : public mitk::AbstractFileWriter
	-{
	-public:
	-
	-
	- FiberBundleDicomWriter();
	- FiberBundleDicomWriter(const FiberBundleDicomWriter & other);
	- FiberBundleDicomWriter * Clone() const override;
	- ~FiberBundleDicomWriter() override;
	-
	- using mitk::AbstractFileWriter::Write;
	- void Write() override;
	-};
	-
	-
	-} // end of namespace mitk
	-
	-#endif //__mitkFiberBundleWriter_h
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleMapper2D.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleMapper2D.cpp
	deleted file mode 100644
	index a57235bd8f..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleMapper2D.cpp
	+++ /dev/null
	@@ -1,280 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkFiberBundleMapper2D.h"
	-#include "mitkBaseRenderer.h"
	-#include "mitkDataNode.h"
	-#include <vtkActor.h>
	-#include <vtkOpenGLPolyDataMapper.h>
	-#include <vtkOpenGLHelper.h>
	-#include <vtkShaderProgram.h>
	-#include <vtkPlane.h>
	-#include <vtkPolyData.h>
	-#include <vtkPointData.h>
	-#include <vtkProperty.h>
	-#include <vtkLookupTable.h>
	-#include <vtkPoints.h>
	-#include <vtkCamera.h>
	-#include <vtkPolyLine.h>
	-#include <vtkRenderer.h>
	-#include <vtkCellArray.h>
	-#include <vtkMatrix4x4.h>
	-#include <vtkTubeFilter.h>
	-#include <mitkPlaneGeometry.h>
	-#include <mitkSliceNavigationController.h>
	-#include <mitkCoreServices.h>
	-
	-class vtkShaderCallback : public vtkCommand
	-{
	-public:
	- static vtkShaderCallback *New()
	- {
	- return new vtkShaderCallback;
	- }
	- mitk::BaseRenderer *renderer;
	- mitk::DataNode *node;
	-
	- void Execute(vtkObject , unsigned long, voidcbo) override
	- {
	- vtkShaderProgram program = reinterpret_cast<vtkShaderProgram>(cbo);
	-
	- float fiberOpacity;
	- bool fiberFading = false;
	- float fiberThickness = 0.0;
	-
	- node->GetOpacity(fiberOpacity, nullptr);
	- node->GetFloatProperty("Fiber2DSliceThickness", fiberThickness);
	- node->GetBoolProperty("Fiber2DfadeEFX", fiberFading);
	-
	- program->SetUniformf("fiberOpacity", fiberOpacity);
	- program->SetUniformi("fiberFadingON", fiberFading);
	- program->SetUniformf("fiberThickness", fiberThickness);
	-
	- if (this->renderer)
	- {
	- //get information about current position of views
	- mitk::SliceNavigationController::Pointer sliceContr = renderer->GetSliceNavigationController();
	- mitk::PlaneGeometry::ConstPointer planeGeo = sliceContr->GetCurrentPlaneGeometry();
	-
	- //generate according cutting planes based on the view position
	- float planeNormal[3];
	- planeNormal[0] = planeGeo->GetNormal()[0];
	- planeNormal[1] = planeGeo->GetNormal()[1];
	- planeNormal[2] = planeGeo->GetNormal()[2];
	-
	- float tmp1 = planeGeo->GetOrigin()[0] * planeNormal[0];
	- float tmp2 = planeGeo->GetOrigin()[1] * planeNormal[1];
	- float tmp3 = planeGeo->GetOrigin()[2] * planeNormal[2];
	- float thickness = tmp1 + tmp2 + tmp3; //attention, correct normalvector
	-
	- float a[4];
	- for (int i = 0; i < 3; ++i)
	- a[i] = planeNormal[i];
	-
	- a[3] = thickness;
	- program->SetUniform4f("slicingPlane", a);
	-
	- }
	- }
	-
	- vtkShaderCallback() { this->renderer = nullptr; }
	-};
	-
	-
	-
	-mitk::FiberBundleMapper2D::FiberBundleMapper2D()
	- : m_LineWidth(1)
	-{
	- m_lut = vtkSmartPointer<vtkLookupTable>::New();
	- m_lut->Build();
	-
	-}
	-
	-mitk::FiberBundleMapper2D::~FiberBundleMapper2D()
	-{
	-}
	-
	-
	-mitk::FiberBundle* mitk::FiberBundleMapper2D::GetInput()
	-{
	- return dynamic_cast< mitk::FiberBundle * > ( GetDataNode()->GetData() );
	-}
	-
	-
	-
	-void mitk::FiberBundleMapper2D::Update(mitk::BaseRenderer * renderer)
	-{
	- bool visible = true;
	- GetDataNode()->GetVisibility(visible, renderer, "visible");
	- if ( !visible )
	- return;
	-
	- // Calculate time step of the input data for the specified renderer (integer value)
	- // this method is implemented in mitkMapper
	- this->CalculateTimeStep( renderer );
	-
	- //check if updates occured in the node or on the display
	- FBXLocalStorage *localStorage = m_LocalStorageHandler.GetLocalStorage(renderer);
	-
	- //set renderer independent shader properties
	- const DataNode::Pointer node = this->GetDataNode();
	- float thickness = 2.0;
	- if(!this->GetDataNode()->GetPropertyValue("Fiber2DSliceThickness",thickness))
	- MITK_INFO << "FIBER2D SLICE THICKNESS PROPERTY ERROR";
	-
	- bool fiberfading = false;
	- if(!this->GetDataNode()->GetPropertyValue("Fiber2DfadeEFX",fiberfading))
	- MITK_INFO << "FIBER2D SLICE FADE EFX PROPERTY ERROR";
	-
	- mitk::FiberBundle* fiberBundle = this->GetInput();
	- if (fiberBundle==nullptr)
	- return;
	-
	- int lineWidth = 1.0;
	- node->GetIntProperty("LineWidth", lineWidth);
	- if (m_LineWidth!=lineWidth)
	- {
	- m_LineWidth = lineWidth;
	- fiberBundle->RequestUpdate2D();
	- }
	-
	- vtkProperty *property = localStorage->m_Actor->GetProperty();
	- property->SetLighting(false);
	-
	- if ( localStorage->m_LastUpdateTime<renderer->GetCurrentWorldPlaneGeometryUpdateTime() \|\| localStorage->m_LastUpdateTime<fiberBundle->GetUpdateTime2D() )
	- {
	- this->UpdateShaderParameter(renderer);
	- this->GenerateDataForRenderer( renderer );
	- }
	-}
	-
	-void mitk::FiberBundleMapper2D::UpdateShaderParameter(mitk::BaseRenderer *)
	-{
	- // see new vtkShaderCallback
	-}
	-
	-// vtkActors and Mappers are feeded here
	-void mitk::FiberBundleMapper2D::GenerateDataForRenderer(mitk::BaseRenderer *renderer)
	-{
	- mitk::FiberBundle* fiberBundle = this->GetInput();
	-
	- //the handler of local storage gets feeded in this method with requested data for related renderwindow
	- FBXLocalStorage *localStorage = m_LocalStorageHandler.GetLocalStorage(renderer);
	-
	- mitk::DataNode* node = this->GetDataNode();
	- if (node == nullptr)
	- return;
	-
	- vtkSmartPointer<vtkPolyData> fiberPolyData = fiberBundle->GetFiberPolyData();
	- if (fiberPolyData == nullptr)
	- return;
	-
	- fiberPolyData->GetPointData()->AddArray(fiberBundle->GetFiberColors());
	- localStorage->m_Mapper->ScalarVisibilityOn();
	- localStorage->m_Mapper->SetScalarModeToUsePointFieldData();
	- localStorage->m_Mapper->SetLookupTable(m_lut); //apply the properties after the slice was set
	- localStorage->m_Actor->GetProperty()->SetOpacity(0.999);
	- localStorage->m_Mapper->SelectColorArray("FIBER_COLORS");
	- localStorage->m_Mapper->SetInputData(fiberPolyData);
	-
	- localStorage->m_Mapper->SetVertexShaderCode(
	- "//VTK::System::Dec\n"
	- "attribute vec4 vertexMC;\n"
	-
	- "//VTK::Normal::Dec\n"
	- "uniform mat4 MCDCMatrix;\n"
	-
	- "//VTK::Color::Dec\n"
	-
	- "varying vec4 positionWorld;\n"
	- "varying vec4 colorVertex;\n"
	-
	- "void main(void)\n"
	- "{\n"
	- " colorVertex = scalarColor;\n"
	- " positionWorld = vertexMC;\n"
	- " gl_Position = MCDCMatrix * vertexMC;\n"
	- "}\n"
	- );
	-
	- localStorage->m_Mapper->SetFragmentShaderCode(
	- "//VTK::System::Dec\n" // always start with this line
	- "//VTK::Output::Dec\n" // always have this line in your FS
	- "uniform vec4 slicingPlane;\n"
	- "uniform float fiberThickness;\n"
	- "uniform int fiberFadingON;\n"
	- "uniform float fiberOpacity;\n"
	-
	- "varying vec4 positionWorld;\n"
	- "varying vec4 colorVertex;\n"
	- "out vec4 out_Color;\n"
	-
	- "void main(void)\n"
	- "{\n"
	- " float r1 = dot(positionWorld.xyz, slicingPlane.xyz) - slicingPlane.w;\n"
	-
	- " if (abs(r1) >= fiberThickness)\n"
	- " discard;\n"
	-
	- " if (fiberFadingON != 0)\n"
	- " {\n"
	- " float x = (r1 + fiberThickness) / (fiberThickness*2.0);\n"
	- " x = 1.0 - x;\n"
	- " out_Color = vec4(colorVertex.xyz*x, fiberOpacity);\n"
	- " }\n"
	- " else{\n"
	- " out_Color = vec4(colorVertex.xyz, fiberOpacity);\n"
	- " }\n"
	- "}\n"
	- );
	-
	- vtkSmartPointer<vtkShaderCallback> myCallback = vtkSmartPointer<vtkShaderCallback>::New();
	- myCallback->renderer = renderer;
	- myCallback->node = this->GetDataNode();
	- localStorage->m_Mapper->AddObserver(vtkCommand::UpdateShaderEvent,myCallback);
	-
	- localStorage->m_Actor->SetMapper(localStorage->m_Mapper);
	- localStorage->m_Actor->GetProperty()->SetLineWidth(m_LineWidth);
	-
	- // We have been modified => save this for next Update()
	- localStorage->m_LastUpdateTime.Modified();
	-}
	-
	-
	-vtkProp* mitk::FiberBundleMapper2D::GetVtkProp(mitk::BaseRenderer *renderer)
	-{
	- this->Update(renderer);
	- return m_LocalStorageHandler.GetLocalStorage(renderer)->m_Actor;
	-}
	-
	-
	-void mitk::FiberBundleMapper2D::SetDefaultProperties(mitk::DataNode* node, mitk::BaseRenderer* renderer, bool overwrite)
	-{
	- Superclass::SetDefaultProperties(node, renderer, overwrite);
	- // node->SetProperty("shader",mitk::ShaderProperty::New("mitkShaderFiberClipping"));
	-
	- //add other parameters to propertylist
	- node->AddProperty( "Fiber2DSliceThickness", mitk::FloatProperty::New(1.0f), renderer, overwrite );
	- node->AddProperty( "Fiber2DfadeEFX", mitk::BoolProperty::New(true), renderer, overwrite );
	- node->AddProperty( "color", mitk::ColorProperty::New(1.0,1.0,1.0), renderer, overwrite);
	-}
	-
	-
	-mitk::FiberBundleMapper2D::FBXLocalStorage::FBXLocalStorage()
	-{
	- m_Actor = vtkSmartPointer<vtkActor>::New();
	- m_Mapper = vtkSmartPointer<MITKFIBERBUNDLEMAPPER2D_POLYDATAMAPPER>::New();
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleMapper2D.h b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleMapper2D.h
	deleted file mode 100644
	index c1daaf50f3..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleMapper2D.h
	+++ /dev/null
	@@ -1,86 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef FiberBundleMAPPER2D_H_HEADER_INCLUDED
	-#define FiberBundleMAPPER2D_H_HEADER_INCLUDED
	-
	-#include <mitkCommon.h>
	-#include <mitkBaseRenderer.h>
	-#include <mitkVtkMapper.h>
	-#include <mitkFiberBundle.h>
	-#include <vtkSmartPointer.h>
	-
	-#define MITKFIBERBUNDLEMAPPER2D_POLYDATAMAPPER vtkOpenGLPolyDataMapper
	-
	-class vtkActor;
	-class mitkBaseRenderer;
	-class MITKFIBERBUNDLEMAPPER2D_POLYDATAMAPPER;
	-class vtkCutter;
	-class vtkPlane;
	-class vtkPolyData;
	-
	-namespace mitk {
	-
	-struct IShaderRepository;
	-
	-class FiberBundleMapper2D : public VtkMapper
	-{
	-
	-public:
	- mitkClassMacro(FiberBundleMapper2D, VtkMapper);
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- mitk::FiberBundle* GetInput();
	- void Update(mitk::BaseRenderer * renderer) override;
	- static void SetDefaultProperties(DataNode* node, BaseRenderer* renderer = nullptr, bool overwrite = false );
	- vtkProp* GetVtkProp(mitk::BaseRenderer* renderer) override;
	-
	- class FBXLocalStorage : public mitk::Mapper::BaseLocalStorage
	- {
	- public:
	- vtkSmartPointer<vtkActor> m_Actor;
	- vtkSmartPointer<MITKFIBERBUNDLEMAPPER2D_POLYDATAMAPPER> m_Mapper;
	- itk::TimeStamp m_LastUpdateTime;
	- FBXLocalStorage();
	-
	- ~FBXLocalStorage() override
	- {
	- }
	- };
	-
	- /** \brief This member holds all three LocalStorages for the three 2D render windows. */
	- mitk::LocalStorageHandler<FBXLocalStorage> m_LocalStorageHandler;
	-
	-protected:
	- FiberBundleMapper2D();
	- ~FiberBundleMapper2D() override;
	-
	- /** Does the actual resampling, without rendering. */
	- void GenerateDataForRenderer(mitk::BaseRenderer*) override;
	-
	- void UpdateShaderParameter(mitk::BaseRenderer*);
	-
	-private:
	- vtkSmartPointer<vtkLookupTable> m_lut;
	-
	- int m_LineWidth;
	-};
	-
	-
	-}//end namespace
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleMapper3D.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleMapper3D.cpp
	deleted file mode 100644
	index a03a227f2e..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleMapper3D.cpp
	+++ /dev/null
	@@ -1,259 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkFiberBundleMapper3D.h"
	-#include <mitkProperties.h>
	-
	-#include <vtkPropAssembly.h>
	-#include <vtkPointData.h>
	-#include <vtkProperty.h>
	-#include <vtkCellArray.h>
	-#include <vtkDepthSortPolyData.h>
	-#include <vtkCamera.h>
	-#include <vtkTubeFilter.h>
	-#include <vtkRibbonFilter.h>
	-#include <vtkLookupTable.h>
	-#include <vtkOpenGLHelper.h>
	-#include <vtkShaderProgram.h>
	-#include <mitkVectorProperty.h>
	-#include <vtkPlane.h>
	-#include <mitkClippingProperty.h>
	-
	-mitk::FiberBundleMapper3D::FiberBundleMapper3D()
	- : m_TubeRadius(0.0)
	- , m_TubeSides(15)
	- , m_LineWidth(1)
	-{
	- m_lut = vtkSmartPointer<vtkLookupTable>::New();
	- m_lut->Build();
	-}
	-
	-
	-mitk::FiberBundleMapper3D::~FiberBundleMapper3D()
	-{
	-
	-}
	-
	-
	-const mitk::FiberBundle* mitk::FiberBundleMapper3D::GetInput()
	-{
	- return static_cast<const mitk::FiberBundle * > ( GetDataNode()->GetData() );
	-}
	-
	-
	-/*
	- This method is called once the mapper gets new input,
	- for UI rotation or changes in colorcoding this method is NOT called
	- */
	-void mitk::FiberBundleMapper3D::InternalGenerateData(mitk::BaseRenderer *renderer)
	-{
	- m_FiberPolyData->GetPointData()->AddArray(m_FiberBundle->GetFiberColors());
	- LocalStorage3D *localStorage = m_LocalStorageHandler.GetLocalStorage(renderer);
	-
	- if (m_TubeRadius>0.0f)
	- {
	- vtkSmartPointer<vtkTubeFilter> tubeFilter = vtkSmartPointer<vtkTubeFilter>::New();
	- tubeFilter->SetInputData(m_FiberPolyData);
	- tubeFilter->SetNumberOfSides(m_TubeSides);
	- tubeFilter->SetRadius(m_TubeRadius);
	- tubeFilter->Update();
	- m_FiberPolyData = tubeFilter->GetOutput();
	- }
	- else if (m_RibbonWidth>0.0f)
	- {
	- vtkSmartPointer<vtkRibbonFilter> tubeFilter = vtkSmartPointer<vtkRibbonFilter>::New();
	- tubeFilter->SetInputData(m_FiberPolyData);
	- tubeFilter->SetWidth(m_RibbonWidth);
	- tubeFilter->Update();
	- m_FiberPolyData = tubeFilter->GetOutput();
	- }
	-
	-// if (tmpopa<1)
	-// {
	-// vtkSmartPointer<vtkDepthSortPolyData> depthSort = vtkSmartPointer<vtkDepthSortPolyData>::New();
	-// depthSort->SetInputData( m_FiberPolyData );
	-// depthSort->SetCamera( renderer->GetVtkRenderer()->GetActiveCamera() );
	-// depthSort->SetDirectionToBackToFront();
	-// depthSort->Update();
	-// localStorage->m_FiberMapper->SetInputConnection(depthSort->GetOutputPort());
	-
	-// }
	-// else
	-// {
	- localStorage->m_FiberMapper->SetInputData(m_FiberPolyData);
	-// }
	-
	- localStorage->m_FiberMapper->SelectColorArray("FIBER_COLORS");
	- localStorage->m_FiberMapper->ScalarVisibilityOn();
	- localStorage->m_FiberMapper->SetScalarModeToUsePointFieldData();
	- localStorage->m_FiberActor->SetMapper(localStorage->m_FiberMapper);
	- localStorage->m_FiberMapper->SetLookupTable(m_lut);
	- localStorage->m_FiberActor->GetProperty()->SetLineWidth(m_LineWidth);
	- localStorage->m_FiberAssembly->AddPart(localStorage->m_FiberActor);
	-
	- DataNode* node = this->GetDataNode();
	- mitk::ClippingProperty* prop = dynamic_cast<mitk::ClippingProperty*>(node->GetProperty("3DClipping"));
	- if (prop==nullptr)
	- {
	- SetDefaultProperties(node, nullptr, false);
	- prop = dynamic_cast<mitk::ClippingProperty*>(node->GetProperty("3DClipping"));
	- }
	-
	- mitk::Vector3D plane_normal = prop->GetNormal();
	- mitk::Point3D plane_origin = prop->GetOrigin();
	- bool flip;
	- node->GetBoolProperty("3DClippingPlaneFlip",flip);
	-
	- if (flip)
	- plane_normal *= -1;
	-
	- vtkSmartPointer<vtkPlane> plane = vtkSmartPointer<vtkPlane>::New();
	- double vp[3], vnormal[3];
	- vp[0] = plane_origin[0]; vp[1] = plane_origin[1]; vp[2] = plane_origin[2];
	- vnormal[0] = plane_normal[0]; vnormal[1] = plane_normal[1]; vnormal[2] = plane_normal[2];
	- plane->SetOrigin(vp);
	- plane->SetNormal(vnormal);
	-
	- localStorage->m_FiberMapper->RemoveAllClippingPlanes();
	- if (plane_normal.GetNorm() > 0.0)
	- localStorage->m_FiberMapper->AddClippingPlane(plane);
	-
	- localStorage->m_LastUpdateTime.Modified();
	-}
	-
	-
	-
	-void mitk::FiberBundleMapper3D::GenerateDataForRenderer( mitk::BaseRenderer *renderer )
	-{
	- bool visible = true;
	- GetDataNode()->GetVisibility(visible, renderer, "visible");
	- if ( !visible )
	- return;
	-
	- const DataNode* node = this->GetDataNode();
	- LocalStorage3D* localStorage = m_LocalStorageHandler.GetLocalStorage(renderer);
	-
	- m_FiberBundle = dynamic_cast<mitk::FiberBundle*>(node->GetData());
	- m_FiberPolyData = m_FiberBundle->GetFiberPolyData();
	-
	- // did any rendering properties change?
	- float tubeRadius = 0;
	- node->GetFloatProperty("shape.tuberadius", tubeRadius);
	- if (m_TubeRadius!=tubeRadius)
	- {
	- m_TubeRadius = tubeRadius;
	- m_FiberBundle->RequestUpdate3D();
	- }
	-
	- int tubeSides = 0;
	- node->GetIntProperty("shape.tubesides", tubeSides);
	- if (m_TubeSides!=tubeSides)
	- {
	- m_TubeSides = tubeSides;
	- m_FiberBundle->RequestUpdate3D();
	- }
	-
	- int lineWidth = 0;
	- node->GetIntProperty("shape.linewidth", lineWidth);
	- if (m_LineWidth!=lineWidth)
	- {
	- m_LineWidth = lineWidth;
	- m_FiberBundle->RequestUpdate3D();
	- }
	-
	- float ribbonWidth = 0;
	- node->GetFloatProperty("shape.ribbonwidth", ribbonWidth);
	- if (m_RibbonWidth!=ribbonWidth)
	- {
	- m_RibbonWidth = ribbonWidth;
	- m_FiberBundle->RequestUpdate3D();
	- }
	-
	- float opacity;
	- this->GetDataNode()->GetOpacity(opacity, nullptr);
	- vtkProperty *property = localStorage->m_FiberActor->GetProperty();
	-
	- float v = 1;
	- node->GetFloatProperty("light.ambient", v);
	- property->SetAmbient(v);
	-
	- node->GetFloatProperty("light.diffuse", v);
	- property->SetDiffuse(v);
	-
	- node->GetFloatProperty("light.specular", v);
	- property->SetSpecular(v);
	-
	- node->GetFloatProperty("light.specularpower", v);
	- property->SetSpecularPower(v);
	-
	- property->SetLighting(true);
	- property->SetOpacity(opacity);
	-
	- if (localStorage->m_LastUpdateTime>=m_FiberBundle->GetUpdateTime3D())
	- return;
	-
	- // Calculate time step of the input data for the specified renderer (integer value)
	- // this method is implemented in mitkMapper
	- this->CalculateTimeStep( renderer );
	- this->InternalGenerateData(renderer);
	-}
	-
	-void mitk::FiberBundleMapper3D::UpdateShaderParameter(mitk::BaseRenderer * )
	-{
	- // see new vtkShaderCallback3D
	-}
	-
	-void mitk::FiberBundleMapper3D::SetDefaultProperties(mitk::DataNode* node, mitk::BaseRenderer* renderer, bool overwrite)
	-{
	- Superclass::SetDefaultProperties(node, renderer, overwrite);
	-
	- mitk::Vector3D plane_vec; plane_vec.Fill(0.0);
	- mitk::Point3D plane_origin; plane_origin.Fill(0.0);
	- node->AddProperty( "3DClipping", mitk::ClippingProperty::New( plane_origin, plane_vec ), renderer, overwrite );
	- node->AddProperty( "3DClippingPlaneId", mitk::IntProperty::New(-1), renderer, overwrite );
	- node->AddProperty( "3DClippingPlaneFlip", mitk::BoolProperty::New( false ), renderer, overwrite );
	-
	- node->AddProperty( "opacity", mitk::FloatProperty::New( 1.0 ), renderer, overwrite);
	- node->AddProperty( "color", mitk::ColorProperty::New(1.0,1.0,1.0), renderer, overwrite);
	- node->AddProperty( "pickable", mitk::BoolProperty::New( true ), renderer, overwrite);
	-
	- node->AddProperty( "shape.linewidth", mitk::IntProperty::New( 1 ), renderer, overwrite );
	- node->AddProperty( "shape.tuberadius",mitk::FloatProperty::New( 0.0 ), renderer, overwrite);
	- node->AddProperty( "shape.tubesides",mitk::IntProperty::New( 15 ), renderer, overwrite);
	- node->AddProperty( "shape.ribbonwidth", mitk::FloatProperty::New( 0.0 ), renderer, overwrite);
	-
	- node->AddProperty( "light.ambient", mitk::FloatProperty::New( 0.05 ), renderer, overwrite);
	- node->AddProperty( "light.diffuse", mitk::FloatProperty::New( 0.9 ), renderer, overwrite);
	- node->AddProperty( "light.specular", mitk::FloatProperty::New( 1.0 ), renderer, overwrite);
	-
	- node->AddProperty( "light.specularpower", mitk::FloatProperty::New( 16.0 ), renderer, overwrite);
	- node->AddProperty( "light.ambientcolor", mitk::ColorProperty::New(1,1,1), renderer, overwrite);
	- node->AddProperty( "light.diffusecolor", mitk::ColorProperty::New(1,1,1), renderer, overwrite);
	- node->AddProperty( "light.specularcolor", mitk::ColorProperty::New(1,1,1), renderer, overwrite);
	-}
	-
	-vtkProp* mitk::FiberBundleMapper3D::GetVtkProp(mitk::BaseRenderer *renderer)
	-{
	- return m_LocalStorageHandler.GetLocalStorage(renderer)->m_FiberAssembly;
	-}
	-
	-mitk::FiberBundleMapper3D::LocalStorage3D::LocalStorage3D()
	-{
	- m_FiberActor = vtkSmartPointer<vtkActor>::New();
	- m_FiberMapper = vtkSmartPointer<vtkOpenGLPolyDataMapper>::New();
	- m_FiberAssembly = vtkSmartPointer<vtkPropAssembly>::New();
	-}
	-
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleMapper3D.h b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleMapper3D.h
	deleted file mode 100644
	index fa70e4f55c..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleMapper3D.h
	+++ /dev/null
	@@ -1,92 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef FiberBundleMapper3D_H_HEADER_INCLUDED
	-#define FiberBundleMapper3D_H_HEADER_INCLUDED
	-
	-#include <mitkVtkMapper.h>
	-#include <mitkFiberBundle.h>
	-#include <vtkOpenGLPolyDataMapper.h>
	-#include <vtkSmartPointer.h>
	-class vtkPropAssembly;
	-class vtkPolyDataMapper;
	-class vtkLookupTable;
	-class vtkOpenGLActor;
	-
	-namespace mitk {
	-
	-//##Documentation
	-//## @brief Mapper for FiberBundle
	-//## @ingroup Mapper
	-
	-class FiberBundleMapper3D : public VtkMapper
	-{
	-public:
	-
	- mitkClassMacro(FiberBundleMapper3D, VtkMapper)
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- const FiberBundle* GetInput();
	- vtkProp GetVtkProp(mitk::BaseRenderer renderer) override; //looks like depricated.. should be replaced bz GetViewProp()
	- static void SetDefaultProperties(DataNode* node, BaseRenderer* renderer = nullptr, bool overwrite = false );
	- void GenerateDataForRenderer(mitk::BaseRenderer* renderer) override;
	-
	- class LocalStorage3D : public mitk::Mapper::BaseLocalStorage
	- {
	- public:
	- vtkSmartPointer<vtkActor> m_FiberActor;
	- vtkSmartPointer<vtkOpenGLPolyDataMapper> m_FiberMapper;
	- vtkSmartPointer<vtkPropAssembly> m_FiberAssembly;
	-
	- itk::TimeStamp m_LastUpdateTime;
	- LocalStorage3D();
	-
	- ~LocalStorage3D() override
	- {
	- }
	- };
	-
	- /** \brief This member holds all three LocalStorages for the 3D render window(s). */
	- mitk::LocalStorageHandler<LocalStorage3D> m_LocalStorageHandler;
	-
	-
	-protected:
	-
	- FiberBundleMapper3D();
	- ~FiberBundleMapper3D() override;
	- void InternalGenerateData(mitk::BaseRenderer *renderer);
	-
	- void UpdateShaderParameter(mitk::BaseRenderer*);
	-
	-private:
	- vtkSmartPointer<vtkLookupTable> m_lut;
	- float m_TubeRadius;
	- int m_TubeSides;
	- int m_LineWidth;
	- float m_RibbonWidth;
	- vtkSmartPointer<vtkPolyData> m_FiberPolyData;
	- mitk::FiberBundle* m_FiberBundle;
	-};
	-
	-} // end namespace mitk
	-
	-
	-
	-
	-#endif /* FiberBundleMapper3D_H_HEADER_INCLUDED */
	-
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleSerializer.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleSerializer.cpp
	deleted file mode 100644
	index 5bd64e40ed..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleSerializer.cpp
	+++ /dev/null
	@@ -1,72 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkFiberBundleSerializer.h"
	-#include "mitkFiberBundle.h"
	-#include "mitkFiberBundleVtkWriter.h"
	-
	-#include <itksys/SystemTools.hxx>
	-#include <mitkIOUtil.h>
	-
	-
	-MITK_REGISTER_SERIALIZER(FiberBundleSerializer)
	-
	-
	-mitk::FiberBundleSerializer::FiberBundleSerializer()
	-{
	-}
	-
	-
	-mitk::FiberBundleSerializer::~FiberBundleSerializer()
	-{
	-}
	-
	-
	-std::string mitk::FiberBundleSerializer::Serialize()
	-{
	- const FiberBundle* fb = dynamic_cast<const FiberBundle*>( m_Data.GetPointer() );
	- if (fb == nullptr)
	- {
	- MITK_ERROR << " Object at " << (const void*) this->m_Data
	- << " is not an mitk::FiberBundle. Cannot serialize as FiberBundle.";
	- return "";
	- }
	-
	- std::string filename( this->GetUniqueFilenameInWorkingDirectory() );
	- filename += "_";
	- filename += m_FilenameHint;
	- filename += ".fib";
	-
	- std::string fullname(m_WorkingDirectory);
	- fullname += "/";
	- fullname += itksys::SystemTools::ConvertToOutputPath(filename.c_str());
	-
	- try
	- {
	- mitk::IOUtil::Save(const_cast<FiberBundle*>(fb),fullname);
	- }
	- catch (std::exception& e)
	- {
	- MITK_ERROR << " Error serializing object at " << (const void*) this->m_Data
	- << " to "
	- << fullname
	- << ": "
	- << e.what();
	- return "";
	- }
	- return filename;
	-}
	-
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleSerializer.h b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleSerializer.h
	deleted file mode 100644
	index eb3790d263..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleSerializer.h
	+++ /dev/null
	@@ -1,39 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef mitkFiberBundleSerializer_h_included
	-#define mitkFiberBundleSerializer_h_included
	-
	-#include "mitkBaseDataSerializer.h"
	-
	-namespace mitk
	-{
	-/**
	- \brief Serializes mitk::Surface for mitk::SceneIO
	-*/
	-class FiberBundleSerializer : public BaseDataSerializer
	-{
	- public:
	- mitkClassMacro( FiberBundleSerializer, BaseDataSerializer );
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- std::string Serialize() override;
	- protected:
	- FiberBundleSerializer();
	- ~FiberBundleSerializer() override;
	-};
	-} // namespace
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleTckReader.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleTckReader.cpp
	deleted file mode 100644
	index 2c427b9039..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleTckReader.cpp
	+++ /dev/null
	@@ -1,164 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkFiberBundleTckReader.h"
	-#include <itkMetaDataObject.h>
	-#include <vtkPolyData.h>
	-#include <vtkDataReader.h>
	-#include <vtkPolyDataReader.h>
	-#include <vtkMatrix4x4.h>
	-#include <vtkPolyLine.h>
	-#include <vtkCellArray.h>
	-#include <vtkDataArray.h>
	-#include <vtkFloatArray.h>
	-#include <vtkCellData.h>
	-#include <vtkPointData.h>
	-#include <itksys/SystemTools.hxx>
	-#include <tinyxml.h>
	-#include <vtkCleanPolyData.h>
	-#include <mitkTrackvis.h>
	-#include <mitkCustomMimeType.h>
	-#include "mitkDiffusionIOMimeTypes.h"
	-#include <vtkTransformPolyDataFilter.h>
	-#include <mitkLexicalCast.h>
	-
	-
	-mitk::FiberBundleTckReader::FiberBundleTckReader()
	- : mitk::AbstractFileReader( mitk::DiffusionIOMimeTypes::FIBERBUNDLE_TCK_MIMETYPE_NAME(), "tck Fiber Bundle Reader (MRtrix format)" )
	-{
	- m_ServiceReg = this->RegisterService();
	-}
	-
	-mitk::FiberBundleTckReader::FiberBundleTckReader(const FiberBundleTckReader &other)
	- :mitk::AbstractFileReader(other)
	-{
	-}
	-
	-mitk::FiberBundleTckReader * mitk::FiberBundleTckReader::Clone() const
	-{
	- return new FiberBundleTckReader(*this);
	-}
	-
	-std::vector<itk::SmartPointer<mitk::BaseData> > mitk::FiberBundleTckReader::Read()
	-{
	-
	- std::vector<itk::SmartPointer<mitk::BaseData> > result;
	- try
	- {
	- const std::string& locale = "C";
	- const std::string& currLocale = setlocale( LC_ALL, nullptr );
	- setlocale(LC_ALL, locale.c_str());
	-
	- std::string filename = this->GetInputLocation();
	-
	- std::string ext = itksys::SystemTools::GetFilenameLastExtension(filename);
	- ext = itksys::SystemTools::LowerCase(ext);
	-
	- if (ext==".tck")
	- {
	- MITK_INFO << "Loading tractogram (MRtrix format): " << itksys::SystemTools::GetFilenameName(filename);
	- std::FILE* filePointer = std::fopen(filename.c_str(),"r+b");
	- std::string header = "";
	-
	- bool header_end = false;
	- int count = 0;
	- while (!header_end)
	- {
	- char c;
	- count += std::fread(&c, 1, 1, filePointer);
	- header += c;
	- if (header.size() >= 3 && header.compare(header.size() - 3, 3, "END") == 0)
	- header_end = true;
	- }
	- MITK_INFO << "TCK Header:";
	- MITK_INFO << header;
	-
	- int header_size = -1;
	- try
	- {
	- std::string delimiter = "file: . ";
	- size_t pos = 0;
	- pos = header.find(delimiter);
	- header.erase(0, pos + delimiter.length());
	- pos = header.find("\n");
	- header_size = boost::lexical_cast<int>(header.substr(0, pos));
	- }
	- catch(...)
	- {
	-
	- }
	-
	- if (header_size==-1)
	- mitkThrow() << "Could not parse header size from " << filename;
	- std::fseek ( filePointer , header_size , SEEK_SET );
	-
	- vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
	- vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	-
	- float tmp[3];
	- count = 1;
	- int fiber_length = 0;
	- while (std::fread((char*)tmp, 1, 12, filePointer)==12)
	- {
	- if (std::isinf(tmp[0]) \|\| std::isinf(tmp[1]) \|\| std::isinf(tmp[1]))
	- break;
	- else if (std::isnan(tmp[0]) \|\| std::isnan(tmp[1]) \|\| std::isnan(tmp[2]))
	- {
	- count++;
	- fiber_length = 0;
	- vtkNewCells->InsertNextCell(container);
	- container = vtkSmartPointer<vtkPolyLine>::New();
	- }
	- else
	- {
	- fiber_length++;
	- vtkIdType id = vtkNewPoints->InsertNextPoint(tmp);
	- container->GetPointIds()->InsertNextId(id);
	- }
	- }
	-
	- vtkSmartPointer<vtkPolyData> fiberPolyData = vtkSmartPointer<vtkPolyData>::New();
	- fiberPolyData->SetPoints(vtkNewPoints);
	- fiberPolyData->SetLines(vtkNewCells);
	-
	- // transform polydata from RAS (MRtrix) to LPS (MITK)
	- mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New();
	- vtkSmartPointer< vtkMatrix4x4 > matrix = vtkSmartPointer< vtkMatrix4x4 >::New();
	- matrix->Identity();
	- matrix->SetElement(0,0,-matrix->GetElement(0,0));
	- matrix->SetElement(1,1,-matrix->GetElement(1,1));
	- geometry->SetIndexToWorldTransformByVtkMatrix(matrix);
	-
	- vtkSmartPointer<vtkTransformPolyDataFilter> transformFilter = vtkSmartPointer<vtkTransformPolyDataFilter>::New();
	- transformFilter->SetInputData(fiberPolyData);
	- transformFilter->SetTransform(geometry->GetVtkTransform());
	- transformFilter->Update();
	-
	- FiberBundle::Pointer fib = FiberBundle::New(transformFilter->GetOutput());
	- result.push_back(fib.GetPointer());
	- }
	-
	- setlocale(LC_ALL, currLocale.c_str());
	- MITK_INFO << "Fiber bundle read";
	- return result;
	- }
	- catch(...)
	- {
	- throw;
	- }
	- return result;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleTckReader.h b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleTckReader.h
	deleted file mode 100644
	index 872a7e8494..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleTckReader.h
	+++ /dev/null
	@@ -1,52 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkFiberBundleTckReader_h
	-#define __mitkFiberBundleTckReader_h
	-
	-#include <mitkCommon.h>
	-#include <mitkFileReader.h>
	-#include <mitkFiberBundle.h>
	-#include <vtkSmartPointer.h>
	-
	-#include <mitkAbstractFileReader.h>
	-
	-namespace mitk
	-{
	-
	- /** \brief
	- */
	-
	- class FiberBundleTckReader : public AbstractFileReader
	- {
	- public:
	-
	- FiberBundleTckReader();
	- ~FiberBundleTckReader() override{}
	- FiberBundleTckReader(const FiberBundleTckReader& other);
	- FiberBundleTckReader * Clone() const override;
	-
	- using mitk::AbstractFileReader::Read;
	- std::vector<itk::SmartPointer<BaseData> > Read() override;
	-
	- private:
	-
	- us::ServiceRegistration<mitk::IFileReader> m_ServiceReg;
	- };
	-
	-} //namespace MITK
	-
	-#endif // __mitkFiberBundleReader_h
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleTrackVisReader.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleTrackVisReader.cpp
	deleted file mode 100644
	index beac4c8317..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleTrackVisReader.cpp
	+++ /dev/null
	@@ -1,87 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkFiberBundleTrackVisReader.h"
	-#include <itkMetaDataObject.h>
	-#include <vtkPolyData.h>
	-#include <vtkDataReader.h>
	-#include <vtkPolyDataReader.h>
	-#include <vtkMatrix4x4.h>
	-#include <vtkPolyLine.h>
	-#include <vtkCellArray.h>
	-#include <vtkDataArray.h>
	-#include <vtkFloatArray.h>
	-#include <vtkCellData.h>
	-#include <vtkPointData.h>
	-#include <itksys/SystemTools.hxx>
	-#include <tinyxml.h>
	-#include <vtkCleanPolyData.h>
	-#include <mitkTrackvis.h>
	-#include <mitkCustomMimeType.h>
	-#include "mitkDiffusionIOMimeTypes.h"
	-
	-
	-mitk::FiberBundleTrackVisReader::FiberBundleTrackVisReader()
	- : mitk::AbstractFileReader( mitk::DiffusionIOMimeTypes::FIBERBUNDLE_TRK_MIMETYPE_NAME(), "TrackVis Fiber Bundle Reader" )
	-{
	- m_ServiceReg = this->RegisterService();
	-}
	-
	-mitk::FiberBundleTrackVisReader::FiberBundleTrackVisReader(const FiberBundleTrackVisReader &other)
	- :mitk::AbstractFileReader(other)
	-{
	-}
	-
	-mitk::FiberBundleTrackVisReader * mitk::FiberBundleTrackVisReader::Clone() const
	-{
	- return new FiberBundleTrackVisReader(*this);
	-}
	-
	-std::vector<itk::SmartPointer<mitk::BaseData> > mitk::FiberBundleTrackVisReader::Read()
	-{
	-
	- std::vector<itk::SmartPointer<mitk::BaseData> > result;
	- try
	- {
	- const std::string& locale = "C";
	- const std::string& currLocale = setlocale( LC_ALL, nullptr );
	- setlocale(LC_ALL, locale.c_str());
	-
	- std::string filename = this->GetInputLocation();
	- MITK_INFO << "Loading tractogram (TrackVis format): " << itksys::SystemTools::GetFilenameName(filename);
	-
	- std::string ext = itksys::SystemTools::GetFilenameLastExtension(filename);
	- ext = itksys::SystemTools::LowerCase(ext);
	-
	- if (ext==".trk")
	- {
	- FiberBundle::Pointer mitk_fib = FiberBundle::New();
	- TrackVisFiberReader reader;
	- reader.open(this->GetInputLocation().c_str());
	- reader.read(mitk_fib.GetPointer());
	- result.push_back(mitk_fib.GetPointer());
	- return result;
	- }
	-
	- setlocale(LC_ALL, currLocale.c_str());
	- MITK_INFO << "Fiber bundle read";
	- }
	- catch(...)
	- {
	- throw;
	- }
	- return result;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleTrackVisReader.h b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleTrackVisReader.h
	deleted file mode 100644
	index 85f4282816..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleTrackVisReader.h
	+++ /dev/null
	@@ -1,52 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkFiberBundleTrackVisReader_h
	-#define __mitkFiberBundleTrackVisReader_h
	-
	-#include <mitkCommon.h>
	-#include <mitkFileReader.h>
	-#include <mitkFiberBundle.h>
	-#include <vtkSmartPointer.h>
	-
	-#include <mitkAbstractFileReader.h>
	-
	-namespace mitk
	-{
	-
	- /** \brief
	- */
	-
	- class FiberBundleTrackVisReader : public AbstractFileReader
	- {
	- public:
	-
	- FiberBundleTrackVisReader();
	- ~FiberBundleTrackVisReader() override{}
	- FiberBundleTrackVisReader(const FiberBundleTrackVisReader& other);
	- FiberBundleTrackVisReader * Clone() const override;
	-
	- using mitk::AbstractFileReader::Read;
	- std::vector<itk::SmartPointer<BaseData> > Read() override;
	-
	- private:
	-
	- us::ServiceRegistration<mitk::IFileReader> m_ServiceReg;
	- };
	-
	-} //namespace MITK
	-
	-#endif // __mitkFiberBundleReader_h
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleTrackVisWriter.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleTrackVisWriter.cpp
	deleted file mode 100644
	index 40a7dccd5c..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleTrackVisWriter.cpp
	+++ /dev/null
	@@ -1,108 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkFiberBundleTrackVisWriter.h"
	-#include <vtkSmartPointer.h>
	-#include <vtkCleanPolyData.h>
	-#include <itksys/SystemTools.hxx>
	-#include <mitkTrackvis.h>
	-#include <itkSize.h>
	-#include <vtkFloatArray.h>
	-#include <vtkCellData.h>
	-#include <vtkPointData.h>
	-#include <mitkAbstractFileWriter.h>
	-#include <mitkCustomMimeType.h>
	-#include "mitkDiffusionIOMimeTypes.h"
	-
	-mitk::FiberBundleTrackVisWriter::FiberBundleTrackVisWriter()
	- : mitk::AbstractFileWriter(mitk::FiberBundle::GetStaticNameOfClass(), mitk::DiffusionIOMimeTypes::FIBERBUNDLE_TRK_MIMETYPE_NAME(), "TrackVis Fiber Bundle Reader")
	-{
	- Options defaultOptions;
	- defaultOptions["Save in LPS space (if unchecked, use RAS)"] = true;
	- this->SetDefaultOptions(defaultOptions);
	-
	- RegisterService();
	-}
	-
	-mitk::FiberBundleTrackVisWriter::FiberBundleTrackVisWriter(const mitk::FiberBundleTrackVisWriter & other)
	- :mitk::AbstractFileWriter(other)
	-{}
	-
	-mitk::FiberBundleTrackVisWriter::~FiberBundleTrackVisWriter()
	-{}
	-
	-mitk::FiberBundleTrackVisWriter * mitk::FiberBundleTrackVisWriter::Clone() const
	-{
	- return new mitk::FiberBundleTrackVisWriter(*this);
	-}
	-
	-void mitk::FiberBundleTrackVisWriter::Write()
	-{
	-
	- std::ostream* out;
	- std::ofstream outStream;
	-
	- if( this->GetOutputStream() )
	- {
	- out = this->GetOutputStream();
	- }else{
	- outStream.open( this->GetOutputLocation().c_str() );
	- out = &outStream;
	- }
	-
	- if ( !out->good() )
	- {
	- mitkThrow() << "Stream not good.";
	- }
	-
	- try
	- {
	- const std::string& locale = "C";
	- const std::string& currLocale = setlocale( LC_ALL, nullptr );
	- setlocale(LC_ALL, locale.c_str());
	-
	- std::locale I("C");
	- out->imbue(I);
	-
	- std::string filename = this->GetOutputLocation().c_str();
	-
	- mitk::FiberBundle::ConstPointer input = dynamic_cast<const mitk::FiberBundle*>(this->GetInput());
	- std::string ext = itksys::SystemTools::GetFilenameLastExtension(this->GetOutputLocation().c_str());
	-
	- // default extension is .fib
	- if(ext == "")
	- {
	- ext = ".trk";
	- this->SetOutputLocation(this->GetOutputLocation() + ext);
	- }
	-
	- Options options = this->GetOptions();
	- bool lps = us::any_cast<bool>(options["Save in LPS space (if unchecked, use RAS)"]);
	-
	- MITK_INFO << "Writing fiber bundle as TRK";
	- TrackVisFiberReader trk;
	- trk.create(filename, input.GetPointer(), lps);
	- trk.writeHdr();
	- trk.append(input.GetPointer());
	-
	- setlocale(LC_ALL, currLocale.c_str());
	- MITK_INFO << "TrackVis Fiber bundle written to " << filename;
	- }
	- catch(...)
	- {
	- throw;
	- }
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleTrackVisWriter.h b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleTrackVisWriter.h
	deleted file mode 100644
	index 264da46dfa..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleTrackVisWriter.h
	+++ /dev/null
	@@ -1,118 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkFiberBundleTrackVisWriter_h
	-#define __mitkFiberBundleTrackVisWriter_h
	-
	-#include <mitkAbstractFileWriter.h>
	-
	-#include "mitkFiberBundle.h"
	-#include <vtkPolyDataWriter.h>
	-
	-
	-
	-namespace mitk
	-{
	-
	-/**
	- * Writes fiber bundles to a file
	- * @ingroup Process
	- */
	-class FiberBundleTrackVisWriter : public mitk::AbstractFileWriter
	-{
	-public:
	-
	-
	- FiberBundleTrackVisWriter();
	- FiberBundleTrackVisWriter(const FiberBundleTrackVisWriter & other);
	- FiberBundleTrackVisWriter * Clone() const override;
	- ~FiberBundleTrackVisWriter() override;
	-
	- using mitk::AbstractFileWriter::Write;
	- void Write() override;
	-
	- static const char* XML_GEOMETRY;
	-
	- static const char* XML_MATRIX_XX;
	-
	- static const char* XML_MATRIX_XY;
	-
	- static const char* XML_MATRIX_XZ;
	-
	- static const char* XML_MATRIX_YX;
	-
	- static const char* XML_MATRIX_YY;
	-
	- static const char* XML_MATRIX_YZ;
	-
	- static const char* XML_MATRIX_ZX;
	-
	- static const char* XML_MATRIX_ZY;
	-
	- static const char* XML_MATRIX_ZZ;
	-
	- static const char* XML_ORIGIN_X;
	-
	- static const char* XML_ORIGIN_Y;
	-
	- static const char* XML_ORIGIN_Z;
	-
	- static const char* XML_SPACING_X;
	-
	- static const char* XML_SPACING_Y;
	-
	- static const char* XML_SPACING_Z;
	-
	- static const char* XML_SIZE_X;
	-
	- static const char* XML_SIZE_Y;
	-
	- static const char* XML_SIZE_Z;
	-
	- static const char* XML_FIBER_BUNDLE;
	-
	- static const char* XML_FIBER;
	-
	- static const char* XML_PARTICLE;
	-
	- static const char* XML_ID;
	-
	- static const char* XML_POS_X;
	-
	- static const char* XML_POS_Y;
	-
	- static const char* XML_POS_Z;
	-
	- static const char* VERSION_STRING;
	-
	- static const char* XML_FIBER_BUNDLE_FILE;
	-
	- static const char* XML_FILE_VERSION;
	-
	- static const char* XML_NUM_FIBERS;
	-
	- static const char* XML_NUM_PARTICLES;
	-
	- static const char* ASCII_FILE;
	-
	- static const char* FILE_NAME;
	-
	-};
	-
	-
	-} // end of namespace mitk
	-
	-#endif //__mitkFiberBundleWriter_h
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleVtkReader.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleVtkReader.cpp
	deleted file mode 100644
	index b7e5333539..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleVtkReader.cpp
	+++ /dev/null
	@@ -1,284 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkFiberBundleVtkReader.h"
	-#include <itkMetaDataObject.h>
	-#include <vtkPolyData.h>
	-#include <vtkDataReader.h>
	-#include <vtkPolyDataReader.h>
	-#include <vtkMatrix4x4.h>
	-#include <vtkPolyLine.h>
	-#include <vtkCellArray.h>
	-#include <vtkDataArray.h>
	-#include <vtkFloatArray.h>
	-#include <vtkCellData.h>
	-#include <vtkPointData.h>
	-#include <itksys/SystemTools.hxx>
	-#include <tinyxml.h>
	-#include <vtkCleanPolyData.h>
	-#include <mitkTrackvis.h>
	-#include <mitkCustomMimeType.h>
	-#include <vtkXMLPolyDataReader.h>
	-#include <vtkXMLDataReader.h>
	-#include "mitkDiffusionIOMimeTypes.h"
	-
	-
	-mitk::FiberBundleVtkReader::FiberBundleVtkReader()
	- : mitk::AbstractFileReader( mitk::DiffusionIOMimeTypes::FIBERBUNDLE_VTK_MIMETYPE_NAME(), "VTK Fiber Bundle Reader" )
	-{
	- m_ServiceReg = this->RegisterService();
	-}
	-
	-mitk::FiberBundleVtkReader::FiberBundleVtkReader(const FiberBundleVtkReader &other)
	- :mitk::AbstractFileReader(other)
	-{
	-}
	-
	-mitk::FiberBundleVtkReader * mitk::FiberBundleVtkReader::Clone() const
	-{
	- return new FiberBundleVtkReader(*this);
	-}
	-
	-
	-std::vector<itk::SmartPointer<mitk::BaseData> > mitk::FiberBundleVtkReader::Read()
	-{
	-
	- std::vector<itk::SmartPointer<mitk::BaseData> > result;
	-
	- const std::string& locale = "C";
	- const std::string& currLocale = setlocale( LC_ALL, nullptr );
	- setlocale(LC_ALL, locale.c_str());
	-
	- std::string filename = this->GetInputLocation();
	-
	- std::string ext = itksys::SystemTools::GetFilenameLastExtension(filename);
	- ext = itksys::SystemTools::LowerCase(ext);
	-
	- try
	- {
	- MITK_INFO << "Loading tractogram (VTK format): " << itksys::SystemTools::GetFilenameName(filename);
	- vtkSmartPointer<vtkPolyDataReader> reader = vtkSmartPointer<vtkPolyDataReader>::New();
	- reader->SetFileName( this->GetInputLocation().c_str() );
	-
	- if (reader->IsFilePolyData())
	- {
	- reader->Update();
	-
	- if ( reader->GetOutput() != nullptr )
	- {
	- vtkSmartPointer<vtkPolyData> fiberPolyData = reader->GetOutput();
	- FiberBundle::Pointer fiberBundle = FiberBundle::New(fiberPolyData);
	-
	- vtkSmartPointer<vtkFloatArray> weights = vtkFloatArray::SafeDownCast(fiberPolyData->GetCellData()->GetArray("FIBER_WEIGHTS"));
	- if (weights!=nullptr)
	- {
	- // float weight=0;
	- for (int i=0; i<weights->GetNumberOfValues(); i++)
	- {
	- if (weights->GetValue(i)<0.0)
	- {
	- MITK_ERROR << "Fiber weight<0 detected! Setting value to 0.";
	- weights->SetValue(i,0);
	- }
	- }
	- // if (!mitk::Equal(weights->GetValue(i),weight,0.00001))
	- // {
	- // MITK_INFO << "Weight: " << weights->GetValue(i);
	- // weight = weights->GetValue(i);
	- // }
	- fiberBundle->SetFiberWeights(weights);
	- }
	-
	- vtkSmartPointer<vtkUnsignedCharArray> fiberColors = vtkUnsignedCharArray::SafeDownCast(fiberPolyData->GetPointData()->GetArray("FIBER_COLORS"));
	- if (fiberColors!=nullptr)
	- fiberBundle->SetFiberColors(fiberColors);
	-
	- result.push_back(fiberBundle.GetPointer());
	- return result;
	- }
	- }
	- else
	- MITK_INFO << "File is not VTK format.";
	- }
	- catch(...)
	- {
	- throw;
	- }
	-
	- try
	- {
	- MITK_INFO << "Trying to load fiber file as VTP format.";
	- vtkSmartPointer<vtkXMLPolyDataReader> reader = vtkSmartPointer<vtkXMLPolyDataReader>::New();
	- reader->SetFileName( this->GetInputLocation().c_str() );
	-
	- if ( reader->CanReadFile(this->GetInputLocation().c_str()) )
	- {
	- reader->Update();
	-
	- if ( reader->GetOutput() != nullptr )
	- {
	- vtkSmartPointer<vtkPolyData> fiberPolyData = reader->GetOutput();
	- FiberBundle::Pointer fiberBundle = FiberBundle::New(fiberPolyData);
	-
	- vtkSmartPointer<vtkFloatArray> weights = vtkFloatArray::SafeDownCast(fiberPolyData->GetCellData()->GetArray("FIBER_WEIGHTS"));
	-
	- if (weights!=nullptr)
	- {
	- // float weight=0;
	- // for (int i=0; i<weights->GetSize(); i++)
	- // if (!mitk::Equal(weights->GetValue(i),weight,0.00001))
	- // {
	- // MITK_INFO << "Weight: " << weights->GetValue(i);
	- // weight = weights->GetValue(i);
	- // }
	- fiberBundle->SetFiberWeights(weights);
	- }
	-
	- vtkSmartPointer<vtkUnsignedCharArray> fiberColors = vtkUnsignedCharArray::SafeDownCast(fiberPolyData->GetPointData()->GetArray("FIBER_COLORS"));
	- if (fiberColors!=nullptr)
	- fiberBundle->SetFiberColors(fiberColors);
	-
	- result.push_back(fiberBundle.GetPointer());
	- return result;
	- }
	- }
	- else
	- MITK_INFO << "File is not VTP format.";
	- }
	- catch(...)
	- {
	- throw;
	- }
	-
	- try
	- {
	- MITK_INFO << "Trying to load fiber file as deprecated XML format.";
	- vtkSmartPointer<vtkPolyData> fiberPolyData = vtkSmartPointer<vtkPolyData>::New();
	- vtkSmartPointer<vtkCellArray> cellArray = vtkSmartPointer<vtkCellArray>::New();
	- vtkSmartPointer<vtkPoints> points = vtkSmartPointer<vtkPoints>::New();
	- TiXmlDocument doc( this->GetInputLocation().c_str() );
	- if(doc.LoadFile())
	- {
	- TiXmlHandle hDoc(&doc);
	- TiXmlElement* pElem;
	- TiXmlHandle hRoot(nullptr);
	- pElem = hDoc.FirstChildElement().Element();
	- // save this for later
	- hRoot = TiXmlHandle(pElem);
	- pElem = hRoot.FirstChildElement("geometry").Element();
	- // read geometry
	- mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New();
	- // read origin
	- mitk::Point3D origin;
	- double temp = 0;
	- pElem->Attribute("origin_x", &temp);
	- origin[0] = temp;
	- pElem->Attribute("origin_y", &temp);
	- origin[1] = temp;
	- pElem->Attribute("origin_z", &temp);
	- origin[2] = temp;
	- geometry->SetOrigin(origin);
	- // read spacing
	- ScalarType spacing[3];
	- pElem->Attribute("spacing_x", &temp);
	- spacing[0] = temp;
	- pElem->Attribute("spacing_y", &temp);
	- spacing[1] = temp;
	- pElem->Attribute("spacing_z", &temp);
	- spacing[2] = temp;
	- geometry->SetSpacing(spacing);
	- // read transform
	- vtkMatrix4x4* m = vtkMatrix4x4::New();
	- pElem->Attribute("xx", &temp);
	- m->SetElement(0,0,temp);
	- pElem->Attribute("xy", &temp);
	- m->SetElement(1,0,temp);
	- pElem->Attribute("xz", &temp);
	- m->SetElement(2,0,temp);
	- pElem->Attribute("yx", &temp);
	- m->SetElement(0,1,temp);
	- pElem->Attribute("yy", &temp);
	- m->SetElement(1,1,temp);
	- pElem->Attribute("yz", &temp);
	- m->SetElement(2,1,temp);
	- pElem->Attribute("zx", &temp);
	- m->SetElement(0,2,temp);
	- pElem->Attribute("zy", &temp);
	- m->SetElement(1,2,temp);
	- pElem->Attribute("zz", &temp);
	- m->SetElement(2,2,temp);
	- m->SetElement(0,3,origin[0]);
	- m->SetElement(1,3,origin[1]);
	- m->SetElement(2,3,origin[2]);
	- m->SetElement(3,3,1);
	- geometry->SetIndexToWorldTransformByVtkMatrix(m);
	- // read bounds
	- float bounds[] = {0, 0, 0, 0, 0, 0};
	- pElem->Attribute("size_x", &temp);
	- bounds[1] = temp;
	- pElem->Attribute("size_y", &temp);
	- bounds[3] = temp;
	- pElem->Attribute("size_z", &temp);
	- bounds[5] = temp;
	- geometry->SetFloatBounds(bounds);
	- geometry->SetImageGeometry(true);
	- pElem = hRoot.FirstChildElement("fiber_bundle").FirstChild().Element();
	- for( ; pElem ; pElem=pElem->NextSiblingElement())
	- {
	- TiXmlElement* pElem2 = pElem->FirstChildElement();
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	- for( ; pElem2; pElem2=pElem2->NextSiblingElement())
	- {
	- Point3D point;
	- pElem2->Attribute("pos_x", &temp);
	- point[0] = temp;
	- pElem2->Attribute("pos_y", &temp);
	- point[1] = temp;
	- pElem2->Attribute("pos_z", &temp);
	- point[2] = temp;
	- geometry->IndexToWorld(point, point);
	- vtkIdType id = points->InsertNextPoint(point.GetDataPointer());
	- container->GetPointIds()->InsertNextId(id);
	- }
	- cellArray->InsertNextCell(container);
	- }
	- fiberPolyData->SetPoints(points);
	- fiberPolyData->SetLines(cellArray);
	- vtkSmartPointer<vtkCleanPolyData> cleaner = vtkSmartPointer<vtkCleanPolyData>::New();
	- cleaner->SetInputData(fiberPolyData);
	- cleaner->Update();
	- fiberPolyData = cleaner->GetOutput();
	- FiberBundle::Pointer image = FiberBundle::New(fiberPolyData);
	- result.push_back(image.GetPointer());
	- return result;
	- }
	- else
	- {
	- MITK_INFO << "File is not deprectaed XML format.";
	- }
	-
	- setlocale(LC_ALL, currLocale.c_str());
	- MITK_INFO << "Fiber bundle read";
	- }
	- catch(...)
	- {
	- throw;
	- }
	-
	- throw "Selected file is no vtk readable fiber format (binary or ascii vtk or vtp file).";
	-
	- return result;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleVtkReader.h b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleVtkReader.h
	deleted file mode 100644
	index b344f3f7de..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleVtkReader.h
	+++ /dev/null
	@@ -1,52 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkFiberBundleVtkReader_h
	-#define __mitkFiberBundleVtkReader_h
	-
	-#include <mitkCommon.h>
	-#include <mitkFileReader.h>
	-#include <mitkFiberBundle.h>
	-#include <vtkSmartPointer.h>
	-
	-#include <mitkAbstractFileReader.h>
	-
	-namespace mitk
	-{
	-
	- /** \brief
	- */
	-
	- class FiberBundleVtkReader : public AbstractFileReader
	- {
	- public:
	-
	- FiberBundleVtkReader();
	- ~FiberBundleVtkReader() override{}
	- FiberBundleVtkReader(const FiberBundleVtkReader& other);
	- FiberBundleVtkReader * Clone() const override;
	-
	- using mitk::AbstractFileReader::Read;
	- std::vector<itk::SmartPointer<BaseData> > Read() override;
	-
	- private:
	-
	- us::ServiceRegistration<mitk::IFileReader> m_ServiceReg;
	- };
	-
	-} //namespace MITK
	-
	-#endif // __mitkFiberBundleReader_h
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleVtkWriter.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleVtkWriter.cpp
	deleted file mode 100644
	index 79ef1381ca..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleVtkWriter.cpp
	+++ /dev/null
	@@ -1,171 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkFiberBundleVtkWriter.h"
	-#include <vtkSmartPointer.h>
	-#include <vtkCleanPolyData.h>
	-#include <itksys/SystemTools.hxx>
	-#include <mitkTrackvis.h>
	-#include <itkSize.h>
	-#include <vtkFloatArray.h>
	-#include <vtkCellData.h>
	-#include <vtkPointData.h>
	-#include <mitkAbstractFileWriter.h>
	-#include <mitkCustomMimeType.h>
	-#include <vtkXMLPolyDataWriter.h>
	-#include "mitkDiffusionIOMimeTypes.h"
	-
	-mitk::FiberBundleVtkWriter::FiberBundleVtkWriter()
	- : mitk::AbstractFileWriter(mitk::FiberBundle::GetStaticNameOfClass(), mitk::DiffusionIOMimeTypes::FIBERBUNDLE_VTK_MIMETYPE_NAME(), "VTK Fiber Bundle Writer")
	-{
	- Options defaultOptions;
	- defaultOptions["Save as binary file"] = true;
	- defaultOptions["Save as xml file (vtp style)"] = false;
	- defaultOptions["Save color information"] = true;
	- defaultOptions["Save fiber weights"] = true;
	- this->SetDefaultOptions(defaultOptions);
	- RegisterService();
	-}
	-
	-mitk::FiberBundleVtkWriter::FiberBundleVtkWriter(const mitk::FiberBundleVtkWriter & other)
	- :mitk::AbstractFileWriter(other)
	-{}
	-
	-mitk::FiberBundleVtkWriter::~FiberBundleVtkWriter()
	-{}
	-
	-mitk::FiberBundleVtkWriter * mitk::FiberBundleVtkWriter::Clone() const
	-{
	- return new mitk::FiberBundleVtkWriter(*this);
	-}
	-
	-void mitk::FiberBundleVtkWriter::Write()
	-{
	-
	- std::ostream* out;
	- std::ofstream outStream;
	-
	- if( this->GetOutputStream() )
	- {
	- out = this->GetOutputStream();
	- }else{
	- outStream.open( this->GetOutputLocation().c_str() );
	- out = &outStream;
	- }
	-
	- if ( !out->good() )
	- {
	- mitkThrow() << "Stream not good.";
	- }
	-
	- try
	- {
	- const std::string& locale = "C";
	- const std::string& currLocale = setlocale( LC_ALL, nullptr );
	- setlocale(LC_ALL, locale.c_str());
	-
	- std::locale I("C");
	- out->imbue(I);
	-
	- std::string filename = this->GetOutputLocation().c_str();
	-
	- mitk::FiberBundle::ConstPointer input = dynamic_cast<const mitk::FiberBundle*>(this->GetInput());
	- std::string ext = itksys::SystemTools::GetFilenameLastExtension(this->GetOutputLocation().c_str());
	- Options options = this->GetOptions();
	-
	- vtkSmartPointer<vtkFloatArray> weights = nullptr;
	- vtkSmartPointer<vtkUnsignedCharArray> fiberColors = nullptr;
	-
	- vtkSmartPointer<vtkPolyData> fibPoly = input->GetFiberPolyData();
	- if (us::any_cast<bool>(options["Save fiber weights"]))
	- {
	- MITK_INFO << "Adding fiber weight information";
	- fibPoly->GetCellData()->AddArray(input->GetFiberWeights());
	- }
	- else if (fibPoly->GetCellData()->HasArray("FIBER_WEIGHTS"))
	- {
	- weights = input->GetFiberWeights();
	- fibPoly->GetCellData()->RemoveArray("FIBER_WEIGHTS");
	- }
	-
	- if (us::any_cast<bool>(options["Save color information"]))
	- {
	- MITK_INFO << "Adding color information";
	- fibPoly->GetPointData()->AddArray(input->GetFiberColors());
	- }
	- else if (fibPoly->GetPointData()->HasArray("FIBER_COLORS"))
	- {
	- fiberColors = input->GetFiberColors();
	- fibPoly->GetPointData()->RemoveArray("FIBER_COLORS");
	- }
	-
	- // default extension is .fib
	- if(ext == "")
	- {
	- ext = ".fib";
	- this->SetOutputLocation(this->GetOutputLocation() + ext);
	- }
	-
	- if (us::any_cast<bool>(options["Save as xml file (vtp style)"]))
	- {
	- vtkSmartPointer<vtkXMLPolyDataWriter> writer = vtkSmartPointer<vtkXMLPolyDataWriter>::New();
	- writer->SetInputData(fibPoly);
	- writer->SetFileName(filename.c_str());
	- if (us::any_cast<bool>(options["Save as binary file"]))
	- {
	- MITK_INFO << "Writing fiber bundle as vtk binary file";
	- writer->SetDataModeToBinary();
	- }
	- else
	- {
	- MITK_INFO << "Writing fiber bundle as vtk ascii file";
	- writer->SetDataModeToAscii();
	- }
	- writer->Write();
	- }
	- else
	- {
	- vtkSmartPointer<vtkPolyDataWriter> writer = vtkSmartPointer<vtkPolyDataWriter>::New();
	- writer->SetInputData(fibPoly);
	- writer->SetFileName(filename.c_str());
	- if (us::any_cast<bool>(options["Save as binary file"]))
	- {
	- MITK_INFO << "Writing fiber bundle as vtk binary file";
	- writer->SetFileTypeToBinary();
	- }
	- else
	- {
	- MITK_INFO << "Writing fiber bundle as vtk ascii file";
	- writer->SetFileTypeToASCII();
	- }
	- writer->Write();
	- }
	-
	- // restore arrays
	- if ( weights!=nullptr )
	- fibPoly->GetPointData()->AddArray(weights);
	-
	- if (fiberColors != nullptr)
	- fibPoly->GetPointData()->AddArray(fiberColors);
	-
	- setlocale(LC_ALL, currLocale.c_str());
	- MITK_INFO << "VTK Fiber bundle written to " << filename;
	- }
	- catch(...)
	- {
	- throw;
	- }
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleVtkWriter.h b/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleVtkWriter.h
	deleted file mode 100644
	index a0c2a7c30e..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberBundleVtkWriter.h
	+++ /dev/null
	@@ -1,118 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkFiberBundleVtkWriter_h
	-#define __mitkFiberBundleVtkWriter_h
	-
	-#include <mitkAbstractFileWriter.h>
	-
	-#include "mitkFiberBundle.h"
	-#include <vtkPolyDataWriter.h>
	-
	-
	-
	-namespace mitk
	-{
	-
	-/**
	- * Writes fiber bundles to a file
	- * @ingroup Process
	- */
	-class FiberBundleVtkWriter : public mitk::AbstractFileWriter
	-{
	-public:
	-
	-
	- FiberBundleVtkWriter();
	- FiberBundleVtkWriter(const FiberBundleVtkWriter & other);
	- FiberBundleVtkWriter * Clone() const override;
	- ~FiberBundleVtkWriter() override;
	-
	- using mitk::AbstractFileWriter::Write;
	- void Write() override;
	-
	- static const char* XML_GEOMETRY;
	-
	- static const char* XML_MATRIX_XX;
	-
	- static const char* XML_MATRIX_XY;
	-
	- static const char* XML_MATRIX_XZ;
	-
	- static const char* XML_MATRIX_YX;
	-
	- static const char* XML_MATRIX_YY;
	-
	- static const char* XML_MATRIX_YZ;
	-
	- static const char* XML_MATRIX_ZX;
	-
	- static const char* XML_MATRIX_ZY;
	-
	- static const char* XML_MATRIX_ZZ;
	-
	- static const char* XML_ORIGIN_X;
	-
	- static const char* XML_ORIGIN_Y;
	-
	- static const char* XML_ORIGIN_Z;
	-
	- static const char* XML_SPACING_X;
	-
	- static const char* XML_SPACING_Y;
	-
	- static const char* XML_SPACING_Z;
	-
	- static const char* XML_SIZE_X;
	-
	- static const char* XML_SIZE_Y;
	-
	- static const char* XML_SIZE_Z;
	-
	- static const char* XML_FIBER_BUNDLE;
	-
	- static const char* XML_FIBER;
	-
	- static const char* XML_PARTICLE;
	-
	- static const char* XML_ID;
	-
	- static const char* XML_POS_X;
	-
	- static const char* XML_POS_Y;
	-
	- static const char* XML_POS_Z;
	-
	- static const char* VERSION_STRING;
	-
	- static const char* XML_FIBER_BUNDLE_FILE;
	-
	- static const char* XML_FILE_VERSION;
	-
	- static const char* XML_NUM_FIBERS;
	-
	- static const char* XML_NUM_PARTICLES;
	-
	- static const char* ASCII_FILE;
	-
	- static const char* FILE_NAME;
	-
	-};
	-
	-
	-} // end of namespace mitk
	-
	-#endif //__mitkFiberBundleWriter_h
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberTrackingObjectFactory.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkFiberTrackingObjectFactory.cpp
	deleted file mode 100644
	index ef3ba90517..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberTrackingObjectFactory.cpp
	+++ /dev/null
	@@ -1,129 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkFiberTrackingObjectFactory.h"
	-
	-
	-mitk::FiberTrackingObjectFactory::FiberTrackingObjectFactory()
	- : CoreObjectFactoryBase()
	-{
	-}
	-
	-mitk::FiberTrackingObjectFactory::~FiberTrackingObjectFactory()
	-{
	-}
	-
	-mitk::Mapper::Pointer mitk::FiberTrackingObjectFactory::CreateMapper(mitk::DataNode* node, MapperSlotId id)
	-{
	- mitk::Mapper::Pointer newMapper=nullptr;
	-
	- if ( id == mitk::BaseRenderer::Standard2D )
	- {
	- std::string classname("FiberBundle");
	- if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0)
	- {
	- newMapper = mitk::FiberBundleMapper2D::New();
	- newMapper->SetDataNode(node);
	- }
	- else if(node->GetData() && std::string("PeakImage").compare(node->GetData()->GetNameOfClass())==0)
	- {
	- newMapper = mitk::PeakImageMapper2D::New();
	- newMapper->SetDataNode(node);
	- }
	-
	- }
	- else if ( id == mitk::BaseRenderer::Standard3D )
	- {
	- std::string classname("FiberBundle");
	- if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0)
	- {
	- newMapper = mitk::FiberBundleMapper3D::New();
	- newMapper->SetDataNode(node);
	- }
	- else if(node->GetData() && std::string("PeakImage").compare(node->GetData()->GetNameOfClass())==0)
	- {
	- newMapper = mitk::PeakImageMapper3D::New();
	- newMapper->SetDataNode(node);
	- }
	- }
	-
	- return newMapper;
	-}
	-
	-void mitk::FiberTrackingObjectFactory::SetDefaultProperties(mitk::DataNode* node)
	-{
	- std::string classname("FiberBundle");
	- if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0)
	- {
	- mitk::FiberBundleMapper3D::SetDefaultProperties(node);
	- mitk::FiberBundleMapper2D::SetDefaultProperties(node);
	- }
	- else if (node->GetData() && std::string("PeakImage").compare(node->GetData()->GetNameOfClass())==0)
	- {
	- mitk::PeakImageMapper3D::SetDefaultProperties(node);
	- mitk::PeakImageMapper2D::SetDefaultProperties(node);
	- }
	-}
	-
	-const char* mitk::FiberTrackingObjectFactory::GetFileExtensions()
	-{
	- std::string fileExtension;
	- this->CreateFileExtensions(m_FileExtensionsMap, fileExtension);
	- return fileExtension.c_str();
	-}
	-
	-mitk::CoreObjectFactoryBase::MultimapType mitk::FiberTrackingObjectFactory::GetFileExtensionsMap()
	-{
	- return m_FileExtensionsMap;
	-}
	-
	-const char* mitk::FiberTrackingObjectFactory::GetSaveFileExtensions()
	-{
	- std::string fileExtension;
	- this->CreateFileExtensions(m_SaveFileExtensionsMap, fileExtension);
	- return fileExtension.c_str();
	-}
	-
	-mitk::CoreObjectFactoryBase::MultimapType mitk::FiberTrackingObjectFactory::GetSaveFileExtensionsMap()
	-{
	- return m_SaveFileExtensionsMap;
	-}
	-
	-void mitk::FiberTrackingObjectFactory::CreateFileExtensionsMap()
	-{
	-
	-}
	-
	-void mitk::FiberTrackingObjectFactory::RegisterIOFactories()
	-{
	-}
	-
	-struct RegisterFiberTrackingObjectFactory{
	- RegisterFiberTrackingObjectFactory()
	- : m_Factory( mitk::FiberTrackingObjectFactory::New() )
	- {
	- mitk::CoreObjectFactory::GetInstance()->RegisterExtraFactory( m_Factory );
	- }
	-
	- ~RegisterFiberTrackingObjectFactory()
	- {
	- mitk::CoreObjectFactory::GetInstance()->UnRegisterExtraFactory( m_Factory );
	- }
	-
	- mitk::FiberTrackingObjectFactory::Pointer m_Factory;
	-};
	-
	-static RegisterFiberTrackingObjectFactory registerFiberTrackingObjectFactory;
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkFiberTrackingObjectFactory.h b/Modules/DiffusionImaging/DiffusionIO/mitkFiberTrackingObjectFactory.h
	deleted file mode 100644
	index d761bf9a82..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkFiberTrackingObjectFactory.h
	+++ /dev/null
	@@ -1,68 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef MITKFIBERTRACKINGOBJECTFACTORY_H
	-#define MITKFIBERTRACKINGOBJECTFACTORY_H
	-
	-#include "mitkCoreObjectFactory.h"
	-
	-#include <mitkFiberBundle.h>
	-#include <mitkFiberBundleMapper3D.h>
	-#include <mitkFiberBundleMapper2D.h>
	-#include <mitkPeakImageMapper2D.h>
	-#include <mitkPeakImageMapper3D.h>
	-
	-namespace mitk {
	-
	-class FiberTrackingObjectFactory : public CoreObjectFactoryBase
	-{
	- public:
	- mitkClassMacro(FiberTrackingObjectFactory,CoreObjectFactoryBase)
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- ~FiberTrackingObjectFactory() override;
	-
	- Mapper::Pointer CreateMapper(mitk::DataNode* node, MapperSlotId slotId) override;
	-
	- void SetDefaultProperties(mitk::DataNode* node) override;
	-
	- const char* GetFileExtensions() override;
	-
	- mitk::CoreObjectFactoryBase::MultimapType GetFileExtensionsMap() override;
	-
	- const char* GetSaveFileExtensions() override;
	-
	- mitk::CoreObjectFactoryBase::MultimapType GetSaveFileExtensionsMap() override;
	-
	- void RegisterIOFactories();
	-
	-protected:
	- FiberTrackingObjectFactory();
	- private:
	- void CreateFileExtensionsMap();
	- std::string m_ExternalFileExtensions;
	- std::string m_InternalFileExtensions;
	- std::string m_SaveFileExtensions;
	- MultimapType m_FileExtensionsMap;
	- MultimapType m_SaveFileExtensionsMap;
	-
	-};
	-
	-}
	-
	-
	-#endif // MITKFIBERTRACKINGOBJECTFACTORY_H
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkNrrdTbssImageIOFactory.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkNrrdTbssImageIOFactory.cpp
	deleted file mode 100644
	index f54b946217..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkNrrdTbssImageIOFactory.cpp
	+++ /dev/null
	@@ -1,51 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkNrrdTbssImageIOFactory.h"
	-#include "mitkIOAdapter.h"
	-#include "mitkNrrdTbssImageReader.h"
	-
	-#include "itkVersion.h"
	-
	-
	-namespace mitk
	-{
	-
	-NrrdTbssImageIOFactory::NrrdTbssImageIOFactory()
	-{
	- typedef NrrdTbssImageReader NrrdTbssVolReaderType;
	- this->RegisterOverride("mitkIOAdapter",
	- "mitkNrrdTbssImageReader",
	- "mitk Tbss Image IO",
	- true,
	- itk::CreateObjectFunction<IOAdapter<NrrdTbssVolReaderType> >::New());
	-}
	-
	-NrrdTbssImageIOFactory::~NrrdTbssImageIOFactory()
	-{
	-}
	-
	-const char* NrrdTbssImageIOFactory::GetITKSourceVersion() const
	-{
	- return ITK_SOURCE_VERSION;
	-}
	-
	-const char* NrrdTbssImageIOFactory::GetDescription() const
	-{
	- return "NrrdTbssImage IO Factory, allows the loading of NRRD Tbss data";
	-}
	-
	-} // end namespace mitk
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkNrrdTbssImageIOFactory.h b/Modules/DiffusionImaging/DiffusionIO/mitkNrrdTbssImageIOFactory.h
	deleted file mode 100644
	index 8808d92688..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkNrrdTbssImageIOFactory.h
	+++ /dev/null
	@@ -1,63 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef __MITK_NRRD_TBSS_VOULMES_IO_FACTORY_H_HEADER__
	-#define __MITK_NRRD_TBSS_VOULMES_IO_FACTORY_H_HEADER__
	-
	-#ifdef _MSC_VER
	-#pragma warning ( disable : 4786 )
	-#endif
	-
	-#include "itkObjectFactoryBase.h"
	-#include "mitkBaseData.h"
	-
	-namespace mitk
	-{
	-//##Documentation
	-//## @brief Create instances of NrrdDiffusionImageReader objects using an object factory.
	-//##
	-class NrrdTbssImageIOFactory : public itk::ObjectFactoryBase
	-{
	-public:
	- /** Standard class typedefs. */
	- typedef NrrdTbssImageIOFactory Self;
	- typedef itk::ObjectFactoryBase Superclass;
	- typedef itk::SmartPointer<Self> Pointer;
	- typedef itk::SmartPointer<const Self> ConstPointer;
	-
	- /** Class methods used to interface with the registered factories. */
	- const char* GetITKSourceVersion(void) const override;
	- const char* GetDescription(void) const override;
	-
	- /** Method for class instantiation. */
	- itkFactorylessNewMacro(Self);
	- static NrrdTbssImageIOFactory* FactoryNew() { return new NrrdTbssImageIOFactory;}
	- /** Run-time type information (and related methods). */
	- itkTypeMacro(NrrdTbssImageIOFactory, ObjectFactoryBase);
	-
	-protected:
	- NrrdTbssImageIOFactory();
	- ~NrrdTbssImageIOFactory() override;
	-
	-private:
	- NrrdTbssImageIOFactory(const Self&); //purposely not implemented
	- void operator=(const Self&); //purposely not implemented
	-
	-};
	-
	-
	-} // end namespace mitk
	-
	-#endif // __MITK_NRRD_TBSS_VOULMES_IO_FACTORY_H_HEADER__
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkNrrdTbssImageWriterFactory.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkNrrdTbssImageWriterFactory.cpp
	deleted file mode 100644
	index 50515ffe4e..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkNrrdTbssImageWriterFactory.cpp
	+++ /dev/null
	@@ -1,50 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkNrrdTbssImageWriterFactory.h"
	-
	-#include "itkCreateObjectFunction.h"
	-#include "itkVersion.h"
	-
	-#include <mitkNrrdTbssImageWriter.h>
	-
	-namespace mitk
	-{
	-
	-NrrdTbssImageWriterFactory::NrrdTbssImageWriterFactory()
	-{
	- this->RegisterOverride("IOWriter",
	- "NrrdTbssImageWriter",
	- "NrrdTbssImage Writer",
	- true,
	- itk::CreateObjectFunction< mitk::NrrdTbssImageWriter >::New());
	-}
	-
	-NrrdTbssImageWriterFactory::~NrrdTbssImageWriterFactory()
	-{
	-}
	-
	-const char* NrrdTbssImageWriterFactory::GetITKSourceVersion() const
	-{
	- return ITK_SOURCE_VERSION;
	-}
	-
	-const char* NrrdTbssImageWriterFactory::GetDescription() const
	-{
	- return "NrrdTbssImageWriterFactory";
	-}
	-
	-} // end namespace mitk
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkNrrdTbssImageWriterFactory.h b/Modules/DiffusionImaging/DiffusionIO/mitkNrrdTbssImageWriterFactory.h
	deleted file mode 100644
	index a9189ddc9a..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkNrrdTbssImageWriterFactory.h
	+++ /dev/null
	@@ -1,54 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef NRRDTBSSIMAGE_WRITERFACTORY_H_HEADER_INCLUDED
	-#define NRRDTBSSIMAGE_WRITERFACTORY_H_HEADER_INCLUDED
	-
	-#include "itkObjectFactoryBase.h"
	-#include "mitkBaseData.h"
	-
	-namespace mitk
	-{
	-
	-class NrrdTbssImageWriterFactory : public itk::ObjectFactoryBase
	-{
	-public:
	-
	- mitkClassMacroItkParent( mitk::NrrdTbssImageWriterFactory, itk::ObjectFactoryBase )
	-
	- /** Class methods used to interface with the registered factories. */
	- const char* GetITKSourceVersion(void) const override;
	- const char* GetDescription(void) const override;
	-
	- /** Method for class instantiation. */
	- itkFactorylessNewMacro(Self);
	-
	-protected:
	- NrrdTbssImageWriterFactory();
	- ~NrrdTbssImageWriterFactory() override;
	-
	-private:
	- NrrdTbssImageWriterFactory(const Self&); //purposely not implemented
	- void operator=(const Self&); //purposely not implemented
	-
	-};
	-
	-} // end namespace mitk
	-
	-#endif // NRRDTBSSIMAGE_WRITERFACTORY_H_HEADER_INCLUDED
	-
	-
	-
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkNrrdTbssRoiImageIOFactory.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkNrrdTbssRoiImageIOFactory.cpp
	deleted file mode 100644
	index 7d81733617..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkNrrdTbssRoiImageIOFactory.cpp
	+++ /dev/null
	@@ -1,51 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkNrrdTbssRoiImageIOFactory.h"
	-#include "mitkIOAdapter.h"
	-#include "mitkNrrdTbssRoiImageReader.h"
	-
	-#include "itkVersion.h"
	-
	-
	-namespace mitk
	-{
	-
	-NrrdTbssRoiImageIOFactory::NrrdTbssRoiImageIOFactory()
	-{
	- typedef NrrdTbssRoiImageReader NrrdTbssRoiVolReaderType;
	- this->RegisterOverride("mitkIOAdapter",
	- "mitkNrrdTbssRoiImageReader",
	- "mitk Tbss Image IO",
	- true,
	- itk::CreateObjectFunction<IOAdapter<NrrdTbssRoiVolReaderType> >::New());
	-}
	-
	-NrrdTbssRoiImageIOFactory::~NrrdTbssRoiImageIOFactory()
	-{
	-}
	-
	-const char* NrrdTbssRoiImageIOFactory::GetITKSourceVersion() const
	-{
	- return ITK_SOURCE_VERSION;
	-}
	-
	-const char* NrrdTbssRoiImageIOFactory::GetDescription() const
	-{
	- return "NrrdTbssImage IO Factory, allows the loading of NRRD Tbss data";
	-}
	-
	-} // end namespace mitk
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkNrrdTbssRoiImageIOFactory.h b/Modules/DiffusionImaging/DiffusionIO/mitkNrrdTbssRoiImageIOFactory.h
	deleted file mode 100644
	index 07bcdf37ab..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkNrrdTbssRoiImageIOFactory.h
	+++ /dev/null
	@@ -1,63 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef __MITK_NRRD_TBSSROI_VOLUMES_IO_FACTORY_H_HEADER__
	-#define __MITK_NRRD_TBSSROI_VOLUMES_IO_FACTORY_H_HEADER__
	-
	-#ifdef _MSC_VER
	-#pragma warning ( disable : 4786 )
	-#endif
	-
	-#include "itkObjectFactoryBase.h"
	-#include "mitkBaseData.h"
	-
	-namespace mitk
	-{
	-//##Documentation
	-//## @brief Create instances of NrrdDiffusionImageReader objects using an object factory.
	-//##
	-class NrrdTbssRoiImageIOFactory : public itk::ObjectFactoryBase
	-{
	-public:
	- /** Standard class typedefs. */
	- typedef NrrdTbssRoiImageIOFactory Self;
	- typedef itk::ObjectFactoryBase Superclass;
	- typedef itk::SmartPointer<Self> Pointer;
	- typedef itk::SmartPointer<const Self> ConstPointer;
	-
	- /** Class methods used to interface with the registered factories. */
	- const char* GetITKSourceVersion(void) const override;
	- const char* GetDescription(void) const override;
	-
	- /** Method for class instantiation. */
	- itkFactorylessNewMacro(Self);
	- static NrrdTbssRoiImageIOFactory* FactoryNew() { return new NrrdTbssRoiImageIOFactory;}
	- /** Run-time type information (and related methods). */
	- itkTypeMacro(NrrdTbssRoiImageIOFactory, ObjectFactoryBase);
	-
	-protected:
	- NrrdTbssRoiImageIOFactory();
	- ~NrrdTbssRoiImageIOFactory() override;
	-
	-private:
	- NrrdTbssRoiImageIOFactory(const Self&); //purposely not implemented
	- void operator=(const Self&); //purposely not implemented
	-
	-};
	-
	-
	-} // end namespace mitk
	-
	-#endif // __MITK_NRRD_TBSS_VOULMES_IO_FACTORY_H_HEADER__
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkNrrdTbssRoiImageWriterFactory.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkNrrdTbssRoiImageWriterFactory.cpp
	deleted file mode 100644
	index 348267d63b..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkNrrdTbssRoiImageWriterFactory.cpp
	+++ /dev/null
	@@ -1,50 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkNrrdTbssRoiImageWriterFactory.h"
	-
	-#include "itkCreateObjectFunction.h"
	-#include "itkVersion.h"
	-
	-#include <mitkNrrdTbssRoiImageWriter.h>
	-
	-namespace mitk
	-{
	-
	-NrrdTbssRoiImageWriterFactory::NrrdTbssRoiImageWriterFactory()
	-{
	- this->RegisterOverride("IOWriter",
	- "NrrdTbssRoiImageWriter",
	- "NrrdTbssRoiImage ROI Writer",
	- true,
	- itk::CreateObjectFunction< mitk::NrrdTbssRoiImageWriter >::New());
	-}
	-
	-NrrdTbssRoiImageWriterFactory::~NrrdTbssRoiImageWriterFactory()
	-{
	-}
	-
	-const char* NrrdTbssRoiImageWriterFactory::GetITKSourceVersion() const
	-{
	- return ITK_SOURCE_VERSION;
	-}
	-
	-const char* NrrdTbssRoiImageWriterFactory::GetDescription() const
	-{
	- return "NrrdTbssRoiImageWriterFactory";
	-}
	-
	-} // end namespace mitk
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkNrrdTbssRoiImageWriterFactory.h b/Modules/DiffusionImaging/DiffusionIO/mitkNrrdTbssRoiImageWriterFactory.h
	deleted file mode 100644
	index 665b03447e..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkNrrdTbssRoiImageWriterFactory.h
	+++ /dev/null
	@@ -1,54 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef NRRDTBSSROIIMAGE_WRITERFACTORY_H_HEADER_INCLUDED
	-#define NRRDTBSSROIIMAGE_WRITERFACTORY_H_HEADER_INCLUDED
	-
	-#include "itkObjectFactoryBase.h"
	-#include "mitkBaseData.h"
	-
	-namespace mitk
	-{
	-
	-class NrrdTbssRoiImageWriterFactory : public itk::ObjectFactoryBase
	-{
	-public:
	-
	- mitkClassMacroItkParent( mitk::NrrdTbssRoiImageWriterFactory, itk::ObjectFactoryBase )
	-
	- /** Class methods used to interface with the registered factories. */
	- const char* GetITKSourceVersion(void) const override;
	- const char* GetDescription(void) const override;
	-
	- /** Method for class instantiation. */
	- itkFactorylessNewMacro(Self)
	-
	-protected:
	- NrrdTbssRoiImageWriterFactory();
	- ~NrrdTbssRoiImageWriterFactory() override;
	-
	-private:
	- NrrdTbssRoiImageWriterFactory(const Self&); //purposely not implemented
	- void operator=(const Self&); //purposely not implemented
	-
	-};
	-
	-} // end namespace mitk
	-
	-#endif // NRRDTBSSIMAGE_WRITERFACTORY_H_HEADER_INCLUDED
	-
	-
	-
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkPeakImageMapper2D.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkPeakImageMapper2D.cpp
	deleted file mode 100644
	index ca85bf8375..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkPeakImageMapper2D.cpp
	+++ /dev/null
	@@ -1,180 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkPeakImageMapper2D.h"
	-#include "mitkBaseRenderer.h"
	-#include "mitkDataNode.h"
	-#include <vtkActor.h>
	-#include <vtkOpenGLPolyDataMapper.h>
	-#include <vtkOpenGLHelper.h>
	-#include <vtkShaderProgram.h>
	-#include <vtkPlane.h>
	-#include <vtkPolyData.h>
	-#include <vtkPointData.h>
	-#include <vtkProperty.h>
	-#include <vtkLookupTable.h>
	-#include <vtkPoints.h>
	-#include <vtkCamera.h>
	-#include <vtkPolyLine.h>
	-#include <vtkRenderer.h>
	-#include <vtkCellArray.h>
	-#include <vtkMatrix4x4.h>
	-#include <vtkTubeFilter.h>
	-#include <mitkPlaneGeometry.h>
	-#include <mitkSliceNavigationController.h>
	-#include <mitkCoreServices.h>
	-
	-
	-mitk::PeakImageMapper2D::PeakImageMapper2D()
	-{
	- m_lut = vtkSmartPointer<vtkLookupTable>::New();
	- m_lut->Build();
	-}
	-
	-mitk::PeakImageMapper2D::~PeakImageMapper2D()
	-{
	-}
	-
	-
	-mitk::PeakImage* mitk::PeakImageMapper2D::GetInput()
	-{
	- return dynamic_cast< mitk::PeakImage * > ( GetDataNode()->GetData() );
	-}
	-
	-void mitk::PeakImageMapper2D::UpdateVtkTransform(mitk::BaseRenderer *)
	-{
	- // don't apply transform since the peak polydata is already in world coordinates.
	- return;
	-}
	-
	-void mitk::PeakImageMapper2D::Update(mitk::BaseRenderer * renderer)
	-{
	- mitk::DataNode* node = this->GetDataNode();
	- if (node == nullptr)
	- return;
	-
	- bool visible = true;
	- node->GetVisibility(visible, renderer, "visible");
	- if ( !visible )
	- return;
	-
	- this->GenerateDataForRenderer( renderer );
	-}
	-
	-// vtkActors and Mappers are feeded here
	-void mitk::PeakImageMapper2D::GenerateDataForRenderer(mitk::BaseRenderer *renderer)
	-{
	- mitk::PeakImage* peakImage = this->GetInput();
	-
	- //the handler of local storage gets feeded in this method with requested data for related renderwindow
	- LocalStorage *localStorage = m_LocalStorageHandler.GetLocalStorage(renderer);
	-
	- vtkSmartPointer<vtkPolyData> polyData = peakImage->GetPolyData();
	- if (polyData == nullptr)
	- return;
	-
	- localStorage->m_Mapper->ScalarVisibilityOn();
	- localStorage->m_Mapper->SetScalarModeToUsePointFieldData();
	- localStorage->m_Mapper->SetLookupTable(m_lut); //apply the properties after the slice was set
	- localStorage->m_Mapper->SelectColorArray("FIBER_COLORS");
	- localStorage->m_Mapper->SetInputData(polyData);
	-
	- mitk::SliceNavigationController::Pointer sliceContr = renderer->GetSliceNavigationController();
	- mitk::PlaneGeometry::ConstPointer planeGeo = sliceContr->GetCurrentPlaneGeometry();
	- mitk::Point3D plane_origin = planeGeo->GetOrigin();
	-
	- mitk::DataNode* node = this->GetDataNode();
	- mitk::Image* image = dynamic_cast<mitk::Image*>(node->GetData());
	- mitk::Vector3D spacing = image->GetGeometry()->GetSpacing();
	-
	- localStorage->m_Mapper->RemoveAllClippingPlanes();
	- float clipping_plane_thickness = 1;
	- if(spacing[0]<spacing[1] && spacing[0]<spacing[2])
	- clipping_plane_thickness = spacing[0];
	- else if (spacing[1] < spacing[2])
	- clipping_plane_thickness = spacing[1];
	- else
	- clipping_plane_thickness = spacing[2];
	- clipping_plane_thickness /= 2.0;
	-
	- mitk::Vector3D plane_normal = planeGeo->GetNormal();
	- plane_normal.Normalize();
	- double vnormal[3];
	- double vp1[3];
	- double vp2[3];
	-
	- vp1[0] = plane_origin[0] - plane_normal[0] * clipping_plane_thickness;
	- vp1[1] = plane_origin[1] - plane_normal[1] * clipping_plane_thickness;
	- vp1[2] = plane_origin[2] - plane_normal[2] * clipping_plane_thickness;
	-
	- vp2[0] = plane_origin[0] + plane_normal[0] * clipping_plane_thickness;
	- vp2[1] = plane_origin[1] + plane_normal[1] * clipping_plane_thickness;
	- vp2[2] = plane_origin[2] + plane_normal[2] * clipping_plane_thickness;
	-
	- {
	- vnormal[0] = vp2[0] - vp1[0];
	- vnormal[1] = vp2[1] - vp1[1];
	- vnormal[2] = vp2[2] - vp1[2];
	-
	- vtkSmartPointer<vtkPlane> plane = vtkSmartPointer<vtkPlane>::New();
	- plane->SetOrigin(vp1);
	- plane->SetNormal(vnormal);
	- localStorage->m_Mapper->AddClippingPlane(plane);
	- }
	- {
	- vnormal[0] = vp1[0] - vp2[0];
	- vnormal[1] = vp1[1] - vp2[1];
	- vnormal[2] = vp1[2] - vp2[2];
	-
	- vtkSmartPointer<vtkPlane> plane = vtkSmartPointer<vtkPlane>::New();
	- plane->SetOrigin(vp2);
	- plane->SetNormal(vnormal);
	- localStorage->m_Mapper->AddClippingPlane(plane);
	- }
	-
	- localStorage->m_PointActor->SetMapper(localStorage->m_Mapper);
	-
	- float linewidth = 1.0;
	- this->GetDataNode()->GetFloatProperty("shape.linewidth",linewidth);
	- localStorage->m_PointActor->GetProperty()->SetLineWidth(linewidth);
	-
	- // We have been modified => save this for next Update()
	- localStorage->m_LastUpdateTime.Modified();
	-}
	-
	-
	-vtkProp* mitk::PeakImageMapper2D::GetVtkProp(mitk::BaseRenderer *renderer)
	-{
	- this->Update(renderer);
	- return m_LocalStorageHandler.GetLocalStorage(renderer)->m_PointActor;
	-}
	-
	-
	-void mitk::PeakImageMapper2D::SetDefaultProperties(mitk::DataNode* node, mitk::BaseRenderer* renderer, bool overwrite)
	-{
	- Superclass::SetDefaultProperties(node, renderer, overwrite);
	-
	- //add other parameters to propertylist
	- node->AddProperty( "color", mitk::ColorProperty::New(1.0,1.0,1.0), renderer, overwrite);
	- node->AddProperty( "shape.linewidth", mitk::FloatProperty::New(1.0), renderer, overwrite);
	-}
	-
	-
	-mitk::PeakImageMapper2D::LocalStorage::LocalStorage()
	-{
	- m_PointActor = vtkSmartPointer<vtkActor>::New();
	- m_Mapper = vtkSmartPointer<MITKPeakImageMapper2D_POLYDATAMAPPER>::New();
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkPeakImageMapper2D.h b/Modules/DiffusionImaging/DiffusionIO/mitkPeakImageMapper2D.h
	deleted file mode 100644
	index 39e97b80e6..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkPeakImageMapper2D.h
	+++ /dev/null
	@@ -1,85 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef PeakImageMapper2D_H_HEADER_INCLUDED
	-#define PeakImageMapper2D_H_HEADER_INCLUDED
	-
	-//MITK Rendering
	-#include <mitkCommon.h>
	-#include <mitkBaseRenderer.h>
	-#include <mitkVtkMapper.h>
	-#include <mitkPeakImage.h>
	-#include <vtkSmartPointer.h>
	-
	-#define MITKPeakImageMapper2D_POLYDATAMAPPER vtkOpenGLPolyDataMapper
	-
	-class vtkActor;
	-class mitkBaseRenderer;
	-class MITKPeakImageMapper2D_POLYDATAMAPPER;
	-class vtkCutter;
	-class vtkPlane;
	-class vtkPolyData;
	-
	-
	-
	-namespace mitk {
	-
	-struct IShaderRepository;
	-
	-class PeakImageMapper2D : public VtkMapper
	-{
	-
	-public:
	- mitkClassMacro(PeakImageMapper2D, VtkMapper)
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- mitk::PeakImage* GetInput();
	- void Update(mitk::BaseRenderer * renderer) override;
	- static void SetDefaultProperties(DataNode* node, BaseRenderer* renderer = nullptr, bool overwrite = false );
	- void UpdateVtkTransform(mitk::BaseRenderer *renderer) override;
	- vtkProp* GetVtkProp(mitk::BaseRenderer* renderer) override;
	-
	- class LocalStorage : public mitk::Mapper::BaseLocalStorage
	- {
	- public:
	- vtkSmartPointer<vtkActor> m_PointActor;
	- vtkSmartPointer<MITKPeakImageMapper2D_POLYDATAMAPPER> m_Mapper;
	-
	- itk::TimeStamp m_LastUpdateTime;
	- LocalStorage();
	-
	- ~LocalStorage() override
	- {
	- }
	- };
	-
	- /** \brief This member holds all three LocalStorages for the three 2D render windows. */
	- mitk::LocalStorageHandler<LocalStorage> m_LocalStorageHandler;
	-
	-protected:
	- PeakImageMapper2D();
	- ~PeakImageMapper2D() override;
	- void GenerateDataForRenderer(mitk::BaseRenderer*) override;
	-
	-private:
	- vtkSmartPointer<vtkLookupTable> m_lut;
	-};
	-
	-
	-}//end namespace
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkPeakImageMapper3D.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkPeakImageMapper3D.cpp
	deleted file mode 100644
	index 73a2b46983..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkPeakImageMapper3D.cpp
	+++ /dev/null
	@@ -1,195 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkPeakImageMapper3D.h"
	-#include "mitkBaseRenderer.h"
	-#include "mitkDataNode.h"
	-#include <vtkActor.h>
	-#include <vtkOpenGLPolyDataMapper.h>
	-#include <vtkOpenGLHelper.h>
	-#include <vtkShaderProgram.h>
	-#include <vtkPlane.h>
	-#include <vtkPolyData.h>
	-#include <vtkPointData.h>
	-#include <vtkProperty.h>
	-#include <vtkLookupTable.h>
	-#include <vtkPoints.h>
	-#include <vtkCamera.h>
	-#include <vtkPolyLine.h>
	-#include <vtkRenderer.h>
	-#include <vtkCellArray.h>
	-#include <vtkMatrix4x4.h>
	-#include <vtkTubeFilter.h>
	-#include <mitkPlaneGeometry.h>
	-#include <mitkSliceNavigationController.h>
	-#include <mitkCoreServices.h>
	-#include <mitkClippingProperty.h>
	-
	-mitk::PeakImageMapper3D::PeakImageMapper3D()
	-{
	- m_lut = vtkSmartPointer<vtkLookupTable>::New();
	- m_lut->Build();
	-}
	-
	-mitk::PeakImageMapper3D::~PeakImageMapper3D()
	-{
	-
	-}
	-
	-
	-mitk::PeakImage* mitk::PeakImageMapper3D::GetInput()
	-{
	- return dynamic_cast< mitk::PeakImage * > ( GetDataNode()->GetData() );
	-}
	-
	-void mitk::PeakImageMapper3D::UpdateVtkTransform(mitk::BaseRenderer *)
	-{
	- // don't apply transform since the peak polydata is already in world coordinates.
	- return;
	-}
	-
	-void mitk::PeakImageMapper3D::Update(mitk::BaseRenderer * renderer)
	-{
	- mitk::DataNode* node = this->GetDataNode();
	- if (node == nullptr)
	- return;
	-
	- bool visible = true;
	- node->GetVisibility(visible, renderer, "visible");
	- if ( !visible )
	- return;
	-
	- this->GenerateDataForRenderer( renderer );
	-}
	-
	-// vtkActors and Mappers are feeded here
	-void mitk::PeakImageMapper3D::GenerateDataForRenderer(mitk::BaseRenderer *renderer)
	-{
	- //the handler of local storage gets feeded in this method with requested data for related renderwindow
	- LocalStorage *localStorage = m_LocalStorageHandler.GetLocalStorage(renderer);
	-
	- bool enabled = false;
	- this->GetDataNode()->GetBoolProperty("Enable3DPeaks",enabled);
	- if (!enabled)
	- {
	- vtkSmartPointer<vtkPolyData> polyData = vtkSmartPointer<vtkPolyData>::New();
	- localStorage->m_Mapper->SetInputData(polyData);
	- localStorage->m_Actor->SetMapper(localStorage->m_Mapper);
	- localStorage->m_Assembly->AddPart(localStorage->m_Actor);
	- return;
	- }
	-
	- mitk::PeakImage* peakImage = this->GetInput();
	- vtkSmartPointer<vtkPolyData> polyData = peakImage->GetPolyData();
	- if (polyData == nullptr)
	- return;
	- float linewidth = 1.0;
	- this->GetDataNode()->GetFloatProperty("shape.linewidth",linewidth);
	-
	- localStorage->m_Mapper->SetInputData(polyData);
	- localStorage->m_Mapper->SelectColorArray("FIBER_COLORS");
	- localStorage->m_Mapper->ScalarVisibilityOn();
	- localStorage->m_Mapper->SetScalarModeToUsePointFieldData();
	- localStorage->m_Actor->SetMapper(localStorage->m_Mapper);
	- localStorage->m_Mapper->SetLookupTable(m_lut);
	- localStorage->m_Actor->GetProperty()->SetLineWidth(linewidth);
	- localStorage->m_Assembly->AddPart(localStorage->m_Actor);
	-
	- const DataNode* node = this->GetDataNode();
	- mitk::ClippingProperty* prop = dynamic_cast<mitk::ClippingProperty*>(node->GetProperty("3DClipping"));
	-
	- mitk::Image* image = dynamic_cast<mitk::Image*>(node->GetData());
	- localStorage->m_Mapper->RemoveAllClippingPlanes();
	- mitk::Vector3D spacing = image->GetGeometry()->GetSpacing();
	- double clipping_plane_thickness = 1;
	- if(spacing[0]<spacing[1] && spacing[0]<spacing[2])
	- clipping_plane_thickness = spacing[0];
	- else if (spacing[1] < spacing[2])
	- clipping_plane_thickness = spacing[1];
	- else
	- clipping_plane_thickness = spacing[2];
	- clipping_plane_thickness /= 2.0;
	-
	- mitk::Vector3D plane_normal = prop->GetNormal();
	- if (plane_normal.GetNorm()>0.0)
	- {
	- plane_normal.Normalize();
	- mitk::Point3D plane_origin = prop->GetOrigin();
	-
	- double vnormal[3];
	- double vp1[3];
	- double vp2[3];
	-
	- vp1[0] = plane_origin[0] + plane_normal[0] * clipping_plane_thickness;
	- vp1[1] = plane_origin[1] + plane_normal[1] * clipping_plane_thickness;
	- vp1[2] = plane_origin[2] + plane_normal[2] * clipping_plane_thickness;
	-
	- vp2[0] = plane_origin[0] - plane_normal[0] * clipping_plane_thickness;
	- vp2[1] = plane_origin[1] - plane_normal[1] * clipping_plane_thickness;
	- vp2[2] = plane_origin[2] - plane_normal[2] * clipping_plane_thickness;
	-
	- {
	- vnormal[0] = vp2[0] - vp1[0];
	- vnormal[1] = vp2[1] - vp1[1];
	- vnormal[2] = vp2[2] - vp1[2];
	-
	- vtkSmartPointer<vtkPlane> plane = vtkSmartPointer<vtkPlane>::New();
	- plane->SetOrigin(vp1);
	- plane->SetNormal(vnormal);
	- localStorage->m_Mapper->AddClippingPlane(plane);
	- }
	- {
	- vnormal[0] = vp1[0] - vp2[0];
	- vnormal[1] = vp1[1] - vp2[1];
	- vnormal[2] = vp1[2] - vp2[2];
	-
	- vtkSmartPointer<vtkPlane> plane = vtkSmartPointer<vtkPlane>::New();
	- plane->SetOrigin(vp2);
	- plane->SetNormal(vnormal);
	- localStorage->m_Mapper->AddClippingPlane(plane);
	- }
	- }
	-
	- // We have been modified => save this for next Update()
	- localStorage->m_LastUpdateTime.Modified();
	-}
	-
	-
	-vtkProp* mitk::PeakImageMapper3D::GetVtkProp(mitk::BaseRenderer *renderer)
	-{
	- return m_LocalStorageHandler.GetLocalStorage(renderer)->m_Assembly;
	-}
	-
	-
	-void mitk::PeakImageMapper3D::SetDefaultProperties(mitk::DataNode* node, mitk::BaseRenderer* renderer, bool overwrite)
	-{
	- Superclass::SetDefaultProperties(node, renderer, overwrite);
	-
	- mitk::Vector3D plane_vec; plane_vec.Fill(0.0);
	- mitk::Point3D plane_origin; plane_origin.Fill(0.0);
	- node->AddProperty( "3DClipping", mitk::ClippingProperty::New( plane_origin, plane_vec ), renderer, overwrite );
	- node->AddProperty( "3DClippingPlaneId", mitk::IntProperty::New(-1), renderer, overwrite );
	- node->AddProperty( "3DClippingPlaneFlip", mitk::BoolProperty::New( false ), renderer, overwrite );
	- node->AddProperty( "Enable3DPeaks", mitk::BoolProperty::New( false ), renderer, overwrite );
	-}
	-
	-
	-mitk::PeakImageMapper3D::LocalStorage::LocalStorage()
	-{
	- m_Actor = vtkSmartPointer<vtkActor>::New();
	- m_Mapper = vtkSmartPointer<MITKPeakImageMapper3D_POLYDATAMAPPER>::New();
	- m_Assembly = vtkSmartPointer<vtkPropAssembly>::New();
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkPeakImageMapper3D.h b/Modules/DiffusionImaging/DiffusionIO/mitkPeakImageMapper3D.h
	deleted file mode 100644
	index 09891bafff..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkPeakImageMapper3D.h
	+++ /dev/null
	@@ -1,85 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef PeakImageMapper3D_H_HEADER_INCLUDED
	-#define PeakImageMapper3D_H_HEADER_INCLUDED
	-
	-//MITK Rendering
	-#include <mitkCommon.h>
	-#include <mitkBaseRenderer.h>
	-#include <mitkVtkMapper.h>
	-#include <mitkPeakImage.h>
	-#include <vtkSmartPointer.h>
	-
	-#define MITKPeakImageMapper3D_POLYDATAMAPPER vtkOpenGLPolyDataMapper
	-
	-class vtkActor;
	-class mitkBaseRenderer;
	-class MITKPeakImageMapper3D_POLYDATAMAPPER;
	-class vtkCutter;
	-class vtkPlane;
	-class vtkPolyData;
	-
	-
	-
	-namespace mitk {
	-
	-struct IShaderRepository;
	-
	-class PeakImageMapper3D : public VtkMapper
	-{
	-
	-public:
	- mitkClassMacro(PeakImageMapper3D, VtkMapper)
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- mitk::PeakImage* GetInput();
	- void Update(mitk::BaseRenderer * renderer) override;
	- static void SetDefaultProperties(DataNode* node, BaseRenderer* renderer = nullptr, bool overwrite = false );
	- void UpdateVtkTransform(mitk::BaseRenderer *renderer) override;
	- vtkProp* GetVtkProp(mitk::BaseRenderer* renderer) override;
	-
	- class LocalStorage : public mitk::Mapper::BaseLocalStorage
	- {
	- public:
	- vtkSmartPointer<vtkActor> m_Actor;
	- vtkSmartPointer<MITKPeakImageMapper3D_POLYDATAMAPPER> m_Mapper;
	- vtkSmartPointer<vtkPropAssembly> m_Assembly;
	-
	- itk::TimeStamp m_LastUpdateTime;
	- LocalStorage();
	-
	- ~LocalStorage() override
	- {
	- }
	- };
	-
	- mitk::LocalStorageHandler<LocalStorage> m_LocalStorageHandler;
	-
	-protected:
	- PeakImageMapper3D();
	- ~PeakImageMapper3D() override;
	- void GenerateDataForRenderer(mitk::BaseRenderer*) override;
	-
	-private:
	- vtkSmartPointer<vtkLookupTable> m_lut;
	-};
	-
	-
	-}//end namespace
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkPlanarFigureCompositeReader.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkPlanarFigureCompositeReader.cpp
	deleted file mode 100644
	index e2710e3e85..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkPlanarFigureCompositeReader.cpp
	+++ /dev/null
	@@ -1,100 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkPlanarFigureCompositeReader.h"
	-#include <itkMetaDataObject.h>
	-#include <itksys/SystemTools.hxx>
	-#include <tinyxml.h>
	-#include <vtkCleanPolyData.h>
	-#include <mitkTrackvis.h>
	-#include <mitkCustomMimeType.h>
	-#include "mitkDiffusionIOMimeTypes.h"
	-#include <boost/property_tree/ptree.hpp>
	-#define RAPIDXML_NO_EXCEPTIONS
	-#include <boost/property_tree/xml_parser.hpp>
	-#include <boost/foreach.hpp>
	-#include <mitkLexicalCast.h>
	-#include <mitkPlanarFigureComposite.h>
	-
	-
	-mitk::PlanarFigureCompositeReader::PlanarFigureCompositeReader()
	- : mitk::AbstractFileReader( mitk::DiffusionIOMimeTypes::PLANARFIGURECOMPOSITE_MIMETYPE(), "Planar Figure Composite Reader" )
	-{
	- m_ServiceReg = this->RegisterService();
	-}
	-
	-mitk::PlanarFigureCompositeReader::PlanarFigureCompositeReader(const PlanarFigureCompositeReader &other)
	- :mitk::AbstractFileReader(other)
	-{
	-}
	-
	-mitk::PlanarFigureCompositeReader * mitk::PlanarFigureCompositeReader::Clone() const
	-{
	- return new PlanarFigureCompositeReader(*this);
	-}
	-
	-
	-std::vector<itk::SmartPointer<mitk::BaseData> > mitk::PlanarFigureCompositeReader::Read()
	-{
	-
	- std::vector<itk::SmartPointer<mitk::BaseData> > result;
	- try
	- {
	- const std::string& locale = "C";
	- const std::string& currLocale = setlocale( LC_ALL, nullptr );
	- setlocale(LC_ALL, locale.c_str());
	-
	- std::string filename = this->GetInputLocation();
	-
	- std::string ext = itksys::SystemTools::GetFilenameLastExtension(filename);
	- ext = itksys::SystemTools::LowerCase(ext);
	-
	- boost::property_tree::ptree tree;
	- boost::property_tree::xml_parser::read_xml(filename, tree);
	- int comptype = tree.get<int>("comptype");
	-
	- mitk::PlanarFigureComposite::Pointer pfc = mitk::PlanarFigureComposite::New();
	- switch(comptype)
	- {
	- case 0:
	- pfc->setOperationType(mitk::PlanarFigureComposite::AND);
	- MITK_INFO << "loading AND composition";
	- break;
	- case 1:
	- pfc->setOperationType(mitk::PlanarFigureComposite::OR);
	- MITK_INFO << "loading OR composition";
	- break;
	- case 2:
	- pfc->setOperationType(mitk::PlanarFigureComposite::NOT);
	- MITK_INFO << "loading NOT composition";
	- break;
	- default:
	- MITK_ERROR << filename << " contains no valid composition type!";
	- }
	-
	- std::vector<itk::SmartPointer<mitk::BaseData> > result;
	- result.push_back(pfc.GetPointer());
	-
	- setlocale(LC_ALL, currLocale.c_str());
	-
	- return result;
	- }
	- catch(...)
	- {
	- throw;
	- }
	- return result;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkPlanarFigureCompositeReader.h b/Modules/DiffusionImaging/DiffusionIO/mitkPlanarFigureCompositeReader.h
	deleted file mode 100644
	index 977f377afd..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkPlanarFigureCompositeReader.h
	+++ /dev/null
	@@ -1,52 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkPlanarFigureCompositeReader_h
	-#define __mitkPlanarFigureCompositeReader_h
	-
	-#include <mitkCommon.h>
	-#include <mitkFileReader.h>
	-#include <mitkFiberBundle.h>
	-#include <vtkSmartPointer.h>
	-
	-#include <mitkAbstractFileReader.h>
	-
	-namespace mitk
	-{
	-
	- /** \brief
	- */
	-
	- class PlanarFigureCompositeReader : public AbstractFileReader
	- {
	- public:
	-
	- PlanarFigureCompositeReader();
	- ~PlanarFigureCompositeReader() override{}
	- PlanarFigureCompositeReader(const PlanarFigureCompositeReader& other);
	- PlanarFigureCompositeReader * Clone() const override;
	-
	- using mitk::AbstractFileReader::Read;
	- std::vector<itk::SmartPointer<BaseData> > Read() override;
	-
	- private:
	-
	- us::ServiceRegistration<mitk::IFileReader> m_ServiceReg;
	- };
	-
	-} //namespace MITK
	-
	-#endif // __mitkFiberBundleReader_h
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkPlanarFigureCompositeSerializer.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkPlanarFigureCompositeSerializer.cpp
	deleted file mode 100644
	index 8b6b57951c..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkPlanarFigureCompositeSerializer.cpp
	+++ /dev/null
	@@ -1,73 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkPlanarFigureCompositeSerializer.h"
	-#include "mitkPlanarFigureComposite.h"
	-#include "mitkPlanarFigureCompositeWriter.h"
	-#include <mitkPlanarFigureComposite.h>
	-
	-#include <itksys/SystemTools.hxx>
	-#include <mitkIOUtil.h>
	-
	-
	-MITK_REGISTER_SERIALIZER(PlanarFigureCompositeSerializer)
	-
	-
	-mitk::PlanarFigureCompositeSerializer::PlanarFigureCompositeSerializer()
	-{
	-}
	-
	-
	-mitk::PlanarFigureCompositeSerializer::~PlanarFigureCompositeSerializer()
	-{
	-}
	-
	-
	-std::string mitk::PlanarFigureCompositeSerializer::Serialize()
	-{
	- const PlanarFigureComposite* fb = dynamic_cast<const PlanarFigureComposite*>( m_Data.GetPointer() );
	- if (fb == nullptr)
	- {
	- MITK_ERROR << " Object at " << (const void*) this->m_Data
	- << " is not an mitk::PlanarFigureComposite. Cannot serialize as PlanarFigureComposite.";
	- return "";
	- }
	-
	- std::string filename( this->GetUniqueFilenameInWorkingDirectory() );
	- filename += "_";
	- filename += m_FilenameHint;
	- filename += ".pfc";
	-
	- std::string fullname(m_WorkingDirectory);
	- fullname += "/";
	- fullname += itksys::SystemTools::ConvertToOutputPath(filename.c_str());
	-
	- try
	- {
	- mitk::IOUtil::Save(fb,fullname);
	- }
	- catch (std::exception& e)
	- {
	- MITK_ERROR << " Error serializing object at " << (const void*) this->m_Data
	- << " to "
	- << fullname
	- << ": "
	- << e.what();
	- return "";
	- }
	- return filename;
	-}
	-
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkPlanarFigureCompositeSerializer.h b/Modules/DiffusionImaging/DiffusionIO/mitkPlanarFigureCompositeSerializer.h
	deleted file mode 100644
	index e6b8fa3a3a..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkPlanarFigureCompositeSerializer.h
	+++ /dev/null
	@@ -1,39 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef mitkPlanarFigureCompositeSerializer_h_included
	-#define mitkPlanarFigureCompositeSerializer_h_included
	-
	-#include "mitkBaseDataSerializer.h"
	-
	-namespace mitk
	-{
	-/**
	- \brief Serializes mitk::PlanarFigureComposite for mitk::SceneIO
	-*/
	-class PlanarFigureCompositeSerializer : public BaseDataSerializer
	-{
	- public:
	- mitkClassMacro( PlanarFigureCompositeSerializer, BaseDataSerializer );
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- std::string Serialize() override;
	- protected:
	- PlanarFigureCompositeSerializer();
	- ~PlanarFigureCompositeSerializer() override;
	-};
	-} // namespace
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkPlanarFigureCompositeWriter.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkPlanarFigureCompositeWriter.cpp
	deleted file mode 100644
	index d2118241d3..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkPlanarFigureCompositeWriter.cpp
	+++ /dev/null
	@@ -1,90 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkPlanarFigureCompositeWriter.h"
	-#include <itksys/SystemTools.hxx>
	-#include <mitkAbstractFileWriter.h>
	-#include <mitkCustomMimeType.h>
	-#include "mitkDiffusionIOMimeTypes.h"
	-#include <boost/property_tree/ptree.hpp>
	-#define RAPIDXML_NO_EXCEPTIONS
	-#include <boost/property_tree/xml_parser.hpp>
	-#include <mitkPlanarFigureComposite.h>
	-
	-mitk::PlanarFigureCompositeWriter::PlanarFigureCompositeWriter()
	- : mitk::AbstractFileWriter(mitk::PlanarFigureComposite::GetStaticNameOfClass(), mitk::DiffusionIOMimeTypes::PLANARFIGURECOMPOSITE_MIMETYPE(), "Planar Figure Composite Writer")
	-{
	- RegisterService();
	-}
	-
	-mitk::PlanarFigureCompositeWriter::PlanarFigureCompositeWriter(const mitk::PlanarFigureCompositeWriter & other)
	- :mitk::AbstractFileWriter(other)
	-{}
	-
	-mitk::PlanarFigureCompositeWriter::~PlanarFigureCompositeWriter()
	-{}
	-
	-mitk::PlanarFigureCompositeWriter * mitk::PlanarFigureCompositeWriter::Clone() const
	-{
	- return new mitk::PlanarFigureCompositeWriter(*this);
	-}
	-
	-void mitk::PlanarFigureCompositeWriter::Write()
	-{
	-
	- std::ostream* out;
	- std::ofstream outStream;
	-
	- if( this->GetOutputStream() )
	- {
	- out = this->GetOutputStream();
	- }else{
	- outStream.open( this->GetOutputLocation().c_str() );
	- out = &outStream;
	- }
	-
	- if ( !out->good() )
	- {
	- mitkThrow() << "Stream not good.";
	- }
	-
	- try
	- {
	- const std::string& locale = "C";
	- const std::string& currLocale = setlocale( LC_ALL, nullptr );
	- setlocale(LC_ALL, locale.c_str());
	-
	- std::locale previousLocale(out->getloc());
	- std::locale I("C");
	- out->imbue(I);
	-
	- std::string filename = this->GetOutputLocation().c_str();
	-
	- mitk::PlanarFigureComposite::ConstPointer input = dynamic_cast<const mitk::PlanarFigureComposite*>(this->GetInput());
	- std::string ext = itksys::SystemTools::GetFilenameLastExtension(this->GetOutputLocation().c_str());
	-
	- boost::property_tree::ptree type;
	- type.put("comptype", input->getOperationType());
	- boost::property_tree::xml_writer_settings<std::string> writerSettings(' ', 2);
	- boost::property_tree::xml_parser::write_xml(filename, type, std::locale(), writerSettings);
	-
	- setlocale(LC_ALL, currLocale.c_str());
	- }
	- catch(...)
	- {
	- throw;
	- }
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkPlanarFigureCompositeWriter.h b/Modules/DiffusionImaging/DiffusionIO/mitkPlanarFigureCompositeWriter.h
	deleted file mode 100644
	index c61931b435..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkPlanarFigureCompositeWriter.h
	+++ /dev/null
	@@ -1,47 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkPlanarFigureCompositeWriter_h
	-#define __mitkPlanarFigureCompositeWriter_h
	-
	-#include <mitkAbstractFileWriter.h>
	-
	-namespace mitk
	-{
	-
	-/**
	- * Writes fiber bundles to a file
	- * @ingroup Process
	- */
	-class PlanarFigureCompositeWriter : public mitk::AbstractFileWriter
	-{
	-public:
	-
	-
	- PlanarFigureCompositeWriter();
	- PlanarFigureCompositeWriter(const PlanarFigureCompositeWriter & other);
	- PlanarFigureCompositeWriter * Clone() const override;
	- ~PlanarFigureCompositeWriter() override;
	-
	- using mitk::AbstractFileWriter::Write;
	- void Write() override;
	-
	-};
	-
	-
	-} // end of namespace mitk
	-
	-#endif //__mitkFiberBundleWriter_h
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkQuantificationObjectFactory.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkQuantificationObjectFactory.cpp
	deleted file mode 100644
	index e1679ec72a..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkQuantificationObjectFactory.cpp
	+++ /dev/null
	@@ -1,172 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkQuantificationObjectFactory.h"
	-
	-#include "mitkTbssImageMapper.h"
	-
	-#include "mitkNrrdTbssImageIOFactory.h"
	-#include "mitkNrrdTbssImageWriterFactory.h"
	-#include "mitkNrrdTbssImageWriter.h"
	-
	-#include "mitkNrrdTbssRoiImageIOFactory.h"
	-#include "mitkNrrdTbssRoiImageWriterFactory.h"
	-#include "mitkNrrdTbssRoiImageWriter.h"
	-
	-#include "mitkGPUVolumeMapper3D.h"
	-
	-typedef char TbssRoiPixelType;
	-typedef float TbssPixelType;
	-typedef int TbssGradientPixelType;
	-
	-mitk::QuantificationObjectFactory::QuantificationObjectFactory()
	- : CoreObjectFactoryBase()
	- , m_NrrdTbssImageIOFactory(mitk::NrrdTbssImageIOFactory::New().GetPointer())
	- , m_NrrdTbssRoiImageIOFactory(mitk::NrrdTbssRoiImageIOFactory::New().GetPointer())
	- , m_NrrdTbssImageWriterFactory(mitk::NrrdTbssImageWriterFactory::New().GetPointer())
	- , m_NrrdTbssRoiImageWriterFactory(mitk::NrrdTbssRoiImageWriterFactory::New().GetPointer())
	-{
	-
	- static bool alreadyDone = false;
	- if (!alreadyDone)
	- {
	- MITK_DEBUG << "QuantificationObjectFactory c'tor" << std::endl;
	-
	- itk::ObjectFactoryBase::RegisterFactory(m_NrrdTbssImageIOFactory);
	- itk::ObjectFactoryBase::RegisterFactory(m_NrrdTbssRoiImageIOFactory);
	-
	- itk::ObjectFactoryBase::RegisterFactory(m_NrrdTbssImageWriterFactory);
	- itk::ObjectFactoryBase::RegisterFactory(m_NrrdTbssRoiImageWriterFactory);
	-
	- m_FileWriters.push_back( NrrdTbssImageWriter::New().GetPointer() );
	- m_FileWriters.push_back( NrrdTbssRoiImageWriter::New().GetPointer() );
	-
	- CreateFileExtensionsMap();
	-
	- alreadyDone = true;
	- }
	-
	-}
	-
	-mitk::QuantificationObjectFactory::~QuantificationObjectFactory()
	-{
	- itk::ObjectFactoryBase::UnRegisterFactory(m_NrrdTbssImageIOFactory);
	- itk::ObjectFactoryBase::RegisterFactory(m_NrrdTbssRoiImageIOFactory);
	-
	- itk::ObjectFactoryBase::UnRegisterFactory(m_NrrdTbssImageWriterFactory);
	- itk::ObjectFactoryBase::UnRegisterFactory(m_NrrdTbssRoiImageWriterFactory);
	-}
	-
	-mitk::Mapper::Pointer mitk::QuantificationObjectFactory::CreateMapper(mitk::DataNode* node, MapperSlotId id)
	-{
	- mitk::Mapper::Pointer newMapper=nullptr;
	-
	- if ( id == mitk::BaseRenderer::Standard2D )
	- {
	- std::string classname = "TbssRoiImage";
	- if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0)
	- {
	- newMapper = mitk::ImageVtkMapper2D::New();
	- newMapper->SetDataNode(node);
	- }
	-
	- classname = "TbssImage";
	- if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0)
	- {
	- newMapper = mitk::TbssImageMapper::New();
	- newMapper->SetDataNode(node);
	- }
	-
	- }
	- else if ( id == mitk::BaseRenderer::Standard3D )
	- {
	- std::string classname = "TbssImage";
	- if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0)
	- {
	- newMapper = mitk::TbssImageMapper::New();
	- newMapper->SetDataNode(node);
	- }
	-
	- }
	-
	- return newMapper;
	-}
	-
	-void mitk::QuantificationObjectFactory::SetDefaultProperties(mitk::DataNode* node)
	-{
	- std::string classname = "TbssRoiImage";
	- if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0)
	- {
	- mitk::ImageVtkMapper2D::SetDefaultProperties(node);
	- }
	-
	- classname = "TbssImage";
	- if(node->GetData() && classname.compare(node->GetData()->GetNameOfClass())==0)
	- {
	- mitk::TbssImageMapper::SetDefaultProperties(node);
	- mitk::GPUVolumeMapper3D::SetDefaultProperties(node);
	- }
	-}
	-
	-const char* mitk::QuantificationObjectFactory::GetFileExtensions()
	-{
	- std::string fileExtension;
	- this->CreateFileExtensions(m_FileExtensionsMap, fileExtension);
	- return fileExtension.c_str();
	-};
	-
	-mitk::CoreObjectFactoryBase::MultimapType mitk::QuantificationObjectFactory::GetFileExtensionsMap()
	-{
	- return m_FileExtensionsMap;
	-}
	-
	-const char* mitk::QuantificationObjectFactory::GetSaveFileExtensions()
	-{
	- std::string fileExtension;
	- this->CreateFileExtensions(m_SaveFileExtensionsMap, fileExtension);
	- return fileExtension.c_str();
	-};
	-
	-mitk::CoreObjectFactoryBase::MultimapType mitk::QuantificationObjectFactory::GetSaveFileExtensionsMap()
	-{
	- return m_SaveFileExtensionsMap;
	-}
	-
	-void mitk::QuantificationObjectFactory::CreateFileExtensionsMap()
	-{
	- m_FileExtensionsMap.insert(std::pair<std::string, std::string>("*.tbss", "TBSS data"));
	- m_FileExtensionsMap.insert(std::pair<std::string, std::string>("*.roi", "TBSS ROI data"));
	-
	- m_SaveFileExtensionsMap.insert(std::pair<std::string, std::string>("*.tbss", "TBSS data"));
	- m_SaveFileExtensionsMap.insert(std::pair<std::string, std::string>("*.roi", "TBSS ROI data"));
	-}
	-
	-struct RegisterQuantificationObjectFactory{
	- RegisterQuantificationObjectFactory()
	- : m_Factory( mitk::QuantificationObjectFactory::New() )
	- {
	- mitk::CoreObjectFactory::GetInstance()->RegisterExtraFactory( m_Factory );
	- }
	-
	- ~RegisterQuantificationObjectFactory()
	- {
	- mitk::CoreObjectFactory::GetInstance()->UnRegisterExtraFactory( m_Factory );
	- }
	-
	- mitk::QuantificationObjectFactory::Pointer m_Factory;
	-};
	-
	-static RegisterQuantificationObjectFactory registerQuantificationObjectFactory;
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkQuantificationObjectFactory.h b/Modules/DiffusionImaging/DiffusionIO/mitkQuantificationObjectFactory.h
	deleted file mode 100644
	index 382adf4402..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkQuantificationObjectFactory.h
	+++ /dev/null
	@@ -1,49 +0,0 @@
	-#ifndef MITKQUANTIFICATIONOBJECTFACTORY_H
	-#define MITKQUANTIFICATIONOBJECTFACTORY_H
	-
	-
	-#include "mitkCoreObjectFactory.h"
	-
	-namespace mitk {
	-
	-class QuantificationObjectFactory : public CoreObjectFactoryBase
	-{
	- public:
	- mitkClassMacro(QuantificationObjectFactory,CoreObjectFactoryBase)
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- ~QuantificationObjectFactory() override;
	-
	- Mapper::Pointer CreateMapper(mitk::DataNode* node, MapperSlotId slotId) override;
	-
	- void SetDefaultProperties(mitk::DataNode* node) override;
	-
	- const char* GetFileExtensions() override;
	-
	- mitk::CoreObjectFactoryBase::MultimapType GetFileExtensionsMap() override;
	-
	- const char* GetSaveFileExtensions() override;
	-
	- mitk::CoreObjectFactoryBase::MultimapType GetSaveFileExtensionsMap() override;
	-
	-protected:
	- QuantificationObjectFactory();
	- private:
	- void CreateFileExtensionsMap();
	- std::string m_ExternalFileExtensions;
	- std::string m_InternalFileExtensions;
	- std::string m_SaveFileExtensions;
	- MultimapType m_FileExtensionsMap;
	- MultimapType m_SaveFileExtensionsMap;
	-
	- itk::ObjectFactoryBase::Pointer m_NrrdTbssImageIOFactory;
	- itk::ObjectFactoryBase::Pointer m_NrrdTbssRoiImageIOFactory;
	-
	- itk::ObjectFactoryBase::Pointer m_NrrdTbssImageWriterFactory;
	- itk::ObjectFactoryBase::Pointer m_NrrdTbssRoiImageWriterFactory;
	-};
	-
	-}
	-
	-#endif // MITKQUANTIFICATIONOBJECTFACTORY_H
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkTractographyForestReader.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkTractographyForestReader.cpp
	deleted file mode 100644
	index 62e63b5edd..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkTractographyForestReader.cpp
	+++ /dev/null
	@@ -1,77 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkTractographyForestReader.h"
	-#include <itkMetaDataObject.h>
	-#include <mitkCustomMimeType.h>
	-#include "mitkDiffusionIOMimeTypes.h"
	-
	-#undef DIFFERENCE
	-#define VIGRA_STATIC_LIB
	-#include <vigra/random_forest.hxx>
	-#include <vigra/random_forest_hdf5_impex.hxx>
	-
	-
	-mitk::TractographyForestReader::TractographyForestReader()
	- : mitk::AbstractFileReader( mitk::DiffusionIOMimeTypes::TRACTOGRAPHYFOREST_MIMETYPE_NAME(), "Tractography Forest" )
	-{
	- m_ServiceReg = this->RegisterService();
	-}
	-
	-mitk::TractographyForestReader::TractographyForestReader(const TractographyForestReader &other)
	- :mitk::AbstractFileReader(other)
	-{
	-}
	-
	-mitk::TractographyForestReader * mitk::TractographyForestReader::Clone() const
	-{
	- return new TractographyForestReader(*this);
	-}
	-
	-
	-std::vector<itk::SmartPointer<mitk::BaseData> > mitk::TractographyForestReader::Read()
	-{
	- std::vector<itk::SmartPointer<mitk::BaseData> > result;
	- std::shared_ptr< vigra::RandomForest<int> > forest;
	-
	- const std::string& locale = "C";
	- const std::string& currLocale = setlocale( LC_ALL, nullptr );
	- setlocale(LC_ALL, locale.c_str());
	-
	- std::string filename = this->GetInputLocation();
	-
	- try
	- {
	- MITK_INFO << "Trying to load random forest file.";
	-
	- forest = std::make_shared< vigra::RandomForest<int> >();
	- vigra::rf_import_HDF5( *forest, filename);
	-
	- mitk::TractographyForest::Pointer mitkForest = mitk::TractographyForest::New(forest);
	- result.push_back(mitkForest.GetPointer());
	- }
	- catch(...)
	- {
	- setlocale(LC_ALL, currLocale.c_str());
	- MITK_INFO << "Reading random forest failed";
	- throw;
	- }
	-
	- setlocale(LC_ALL, currLocale.c_str());
	- MITK_INFO << "Random forest read";
	-
	- return result;
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkTractographyForestReader.h b/Modules/DiffusionImaging/DiffusionIO/mitkTractographyForestReader.h
	deleted file mode 100644
	index 6a1b71d162..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkTractographyForestReader.h
	+++ /dev/null
	@@ -1,50 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkTractographyForestReader_h
	-#define __mitkTractographyForestReader_h
	-
	-#include <mitkCommon.h>
	-#include <mitkFileReader.h>
	-#include <mitkAbstractFileReader.h>
	-#include <mitkTractographyForest.h>
	-
	-namespace mitk
	-{
	-
	- /** \brief
	- */
	-
	- class TractographyForestReader : public AbstractFileReader
	- {
	- public:
	-
	- TractographyForestReader();
	- ~TractographyForestReader() override{}
	- TractographyForestReader(const TractographyForestReader& other);
	- TractographyForestReader * Clone() const override;
	-
	- using mitk::AbstractFileReader::Read;
	- std::vector<itk::SmartPointer<BaseData> > Read() override;
	-
	- private:
	-
	- us::ServiceRegistration<mitk::IFileReader> m_ServiceReg;
	- };
	-
	-} //namespace MITK
	-
	-#endif // __mitkFiberBundleReader_h
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkTractographyForestSerializer.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkTractographyForestSerializer.cpp
	deleted file mode 100644
	index b26c6ce347..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkTractographyForestSerializer.cpp
	+++ /dev/null
	@@ -1,73 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkTractographyForestSerializer.h"
	-#include "mitkTractographyForest.h"
	-#include "mitkTractographyForestWriter.h"
	-#include <mitkTractographyForest.h>
	-
	-#include <itksys/SystemTools.hxx>
	-#include <mitkIOUtil.h>
	-
	-
	-MITK_REGISTER_SERIALIZER(TractographyForestSerializer)
	-
	-
	-mitk::TractographyForestSerializer::TractographyForestSerializer()
	-{
	-}
	-
	-
	-mitk::TractographyForestSerializer::~TractographyForestSerializer()
	-{
	-}
	-
	-
	-std::string mitk::TractographyForestSerializer::Serialize()
	-{
	- const TractographyForest* fb = dynamic_cast<const TractographyForest*>( m_Data.GetPointer() );
	- if (fb == nullptr)
	- {
	- MITK_ERROR << " Object at " << (const void*) this->m_Data
	- << " is not an mitk::TractographyForest. Cannot serialize as TractographyForest.";
	- return "";
	- }
	-
	- std::string filename( this->GetUniqueFilenameInWorkingDirectory() );
	- filename += "_";
	- filename += m_FilenameHint;
	- filename += ".rf";
	-
	- std::string fullname(m_WorkingDirectory);
	- fullname += "/";
	- fullname += itksys::SystemTools::ConvertToOutputPath(filename.c_str());
	-
	- try
	- {
	- mitk::IOUtil::Save(fb,fullname);
	- }
	- catch (std::exception& e)
	- {
	- MITK_ERROR << " Error serializing object at " << (const void*) this->m_Data
	- << " to "
	- << fullname
	- << ": "
	- << e.what();
	- return "";
	- }
	- return filename;
	-}
	-
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkTractographyForestSerializer.h b/Modules/DiffusionImaging/DiffusionIO/mitkTractographyForestSerializer.h
	deleted file mode 100644
	index 4616749dbc..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkTractographyForestSerializer.h
	+++ /dev/null
	@@ -1,39 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef mitkTractographyForestSerializer_h_included
	-#define mitkTractographyForestSerializer_h_included
	-
	-#include "mitkBaseDataSerializer.h"
	-
	-namespace mitk
	-{
	-/**
	- \brief Serializes mitk::TractographyForest for mitk::SceneIO
	-*/
	-class TractographyForestSerializer : public BaseDataSerializer
	-{
	- public:
	- mitkClassMacro( TractographyForestSerializer, BaseDataSerializer );
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- std::string Serialize() override;
	- protected:
	- TractographyForestSerializer();
	- ~TractographyForestSerializer() override;
	-};
	-} // namespace
	-#endif
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkTractographyForestWriter.cpp b/Modules/DiffusionImaging/DiffusionIO/mitkTractographyForestWriter.cpp
	deleted file mode 100644
	index 79c520a99c..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkTractographyForestWriter.cpp
	+++ /dev/null
	@@ -1,91 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkTractographyForestWriter.h"
	-#include <mitkAbstractFileWriter.h>
	-#include <mitkCustomMimeType.h>
	-#include <mitkDiffusionIOMimeTypes.h>
	-#include <mitkTractographyForest.h>
	-
	-//#undef DIFFERENCE
	-//#define VIGRA_STATIC_LIB
	-//#include <vigra/random_forest.hxx>
	-#include <vigra/random_forest_hdf5_impex.hxx>
	-
	-mitk::TractographyForestWriter::TractographyForestWriter()
	- : mitk::AbstractFileWriter(mitk::TractographyForest::GetStaticNameOfClass(), mitk::DiffusionIOMimeTypes::TRACTOGRAPHYFOREST_MIMETYPE_NAME(), "Tractography Forest")
	-{
	- RegisterService();
	-}
	-
	-mitk::TractographyForestWriter::TractographyForestWriter(const mitk::TractographyForestWriter & other)
	- :mitk::AbstractFileWriter(other)
	-{}
	-
	-mitk::TractographyForestWriter::~TractographyForestWriter()
	-{}
	-
	-mitk::TractographyForestWriter * mitk::TractographyForestWriter::Clone() const
	-{
	- return new mitk::TractographyForestWriter(*this);
	-}
	-
	-void mitk::TractographyForestWriter::Write()
	-{
	-
	- std::ostream* out;
	- std::ofstream outStream;
	-
	- if( this->GetOutputStream() )
	- {
	- out = this->GetOutputStream();
	- }else{
	- outStream.open( this->GetOutputLocation().c_str() );
	- out = &outStream;
	- }
	-
	- if ( !out->good() )
	- {
	- mitkThrow() << "Stream not good.";
	- }
	-
	-
	- const std::string& locale = "C";
	- const std::string& currLocale = setlocale( LC_ALL, nullptr );
	- setlocale(LC_ALL, locale.c_str());
	-
	- std::locale previousLocale(out->getloc());
	- std::locale I("C");
	- out->imbue(I);
	-
	- try
	- {
	- std::string filename = this->GetOutputLocation().c_str();
	- mitk::TractographyForest::ConstPointer input = dynamic_cast<const mitk::TractographyForest*>(this->GetInput());
	-
	- MITK_INFO << "Saving forest to " << filename;
	- vigra::rf_export_HDF5( *input->GetForest(), filename, "" );
	-
	- setlocale(LC_ALL, currLocale.c_str());
	- MITK_INFO << "Forest saved successfully.";
	- }
	- catch(...)
	- {
	- setlocale(LC_ALL, currLocale.c_str());
	- MITK_INFO << "Forest could not be saved.";
	- throw;
	- }
	-}
	diff --git a/Modules/DiffusionImaging/DiffusionIO/mitkTractographyForestWriter.h b/Modules/DiffusionImaging/DiffusionIO/mitkTractographyForestWriter.h
	deleted file mode 100644
	index 9ed381a79d..0000000000
	--- a/Modules/DiffusionImaging/DiffusionIO/mitkTractographyForestWriter.h
	+++ /dev/null
	@@ -1,52 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkTractographyForestWriter_h
	-#define __mitkTractographyForestWriter_h
	-
	-#include <mitkAbstractFileWriter.h>
	-
	-#include "mitkFiberBundle.h"
	-#include <vtkPolyDataWriter.h>
	-
	-
	-
	-namespace mitk
	-{
	-
	-/**
	- * Writes random forests used for fiber tractography
	- * @ingroup Process
	- */
	-class TractographyForestWriter : public mitk::AbstractFileWriter
	-{
	-public:
	-
	-
	- TractographyForestWriter();
	- TractographyForestWriter(const TractographyForestWriter & other);
	- TractographyForestWriter * Clone() const override;
	- ~TractographyForestWriter() override;
	-
	- using mitk::AbstractFileWriter::Write;
	- void Write() override;
	-
	-};
	-
	-
	-} // end of namespace mitk
	-
	-#endif //__mitkFiberBundleWriter_h
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/ClusteringMetrics/mitkClusteringMetric.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/ClusteringMetrics/mitkClusteringMetric.h
	deleted file mode 100644
	index 9bbf13b8c6..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/ClusteringMetrics/mitkClusteringMetric.h
	+++ /dev/null
	@@ -1,61 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _ClusteringMetric
	-#define _ClusteringMetric
	-
	-#include <mitkDiffusionFunctionCollection.h>
	-
	-namespace mitk
	-{
	-
	-/**
	-* \brief Base class for fiber clustering metrics */
	-
	-class ClusteringMetric
	-{
	-
	-public:
	-
	- ClusteringMetric()
	- : m_Scale(1.0)
	- {}
	- virtual ~ClusteringMetric(){}
	-
	- virtual float CalculateDistance(vnl_matrix<float>& s, vnl_matrix<float>& t, bool &flipped) = 0;
	-
	- float GetScale() const;
	- void SetScale(float Scale);
	-
	-protected:
	-
	- float m_Scale;
	-
	-};
	-
	-float ClusteringMetric::GetScale() const
	-{
	- return m_Scale;
	-}
	-
	-void ClusteringMetric::SetScale(float Scale)
	-{
	- m_Scale = Scale;
	-}
	-
	-}
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/ClusteringMetrics/mitkClusteringMetricAnatomic.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/ClusteringMetrics/mitkClusteringMetricAnatomic.h
	deleted file mode 100644
	index 8603078662..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/ClusteringMetrics/mitkClusteringMetricAnatomic.h
	+++ /dev/null
	@@ -1,199 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _ClusteringMetricAnatomic
	-#define _ClusteringMetricAnatomic
	-
	-#include <mitkClusteringMetric.h>
	-#include <itkImage.h>
	-#include <itkImageRegionConstIterator.h>
	-#include <itkNumericTraits.h>
	-
	-namespace mitk
	-{
	-
	-/**
	-* \brief Fiber clustering metric based on white matter parcellation histograms along the tracts (Siless et al. https://www.ncbi.nlm.nih.gov/pubmed/29100937) */
	-
	-class ClusteringMetricAnatomic : public ClusteringMetric
	-{
	-
	-public:
	-
	- typedef itk::Image<short, 3> ItkShortImgType;
	-
	- ClusteringMetricAnatomic()
	- : m_Radius(1)
	- {}
	- virtual ~ClusteringMetricAnatomic(){}
	-
	- float CalculateDistance(vnl_matrix<float>& s, vnl_matrix<float>& t, bool &flipped)
	- {
	- vnl_matrix<float> hist1; hist1.set_size( (2m_Radius+1)(2m_Radius+1)(2*m_Radius+1), m_NumLabels ); hist1.fill(0);
	- vnl_matrix<float> hist2; hist2.set_size( (2m_Radius+1)(2m_Radius+1)(2*m_Radius+1), m_NumLabels ); hist2.fill(0);
	-
	-
	- float d_direct = 0;
	- float d_flipped = 0;
	-
	- vnl_vector<float> dists_d; dists_d.set_size(s.cols());
	- vnl_vector<float> dists_f; dists_f.set_size(s.cols());
	-
	- for (unsigned int i=0; i<s.cols(); ++i)
	- {
	- itk::Point<float, 3> p;
	- p[0] = s[0][i];
	- p[1] = s[1][i];
	- p[2] = s[2][i];
	- GetHistogramAtPoint(p, hist1);
	-
	- p[0] = t[0][i];
	- p[1] = t[1][i];
	- p[2] = t[2][i];
	- GetHistogramAtPoint(p, hist2);
	-
	- d_direct += (s.get_column(i)-t.get_column(i)).magnitude();
	- d_flipped += (s.get_column(i)-t.get_column(s.cols()-i-1)).magnitude();
	- }
	-
	-// float eudist = 0;
	- if (d_direct>d_flipped)
	- {
	- flipped = true;
	-// eudist = d_flipped/s.cols();
	- }
	- else
	- {
	- flipped = false;
	-// eudist = d_direct/s.cols();
	- }
	-
	- float label_intersection = 0;
	- for (unsigned int c=0; c<hist1.cols(); ++c)
	- {
	- bool l1 = false;
	- bool l2 = false;
	- for (unsigned int r=0; r<hist1.rows(); ++r)
	- {
	- if (hist1[r][c]>0)
	- l1 = true;
	- if (hist2[r][c]>0)
	- l2 = true;
	- if (l1 && l2)
	- {
	- label_intersection += 1;
	- break;
	- }
	- }
	- }
	-
	- float similarity = 0;
	- if (label_intersection>0)
	- {
	- hist1.normalize_rows();
	- hist2.normalize_rows();
	- label_intersection /= m_NumLabels;
	-
	- for (unsigned int l=0; l<hist1.rows(); ++l)
	- similarity += dot_product( hist1.get_row(l), hist2.get_row(l) );
	- similarity /= hist1.rows();
	- similarity *= label_intersection;
	- }
	-
	- if (similarity>0)
	- return m_Scale*0.2/similarity;
	- else
	- return 9999;
	- }
	-
	- void GetHistogramAtPoint(itk::Point<float, 3>& itkP, vnl_matrix<float>& hist)
	- {
	- int parc_idx = 0;
	- for (auto parc : m_Parcellations)
	- {
	- int dir_idx=0;
	- itk::Index<3> tmp_idx;
	- itk::Index<3> idx;
	- parc->TransformPhysicalPointToIndex(itkP, idx);
	- if (!parc->GetLargestPossibleRegion().IsInside(idx))
	- continue;
	-
	- short label = parc->GetPixel(idx);
	- short S0 = label;
	- hist[dir_idx][m_LabelMaps.at(parc_idx).at(label)] += 1;
	-
	- for (int x=-m_Radius; x<=m_Radius; ++x)
	- for (int y=-m_Radius; y<=m_Radius; ++y)
	- for (int z=-m_Radius; z<=m_Radius; ++z)
	- {
	- if (x==0 && y==0 && z==0)
	- continue;
	-
	- ++dir_idx;
	-
	- for (int d=1; d<5; ++d)
	- {
	- tmp_idx[0] = idx[0] + x*d;
	- tmp_idx[1] = idx[1] + y*d;
	- tmp_idx[2] = idx[2] + z*d;
	- if (!parc->GetLargestPossibleRegion().IsInside(tmp_idx))
	- break;
	- label = parc->GetPixel(tmp_idx);
	-
	- if (label!=S0)
	- {
	- hist[dir_idx][m_LabelMaps.at(parc_idx).at(label)] += 1;
	- break;
	- }
	- }
	- }
	- ++parc_idx;
	- }
	- }
	-
	- void SetParcellations(const std::vector<ItkShortImgType::Pointer> &Parcellations)
	- {
	- m_Parcellations = Parcellations;
	- m_NumLabels = 0;
	-
	- for (auto parc : m_Parcellations)
	- {
	- std::map< short, short > label_map;
	- itk::ImageRegionConstIterator<ItkShortImgType> it(parc, parc->GetLargestPossibleRegion());
	- while (!it.IsAtEnd())
	- {
	- if (label_map.count(it.Get())==0)
	- {
	- label_map.insert( std::pair< short, short >( it.Get(), m_NumLabels) );
	- ++m_NumLabels;
	- }
	- ++it;
	- }
	- m_LabelMaps.push_back(label_map);
	- }
	- }
	-
	-protected:
	-
	- std::vector< ItkShortImgType::Pointer > m_Parcellations;
	- short m_NumLabels;
	- int m_Radius;
	- std::vector< std::map< short, short > > m_LabelMaps;
	-};
	-
	-}
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/ClusteringMetrics/mitkClusteringMetricEuclideanMax.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/ClusteringMetrics/mitkClusteringMetricEuclideanMax.h
	deleted file mode 100644
	index ecd02c745a..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/ClusteringMetrics/mitkClusteringMetricEuclideanMax.h
	+++ /dev/null
	@@ -1,71 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _ClusteringMetricEuMax
	-#define _ClusteringMetricEuMax
	-
	-#include <mitkClusteringMetric.h>
	-
	-namespace mitk
	-{
	-
	-/**
	-* \brief Fiber clustering metric based on the euclidean maximum distance between tracts */
	-
	-class ClusteringMetricEuclideanMax : public ClusteringMetric
	-{
	-
	-public:
	-
	- ClusteringMetricEuclideanMax(){}
	- virtual ~ClusteringMetricEuclideanMax(){}
	-
	- float CalculateDistance(vnl_matrix<float>& s, vnl_matrix<float>& t, bool &flipped)
	- {
	- float d_direct = 0;
	- float d_flipped = 0;
	-
	- vnl_vector<float> dists_d; dists_d.set_size(s.cols());
	- vnl_vector<float> dists_f; dists_f.set_size(s.cols());
	-
	- for (unsigned int i=0; i<s.cols(); ++i)
	- {
	- dists_d[i] = (s.get_column(i)-t.get_column(i)).magnitude();
	- d_direct += dists_d[i];
	-
	- dists_f[i] = (s.get_column(i)-t.get_column(s.cols()-i-1)).magnitude();
	- d_flipped += dists_f[i];
	- }
	-
	- if (d_direct>d_flipped)
	- {
	- float d = dists_f.max_value();
	- flipped = true;
	- return m_Scale*d;
	- }
	-
	- float d = dists_d.max_value();
	- flipped = false;
	- return m_Scale*d;
	- }
	-
	-protected:
	-
	-};
	-
	-}
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/ClusteringMetrics/mitkClusteringMetricEuclideanMean.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/ClusteringMetrics/mitkClusteringMetricEuclideanMean.h
	deleted file mode 100644
	index 456b7bfce0..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/ClusteringMetrics/mitkClusteringMetricEuclideanMean.h
	+++ /dev/null
	@@ -1,62 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _ClusteringMetricEuMean
	-#define _ClusteringMetricEuMean
	-
	-#include <mitkClusteringMetric.h>
	-
	-namespace mitk
	-{
	-
	-/**
	-* \brief Fiber clustering metric based on the mean euclidean distance between tracts */
	-
	-class ClusteringMetricEuclideanMean : public ClusteringMetric
	-{
	-
	-public:
	-
	- ClusteringMetricEuclideanMean(){}
	- virtual ~ClusteringMetricEuclideanMean(){}
	-
	- float CalculateDistance(vnl_matrix<float>& s, vnl_matrix<float>& t, bool &flipped)
	- {
	- float d_direct = 0;
	- float d_flipped = 0;
	-
	- for (unsigned int i=0; i<s.cols(); ++i)
	- {
	- d_direct += (s.get_column(i)-t.get_column(i)).magnitude();
	- d_flipped += (s.get_column(i)-t.get_column(s.cols()-i-1)).magnitude();
	- }
	-
	- if (d_direct>d_flipped)
	- {
	- flipped = true;
	- return m_Scale*d_flipped/s.cols();
	- }
	- flipped = false;
	- return m_Scale*d_direct/s.cols();
	- }
	-
	-protected:
	-
	-};
	-
	-}
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/ClusteringMetrics/mitkClusteringMetricEuclideanStd.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/ClusteringMetrics/mitkClusteringMetricEuclideanStd.h
	deleted file mode 100644
	index 565938ece4..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/ClusteringMetrics/mitkClusteringMetricEuclideanStd.h
	+++ /dev/null
	@@ -1,77 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _ClusteringMetricEuStd
	-#define _ClusteringMetricEuStd
	-
	-#include <mitkClusteringMetric.h>
	-
	-namespace mitk
	-{
	-
	-/**
	-* \brief Fiber clustering metric based on the euclidean distance between tracts and the corresponding standard deviation of the distances */
	-
	-class ClusteringMetricEuclideanStd : public ClusteringMetric
	-{
	-
	-public:
	-
	- ClusteringMetricEuclideanStd(){}
	- virtual ~ClusteringMetricEuclideanStd(){}
	-
	- float CalculateDistance(vnl_matrix<float>& s, vnl_matrix<float>& t, bool &flipped)
	- {
	- float d_direct = 0;
	- float d_flipped = 0;
	-
	- vnl_vector<float> dists_d; dists_d.set_size(s.cols());
	- vnl_vector<float> dists_f; dists_f.set_size(s.cols());
	-
	- for (unsigned int i=0; i<s.cols(); ++i)
	- {
	- dists_d[i] = (s.get_column(i)-t.get_column(i)).magnitude();
	- d_direct += dists_d[i];
	-
	- dists_f[i] = (s.get_column(i)-t.get_column(s.cols()-i-1)).magnitude();
	- d_flipped += dists_f[i];
	- }
	-
	- if (d_direct>d_flipped)
	- {
	- float d = d_flipped/s.cols();
	- dists_f -= d;
	- d += dists_f.magnitude();
	-
	- flipped = true;
	- return m_Scale*d/2;
	- }
	-
	- float d = d_direct/s.cols();
	- dists_d -= d;
	- d += dists_d.magnitude();
	-
	- flipped = false;
	- return m_Scale*d/2;
	- }
	-
	-protected:
	-
	-};
	-
	-}
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/ClusteringMetrics/mitkClusteringMetricInnerAngles.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/ClusteringMetrics/mitkClusteringMetricInnerAngles.h
	deleted file mode 100644
	index 5581cb9aa3..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/ClusteringMetrics/mitkClusteringMetricInnerAngles.h
	+++ /dev/null
	@@ -1,125 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _ClusteringMetricInnerAngles
	-#define _ClusteringMetricInnerAngles
	-
	-#include <mitkClusteringMetric.h>
	-
	-namespace mitk
	-{
	-
	-/**
	-* \brief Fiber clustering metric based on the angles between certain parts of the streamline */
	-
	-class ClusteringMetricInnerAngles : public ClusteringMetric
	-{
	-
	-public:
	-
	- ClusteringMetricInnerAngles(){}
	- virtual ~ClusteringMetricInnerAngles(){}
	-
	- float CalculateDistance(vnl_matrix<float>& s, vnl_matrix<float>& t, bool &flipped)
	- {
	- int p1 = 0;
	- int p2 = s.cols()/4;
	- int p3 = s.cols()/2;
	- int p4 = 3*s.cols()/4;
	- int p5 = s.cols()-1;
	-
	- float a1_s = 0;
	- float a2_s = 0;
	- float a3_s = 0;
	- float a1_t = 0;
	- float a2_t = 0;
	- float a3_t = 0;
	-
	- {
	- vnl_vector<float> v1 = s.get_column(p1)-s.get_column(p2); v1.normalize();
	- vnl_vector<float> v2 = s.get_column(p3)-s.get_column(p2); v2.normalize();
	- a1_s = dot_product(v1,v2);
	- a1_s = std::acos( a1_s ) * 180.0/itk::Math::pi;
	- }
	-
	- {
	- vnl_vector<float> v1 = s.get_column(p1)-s.get_column(p3); v1.normalize();
	- vnl_vector<float> v2 = s.get_column(p5)-s.get_column(p3); v2.normalize();
	- a2_s = dot_product(v1,v2);
	- a2_s = std::acos( a2_s ) * 180.0/itk::Math::pi;
	- }
	-
	- {
	- vnl_vector<float> v1 = s.get_column(p3)-s.get_column(p4); v1.normalize();
	- vnl_vector<float> v2 = s.get_column(p5)-s.get_column(p4); v2.normalize();
	- a3_s = dot_product(v1,v2);
	- a3_s = std::acos( a3_s ) * 180.0/itk::Math::pi;
	- }
	-
	- //
	- {
	- vnl_vector<float> v1 = t.get_column(p1)-t.get_column(p2); v1.normalize();
	- vnl_vector<float> v2 = t.get_column(p3)-t.get_column(p2); v2.normalize();
	- a1_t = dot_product(v1,v2);
	- a1_t = std::acos( a1_t ) * 180.0/itk::Math::pi;
	- }
	-
	- {
	- vnl_vector<float> v1 = t.get_column(p1)-t.get_column(p3); v1.normalize();
	- vnl_vector<float> v2 = t.get_column(p5)-t.get_column(p3); v2.normalize();
	- a2_t = dot_product(v1,v2);
	- a2_t = std::acos( a2_t ) * 180.0/itk::Math::pi;
	- }
	-
	- {
	- vnl_vector<float> v1 = t.get_column(p3)-t.get_column(p4); v1.normalize();
	- vnl_vector<float> v2 = t.get_column(p5)-t.get_column(p4); v2.normalize();
	- a3_t = dot_product(v1,v2);
	- a3_t = std::acos( a3_t ) * 180.0/itk::Math::pi;
	- }
	-
	- float d_direct = 0;
	- float d_flipped = 0;
	-
	- int inc = s.cols()/4;
	- for (unsigned int i=0; i<s.cols(); i += inc)
	- {
	- d_direct += (s.get_column(i)-t.get_column(i)).magnitude();
	- d_flipped += (s.get_column(i)-t.get_column(s.cols()-i-1)).magnitude();
	- }
	-
	- if (d_direct>d_flipped)
	- {
	- flipped = true;
	- float d1 = std::fabs(a1_s-a3_t);
	- float d2 = std::fabs(a2_s-a2_t);
	- float d3 = std::fabs(a3_s-a1_t);
	- return m_Scale * std::max( d1, std::max(d2,d3) );
	- }
	- flipped = false;
	- float d1 = std::fabs(a1_s-a1_t);
	- float d2 = std::fabs(a2_s-a2_t);
	- float d3 = std::fabs(a3_s-a3_t);
	- return m_Scale * std::max( d1, std::max(d2,d3) );
	- }
	-
	-protected:
	-
	-};
	-
	-}
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/ClusteringMetrics/mitkClusteringMetricLength.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/ClusteringMetrics/mitkClusteringMetricLength.h
	deleted file mode 100644
	index 988208084f..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/ClusteringMetrics/mitkClusteringMetricLength.h
	+++ /dev/null
	@@ -1,72 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _ClusteringMetricLength
	-#define _ClusteringMetricLength
	-
	-#include <mitkClusteringMetric.h>
	-
	-namespace mitk
	-{
	-
	-/**
	-* \brief Fiber clustering metric based on the angles between certain parts of the streamline */
	-
	-class ClusteringMetricLength : public ClusteringMetric
	-{
	-
	-public:
	-
	- ClusteringMetricLength(){}
	- virtual ~ClusteringMetricLength(){}
	-
	- float CalculateDistance(vnl_matrix<float>& s, vnl_matrix<float>& t, bool &flipped)
	- {
	- float l1 = 0;
	- float l2 = 0;
	-
	- float d_direct = 0;
	- float d_flipped = 0;
	-
	- int inc = s.cols()/4;
	- for (unsigned int i=0; i<s.cols(); i += inc)
	- {
	- d_direct += (s.get_column(i)-t.get_column(i)).magnitude();
	- d_flipped += (s.get_column(i)-t.get_column(s.cols()-i-1)).magnitude();
	-
	- if (i<s.cols()-1)
	- {
	- l1 += (s.get_column(i+1)-s.get_column(i)).magnitude();
	- l2 += (t.get_column(i+1)-t.get_column(i)).magnitude();
	- }
	- }
	-
	- if (d_direct>d_flipped)
	- {
	- flipped = true;
	- return m_Scale * std::fabs(l1-l2);
	- }
	- flipped = false;
	- return m_Scale * std::fabs(l1-l2);
	- }
	-
	-protected:
	-
	-};
	-
	-}
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/ClusteringMetrics/mitkClusteringMetricScalarMap.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/ClusteringMetrics/mitkClusteringMetricScalarMap.h
	deleted file mode 100644
	index ec433340fa..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/ClusteringMetrics/mitkClusteringMetricScalarMap.h
	+++ /dev/null
	@@ -1,132 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _ClusteringMetricScalarMap
	-#define _ClusteringMetricScalarMap
	-
	-#include <mitkClusteringMetric.h>
	-#include <itkImage.h>
	-#include <itkImageRegionConstIterator.h>
	-#include <itkNumericTraits.h>
	-#include <mitkTrackingDataHandler.h>
	-
	-namespace mitk
	-{
	-
	-/**
	-* \brief Fiber clustering metric based on the scalar image values along a tract */
	-
	-class ClusteringMetricScalarMap : public ClusteringMetric
	-{
	-
	-public:
	-
	- typedef itk::Image<float, 3> ItkFloatImgType;
	-
	- ClusteringMetricScalarMap()
	- {
	- m_Interpolator = itk::LinearInterpolateImageFunction< ItkFloatImgType, float >::New();
	- this->m_Scale = 30;
	- }
	- virtual ~ClusteringMetricScalarMap(){}
	-
	- float CalculateDistance(vnl_matrix<float>& s, vnl_matrix<float>& t, bool &flipped)
	- {
	- float d_direct = 0;
	- float d_flipped = 0;
	- float map_distance = 0;
	-
	- vnl_vector<float> dists_d; dists_d.set_size(s.cols());
	- vnl_vector<float> dists_f; dists_f.set_size(s.cols());
	-
	- int inc = s.cols()/4;
	- for (unsigned int i=0; i<s.cols(); i += inc)
	- {
	- d_direct += (s.get_column(i)-t.get_column(i)).magnitude();
	- d_flipped += (s.get_column(i)-t.get_column(s.cols()-i-1)).magnitude();
	- }
	-
	- if (d_direct>d_flipped)
	- {
	- flipped = true;
	-
	- for (unsigned int i=0; i<s.cols(); ++i)
	- {
	- itk::Point<float, 3> p;
	- p[0] = s[0][i];
	- p[1] = s[1][i];
	- p[2] = s[2][i];
	- vnl_vector<float> vals1 = GetImageValuesAtPoint(p);
	-
	- p[0] = t[0][s.cols()-i-1];
	- p[1] = t[1][s.cols()-i-1];
	- p[2] = t[2][s.cols()-i-1];
	- vnl_vector<float> vals2 = GetImageValuesAtPoint(p);
	-
	- map_distance += (vals1-vals2).magnitude();
	- }
	- }
	- else
	- {
	- flipped = false;
	-
	- for (unsigned int i=0; i<s.cols(); ++i)
	- {
	- itk::Point<float, 3> p;
	- p[0] = s[0][i];
	- p[1] = s[1][i];
	- p[2] = s[2][i];
	- vnl_vector<float> vals1 = GetImageValuesAtPoint(p);
	-
	- p[0] = t[0][i];
	- p[1] = t[1][i];
	- p[2] = t[2][i];
	- vnl_vector<float> vals2 = GetImageValuesAtPoint(p);
	-
	- map_distance += (vals1-vals2).magnitude();
	- }
	- }
	-
	- return m_Scale*map_distance;
	- }
	-
	- vnl_vector<float> GetImageValuesAtPoint(itk::Point<float, 3>& itkP)
	- {
	- vnl_vector<float> vals; vals.set_size(m_ScalarMaps.size());
	- int c = 0;
	- for (auto map : m_ScalarMaps)
	- {
	- m_Interpolator->SetInputImage(map);
	- vals[c] = mitk::imv::GetImageValue<float>(itkP, true, m_Interpolator);
	- ++c;
	- }
	- return vals;
	- }
	-
	- void SetImages(const std::vector<ItkFloatImgType::Pointer> &Parcellations)
	- {
	- m_ScalarMaps = Parcellations;
	- }
	-
	-protected:
	-
	- std::vector< ItkFloatImgType::Pointer > m_ScalarMaps;
	- itk::LinearInterpolateImageFunction< ItkFloatImgType, float >::Pointer m_Interpolator;
	-};
	-
	-}
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkEnergyComputer.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkEnergyComputer.cpp
	deleted file mode 100644
	index e752d19a2d..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkEnergyComputer.cpp
	+++ /dev/null
	@@ -1,170 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkEnergyComputer.h"
	-#include <vnl/vnl_copy.h>
	-#include <itkNumericTraits.h>
	-
	-using namespace mitk;
	-
	-EnergyComputer::EnergyComputer(ItkFloatImageType* mask, ParticleGrid* particleGrid, SphereInterpolator* interpolator, ItkRandGenType* randGen)
	- : m_UseTrilinearInterpolation(true)
	-{
	- m_ParticleGrid = particleGrid;
	- m_RandGen = randGen;
	- m_SphereInterpolator = interpolator;
	- m_Mask = mask;
	-
	- m_ParticleLength = m_ParticleGrid->m_ParticleLength;
	- m_SquaredParticleLength = m_ParticleLength*m_ParticleLength;
	-
	- m_Size[0] = mask->GetLargestPossibleRegion().GetSize()[0];
	- m_Size[1] = mask->GetLargestPossibleRegion().GetSize()[1];
	- m_Size[2] = mask->GetLargestPossibleRegion().GetSize()[2];
	-
	- if (m_Size[0]<3 \|\| m_Size[1]<3 \|\| m_Size[2]<3)
	- m_UseTrilinearInterpolation = false;
	-
	- m_Spacing[0] = mask->GetSpacing()[0];
	- m_Spacing[1] = mask->GetSpacing()[1];
	- m_Spacing[2] = mask->GetSpacing()[2];
	-
	- // get rotation matrix
	- vnl_matrix<double> temp = mask->GetDirection().GetVnlMatrix();
	- vnl_matrix<float> directionMatrix; directionMatrix.set_size(3,3);
	- vnl_copy(temp, directionMatrix);
	- vnl_matrix_fixed<float, 3, 3> I = directionMatrix*directionMatrix.transpose();
	- for (int i = 0; i < 3; i++)
	- for (int j = 0; j < 3; j++)
	- I[i][j] = fabs(I[i][j]);
	- if(!I.is_identity(0.001))
	- {
	- fprintf(stderr,"EnergyComputer: image direction is not a rotation matrix. Tracking not possible!\n");
	- std::cout << directionMatrix << std::endl;
	- }
	- m_RotationMatrix = directionMatrix;
	-
	- if (ODF_SAMPLING_SIZE != m_SphereInterpolator->nverts)
	- fprintf(stderr,"EnergyComputer: error during init: data does not match with interpolation scheme\n");
	-
	- int totsz = m_Size[0]m_Size[1]m_Size[2];
	- m_CumulatedSpatialProbability.resize(totsz + 1, 0.0);
	- m_ActiveIndices.resize(totsz, 0);
	-
	- // calculate active voxels and cumulate probabilities
	- m_NumActiveVoxels = 0;
	- m_CumulatedSpatialProbability[0] = 0;
	- for (int x = 0; x < m_Size[0];x++)
	- for (int y = 0; y < m_Size[1];y++)
	- for (int z = 0; z < m_Size[2];z++)
	- {
	- int idx = x+(y+zm_Size[1])m_Size[0];
	- ItkFloatImageType::IndexType index;
	- index[0] = x; index[1] = y; index[2] = z;
	- if (m_Mask->GetPixel(index) > 0.5)
	- {
	- m_CumulatedSpatialProbability[m_NumActiveVoxels+1] = m_CumulatedSpatialProbability[m_NumActiveVoxels] + m_Mask->GetPixel(index);
	- m_ActiveIndices[m_NumActiveVoxels] = idx;
	- m_NumActiveVoxels++;
	- }
	- }
	- for (int k = 0; k < m_NumActiveVoxels; k++)
	- m_CumulatedSpatialProbability[k] /= m_CumulatedSpatialProbability[m_NumActiveVoxels];
	-
	- std::cout << "EnergyComputer: " << m_NumActiveVoxels << " active voxels found" << std::endl;
	-}
	-
	-void EnergyComputer::SetParameters(float particleWeight, float particleWidth, float connectionPotential, float curvThres, float inexBalance, float particlePotential)
	-{
	- m_ParticleChemicalPotential = particlePotential;
	- m_ConnectionPotential = connectionPotential;
	- m_ParticleWeight = particleWeight;
	-
	- float bal = 1/(1+exp(-inexBalance));
	- m_ExtStrength = 2*bal;
	- m_IntStrength = 2*(1-bal)/m_SquaredParticleLength;
	-
	- m_CurvatureThreshold = curvThres;
	-
	- float sigma_s = particleWidth;
	- m_SigmaInv = 1/(2sigma_ssigma_s);
	-}
	-
	-// draw random position from active voxels
	-void EnergyComputer::DrawRandomPosition(vnl_vector_fixed<float, 3>& R)
	-{
	- float r = static_cast<float>(m_RandGen->GetVariate());
	- int j;
	- int rl = 1;
	- int rh = m_NumActiveVoxels;
	- while(rh != rl)
	- {
	- j = rl + (rh-rl)/2;
	- if (r < m_CumulatedSpatialProbability[j])
	- {
	- rh = j;
	- continue;
	- }
	- if (r > m_CumulatedSpatialProbability[j])
	- {
	- rl = j+1;
	- continue;
	- }
	- break;
	- }
	- R[0] = m_Spacing[0]*((float)(m_ActiveIndices[rh-1] % m_Size[0]) + m_RandGen->GetVariate());
	- R[1] = m_Spacing[1]*((float)((m_ActiveIndices[rh-1]/m_Size[0]) % m_Size[1]) + m_RandGen->GetVariate());
	- R[2] = m_Spacing[2]((float)(m_ActiveIndices[rh-1]/(m_Size[0]m_Size[1])) + m_RandGen->GetVariate());
	-}
	-
	-// return spatial probability of position
	-float EnergyComputer::SpatProb(vnl_vector_fixed<float, 3> pos)
	-{
	- ItkFloatImageType::IndexType index;
	- index[0] = floor(pos[0]/m_Spacing[0]);
	- index[1] = floor(pos[1]/m_Spacing[1]);
	- index[2] = floor(pos[2]/m_Spacing[2]);
	-
	- if (m_Mask->GetLargestPossibleRegion().IsInside(index)) // is inside image?
	- return m_Mask->GetPixel(index);
	- else
	- return 0;
	-}
	-
	-float EnergyComputer::CalcI0(float x)
	-{
	- // BESSEL_APPROXCOEFF[0] = -0.1714;
	- // BESSEL_APPROXCOEFF[1] = 0.5332;
	- // BESSEL_APPROXCOEFF[2] = -1.4889;
	- // BESSEL_APPROXCOEFF[3] = 2.0389;
	- float y = x*x;
	- float erg = -0.1714;
	- erg += y*0.5332;
	- erg += yy-1.4889;
	- erg += yyy*2.0389;
	- return erg;
	-}
	-
	-float EnergyComputer::mexp(float x)
	-{
	- return((x>=7.0) ? 0 : ((x>=5.0) ? (-0.0029x+0.0213) : ((x>=3.0) ? (-0.0215x+0.1144) : ((x>=2.0) ? (-0.0855x+0.3064) : ((x>=1.0) ? (-0.2325x+0.6004) : ((x>=0.5) ? (-0.4773x+0.8452) : ((x>=0.0) ? (-0.7869x+1.0000) : 1 )))))));
	- // return exp(-x);
	-}
	-
	-int EnergyComputer::GetNumActiveVoxels()
	-{
	- return m_NumActiveVoxels;
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkEnergyComputer.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkEnergyComputer.h
	deleted file mode 100644
	index ca02e08a41..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkEnergyComputer.h
	+++ /dev/null
	@@ -1,85 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _ENCOMP
	-#define _ENCOMP
	-
	-#include <MitkFiberTrackingExports.h>
	-#include <itkOrientationDistributionFunction.h>
	-#include <mitkParticleGrid.h>
	-#include <mitkSphereInterpolator.h>
	-#include <itkMersenneTwisterRandomVariateGenerator.h>
	-
	-using namespace mitk;
	-
	-/**
	-* \brief Calculates internal and external energy of the new particle configuration proposal. */
	-
	-class MITKFIBERTRACKING_EXPORT EnergyComputer
	-{
	-
	-public:
	-
	- typedef itk::Image<float, 3> ItkFloatImageType;
	- typedef itk::Statistics::MersenneTwisterRandomVariateGenerator ItkRandGenType;
	-
	- EnergyComputer(ItkFloatImageType* mask, ParticleGrid* particleGrid, SphereInterpolator* interpolator, ItkRandGenType* randGen);
	- void SetParameters(float particleWeight, float particleWidth, float connectionPotential, float curvThres, float inexBalance, float particlePotential);
	-
	- // get random position inside mask
	- void DrawRandomPosition(vnl_vector_fixed<float, 3>& R);
	-
	- // external energy calculation
	- virtual float ComputeExternalEnergy(vnl_vector_fixed<float, 3>& R, vnl_vector_fixed<float, 3>& N, Particle* dp) =0;
	-
	- // internal energy calculation
	- virtual float ComputeInternalEnergyConnection(Particle *p1,int ep1) = 0;
	- virtual float ComputeInternalEnergyConnection(Particle p1,int ep1, Particle p2, int ep2) = 0;
	- virtual float ComputeInternalEnergy(Particle *dp) = 0;
	-
	- int GetNumActiveVoxels();
	-
	-protected:
	-
	- vnl_matrix_fixed<float, 3, 3> m_RotationMatrix;
	- SphereInterpolator* m_SphereInterpolator;
	- ParticleGrid* m_ParticleGrid;
	- ItkRandGenType* m_RandGen;
	- ItkFloatImageType* m_Mask;
	- vnl_vector_fixed<int, 3> m_Size;
	- vnl_vector_fixed<float, 3> m_Spacing;
	- std::vector< float > m_CumulatedSpatialProbability;
	- std::vector< int > m_ActiveIndices; // indices inside mask
	-
	- bool m_UseTrilinearInterpolation; // is deactivated if less than 3 image slices are available
	- int m_NumActiveVoxels; // voxels inside mask
	- float m_ConnectionPotential; // larger value results in larger energy value -> higher proposal acceptance probability
	- float m_ParticleChemicalPotential; // larger value results in larger energy value -> higher proposal acceptance probability
	- float m_SigmaInv;
	- float m_ParticleWeight; // defines how much one particle contributes to the artificial signal
	- float m_ExtStrength; // weighting factor for external energy
	- float m_IntStrength; // weighting factor for internal energy
	- float m_ParticleLength; // particle length
	- float m_SquaredParticleLength; // squared particle length
	- float m_CurvatureThreshold; // maximum angle accepted between two connected particles
	-
	- float SpatProb(vnl_vector_fixed<float, 3> pos);
	- float EvaluateOdf(vnl_vector_fixed<float, 3> &pos, vnl_vector_fixed<float, 3> dir);
	- float CalcI0(float x);
	- float mexp(float x);
	-};
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkFiberBuilder.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkFiberBuilder.cpp
	deleted file mode 100644
	index 40ed391393..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkFiberBuilder.cpp
	+++ /dev/null
	@@ -1,138 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkFiberBuilder.h"
	-
	-using namespace mitk;
	-
	-FiberBuilder::FiberBuilder(ParticleGrid* grid, ItkFloatImageType* image)
	-{
	- m_Grid = grid;
	- m_Image = image;
	- m_FiberLength = 0;
	-}
	-
	-FiberBuilder::~FiberBuilder()
	-{
	-
	-}
	-
	-vtkSmartPointer<vtkPolyData> FiberBuilder::iterate(int minFiberLength)
	-{
	- m_VtkCellArray = vtkSmartPointer<vtkCellArray>::New();
	- m_VtkPoints = vtkSmartPointer<vtkPoints>::New();
	-
	- int cur_label = 1;
	- int numFibers = 0;
	- m_FiberLength = 0;
	- for (int k = 0; k < m_Grid->m_NumParticles;k++)
	- {
	- Particle *dp = m_Grid->GetParticle(k);
	- if (dp->label == 0)
	- {
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	- dp->label = cur_label;
	- LabelPredecessors(dp, -1, container);
	- LabelSuccessors(dp, 1, container);
	- cur_label++;
	- if(m_FiberLength >= minFiberLength)
	- {
	- m_VtkCellArray->InsertNextCell(container);
	- numFibers++;
	- }
	- m_FiberLength = 0;
	- }
	- }
	- for (int k = 0; k < m_Grid->m_NumParticles;k++)
	- {
	- Particle *dp = m_Grid->GetParticle(k);
	- dp->label = 0;
	- }
	-
	- vtkSmartPointer<vtkPolyData> fiberPolyData = vtkSmartPointer<vtkPolyData>::New();
	- fiberPolyData->SetPoints(m_VtkPoints);
	- fiberPolyData->SetLines(m_VtkCellArray);
	- return fiberPolyData;
	-}
	-
	-void FiberBuilder::LabelPredecessors(Particle* p, int ep, vtkPolyLine* container)
	-{
	- Particle* p2 = nullptr;
	- if (ep==1)
	- p2 = m_Grid->GetParticle(p->pID);
	- else
	- p2 = m_Grid->GetParticle(p->mID);
	-
	- if (p2!=nullptr && p2->label==0)
	- {
	- p2->label = 1; // assign particle to current fiber
	-
	- if (p2->pID==p->ID)
	- LabelPredecessors(p2, -1, container);
	- else if (p2->mID==p->ID)
	- LabelPredecessors(p2, 1, container);
	- else
	- std::cout << "FiberBuilder: connection inconsistent (LabelPredecessors)" << std::endl;
	- }
	-
	- AddPoint(p, container);
	-}
	-
	-
	-void FiberBuilder::LabelSuccessors(Particle* p, int ep, vtkPolyLine* container)
	-{
	- AddPoint(p, container);
	-
	- Particle* p2 = nullptr;
	- if (ep==1)
	- p2 = m_Grid->GetParticle(p->pID);
	- else
	- p2 = m_Grid->GetParticle(p->mID);
	-
	- if (p2!=nullptr && p2->label==0)
	- {
	- p2->label = 1; // assign particle to current fiber
	-
	- if (p2->pID==p->ID)
	- LabelSuccessors(p2, -1, container);
	- else if (p2->mID==p->ID)
	- LabelSuccessors(p2, 1, container);
	- else
	- std::cout << "FiberBuilder: connection inconsistent (LabelPredecessors)" << std::endl;
	- }
	-}
	-
	-void FiberBuilder::AddPoint(Particle *dp, vtkSmartPointer<vtkPolyLine> container)
	-{
	- if (dp->label!=1)
	- return;
	-
	- dp->label = 2;
	-
	- itk::ContinuousIndex<float, 3> index;
	- index[0] = dp->GetPos()[0]/m_Image->GetSpacing()[0]-0.5;
	- index[1] = dp->GetPos()[1]/m_Image->GetSpacing()[1]-0.5;
	- index[2] = dp->GetPos()[2]/m_Image->GetSpacing()[2]-0.5;
	- itk::Point<float> point;
	- m_Image->TransformContinuousIndexToPhysicalPoint( index, point );
	- vtkIdType id = m_VtkPoints->InsertNextPoint(point.GetDataPointer());
	- container->GetPointIds()->InsertNextId(id);
	-
	- if(container->GetNumberOfPoints()>1)
	- m_FiberLength += m_LastPoint.EuclideanDistanceTo(point);
	-
	- m_LastPoint = point;
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkFiberBuilder.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkFiberBuilder.h
	deleted file mode 100644
	index 807980d77a..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkFiberBuilder.h
	+++ /dev/null
	@@ -1,68 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef _BUILDFIBRES
	-#define _BUILDFIBRES
	-
	-// MITK
	-#include <MitkFiberTrackingExports.h>
	-#include <mitkParticleGrid.h>
	-
	-// VTK
	-#include <vtkSmartPointer.h>
	-#include <vtkPolyData.h>
	-#include <vtkCellArray.h>
	-#include <vtkPoints.h>
	-#include <vtkPolyLine.h>
	-#include <vtkCleanPolyData.h>
	-
	-#include <itkImage.h>
	-
	-namespace mitk
	-{
	-
	-/**
	-* \brief Gnerates actual fiber structure (vtkPolyData) from the particle grid content. */
	-
	-class MITKFIBERTRACKING_EXPORT FiberBuilder
	-{
	-public:
	-
	- typedef itk::Image<float, 3> ItkFloatImageType;
	-
	- FiberBuilder(ParticleGrid* grid, ItkFloatImageType* image);
	- ~FiberBuilder();
	-
	- vtkSmartPointer<vtkPolyData> iterate(int minFiberLength);
	-
	-protected:
	-
	- void AddPoint(Particle *dp, vtkSmartPointer<vtkPolyLine> container);
	-
	- void LabelPredecessors(Particle* p, int ep, vtkPolyLine* container);
	- void LabelSuccessors(Particle* p, int ep, vtkPolyLine* container);
	-
	- itk::Point<float> m_LastPoint;
	- float m_FiberLength;
	- ItkFloatImageType::Pointer m_Image;
	- ParticleGrid* m_Grid;
	- vtkSmartPointer<vtkCellArray> m_VtkCellArray;
	- vtkSmartPointer<vtkPoints> m_VtkPoints;
	-
	-};
	-
	-}
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkGibbsEnergyComputer.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkGibbsEnergyComputer.cpp
	deleted file mode 100644
	index 2841ec0f1a..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkGibbsEnergyComputer.cpp
	+++ /dev/null
	@@ -1,219 +0,0 @@
	-#include <mitkGibbsEnergyComputer.h>
	-
	-#include <vnl/vnl_vector_fixed.h>
	-#include <vnl/vnl_copy.h>
	-#include <itkNumericTraits.h>
	-#include <MitkFiberTrackingExports.h>
	-#include <itkMersenneTwisterRandomVariateGenerator.h>
	-
	-using namespace mitk;
	-
	-GibbsEnergyComputer::GibbsEnergyComputer(ItkOdfImgType* OdfImage, ItkFloatImageType* mask, ParticleGrid* particleGrid, SphereInterpolator* interpolator, ItkRandGenType* randGen)
	-:EnergyComputer(mask, particleGrid, interpolator, randGen)
	-
	-{
	- m_Image = OdfImage;
	-}
	-
	-GibbsEnergyComputer::~GibbsEnergyComputer()
	-{
	-
	-}
	-
	-float GibbsEnergyComputer::EvaluateOdf(vnl_vector_fixed<float, 3>& pos, vnl_vector_fixed<float, 3> dir)
	-{
	- const int sampleSteps = 10; // evaluate ODF at 2*sampleSteps+1 positions along dir
	- vnl_vector_fixed<float, 3> samplePos; // current position to evaluate
	- float result = 0; // average of sampled ODF values
	- int xint, yint, zint; // voxel containing samplePos
	-
	- // rotate particle direction according to image rotation
	- dir = m_RotationMatrix*dir;
	-
	- // get interpolation for rotated direction
	- m_SphereInterpolator->getInterpolation(dir);
	-
	- // sample ODF values along particle direction
	- for (int i=-sampleSteps; i <= sampleSteps;i++)
	- {
	- samplePos = pos + (dir * m_ParticleLength) * ((float)i/sampleSteps);
	-
	- if (!m_UseTrilinearInterpolation) // image has not enough slices to use trilinear interpolation
	- {
	- ItkOdfImgType::IndexType index;
	- index[0] = floor(pos[0]/m_Spacing[0]);
	- index[1] = floor(pos[1]/m_Spacing[1]);
	- index[2] = floor(pos[2]/m_Spacing[2]);
	- if (m_Image->GetLargestPossibleRegion().IsInside(index))
	- {
	- result += (m_Image->GetPixel(index)[m_SphereInterpolator->idx[0]-1]*m_SphereInterpolator->interpw[0] +
	- m_Image->GetPixel(index)[m_SphereInterpolator->idx[1]-1]*m_SphereInterpolator->interpw[1] +
	- m_Image->GetPixel(index)[m_SphereInterpolator->idx[2]-1]* m_SphereInterpolator->interpw[2]);
	- }
	- }
	- else // use trilinear interpolation
	- {
	- float Rx = samplePos[0]/m_Spacing[0]-0.5;
	- float Ry = samplePos[1]/m_Spacing[1]-0.5;
	- float Rz = samplePos[2]/m_Spacing[2]-0.5;
	-
	- xint = floor(Rx);
	- yint = floor(Ry);
	- zint = floor(Rz);
	-
	- if (xint >= 0 && xint < m_Size[0]-1 && yint >= 0 && yint < m_Size[1]-1 && zint >= 0 && zint < m_Size[2]-1)
	- {
	- float xfrac = Rx-xint;
	- float yfrac = Ry-yint;
	- float zfrac = Rz-zint;
	-
	- ItkOdfImgType::IndexType index;
	- float weight;
	-
	- weight = (1-xfrac)(1-yfrac)(1-zfrac);
	- index[0] = xint; index[1] = yint; index[2] = zint;
	- result += (m_Image->GetPixel(index)[m_SphereInterpolator->idx[0]-1]*m_SphereInterpolator->interpw[0] +
	- m_Image->GetPixel(index)[m_SphereInterpolator->idx[1]-1]*m_SphereInterpolator->interpw[1] +
	- m_Image->GetPixel(index)[m_SphereInterpolator->idx[2]-1]* m_SphereInterpolator->interpw[2])*weight;
	-
	- weight = (xfrac)(1-yfrac)(1-zfrac);
	- index[0] = xint+1; index[1] = yint; index[2] = zint;
	- result += (m_Image->GetPixel(index)[m_SphereInterpolator->idx[0]-1]*m_SphereInterpolator->interpw[0] +
	- m_Image->GetPixel(index)[m_SphereInterpolator->idx[1]-1]*m_SphereInterpolator->interpw[1] +
	- m_Image->GetPixel(index)[m_SphereInterpolator->idx[2]-1]* m_SphereInterpolator->interpw[2])*weight;
	-
	- weight = (1-xfrac)(yfrac)(1-zfrac);
	- index[0] = xint; index[1] = yint+1; index[2] = zint;
	- result += (m_Image->GetPixel(index)[m_SphereInterpolator->idx[0]-1]*m_SphereInterpolator->interpw[0] +
	- m_Image->GetPixel(index)[m_SphereInterpolator->idx[1]-1]*m_SphereInterpolator->interpw[1] +
	- m_Image->GetPixel(index)[m_SphereInterpolator->idx[2]-1]* m_SphereInterpolator->interpw[2])*weight;
	-
	- weight = (1-xfrac)(1-yfrac)(zfrac);
	- index[0] = xint; index[1] = yint; index[2] = zint+1;
	- result += (m_Image->GetPixel(index)[m_SphereInterpolator->idx[0]-1]*m_SphereInterpolator->interpw[0] +
	- m_Image->GetPixel(index)[m_SphereInterpolator->idx[1]-1]*m_SphereInterpolator->interpw[1] +
	- m_Image->GetPixel(index)[m_SphereInterpolator->idx[2]-1]* m_SphereInterpolator->interpw[2])*weight;
	-
	- weight = (xfrac)(yfrac)(1-zfrac);
	- index[0] = xint+1; index[1] = yint+1; index[2] = zint;
	- result += (m_Image->GetPixel(index)[m_SphereInterpolator->idx[0]-1]*m_SphereInterpolator->interpw[0] +
	- m_Image->GetPixel(index)[m_SphereInterpolator->idx[1]-1]*m_SphereInterpolator->interpw[1] +
	- m_Image->GetPixel(index)[m_SphereInterpolator->idx[2]-1]* m_SphereInterpolator->interpw[2])*weight;
	-
	- weight = (1-xfrac)(yfrac)(zfrac);
	- index[0] = xint; index[1] = yint+1; index[2] = zint+1;
	- result += (m_Image->GetPixel(index)[m_SphereInterpolator->idx[0]-1]*m_SphereInterpolator->interpw[0] +
	- m_Image->GetPixel(index)[m_SphereInterpolator->idx[1]-1]*m_SphereInterpolator->interpw[1] +
	- m_Image->GetPixel(index)[m_SphereInterpolator->idx[2]-1]* m_SphereInterpolator->interpw[2])*weight;
	-
	- weight = (xfrac)(1-yfrac)(zfrac);
	- index[0] = xint+1; index[1] = yint; index[2] = zint+1;
	- result += (m_Image->GetPixel(index)[m_SphereInterpolator->idx[0]-1]*m_SphereInterpolator->interpw[0] +
	- m_Image->GetPixel(index)[m_SphereInterpolator->idx[1]-1]*m_SphereInterpolator->interpw[1] +
	- m_Image->GetPixel(index)[m_SphereInterpolator->idx[2]-1]* m_SphereInterpolator->interpw[2])*weight;
	-
	- weight = (xfrac)(yfrac)(zfrac);
	- index[0] = xint+1; index[1] = yint+1; index[2] = zint+1;
	- result += (m_Image->GetPixel(index)[m_SphereInterpolator->idx[0]-1]*m_SphereInterpolator->interpw[0] +
	- m_Image->GetPixel(index)[m_SphereInterpolator->idx[1]-1]*m_SphereInterpolator->interpw[1] +
	- m_Image->GetPixel(index)[m_SphereInterpolator->idx[2]-1]* m_SphereInterpolator->interpw[2])*weight;
	- }
	- }
	- }
	- result /= (2*sampleSteps+1); // average result over taken samples
	- return result;
	-}
	-
	-float GibbsEnergyComputer::ComputeExternalEnergy(vnl_vector_fixed<float, 3> &R, vnl_vector_fixed<float, 3> &N, Particle *dp)
	-{
	- if (SpatProb(R) == 0) // check if position is inside mask
	- return itk::NumericTraits<float>::NonpositiveMin();
	-
	- float odfVal = EvaluateOdf(R, N); // evaluate ODF in given direction
	-
	- float modelVal = 0;
	- m_ParticleGrid->ComputeNeighbors(R); // retrieve neighbouring particles from particle grid
	- Particle* neighbour = m_ParticleGrid->GetNextNeighbor();
	- while (neighbour!=nullptr) // iterate over nieghbouring particles
	- {
	- if (dp != neighbour) // don't evaluate against itself
	- {
	- // see Reisert et al. "Global Reconstruction of Neuronal Fibers", MICCAI 2009
	- float dot = fabs( dot_product(N,neighbour->GetDir()) );
	- float I_0 = CalcI0(dot) + m_ParticleChemicalPotential;
	-
	- float dpos = (neighbour->GetPos()-R).squared_magnitude();
	- float pos_w = exp(-dpos*m_SigmaInv);
	-
	- modelVal += pos_w*I_0;
	- }
	- neighbour = m_ParticleGrid->GetNextNeighbor();
	- }
	- modelVal += CalcI0(1.0)+m_ParticleChemicalPotential;
	-
	- float energy = 2*odfVal/m_ParticleWeight - modelVal;
	- return energy*m_ExtStrength;
	-}
	-
	-float GibbsEnergyComputer::ComputeInternalEnergy(Particle *dp)
	-{
	- float energy = 0;
	-
	- if (dp->pID != -1) // has predecessor
	- energy += ComputeInternalEnergyConnection(dp,+1);
	- if (dp->mID != -1) // has successor
	- energy += ComputeInternalEnergyConnection(dp,-1);
	-
	- return energy;
	-}
	-
	-float GibbsEnergyComputer::ComputeInternalEnergyConnection(Particle *p1,int ep1)
	-{
	- Particle *p2 = nullptr;
	- int ep2 = 0;
	-
	- if (ep1 == 1)
	- p2 = m_ParticleGrid->GetParticle(p1->pID); // get predecessor
	- else
	- p2 = m_ParticleGrid->GetParticle(p1->mID); // get successor
	-
	- // check in which direction the connected particle is pointing
	- if (p2->mID == p1->ID)
	- ep2 = -1;
	- else if (p2->pID == p1->ID)
	- ep2 = 1;
	- else
	- std::cout << "EnergyComputer: Connections are inconsistent!" << std::endl;
	-
	- return ComputeInternalEnergyConnection(p1,ep1,p2,ep2);
	-}
	-
	-float GibbsEnergyComputer::ComputeInternalEnergyConnection(Particle p1,int ep1, Particle p2, int ep2)
	-{
	- // see Reisert et al. "Global Reconstruction of Neuronal Fibers", MICCAI 2009
	- if ((dot_product(p1->GetDir(),p2->GetDir()))ep1ep2 > -m_CurvatureThreshold) // angle between particles is too sharp
	- return itk::NumericTraits<float>::NonpositiveMin();
	-
	- // calculate the endpoints of the two particles
	- vnl_vector_fixed<float, 3> endPoint1 = p1->GetPos() + (p1->GetDir() * (m_ParticleLength * ep1));
	- vnl_vector_fixed<float, 3> endPoint2 = p2->GetPos() + (p2->GetDir() * (m_ParticleLength * ep2));
	-
	- // check if endpoints are too far apart to connect
	- if ((endPoint1-endPoint2).squared_magnitude() > m_SquaredParticleLength)
	- return itk::NumericTraits<float>::NonpositiveMin();
	-
	- // calculate center point of the two particles
	- vnl_vector_fixed<float, 3> R = (p2->GetPos() + p1->GetPos()); R *= 0.5;
	-
	- // they are not allowed to connect if the mask image does not allow it
	- if (SpatProb(R) == 0)
	- return itk::NumericTraits<float>::NonpositiveMin();
	-
	- // get distances of endpoints to center point
	- float norm1 = (endPoint1-R).squared_magnitude();
	- float norm2 = (endPoint2-R).squared_magnitude();
	-
	- // calculate actual internal energy
	- float energy = (m_ConnectionPotential-norm1-norm2)*m_IntStrength;
	- return energy;
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkGibbsEnergyComputer.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkGibbsEnergyComputer.h
	deleted file mode 100644
	index df1ddee5a8..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkGibbsEnergyComputer.h
	+++ /dev/null
	@@ -1,46 +0,0 @@
	-#ifndef GIBBSENERGYCOMPUTER_H
	-#define GIBBSENERGYCOMPUTER_H
	-
	-#include <MitkFiberTrackingExports.h>
	-#include <itkOrientationDistributionFunction.h>
	-#include <mitkParticleGrid.h>
	-#include <mitkSphereInterpolator.h>
	-#include <itkMersenneTwisterRandomVariateGenerator.h>
	-
	-#include "mitkEnergyComputer.h"
	-
	-
	-using namespace mitk;
	-
	-/**
	-* \brief ODF lookuptable based energy computer. */
	-
	-class MITKFIBERTRACKING_EXPORT GibbsEnergyComputer : public EnergyComputer
	-{
	- public:
	-
	- typedef itk::Vector<float, ODF_SAMPLING_SIZE> OdfVectorType;
	- typedef itk::Image<OdfVectorType, 3> ItkOdfImgType;
	- typedef itk::Image<float, 3> ItkFloatImageType;
	- typedef itk::Statistics::MersenneTwisterRandomVariateGenerator ItkRandGenType;
	-
	- GibbsEnergyComputer(ItkOdfImgType* OdfImage, ItkFloatImageType* mask, ParticleGrid* particleGrid, SphereInterpolator* interpolator, ItkRandGenType* randGen);
	-
	- virtual ~GibbsEnergyComputer();
	-
	- // external energy calculation
	- float ComputeExternalEnergy(vnl_vector_fixed<float, 3>& R, vnl_vector_fixed<float, 3>& N, Particle* dp) override;
	-
	- // internal energy calculation
	- float ComputeInternalEnergyConnection(Particle *p1,int ep1) override;
	- float ComputeInternalEnergyConnection(Particle p1,int ep1, Particle p2, int ep2) override;
	- float ComputeInternalEnergy(Particle *dp) override;
	-
	- float EvaluateOdf(vnl_vector_fixed<float, 3>& pos, vnl_vector_fixed<float, 3> dir);
	- protected:
	-
	- ItkOdfImgType* m_Image;
	-
	-};
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkMetropolisHastingsSampler.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkMetropolisHastingsSampler.cpp
	deleted file mode 100644
	index 721392252c..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkMetropolisHastingsSampler.cpp
	+++ /dev/null
	@@ -1,499 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkMetropolisHastingsSampler.h"
	-
	-using namespace mitk;
	-
	-MetropolisHastingsSampler::MetropolisHastingsSampler(ParticleGrid* grid, EnergyComputer* enComp, ItkRandGenType* randGen, float curvThres)
	- : m_ExTemp(0.01)
	- , m_BirthProb(0.25)
	- , m_DeathProb(0.05)
	- , m_ShiftProb(0.15)
	- , m_OptShiftProb(0.1)
	- , m_ConnectionProb(0.45)
	- , m_TractProb(0.5)
	- , m_DelProb(0.1)
	- , m_ChempotParticle(0.0)
	- , m_AcceptedProposals(0)
	-{
	- m_RandGen = randGen;
	- m_ParticleGrid = grid;
	- m_EnergyComputer = enComp;
	-
	- m_ParticleLength = m_ParticleGrid->m_ParticleLength;
	- m_DistanceThreshold = m_ParticleLength*m_ParticleLength;
	- m_Sigma = m_ParticleLength/8.0;
	- m_Gamma = 1/(m_Sigmam_Sigma2);
	- m_Z = pow(2itk::Math::pim_Sigma,3.0/2.0)(itk::Math::pim_Sigma/m_ParticleLength);
	-
	- m_CurvatureThreshold = curvThres;
	- m_StopProb = exp(-1/m_TractProb);
	-}
	-
	-void MetropolisHastingsSampler::SetProbabilities(float birth, float death, float shift, float optShift, float connect)
	-{
	- m_BirthProb = birth;
	- m_DeathProb = death;
	- m_ShiftProb = shift;
	- m_OptShiftProb = optShift;
	- m_ConnectionProb = connect;
	- float sum = m_BirthProb+m_DeathProb+m_ShiftProb+m_OptShiftProb+m_ConnectionProb;
	- if (sum!=1 && sum>mitk::eps)
	- {
	- m_BirthProb /= sum;
	- m_DeathProb /= sum;
	- m_ShiftProb /= sum;
	- m_OptShiftProb /= sum;
	- m_ConnectionProb /= sum;
	- }
	- std::cout << "Update proposal probabilities" << std::endl;
	- std::cout << "Birth: " << m_BirthProb << std::endl;
	- std::cout << "Death: " << m_DeathProb << std::endl;
	- std::cout << "Shift: " << m_ShiftProb << std::endl;
	- std::cout << "Optimal shift: " << m_OptShiftProb << std::endl;
	- std::cout << "Connection: " << m_ConnectionProb << std::endl;
	-}
	-
	-// print proposal times
	-void MetropolisHastingsSampler::PrintProposalTimes()
	-{
	- double sum = m_BirthTime.GetTotal()+m_DeathTime.GetTotal()+m_ShiftTime.GetTotal()+m_OptShiftTime.GetTotal()+m_ConnectionTime.GetTotal();
	- std::cout << "Proposal time probes (toal%/mean)" << std::endl;
	- std::cout << "Birth: " << 100m_BirthTime.GetTotal()/sum << "/" << m_BirthTime.GetMean()1000 << std::endl;
	- std::cout << "Death: " << 100m_DeathTime.GetTotal()/sum << "/" << m_DeathTime.GetMean()1000 << std::endl;
	- std::cout << "Shift: " << 100m_ShiftTime.GetTotal()/sum << "/" << m_ShiftTime.GetMean()1000 << std::endl;
	- std::cout << "Optimal shift: " << 100m_OptShiftTime.GetTotal()/sum << " - " << m_OptShiftTime.GetMean()1000 << std::endl;
	- std::cout << "Connection: " << 100m_ConnectionTime.GetTotal()/sum << "/" << m_ConnectionTime.GetMean()1000 << std::endl;
	-}
	-
	-// update temperature of simulated annealing process
	-void MetropolisHastingsSampler::SetTemperature(float val)
	-{
	- m_InTemp = val;
	- m_Density = exp(-m_ChempotParticle/m_InTemp);
	-}
	-
	-// add small random number drawn from gaussian to each vector element
	-void MetropolisHastingsSampler::DistortVector(float sigma, vnl_vector_fixed<float, 3>& vec)
	-{
	- vec[0] += m_RandGen->GetNormalVariate(0.0, sigma);
	- vec[1] += m_RandGen->GetNormalVariate(0.0, sigma);
	- vec[2] += m_RandGen->GetNormalVariate(0.0, sigma);
	-}
	-
	-// generate normalized random vector
	-vnl_vector_fixed<float, 3> MetropolisHastingsSampler::GetRandomDirection()
	-{
	- vnl_vector_fixed<float, 3> vec;
	- vec[0] = m_RandGen->GetNormalVariate();
	- vec[1] = m_RandGen->GetNormalVariate();
	- vec[2] = m_RandGen->GetNormalVariate();
	- vec.normalize();
	- return vec;
	-}
	-
	-// generate actual proposal (birth, death, shift and connection of particle)
	-void MetropolisHastingsSampler::MakeProposal()
	-{
	- float randnum = m_RandGen->GetVariate();
	-
	- // Birth Proposal
	- if (randnum < m_BirthProb)
	- {
	- m_BirthTime.Start();
	- vnl_vector_fixed<float, 3> R;
	- m_EnergyComputer->DrawRandomPosition(R);
	- vnl_vector_fixed<float, 3> N = GetRandomDirection();
	- Particle prop;
	- prop.GetPos() = R;
	- prop.GetDir() = N;
	-
	- float prob = m_Density * m_DeathProb /((m_BirthProb)*(m_ParticleGrid->m_NumParticles+1));
	-
	- float ex_energy = m_EnergyComputer->ComputeExternalEnergy(R,N,nullptr);
	- float in_energy = m_EnergyComputer->ComputeInternalEnergy(&prop);
	- prob *= exp((in_energy/m_InTemp+ex_energy/m_ExTemp)) ;
	-
	- if (prob > 1 \|\| m_RandGen->GetVariate() < prob)
	- {
	- Particle *p = m_ParticleGrid->NewParticle(R);
	- if (p!=nullptr)
	- {
	- p->GetPos() = R;
	- p->GetDir() = N;
	- m_AcceptedProposals++;
	- }
	- }
	- m_BirthTime.Stop();
	- }
	- // Death Proposal
	- else if (randnum < m_BirthProb+m_DeathProb)
	- {
	- m_DeathTime.Start();
	- if (m_ParticleGrid->m_NumParticles > 0)
	- {
	- int pnum = m_RandGen->GetIntegerVariate()%m_ParticleGrid->m_NumParticles;
	- Particle *dp = m_ParticleGrid->GetParticle(pnum);
	- if (dp->pID == -1 && dp->mID == -1)
	- {
	- float ex_energy = m_EnergyComputer->ComputeExternalEnergy(dp->GetPos(),dp->GetDir(),dp);
	- float in_energy = m_EnergyComputer->ComputeInternalEnergy(dp);
	-
	- float prob = m_ParticleGrid->m_NumParticles * (m_BirthProb) /(m_Densitym_DeathProb); //SpatProb(dp->R);
	- prob *= exp(-(in_energy/m_InTemp+ex_energy/m_ExTemp)) ;
	- if (prob > 1 \|\| m_RandGen->GetVariate() < prob)
	- {
	- m_ParticleGrid->RemoveParticle(pnum);
	- m_AcceptedProposals++;
	- }
	- }
	- }
	- m_DeathTime.Stop();
	- }
	- // Shift Proposal
	- else if (randnum < m_BirthProb+m_DeathProb+m_ShiftProb)
	- {
	- if (m_ParticleGrid->m_NumParticles > 0)
	- {
	- m_ShiftTime.Start();
	- int pnum = m_RandGen->GetIntegerVariate()%m_ParticleGrid->m_NumParticles;
	- Particle *p = m_ParticleGrid->GetParticle(pnum);
	- Particle prop_p = *p;
	-
	- DistortVector(m_Sigma, prop_p.GetPos());
	- DistortVector(m_Sigma/(2*m_ParticleLength), prop_p.GetDir());
	- prop_p.GetDir().normalize();
	-
	-
	- float ex_energy = m_EnergyComputer->ComputeExternalEnergy(prop_p.GetPos(),prop_p.GetDir(),p)
	- - m_EnergyComputer->ComputeExternalEnergy(p->GetPos(),p->GetDir(),p);
	- float in_energy = m_EnergyComputer->ComputeInternalEnergy(&prop_p) - m_EnergyComputer->ComputeInternalEnergy(p);
	-
	- float prob = exp(ex_energy/m_ExTemp+in_energy/m_InTemp);
	- if (m_RandGen->GetVariate() < prob)
	- {
	- vnl_vector_fixed<float, 3> Rtmp = p->GetPos();
	- vnl_vector_fixed<float, 3> Ntmp = p->GetDir();
	- p->GetPos() = prop_p.GetPos();
	- p->GetDir() = prop_p.GetDir();
	- if (!m_ParticleGrid->TryUpdateGrid(pnum))
	- {
	- p->GetPos() = Rtmp;
	- p->GetDir() = Ntmp;
	- }
	- m_AcceptedProposals++;
	- }
	- m_ShiftTime.Stop();
	- }
	- }
	- // Optimal Shift Proposal
	- else if (randnum < m_BirthProb+m_DeathProb+m_ShiftProb+m_OptShiftProb)
	- {
	- if (m_ParticleGrid->m_NumParticles > 0)
	- {
	- m_OptShiftTime.Start();
	- int pnum = m_RandGen->GetIntegerVariate()%m_ParticleGrid->m_NumParticles;
	- Particle *p = m_ParticleGrid->GetParticle(pnum);
	-
	- bool no_proposal = false;
	- Particle prop_p = *p;
	- if (p->pID != -1 && p->mID != -1)
	- {
	- Particle *plus = m_ParticleGrid->GetParticle(p->pID);
	- int ep_plus = (plus->pID == p->ID)? 1 : -1;
	- Particle *minus = m_ParticleGrid->GetParticle(p->mID);
	- int ep_minus = (minus->pID == p->ID)? 1 : -1;
	- prop_p.GetPos() = (plus->GetPos() + plus->GetDir() * (m_ParticleLength * ep_plus) + minus->GetPos() + minus->GetDir() * (m_ParticleLength * ep_minus));
	- prop_p.GetPos() *= 0.5;
	- prop_p.GetDir() = plus->GetPos() - minus->GetPos();
	- prop_p.GetDir().normalize();
	- }
	- else if (p->pID != -1)
	- {
	- Particle *plus = m_ParticleGrid->GetParticle(p->pID);
	- int ep_plus = (plus->pID == p->ID)? 1 : -1;
	- prop_p.GetPos() = plus->GetPos() + plus->GetDir() * (m_ParticleLength * ep_plus * 2);
	- prop_p.GetDir() = plus->GetDir();
	- }
	- else if (p->mID != -1)
	- {
	- Particle *minus = m_ParticleGrid->GetParticle(p->mID);
	- int ep_minus = (minus->pID == p->ID)? 1 : -1;
	- prop_p.GetPos() = minus->GetPos() + minus->GetDir() * (m_ParticleLength * ep_minus * 2);
	- prop_p.GetDir() = minus->GetDir();
	- }
	- else
	- no_proposal = true;
	-
	- if (!no_proposal)
	- {
	- float cos = dot_product(prop_p.GetDir(), p->GetDir());
	- float p_rev = exp(-((prop_p.GetPos()-p->GetPos()).squared_magnitude() + (1-coscos))m_Gamma)/m_Z;
	-
	- float ex_energy = m_EnergyComputer->ComputeExternalEnergy(prop_p.GetPos(),prop_p.GetDir(),p)
	- - m_EnergyComputer->ComputeExternalEnergy(p->GetPos(),p->GetDir(),p);
	- float in_energy = m_EnergyComputer->ComputeInternalEnergy(&prop_p) - m_EnergyComputer->ComputeInternalEnergy(p);
	-
	- float prob = exp(ex_energy/m_ExTemp+in_energy/m_InTemp)m_ShiftProbp_rev/(m_OptShiftProb+m_ShiftProb*p_rev);
	-
	- if (m_RandGen->GetVariate() < prob)
	- {
	- vnl_vector_fixed<float, 3> Rtmp = p->GetPos();
	- vnl_vector_fixed<float, 3> Ntmp = p->GetDir();
	- p->GetPos() = prop_p.GetPos();
	- p->GetDir() = prop_p.GetDir();
	- if (!m_ParticleGrid->TryUpdateGrid(pnum))
	- {
	- p->GetPos() = Rtmp;
	- p->GetDir() = Ntmp;
	- }
	- m_AcceptedProposals++;
	- }
	- }
	- m_OptShiftTime.Stop();
	- }
	- }
	- // Connection Proposal
	- else
	- {
	- if (m_ParticleGrid->m_NumParticles > 0)
	- {
	- m_ConnectionTime.Start();
	- int pnum = m_RandGen->GetIntegerVariate()%m_ParticleGrid->m_NumParticles;
	- Particle *p = m_ParticleGrid->GetParticle(pnum);
	-
	- EndPoint P;
	- P.p = p;
	- P.ep = (m_RandGen->GetVariate() > 0.5)? 1 : -1; // direction of the new tract
	-
	- RemoveAndSaveTrack(P); // remove old tract and save it for later
	- if (m_BackupTrack.m_Probability != 0)
	- {
	- MakeTrackProposal(P); // propose new tract starting from P
	-
	- float prob = (m_ProposalTrack.m_Energy-m_BackupTrack.m_Energy)/m_InTemp ;
	-
	- prob = exp(prob)(m_BackupTrack.m_Probability pow(m_DelProb,m_ProposalTrack.m_Length))
	- /(m_ProposalTrack.m_Probability * pow(m_DelProb,m_BackupTrack.m_Length));
	- if (m_RandGen->GetVariate() < prob)
	- {
	- ImplementTrack(m_ProposalTrack); // accept proposed tract
	- m_AcceptedProposals++;
	- }
	- else
	- {
	- ImplementTrack(m_BackupTrack); // reject proposed tract and restore old one
	- }
	- }
	- else
	- ImplementTrack(m_BackupTrack);
	- m_ConnectionTime.Stop();
	- }
	- }
	-}
	-
	-// establish connections between particles stored in input Track
	-void MetropolisHastingsSampler::ImplementTrack(Track &T)
	-{
	- for (int k = 1; k < T.m_Length;k++)
	- m_ParticleGrid->CreateConnection(T.track[k-1].p,T.track[k-1].ep,T.track[k].p,-T.track[k].ep);
	-}
	-
	-// remove pending track from random particle, save it in m_BackupTrack and calculate its probability
	-void MetropolisHastingsSampler::RemoveAndSaveTrack(EndPoint P)
	-{
	- EndPoint Current = P;
	- int cnt = 0;
	- float energy = 0;
	- float AccumProb = 1.0;
	- m_BackupTrack.track[cnt] = Current;
	- EndPoint Next;
	-
	- for (;;)
	- {
	- Next.p = nullptr;
	- if (Current.ep == 1)
	- {
	- if (Current.p->pID != -1)
	- {
	- Next.p = m_ParticleGrid->GetParticle(Current.p->pID);
	- Current.p->pID = -1;
	- m_ParticleGrid->m_NumConnections--;
	- }
	- }
	- else if (Current.ep == -1)
	- {
	- if (Current.p->mID != -1)
	- {
	- Next.p = m_ParticleGrid->GetParticle(Current.p->mID);
	- Current.p->mID = -1;
	- m_ParticleGrid->m_NumConnections--;
	- }
	- }
	- else
	- { fprintf(stderr,"MetropolisHastingsSampler_randshift: Connection inconsistent 3\n"); break; }
	-
	- if (Next.p == nullptr) // no successor
	- {
	- Next.ep = 0; // mark as empty successor
	- break;
	- }
	- else
	- {
	- if (Next.p->pID == Current.p->ID)
	- {
	- Next.p->pID = -1;
	- Next.ep = 1;
	- }
	- else if (Next.p->mID == Current.p->ID)
	- {
	- Next.p->mID = -1;
	- Next.ep = -1;
	- }
	- else
	- { fprintf(stderr,"MetropolisHastingsSampler_randshift: Connection inconsistent 4\n"); break; }
	- }
	-
	- ComputeEndPointProposalDistribution(Current);
	- AccumProb *= (m_SimpSamp.probFor(Next));
	-
	- if (Next.p == nullptr) // no successor -> break
	- break;
	-
	- energy += m_EnergyComputer->ComputeInternalEnergyConnection(Current.p,Current.ep,Next.p,Next.ep);
	-
	- Current = Next;
	- Current.ep *= -1;
	- cnt++;
	- m_BackupTrack.track[cnt] = Current;
	-
	- if (m_RandGen->GetVariate() > m_DelProb)
	- break;
	- }
	- m_BackupTrack.m_Energy = energy;
	- m_BackupTrack.m_Probability = AccumProb;
	- m_BackupTrack.m_Length = cnt+1;
	-}
	-
	-// generate new track using kind of a local tracking starting from P in the given direction, store it in m_ProposalTrack and calculate its probability
	-void MetropolisHastingsSampler::MakeTrackProposal(EndPoint P)
	-{
	- EndPoint Current = P;
	- int cnt = 0;
	- float energy = 0;
	- float AccumProb = 1.0;
	- m_ProposalTrack.track[cnt++] = Current;
	- Current.p->label = 1;
	-
	- for (;;)
	- {
	- // next candidate is already connected
	- if ((Current.ep == 1 && Current.p->pID != -1) \|\| (Current.ep == -1 && Current.p->mID != -1))
	- break;
	-
	- // track too long
	-// if (cnt > 250)
	-// break;
	-
	- ComputeEndPointProposalDistribution(Current);
	-
	- int k = m_SimpSamp.draw(m_RandGen->GetVariate());
	-
	- // stop tracking proposed
	- if (k==0)
	- break;
	-
	- EndPoint Next = m_SimpSamp.objs[k];
	- float probability = m_SimpSamp.probFor(k);
	-
	- // accumulate energy and proposal distribution
	- energy += m_EnergyComputer->ComputeInternalEnergyConnection(Current.p,Current.ep,Next.p,Next.ep);
	- AccumProb *= probability;
	-
	- // track to next endpoint
	- Current = Next;
	- Current.ep *= -1;
	-
	- Current.p->label = 1; // put label to avoid loops
	- m_ProposalTrack.track[cnt++] = Current;
	- }
	-
	- m_ProposalTrack.m_Energy = energy;
	- m_ProposalTrack.m_Probability = AccumProb;
	- m_ProposalTrack.m_Length = cnt;
	-
	- // clear labels
	- for (int j = 0; j < m_ProposalTrack.m_Length;j++)
	- m_ProposalTrack.track[j].p->label = 0;
	-}
	-
	-// get neigbouring particles of P and calculate the according connection probabilities
	-void MetropolisHastingsSampler::ComputeEndPointProposalDistribution(EndPoint P)
	-{
	- Particle *p = P.p;
	- int ep = P.ep;
	-
	- float dist,dot;
	- vnl_vector_fixed<float, 3> R = p->GetPos() + (p->GetDir() * (ep*m_ParticleLength) );
	- m_ParticleGrid->ComputeNeighbors(R);
	- m_SimpSamp.clear();
	-
	- m_SimpSamp.add(m_StopProb,EndPoint(nullptr,0));
	-
	- for (;;)
	- {
	- Particle *p2 = m_ParticleGrid->GetNextNeighbor();
	- if (p2 == nullptr) break;
	- if (p!=p2 && p2->label == 0)
	- {
	- if (p2->mID == -1)
	- {
	- dist = (p2->GetPos() - p2->GetDir() * m_ParticleLength - R).squared_magnitude();
	- if (dist < m_DistanceThreshold)
	- {
	- dot = dot_product(p2->GetDir(),p->GetDir()) * ep;
	- if (dot > m_CurvatureThreshold)
	- {
	- float en = m_EnergyComputer->ComputeInternalEnergyConnection(p,ep,p2,-1);
	- m_SimpSamp.add(exp(en/m_TractProb),EndPoint(p2,-1));
	- }
	- }
	- }
	- if (p2->pID == -1)
	- {
	- dist = (p2->GetPos() + p2->GetDir() * m_ParticleLength - R).squared_magnitude();
	- if (dist < m_DistanceThreshold)
	- {
	- dot = dot_product(p2->GetDir(),p->GetDir()) * (-ep);
	- if (dot > m_CurvatureThreshold)
	- {
	- float en = m_EnergyComputer->ComputeInternalEnergyConnection(p,ep,p2,+1);
	- m_SimpSamp.add(exp(en/m_TractProb),EndPoint(p2,+1));
	- }
	- }
	- }
	- }
	- }
	-}
	-
	-// return number of accepted proposals
	-int MetropolisHastingsSampler::GetNumAcceptedProposals()
	-{
	- return m_AcceptedProposals;
	-}
	-
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkMetropolisHastingsSampler.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkMetropolisHastingsSampler.h
	deleted file mode 100644
	index ca1cad3488..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkMetropolisHastingsSampler.h
	+++ /dev/null
	@@ -1,110 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _SAMPLER
	-#define _SAMPLER
	-
	-// MITK
	-#include <MitkFiberTrackingExports.h>
	-#include <mitkParticleGrid.h>
	-#include <mitkEnergyComputer.h>
	-#include <mitkSimpSamp.h>
	-
	-// ITK
	-#include <itkImage.h>
	-#include <itkTimeProbe.h>
	-#include <itkMersenneTwisterRandomVariateGenerator.h>
	-
	-// MISC
	-#include <fstream>
	-
	-namespace mitk
	-{
	-
	-/**
	-* \brief Generates ne proposals of particle configurations. */
	-
	-class MITKFIBERTRACKING_EXPORT MetropolisHastingsSampler
	-{
	-public:
	-
	- typedef itk::Image< float, 3 > ItkFloatImageType;
	- typedef itk::Statistics::MersenneTwisterRandomVariateGenerator ItkRandGenType;
	-
	- MetropolisHastingsSampler(ParticleGrid* grid, EnergyComputer* enComp, ItkRandGenType* randGen, float curvThres);
	- void SetTemperature(float val);
	-
	- void MakeProposal(); ///< make proposal for birth/death/shift/connection of particles
	- int GetNumAcceptedProposals();
	- void SetProbabilities(float birth, float death, float shift, float optShift, float connect); ///< update the probabilities of the single proposals
	- void PrintProposalTimes(); ///< print the state of the proposal time probes
	-
	-protected:
	-
	- /** connection proposal related methods */
	- void ImplementTrack(Track& T);
	- void RemoveAndSaveTrack(EndPoint P);
	- void MakeTrackProposal(EndPoint P);
	- void ComputeEndPointProposalDistribution(EndPoint P);
	-
	- /** generate random vectors */
	- void DistortVector(float sigma, vnl_vector_fixed<float, 3>& vec);
	- vnl_vector_fixed<float, 3> GetRandomDirection();
	-
	- ItkRandGenType* m_RandGen; ///< random generator
	- Track m_ProposalTrack; ///< stores proposal track
	- Track m_BackupTrack; ///< stores track removed for new proposal traCK
	- SimpSamp m_SimpSamp; ///< neighbouring particles and their probabilities for the local tracking
	-
	- float m_InTemp; ///< simulated annealing temperature
	- float m_ExTemp; ///< simulated annealing temperature
	- float m_Density;
	-
	- float m_BirthProb; ///< probability for particle birth
	- float m_DeathProb; ///< probability for particle death
	- float m_ShiftProb; ///< probability for particle shift
	- float m_OptShiftProb; ///< probability for optimal particle shift
	- float m_ConnectionProb; ///< probability for particle connection proposal
	-
	- float m_Sigma;
	- float m_Gamma;
	- float m_Z;
	-
	- float m_DistanceThreshold; ///< threshold for maximum distance between connected particles
	- float m_CurvatureThreshold; ///< threshold for maximum angle between connected particles
	- float m_TractProb;
	- float m_StopProb;
	- float m_DelProb;
	- float m_ParticleLength;
	- float m_ChempotParticle;
	-
	- ParticleGrid* m_ParticleGrid; ///< storest all particles
	- EnergyComputer* m_EnergyComputer; ///< computes internal and external energy of particles
	- unsigned int m_AcceptedProposals; ///< counts accepted proposals
	-
	- /** Time probes for the single proposals */
	- itk::TimeProbe m_BirthTime;
	- itk::TimeProbe m_DeathTime;
	- itk::TimeProbe m_ShiftTime;
	- itk::TimeProbe m_OptShiftTime;
	- itk::TimeProbe m_ConnectionTime;
	-};
	-
	-}
	-
	-#endif
	-
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkParticle.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkParticle.h
	deleted file mode 100644
	index 31720194c3..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkParticle.h
	+++ /dev/null
	@@ -1,90 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _PARTICLE
	-#define _PARTICLE
	-
	-#include <MitkFiberTrackingExports.h>
	-#include <vnl/vnl_vector_fixed.h>
	-
	-
	-namespace mitk
	-{
	-
	-/**
	-* \brief A particle is the basic element of the Gibbs fiber tractography method. */
	-
	-class MITKFIBERTRACKING_EXPORT Particle
	-{
	-public:
	-
	- Particle()
	- {
	- label = 0;
	- pID = -1;
	- mID = -1;
	- }
	-
	- ~Particle()
	- {
	- }
	-
	- int gridindex; // index in the grid where it is living
	- int ID; // particle ID
	- int pID; // successor ID
	- int mID; // predecessor ID
	- unsigned char label; // label used in the fiber building process
	-
	- vnl_vector_fixed<float, 3>& GetPos()
	- {
	- return pos;
	- }
	-
	- vnl_vector_fixed<float, 3>& GetDir()
	- {
	- return dir;
	- }
	-
	-private:
	- // this pragma ignores the following warning:
	- // warning C4251: 'mitk::Particle::pos' : class 'ATL::CStringT' needs to have dll-interface to be used by clients of class 'Particle'
	- vnl_vector_fixed<float, 3> pos; // particle position (world coordinates. corner based voxels. not accounted for image rotation.
	- vnl_vector_fixed<float, 3> dir; // normalized direction vector
	-};
	-
	-class MITKFIBERTRACKING_EXPORT EndPoint
	-{
	-public:
	- EndPoint()
	- {}
	-
	- EndPoint(Particle *p,int ep)
	- {
	- this->p = p;
	- this->ep = ep;
	- }
	- Particle *p;
	- int ep;
	-
	- inline bool operator==(EndPoint P)
	- {
	- return (P.p == p) && (P.ep == ep);
	- }
	-};
	-
	-}
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkParticleGrid.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkParticleGrid.cpp
	deleted file mode 100644
	index 2242b7a372..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkParticleGrid.cpp
	+++ /dev/null
	@@ -1,420 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#include "mitkParticleGrid.h"
	-#include <cstdlib>
	-#include <cstdio>
	-
	-using namespace mitk;
	-
	-ParticleGrid::ParticleGrid(ItkFloatImageType* image, float particleLength, int cellCapacity)
	-{
	- // initialize counters
	- m_NumParticles = 0;
	- m_NumConnections = 0;
	- m_NumCellOverflows = 0;
	- m_ParticleLength = particleLength;
	-
	- // define isotropic grid from voxel spacing and particle length
	- float cellSize = 2*m_ParticleLength;
	- m_GridSize[0] = image->GetLargestPossibleRegion().GetSize()[0]*image->GetSpacing()[0]/cellSize +1;
	- m_GridSize[1] = image->GetLargestPossibleRegion().GetSize()[1]*image->GetSpacing()[1]/cellSize +1;
	- m_GridSize[2] = image->GetLargestPossibleRegion().GetSize()[2]*image->GetSpacing()[2]/cellSize +1;
	- m_GridScale[0] = 1/cellSize;
	- m_GridScale[1] = 1/cellSize;
	- m_GridScale[2] = 1/cellSize;
	-
	- m_CellCapacity = cellCapacity; // maximum number of particles per grid cell
	- m_ContainerCapacity = 100000; // initial particle container capacity
	- unsigned long numCells = m_GridSize[0]m_GridSize[1]m_GridSize[2]; // number of grid cells
	- unsigned long gridSize = numCells*m_CellCapacity;
	- if ( (unsigned long)itk::NumericTraits<int>::max()<gridSize )
	- throw std::bad_alloc();
	-
	- m_Particles.resize(m_ContainerCapacity); // allocate and initialize particles
	- m_Grid.resize(gridSize, nullptr); // allocate and initialize particle grid
	- m_OccupationCount.resize(numCells, 0); // allocate and initialize occupation counter array
	- m_NeighbourTracker.cellidx.resize(8, 0); // allocate and initialize neighbour tracker
	- m_NeighbourTracker.cellidx_c.resize(8, 0);
	-
	- for (int i = 0;i < m_ContainerCapacity;i++) // initialize particle IDs
	- m_Particles[i].ID = i;
	-
	- std::cout << "ParticleGrid: allocated " << (sizeof(Particle)m_ContainerCapacity + sizeof(Particle)m_GridSize[0]m_GridSize[1]*m_GridSize[2])/1048576 << "mb for " << m_ContainerCapacity/1000 << "k particles." << std::endl;
	-}
	-
	-ParticleGrid::~ParticleGrid()
	-{
	-
	-}
	-
	-// remove all particles
	-void ParticleGrid::ResetGrid()
	-{
	- // initialize counters
	- m_NumParticles = 0;
	- m_NumConnections = 0;
	- m_NumCellOverflows = 0;
	- m_Particles.clear();
	- m_Grid.clear();
	- m_OccupationCount.clear();
	- m_NeighbourTracker.cellidx.clear();
	- m_NeighbourTracker.cellidx_c.clear();
	-
	- int numCells = m_GridSize[0]m_GridSize[1]m_GridSize[2]; // number of grid cells
	-
	- m_Particles.resize(m_ContainerCapacity); // allocate and initialize particles
	- m_Grid.resize(numCells*m_CellCapacity, nullptr); // allocate and initialize particle grid
	- m_OccupationCount.resize(numCells, 0); // allocate and initialize occupation counter array
	- m_NeighbourTracker.cellidx.resize(8, 0); // allocate and initialize neighbour tracker
	- m_NeighbourTracker.cellidx_c.resize(8, 0);
	-
	- for (int i = 0;i < m_ContainerCapacity;i++) // initialize particle IDs
	- m_Particles[i].ID = i;
	-}
	-
	-bool ParticleGrid::ReallocateGrid()
	-{
	- int new_capacity = m_ContainerCapacity + 100000; // increase container capacity by 100k particles
	- try
	- {
	- m_Particles.resize(new_capacity); // reallocate particles
	-
	- for (int i = 0; i<m_ContainerCapacity; i++) // update particle addresses (changed during reallocation)
	- m_Grid[m_Particles[i].gridindex] = &m_Particles[i];
	-
	- for (int i = m_ContainerCapacity; i < new_capacity; i++) // initialize IDs of ne particles
	- m_Particles[i].ID = i;
	-
	- m_ContainerCapacity = new_capacity; // update member variable
	- //std::cout << "ParticleGrid: allocated " << (sizeof(Particle)m_ContainerCapacity + sizeof(Particle)m_GridSize[0]m_GridSize[1]*m_GridSize[2])/1048576 << "mb for " << m_ContainerCapacity/1000 << "k particles." << std::endl;
	- }
	- catch(...)
	- {
	- std::cout << "ParticleGrid: allocation of " << (sizeof(Particle)new_capacity + sizeof(Particle)m_GridSize[0]m_GridSize[1]*m_GridSize[2])/1048576 << "mb for " << new_capacity/1000 << "k particles failed!" << std::endl;
	- return false;
	- }
	- return true;
	-}
	-
	-Particle* ParticleGrid::GetParticle(int ID)
	-{
	- if (ID!=-1)
	- return &m_Particles[ID];
	- return nullptr;
	-}
	-
	-
	-Particle* ParticleGrid::NewParticle(vnl_vector_fixed<float, 3> R)
	-{
	- if (m_NumParticles >= m_ContainerCapacity)
	- {
	- if (!ReallocateGrid())
	- return nullptr;
	- }
	-
	- int xint = int(R[0]*m_GridScale[0]);
	- if (xint < 0)
	- return nullptr;
	- if (xint >= m_GridSize[0])
	- return nullptr;
	- int yint = int(R[1]*m_GridScale[1]);
	- if (yint < 0)
	- return nullptr;
	- if (yint >= m_GridSize[1])
	- return nullptr;
	- int zint = int(R[2]*m_GridScale[2]);
	- if (zint < 0)
	- return nullptr;
	- if (zint >= m_GridSize[2])
	- return nullptr;
	-
	- int idx = xint + m_GridSize[0](yint + m_GridSize[1]zint);
	- if (m_OccupationCount[idx] < m_CellCapacity)
	- {
	- Particle *p = &(m_Particles[m_NumParticles]);
	- p->GetPos() = R;
	- p->mID = -1;
	- p->pID = -1;
	- m_NumParticles++;
	- p->gridindex = m_CellCapacity*idx + m_OccupationCount[idx];
	- m_Grid[p->gridindex] = p;
	- m_OccupationCount[idx]++;
	- return p;
	- }
	- else
	- {
	- m_NumCellOverflows++;
	- return nullptr;
	- }
	-}
	-
	-bool ParticleGrid::TryUpdateGrid(int k)
	-{
	- Particle* p = &(m_Particles[k]);
	-
	- int xint = int(p->GetPos()[0]*m_GridScale[0]);
	- if (xint < 0)
	- return false;
	- if (xint >= m_GridSize[0])
	- return false;
	- int yint = int(p->GetPos()[1]*m_GridScale[1]);
	- if (yint < 0)
	- return false;
	- if (yint >= m_GridSize[1])
	- return false;
	- int zint = int(p->GetPos()[2]*m_GridScale[2]);
	- if (zint < 0)
	- return false;
	- if (zint >= m_GridSize[2])
	- return false;
	-
	- int idx = xint + m_GridSize[0](yint+ zintm_GridSize[1]);
	- int cellidx = p->gridindex/m_CellCapacity;
	- if (idx != cellidx) // cell has changed
	- {
	-
	- if (m_OccupationCount[idx] < m_CellCapacity)
	- {
	- // remove from old position in grid;
	- int grdindex = p->gridindex;
	- m_Grid[grdindex] = m_Grid[cellidx*m_CellCapacity + m_OccupationCount[cellidx]-1];
	- m_Grid[grdindex]->gridindex = grdindex;
	- m_OccupationCount[cellidx]--;
	-
	- // insert at new position in grid
	- p->gridindex = idx*m_CellCapacity + m_OccupationCount[idx];
	- m_Grid[p->gridindex] = p;
	- m_OccupationCount[idx]++;
	- return true;
	- }
	- else
	- {
	- m_NumCellOverflows++;
	- return false;
	- }
	- }
	- return true;
	-}
	-
	-void ParticleGrid::RemoveParticle(int k)
	-{
	- Particle* p = &(m_Particles[k]);
	- int gridIndex = p->gridindex;
	- int cellIdx = gridIndex/m_CellCapacity;
	- int idx = gridIndex%m_CellCapacity;
	-
	- // remove pending connections
	- if (p->mID != -1)
	- DestroyConnection(p,-1);
	- if (p->pID != -1)
	- DestroyConnection(p,+1);
	-
	- // remove from grid
	- if (idx < m_OccupationCount[cellIdx]-1)
	- {
	- m_Grid[gridIndex] = m_Grid[cellIdx*m_CellCapacity+m_OccupationCount[cellIdx]-1];
	- m_Grid[cellIdx*m_CellCapacity+m_OccupationCount[cellIdx]-1] = nullptr;
	- m_Grid[gridIndex]->gridindex = gridIndex;
	- }
	- m_OccupationCount[cellIdx]--;
	-
	- // remove from container
	- if (k < m_NumParticles-1)
	- {
	- Particle* last = &m_Particles[m_NumParticles-1]; // last particle
	-
	- // update connections of last particle because its index is changing
	- if (last->mID!=-1)
	- {
	- if ( m_Particles[last->mID].mID == m_NumParticles-1 )
	- m_Particles[last->mID].mID = k;
	- else if ( m_Particles[last->mID].pID == m_NumParticles-1 )
	- m_Particles[last->mID].pID = k;
	- }
	- if (last->pID!=-1)
	- {
	- if ( m_Particles[last->pID].mID == m_NumParticles-1 )
	- m_Particles[last->pID].mID = k;
	- else if ( m_Particles[last->pID].pID == m_NumParticles-1 )
	- m_Particles[last->pID].pID = k;
	- }
	-
	- m_Particles[k] = m_Particles[m_NumParticles-1]; // move very last particle to empty slot
	- m_Particles[m_NumParticles-1].ID = m_NumParticles-1; // update ID of removed particle to match the index
	- m_Particles[k].ID = k; // update ID of moved particle
	- m_Grid[m_Particles[k].gridindex] = &m_Particles[k]; // update address of moved particle
	- }
	- m_NumParticles--;
	-}
	-
	-void ParticleGrid::ComputeNeighbors(vnl_vector_fixed<float, 3> &R)
	-{
	- float xfrac = R[0]*m_GridScale[0];
	- float yfrac = R[1]*m_GridScale[1];
	- float zfrac = R[2]*m_GridScale[2];
	- int xint = int(xfrac);
	- int yint = int(yfrac);
	- int zint = int(zfrac);
	-
	- int dx = -1;
	- if (xfrac-xint > 0.5) dx = 1;
	- if (xint <= 0) { xint = 0; dx = 1; }
	- if (xint >= m_GridSize[0]-1) { xint = m_GridSize[0]-1; dx = -1; }
	- if (m_GridSize[0] <= 1) { dx = 0; } // Necessary with 2d images (bug 15416)
	-
	- int dy = -1;
	- if (yfrac-yint > 0.5) dy = 1;
	- if (yint <= 0) {yint = 0; dy = 1; }
	- if (yint >= m_GridSize[1]-1) {yint = m_GridSize[1]-1; dy = -1;}
	- if (m_GridSize[1] <= 1) { dy = 0; } // Necessary with 2d images (bug 15416)
	-
	- int dz = -1;
	- if (zfrac-zint > 0.5) dz = 1;
	- if (zint <= 0) {zint = 0; dz = 1; }
	- if (zint >= m_GridSize[2]-1) {zint = m_GridSize[2]-1; dz = -1;}
	- if (m_GridSize[2] <= 1) { dz = 0; } // Necessary with 2d images (bug 15416)
	-
	-
	- m_NeighbourTracker.cellidx[0] = xint + m_GridSize[0](yint+zintm_GridSize[1]);
	- m_NeighbourTracker.cellidx[1] = m_NeighbourTracker.cellidx[0] + dx;
	- m_NeighbourTracker.cellidx[2] = m_NeighbourTracker.cellidx[1] + dy*m_GridSize[0];
	- m_NeighbourTracker.cellidx[3] = m_NeighbourTracker.cellidx[2] - dx;
	- m_NeighbourTracker.cellidx[4] = m_NeighbourTracker.cellidx[0] + dzm_GridSize[0]m_GridSize[1];
	- m_NeighbourTracker.cellidx[5] = m_NeighbourTracker.cellidx[4] + dx;
	- m_NeighbourTracker.cellidx[6] = m_NeighbourTracker.cellidx[5] + dy*m_GridSize[0];
	- m_NeighbourTracker.cellidx[7] = m_NeighbourTracker.cellidx[6] - dx;
	-
	-
	- m_NeighbourTracker.cellidx_c[0] = m_CellCapacity*m_NeighbourTracker.cellidx[0];
	- m_NeighbourTracker.cellidx_c[1] = m_CellCapacity*m_NeighbourTracker.cellidx[1];
	- m_NeighbourTracker.cellidx_c[2] = m_CellCapacity*m_NeighbourTracker.cellidx[2];
	- m_NeighbourTracker.cellidx_c[3] = m_CellCapacity*m_NeighbourTracker.cellidx[3];
	- m_NeighbourTracker.cellidx_c[4] = m_CellCapacity*m_NeighbourTracker.cellidx[4];
	- m_NeighbourTracker.cellidx_c[5] = m_CellCapacity*m_NeighbourTracker.cellidx[5];
	- m_NeighbourTracker.cellidx_c[6] = m_CellCapacity*m_NeighbourTracker.cellidx[6];
	- m_NeighbourTracker.cellidx_c[7] = m_CellCapacity*m_NeighbourTracker.cellidx[7];
	-
	- m_NeighbourTracker.cellcnt = 0;
	- m_NeighbourTracker.pcnt = 0;
	-}
	-
	-Particle* ParticleGrid::GetNextNeighbor()
	-{
	- if (m_NeighbourTracker.pcnt < m_OccupationCount[m_NeighbourTracker.cellidx[m_NeighbourTracker.cellcnt]])
	- {
	- return m_Grid[m_NeighbourTracker.cellidx_c[m_NeighbourTracker.cellcnt] + (m_NeighbourTracker.pcnt++)];
	- }
	- else
	- {
	- for(;;)
	- {
	- m_NeighbourTracker.cellcnt++;
	- if (m_NeighbourTracker.cellcnt >= 8)
	- return nullptr;
	- if (m_OccupationCount[m_NeighbourTracker.cellidx[m_NeighbourTracker.cellcnt]] > 0)
	- break;
	- }
	- m_NeighbourTracker.pcnt = 1;
	- return m_Grid[m_NeighbourTracker.cellidx_c[m_NeighbourTracker.cellcnt]];
	- }
	-}
	-
	-void ParticleGrid::CreateConnection(Particle P1,int ep1, Particle P2, int ep2)
	-{
	- if (ep1 == -1)
	- P1->mID = P2->ID;
	- else
	- P1->pID = P2->ID;
	-
	- if (ep2 == -1)
	- P2->mID = P1->ID;
	- else
	- P2->pID = P1->ID;
	-
	- m_NumConnections++;
	-}
	-
	-void ParticleGrid::DestroyConnection(Particle P1,int ep1, Particle P2, int ep2)
	-{
	- if (ep1 == -1)
	- P1->mID = -1;
	- else
	- P1->pID = -1;
	-
	- if (ep2 == -1)
	- P2->mID = -1;
	- else
	- P2->pID = -1;
	- m_NumConnections--;
	-}
	-
	-void ParticleGrid::DestroyConnection(Particle *P1,int ep1)
	-{
	-
	- Particle *P2 = nullptr;
	- if (ep1 == 1)
	- {
	- P2 = &m_Particles[P1->pID];
	- P1->pID = -1;
	- }
	- else
	- {
	- P2 = &m_Particles[P1->mID];
	- P1->mID = -1;
	- }
	-
	- if (P2->mID == P1->ID)
	- P2->mID = -1;
	- else
	- P2->pID = -1;
	-
	- m_NumConnections--;
	-}
	-
	-bool ParticleGrid::CheckConsistency()
	-{
	- for (int i=0; i<m_NumParticles; i++)
	- {
	- Particle* p = &m_Particles[i];
	- if (p->ID != i)
	- {
	- std::cout << "Particle ID error!" << std::endl;
	- return false;
	- }
	-
	- if (p->mID!=-1)
	- {
	- Particle* p2 = &m_Particles[p->mID];
	- if (p2->mID!=p->ID && p2->pID!=p->ID)
	- {
	- std::cout << "Connection inconsistent!" << std::endl;
	- return false;
	- }
	- }
	- if (p->pID!=-1)
	- {
	- Particle* p2 = &m_Particles[p->pID];
	- if (p2->mID!=p->ID && p2->pID!=p->ID)
	- {
	- std::cout << "Connection inconsistent!" << std::endl;
	- return false;
	- }
	- }
	- }
	- return true;
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkParticleGrid.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkParticleGrid.h
	deleted file mode 100644
	index 3a42f3f94c..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkParticleGrid.h
	+++ /dev/null
	@@ -1,124 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _PARTICLEGRID
	-#define _PARTICLEGRID
	-
	-// MITK
	-#include <MitkFiberTrackingExports.h>
	-#include <mitkParticle.h>
	-
	-// ITK
	-#include <itkImage.h>
	-
	-namespace mitk
	-{
	-
	-/**
	-* \brief Contains and manages particles. */
	-
	-class MITKFIBERTRACKING_EXPORT ParticleGrid
	-{
	-
	-public:
	-
	- typedef itk::Image< float, 3 > ItkFloatImageType;
	-
	- int m_NumParticles; // number of particles
	- int m_NumConnections; // number of connections
	- int m_NumCellOverflows; // number of cell overflows
	- float m_ParticleLength;
	-
	- ParticleGrid(ItkFloatImageType* image, float particleLength, int cellCapacity);
	- ~ParticleGrid();
	-
	- Particle* GetParticle(int ID);
	-
	- Particle* NewParticle(vnl_vector_fixed<float, 3> R);
	- bool TryUpdateGrid(int k);
	- void RemoveParticle(int k);
	-
	- void ComputeNeighbors(vnl_vector_fixed<float, 3> &R);
	- Particle* GetNextNeighbor();
	-
	- void CreateConnection(Particle P1,int ep1, Particle P2, int ep2);
	- void DestroyConnection(Particle P1,int ep1, Particle P2, int ep2);
	- void DestroyConnection(Particle *P1,int ep1);
	-
	- bool CheckConsistency();
	- void ResetGrid();
	-
	-protected:
	-
	- bool ReallocateGrid();
	-
	- std::vector< Particle* > m_Grid; // the grid
	- std::vector< Particle > m_Particles; // particle container
	- std::vector< int > m_OccupationCount; // number of particles per grid cell
	-
	- int m_ContainerCapacity; // maximal number of particles
	-
	- vnl_vector_fixed< int, 3 > m_GridSize; // grid dimensions
	- vnl_vector_fixed< float, 3 > m_GridScale; // scaling factor for grid
	-
	- int m_CellCapacity; // particle capacity of single cell in grid
	-
	- struct NeighborTracker // to run over the neighbors
	- {
	- std::vector< int > cellidx;
	- std::vector< int > cellidx_c;
	- int cellcnt;
	- int pcnt;
	- } m_NeighbourTracker;
	-
	-};
	-
	-class MITKFIBERTRACKING_EXPORT Track
	-{
	-public:
	- std::vector< EndPoint > track;
	- float m_Energy;
	- float m_Probability;
	- int m_Length;
	-
	- Track()
	- {
	- track.resize(1000);
	- }
	-
	- ~Track(){}
	-
	- void clear()
	- {
	- m_Length = 0;
	- m_Energy = 0;
	- m_Probability = 1;
	- }
	-
	- bool isequal(Track& t)
	- {
	- for (int i = 0; i < m_Length;i++)
	- {
	- if (track[i].p != t.track[i].p \|\| track[i].ep != t.track[i].ep)
	- return false;
	- }
	- return true;
	- }
	-};
	-
	-}
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkSimpSamp.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkSimpSamp.h
	deleted file mode 100644
	index 5a6ad5119a..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkSimpSamp.h
	+++ /dev/null
	@@ -1,122 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _SIMPSAMP
	-#define _SIMPSAMP
	-
	-#include <MitkFiberTrackingExports.h>
	-#include <mitkParticle.h>
	-#include <cstdlib>
	-
	-namespace mitk
	-{
	-
	-/**
	-* \brief Samples new tract from surrounding fiber segments. */
	-
	-class MITKFIBERTRACKING_EXPORT SimpSamp
	-{
	-
	- float *P;
	- int cnt;
	-
	-public:
	- EndPoint* objs;
	-
	-
	- SimpSamp()
	- {
	- P = (float) malloc(sizeof(float)1000);
	- objs = (EndPoint) malloc(sizeof(EndPoint)1000);
	- }
	- ~SimpSamp()
	- {
	- free(P);
	- free(objs);
	- }
	-
	- inline void clear()
	- {
	- cnt = 1;
	- P[0] = 0;
	- }
	-
	- inline void add(float p, EndPoint obj)
	- {
	- P[cnt] = P[cnt-1] + p;
	- objs[cnt-1] = obj;
	- cnt++;
	- }
	-
	- inline int draw(float prob)
	- {
	- float r = prob*P[cnt-1];
	- int j;
	- int rl = 1;
	- int rh = cnt-1;
	- while(rh != rl)
	- {
	- j = rl + (rh-rl)/2;
	- if (r < P[j])
	- {
	- rh = j;
	- continue;
	- }
	- if (r > P[j])
	- {
	- rl = j+1;
	- continue;
	- }
	- break;
	- }
	- return rh-1;
	- }
	-
	- inline EndPoint drawObj(float prob)
	- {
	- return objs[draw(prob)];
	- }
	-
	- inline bool isempty()
	- {
	- if (cnt == 1)
	- return true;
	- else
	- return false;
	- }
	-
	-
	- float probFor(int idx)
	- {
	- return (P[idx+1]-P[idx])/P[cnt-1];
	- }
	-
	- float probFor(EndPoint& t)
	- {
	- for (int i = 1; i< cnt;i++)
	- {
	- if (t == objs[i-1])
	- return probFor(i-1);
	- }
	- return 0;
	- }
	-};
	-
	-}
	-
	-#endif
	-
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkSphereInterpolator.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkSphereInterpolator.cpp
	deleted file mode 100644
	index 79eee307fc..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkSphereInterpolator.cpp
	+++ /dev/null
	@@ -1,173 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkSphereInterpolator.h"
	-
	-#include <usGetModuleContext.h>
	-#include <usModuleContext.h>
	-#include <usModule.h>
	-#include <usModuleResource.h>
	-#include <usModuleResourceStream.h>
	-
	-#include <mitkOdfImage.h>
	-
	-#include <fstream>
	-#include <exception>
	-
	-static const std::string BaryCoordsFileName = "FiberTrackingLUTBaryCoords.bin";
	-static const std::string IndicesFileName = "FiberTrackingLUTIndices.bin";
	-
	-SphereInterpolator::SphereInterpolator(const std::string& lutPath)
	-{
	- m_ValidState = true;
	- if (lutPath.length()==0)
	- {
	- if (!LoadLookuptables())
	- {
	- m_ValidState = false;
	- return;
	- }
	- }
	- else
	- {
	- if (!LoadLookuptables(lutPath))
	- {
	- m_ValidState = false;
	- return;
	- }
	- }
	-
	- size = 301;
	- sN = (size-1)/2;
	- nverts = ODF_SAMPLING_SIZE;
	- beta = 0.5;
	-
	- inva = (sqrt(1+beta)-sqrt(beta));
	- b = 1/(1-sqrt(1/beta + 1));
	-}
	-
	-SphereInterpolator::~SphereInterpolator()
	-{
	-
	-}
	-
	-bool SphereInterpolator::LoadLookuptables(const std::string& lutPath)
	-{
	- MITK_INFO << "SphereInterpolator: loading lookuptables from custom path: " << lutPath;
	-
	- std::string path = lutPath; path.append(BaryCoordsFileName);
	- std::ifstream BaryCoordsStream;
	- BaryCoordsStream.open(path.c_str(), ios::in \| ios::binary);
	- MITK_INFO << "SphereInterpolator: 1 " << path;
	- if (!BaryCoordsStream.is_open())
	- {
	- MITK_INFO << "SphereInterpolator: could not load FiberTrackingLUTBaryCoords.bin from " << path;
	- return false;
	- }
	-
	- ifstream IndicesStream;
	- path = lutPath; path.append("FiberTrackingLUTIndices.bin");
	- IndicesStream.open(path.c_str(), ios::in \| ios::binary);
	- MITK_INFO << "SphereInterpolator: 1 " << path;
	- if (!IndicesStream.is_open())
	- {
	- MITK_INFO << "SphereInterpolator: could not load FiberTrackingLUTIndices.bin from " << path;
	- return false;
	- }
	-
	- if (LoadLookuptables(BaryCoordsStream, IndicesStream))
	- {
	- MITK_INFO << "SphereInterpolator: first and second lut loaded successfully";
	- return true;
	- }
	-
	- return false;
	-}
	-
	-bool SphereInterpolator::LoadLookuptables()
	-{
	- MITK_INFO << "SphereInterpolator: loading lookuptables";
	-
	- us::Module* module = us::GetModuleContext()->GetModule();
	- us::ModuleResource BaryCoordsRes = module->GetResource(BaryCoordsFileName);
	- if (!BaryCoordsRes.IsValid())
	- {
	- MITK_INFO << "Could not retrieve resource " << BaryCoordsFileName;
	- return false;
	- }
	-
	- us::ModuleResource IndicesRes = module->GetResource(IndicesFileName);
	- if (!IndicesRes)
	- {
	- MITK_INFO << "Could not retrieve resource " << IndicesFileName;
	- return false;
	- }
	-
	- us::ModuleResourceStream BaryCoordsStream(BaryCoordsRes, std::ios_base::binary);
	- us::ModuleResourceStream IndicesStream(IndicesRes, std::ios_base::binary);
	- return LoadLookuptables(BaryCoordsStream, IndicesStream);
	-}
	-
	-bool SphereInterpolator::LoadLookuptables(std::istream& BaryCoordsStream, std::istream& IndicesStream)
	-{
	- if (BaryCoordsStream)
	- {
	- try
	- {
	- float tmp;
	- BaryCoordsStream.seekg (0, ios::beg);
	- while (!BaryCoordsStream.eof())
	- {
	- BaryCoordsStream.read((char *)&tmp, sizeof(tmp));
	- barycoords.push_back(tmp);
	- }
	- }
	- catch (const std::exception& e)
	- {
	- MITK_INFO << e.what();
	- }
	- }
	- else
	- {
	- MITK_INFO << "SphereInterpolator: could not load FiberTrackingLUTBaryCoords.bin";
	- return false;
	- }
	-
	- if (IndicesStream)
	- {
	- try
	- {
	- int tmp;
	- IndicesStream.seekg (0, ios::beg);
	- while (!IndicesStream.eof())
	- {
	- IndicesStream.read((char *)&tmp, sizeof(tmp));
	- indices.push_back(tmp);
	- }
	- }
	- catch (const std::exception& e)
	- {
	- MITK_INFO << e.what();
	- }
	- }
	- else
	- {
	- MITK_INFO << "SphereInterpolator: could not load FiberTrackingLUTIndices.bin";
	- return false;
	- }
	-
	- return true;
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkSphereInterpolator.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkSphereInterpolator.h
	deleted file mode 100644
	index b4304c3d1f..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/GibbsTracking/mitkSphereInterpolator.h
	+++ /dev/null
	@@ -1,164 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _SPHEREINTERPOLATOR
	-#define _SPHEREINTERPOLATOR
	-
	-#include <MitkFiberTrackingExports.h>
	-#include <vnl/vnl_vector_fixed.h>
	-#include <vector>
	-
	-/**
	- * \brief Lookuptable based trilinear interpolation of spherically arranged scalar values.
	- */
	-class MITKFIBERTRACKING_EXPORT SphereInterpolator
	-{
	-
	-public:
	-
	- int size; // size of LUT
	- int sN; // (sizeofLUT-1)/2
	- int nverts; // number of data vertices
	- float beta;
	- float inva;
	- float b;
	- bool m_ValidState;
	-
	- std::vector< float > barycoords;
	- std::vector< int > indices;
	- vnl_vector_fixed< int, 3 > idx;
	- vnl_vector_fixed< float, 3 > interpw;
	-
	- SphereInterpolator(const std::string& lutPath);
	-
	- inline bool IsInValidState() const
	- {
	- return m_ValidState;
	- }
	-
	- ~SphereInterpolator();
	-
	- inline void getInterpolation(const vnl_vector_fixed<float, 3>& N)
	- {
	- float nx = N[0];
	- float ny = N[1];
	- float nz = N[2];
	-
	- if (nz > 0.5)
	- {
	- int x = float2int(nx);
	- int y = float2int(ny);
	- int i = 36(x+y*size); // (:,1,x,y)
	- idx[0] = indices[i];
	- idx[1] = indices[i+1];
	- idx[2] = indices[i+2];
	- interpw[0] = barycoords[i];
	- interpw[1] = barycoords[i+1];
	- interpw[2] = barycoords[i+2];
	- return;
	- }
	- if (nz < -0.5)
	- {
	- int x = float2int(nx);
	- int y = float2int(ny);
	- int i = 3(1+6(x+y*size)); // (:,2,x,y)
	- idx[0] = indices[i];
	- idx[1] = indices[i+1];
	- idx[2] = indices[i+2];
	- interpw[0] = barycoords[i];
	- interpw[1] = barycoords[i+1];
	- interpw[2] = barycoords[i+2];
	- return;
	- }
	- if (nx > 0.5)
	- {
	- int z = float2int(nz);
	- int y = float2int(ny);
	- int i = 3(2+6(z+y*size)); // (:,2,x,y)
	- idx[0] = indices[i];
	- idx[1] = indices[i+1];
	- idx[2] = indices[i+2];
	- interpw[0] = barycoords[i];
	- interpw[1] = barycoords[i+1];
	- interpw[2] = barycoords[i+2];
	- return;
	- }
	- if (nx < -0.5)
	- {
	- int z = float2int(nz);
	- int y = float2int(ny);
	- int i = 3(3+6(z+y*size)); // (:,2,x,y)
	- idx[0] = indices[i];
	- idx[1] = indices[i+1];
	- idx[2] = indices[i+2];
	- interpw[0] = barycoords[i];
	- interpw[1] = barycoords[i+1];
	- interpw[2] = barycoords[i+2];
	- return;
	- }
	- if (ny > 0)
	- {
	- int x = float2int(nx);
	- int z = float2int(nz);
	- int i = 3(4+6(x+z*size)); // (:,1,x,y)
	- idx[0] = indices[i];
	- idx[1] = indices[i+1];
	- idx[2] = indices[i+2];
	- interpw[0] = barycoords[i];
	- interpw[1] = barycoords[i+1];
	- interpw[2] = barycoords[i+2];
	- return;
	- }
	- else
	- {
	- int x = float2int(nx);
	- int z = float2int(nz);
	- int i = 3(5+6(x+z*size)); // (:,1,x,y)
	- idx[0] = indices[i];
	- idx[1] = indices[i+1];
	- idx[2] = indices[i+2];
	- interpw[0] = barycoords[i];
	- interpw[1] = barycoords[i+1];
	- interpw[2] = barycoords[i+2];
	- return;
	- }
	- }
	-
	-protected:
	-
	- bool LoadLookuptables(const std::string& lutPath);
	-
	- bool LoadLookuptables();
	-
	- bool LoadLookuptables(std::istream& BaryCoordsStream, std::istream& IndicesStream);
	-
	- inline float invrescale(float f) const
	- {
	- float x = (fabs(f)-b)*inva;
	- if (f>0)
	- return (x*x-beta);
	- else
	- return beta - x*x;
	- }
	-
	- inline int float2int(float x) const
	- {
	- return int((invrescale(x)+1)*sN-0.5);
	- }
	-
	-};
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/StochasticTracking/StochasticTractographyFilter.cxx b/Modules/DiffusionImaging/FiberTracking/Algorithms/StochasticTracking/StochasticTractographyFilter.cxx
	deleted file mode 100644
	index 0772463e52..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/StochasticTracking/StochasticTractographyFilter.cxx
	+++ /dev/null
	@@ -1,570 +0,0 @@
	-#include "itkStochasticTractographyFilter.h"
	-#include "itkVectorImage.h"
	-#include "itkImageSeriesReader.h" //this is needed for itk::ExposeMetaData()
	-#include "itkImageFileReader.h"
	-#include "itkImageFileWriter.h"
	-#include "itkMetaDataDictionary.h"
	-#include "itkAddImageFilter.h"
	-#include "itkUnaryFunctorImageFilter.h"
	-#include <iostream>
	-#include <vector>
	-#include "itkImageRegionConstIterator.h"
	-#include "StochasticTractographyFilterCLP.h"
	-#include "itkTensorFractionalAnisotropyImageFilter.h"
	-#include "itkPathIterator.h"
	-#include <string>
	-#include <fstream>
	-
	-std::string stripExtension(const std::string& fileName){
	- const int length = fileName.length();
	- for (int i=0; i!=length; ++i){
	- if (fileName[i]=='.'){
	- return fileName.substr(0,i);
	- }
	- }
	- return fileName;
	-}
	-
	-
	-template< class TTOContainerType >
	-bool SamplingDirections(const char* fn, typename TTOContainerType::Pointer directions){
	- char str[100];
	- double x,y,z;
	- std::ifstream m_file;
	- typename TTOContainerType::Element direction;
	-
	- //open the file
	- m_file.open(fn);
	- if(!m_file.is_open()){
	- std::cerr<<"Problems opening: "<< fn << std::endl;
	- return false;
	- }
	- else{
	- //load file info into valid itk representation
	- //assume all entries in the file describe a vector of length 1
	- //each line is arranged [x, y, z]
	- unsigned int directioncount=0;
	-
	- while(!m_file.getline(str, 100, '\n').eof()){
	- for(int i=0;i<3;i++){
	- sscanf(str,"%lf %lf %lf",&x,&y,&z);
	- direction[0]=x;
	- direction[1]=y;
	- direction[2]=z;
	- }
	- directions->InsertElement(directioncount++,direction);
	- }
	- }
	-
	- //close file
	- m_file.close();
	- return true;
	-}
	-
	-template< class TractContainerType >
	-bool WriteTractContainerToFile( const char* fn, TractContainerType* tractcontainer ){
	- std::ofstream tractfile( fn, std::ios::out \| std::ios::binary );
	- tractfile.seekp(0);
	- if(tractfile.is_open()){
	- for(int i=0; i<tractcontainer->Size(); i++ ){
	- typename TractContainerType::Element tract =
	- tractcontainer->GetElement(i);
	-
	- typename TractContainerType::Element::ObjectType::VertexListType::ConstPointer vertexlist =
	- tract->GetVertexList();
	-
	- for(int j=0; j<vertexlist->Size(); j++){
	- typename TractContainerType::Element::ObjectType::VertexListType::Element vertex =
	- vertexlist->GetElement(j);
	- tractfile.write((char*)&vertex[0], sizeof(vertex[0]));
	- tractfile.write((char*)&vertex[1], sizeof(vertex[1]));
	- tractfile.write((char*)&vertex[2], sizeof(vertex[2]));
	- }
	- double endoftractsymbol = 0.0;
	- tractfile.write((char*)&endoftractsymbol, sizeof(endoftractsymbol));
	- tractfile.write((char*)&endoftractsymbol, sizeof(endoftractsymbol));
	- tractfile.write((char*)&endoftractsymbol, sizeof(endoftractsymbol));
	- }
	-
	- tractfile.close();
	- return true;
	- }
	- else{
	- std::cerr<<"Problems opening file to write tracts\n";
	- return false;
	- }
	-}
	-template< class FAContainerType >
	-bool WriteScalarContainerToFile( const char* fn, FAContainerType* facontainer ){
	- std::ofstream fafile( fn, std::ios::out );
	- std::locale C("C"); // define standard locale
	- fafile.imbue(C); // switch the stream to standard locale
	-
	- if(fafile.is_open()){
	- for(int i=0; i<facontainer->Size(); i++){
	- fafile<<facontainer->GetElement(i)<<std::endl;
	- }
	- fafile.close();
	- return true;
	- }
	- else{
	- std::cerr<<"Problems opening file to write FA value\n";
	- return false;
	- }
	-}
	-
	-namespace Functor {
	-
	-template< class TInput, class TOutput>
	-class ZeroDWITest
	-{
	-public:
	- ZeroDWITest() {};
	- ~ZeroDWITest() {};
	- bool operator!=( const ZeroDWITest & ) const
	- {
	- return false;
	- }
	- bool operator==( const ZeroDWITest & other ) const
	- {
	- return !(*this != other);
	- }
	- inline TOutput operator()( const TInput & A )
	- {
	- /*for(int i=0;i<A.GetSize();i++){
	- if(A[0]<100){
	- std::cout<<"Invalid Voxel\n";
	- return 0;
	- }
	- }
	- */
	- return 10;
	- }
	-};
	-
	-template< class TInput, class TOutput>
	-class ScalarMultiply
	-{
	-public:
	- ScalarMultiply() {};
	- ~ScalarMultiply() {};
	- bool operator!=( const ScalarMultiply & ) const
	- {
	- return false;
	- }
	- bool operator==( const ScalarMultiply & other ) const
	- {
	- return !(*this != other);
	- }
	- inline TOutput operator()( const TInput & A )
	- {
	- /*for(int i=0;i<A.GetSize();i++){
	- if(A[0]<100){
	- std::cout<<"Invalid Voxel\n";
	- return 0;
	- }
	- }
	- */
	- return A*1000;
	- }
	-};
	-
	-}
	-
	-int main(int argc, char* argv[]){
	- PARSE_ARGS;
	- //define the input/output types
	- typedef itk::VectorImage< unsigned short int, 3 > DWIVectorImageType;
	- typedef itk::Image< float, 3 > WMPImageType;
	- typedef itk::Image< short int, 3 > ROIImageType;
	- typedef itk::Image< unsigned int, 3 > CImageType;
	-
	- //define an iterator for the ROI image
	- typedef itk::ImageRegionConstIterator< ROIImageType > ROIImageIteratorType;
	-
	- //define reader and writer
	- typedef itk::ImageFileReader< DWIVectorImageType > DWIVectorImageReaderType;
	- typedef itk::ImageFileReader< WMPImageType > WMPImageReaderType;
	- typedef itk::ImageFileReader< ROIImageType > ROIImageReaderType;
	- typedef itk::ImageFileWriter< CImageType > CImageWriterType;
	- typedef itk::ImageFileWriter< WMPImageType > WMPImageWriterType;
	-
	- //define metadata dictionary types
	- typedef itk::MetaDataDictionary DictionaryType;
	- typedef DictionaryType::ConstIterator DictionaryIteratorType;
	-
	- //define a probabilistic tractography filter type and associated bValue,
	- //gradient direction, and measurement frame types
	- typedef itk::StochasticTractographyFilter< DWIVectorImageType, WMPImageType,
	- CImageType >
	- PTFilterType;
	- typedef PTFilterType::bValueContainerType bValueContainerType;
	- typedef PTFilterType::GradientDirectionContainerType GDContainerType;
	- typedef PTFilterType::MeasurementFrameType MeasurementFrameType;
	-
	- //define a filter to generate a mask image that excludes zero dwi values
	- typedef Functor::ZeroDWITest< DWIVectorImageType::PixelType, WMPImageType::PixelType >
	- ZeroDWITestType;
	- typedef itk::UnaryFunctorImageFilter< DWIVectorImageType, WMPImageType,
	- ZeroDWITestType > ExcludeZeroDWIFilterType;
	-
	- //FA stuff
	- typedef itk::Image< double, 3 > FAImageType;
	- typedef itk::TensorFractionalAnisotropyImageFilter< PTFilterType::OutputTensorImageType,
	- FAImageType > FAFilterType;
	- typedef itk::ImageFileWriter< FAImageType > FAImageWriterType;
	-
	- //define a filter to multiply a FA image by 1000
	- typedef Functor::ScalarMultiply< FAImageType::PixelType, FAImageType::PixelType >
	- ScalarMultiplyType;
	- typedef itk::UnaryFunctorImageFilter< FAImageType, FAImageType,
	- ScalarMultiplyType > MultiplyFAFilterType;
	-
	- //define AddImageFilterType to accumulate the connectivity maps of the pixels in the ROI
	- typedef itk::AddImageFilter< CImageType, CImageType, CImageType> AddImageFilterType;
	-
	- //parse command line arguments
	- //if(argc < 3){
	- // std::cerr << "Usage: " << argv[0];
	- // std::cerr<< " DWIFile(.nhdr) ROIFile(.nhdr) ConnectivityFile(.nhdr) ";
	- // std::cerr<< "LabelNumber NumberOfTracts MaxTractLength MaxLikelihoodCacheSize\n";
	- // return EXIT_FAILURE;
	- //}
	- /*
	- char* dwifilename = argv[1];
	- char* roifilename = argv[2];
	- char* cfilename = argv[3];
	- unsigned int labelnumber = atoi(argv[4]);
	- unsigned int totaltracts = atoi(argv[5]);
	- unsigned int maxtractlength = atoi(argv[6]);
	- unsigned int maxlikelihoodcachesize = atoi(argv[7]);
	- */
	- //setup output stat files
	- std::string fafilename = outputprefix + "_CONDFAValues.txt";
	- //sprintf( fafilename, "%s_CONDFAValues.txt", outputprefix.c_str() );
	- std::string lengthfilename = outputprefix + "_CONDLENGTHValues.txt";
	- //sprintf( lengthfilename, "%s_CONDLENGTHValues.txt", outputprefix.c_str() );
	-
	- //open these files
	- std::ofstream fafile( fafilename.c_str() );
	- std::locale C("C"); // define standard locale
	- fafile.imbue(C); // switch the stream to standard locale
	-
	- if(!fafile.is_open()){
	- std::cerr<<"Could not open FA file!\n";
	- return EXIT_FAILURE;
	- }
	-
	- std::ofstream lengthfile( lengthfilename.c_str() );
	- lengthfile.imbue(C); // switch the stream to standard locale
	- //if(!lengthfile.is_open()){
	- // std::cerr<<"Could not open Length file!\n";
	- // return EXIT_FAILURE;
	- // }
	-
	- //read in the DWI image
	- DWIVectorImageReaderType::Pointer dwireaderPtr = DWIVectorImageReaderType::New();
	- dwireaderPtr->SetFileName(dwifilename);
	- dwireaderPtr->Update();
	-
	- //Obtain bValue, gradient directions and measurement frame from metadata dictionary
	- DictionaryType& dictionary = dwireaderPtr->GetMetaDataDictionary();
	- bValueContainerType::Pointer bValuesPtr = bValueContainerType::New();
	- MeasurementFrameType measurement_frame;
	- GDContainerType::Pointer gradientsPtr = GDContainerType::New();
	- bValueContainerType::Element scaling_bValue = 0;
	- GDContainerType::Element g_i;
	-
	- //bad choice of variable names: dictit->first refers to the key in the Map
	- //dictit->second refers to the Value associated with that Key
	- for(DictionaryIteratorType dictit = dictionary.Begin();
	- dictit!=dictionary.End();
	- ++dictit){
	- if(dictit->first.find("DWMRI_gradient") != std::string::npos){
	- std::string metaDataValue;
	- itk::ExposeMetaData< std::string > (dictionary, dictit->first, metaDataValue);
	- sscanf(metaDataValue.c_str(), "%lf %lf %lf\n", &g_i[0], &g_i[1], &g_i[2]);
	- //normalize the gradient vector
	- gradientsPtr->InsertElement( gradientsPtr->Size(), g_i.normalize() );
	- }
	- else if(dictit->first.find("DWMRI_b-value") != std::string::npos){
	- std::string metaDataValue;
	- itk::ExposeMetaData< std::string >(dictionary, dictit->first, metaDataValue);
	- scaling_bValue = atof(metaDataValue.c_str());
	- }
	- else if(dictit->first.find("NRRD_measurement frame") != std::string::npos){
	- std::vector< std::vector < double > > metaDataValue;
	- itk::ExposeMetaData< std::vector< std::vector<double> > >
	- (dictionary, dictit->first, metaDataValue);
	- for(int i=0;i<3;i++){
	- for(int j=0;j<3;j++)
	- measurement_frame(i,j) = metaDataValue[j][i];
	- }
	- }
	- else{
	- std::cout << dictit->first << std::endl;
	- }
	- }
	-
	- //check to see if bValue, gradients, or measurement frame is missing
	- if(scaling_bValue == 0){
	- std::cerr << "scaling_bValue should never be 0, possibly not found in Nrrd header\n";
	- return EXIT_FAILURE;
	- }
	- else if(gradientsPtr->Size() == 0){
	- std::cerr <<"no gradients were found!";
	- return EXIT_FAILURE;
	- }
	- else if(measurement_frame.size() == 0){
	- std::cerr <<"no measurement frame was found!";
	- return EXIT_FAILURE;
	- }
	- //correct the measurement frame
	-
	- std::cout << scaling_bValue << std::endl;
	- for(unsigned int i=0; i<gradientsPtr->Size(); i++)
	- std::cout << gradientsPtr->GetElement(i) << std::endl;
	-
	- //std::cout << measurement_frame <<std::endl;
	-
	- for(unsigned int i=0; i<measurement_frame.rows(); i++){
	- for(unsigned int j=0; j<measurement_frame.columns(); j++){
	- std::cout<<measurement_frame(i,j) << " ";
	- }
	- std::cout << std::endl;
	- }
	-
	- //correct the measurement frame since the image is now in LPS from RAS frame
	- //NRRDIO should do this, but we do it here as a work around
	-
	- //fill up bValue container with the scaling_bValue;
	- for(unsigned int i=0; i<gradientsPtr->Size() ;i++){
	- if(gradientsPtr->GetElement(i).squared_magnitude() == 0){
	- bValuesPtr->InsertElement(i, 0);
	- }
	- else{
	- //this matters in the calculations for the constrained model but not the tensor model
	- //since a gradient direction of all zeros handles it
	- bValuesPtr->InsertElement(i, scaling_bValue);
	- }
	- }
	-
	- //setup the ROI image reader
	- ROIImageReaderType::Pointer roireaderPtr = ROIImageReaderType::New();
	- roireaderPtr->SetFileName(roifilename);
	- roireaderPtr->Update();
	-
	- //setup the white matter probability image reader
	- WMPImageReaderType::Pointer wmpreader = WMPImageReaderType::New();
	- wmpreader->SetFileName(wmpfilename);
	- wmpreader->Update();
	-
	- //optionally set the origins of these images to be the same as the DWI
	- if(recenteroriginswitch==true){
	- roireaderPtr->GetOutput()->SetOrigin( dwireaderPtr->GetOutput()->GetOrigin() );
	- wmpreader->GetOutput()->SetOrigin( dwireaderPtr->GetOutput()->GetOrigin() );
	- }
	- /*
	- //set list of directions
	- typedef PTFilterType::TractOrientationContainerType TOCType;
	- TOCType::Pointer directionsPtr = TOCType::New();
	-
	- if(SamplingDirections<TOCType>("SD.txt", directionsPtr));
	- else return EXIT_FAILURE;
	- */
	- /*
	- //write out the directions
	- std::ofstream outfile("crapola.txt");
	-
	-
	- for(int i=0; i<directionsPtr->Size(); i++){
	- TOCType::Element dir = directionsPtr->GetElement(i);
	- outfile<<"{"<<dir[0]<<", "<<dir[1]<<", "<<dir[2]<<"},"<<std::endl;
	- }
	- outfile.close();
	- */
	-
	- //Create a default Mask Image which
	- //excludes DWI pixels which contain values that are zero
	- //ExcludeZeroDWIFilterType::Pointer ezdwifilter = ExcludeZeroDWIFilterType::New();
	- //ezdwifilter->SetInput( dwireaderPtr->GetOutput() );
	- //std::cout<<"Start mask image\n";
	- //write out the mask image
	- //MaskImageWriterType::Pointer maskwriterPtr = MaskImageWriterType::New();
	- //maskwriterPtr->SetInput( ezdwifilter->GetOutput() );
	- //maskwriterPtr->SetFileName( "maskimage.nhdr" );
	- //maskwriterPtr->Update();
	- //std::cout<<"Finish the mask image\n";
	-
	- std::cout<<"Create PTFilter\n";
	- //Setup the PTFilter
	- PTFilterType::Pointer ptfilterPtr = PTFilterType::New();
	- ptfilterPtr->SetInput( dwireaderPtr->GetOutput() );
	- //ptfilterPtr->SetMaskImageInput( ezdwifilter->GetOutput() );
	- ptfilterPtr->SetWhiteMatterProbabilityImageInput( wmpreader->GetOutput() );
	- ptfilterPtr->SetbValues(bValuesPtr);
	- ptfilterPtr->SetGradients( gradientsPtr );
	- ptfilterPtr->SetMeasurementFrame( measurement_frame );
	- //ptfilterPtr->SetSampleDirections(directionsPtr);
	- ptfilterPtr->SetMaxTractLength( maxtractlength );
	- ptfilterPtr->SetTotalTracts( totaltracts );
	- ptfilterPtr->SetMaxLikelihoodCacheSize( maxlikelihoodcachesize );
	- if(totalthreads!=0) ptfilterPtr->SetNumberOfThreads( totalthreads );
	-
	- //calculate the tensor image
	- ptfilterPtr->GenerateTensorImageOutput();
	-
	- //Setup the FAImageFilter
	- FAFilterType::Pointer fafilter = FAFilterType::New();
	-
	- fafilter->SetInput( ptfilterPtr->GetOutputTensorImage() );
	- fafilter->Update();
	-
	- //Setup the FA container to hold FA values for tracts of interest
	- typedef itk::VectorContainer< unsigned int, double > FAContainerType;
	- //FAContainerType::Pointer facontainer = FAContainerType::New();
	-
	- //Setup the length container to hold lengths for tracts of interest
	- typedef itk::VectorContainer< unsigned int, unsigned int > LengthContainerType;
	- //LengthContainerType::Pointer lengthcontainer = LengthContainerType::New();
	-
	- //Setup the AddImageFilter
	- AddImageFilterType::Pointer addimagefilterPtr = AddImageFilterType::New();
	-
	- //Create a zeroed Connectivity Image
	- CImageType::Pointer accumulatedcimagePtr = CImageType::New();
	- accumulatedcimagePtr->CopyInformation( dwireaderPtr->GetOutput() );
	- accumulatedcimagePtr->SetBufferedRegion( dwireaderPtr->GetOutput()->GetBufferedRegion() );
	- accumulatedcimagePtr->SetRequestedRegion( dwireaderPtr->GetOutput()->GetRequestedRegion() );
	- accumulatedcimagePtr->Allocate();
	- accumulatedcimagePtr->FillBuffer(0);
	-
	- //Create another Connectivity Map for just the tracts
	- //which make it to the second ROI
	- CImageType::Pointer conditionedcimagePtr = CImageType::New();
	- conditionedcimagePtr->CopyInformation( dwireaderPtr->GetOutput() );
	- conditionedcimagePtr->SetBufferedRegion( dwireaderPtr->GetOutput()->GetBufferedRegion() );
	- conditionedcimagePtr->SetRequestedRegion( dwireaderPtr->GetOutput()->GetRequestedRegion() );
	- conditionedcimagePtr->Allocate();
	- conditionedcimagePtr->FillBuffer(0);
	-
	- //graft this onto the output of the addimagefilter
	- addimagefilterPtr->GraftOutput(accumulatedcimagePtr);
	- addimagefilterPtr->SetInput1(ptfilterPtr->GetOutput());
	- addimagefilterPtr->SetInput2(addimagefilterPtr->GetOutput());
	-
	- ROIImageIteratorType ROIImageIt( roireaderPtr->GetOutput(),
	- roireaderPtr->GetOutput()->GetRequestedRegion() );
	- for(ROIImageIt.GoToBegin(); !ROIImageIt.IsAtEnd(); ++ROIImageIt){
	- if(ROIImageIt.Get() == labelnumber){
	- std::cout << "PixelIndex: "<< ROIImageIt.GetIndex() << std::endl;
	- ptfilterPtr->SetSeedIndex( ROIImageIt.GetIndex() );
	- //ptfilterPtr->GenerateTractContainerOutput();
	- //write out the tract info
	-
	- //WriteTractContainerToFile( filename, ptfilterPtr->GetOutputTractContainer() );
	- addimagefilterPtr->Update();
	-
	- std::cout<<"Calculate Statistics\n";
	- //calculate the FA stats for tracts which pass through a second ROI
	- PTFilterType::TractContainerType::Pointer tractcontainer =
	- ptfilterPtr->GetOutputTractContainer();
	-
	- typedef itk::PathIterator< ROIImageType, PTFilterType::TractType >
	- ROITractIteratorType;
	-
	- for(int i=0; i<tractcontainer->Size(); i++ ){
	- PTFilterType::TractType::Pointer currtract = tractcontainer->GetElement(i);
	- ROITractIteratorType roitractIt( roireaderPtr->GetOutput(),
	- currtract );
	-
	- for(roitractIt.GoToBegin(); !roitractIt.IsAtEnd(); ++roitractIt){
	- if(roitractIt.Get() == endlabelnumber){
	- double accumFA=0;
	- unsigned int stepcount=0;
	- //integrate fa along length of tract
	- for(double t=0; t<currtract->EndOfInput(); t+=0.2){
	- stepcount++;
	- //std::cout<<fafilter->GetOutput()->GetPixel(roitractIt.GetIndex())<<std::endl;
	- accumFA+=fafilter->GetOutput()->GetPixel(currtract->EvaluateToIndex(t));
	- }
	- fafile<<accumFA/((double)stepcount)<<std::endl;
	- lengthfile<<tractcontainer->GetElement(i)->EndOfInput()<<std::endl;
	- if(fafile.fail() \|\| lengthfile.fail() ){
	- std::cerr<<"Error writing to text files\n";
	- return EXIT_FAILURE;
	- }
	- //lengthcontainer->InsertElement( lengthcontainer->Size(),
	- //(unsigned int) tractcontainer->GetElement(i)->EndOfInput() );
	- //facontainer->InsertElement( facontainer->Size(), accumFA/((double)stepcount) );
	-
	- //color in the tracts
	- for(roitractIt.GoToBegin(); !roitractIt.IsAtEnd(); ++roitractIt){
	- conditionedcimagePtr->GetPixel(roitractIt.GetIndex())++;
	- }
	- break;
	- }
	- }
	- }
	- }
	- }
	-
	- std::cout<<"DWI image origin:"<< dwireaderPtr->GetOutput()->GetOrigin() <<std::endl;
	- std::cout<<"ROI image origin:"<< roireaderPtr->GetOutput()->GetOrigin() <<std::endl;
	- std::cout<<"wmp image origin:"<< wmpreader->GetOutput()->GetOrigin() <<std::endl;
	- if(outputimageswitch){
	- //Write out the Connectivity Map
	- std::string cfilename = outputprefix + "_CMAP.nhdr";
	- //sprintf(cfilename, "%s_CMAP.nhdr", outputprefix.c_str() );
	- CImageWriterType::Pointer writerPtr = CImageWriterType::New();
	- writerPtr->SetInput( accumulatedcimagePtr );
	- writerPtr->SetFileName( cfilename.c_str() );
	- writerPtr->Update();
	-
	- //Write out TensorImage
	- std::string tensorimagefilename = outputprefix + "_TENSOR.nhdr";
	- //sprintf(tensorimagefilename, "%s_TENSOR.nhdr", outputprefix.c_str() );
	- typedef itk::ImageFileWriter< PTFilterType::OutputTensorImageType > TensorImageWriterType;
	- TensorImageWriterType::Pointer tensorwriter = TensorImageWriterType::New();
	- tensorwriter->SetInput( ptfilterPtr->GetOutputTensorImage() );
	- tensorwriter->SetFileName( tensorimagefilename.c_str() );
	- tensorwriter->Update();
	-
	- //Create a default Mask Image which
	- //excludes DWI pixels which contain values that are zero
	- MultiplyFAFilterType::Pointer multFAfilter = MultiplyFAFilterType::New();
	- multFAfilter->SetInput( fafilter->GetOutput() );
	- //write out the FA image
	- std::string faimagefilename = outputprefix + "_FA.nhdr";
	- //sprintf(faimagefilename, "%s_FA.nhdr", outputprefix.c_str() );
	- FAImageWriterType::Pointer fawriter = FAImageWriterType::New();
	- fawriter->SetInput( multFAfilter->GetOutput() );
	- fawriter->SetFileName( faimagefilename.c_str() );
	- fawriter->Update();
	-
	- //Write out the conditioned connectivity map
	- CImageWriterType::Pointer condcmapwriterPtr = CImageWriterType::New();
	- condcmapwriterPtr->SetInput( conditionedcimagePtr );
	- std::string condcmapfilename = outputprefix + "_COND.nhdr";
	- //sprintf(condcmapfilename, "%s_COND.nhdr", outputprefix.c_str());
	- condcmapwriterPtr->SetFileName( condcmapfilename );
	- condcmapwriterPtr->Update();
	- }
	- //close files
	- fafile.close();
	- lengthfile.close();
	- if(fafile.fail() \|\| lengthfile.fail() ){
	- std::cerr<<"Error closing text files\n";
	- return EXIT_FAILURE;
	- }
	- //Write out FA container
	- //char fafilename[100];
	- //sprintf( fafilename, "%s_CONDFAValues.txt", outputprefix.c_str() );
	- //WriteScalarContainerToFile< FAContainerType >( fafilename, facontainer );
	-
	- //Write out tract length container
	- //char lengthfilename[100];
	- //sprintf( lengthfilename, "%s_CONDLENGTHValues.txt", outputprefix.c_str() );
	- //WriteScalarContainerToFile< LengthContainerType >( lengthfilename, lengthcontainer );
	- return EXIT_SUCCESS;
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/StochasticTracking/StochasticTractographyFilter.xml b/Modules/DiffusionImaging/FiberTracking/Algorithms/StochasticTracking/StochasticTractographyFilter.xml
	deleted file mode 100644
	index 6b797da757..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/StochasticTracking/StochasticTractographyFilter.xml
	+++ /dev/null
	@@ -1,160 +0,0 @@
	-<?xml version="1.0" encoding="utf-8"?>
	-<executable>
	- <category>filtering</category>
	- <title>Stochastic Tractography Filter</title>
	- <description>
	- Generates a map of connectivity probabilities from a DWI volume.
	- </description>
	- <version>1.0</version>
	- <documentationurl></documentationurl>
	- <license></license>
	- <contributor>Tri Ngo</contributor>
	-
	- <parameters>
	- <label>
	- Stochastic Tractography Parameters
	- </label>
	- <description>
	- Parameters for the Stochastic Tractography algorithm
	- </description>
	-
	- <integer>
	- <name>labelnumber</name>
	- <flag>l</flag>
	- <longflag>labelnumber</longflag>
	- <description>Label Number to use as seed points</description>
	- <label>Seed Point(s) Label Number</label>
	- <default>0</default>
	- <constraints>
	- <minimum>0</minimum>
	- <step>1</step>
	- </constraints>
	- </integer>
	-
	- <integer>
	- <name>endlabelnumber</name>
	- <flag>e</flag>
	- <longflag>endlabelnumber</longflag>
	- <description>Label Number to use as end region</description>
	- <label>End Region Label Number</label>
	- <default>1</default>
	- <constraints>
	- <minimum>0</minimum>
	- <step>1</step>
	- </constraints>
	- </integer>
	-
	- <integer>
	- <name>totaltracts</name>
	- <flag>t</flag>
	- <longflag>totaltracts</longflag>
	- <description>Number of Sample Tracts</description>
	- <label>Total Tracts</label>
	- <default>100</default>
	- <constraints>
	- <minimum>0</minimum>
	- <step>1</step>
	- </constraints>
	- </integer>
	-
	- <integer>
	- <name>maxtractlength</name>
	- <flag>m</flag>
	- <longflag>maxtractlength</longflag>
	- <description>Maximum Length of Sample Tract</description>
	- <label>Maximum Tract Length</label>
	- <default>100</default>
	- <constraints>
	- <minimum>0</minimum>
	- <step>1</step>
	- </constraints>
	- </integer>
	- <integer>
	- <name>stepsize</name>
	- <flag>s</flag>
	- <longflag>stepsize</longflag>
	- <description>The length of each segment of the tract in mm</description>
	- <label>Step Size(mm)</label>
	- <default>1</default>
	- <constraints>
	- <minimum>0.1</minimum>
	- <step>0.1</step>
	- </constraints>
	- </integer>
	- <integer>
	- <name>maxlikelihoodcachesize</name>
	- <flag>c</flag>
	- <longflag>maxlikelihoodcachesize</longflag>
	- <description>Maximum Size of Likelihood Cache</description>
	- <label>Maximum Cache Size</label>
	- <default>100</default>
	- <constraints>
	- <minimum>0</minimum>
	- <step>1</step>
	- </constraints>
	- </integer>
	- <string>
	- <name>outputprefix</name>
	- <flag>o</flag>
	- <longflag>outputprefix</longflag>
	- <description>Prefix for the output files</description>
	- <label>Output Filename Prefix</label>
	- <default>"Output"</default>
	- </string>
	- <boolean>
	- <name>outputimageswitch</name>
	- <flag>i</flag>
	- <default>false</default>
	- <longflag>outputimageswitch</longflag>
	- <label>Produce Output Images</label>
	- <description>Output Tensor, FA maps and Connectivity Maps</description>
	- </boolean>
	- <boolean>
	- <name>recenteroriginswitch</name>
	- <flag>r</flag>
	- <default>false</default>
	- <longflag>recenteroriginswitch</longflag>
	- <label>Recenter Image Origins</label>
	- <description>Ignore the origins of the ROI and WM mask and set it to be the same as the DWI image origin</description>
	- </boolean>
	- <integer>
	- <name>totalthreads</name>
	- <flag>j</flag>
	- <longflag>totalthreads</longflag>
	- <description>Total number of threads to use. Default value of zero sets number of threads to number of CPUs</description>
	- <label>Total Threads</label>
	- <default>0</default>
	- <constraints>
	- <minimum>0</minimum>
	- <step>1</step>
	- </constraints>
	- </integer>
	- </parameters>
	-
	- <parameters>
	- <label>IO</label>
	- <description>Input/output parameters</description>
	- <image type="diffusion-weighted">
	- <name>dwifilename</name>
	- <label>Input Volume</label>
	- <channel>input</channel>
	- <index>0</index>
	- <description>Input DWI volume to be filtered</description>
	- </image>
	- <image>
	- <name>wmpfilename</name>
	- <label>Input White Matter Probability Volume</label>
	- <channel>input</channel>
	- <index>1</index>
	- <description>Input Mask volume that provides the probability that the voxel is white matter </description>
	- </image>
	- <image>
	- <name>roifilename</name>
	- <label>Input ROI Volume</label>
	- <channel>input</channel>
	- <index>2</index>
	- <description>Input ROI volume used to seed algorithm</description>
	- </image>
	- </parameters>
	-
	-</executable>
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/StochasticTracking/itkSlowPolyLineParametricPath.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/StochasticTracking/itkSlowPolyLineParametricPath.h
	deleted file mode 100644
	index b4b2061d0b..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/StochasticTracking/itkSlowPolyLineParametricPath.h
	+++ /dev/null
	@@ -1,128 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef _itkSlowPolyLineParametricPathPath_h
	-#define _itkSlowPolyLineParametricPathPath_h
	-
	-#include "itkPolyLineParametricPath.h"
	-#include "itkVectorContainer.h"
	-#include "itkContinuousIndex.h"
	-#include "itkIndex.h"
	-#include "itkOffset.h"
	-#include "itkVector.h"
	-
	-namespace itk
	-{
	-
	-
	-/** \class SlowPolyLineParametricPath
	- * \brief Represent a path of line segments through ND Space
	- *
	- * This class is intended to represent parametric paths through an image, where
	- * the paths are composed of line segments. Each line segment traverses one
	- * unit of input. A classic application of this class is the representation of
	- * contours in 2D images, especially when the contours only need to be
	- * approximately correct. Another use of a path is to guide the movement of an
	- * iterator through an image.
	- *
	- * \sa EllipseParametricPath
	- * \sa FourierSeriesPath
	- * \sa OrthogonallyCorrectedParametricPath
	- * \sa ParametricPath
	- * \sa ChainCodePath
	- * \sa Path
	- * \sa ContinuousIndex
	- * \sa Index
	- * \sa Offset
	- * \sa Vector
	- *
	- * \ingroup PathObjects
	- */
	-template <unsigned int VDimension>
	-class ITK_EXPORT SlowPolyLineParametricPath : public
	-PolyLineParametricPath< VDimension >
	-{
	-public:
	- /** Standard class typedefs. */
	- typedef SlowPolyLineParametricPath Self;
	- typedef PolyLineParametricPath<VDimension> Superclass;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	-
	- /** Run-time type information (and related methods). */
	- itkTypeMacro(SlowPolyLineParametricPath, PolyLineParametricPath);
	-
	- /** Input type */
	- typedef typename Superclass::InputType InputType;
	-
	- /** Output type */
	- typedef typename Superclass::OutputType OutputType;
	-
	-
	- /** Basic data-structure types used */
	- typedef typename Superclass::ContinuousIndexType ContinuousIndexType;
	- typedef typename Superclass::IndexType IndexType;
	- typedef typename Superclass::OffsetType OffsetType;
	- typedef typename Superclass::PointType PointType;
	- typedef typename Superclass::VectorType VectorType;
	- typedef typename Superclass::VertexType VertexType;
	- typedef typename Superclass::VertexListType VertexListType;
	- typedef typename Superclass::VertexListPointer VertexListPointer;
	-
	- /** Increment the input variable passed by reference such that the ND index of
	- * the path moves to its next vertex-connected (8-connected in 2D) neighbor.
	- * Return the Index-space offset of the path from its prior input to its new
	- * input. If the path is unable to increment, input is not changed and an
	- * offset of Zero is returned. Children are not required to implement bounds
	- * checking.
	- *
	- * This is a fairly slow, iterative algorithm that numerically converges to
	- * the next index along the path, in a vertex-connected (8-connected in 2D)
	- * fashion. When possible, children of this class should overload this
	- * function with something more efficient.
	- *
	- * WARNING: This default implementation REQUIRES that the ND endpoint of
	- * the path be either unique or coincident only with the startpoint, since it
	- * uses the endpoint as a stopping condition. */
	- virtual OffsetType IncrementInput(InputType & input) const;
	-
	-
	- ///** Evaluate the first derivative of the ND output with respect to the 1D
	- // * input. This is an exact, algebraic function. */
	- //virtual VectorType EvaluateDerivative(const InputType & input) const;
	-
	-
	- /** New() method for dynamic construction */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	-
	-protected:
	- SlowPolyLineParametricPath();
	- ~SlowPolyLineParametricPath(){}
	- void PrintSelf(std::ostream& os, Indent indent) const;
	-
	-private:
	- SlowPolyLineParametricPath(const Self&); //purposely not implemented
	- void operator=(const Self&); //purposely not implemented
	-};
	-
	-} // namespace itk
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkSlowPolyLineParametricPath.txx"
	-#endif
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/StochasticTracking/itkSlowPolyLineParametricPath.txx b/Modules/DiffusionImaging/FiberTracking/Algorithms/StochasticTracking/itkSlowPolyLineParametricPath.txx
	deleted file mode 100644
	index 18fb919896..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/StochasticTracking/itkSlowPolyLineParametricPath.txx
	+++ /dev/null
	@@ -1,130 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef _itkSlowPolyLineParametricPath_txx
	-#define _itkSlowPolyLineParametricPath_txx
	-
	-#include "itkSlowPolyLineParametricPath.h"
	-#include <math.h>
	-
	-
	-
	-namespace itk
	-{
	-
	-//template<unsigned int VDimension>
	-//typename SlowPolyLineParametricPath<VDimension>::VectorType
	-//SlowPolyLineParametricPath<VDimension>
	-//::EvaluateDerivative(const InputType & input) const
	-//{
	-//}
	-
	-
	-
	-/**
	- * Constructor
	- */
	-template <unsigned int VDimension>
	-SlowPolyLineParametricPath<VDimension>
	-::SlowPolyLineParametricPath()
	-{
	- this->SetDefaultInputStepSize( 0.3 );
	-}
	-
	-
	-template<unsigned int VDimension>
	-typename SlowPolyLineParametricPath<VDimension>::OffsetType
	-SlowPolyLineParametricPath<VDimension>
	-::IncrementInput(InputType & input) const
	-{
	- int iterationCount;
	- bool tooSmall;
	- bool tooBig;
	- InputType inputStepSize;
	- InputType finalInputValue;
	- OffsetType offset;
	- IndexType currentImageIndex;
	- IndexType nextImageIndex;
	- IndexType finalImageIndex;
	-
	- iterationCount = 0;
	- inputStepSize = this->GetDefaultInputStepSize();
	-
	- // Are we already at (or past) the end of the input?
	- finalInputValue = this->EndOfInput();
	- currentImageIndex = this->EvaluateToIndex( input );
	- finalImageIndex = this->EvaluateToIndex( finalInputValue );
	- offset = finalImageIndex - currentImageIndex;
	- if( ( offset == this->GetZeroOffset() && input != this->StartOfInput() ) \|\|
	- ( input >=finalInputValue ) )
	- {
	- return this->GetZeroOffset();
	- }
	-
	- do
	- {
	- if( iterationCount++ > 10000 ) {return this->GetZeroOffset(); itkExceptionMacro(<<"Too many iterations");}
	-
	- nextImageIndex = this->EvaluateToIndex( input + inputStepSize );
	- offset = nextImageIndex - currentImageIndex;
	-
	- tooBig = false;
	- tooSmall = ( offset == this->GetZeroOffset() );
	- if( tooSmall )
	- {
	- // increase the input step size, but don't go past the end of the input
	- inputStepSize *= 2;
	- if( (input + inputStepSize) >= finalInputValue ){
	- //inputStepSize = finalInputValue - input;
	- inputStepSize += this->GetDefaultInputStepSize();
	- }
	- }
	- else
	- {
	- // Search for an offset dimension that is too big
	- for( unsigned int i=0; i<VDimension && !tooBig; i++ )
	- {
	- tooBig = ( offset[i] >= 2 \|\| offset[i] <= -2 );
	- }
	-
	- if( tooBig ){
	- //inputStepSize /= 1.5;
	- inputStepSize -= (this->GetDefaultInputStepSize()/0.5);
	- }
	- }
	- }
	- while( tooSmall \|\| tooBig );
	-
	- input += inputStepSize;
	- return offset;
	-}
	-
	-
	-/**
	- * Standard "PrintSelf" method
	- */
	-template <unsigned int VDimension>
	-void
	-SlowPolyLineParametricPath<VDimension>
	-::PrintSelf( std::ostream& os, Indent indent) const
	-{
	- Superclass::PrintSelf( os, indent );
	-}
	-
	-
	-
	-} // end namespaceitk
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/StochasticTracking/itkStochasticTractographyFilter_SD.txx b/Modules/DiffusionImaging/FiberTracking/Algorithms/StochasticTracking/itkStochasticTractographyFilter_SD.txx
	deleted file mode 100644
	index 1943f4ea87..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/StochasticTracking/itkStochasticTractographyFilter_SD.txx
	+++ /dev/null
	@@ -1,2601 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#include "itkStochasticTractographyFilter.h"
	-
	-namespace itk{
	-
	-template< class TInputDWIImage, class TInputMaskImage, class TOutputConnectivityImage >
	-void
	-StochasticTractographyFilter< TInputDWIImage, TInputMaskImage, TOutputConnectivityImage >
	-::LoadDefaultSampleDirections( void ){
	- const unsigned int totalsd = 2562;
	- double sdarray[totalsd][3] = {
	- {0.850651, 0.525731, 6.12323e-17},
	- {-0.850651, 0.525731, 6.12323e-17},
	- {-0.850651 , -0.525731, 6.12323e-17},
	- {0.850651, -0.525731, 6.12323e-17},
	- {0.525731, 0, 0.850651},
	- {0.525731, 0, -0.850651},
	- {-0.525731, 6.43835e-17, -0.850651},
	- {-0.525731, 6.43835e-17, 0.850651},
	- {5.20873e-17, 0.850651, 0.525731},
	- {5.20873e-17, -0.850651, 0.525731},
	- {5.20873e-17, -0.850651, -0.525731},
	- {5.20873e-17, 0.850651, -0.525731},
	- {0, 0, 1},
	- {-0.309017, 0.5, 0.809017 },
	- {0.309017, 0.5, 0.809017},
	- {0.309017, -0.5, 0.809017},
	- {-0.309017, -0.5, 0.809017},
	- {0.309017, 0.5, -0.809017},
	- {-0.309017, 0.5, -0.809017},
	- {1.22465e-16, 0, -1},
	- {-0.309017 , -0.5, -0.809017},
	- {0.309017, -0.5, -0.809017},
	- {1, 0, 6.12323e-17},
	- {0.809017, -0.309017, 0.5},
	- {0.809017, 0.309017, 0.5},
	- {0.809017, 0.309017, -0.5},
	- {0.809017, -0.309017, -0.5 },
	- {-1, 1.22465e-16, 6.12323e-17},
	- {-0.809017, 0.309017, 0.5},
	- {-0.809017, -0.309017, 0.5},
	- {-0.809017, -0.309017, -0.5},
	- {-0.809017, 0.309017, -0.5},
	- {6.12323e-17, 1, 6.12323e-17 },
	- {0.5, 0.809017, -0.309017},
	- {0.5, 0.809017, 0.309017},
	- {-0.5, 0.809017, 0.309017},
	- {-0.5, 0.809017, -0.309017},
	- {0.5, -0.809017, 0.309017},
	- {0.5, -0.809017, -0.309017},
	- { 6.12323e-17, -1, 6.12323e-17},
	- {-0.5, -0.809017, -0.309017},
	- {-0.5, -0.809017, 0.309017},
	- {0.273267, 0, 0.961938},
	- {0.16246, 0.262866, 0.951057},
	- {0.433889, 0.259892, 0.862668},
	- {- 0.273267, 3.34655e-17, 0.961938},
	- {-0.433889, 0.259892, 0.862668},
	- {-0.16246, 0.262866, 0.951057},
	- {-8.4544e-17, 0.525731, 0.850651},
	- {-0.160622, 0.702046, 0.69378},
	- {0.160622, 0.702046, 0.69378},
	- {0.433889, -0.259892, 0.862668},
	- {0.16246, -0.262866, 0.951057},
	- {0.160622, -0.702046, 0.69378},
	- {-0.160622, -0.702046, 0.69378},
	- {-8.4544e-17, -0.525731, 0.850651},
	- {-0.16246 , -0.262866, 0.951057},
	- {-0.433889, -0.259892, 0.862668},
	- {0.433889, 0.259892, -0.862668},
	- {0.16246, 0.262866, -0.951057},
	- {0.273267, 0, -0.961938},
	- {0.160622, 0.702046, -0.69378},
	- {- 0.160622, 0.702046, -0.69378},
	- {-8.4544e-17, 0.525731, -0.850651},
	- {-0.16246, 0.262866, -0.951057},
	- {-0.433889, 0.259892, -0.862668},
	- {-0.273267, 3.34655e-17, -0.961938},
	- {0.16246, -0.262866 , -0.951057},
	- {0.433889, -0.259892, -0.862668},
	- {-0.433889, -0.259892, -0.862668},
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	- {0.790112, -0.545109, -0.280319},
	- {0.414273, -0.536784, -0.735011},
	- {0.470917, -0.628313, -0.619242},
	- {0.443957, -0.584716, -0.678977},
	- {0.485208, -0.51797, -0.704471},
	- { 0.552418, -0.496441, -0.669612},
	- {0.51797, -0.704471, -0.485208},
	- {0.496441, -0.669612, -0.552418},
	- {0.536784, -0.735011, -0.414273},
	- {0.584716, -0.678977, -0.443957},
	- {0.628313, -0.619242 , -0.470917},
	- {0.619242, -0.470917, -0.628313},
	- {0.678977, -0.443957, -0.584716},
	- {0.669612, -0.552418, -0.496441},
	- {0.704471, -0.485208, -0.51797},
	- {0.735011, -0.414273, -0.536784},
	- {0.54065, -0.607478, -0.581952},
	- {0.607478, -0.581952, -0.54065},
	- {0.581952, -0.54065, -0.607478},
	- {-0.551859, 0.106494, 0.82711},
	- {-0.634579, 0.187432, 0.749786},
	- {-0.594895, 0.147414 , 0.79017},
	- {-0.529135, 0.172532, 0.830812},
	- {-0.504209, 0.237229, 0.830359},
	- {-0.705236, 0.267381, 0.65662},
	- {-0.672319, 0.2289, 0.703983},
	- {-0.760406, 0.341435, 0.552454},
	- {-0.734794 , 0.305212, 0.605741},
	- {-0.678913, 0.334692, 0.653497},
	- {-0.649448, 0.399769, 0.64684},
	- {-0.619186, 0.361592, 0.697037},
	- {-0.476226, 0.303801, 0.825175},
	- {-0.446977, 0.366027, 0.816233},
	- {-0.553372, 0.38673, 0.737712},
	- {-0.522499, 0.448259, 0.725299},
	- {-0.48624, 0.408286, 0.772575},
	- {-0.415597, 0.427135, 0.803016},
	- {-0.382683, 0.485712, 0.785899},
	- {-0.610926, 0.25518 , 0.749435},
	- {-0.583691, 0.322141, 0.745338},
	- {-0.545109, 0.280319, 0.790112},
	- {-0.803016, 0.415597, 0.427135},
	- {-0.785899, 0.382683, 0.485712},
	- {-0.825175, 0.476226, 0.303801},
	- {- 0.816233, 0.446977, 0.366027},
	- {-0.772575, 0.48624, 0.408286},
	- {-0.737712, 0.553372, 0.38673},
	- {-0.725299, 0.522499, 0.448259},
	- {-0.830812, 0.529135, 0.172532},
	- {-0.830359, 0.504209, 0.237229 },
	- {-0.82711, 0.551859, 0.106494},
	- {-0.79017, 0.594895, 0.147414},
	- {-0.749786, 0.634579, 0.187432},
	- {-0.697037, 0.619186, 0.361592},
	- {-0.653497, 0.678913, 0.334692},
	- {-0.64684, 0.649448 , 0.399769},
	- {-0.703983, 0.672319, 0.2289},
	- {-0.65662, 0.705236, 0.267381},
	- {-0.605741, 0.734794, 0.305212},
	- {-0.552454, 0.760406, 0.341435},
	- {-0.790112, 0.545109, 0.280319},
	- {-0.749435 , 0.610926, 0.25518},
	- {-0.745338, 0.583691, 0.322141},
	- {-0.341435, 0.552454, 0.760406},
	- {-0.305212, 0.605741, 0.734794},
	- {-0.399769, 0.64684, 0.649448},
	- {-0.361592, 0.697037, 0.619186},
	- {-0.334692, 0.653497, 0.678913},
	- {-0.267381, 0.65662, 0.705236},
	- {-0.2289, 0.703983, 0.672319},
	- {-0.448259, 0.725299, 0.522499},
	- {-0.408286, 0.772575, 0.48624},
	- {-0.38673, 0.737712, 0.553372},
	- {-0.485712, 0.785899, 0.382683},
	- {-0.427135, 0.803016, 0.415597},
	- {-0.366027, 0.816233, 0.446977},
	- {-0.303801, 0.825175, 0.476226},
	- {-0.187432, 0.749786, 0.634579},
	- {-0.147414 , 0.79017, 0.594895},
	- {-0.237229, 0.830359, 0.504209},
	- {-0.172532, 0.830812, 0.529135},
	- {-0.106494, 0.82711, 0.551859},
	- {-0.322141, 0.745338, 0.583691},
	- {-0.280319, 0.790112, 0.545109},
	- {-0.25518, 0.749435, 0.610926},
	- {-0.735011, 0.414273, 0.536784},
	- {-0.669612, 0.552418, 0.496441},
	- {-0.704471, 0.485208, 0.51797},
	- {-0.678977, 0.443957, 0.584716},
	- {-0.619242, 0.470917 , 0.628313},
	- {-0.584716, 0.678977, 0.443957},
	- {-0.628313, 0.619242, 0.470917},
	- {-0.536784, 0.735011, 0.414273},
	- {-0.51797, 0.704471, 0.485208},
	- {-0.496441, 0.669612, 0.552418},
	- {- 0.552418, 0.496441, 0.669612},
	- {-0.485208, 0.51797, 0.704471},
	- {-0.470917, 0.628313, 0.619242},
	- {-0.443957, 0.584716, 0.678977},
	- {-0.414273, 0.536784, 0.735011},
	- {-0.607478, 0.581952, 0.54065 },
	- {-0.54065, 0.607478, 0.581952},
	- {-0.581952, 0.54065, 0.607478},
	- {-0.551859, 0.106494, -0.82711},
	- {-0.504209, 0.237229, -0.830359},
	- {-0.529135, 0.172532, -0.830812},
	- {-0.594895, 0.147414, -0.79017},
	- {-0.634579, 0.187432, -0.749786},
	- {-0.446977, 0.366027, -0.816233},
	- {-0.476226, 0.303801, -0.825175},
	- {-0.382683, 0.485712, -0.785899},
	- {-0.415597, 0.427135, -0.803016 },
	- {-0.48624, 0.408286, -0.772575},
	- {-0.522499, 0.448259, -0.725299},
	- {-0.553372, 0.38673, -0.737712},
	- {-0.672319, 0.2289, -0.703983},
	- {-0.705236, 0.267381, -0.65662},
	- {-0.619186, 0.361592, -0.697037},
	- {-0.649448, 0.399769, -0.64684},
	- {-0.678913, 0.334692, -0.653497},
	- {-0.734794, 0.305212, -0.605741},
	- {-0.760406, 0.341435, -0.552454},
	- {-0.545109, 0.280319, -0.790112 },
	- {-0.583691, 0.322141, -0.745338},
	- {-0.610926, 0.25518, -0.749435},
	- {-0.305212, 0.605741, -0.734794},
	- {-0.341435, 0.552454, -0.760406},
	- {-0.2289, 0.703983, -0.672319},
	- {-0.267381 , 0.65662, -0.705236},
	- {-0.334692, 0.653497, -0.678913},
	- {-0.361592, 0.697037, -0.619186},
	- {-0.399769, 0.64684, -0.649448},
	- {-0.147414, 0.79017, -0.594895},
	- {-0.187432, 0.749786, -0.634579 },
	- {-0.106494, 0.82711, -0.551859},
	- {-0.172532, 0.830812, -0.529135},
	- {-0.237229, 0.830359, -0.504209},
	- {-0.38673, 0.737712, -0.553372},
	- {-0.408286, 0.772575, -0.48624},
	- {-0.448259 , 0.725299, -0.522499},
	- {-0.303801, 0.825175, -0.476226},
	- {-0.366027, 0.816233, -0.446977},
	- {-0.427135, 0.803016, -0.415597},
	- {-0.485712, 0.785899, -0.382683},
	- {-0.25518, 0.749435, -0.610926 },
	- {-0.280319, 0.790112, -0.545109},
	- {-0.322141, 0.745338, -0.583691},
	- {-0.785899, 0.382683, -0.485712},
	- {-0.803016, 0.415597, -0.427135},
	- {-0.725299, 0.522499, -0.448259},
	- {-0.737712 , 0.553372, -0.38673},
	- {-0.772575, 0.48624, -0.408286},
	- {-0.816233, 0.446977, -0.366027},
	- {-0.825175, 0.476226, -0.303801},
	- {-0.64684, 0.649448, -0.399769},
	- {-0.653497, 0.678913, -0.334692 },
	- {-0.697037, 0.619186, -0.361592},
	- {-0.552454, 0.760406, -0.341435},
	- {-0.605741, 0.734794, -0.305212},
	- {-0.65662, 0.705236, -0.267381},
	- {-0.703983, 0.672319, -0.2289},
	- {-0.830359 , 0.504209, -0.237229},
	- {-0.830812, 0.529135, -0.172532},
	- {-0.749786, 0.634579, -0.187432},
	- {-0.79017, 0.594895, -0.147414},
	- {-0.82711, 0.551859, -0.106494},
	- {-0.745338, 0.583691, -0.322141 },
	- {-0.749435, 0.610926, -0.25518},
	- {-0.790112, 0.545109, -0.280319},
	- {-0.414273, 0.536784, -0.735011},
	- {-0.470917, 0.628313, -0.619242},
	- {-0.443957, 0.584716, -0.678977},
	- {-0.485208 , 0.51797, -0.704471},
	- {-0.552418, 0.496441, -0.669612},
	- {-0.51797, 0.704471, -0.485208},
	- {-0.496441, 0.669612, -0.552418},
	- {-0.536784, 0.735011, -0.414273},
	- {-0.584716, 0.678977, -0.443957 },
	- {-0.628313, 0.619242, -0.470917},
	- {-0.619242, 0.470917, -0.628313},
	- {-0.678977, 0.443957, -0.584716},
	- {-0.669612, 0.552418, -0.496441},
	- {-0.704471, 0.485208, -0.51797},
	- {-0.735011 , 0.414273, -0.536784},
	- {-0.54065, 0.607478, -0.581952},
	- {-0.607478, 0.581952, -0.54065},
	- {-0.581952, 0.54065, -0.607478},
	- {-0.551859, -0.106494, 0.82711},
	- {-0.504209, -0.237229, 0.830359 },
	- {-0.529135, -0.172532, 0.830812},
	- {-0.594895, -0.147414, 0.79017},
	- {-0.634579, -0.187432, 0.749786},
	- {-0.446977, -0.366027, 0.816233},
	- {-0.476226, -0.303801, 0.825175},
	- {-0.382683 , -0.485712, 0.785899},
	- {-0.415597, -0.427135, 0.803016},
	- {-0.48624, -0.408286, 0.772575},
	- {-0.522499, -0.448259, 0.725299},
	- {-0.553372, -0.38673, 0.737712},
	- {-0.672319, -0.2289, 0.703983 },
	- {-0.705236, -0.267381, 0.65662},
	- {-0.619186, -0.361592, 0.697037},
	- {-0.649448, -0.399769, 0.64684},
	- {-0.678913, -0.334692, 0.653497},
	- {-0.734794, -0.305212, 0.605741},
	- {-0.760406 , -0.341435, 0.552454},
	- {-0.545109, -0.280319, 0.790112},
	- {-0.583691, -0.322141, 0.745338},
	- {-0.610926, -0.25518, 0.749435},
	- {-0.305212, -0.605741, 0.734794},
	- {-0.341435, -0.552454, 0.760406 },
	- {-0.2289, -0.703983, 0.672319},
	- {-0.267381, -0.65662, 0.705236},
	- {-0.334692, -0.653497, 0.678913},
	- {-0.361592, -0.697037, 0.619186},
	- {-0.399769, -0.64684, 0.649448},
	- {-0.147414 , -0.79017, 0.594895},
	- {-0.187432, -0.749786, 0.634579},
	- {-0.106494, -0.82711, 0.551859},
	- {-0.172532, -0.830812, 0.529135},
	- {-0.237229, -0.830359, 0.504209},
	- {-0.38673, -0.737712, 0.553372 },
	- {-0.408286, -0.772575, 0.48624},
	- {-0.448259, -0.725299, 0.522499},
	- {-0.303801, -0.825175, 0.476226},
	- {-0.366027, -0.816233, 0.446977},
	- {-0.427135, -0.803016, 0.415597},
	- {-0.485712 , -0.785899, 0.382683},
	- {-0.25518, -0.749435, 0.610926},
	- {-0.280319, -0.790112, 0.545109},
	- {-0.322141, -0.745338, 0.583691},
	- {-0.785899, -0.382683, 0.485712},
	- {-0.803016, -0.415597, 0.427135 },
	- {-0.725299, -0.522499, 0.448259},
	- {-0.737712, -0.553372, 0.38673},
	- {-0.772575, -0.48624, 0.408286},
	- {-0.816233, -0.446977, 0.366027},
	- {-0.825175, -0.476226, 0.303801},
	- {-0.64684 , -0.649448, 0.399769},
	- {-0.653497, -0.678913, 0.334692},
	- {-0.697037, -0.619186, 0.361592},
	- {-0.552454, -0.760406, 0.341435},
	- {-0.605741, -0.734794, 0.305212},
	- {-0.65662, -0.705236, 0.267381 },
	- {-0.703983, -0.672319, 0.2289},
	- {-0.830359, -0.504209, 0.237229},
	- {-0.830812, -0.529135, 0.172532},
	- {-0.749786, -0.634579, 0.187432},
	- {-0.79017, -0.594895, 0.147414},
	- {-0.82711 , -0.551859, 0.106494},
	- {-0.745338, -0.583691, 0.322141},
	- {-0.749435, -0.610926, 0.25518},
	- {-0.790112, -0.545109, 0.280319},
	- {-0.414273, -0.536784, 0.735011},
	- {-0.470917, -0.628313, 0.619242 },
	- {-0.443957, -0.584716, 0.678977},
	- {-0.485208, -0.51797, 0.704471},
	- {-0.552418, -0.496441, 0.669612},
	- {-0.51797, -0.704471, 0.485208},
	- {-0.496441, -0.669612, 0.552418},
	- {-0.536784 , -0.735011, 0.414273},
	- {-0.584716, -0.678977, 0.443957},
	- {-0.628313, -0.619242, 0.470917},
	- {-0.619242, -0.470917, 0.628313},
	- {-0.678977, -0.443957, 0.584716},
	- {-0.669612, -0.552418, 0.496441 },
	- {-0.704471, -0.485208, 0.51797},
	- {-0.735011, -0.414273, 0.536784},
	- {-0.54065, -0.607478, 0.581952},
	- {-0.607478, -0.581952, 0.54065},
	- {-0.581952, -0.54065, 0.607478},
	- {-0.551859 , -0.106494, -0.82711},
	- {-0.634579, -0.187432, -0.749786},
	- {-0.594895, -0.147414, -0.79017},
	- {-0.529135, -0.172532, -0.830812},
	- {-0.504209, -0.237229, -0.830359},
	- {-0.705236, -0.267381, - 0.65662},
	- {-0.672319, -0.2289, -0.703983},
	- {-0.760406, -0.341435, -0.552454},
	- {-0.734794, -0.305212, -0.605741},
	- {-0.678913, -0.334692, -0.653497},
	- {-0.649448, -0.399769, -0.64684},
	- {- 0.619186, -0.361592, -0.697037},
	- {-0.476226, -0.303801, -0.825175},
	- {-0.446977, -0.366027, -0.816233},
	- {-0.553372, -0.38673, -0.737712},
	- {-0.522499, -0.448259, -0.725299},
	- {-0.48624, -0.408286 , -0.772575},
	- {-0.415597, -0.427135, -0.803016},
	- {-0.382683, -0.485712, -0.785899},
	- {-0.610926, -0.25518, -0.749435},
	- {-0.583691, -0.322141, -0.745338},
	- {-0.545109, -0.280319, -0.790112},
	- {-0.803016, -0.415597, -0.427135},
	- {-0.785899, -0.382683, -0.485712},
	- {-0.825175, -0.476226, -0.303801},
	- {-0.816233, -0.446977, -0.366027},
	- {-0.772575, -0.48624, -0.408286},
	- {-0.737712 , -0.553372, -0.38673},
	- {-0.725299, -0.522499, -0.448259},
	- {-0.830812, -0.529135, -0.172532},
	- {-0.830359, -0.504209, -0.237229},
	- {-0.82711, -0.551859, -0.106494},
	- {-0.79017, -0.594895, - 0.147414},
	- {-0.749786, -0.634579, -0.187432},
	- {-0.697037, -0.619186, -0.361592},
	- {-0.653497, -0.678913, -0.334692},
	- {-0.64684, -0.649448, -0.399769},
	- {-0.703983, -0.672319, -0.2289},
	- {-0.65662, -0.705236, -0.267381},
	- {-0.605741, -0.734794, -0.305212},
	- {-0.552454, -0.760406, -0.341435},
	- {-0.790112, -0.545109, -0.280319},
	- {-0.749435, -0.610926, -0.25518},
	- {-0.745338 , -0.583691, -0.322141},
	- {-0.341435, -0.552454, -0.760406},
	- {-0.305212, -0.605741, -0.734794},
	- {-0.399769, -0.64684, -0.649448},
	- {-0.361592, -0.697037, -0.619186},
	- {-0.334692, -0.653497, - 0.678913},
	- {-0.267381, -0.65662, -0.705236},
	- {-0.2289, -0.703983, -0.672319},
	- {-0.448259, -0.725299, -0.522499},
	- {-0.408286, -0.772575, -0.48624},
	- {-0.38673, -0.737712, -0.553372},
	- {- 0.485712, -0.785899, -0.382683},
	- {-0.427135, -0.803016, -0.415597},
	- {-0.366027, -0.816233, -0.446977},
	- {-0.303801, -0.825175, -0.476226},
	- {-0.187432, -0.749786, -0.634579},
	- {-0.147414, - 0.79017, -0.594895},
	- {-0.237229, -0.830359, -0.504209},
	- {-0.172532, -0.830812, -0.529135},
	- {-0.106494, -0.82711, -0.551859},
	- {-0.322141, -0.745338, -0.583691},
	- {-0.280319, -0.790112, -0.545109 },
	- {-0.25518, -0.749435, -0.610926},
	- {-0.735011, -0.414273, -0.536784},
	- {-0.669612, -0.552418, -0.496441},
	- {-0.704471, -0.485208, -0.51797},
	- {-0.678977, -0.443957, -0.584716},
	- {-0.619242 , -0.470917, -0.628313},
	- {-0.584716, -0.678977, -0.443957},
	- {-0.628313, -0.619242, -0.470917},
	- {-0.536784, -0.735011, -0.414273},
	- {-0.51797, -0.704471, -0.485208},
	- {-0.496441, -0.669612, - 0.552418},
	- {-0.552418, -0.496441, -0.669612},
	- {-0.485208, -0.51797, -0.704471},
	- {-0.470917, -0.628313, -0.619242},
	- {-0.443957, -0.584716, -0.678977},
	- {-0.414273, -0.536784, -0.735011},
	- {-0.607478, -0.581952, -0.54065},
	- {-0.54065, -0.607478, -0.581952},
	- {-0.581952, -0.54065, -0.607478}
	- };
	- TractOrientationContainerType::Pointer sdcontainerptr =
	- TractOrientationContainerType::New();
	-
	- for(unsigned int i = 0; i<totalsd; i++){
	- TractOrientationContainerType::Element dir(
	- sdarray[i][0], sdarray[i][1], sdarray[i][2]);
	- sdcontainerptr->InsertElement(i, dir);
	- }
	-
	- this->SetSampleDirections( sdcontainerptr );
	-}
	-
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingDataHandler.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingDataHandler.cpp
	deleted file mode 100644
	index bae0ea1b8d..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingDataHandler.cpp
	+++ /dev/null
	@@ -1,27 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkTrackingDataHandler.h"
	-
	-namespace mitk
	-{
	-TrackingDataHandler::TrackingDataHandler()
	- : m_RngItk(ItkRngType::New())
	- , m_NeedsDataInit(true)
	-{
	-
	-}
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingDataHandler.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingDataHandler.h
	deleted file mode 100644
	index a61bbf7ed9..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingDataHandler.h
	+++ /dev/null
	@@ -1,116 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _TrackingDataHandler
	-#define _TrackingDataHandler
	-
	-#include <MitkFiberTrackingExports.h>
	-#include <boost/random/discrete_distribution.hpp>
	-#include <boost/random/mersenne_twister.hpp>
	-#include <boost/random/variate_generator.hpp>
	-#include <deque>
	-#include <itkImage.h>
	-#include <itkLinearInterpolateImageFunction.h>
	-#include <itkMersenneTwisterRandomVariateGenerator.h>
	-#include <itkPoint.h>
	-#include <mitkBaseData.h>
	-#include <mitkDiffusionFunctionCollection.h>
	-#include <mitkStreamlineTractographyParameters.h>
	-
	-namespace mitk
	-{
	- /**
	- * \brief Abstract class for tracking handler. A tracking handler deals with determining the next progression
	- * direction of a streamline fiber. There are different handlers for tensor images, peak images, ... */
	-
	- class MITKFIBERTRACKING_EXPORT TrackingDataHandler
	- {
	- public:
	- TrackingDataHandler();
	- virtual ~TrackingDataHandler() {}
	-
	- typedef itk::Statistics::MersenneTwisterRandomVariateGenerator ItkRngType;
	- typedef boost::mt19937 BoostRngType;
	- typedef itk::Image<unsigned char, 3> ItkUcharImgType;
	- typedef itk::Image<short, 3> ItkShortImgType;
	- typedef itk::Image<float, 3> ItkFloatImgType;
	- typedef itk::Image<double, 3> ItkDoubleImgType;
	- typedef vnl_vector_fixed<float, 3> TrackingDirectionType;
	- typedef mitk::StreamlineTractographyParameters::MODE MODE;
	-
	- virtual TrackingDirectionType ProposeDirection(
	- const itk::Point<float, 3> &pos,
	- std::deque<TrackingDirectionType> &olddirs,
	- itk::Index<3> &oldIndex) = 0; ///< predicts next progression direction at the given position
	-
	- virtual void InitForTracking() = 0;
	- virtual itk::Vector<double, 3> GetSpacing() = 0;
	- virtual itk::Point<float, 3> GetOrigin() = 0;
	- virtual itk::Matrix<double, 3, 3> GetDirection() = 0;
	- virtual itk::ImageRegion<3> GetLargestPossibleRegion() = 0;
	- virtual bool WorldToIndex(itk::Point<float, 3> &pos, itk::Index<3> &index) = 0;
	-
	- void SetParameters(std::shared_ptr<mitk::StreamlineTractographyParameters> parameters)
	- {
	- m_Parameters = parameters;
	-
	- if (m_Parameters->m_FixRandomSeed)
	- {
	- m_Rng.seed(0);
	- std::srand(0);
	- m_RngItk->SetSeed(0);
	- }
	- else
	- {
	- m_Rng.seed();
	- m_RngItk->SetSeed();
	- std::srand(std::time(nullptr));
	- }
	- }
	-
	- double GetRandDouble(const double &a, const double &b) { return m_RngItk->GetUniformVariate(a, b); }
	-
	- protected:
	- void CalculateMinVoxelSize()
	- {
	- itk::Vector<double, 3> imageSpacing = this->GetSpacing();
	- float minVoxelSize = 0;
	- if (imageSpacing[0] < imageSpacing[1] && imageSpacing[0] < imageSpacing[2])
	- minVoxelSize = static_cast<float>(imageSpacing[0]);
	- else if (imageSpacing[1] < imageSpacing[2])
	- minVoxelSize = static_cast<float>(imageSpacing[1]);
	- else
	- minVoxelSize = static_cast<float>(imageSpacing[2]);
	-
	- if (m_Parameters == nullptr)
	- mitkThrow() << "No tractography parameter opbect set!";
	-
	- m_Parameters->SetMinVoxelSizeMm(minVoxelSize);
	- }
	-
	- BoostRngType m_Rng;
	- ItkRngType::Pointer m_RngItk;
	- bool m_NeedsDataInit;
	- std::shared_ptr<mitk::StreamlineTractographyParameters> m_Parameters;
	-
	- void DataModified() { m_NeedsDataInit = true; }
	-
	- vnl_matrix_fixed<float, 3, 3> m_FloatImageRotation;
	- };
	-
	-} // namespace mitk
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerOdf.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerOdf.cpp
	deleted file mode 100644
	index 503a0143c5..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerOdf.cpp
	+++ /dev/null
	@@ -1,307 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkTrackingHandlerOdf.h"
	-#include <itkDiffusionOdfGeneralizedFaImageFilter.h>
	-#include <itkImageRegionIterator.h>
	-#include <itkPointShell.h>
	-#include <omp.h>
	-#include <cmath>
	-
	-namespace mitk
	-{
	-
	-TrackingHandlerOdf::TrackingHandlerOdf()
	- : m_NumProbSamples(1)
	- , m_OdfFromTensor(false)
	-{
	- m_GfaInterpolator = itk::LinearInterpolateImageFunction< itk::Image< float, 3 >, float >::New();
	- m_OdfInterpolator = itk::LinearInterpolateImageFunction< itk::Image< ItkOdfImageType::PixelType, 3 >, float >::New();
	-}
	-
	-TrackingHandlerOdf::~TrackingHandlerOdf()
	-{
	-}
	-
	-bool TrackingHandlerOdf::WorldToIndex(itk::Point<float, 3>& pos, itk::Index<3>& index)
	-{
	- m_OdfImage->TransformPhysicalPointToIndex(pos, index);
	- return m_OdfImage->GetLargestPossibleRegion().IsInside(index);
	-}
	-
	-void TrackingHandlerOdf::InitForTracking()
	-{
	- MITK_INFO << "Initializing ODF tracker.";
	-
	- if (m_NeedsDataInit)
	- {
	- m_OdfHemisphereIndices.clear();
	- itk::OrientationDistributionFunction< float, ODF_SAMPLING_SIZE > odf;
	- vnl_vector_fixed<double,3> ref; ref.fill(0); ref[0]=1;
	-
	- for (int i=0; i<ODF_SAMPLING_SIZE; i++)
	- if (dot_product(ref, odf.GetDirection(i))>0)
	- m_OdfHemisphereIndices.push_back(i);
	- m_OdfFloatDirs.set_size(m_OdfHemisphereIndices.size(), 3);
	-
	- auto double_dir = m_OdfImage->GetDirection().GetVnlMatrix();
	- for (int r=0; r<3; r++)
	- for (int c=0; c<3; c++)
	- {
	- m_FloatImageRotation[r][c] = double_dir[r][c];
	- }
	-
	- for (unsigned int i=0; i<m_OdfHemisphereIndices.size(); i++)
	- {
	- m_OdfFloatDirs[i][0] = odf.GetDirection(m_OdfHemisphereIndices[i])[0];
	- m_OdfFloatDirs[i][1] = odf.GetDirection(m_OdfHemisphereIndices[i])[1];
	- m_OdfFloatDirs[i][2] = odf.GetDirection(m_OdfHemisphereIndices[i])[2];
	- }
	-
	- if (m_GfaImage.IsNull())
	- {
	- MITK_INFO << "Calculating GFA image.";
	- typedef itk::DiffusionOdfGeneralizedFaImageFilter<float,float,ODF_SAMPLING_SIZE> GfaFilterType;
	- GfaFilterType::Pointer gfaFilter = GfaFilterType::New();
	- gfaFilter->SetInput(m_OdfImage);
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_STANDARD);
	- gfaFilter->Update();
	- m_GfaImage = gfaFilter->GetOutput();
	- }
	-
	- this->CalculateMinVoxelSize();
	- m_NeedsDataInit = false;
	- }
	-
	- if (m_OdfFromTensor)
	- {
	- m_Parameters->m_OdfCutoff = 0;
	- m_Parameters->m_SharpenOdfs = false;
	- }
	-
	- m_GfaInterpolator->SetInputImage(m_GfaImage);
	- m_OdfInterpolator->SetInputImage(m_OdfImage);
	-
	- std::cout << "TrackingHandlerOdf - GFA threshold: " << m_Parameters->m_Cutoff << std::endl;
	- std::cout << "TrackingHandlerOdf - ODF threshold: " << m_Parameters->m_OdfCutoff << std::endl;
	- if (m_Parameters->m_SharpenOdfs)
	- std::cout << "TrackingHandlerOdf - Sharpening ODfs" << std::endl;
	-}
	-
	-int TrackingHandlerOdf::SampleOdf(vnl_vector< float >& probs, vnl_vector< float >& angles)
	-{
	- boost::random::discrete_distribution<int, float> dist(probs.begin(), probs.end());
	- int sampled_idx = 0;
	- int max_sample_idx = -1;
	- float max_prob = 0;
	- int trials = 0;
	-
	- for (int i=0; i<m_NumProbSamples; i++) // we sample m_NumProbSamples times and retain the sample with maximum probabilty
	- {
	- trials++;
	-#pragma omp critical
	- {
	- boost::random::variate_generator<boost::random::mt19937&, boost::random::discrete_distribution<int,float>> sampler(m_Rng, dist);
	- sampled_idx = sampler();
	- }
	- if (probs[sampled_idx]>max_prob && probs[sampled_idx]>m_Parameters->m_OdfCutoff && fabs(angles[sampled_idx])>=m_Parameters->GetAngularThresholdDot())
	- {
	- max_prob = probs[sampled_idx];
	- max_sample_idx = sampled_idx;
	- }
	- else if ( (probs[sampled_idx]<=m_Parameters->m_OdfCutoff \|\| fabs(angles[sampled_idx])<m_Parameters->GetAngularThresholdDot()) && trials<50) // we allow 50 trials to exceed the ODF threshold
	- i--;
	- }
	-
	- return max_sample_idx;
	-}
	-
	-void TrackingHandlerOdf::SetIsOdfFromTensor(bool OdfFromTensor)
	-{
	- m_OdfFromTensor = OdfFromTensor;
	-}
	-
	-bool TrackingHandlerOdf::GetIsOdfFromTensor() const
	-{
	- return m_OdfFromTensor;
	-}
	-
	-vnl_vector_fixed<float,3> TrackingHandlerOdf::ProposeDirection(const itk::Point<float, 3>& pos, std::deque<vnl_vector_fixed<float, 3> >& olddirs, itk::Index<3>& oldIndex)
	-{
	-
	- vnl_vector_fixed<float,3> output_direction; output_direction.fill(0);
	-
	- itk::Index<3> idx;
	- m_OdfImage->TransformPhysicalPointToIndex(pos, idx);
	-
	- if ( !m_OdfImage->GetLargestPossibleRegion().IsInside(idx) )
	- return output_direction;
	-
	- // check GFA threshold for termination
	- float gfa = mitk::imv::GetImageValue<float>(pos, m_Parameters->m_InterpolateTractographyData, m_GfaInterpolator);
	- if (gfa<m_Parameters->m_Cutoff)
	- return output_direction;
	-
	- vnl_vector_fixed<float,3> last_dir;
	- if (!olddirs.empty())
	- last_dir = olddirs.back();
	-
	- if (!m_Parameters->m_InterpolateTractographyData && oldIndex==idx)
	- return last_dir;
	-
	- ItkOdfImageType::PixelType odf_values = mitk::imv::GetImageValue<ItkOdfImageType::PixelType>(pos, m_Parameters->m_InterpolateTractographyData, m_OdfInterpolator);
	- vnl_vector< float > probs; probs.set_size(m_OdfHemisphereIndices.size());
	- vnl_vector< float > angles; angles.set_size(m_OdfHemisphereIndices.size()); angles.fill(1.0);
	-
	- // Find ODF maximum and remove <0 values
	- float max_odf_val = 0;
	- float min_odf_val = 999;
	- int max_idx_d = -1;
	- int c = 0;
	- for (int i : m_OdfHemisphereIndices)
	- {
	- if (odf_values[i]<0)
	- odf_values[i] = 0;
	-
	- if (odf_values[i]>max_odf_val)
	- {
	- max_odf_val = odf_values[i];
	- max_idx_d = c;
	- }
	- if (odf_values[i]<min_odf_val)
	- min_odf_val = odf_values[i];
	-
	- probs[c] = odf_values[i];
	- c++;
	- }
	-
	- if (m_Parameters->m_SharpenOdfs)
	- {
	- // sharpen ODF
	- probs -= min_odf_val;
	- probs /= (max_odf_val-min_odf_val);
	- for (unsigned int i=0; i<probs.size(); i++)
	- probs[i] = pow(probs[i], 4);
	- float odf_sum = probs.sum();
	- if (odf_sum>0)
	- {
	- probs /= odf_sum;
	- max_odf_val /= odf_sum;
	- }
	- }
	-
	- // no previous direction
	- if (max_odf_val>m_Parameters->m_OdfCutoff && (olddirs.empty() \|\| last_dir.magnitude()<=0.5))
	- {
	- if (m_Parameters->m_Mode==MODE::DETERMINISTIC) // return maximum peak
	- {
	- output_direction = m_OdfFloatDirs.get_row(max_idx_d);
	- return output_direction * max_odf_val;
	- }
	- else if (m_Parameters->m_Mode==MODE::PROBABILISTIC) // sample from complete ODF
	- {
	- int max_sample_idx = SampleOdf(probs, angles);
	- if (max_sample_idx>=0)
	- output_direction = m_OdfFloatDirs.get_row(max_sample_idx) * probs[max_sample_idx];
	- return output_direction;
	- }
	- }
	- else if (max_odf_val<=m_Parameters->m_OdfCutoff) // return (0,0,0)
	- {
	- return output_direction;
	- }
	-
	- // correct previous direction
	- if (m_Parameters->m_FlipX)
	- last_dir[0] *= -1;
	- if (m_Parameters->m_FlipY)
	- last_dir[1] *= -1;
	- if (m_Parameters->m_FlipZ)
	- last_dir[2] *= -1;
	-
	- // calculate angles between previous direction and ODF directions
	- angles = m_OdfFloatDirs*last_dir;
	-
	- float probs_sum = 0;
	- float max_prob = 0;
	- for (unsigned int i=0; i<m_OdfHemisphereIndices.size(); i++)
	- {
	- float odf_val = probs[i];
	- float angle = angles[i];
	- float abs_angle = fabs(angle);
	-
	- odf_val *= abs_angle; // weight probabilities according to deviation from last direction
	- if (m_Parameters->m_Mode==MODE::DETERMINISTIC && odf_val>max_prob && odf_val>m_Parameters->m_OdfCutoff)
	- {
	- // use maximum peak of the ODF weighted with the directional prior
	- max_prob = odf_val;
	- vnl_vector_fixed<float,3> d = m_OdfFloatDirs.get_row(i);
	- if (angle<0)
	- d *= -1;
	- output_direction = odf_val*d;
	- }
	- else if (m_Parameters->m_Mode==MODE::PROBABILISTIC)
	- {
	- // update ODF probabilties with the ODF values pow(abs_angle, m_DirPriorPower)
	- probs[i] = odf_val;
	- probs_sum += probs[i];
	- }
	- }
	-
	- // do probabilistic sampling
	- if (m_Parameters->m_Mode==MODE::PROBABILISTIC && probs_sum>0.0001)
	- {
	- int max_sample_idx = SampleOdf(probs, angles);
	- if (max_sample_idx>=0)
	- {
	- output_direction = m_OdfFloatDirs.get_row(max_sample_idx);
	- if (angles[max_sample_idx]<0)
	- output_direction *= -1;
	- output_direction *= probs[max_sample_idx];
	- }
	- }
	-
	- // check hard angular threshold
	- float mag = output_direction.magnitude();
	- if (mag>=0.0001)
	- {
	- output_direction.normalize();
	- float a = dot_product(output_direction, last_dir);
	- if (a<m_Parameters->GetAngularThresholdDot())
	- output_direction.fill(0);
	- }
	- else
	- output_direction.fill(0);
	-
	- if (m_Parameters->m_FlipX)
	- output_direction[0] *= -1;
	- if (m_Parameters->m_FlipY)
	- output_direction[1] *= -1;
	- if (m_Parameters->m_FlipZ)
	- output_direction[2] *= -1;
	- if (m_Parameters->m_ApplyDirectionMatrix)
	- output_direction = m_FloatImageRotation*output_direction;
	-
	- return output_direction;
	-}
	-
	-void TrackingHandlerOdf::SetNumProbSamples(int NumProbSamples)
	-{
	- m_NumProbSamples = NumProbSamples;
	-}
	-
	-}
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerOdf.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerOdf.h
	deleted file mode 100644
	index 4a70fd4f0c..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerOdf.h
	+++ /dev/null
	@@ -1,80 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _TrackingHandlerOdf
	-#define _TrackingHandlerOdf
	-
	-#include "mitkTrackingDataHandler.h"
	-#include <mitkOdfImage.h>
	-#include <mitkTensorImage.h>
	-#include <itkOrientationDistributionFunction.h>
	-#include <MitkFiberTrackingExports.h>
	-
	-namespace mitk
	-{
	-
	-/**
	-* \brief Enables streamline tracking on sampled ODF images. */
	-
	-class MITKFIBERTRACKING_EXPORT TrackingHandlerOdf : public TrackingDataHandler
	-{
	-
	-public:
	-
	- TrackingHandlerOdf();
	- ~TrackingHandlerOdf() override;
	-
	- typedef OdfImage::ItkOdfImageType ItkOdfImageType;
	- typedef itk::Image< vnl_vector_fixed<float,3>, 3> ItkPDImgType;
	-
	-
	- void InitForTracking() override; ///< calls InputDataValidForTracking() and creates feature images
	- vnl_vector_fixed<float,3> ProposeDirection(const itk::Point<float, 3>& pos, std::deque< vnl_vector_fixed<float,3> >& olddirs, itk::Index<3>& oldIndex) override; ///< predicts next progression direction at the given position
	- bool WorldToIndex(itk::Point<float, 3>& pos, itk::Index<3>& index) override;
	-
	- void SetOdfImage( ItkOdfImageType::Pointer img ){ m_OdfImage = img; DataModified(); }
	- void SetGfaImage( ItkFloatImgType::Pointer img ){ m_GfaImage = img; DataModified(); }
	-
	- ItkUcharImgType::SpacingType GetSpacing() override{ return m_OdfImage->GetSpacing(); }
	- itk::Point<float,3> GetOrigin() override{ return m_OdfImage->GetOrigin(); }
	- ItkUcharImgType::DirectionType GetDirection() override{ return m_OdfImage->GetDirection(); }
	- ItkUcharImgType::RegionType GetLargestPossibleRegion() override{ return m_OdfImage->GetLargestPossibleRegion(); }
	-
	- int OdfPower() const;
	- void SetNumProbSamples(int NumProbSamples);
	-
	- bool GetIsOdfFromTensor() const;
	- void SetIsOdfFromTensor(bool OdfFromTensor);
	-
	-protected:
	-
	- int SampleOdf(vnl_vector< float >& probs, vnl_vector< float >& angles);
	-
	- ItkFloatImgType::Pointer m_GfaImage; ///< GFA image used to determine streamline termination.
	- ItkOdfImageType::Pointer m_OdfImage; ///< Input odf image.
	- ItkOdfImageType::Pointer m_WorkingOdfImage; ///< Modified odf image.
	- std::vector< int > m_OdfHemisphereIndices;
	- vnl_matrix< float > m_OdfFloatDirs;
	- int m_NumProbSamples;
	- bool m_OdfFromTensor;
	-
	- itk::LinearInterpolateImageFunction< itk::Image< float, 3 >, float >::Pointer m_GfaInterpolator;
	- itk::LinearInterpolateImageFunction< itk::Image< ItkOdfImageType::PixelType, 3 >, float >::Pointer m_OdfInterpolator;
	-};
	-
	-}
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerPeaks.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerPeaks.cpp
	deleted file mode 100644
	index efa67a9145..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerPeaks.cpp
	+++ /dev/null
	@@ -1,306 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkTrackingHandlerPeaks.h"
	-
	-namespace mitk
	-{
	-
	-TrackingHandlerPeaks::TrackingHandlerPeaks()
	-{
	-
	-}
	-
	-TrackingHandlerPeaks::~TrackingHandlerPeaks()
	-{
	-}
	-
	-bool TrackingHandlerPeaks::WorldToIndex(itk::Point<float, 3>& pos, itk::Index<3>& index)
	-{
	- m_DummyImage->TransformPhysicalPointToIndex(pos, index);
	- return m_DummyImage->GetLargestPossibleRegion().IsInside(index);
	-}
	-
	-void TrackingHandlerPeaks::InitForTracking()
	-{
	- MITK_INFO << "Initializing peak tracker.";
	-
	- if (m_NeedsDataInit)
	- {
	- itk::Vector<double, 4> spacing4 = m_PeakImage->GetSpacing();
	- itk::Point<float, 4> origin4 = m_PeakImage->GetOrigin();
	- itk::Matrix<double, 4, 4> direction4 = m_PeakImage->GetDirection();
	- itk::ImageRegion<4> imageRegion4 = m_PeakImage->GetLargestPossibleRegion();
	-
	- spacing3[0] = spacing4[0]; spacing3[1] = spacing4[1]; spacing3[2] = spacing4[2];
	- origin3[0] = origin4[0]; origin3[1] = origin4[1]; origin3[2] = origin4[2];
	- for (int r=0; r<3; r++)
	- for (int c=0; c<3; c++)
	- {
	- direction3[r][c] = direction4[r][c];
	- m_FloatImageRotation[r][c] = direction4[r][c];
	- }
	- imageRegion3.SetSize(0, imageRegion4.GetSize()[0]);
	- imageRegion3.SetSize(1, imageRegion4.GetSize()[1]);
	- imageRegion3.SetSize(2, imageRegion4.GetSize()[2]);
	-
	- m_DummyImage = ItkUcharImgType::New();
	- m_DummyImage->SetSpacing( spacing3 );
	- m_DummyImage->SetOrigin( origin3 );
	- m_DummyImage->SetDirection( direction3 );
	- m_DummyImage->SetRegions( imageRegion3 );
	- m_DummyImage->Allocate();
	- m_DummyImage->FillBuffer(0.0);
	-
	- m_NumDirs = imageRegion4.GetSize(3)/3;
	-
	- this->CalculateMinVoxelSize();
	- m_NeedsDataInit = false;
	- }
	-
	- std::cout << "TrackingHandlerPeaks - Peak threshold: " << m_Parameters->m_Cutoff << std::endl;
	- if (m_Parameters->m_Mode == MODE::PROBABILISTIC)
	- std::cout << "TrackingHandlerPeaks - Peak jitter: " << m_Parameters->m_PeakJitter << std::endl;
	-}
	-
	-vnl_vector_fixed<float,3> TrackingHandlerPeaks::GetMatchingDirection(itk::Index<3> idx3, vnl_vector_fixed<float,3>& oldDir)
	-{
	- vnl_vector_fixed<float,3> out_dir; out_dir.fill(0);
	- float angle = 0;
	- float mag = oldDir.magnitude();
	- if (mag<mitk::eps)
	- {
	- bool found = false;
	-
	- if (!m_Parameters->m_FixRandomSeed)
	- {
	- // try m_NumDirs times to get a non-zero random direction
	- for (int j=0; j<m_NumDirs; j++)
	- {
	- int i = 0;
	-#pragma omp critical
	- i = m_RngItk->GetIntegerVariate(m_NumDirs-1);
	- out_dir = GetDirection(idx3, i);
	-
	- if (out_dir.magnitude()>mitk::eps)
	- {
	- oldDir[0] = out_dir[0];
	- oldDir[1] = out_dir[1];
	- oldDir[2] = out_dir[2];
	- found = true;
	- break;
	- }
	- }
	- }
	-
	- if (!found)
	- {
	- // if you didn't find a non-zero random direction, take first non-zero direction you find
	- for (int i=0; i<m_NumDirs; i++)
	- {
	- out_dir = GetDirection(idx3, i);
	- if (out_dir.magnitude()>mitk::eps)
	- {
	- oldDir[0] = out_dir[0];
	- oldDir[1] = out_dir[1];
	- oldDir[2] = out_dir[2];
	- break;
	- }
	- }
	- }
	- }
	- else
	- {
	- for (int i=0; i<m_NumDirs; i++)
	- {
	- vnl_vector_fixed<float,3> dir = GetDirection(idx3, i);
	- mag = dir.magnitude();
	- if (mag>mitk::eps)
	- dir.normalize();
	- float a = dot_product(dir, oldDir);
	- if (fabs(a)>angle)
	- {
	- angle = fabs(a);
	- if (a<0)
	- out_dir = -dir;
	- else
	- out_dir = dir;
	- out_dir *= mag;
	- out_dir *= angle; // shrink contribution of direction if is less parallel to previous direction
	- }
	- }
	- }
	-
	- return out_dir;
	-}
	-
	-vnl_vector_fixed<float,3> TrackingHandlerPeaks::GetDirection(itk::Index<3> idx3, int dirIdx)
	-{
	- vnl_vector_fixed<float,3> dir; dir.fill(0.0);
	- if ( !m_DummyImage->GetLargestPossibleRegion().IsInside(idx3) )
	- return dir;
	-
	- PeakImgType::IndexType idx4;
	- idx4.SetElement(0,idx3[0]);
	- idx4.SetElement(1,idx3[1]);
	- idx4.SetElement(2,idx3[2]);
	-
	- for (int k=0; k<3; k++)
	- {
	- idx4.SetElement(3, dirIdx*3 + k);
	- dir[k] = m_PeakImage->GetPixel(idx4);
	- }
	-
	- if (m_Parameters->m_FlipX)
	- dir[0] *= -1;
	- if (m_Parameters->m_FlipY)
	- dir[1] *= -1;
	- if (m_Parameters->m_FlipZ)
	- dir[2] *= -1;
	- if (m_Parameters->m_ApplyDirectionMatrix)
	- dir = m_FloatImageRotation*dir;
	-
	- return dir;
	-}
	-
	-vnl_vector_fixed<float,3> TrackingHandlerPeaks::GetDirection(itk::Point<float, 3> itkP, bool interpolate, vnl_vector_fixed<float,3> oldDir){
	- // transform physical point to index coordinates
	- itk::Index<3> idx3;
	- itk::ContinuousIndex< float, 3> cIdx;
	- m_DummyImage->TransformPhysicalPointToIndex(itkP, idx3);
	- m_DummyImage->TransformPhysicalPointToContinuousIndex(itkP, cIdx);
	-
	- vnl_vector_fixed<float,3> dir; dir.fill(0.0);
	- if ( !m_DummyImage->GetLargestPossibleRegion().IsInside(idx3) )
	- return dir;
	-
	- if (interpolate)
	- {
	- float frac_x = cIdx[0] - idx3[0];
	- float frac_y = cIdx[1] - idx3[1];
	- float frac_z = cIdx[2] - idx3[2];
	- if (frac_x<0)
	- {
	- idx3[0] -= 1;
	- frac_x += 1;
	- }
	- if (frac_y<0)
	- {
	- idx3[1] -= 1;
	- frac_y += 1;
	- }
	- if (frac_z<0)
	- {
	- idx3[2] -= 1;
	- frac_z += 1;
	- }
	- frac_x = 1-frac_x;
	- frac_y = 1-frac_y;
	- frac_z = 1-frac_z;
	-
	- // int coordinates inside image?
	- if (idx3[0] >= 0 && idx3[0] < static_cast<itk::IndexValueType>(m_DummyImage->GetLargestPossibleRegion().GetSize(0) - 1) &&
	- idx3[1] >= 0 && idx3[1] < static_cast<itk::IndexValueType>(m_DummyImage->GetLargestPossibleRegion().GetSize(1) - 1) &&
	- idx3[2] >= 0 && idx3[2] < static_cast<itk::IndexValueType>(m_DummyImage->GetLargestPossibleRegion().GetSize(2) - 1))
	- {
	- // trilinear interpolation
	- vnl_vector_fixed<float, 8> interpWeights;
	- interpWeights[0] = ( frac_x)( frac_y)( frac_z);
	- interpWeights[1] = (1-frac_x)( frac_y)( frac_z);
	- interpWeights[2] = ( frac_x)(1-frac_y)( frac_z);
	- interpWeights[3] = ( frac_x)( frac_y)(1-frac_z);
	- interpWeights[4] = (1-frac_x)(1-frac_y)( frac_z);
	- interpWeights[5] = ( frac_x)(1-frac_y)(1-frac_z);
	- interpWeights[6] = (1-frac_x)( frac_y)(1-frac_z);
	- interpWeights[7] = (1-frac_x)(1-frac_y)(1-frac_z);
	-
	- dir = GetMatchingDirection(idx3, oldDir) * interpWeights[0];
	-
	- itk::Index<3> tmpIdx = idx3; tmpIdx[0]++;
	- dir += GetMatchingDirection(tmpIdx, oldDir) * interpWeights[1];
	-
	- tmpIdx = idx3; tmpIdx[1]++;
	- dir += GetMatchingDirection(tmpIdx, oldDir) * interpWeights[2];
	-
	- tmpIdx = idx3; tmpIdx[2]++;
	- dir += GetMatchingDirection(tmpIdx, oldDir) * interpWeights[3];
	-
	- tmpIdx = idx3; tmpIdx[0]++; tmpIdx[1]++;
	- dir += GetMatchingDirection(tmpIdx, oldDir) * interpWeights[4];
	-
	- tmpIdx = idx3; tmpIdx[1]++; tmpIdx[2]++;
	- dir += GetMatchingDirection(tmpIdx, oldDir) * interpWeights[5];
	-
	- tmpIdx = idx3; tmpIdx[2]++; tmpIdx[0]++;
	- dir += GetMatchingDirection(tmpIdx, oldDir) * interpWeights[6];
	-
	- tmpIdx = idx3; tmpIdx[0]++; tmpIdx[1]++; tmpIdx[2]++;
	- dir += GetMatchingDirection(tmpIdx, oldDir) * interpWeights[7];
	- }
	- }
	- else
	- dir = GetMatchingDirection(idx3, oldDir);
	-
	- return dir;
	-}
	-
	-vnl_vector_fixed<float,3> TrackingHandlerPeaks::ProposeDirection(const itk::Point<float, 3>& pos, std::deque<vnl_vector_fixed<float, 3> >& olddirs, itk::Index<3>& oldIndex)
	-{
	- // CHECK: wann wird wo normalisiert
	- vnl_vector_fixed<float,3> output_direction; output_direction.fill(0);
	-
	- itk::Index<3> index;
	- m_DummyImage->TransformPhysicalPointToIndex(pos, index);
	-
	- vnl_vector_fixed<float,3> oldDir; oldDir.fill(0.0);
	- if (!olddirs.empty())
	- oldDir = olddirs.back();
	- float old_mag = oldDir.magnitude();
	-
	- if (!m_Parameters->m_InterpolateTractographyData && oldIndex==index)
	- return oldDir;
	-
	- output_direction = GetDirection(pos, m_Parameters->m_InterpolateTractographyData, oldDir);
	- float mag = output_direction.magnitude();
	-
	- if (mag>=m_Parameters->m_Cutoff)
	- {
	- if (m_Parameters->m_Mode == MODE::PROBABILISTIC)
	- {
	- output_direction[0] += this->m_RngItk->GetNormalVariate(0, fabs(output_direction[0])*m_Parameters->m_PeakJitter);
	- output_direction[1] += this->m_RngItk->GetNormalVariate(0, fabs(output_direction[1])*m_Parameters->m_PeakJitter);
	- output_direction[2] += this->m_RngItk->GetNormalVariate(0, fabs(output_direction[2])*m_Parameters->m_PeakJitter);
	- mag = output_direction.magnitude();
	- }
	-
	- output_direction.normalize();
	-
	- float a = 1;
	- if (old_mag>0.5)
	- a = dot_product(output_direction, oldDir);
	- if (a>=m_Parameters->GetAngularThresholdDot())
	- output_direction *= mag;
	- else
	- output_direction.fill(0);
	- }
	- else
	- output_direction.fill(0);
	-
	- return output_direction;
	-}
	-
	-}
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerPeaks.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerPeaks.h
	deleted file mode 100644
	index 6143ac66f2..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerPeaks.h
	+++ /dev/null
	@@ -1,71 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _TrackingHandlerPeaks
	-#define _TrackingHandlerPeaks
	-
	-#include "mitkTrackingDataHandler.h"
	-#include <itkDiffusionTensor3D.h>
	-#include <MitkFiberTrackingExports.h>
	-
	-namespace mitk
	-{
	-
	-/**
	-* \brief Enables deterministic streamline tracking on MRtrix style peak images (4D float images) */
	-
	-class MITKFIBERTRACKING_EXPORT TrackingHandlerPeaks : public TrackingDataHandler
	-{
	-
	-public:
	-
	- TrackingHandlerPeaks();
	- ~TrackingHandlerPeaks() override;
	-
	- typedef itk::Image< float, 4 > PeakImgType; ///< MRtrix peak image type
	-
	-
	- void InitForTracking() override; ///< calls InputDataValidForTracking() and creates feature images
	- vnl_vector_fixed<float,3> ProposeDirection(const itk::Point<float, 3>& pos, std::deque< vnl_vector_fixed<float,3> >& olddirs, itk::Index<3>& oldIndex) override; ///< predicts next progression direction at the given position
	- bool WorldToIndex(itk::Point<float, 3>& pos, itk::Index<3>& index) override;
	-
	- void SetPeakImage( PeakImgType::Pointer image ){ m_PeakImage = image; DataModified(); }
	-
	- itk::Vector<double, 3> GetSpacing() override{ return spacing3; }
	- itk::Point<float,3> GetOrigin() override{ return origin3; }
	- itk::Matrix<double, 3, 3> GetDirection() override{ return direction3; }
	- itk::ImageRegion<3> GetLargestPossibleRegion() override{ return imageRegion3; }
	-
	-protected:
	-
	- vnl_vector_fixed<float,3> GetDirection(itk::Point<float, 3> itkP, bool interpolate, vnl_vector_fixed<float,3> oldDir);
	- vnl_vector_fixed<float,3> GetMatchingDirection(itk::Index<3> idx3, vnl_vector_fixed<float,3>& oldDir);
	- vnl_vector_fixed<float,3> GetDirection(itk::Index<3> idx3, int dirIdx);
	-
	- PeakImgType::ConstPointer m_PeakImage;
	- int m_NumDirs;
	-
	- itk::Vector<double, 3> spacing3;
	- itk::Point<float, 3> origin3;
	- itk::Matrix<double, 3, 3> direction3;
	- itk::ImageRegion<3> imageRegion3;
	-
	- ItkUcharImgType::Pointer m_DummyImage;
	-};
	-
	-}
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerRandomForest.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerRandomForest.cpp
	deleted file mode 100644
	index f8375e26d6..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerRandomForest.cpp
	+++ /dev/null
	@@ -1,909 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _TrackingForestHandler_cpp
	-#define _TrackingForestHandler_cpp
	-
	-#include "mitkTrackingHandlerRandomForest.h"
	-#include <itkTractDensityImageFilter.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-
	-namespace mitk
	-{
	-template< int ShOrder, int NumberOfSignalFeatures >
	-TrackingHandlerRandomForest< ShOrder, NumberOfSignalFeatures >::TrackingHandlerRandomForest()
	- : m_WmSampleDistance(-1)
	- , m_NumTrees(30)
	- , m_MaxTreeDepth(25)
	- , m_SampleFraction(1.0)
	- , m_NumberOfSamples(0)
	- , m_GmSamplesPerVoxel(-1)
	- , m_BidirectionalFiberSampling(false)
	- , m_ZeroDirWmFeatures(true)
	- , m_MaxNumWmSamples(-1)
	-{
	- vnl_vector_fixed<float,3> ref; ref.fill(0); ref[0]=1;
	-
	- itk::OrientationDistributionFunction< float, 200 > odf;
	- m_DirectionContainer.clear();
	- for (unsigned int i = 0; i<odf.GetNumberOfComponents(); i++)
	- {
	- vnl_vector_fixed<float,3> odf_dir;
	- odf_dir[0] = odf.GetDirection(i)[0];
	- odf_dir[1] = odf.GetDirection(i)[1];
	- odf_dir[2] = odf.GetDirection(i)[2];
	- if (dot_product(ref, odf_dir)>0) // only used directions on one hemisphere
	- m_DirectionContainer.push_back(odf_dir); // store indices for later mapping the classifier output to the actual direction
	- }
	-
	-
	- m_OdfFloatDirs.set_size(m_DirectionContainer.size(), 3);
	-
	- for (unsigned int i=0; i<m_DirectionContainer.size(); i++)
	- {
	- m_OdfFloatDirs[i][0] = m_DirectionContainer.at(i)[0];
	- m_OdfFloatDirs[i][1] = m_DirectionContainer.at(i)[1];
	- m_OdfFloatDirs[i][2] = m_DirectionContainer.at(i)[2];
	- }
	-}
	-
	-template< int ShOrder, int NumberOfSignalFeatures >
	-TrackingHandlerRandomForest< ShOrder, NumberOfSignalFeatures >::~TrackingHandlerRandomForest()
	-{
	-}
	-
	-template< int ShOrder, int NumberOfSignalFeatures >
	-bool TrackingHandlerRandomForest< ShOrder, NumberOfSignalFeatures >::WorldToIndex(itk::Point<float, 3>& pos, itk::Index<3>& index)
	-{
	- m_DwiFeatureImages.at(0)->TransformPhysicalPointToIndex(pos, index);
	- return m_DwiFeatureImages.at(0)->GetLargestPossibleRegion().IsInside(index);
	-}
	-
	-template< int ShOrder, int NumberOfSignalFeatures >
	-void TrackingHandlerRandomForest< ShOrder, NumberOfSignalFeatures >::InputDataValidForTracking()
	-{
	- if (m_InputDwis.empty())
	- mitkThrow() << "No diffusion-weighted images set!";
	- if (!IsForestValid())
	- mitkThrow() << "No or invalid random forest detected!";
	-}
	-
	-template< int ShOrder, int NumberOfSignalFeatures>
	-template<typename T>
	-typename std::enable_if< NumberOfSignalFeatures <=99, T >::type TrackingHandlerRandomForest< ShOrder, NumberOfSignalFeatures >::InitDwiImageFeatures(mitk::Image::Pointer mitk_dwi)
	-{
	- MITK_INFO << "Calculating spherical harmonics features";
	- typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,ShOrder, 2*NumberOfSignalFeatures> InterpolationFilterType;
	-
	- typename InterpolationFilterType::Pointer filter = InterpolationFilterType::New();
	- filter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(mitk_dwi));
	- filter->SetGradientImage( mitk::DiffusionPropertyHelper::GetOriginalGradientContainer(mitk_dwi), mitk::DiffusionPropertyHelper::GetItkVectorImage(mitk_dwi) );
	- filter->SetLambda(0.006);
	- filter->SetNormalizationMethod(InterpolationFilterType::QBAR_RAW_SIGNAL);
	- filter->Update();
	-
	- m_DwiFeatureImages.push_back(filter->GetCoefficientImage());
	- return true;
	-}
	-
	-template< int ShOrder, int NumberOfSignalFeatures>
	-template<typename T>
	-typename std::enable_if< NumberOfSignalFeatures >=100, T >::type TrackingHandlerRandomForest< ShOrder, NumberOfSignalFeatures >::InitDwiImageFeatures(mitk::Image::Pointer mitk_dwi)
	-{
	- MITK_INFO << "Interpolating raw dwi signal features";
	- typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,ShOrder, 2*NumberOfSignalFeatures> InterpolationFilterType;
	-
	- typename InterpolationFilterType::Pointer filter = InterpolationFilterType::New();
	- filter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(mitk_dwi));
	- filter->SetGradientImage( mitk::DiffusionPropertyHelper::GetOriginalGradientContainer(mitk_dwi), mitk::DiffusionPropertyHelper::GetItkVectorImage(mitk_dwi) );
	- filter->SetLambda(0.006);
	- filter->SetNormalizationMethod(InterpolationFilterType::QBAR_RAW_SIGNAL);
	- filter->Update();
	-
	- typename DwiFeatureImageType::Pointer dwiFeatureImage = DwiFeatureImageType::New();
	- dwiFeatureImage->SetSpacing(filter->GetOutput()->GetSpacing());
	- dwiFeatureImage->SetOrigin(filter->GetOutput()->GetOrigin());
	- dwiFeatureImage->SetDirection(filter->GetOutput()->GetDirection());
	- dwiFeatureImage->SetLargestPossibleRegion(filter->GetOutput()->GetLargestPossibleRegion());
	- dwiFeatureImage->SetBufferedRegion(filter->GetOutput()->GetLargestPossibleRegion());
	- dwiFeatureImage->SetRequestedRegion(filter->GetOutput()->GetLargestPossibleRegion());
	- dwiFeatureImage->Allocate();
	-
	- // get signal values and store them in the feature image
	- vnl_vector_fixed<double,3> ref; ref.fill(0); ref[0]=1;
	- itk::OrientationDistributionFunction< float, 2*NumberOfSignalFeatures > odf;
	- itk::ImageRegionIterator< typename InterpolationFilterType::OutputImageType > it(filter->GetOutput(), filter->GetOutput()->GetLargestPossibleRegion());
	- while(!it.IsAtEnd())
	- {
	- typename DwiFeatureImageType::PixelType pix;
	- int f = 0;
	- for (unsigned int i = 0; i<odf.GetNumberOfComponents(); i++)
	- {
	- if (dot_product(ref, odf.GetDirection(i))>0) // only used directions on one hemisphere
	- {
	- pix[f] = it.Get()[i];
	- f++;
	- }
	- }
	- dwiFeatureImage->SetPixel(it.GetIndex(), pix);
	- ++it;
	- }
	- m_DwiFeatureImages.push_back(dwiFeatureImage);
	- return true;
	-}
	-
	-template< int ShOrder, int NumberOfSignalFeatures >
	-void TrackingHandlerRandomForest< ShOrder, NumberOfSignalFeatures >::InitForTracking()
	-{
	- MITK_INFO << "Initializing random forest tracker.";
	- if (m_NeedsDataInit)
	- {
	- InputDataValidForTracking();
	- m_DwiFeatureImages.clear();
	- InitDwiImageFeatures<>(m_InputDwis.at(0));
	-
	- // initialize interpolators
	- m_DwiFeatureImageInterpolator = DwiFeatureImageInterpolatorType::New();
	- m_DwiFeatureImageInterpolator->SetInputImage(m_DwiFeatureImages.at(0));
	-
	- m_AdditionalFeatureImageInterpolators.clear();
	- for (auto afi_vec : m_AdditionalFeatureImages)
	- {
	- std::vector< FloatImageInterpolatorType::Pointer > v;
	- for (auto img : afi_vec)
	- {
	- FloatImageInterpolatorType::Pointer interp = FloatImageInterpolatorType::New();
	- interp->SetInputImage(img);
	- v.push_back(interp);
	- }
	- m_AdditionalFeatureImageInterpolators.push_back(v);
	- }
	-
	- auto double_dir = m_DwiFeatureImages.at(0)->GetDirection().GetVnlMatrix();
	- for (int r=0; r<3; r++)
	- for (int c=0; c<3; c++)
	- {
	- m_FloatImageRotation[r][c] = double_dir[r][c];
	- }
	-
	- this->CalculateMinVoxelSize();
	- m_NeedsDataInit = false;
	- }
	-}
	-
	-template< int ShOrder, int NumberOfSignalFeatures >
	-vnl_vector_fixed<float,3> TrackingHandlerRandomForest< ShOrder, NumberOfSignalFeatures >::ProposeDirection(const itk::Point<float, 3>& pos, std::deque<vnl_vector_fixed<float, 3> >& olddirs, itk::Index<3>& oldIndex)
	-{
	-
	- vnl_vector_fixed<float,3> output_direction; output_direction.fill(0);
	-
	- itk::Index<3> idx;
	- m_DwiFeatureImages.at(0)->TransformPhysicalPointToIndex(pos, idx);
	-
	- bool check_last_dir = false;
	- vnl_vector_fixed<float,3> last_dir;
	- if (!olddirs.empty())
	- {
	- last_dir = olddirs.back();
	- if (last_dir.magnitude()>0.5)
	- check_last_dir = true;
	- }
	-
	- if (!m_Parameters->m_InterpolateTractographyData && oldIndex==idx)
	- return last_dir;
	-
	- // store feature pixel values in a vigra data type
	- vigra::MultiArray<2, float> featureData = vigra::MultiArray<2, float>( vigra::Shape2(1,m_Forest->GetNumFeatures()) );
	- featureData.init(0.0);
	- typename DwiFeatureImageType::PixelType dwiFeaturePixel = mitk::imv::GetImageValue< typename DwiFeatureImageType::PixelType >(pos, m_Parameters->m_InterpolateTractographyData, m_DwiFeatureImageInterpolator);
	- for (unsigned int f=0; f<NumberOfSignalFeatures; f++)
	- featureData(0,f) = dwiFeaturePixel[f];
	-
	- vnl_matrix_fixed<double,3,3> direction_matrix = m_DwiFeatureImages.at(0)->GetDirection().GetVnlMatrix();
	- vnl_matrix_fixed<double,3,3> inverse_direction_matrix = m_DwiFeatureImages.at(0)->GetInverseDirection().GetVnlMatrix();
	-
	- // append normalized previous direction(s) to feature vector
	- int i = 0;
	- vnl_vector_fixed<double,3> ref; ref.fill(0); ref[0]=1;
	-
	- for (auto d : olddirs)
	- {
	- vnl_vector_fixed<double,3> tempD;
	- tempD[0] = d[0]; tempD[1] = d[1]; tempD[2] = d[2];
	-
	- if (m_Parameters->m_FlipX)
	- tempD[0] *= -1;
	- if (m_Parameters->m_FlipY)
	- tempD[1] *= -1;
	- if (m_Parameters->m_FlipZ)
	- tempD[2] *= -1;
	-
	- tempD = inverse_direction_matrix * tempD;
	- last_dir[0] = tempD[0];
	- last_dir[1] = tempD[1];
	- last_dir[2] = tempD[2];
	-
	- int c = 0;
	- for (int f=NumberOfSignalFeatures+3i; f<NumberOfSignalFeatures+3(i+1); f++)
	- {
	- if (dot_product(ref, tempD)<0)
	- featureData(0,f) = -tempD[c];
	- else
	- featureData(0,f) = tempD[c];
	- c++;
	- }
	- i++;
	- }
	-
	- // additional feature images
	- if (m_AdditionalFeatureImages.size()>0)
	- {
	- int c = 0;
	- for (auto interpolator : m_AdditionalFeatureImageInterpolators.at(0))
	- {
	- float v = mitk::imv::GetImageValue<float>(pos, false, interpolator);
	- featureData(0,NumberOfSignalFeatures+m_Parameters->m_NumPreviousDirections*3+c) = v;
	- c++;
	- }
	- }
	-
	- // perform classification
	- vigra::MultiArray<2, float> probs(vigra::Shape2(1, m_Forest->GetNumClasses()));
	- m_Forest->PredictProbabilities(featureData, probs);
	-
	- vnl_vector< float > angles = m_OdfFloatDirs*last_dir;
	- vnl_vector< float > probs2; probs2.set_size(m_DirectionContainer.size()); probs2.fill(0.0); // used for probabilistic direction sampling
	- float probs_sum = 0;
	-
	- float pNonFib = 0; // probability that we left the white matter
	- float w = 0; // weight of the predicted direction
	-
	- for (int i=0; i<m_Forest->GetNumClasses(); i++) // for each class (number of possible directions + out-of-wm class)
	- {
	- if (probs(0,i)>0) // if probability of respective class is 0, do nothing
	- {
	- // get label of class (does not correspond to the loop variable i)
	- unsigned int classLabel = m_Forest->IndexToClassLabel(i);
	-
	- if (classLabel<m_DirectionContainer.size()) // does class label correspond to a direction or to the out-of-wm class?
	- {
	- float angle = angles[classLabel];
	- float abs_angle = fabs(angle);
	-
	- if (m_Parameters->m_Mode==MODE::PROBABILISTIC)
	- {
	- probs2[classLabel] = probs(0,i);
	- if (check_last_dir)
	- probs2[classLabel] *= abs_angle;
	- probs_sum += probs2[classLabel];
	- }
	- else if (m_Parameters->m_Mode==MODE::DETERMINISTIC)
	- {
	- vnl_vector_fixed<float,3> d = m_DirectionContainer.at(classLabel); // get direction vector assiciated with the respective direction index
	- if (check_last_dir) // do we have a previous streamline direction or did we just start?
	- {
	- if (abs_angle>=m_Parameters->GetAngularThresholdDot()) // is angle between the directions smaller than our hard threshold?
	- {
	- if (angle<0) // make sure we don't walk backwards
	- d *= -1;
	- float w_i = probs(0,i)*abs_angle;
	- output_direction += w_i*d; // weight contribution to output direction with its probability and the angular deviation from the previous direction
	- w += w_i; // increase output weight of the final direction
	- }
	- }
	- else
	- {
	- output_direction += probs(0,i)*d;
	- w += probs(0,i);
	- }
	- }
	- }
	- else
	- pNonFib += probs(0,i); // probability that we are not in the white matter anymore
	- }
	- }
	-
	-
	- if (m_Parameters->m_Mode==MODE::PROBABILISTIC && pNonFib<0.5)
	- {
	- boost::random::discrete_distribution<int, float> dist(probs2.begin(), probs2.end());
	- int sampled_idx = 0;
	-
	- for (int i=0; i<50; i++) // we allow 50 trials to exceed m_AngularThreshold
	- {
	- #pragma omp critical
	- {
	- boost::random::variate_generator<boost::random::mt19937&, boost::random::discrete_distribution<int,float>> sampler(m_Rng, dist);
	- sampled_idx = sampler();
	- }
	-
	- if ( probs2[sampled_idx]>0.1 && (!check_last_dir \|\| (check_last_dir && fabs(angles[sampled_idx])>=m_Parameters->GetAngularThresholdDot())) )
	- break;
	- }
	-
	- output_direction = m_DirectionContainer.at(sampled_idx);
	- w = probs2[sampled_idx];
	- if (check_last_dir && angles[sampled_idx]<0) // make sure we don't walk backwards
	- output_direction *= -1;
	- }
	-
	- // if we did not find a suitable direction, make sure that we return (0,0,0)
	- if (pNonFib>w && w>0)
	- output_direction.fill(0.0);
	- else
	- {
	- vnl_vector_fixed<double,3> tempD;
	- tempD[0] = output_direction[0]; tempD[1] = output_direction[1]; tempD[2] = output_direction[2];
	- tempD = direction_matrix * tempD;
	- output_direction[0] = tempD[0];
	- output_direction[1] = tempD[1];
	- output_direction[2] = tempD[2];
	-
	- if (m_Parameters->m_FlipX)
	- output_direction[0] *= -1;
	- if (m_Parameters->m_FlipY)
	- output_direction[1] *= -1;
	- if (m_Parameters->m_FlipZ)
	- output_direction[2] *= -1;
	- if (m_Parameters->m_ApplyDirectionMatrix)
	- output_direction = m_FloatImageRotation*output_direction;
	- }
	-
	- return output_direction * w;
	-}
	-
	-template< int ShOrder, int NumberOfSignalFeatures >
	-void TrackingHandlerRandomForest< ShOrder, NumberOfSignalFeatures >::StartTraining()
	-{
	- m_StartTime = std::chrono::system_clock::now();
	- InputDataValidForTraining();
	- InitForTraining();
	- CalculateTrainingSamples();
	-
	- MITK_INFO << "Maximum tree depths: " << m_MaxTreeDepth;
	- MITK_INFO << "Sample fraction per tree: " << m_SampleFraction;
	- MITK_INFO << "Number of trees: " << m_NumTrees;
	-
	- DefaultSplitType splitter;
	- splitter.UsePointBasedWeights(true);
	- splitter.SetWeights(m_Weights);
	- splitter.UseRandomSplit(false);
	- splitter.SetPrecision(mitk::eps);
	- splitter.SetMaximumTreeDepth(m_MaxTreeDepth);
	-
	- std::vector< std::shared_ptr< vigra::RandomForest<int> > > trees;
	- int count = 0;
	-#pragma omp parallel for
	- for (int i = 0; i < m_NumTrees; ++i)
	- {
	- std::shared_ptr< vigra::RandomForest<int> > lrf = std::make_shared< vigra::RandomForest<int> >();
	- lrf->set_options().use_stratification(vigra::RF_NONE); // How the data should be made equal
	- lrf->set_options().sample_with_replacement(true); // if sampled with replacement or not
	- lrf->set_options().samples_per_tree(m_SampleFraction); // Fraction of samples that are used to train a tree
	- lrf->set_options().tree_count(1); // Number of trees that are calculated;
	- lrf->set_options().min_split_node_size(5); // Minimum number of datapoints that must be in a node
	- lrf->ext_param_.max_tree_depth = m_MaxTreeDepth;
	-
	- lrf->learn(m_FeatureData, m_LabelData,vigra::rf::visitors::VisitorBase(),splitter);
	-#pragma omp critical
	- {
	- count++;
	- MITK_INFO << "Tree " << count << " finished training.";
	- trees.push_back(lrf);
	- }
	- }
	-
	- for (int i = 1; i < m_NumTrees; ++i)
	- trees.at(0)->trees_.push_back(trees.at(i)->trees_[0]);
	-
	- std::shared_ptr< vigra::RandomForest<int> > forest = trees.at(0);
	- forest->options_.tree_count_ = m_NumTrees;
	- m_Forest = mitk::TractographyForest::New(forest);
	- MITK_INFO << "Training finsihed";
	-
	- m_EndTime = std::chrono::system_clock::now();
	- std::chrono::hours hh = std::chrono::duration_cast<std::chrono::hours>(m_EndTime - m_StartTime);
	- std::chrono::minutes mm = std::chrono::duration_cast<std::chrono::minutes>(m_EndTime - m_StartTime);
	- mm %= 60;
	- MITK_INFO << "Training took " << hh.count() << "h and " << mm.count() << "m";
	-}
	-
	-template< int ShOrder, int NumberOfSignalFeatures >
	-void TrackingHandlerRandomForest< ShOrder, NumberOfSignalFeatures >::InputDataValidForTraining()
	-{
	- if (m_InputDwis.empty())
	- mitkThrow() << "No diffusion-weighted images set!";
	- if (m_Tractograms.empty())
	- mitkThrow() << "No tractograms set!";
	- if (m_InputDwis.size()!=m_Tractograms.size())
	- mitkThrow() << "Unequal number of diffusion-weighted images and tractograms detected!";
	-}
	-
	-template< int ShOrder, int NumberOfSignalFeatures >
	-bool TrackingHandlerRandomForest< ShOrder, NumberOfSignalFeatures >::IsForestValid()
	-{
	- int additional_features = 0;
	- if (m_AdditionalFeatureImages.size()>0)
	- additional_features = m_AdditionalFeatureImages.at(0).size();
	-
	- if (!m_Forest)
	- MITK_INFO << "No forest available!";
	- else
	- {
	- if (m_Forest->GetNumTrees() <= 0)
	- MITK_ERROR << "Forest contains no trees!";
	- if ( m_Forest->GetNumFeatures() != static_cast<int>(NumberOfSignalFeatures+3*m_Parameters->m_NumPreviousDirections+additional_features) )
	- MITK_ERROR << "Wrong number of features in forest: got " << m_Forest->GetNumFeatures() << ", expected " << (NumberOfSignalFeatures+3*m_Parameters->m_NumPreviousDirections+additional_features);
	- }
	-
	- if(m_Forest && m_Forest->GetNumTrees()>0 && m_Forest->GetNumFeatures() == static_cast<int>(NumberOfSignalFeatures+3*m_Parameters->m_NumPreviousDirections+additional_features))
	- return true;
	-
	- return false;
	-}
	-
	-template< int ShOrder, int NumberOfSignalFeatures >
	-void TrackingHandlerRandomForest< ShOrder, NumberOfSignalFeatures >::InitForTraining()
	-{
	- MITK_INFO << "Spherical signal interpolation and sampling ...";
	- for (unsigned int i=0; i<m_InputDwis.size(); i++)
	- {
	- InitDwiImageFeatures<>(m_InputDwis.at(i));
	-
	- if (i>=m_AdditionalFeatureImages.size())
	- {
	- m_AdditionalFeatureImages.push_back(std::vector< ItkFloatImgType::Pointer >());
	- }
	-
	- if (i>=m_FiberVolumeModImages.size())
	- {
	- ItkFloatImgType::Pointer img = ItkFloatImgType::New();
	- img->SetSpacing( m_DwiFeatureImages.at(i)->GetSpacing() );
	- img->SetOrigin( m_DwiFeatureImages.at(i)->GetOrigin() );
	- img->SetDirection( m_DwiFeatureImages.at(i)->GetDirection() );
	- img->SetLargestPossibleRegion( m_DwiFeatureImages.at(i)->GetLargestPossibleRegion() );
	- img->SetBufferedRegion( m_DwiFeatureImages.at(i)->GetLargestPossibleRegion() );
	- img->SetRequestedRegion( m_DwiFeatureImages.at(i)->GetLargestPossibleRegion() );
	- img->Allocate();
	- img->FillBuffer(1);
	- m_FiberVolumeModImages.push_back(img);
	- }
	-
	- if (m_FiberVolumeModImages.at(i)==nullptr)
	- {
	- m_FiberVolumeModImages.at(i) = ItkFloatImgType::New();
	- m_FiberVolumeModImages.at(i)->SetSpacing( m_DwiFeatureImages.at(i)->GetSpacing() );
	- m_FiberVolumeModImages.at(i)->SetOrigin( m_DwiFeatureImages.at(i)->GetOrigin() );
	- m_FiberVolumeModImages.at(i)->SetDirection( m_DwiFeatureImages.at(i)->GetDirection() );
	- m_FiberVolumeModImages.at(i)->SetLargestPossibleRegion( m_DwiFeatureImages.at(i)->GetLargestPossibleRegion() );
	- m_FiberVolumeModImages.at(i)->SetBufferedRegion( m_DwiFeatureImages.at(i)->GetLargestPossibleRegion() );
	- m_FiberVolumeModImages.at(i)->SetRequestedRegion( m_DwiFeatureImages.at(i)->GetLargestPossibleRegion() );
	- m_FiberVolumeModImages.at(i)->Allocate();
	- m_FiberVolumeModImages.at(i)->FillBuffer(1);
	- }
	-
	- if (i>=m_MaskImages.size())
	- {
	- ItkUcharImgType::Pointer newMask = ItkUcharImgType::New();
	- newMask->SetSpacing( m_DwiFeatureImages.at(i)->GetSpacing() );
	- newMask->SetOrigin( m_DwiFeatureImages.at(i)->GetOrigin() );
	- newMask->SetDirection( m_DwiFeatureImages.at(i)->GetDirection() );
	- newMask->SetLargestPossibleRegion( m_DwiFeatureImages.at(i)->GetLargestPossibleRegion() );
	- newMask->SetBufferedRegion( m_DwiFeatureImages.at(i)->GetLargestPossibleRegion() );
	- newMask->SetRequestedRegion( m_DwiFeatureImages.at(i)->GetLargestPossibleRegion() );
	- newMask->Allocate();
	- newMask->FillBuffer(1);
	- m_MaskImages.push_back(newMask);
	- }
	-
	- if (m_MaskImages.at(i)==nullptr)
	- {
	- m_MaskImages.at(i) = ItkUcharImgType::New();
	- m_MaskImages.at(i)->SetSpacing( m_DwiFeatureImages.at(i)->GetSpacing() );
	- m_MaskImages.at(i)->SetOrigin( m_DwiFeatureImages.at(i)->GetOrigin() );
	- m_MaskImages.at(i)->SetDirection( m_DwiFeatureImages.at(i)->GetDirection() );
	- m_MaskImages.at(i)->SetLargestPossibleRegion( m_DwiFeatureImages.at(i)->GetLargestPossibleRegion() );
	- m_MaskImages.at(i)->SetBufferedRegion( m_DwiFeatureImages.at(i)->GetLargestPossibleRegion() );
	- m_MaskImages.at(i)->SetRequestedRegion( m_DwiFeatureImages.at(i)->GetLargestPossibleRegion() );
	- m_MaskImages.at(i)->Allocate();
	- m_MaskImages.at(i)->FillBuffer(1);
	- }
	- }
	-
	- // initialize interpolators
	- m_AdditionalFeatureImageInterpolators.clear();
	- for (auto afi_vec : m_AdditionalFeatureImages)
	- {
	- std::vector< FloatImageInterpolatorType::Pointer > v;
	- for (auto img : afi_vec)
	- {
	- FloatImageInterpolatorType::Pointer interp = FloatImageInterpolatorType::New();
	- interp->SetInputImage(img);
	- v.push_back(interp);
	- }
	- m_AdditionalFeatureImageInterpolators.push_back(v);
	- }
	-
	- MITK_INFO << "Resampling fibers and calculating number of samples ...";
	- m_NumberOfSamples = 0;
	- m_SampleUsage.clear();
	- for (unsigned int t=0; t<m_Tractograms.size(); t++)
	- {
	- ItkUcharImgType::Pointer mask = m_MaskImages.at(t);
	- ItkUcharImgType::Pointer wmmask;
	- if (t<m_WhiteMatterImages.size() && m_WhiteMatterImages.at(t)!=nullptr)
	- wmmask = m_WhiteMatterImages.at(t);
	- else
	- {
	- MITK_INFO << "No white-matter mask found. Using fiber envelope.";
	- itk::TractDensityImageFilter< ItkUcharImgType >::Pointer env = itk::TractDensityImageFilter< ItkUcharImgType >::New();
	- env->SetFiberBundle(m_Tractograms.at(t));
	- env->SetInputImage(mask);
	- env->SetBinaryOutput(true);
	- env->SetUseImageGeometry(true);
	- env->Update();
	- wmmask = env->GetOutput();
	- if (t>=m_WhiteMatterImages.size())
	- m_WhiteMatterImages.push_back(wmmask);
	- else
	- m_WhiteMatterImages.at(t) = wmmask;
	- }
	-
	- // Calculate white-matter samples
	- if (m_WmSampleDistance<0)
	- {
	- typename DwiFeatureImageType::Pointer image = m_DwiFeatureImages.at(t);
	- float minSpacing = 1;
	- if(image->GetSpacing()[0]<image->GetSpacing()[1] && image->GetSpacing()[0]<image->GetSpacing()[2])
	- minSpacing = image->GetSpacing()[0];
	- else if (image->GetSpacing()[1] < image->GetSpacing()[2])
	- minSpacing = image->GetSpacing()[1];
	- else
	- minSpacing = image->GetSpacing()[2];
	- m_WmSampleDistance = minSpacing*0.5;
	- }
	-
	- m_Tractograms.at(t)->ResampleLinear(m_WmSampleDistance);
	-
	- int wmSamples = m_Tractograms.at(t)->GetNumberOfPoints()-2*m_Tractograms.at(t)->GetNumFibers();
	- if (m_BidirectionalFiberSampling)
	- wmSamples *= 2;
	- if (m_ZeroDirWmFeatures)
	- wmSamples *= (m_Parameters->m_NumPreviousDirections+1);
	-
	- MITK_INFO << "White matter samples available: " << wmSamples;
	-
	- // upper limit for samples
	- if (m_MaxNumWmSamples>0 && wmSamples>m_MaxNumWmSamples)
	- {
	- if ((float)m_MaxNumWmSamples/wmSamples > 0.8)
	- {
	- m_SampleUsage.push_back(std::vector<bool>(wmSamples, true));
	- m_NumberOfSamples += wmSamples;
	- }
	- else
	- {
	- m_SampleUsage.push_back(std::vector<bool>(wmSamples, false));
	- m_NumberOfSamples += m_MaxNumWmSamples;
	- wmSamples = m_MaxNumWmSamples;
	- MITK_INFO << "Limiting white matter samples to: " << m_MaxNumWmSamples;
	-
	- itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer randgen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New();
	- randgen->SetSeed();
	- int c = 0;
	- while (c<m_MaxNumWmSamples)
	- {
	- int idx = randgen->GetIntegerVariate(m_MaxNumWmSamples-1);
	- if (m_SampleUsage[t][idx]==false)
	- {
	- m_SampleUsage[t][idx]=true;
	- ++c;
	- }
	- }
	- }
	- }
	- else
	- {
	- m_SampleUsage.push_back(std::vector<bool>(wmSamples, true));
	- m_NumberOfSamples += wmSamples;
	- }
	-
	- // calculate gray-matter samples
	- itk::ImageRegionConstIterator<ItkUcharImgType> it(wmmask, wmmask->GetLargestPossibleRegion());
	- int OUTOFWM = 0;
	- while(!it.IsAtEnd())
	- {
	- if (it.Get()==0 && mask->GetPixel(it.GetIndex())>0)
	- OUTOFWM++;
	- ++it;
	- }
	- MITK_INFO << "Non-white matter voxels: " << OUTOFWM;
	-
	- if (m_GmSamplesPerVoxel>0)
	- {
	- m_GmSamples.push_back(m_GmSamplesPerVoxel);
	- m_NumberOfSamples += m_GmSamplesPerVoxel*OUTOFWM;
	- }
	- else if (OUTOFWM>0)
	- {
	- int gm_per_voxel = 0.5+(float)wmSamples/(float)OUTOFWM;
	- if (gm_per_voxel<=0)
	- gm_per_voxel = 1;
	- m_GmSamples.push_back(gm_per_voxel);
	- m_NumberOfSamples += m_GmSamples.back()*OUTOFWM;
	- MITK_INFO << "Non-white matter samples per voxel: " << m_GmSamples.back();
	- }
	- else
	- {
	- m_GmSamples.push_back(0);
	- }
	- MITK_INFO << "Non-white matter samples: " << m_GmSamples.back()*OUTOFWM;
	- }
	- MITK_INFO << "Number of samples: " << m_NumberOfSamples;
	-}
	-
	-template< int ShOrder, int NumberOfSignalFeatures >
	-void TrackingHandlerRandomForest< ShOrder, NumberOfSignalFeatures >::CalculateTrainingSamples()
	-{
	- vnl_vector_fixed<float,3> ref; ref.fill(0); ref[0]=1;
	-
	- m_FeatureData.reshape( vigra::Shape2(m_NumberOfSamples, NumberOfSignalFeatures+m_Parameters->m_NumPreviousDirections*3+m_AdditionalFeatureImages.at(0).size()) );
	- m_LabelData.reshape( vigra::Shape2(m_NumberOfSamples,1) );
	- m_Weights.reshape( vigra::Shape2(m_NumberOfSamples,1) );
	- MITK_INFO << "Number of features: " << m_FeatureData.shape(1);
	-
	- itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer m_RandGen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New();
	- m_RandGen->SetSeed();
	- MITK_INFO << "Creating training data ...";
	- unsigned int sampleCounter = 0;
	- for (unsigned int t=0; t<m_Tractograms.size(); t++)
	- {
	- ItkFloatImgType::Pointer fiber_folume = m_FiberVolumeModImages.at(t);
	- FloatImageInterpolatorType::Pointer volume_interpolator = FloatImageInterpolatorType::New();
	- volume_interpolator->SetInputImage(fiber_folume);
	- typename DwiFeatureImageType::Pointer image = m_DwiFeatureImages.at(t);
	- typename DwiFeatureImageInterpolatorType::Pointer dwi_interp = DwiFeatureImageInterpolatorType::New();
	- dwi_interp->SetInputImage(image);
	-
	- ItkUcharImgType::Pointer wmMask = m_WhiteMatterImages.at(t);
	- ItkUcharImgType::Pointer mask;
	- if (t<m_MaskImages.size())
	- mask = m_MaskImages.at(t);
	-
	- // non-white matter samples
	- itk::ImageRegionConstIterator<ItkUcharImgType> it(wmMask, wmMask->GetLargestPossibleRegion());
	- while(!it.IsAtEnd())
	- {
	- if (it.Get()==0 && (mask.IsNull() \|\| (mask.IsNotNull() && mask->GetPixel(it.GetIndex())>0)))
	- {
	- typename DwiFeatureImageType::PixelType pix = image->GetPixel(it.GetIndex());
	-
	- // random directions
	- for (unsigned int i=0; i<m_GmSamples.at(t); i++)
	- {
	- // diffusion signal features
	- for (unsigned int f=0; f<NumberOfSignalFeatures; f++)
	- {
	- m_FeatureData(sampleCounter,f) = pix[f];
	- if(m_FeatureData(sampleCounter,f)!=m_FeatureData(sampleCounter,f))
	- m_FeatureData(sampleCounter,f) = 0;
	- }
	-
	- // direction feature
	- int num_zero_dirs = m_RandGen->GetIntegerVariate(m_Parameters->m_NumPreviousDirections); // how many directions should be zero?
	- for (unsigned int i=0; i<m_Parameters->m_NumPreviousDirections; i++)
	- {
	- int c=0;
	- vnl_vector_fixed<float,3> probe;
	- if (static_cast<int>(i)<num_zero_dirs)
	- probe.fill(0.0);
	- else
	- {
	- probe[0] = m_RandGen->GetVariate()*2-1;
	- probe[1] = m_RandGen->GetVariate()*2-1;
	- probe[2] = m_RandGen->GetVariate()*2-1;
	- probe.normalize();
	- if (dot_product(ref, probe)<0)
	- probe *= -1;
	- }
	- for (unsigned int f=NumberOfSignalFeatures+3i; f<NumberOfSignalFeatures+3(i+1); f++)
	- {
	- m_FeatureData(sampleCounter,f) = probe[c];
	- c++;
	- }
	- }
	-
	- // additional feature images
	- int add_feat_c = 0;
	- for (auto interpolator : m_AdditionalFeatureImageInterpolators.at(t))
	- {
	- itk::Point<float, 3> itkP;
	- image->TransformIndexToPhysicalPoint(it.GetIndex(), itkP);
	- float v = mitk::imv::GetImageValue<float>(itkP, false, interpolator);
	- m_FeatureData(sampleCounter,NumberOfSignalFeatures+m_Parameters->m_NumPreviousDirections*3+add_feat_c) = v;
	- add_feat_c++;
	- }
	-
	- // label and sample weight
	- m_LabelData(sampleCounter,0) = m_DirectionContainer.size();
	- m_Weights(sampleCounter,0) = 1.0;
	- sampleCounter++;
	- }
	- }
	- ++it;
	- }
	-
	- unsigned int num_gm_samples = sampleCounter;
	- // white matter samples
	- mitk::FiberBundle::Pointer fib = m_Tractograms.at(t);
	- vtkSmartPointer< vtkPolyData > polyData = fib->GetFiberPolyData();
	- vnl_vector_fixed<float,3> zero_dir; zero_dir.fill(0.0);
	- for (unsigned int i=0; i<fib->GetNumFibers(); i++)
	- {
	- vtkCell* cell = polyData->GetCell(i);
	- int numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	- float fiber_weight = fib->GetFiberWeight(i);
	-
	- for (int n = 0; n <= static_cast<int>(m_Parameters->m_NumPreviousDirections); ++n)
	- {
	- if (!m_ZeroDirWmFeatures)
	- n = m_Parameters->m_NumPreviousDirections;
	- for (bool reverse : {false, true})
	- {
	- for (int j=1; j<numPoints-1; j++)
	- {
	- if (!m_SampleUsage[t][sampleCounter-num_gm_samples])
	- continue;
	-
	- itk::Point<float, 3> itkP1, itkP2;
	-
	- int num_nonzero_dirs = m_Parameters->m_NumPreviousDirections;
	- if (!reverse)
	- num_nonzero_dirs = std::min(n, j);
	- else
	- num_nonzero_dirs = std::min(n, numPoints-j-1);
	-
	- vnl_vector_fixed<float,3> dir;
	- // zero directions
	- for (unsigned int k=0; k<m_Parameters->m_NumPreviousDirections-num_nonzero_dirs; k++)
	- {
	- dir.fill(0.0);
	- int c = 0;
	- for (unsigned int f=NumberOfSignalFeatures+3k; f<NumberOfSignalFeatures+3(k+1); f++)
	- {
	- m_FeatureData(sampleCounter,f) = dir[c];
	- c++;
	- }
	- }
	-
	- // nonzero directions
	- for (int k=0; k<num_nonzero_dirs; k++)
	- {
	- double* p = nullptr;
	- int n_idx = num_nonzero_dirs-k;
	- if (!reverse)
	- {
	- p = points->GetPoint(j-n_idx);
	- itkP1[0] = p[0]; itkP1[1] = p[1]; itkP1[2] = p[2];
	- p = points->GetPoint(j-n_idx+1);
	- itkP2[0] = p[0]; itkP2[1] = p[1]; itkP2[2] = p[2];
	- }
	- else
	- {
	- p = points->GetPoint(j+n_idx);
	- itkP1[0] = p[0]; itkP1[1] = p[1]; itkP1[2] = p[2];
	- p = points->GetPoint(j+n_idx-1);
	- itkP2[0] = p[0]; itkP2[1] = p[1]; itkP2[2] = p[2];
	- }
	-
	- dir[0]=itkP1[0]-itkP2[0];
	- dir[1]=itkP1[1]-itkP2[1];
	- dir[2]=itkP1[2]-itkP2[2];
	-
	- if (dir.magnitude()<0.0001)
	- mitkThrow() << "streamline error!";
	- dir.normalize();
	- if (dir[0]!=dir[0] \|\| dir[1]!=dir[1] \|\| dir[2]!=dir[2])
	- mitkThrow() << "ERROR: NaN direction!";
	-
	- if (dot_product(ref, dir)<0)
	- dir *= -1;
	-
	- int c = 0;
	- for (unsigned int f=NumberOfSignalFeatures+3(k+m_Parameters->m_NumPreviousDirections-num_nonzero_dirs); f<NumberOfSignalFeatures+3(k+1+m_Parameters->m_NumPreviousDirections-num_nonzero_dirs); f++)
	- {
	- m_FeatureData(sampleCounter,f) = dir[c];
	- c++;
	- }
	- }
	-
	- // get target direction
	- double* p = points->GetPoint(j);
	- itkP1[0] = p[0]; itkP1[1] = p[1]; itkP1[2] = p[2];
	- if (reverse)
	- {
	- p = points->GetPoint(j-1);
	- itkP2[0] = p[0]; itkP2[1] = p[1]; itkP2[2] = p[2];
	- }
	- else
	- {
	- p = points->GetPoint(j+1);
	- itkP2[0] = p[0]; itkP2[1] = p[1]; itkP2[2] = p[2];
	- }
	- dir[0]=itkP2[0]-itkP1[0];
	- dir[1]=itkP2[1]-itkP1[1];
	- dir[2]=itkP2[2]-itkP1[2];
	-
	- if (dir.magnitude()<0.0001)
	- mitkThrow() << "streamline error!";
	- dir.normalize();
	- if (dir[0]!=dir[0] \|\| dir[1]!=dir[1] \|\| dir[2]!=dir[2])
	- mitkThrow() << "ERROR: NaN direction!";
	- if (dot_product(ref, dir)<0)
	- dir *= -1;
	-
	- // image features
	- float volume_mod = mitk::imv::GetImageValue<float>(itkP1, false, volume_interpolator);
	-
	- // diffusion signal features
	- typename DwiFeatureImageType::PixelType pix = mitk::imv::GetImageValue< typename DwiFeatureImageType::PixelType >(itkP1, m_Parameters->m_InterpolateTractographyData, dwi_interp);
	- for (unsigned int f=0; f<NumberOfSignalFeatures; f++)
	- m_FeatureData(sampleCounter,f) = pix[f];
	-
	- // additional feature images
	- int add_feat_c = 0;
	- for (auto interpolator : m_AdditionalFeatureImageInterpolators.at(t))
	- {
	- float v = mitk::imv::GetImageValue<float>(itkP1, false, interpolator);
	- add_feat_c++;
	- m_FeatureData(sampleCounter,NumberOfSignalFeatures+2+add_feat_c) = v;
	- }
	-
	- // set label values
	- float angle = 0;
	- float m = dir.magnitude();
	- if (m>0.0001)
	- {
	- int l = 0;
	- for (auto d : m_DirectionContainer)
	- {
	- float a = fabs(dot_product(dir, d));
	- if (a>angle)
	- {
	- m_LabelData(sampleCounter,0) = l;
	- m_Weights(sampleCounter,0) = fiber_weight*volume_mod;
	- angle = a;
	- }
	- l++;
	- }
	- }
	-
	- sampleCounter++;
	- }
	- if (!m_BidirectionalFiberSampling) // don't sample fibers backward
	- break;
	- }
	- }
	- }
	- }
	- m_Tractograms.clear();
	- MITK_INFO << "done";
	-}
	-
	-}
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerRandomForest.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerRandomForest.h
	deleted file mode 100644
	index 136c6be6f0..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerRandomForest.h
	+++ /dev/null
	@@ -1,163 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _TrackingForestHandler
	-#define _TrackingForestHandler
	-
	-#include <mitkTrackingDataHandler.h>
	-
	-#include <mitkFiberBundle.h>
	-#include <itkAnalyticalDiffusionQballReconstructionImageFilter.h>
	-#include <itkOrientationDistributionFunction.h>
	-#include <itkMersenneTwisterRandomVariateGenerator.h>
	-#include <itkOrientationDistributionFunction.h>
	-#include <chrono>
	-
	-#include <mitkTractographyForest.h>
	-
	-#undef DIFFERENCE
	-#define VIGRA_STATIC_LIB
	-#include <vigra/random_forest.hxx>
	-#include <vigra/multi_array.hxx>
	-#include <vigra/random_forest_hdf5_impex.hxx>
	-#include <mitkLinearSplitting.h>
	-#include <mitkThresholdSplit.h>
	-#include <mitkImpurityLoss.h>
	-
	-#define _USE_MATH_DEFINES
	-#include <cmath>
	-
	-namespace mitk
	-{
	-
	-/**
	-* \brief Manages random forests for fiber tractography. The preparation of the features from the inputa data and the training process are handled here. The data preprocessing and actual prediction for the tracking process is also performed here. The tracking itself is performed in MLBSTrackingFilter. */
	-
	-template< int ShOrder, int NumberOfSignalFeatures >
	-class TrackingHandlerRandomForest : public TrackingDataHandler
	-{
	-
	-public:
	-
	-
	- TrackingHandlerRandomForest();
	- ~TrackingHandlerRandomForest() override;
	-
	- typedef itk::Image< itk::Vector< float, NumberOfSignalFeatures > , 3 > DwiFeatureImageType;
	- typedef itk::LinearInterpolateImageFunction< DwiFeatureImageType, float > DwiFeatureImageInterpolatorType;
	- typedef itk::LinearInterpolateImageFunction< ItkFloatImgType, float > FloatImageInterpolatorType;
	-
	- typedef mitk::ThresholdSplit<mitk::LinearSplitting< mitk::ImpurityLoss<> >,int,vigra::ClassificationTag> DefaultSplitType;
	-
	- void SetDwis( std::vector< Image::Pointer > images ){ m_InputDwis = images; DataModified(); }
	- void AddDwi( Image::Pointer img ){ m_InputDwis.push_back(img); DataModified(); }
	- void SetTractograms( std::vector< FiberBundle::Pointer > tractograms )
	- {
	- m_Tractograms.clear();
	- for (auto fib : tractograms)
	- m_Tractograms.push_back(fib);
	- DataModified();
	- }
	- void SetMaskImages( std::vector< ItkUcharImgType::Pointer > images ){ m_MaskImages = images; DataModified(); }
	- void SetWhiteMatterImages( std::vector< ItkUcharImgType::Pointer > images ){ m_WhiteMatterImages = images; DataModified(); }
	- void SetFiberVolumeModImages( std::vector< ItkFloatImgType::Pointer > images ){ m_FiberVolumeModImages = images; DataModified(); }
	- void SetAdditionalFeatureImages( std::vector< std::vector< ItkFloatImgType::Pointer > > images ){ m_AdditionalFeatureImages = images; DataModified(); }
	-
	- void StartTraining();
	-
	- void SetForest(mitk::TractographyForest::Pointer forest){ m_Forest = forest; }
	- void SetMaxNumWmSamples(int num){ m_MaxNumWmSamples=num; }
	- void SetNumTrees(int num){ m_NumTrees = num; }
	- void SetMaxTreeDepth(int depth){ m_MaxTreeDepth = depth; }
	- void SetFiberSamplingStep(float step){ m_WmSampleDistance = step; }
	- void SetGrayMatterSamplesPerVoxel(int samples){ m_GmSamplesPerVoxel = samples; }
	- void SetSampleFraction(float fraction){ m_SampleFraction = fraction; }
	- void SetBidirectionalFiberSampling(bool val) { m_BidirectionalFiberSampling = val; }
	- void SetZeroDirWmFeatures(bool val) { m_ZeroDirWmFeatures = val; }
	-
	- void InitForTracking() override; ///< calls InputDataValidForTracking() and creates feature images
	- vnl_vector_fixed<float,3> ProposeDirection(const itk::Point<float, 3>& pos, std::deque< vnl_vector_fixed<float,3> >& olddirs, itk::Index<3>& oldIndex) override; ///< predicts next progression direction at the given position
	- bool WorldToIndex(itk::Point<float, 3>& pos, itk::Index<3>& index) override;
	-
	- bool IsForestValid(); ///< true is forest is not null, has more than 0 trees and the correct number of features (NumberOfSignalFeatures + 3)
	-
	- mitk::TractographyForest::Pointer GetForest(){ return m_Forest; }
	-
	- ItkUcharImgType::SpacingType GetSpacing() override{ return m_DwiFeatureImages.at(0)->GetSpacing(); }
	- itk::Point<float,3> GetOrigin() override{ return m_DwiFeatureImages.at(0)->GetOrigin(); }
	- ItkUcharImgType::DirectionType GetDirection() override{ return m_DwiFeatureImages.at(0)->GetDirection(); }
	- ItkUcharImgType::RegionType GetLargestPossibleRegion() override{ return m_DwiFeatureImages.at(0)->GetLargestPossibleRegion(); }
	-
	-protected:
	-
	- void InputDataValidForTracking(); ///< check if raw data is set and tracking forest is valid
	-
	- template<typename T=bool>
	- typename std::enable_if<NumberOfSignalFeatures <= 99, T>::type InitDwiImageFeatures(mitk::Image::Pointer mitk_dwi);
	-
	- template<typename T=bool>
	- typename std::enable_if<NumberOfSignalFeatures >= 100, T>::type InitDwiImageFeatures(mitk::Image::Pointer mitk_dwi);
	-
	- void InputDataValidForTraining(); ///< Check if everything is tehere for training (raw datasets, fiber tracts)
	- void InitForTraining(); ///< Generate masks if necessary, resample fibers, spherically interpolate raw DWIs
	- void CalculateTrainingSamples(); ///< Calculate GM and WM features using the interpolated raw data, the WM masks and the fibers
	-
	- std::vector< Image::Pointer > m_InputDwis; ///< original input DWI data
	- mitk::TractographyForest::Pointer m_Forest; ///< random forest classifier
	- std::chrono::time_point<std::chrono::system_clock> m_StartTime;
	- std::chrono::time_point<std::chrono::system_clock> m_EndTime;
	-
	-
	- std::vector< typename DwiFeatureImageType::Pointer > m_DwiFeatureImages;
	- std::vector< std::vector< ItkFloatImgType::Pointer > > m_AdditionalFeatureImages;
	-
	- std::vector< ItkFloatImgType::Pointer > m_FiberVolumeModImages; ///< used to correct the fiber density
	- std::vector< FiberBundle::Pointer > m_Tractograms; ///< training tractograms
	- std::vector< ItkUcharImgType::Pointer > m_MaskImages; ///< binary mask images to constrain training to a certain area (e.g. brain mask)
	- std::vector< ItkUcharImgType::Pointer > m_WhiteMatterImages; ///< defines white matter voxels. if not set, theses mask images are automatically generated from the input tractograms
	-
	- float m_WmSampleDistance; ///< deterines the number of white matter samples (distance of sampling points on each fiber).
	- int m_NumTrees; ///< number of trees in random forest
	- int m_MaxTreeDepth; ///< limits the tree depth
	- float m_SampleFraction; ///< fraction of samples used to train each tree
	- unsigned int m_NumberOfSamples; ///< stores overall number of samples used for training
	- std::vector< unsigned int > m_GmSamples; ///< number of gray matter samples
	- int m_GmSamplesPerVoxel; ///< number of gray matter samplees per voxel. if -1, then the number is automatically chosen to gain an overall number of GM samples close to the number of WM samples.
	- vigra::MultiArray<2, float> m_FeatureData; ///< vigra container for training features
	-
	- // only for tracking
	- vigra::MultiArray<2, float> m_LabelData; ///< vigra container for training labels
	- vigra::MultiArray<2, double> m_Weights; ///< vigra container for training sample weights
	- std::vector< vnl_vector_fixed<float,3> > m_DirectionContainer;
	- vnl_matrix< float > m_OdfFloatDirs;
	-
	- bool m_BidirectionalFiberSampling;
	- bool m_ZeroDirWmFeatures;
	- int m_MaxNumWmSamples;
	- std::vector< std::vector< bool > > m_SampleUsage;
	-
	- vnl_matrix_fixed<float,3,3> m_ImageDirection;
	- vnl_matrix_fixed<float,3,3> m_ImageDirectionInverse;
	-
	- typename DwiFeatureImageInterpolatorType::Pointer m_DwiFeatureImageInterpolator;
	- std::vector< std::vector< FloatImageInterpolatorType::Pointer > > m_AdditionalFeatureImageInterpolators;
	-};
	-
	-}
	-
	-#include "mitkTrackingHandlerRandomForest.cpp"
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerTensor.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerTensor.cpp
	deleted file mode 100644
	index b68d185e93..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerTensor.cpp
	+++ /dev/null
	@@ -1,378 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkTrackingHandlerTensor.h"
	-
	-namespace mitk
	-{
	-
	-TrackingHandlerTensor::TrackingHandlerTensor()
	- : m_InterpolateTensors(true)
	- , m_NumberOfInputs(0)
	-{
	- m_FaInterpolator = itk::LinearInterpolateImageFunction< itk::Image< float, 3 >, float >::New();
	-}
	-
	-TrackingHandlerTensor::~TrackingHandlerTensor()
	-{
	-}
	-
	-void TrackingHandlerTensor::InitForTracking()
	-{
	- MITK_INFO << "Initializing tensor tracker.";
	-
	- if (m_NeedsDataInit)
	- {
	- m_NumberOfInputs = m_TensorImages.size();
	- for (int i=0; i<m_NumberOfInputs; i++)
	- {
	- ItkPDImgType::Pointer pdImage = ItkPDImgType::New();
	- pdImage->SetSpacing( m_TensorImages.at(0)->GetSpacing() );
	- pdImage->SetOrigin( m_TensorImages.at(0)->GetOrigin() );
	- pdImage->SetDirection( m_TensorImages.at(0)->GetDirection() );
	- pdImage->SetRegions( m_TensorImages.at(0)->GetLargestPossibleRegion() );
	- pdImage->Allocate();
	- m_PdImage.push_back(pdImage);
	-
	- ItkDoubleImgType::Pointer emaxImage = ItkDoubleImgType::New();
	- emaxImage->SetSpacing( m_TensorImages.at(0)->GetSpacing() );
	- emaxImage->SetOrigin( m_TensorImages.at(0)->GetOrigin() );
	- emaxImage->SetDirection( m_TensorImages.at(0)->GetDirection() );
	- emaxImage->SetRegions( m_TensorImages.at(0)->GetLargestPossibleRegion() );
	- emaxImage->Allocate();
	- emaxImage->FillBuffer(1.0);
	- m_EmaxImage.push_back(emaxImage);
	- }
	-
	- bool useUserFaImage = true;
	- if (m_FaImage.IsNull())
	- {
	- m_FaImage = ItkFloatImgType::New();
	- m_FaImage->SetSpacing( m_TensorImages.at(0)->GetSpacing() );
	- m_FaImage->SetOrigin( m_TensorImages.at(0)->GetOrigin() );
	- m_FaImage->SetDirection( m_TensorImages.at(0)->GetDirection() );
	- m_FaImage->SetRegions( m_TensorImages.at(0)->GetLargestPossibleRegion() );
	- m_FaImage->Allocate();
	- m_FaImage->FillBuffer(0.0);
	- useUserFaImage = false;
	- }
	-
	- typedef itk::DiffusionTensor3D<float> TensorType;
	-
	- for (int x=0; x<(int)m_TensorImages.at(0)->GetLargestPossibleRegion().GetSize()[0]; x++)
	- for (int y=0; y<(int)m_TensorImages.at(0)->GetLargestPossibleRegion().GetSize()[1]; y++)
	- for (int z=0; z<(int)m_TensorImages.at(0)->GetLargestPossibleRegion().GetSize()[2]; z++)
	- {
	- ItkTensorImageType::IndexType index;
	- index[0] = x; index[1] = y; index[2] = z;
	- for (int i=0; i<m_NumberOfInputs; i++)
	- {
	- TensorType::EigenValuesArrayType eigenvalues;
	- TensorType::EigenVectorsMatrixType eigenvectors;
	-
	- ItkTensorImageType::PixelType tensor;
	- vnl_vector_fixed<float,3> dir;
	- tensor = m_TensorImages.at(i)->GetPixel(index);
	- tensor.ComputeEigenAnalysis(eigenvalues, eigenvectors);
	-
	- dir[0] = eigenvectors(2, 0);
	- dir[1] = eigenvectors(2, 1);
	- dir[2] = eigenvectors(2, 2);
	- if (dir.magnitude()>mitk::eps)
	- dir.normalize();
	- else
	- dir.fill(0.0);
	-
	- m_PdImage.at(i)->SetPixel(index, dir);
	- if (!useUserFaImage)
	- m_FaImage->SetPixel(index, m_FaImage->GetPixel(index)+tensor.GetFractionalAnisotropy());
	- m_EmaxImage.at(i)->SetPixel(index, 2/eigenvalues[2]);
	- }
	- if (!useUserFaImage)
	- m_FaImage->SetPixel(index, m_FaImage->GetPixel(index)/m_NumberOfInputs);
	- }
	-
	- auto double_dir = m_TensorImages.at(0)->GetDirection().GetVnlMatrix();
	- for (int r=0; r<3; r++)
	- for (int c=0; c<3; c++)
	- {
	- m_FloatImageRotation[r][c] = double_dir[r][c];
	- }
	-
	- this->CalculateMinVoxelSize();
	- m_NeedsDataInit = false;
	- }
	-
	-
	- if (m_Parameters->m_F+m_Parameters->m_G>1.0)
	- {
	- float temp = m_Parameters->m_F+m_Parameters->m_G;
	- m_Parameters->m_F /= temp;
	- m_Parameters->m_G /= temp;
	- }
	-
	- m_FaInterpolator->SetInputImage(m_FaImage);
	-
	- std::cout << "TrackingHandlerTensor - FA threshold: " << m_Parameters->m_Cutoff << std::endl;
	- std::cout << "TrackingHandlerTensor - f: " << m_Parameters->m_F << std::endl;
	- std::cout << "TrackingHandlerTensor - g: " << m_Parameters->m_G << std::endl;
	-}
	-
	-vnl_vector_fixed<float,3> TrackingHandlerTensor::GetMatchingDirection(itk::Index<3> idx, vnl_vector_fixed<float,3>& oldDir, int& image_num)
	-{
	- vnl_vector_fixed<float,3> out_dir; out_dir.fill(0);
	- float angle = 0;
	- float mag = oldDir.magnitude();
	- if (mag<mitk::eps)
	- {
	- for (unsigned int i=0; i<m_PdImage.size(); i++)
	- {
	- out_dir = m_PdImage.at(i)->GetPixel(idx);
	-
	- if (out_dir.magnitude()>0.5)
	- {
	- image_num = i;
	- oldDir[0] = out_dir[0];
	- oldDir[1] = out_dir[1];
	- oldDir[2] = out_dir[2];
	- break;
	- }
	- }
	- }
	- else
	- {
	- for (unsigned int i=0; i<m_PdImage.size(); i++)
	- {
	- vnl_vector_fixed<float,3> dir = m_PdImage.at(i)->GetPixel(idx);
	-
	- float a = dot_product(dir, oldDir);
	- if (fabs(a)>angle)
	- {
	- image_num = i;
	- angle = fabs(a);
	- if (a<0)
	- out_dir = -dir;
	- else
	- out_dir = dir;
	- out_dir *= angle; // shrink contribution of direction if is less parallel to previous direction
	- }
	- }
	- }
	-
	- return out_dir;
	-}
	-
	-bool TrackingHandlerTensor::WorldToIndex(itk::Point<float, 3>& pos, itk::Index<3>& index)
	-{
	- m_TensorImages.at(0)->TransformPhysicalPointToIndex(pos, index);
	- return m_TensorImages.at(0)->GetLargestPossibleRegion().IsInside(index);
	-}
	-
	-vnl_vector_fixed<float,3> TrackingHandlerTensor::GetDirection(itk::Point<float, 3> itkP, vnl_vector_fixed<float,3> oldDir, TensorType& tensor)
	-{
	- // transform physical point to index coordinates
	- itk::Index<3> idx;
	- itk::ContinuousIndex< float, 3> cIdx;
	- m_FaImage->TransformPhysicalPointToIndex(itkP, idx);
	- m_FaImage->TransformPhysicalPointToContinuousIndex(itkP, cIdx);
	-
	- vnl_vector_fixed<float,3> dir; dir.fill(0.0);
	- if ( !m_FaImage->GetLargestPossibleRegion().IsInside(idx) )
	- return dir;
	-
	- int image_num = -1;
	- if (!m_Parameters->m_InterpolateTractographyData)
	- {
	- dir = GetMatchingDirection(idx, oldDir, image_num);
	- if (image_num>=0)
	- tensor = m_TensorImages[image_num]->GetPixel(idx) * m_EmaxImage[image_num]->GetPixel(idx);
	- }
	- else
	- {
	- float frac_x = cIdx[0] - idx[0];
	- float frac_y = cIdx[1] - idx[1];
	- float frac_z = cIdx[2] - idx[2];
	- if (frac_x<0)
	- {
	- idx[0] -= 1;
	- frac_x += 1;
	- }
	- if (frac_y<0)
	- {
	- idx[1] -= 1;
	- frac_y += 1;
	- }
	- if (frac_z<0)
	- {
	- idx[2] -= 1;
	- frac_z += 1;
	- }
	- frac_x = 1-frac_x;
	- frac_y = 1-frac_y;
	- frac_z = 1-frac_z;
	-
	- // int coordinates inside image?
	- if (idx[0] >= 0 && idx[0] < static_cast<itk::IndexValueType>(m_FaImage->GetLargestPossibleRegion().GetSize(0) - 1) &&
	- idx[1] >= 0 && idx[1] < static_cast<itk::IndexValueType>(m_FaImage->GetLargestPossibleRegion().GetSize(1) - 1) &&
	- idx[2] >= 0 && idx[2] < static_cast<itk::IndexValueType>(m_FaImage->GetLargestPossibleRegion().GetSize(2) - 1))
	- {
	- // trilinear interpolation
	- vnl_vector_fixed<float, 8> interpWeights;
	- interpWeights[0] = ( frac_x)( frac_y)( frac_z);
	- interpWeights[1] = (1-frac_x)( frac_y)( frac_z);
	- interpWeights[2] = ( frac_x)(1-frac_y)( frac_z);
	- interpWeights[3] = ( frac_x)( frac_y)(1-frac_z);
	- interpWeights[4] = (1-frac_x)(1-frac_y)( frac_z);
	- interpWeights[5] = ( frac_x)(1-frac_y)(1-frac_z);
	- interpWeights[6] = (1-frac_x)( frac_y)(1-frac_z);
	- interpWeights[7] = (1-frac_x)(1-frac_y)(1-frac_z);
	-
	- dir = GetMatchingDirection(idx, oldDir, image_num) * interpWeights[0];
	- if (image_num>=0)
	- tensor += m_TensorImages[image_num]->GetPixel(idx) * m_EmaxImage[image_num]->GetPixel(idx) * interpWeights[0];
	-
	- itk::Index<3> tmpIdx = idx; tmpIdx[0]++;
	- dir += GetMatchingDirection(tmpIdx, oldDir, image_num) * interpWeights[1];
	- if (image_num>=0)
	- tensor += m_TensorImages[image_num]->GetPixel(tmpIdx) * m_EmaxImage[image_num]->GetPixel(tmpIdx) * interpWeights[1];
	-
	- tmpIdx = idx; tmpIdx[1]++;
	- dir += GetMatchingDirection(tmpIdx, oldDir, image_num) * interpWeights[2];
	- if (image_num>=0)
	- tensor += m_TensorImages[image_num]->GetPixel(tmpIdx) * m_EmaxImage[image_num]->GetPixel(tmpIdx) * interpWeights[2];
	-
	- tmpIdx = idx; tmpIdx[2]++;
	- dir += GetMatchingDirection(tmpIdx, oldDir, image_num) * interpWeights[3];
	- if (image_num>=0)
	- tensor += m_TensorImages[image_num]->GetPixel(tmpIdx) * m_EmaxImage[image_num]->GetPixel(tmpIdx) * interpWeights[3];
	-
	- tmpIdx = idx; tmpIdx[0]++; tmpIdx[1]++;
	- dir += GetMatchingDirection(tmpIdx, oldDir, image_num) * interpWeights[4];
	- if (image_num>=0)
	- tensor += m_TensorImages[image_num]->GetPixel(tmpIdx) * m_EmaxImage[image_num]->GetPixel(tmpIdx) * interpWeights[4];
	-
	- tmpIdx = idx; tmpIdx[1]++; tmpIdx[2]++;
	- dir += GetMatchingDirection(tmpIdx, oldDir, image_num) * interpWeights[5];
	- if (image_num>=0)
	- tensor += m_TensorImages[image_num]->GetPixel(tmpIdx) * m_EmaxImage[image_num]->GetPixel(tmpIdx) * interpWeights[5];
	-
	- tmpIdx = idx; tmpIdx[2]++; tmpIdx[0]++;
	- dir += GetMatchingDirection(tmpIdx, oldDir, image_num) * interpWeights[6];
	- if (image_num>=0)
	- tensor += m_TensorImages[image_num]->GetPixel(tmpIdx) * m_EmaxImage[image_num]->GetPixel(tmpIdx) * interpWeights[6];
	-
	- tmpIdx = idx; tmpIdx[0]++; tmpIdx[1]++; tmpIdx[2]++;
	- dir += GetMatchingDirection(tmpIdx, oldDir, image_num) * interpWeights[7];
	- if (image_num>=0)
	- tensor += m_TensorImages[image_num]->GetPixel(tmpIdx) * m_EmaxImage[image_num]->GetPixel(tmpIdx) * interpWeights[7];
	- }
	- }
	-
	- return dir;
	-}
	-
	-vnl_vector_fixed<float,3> TrackingHandlerTensor::GetLargestEigenvector(TensorType& tensor)
	-{
	- vnl_vector_fixed<float,3> dir;
	- TensorType::EigenValuesArrayType eigenvalues;
	- TensorType::EigenVectorsMatrixType eigenvectors;
	- tensor.ComputeEigenAnalysis(eigenvalues, eigenvectors);
	- dir[0] = eigenvectors(2, 0);
	- dir[1] = eigenvectors(2, 1);
	- dir[2] = eigenvectors(2, 2);
	- if (dir.magnitude()<mitk::eps)
	- dir.fill(0.0);
	-
	- return dir;
	-}
	-
	-vnl_vector_fixed<float,3> TrackingHandlerTensor::ProposeDirection(const itk::Point<float, 3>& pos, std::deque<vnl_vector_fixed<float, 3> >& olddirs, itk::Index<3>& oldIndex)
	-{
	- vnl_vector_fixed<float,3> output_direction; output_direction.fill(0);
	- TensorType tensor; tensor.Fill(0);
	-
	- try
	- {
	- itk::Index<3> index;
	- m_TensorImages.at(0)->TransformPhysicalPointToIndex(pos, index);
	-
	- float fa = mitk::imv::GetImageValue<float>(pos, m_Parameters->m_InterpolateTractographyData, m_FaInterpolator);
	- if (fa<m_Parameters->m_Cutoff)
	- return output_direction;
	-
	- vnl_vector_fixed<float,3> oldDir; oldDir.fill(0.0);
	- if (!olddirs.empty())
	- oldDir = olddirs.back();
	-
	- if (m_Parameters->m_FlipX)
	- oldDir[0] *= -1;
	- if (m_Parameters->m_FlipY)
	- oldDir[1] *= -1;
	- if (m_Parameters->m_FlipZ)
	- oldDir[2] *= -1;
	-
	- float old_mag = oldDir.magnitude();
	-
	- if (!m_Parameters->m_InterpolateTractographyData && oldIndex==index)
	- return oldDir;
	-
	- output_direction = GetDirection(pos, oldDir, tensor);
	- float mag = output_direction.magnitude();
	-
	- if (mag>=mitk::eps)
	- {
	- output_direction.normalize();
	-
	- if (old_mag>0.5 && m_Parameters->m_G>mitk::eps) // TEND tracking
	- {
	-
	- output_direction[0] = m_Parameters->m_Foutput_direction[0] + (1-m_Parameters->m_F)( (1-m_Parameters->m_G)oldDir[0] + m_Parameters->m_G(tensor[0]oldDir[0] + tensor[1]oldDir[1] + tensor[2]*oldDir[2]));
	- output_direction[1] = m_Parameters->m_Foutput_direction[1] + (1-m_Parameters->m_F)( (1-m_Parameters->m_G)oldDir[1] + m_Parameters->m_G(tensor[1]oldDir[0] + tensor[3]oldDir[1] + tensor[4]*oldDir[2]));
	- output_direction[2] = m_Parameters->m_Foutput_direction[2] + (1-m_Parameters->m_F)( (1-m_Parameters->m_G)oldDir[2] + m_Parameters->m_G(tensor[2]oldDir[0] + tensor[4]oldDir[1] + tensor[5]*oldDir[2]));
	- output_direction.normalize();
	- }
	-
	- float a = 1;
	- if (old_mag>0.5)
	- a = dot_product(output_direction, oldDir);
	- if (a>=m_Parameters->GetAngularThresholdDot())
	- output_direction *= mag;
	- else
	- output_direction.fill(0);
	- }
	- else
	- output_direction.fill(0);
	-
	- }
	- catch(...)
	- {
	-
	- }
	-
	- if (m_Parameters->m_FlipX)
	- output_direction[0] *= -1;
	- if (m_Parameters->m_FlipY)
	- output_direction[1] *= -1;
	- if (m_Parameters->m_FlipZ)
	- output_direction[2] *= -1;
	- if (m_Parameters->m_ApplyDirectionMatrix)
	- output_direction = m_FloatImageRotation*output_direction;
	-
	- return output_direction;
	-}
	-
	-}
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerTensor.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerTensor.h
	deleted file mode 100644
	index 6175bec856..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerTensor.h
	+++ /dev/null
	@@ -1,80 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _TrackingHandlerTensor
	-#define _TrackingHandlerTensor
	-
	-#include "mitkTrackingDataHandler.h"
	-#include <itkDiffusionTensor3D.h>
	-#include <MitkFiberTrackingExports.h>
	-#include <mitkTensorImage.h>
	-#include <itkLinearInterpolateImageFunction.h>
	-
	-namespace mitk
	-{
	-
	-/**
	-* \brief Enables streamline tracking on tensor images. Supports multi tensor tracking by adding multiple tensor images. */
	-
	-class MITKFIBERTRACKING_EXPORT TrackingHandlerTensor : public TrackingDataHandler
	-{
	-
	-public:
	-
	- TrackingHandlerTensor();
	- ~TrackingHandlerTensor() override;
	-
	- typedef TensorImage::PixelType TensorType;
	- typedef TensorImage::ItkTensorImageType ItkTensorImageType;
	- typedef itk::Image< vnl_vector_fixed<float,3>, 3> ItkPDImgType;
	-
	-
	- void InitForTracking() override; ///< calls InputDataValidForTracking() and creates feature images
	- vnl_vector_fixed<float,3> ProposeDirection(const itk::Point<float, 3>& pos, std::deque< vnl_vector_fixed<float,3> >& olddirs, itk::Index<3>& oldIndex) override; ///< predicts next progression direction at the given position
	- bool WorldToIndex(itk::Point<float, 3>& pos, itk::Index<3>& index) override;
	-
	- void AddTensorImage( ItkTensorImageType::ConstPointer img ){ m_TensorImages.push_back(img); DataModified(); }
	- void SetTensorImage( ItkTensorImageType::ConstPointer img ){ m_TensorImages.clear(); m_TensorImages.push_back(img); DataModified(); }
	- void ClearTensorImages(){ m_TensorImages.clear(); DataModified(); }
	- void SetFaImage( ItkFloatImgType::Pointer img ){ m_FaImage = img; DataModified(); }
	- void SetInterpolateTensors( bool interpolateTensors ){ m_InterpolateTensors = interpolateTensors; }
	- int GetNumTensorImages() const { return m_TensorImages.size(); }
	-
	-
	- ItkUcharImgType::SpacingType GetSpacing() override{ return m_FaImage->GetSpacing(); }
	- itk::Point<float,3> GetOrigin() override{ return m_FaImage->GetOrigin(); }
	- ItkUcharImgType::DirectionType GetDirection() override{ return m_FaImage->GetDirection(); }
	- ItkUcharImgType::RegionType GetLargestPossibleRegion() override{ return m_FaImage->GetLargestPossibleRegion(); }
	-
	-protected:
	-
	- vnl_vector_fixed<float,3> GetMatchingDirection(itk::Index<3> idx, vnl_vector_fixed<float,3>& oldDir, int& image_num);
	- vnl_vector_fixed<float,3> GetDirection(itk::Point<float, 3> itkP, vnl_vector_fixed<float,3> oldDir, TensorType& tensor);
	- vnl_vector_fixed<float,3> GetLargestEigenvector(TensorType& tensor);
	-
	- std::vector< ItkDoubleImgType::Pointer > m_EmaxImage; ///< Stores largest eigenvalues per voxel (one for each tensor)
	- ItkFloatImgType::Pointer m_FaImage; ///< FA image used to determine streamline termination.
	- std::vector< ItkPDImgType::Pointer > m_PdImage; ///< Stores principal direction of each tensor in each voxel.
	- std::vector< ItkTensorImageType::ConstPointer > m_TensorImages; ///< Input tensor images. For multi tensor tracking provide multiple tensor images.
	- bool m_InterpolateTensors; ///< If false, then the peaks are interpolated. Otherwiese, The tensors are interpolated.
	- int m_NumberOfInputs;
	-
	- itk::LinearInterpolateImageFunction< itk::Image< float, 3 >, float >::Pointer m_FaInterpolator;
	-};
	-
	-}
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkEvaluateDirectionImagesFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkEvaluateDirectionImagesFilter.cpp
	deleted file mode 100755
	index 7ee6a0877f..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkEvaluateDirectionImagesFilter.cpp
	+++ /dev/null
	@@ -1,332 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkEvaluateDirectionImagesFilter_cpp
	-#define __itkEvaluateDirectionImagesFilter_cpp
	-
	-#include "itkEvaluateDirectionImagesFilter.h"
	-#include <itkImageRegionConstIterator.h>
	-#include <itkImageRegionIterator.h>
	-#include <itkImageDuplicator.h>
	-#include <boost/progress.hpp>
	-
	-namespace itk {
	-
	-template< class PixelType >
	-ComparePeakImagesFilter< PixelType >
	-::ComparePeakImagesFilter():
	- m_IgnoreMissingRefDirections(false),
	- m_IgnoreMissingTestDirections(false),
	- m_Eps(0.0001)
	-{
	- this->SetNumberOfIndexedOutputs(2);
	-}
	-
	-template< class PixelType >
	-void ComparePeakImagesFilter< PixelType >::GenerateData()
	-{
	- if (m_TestImage.IsNull() \|\| m_ReferenceImage.IsNull())
	- mitkThrow() << "Test or reference image not set!";
	-// if (m_TestImage->GetLargestPossibleRegion().GetSize()!=m_ReferenceImage->GetLargestPossibleRegion().GetSize())
	-// mitkThrow() << "Test and reference image need to have same sizes!";
	-
	- Vector<float, 4> spacing4 = m_TestImage->GetSpacing();
	- Point<float, 4> origin4 = m_TestImage->GetOrigin();
	- Matrix<double, 4, 4> direction4 = m_TestImage->GetDirection();
	- ImageRegion<4> imageRegion4 = m_TestImage->GetLargestPossibleRegion();
	-
	- Vector<double, 3> spacing3;
	- Point<float, 3> origin3;
	- Matrix<double, 3, 3> direction3;
	- ImageRegion<3> imageRegion3;
	-
	- spacing3[0] = spacing4[0]; spacing3[1] = spacing4[1]; spacing3[2] = spacing4[2];
	- origin3[0] = origin4[0]; origin3[1] = origin4[1]; origin3[2] = origin4[2];
	- for (int r=0; r<3; r++)
	- for (int c=0; c<3; c++)
	- direction3[r][c] = direction4[r][c];
	- imageRegion3.SetSize(0, imageRegion4.GetSize()[0]);
	- imageRegion3.SetSize(1, imageRegion4.GetSize()[1]);
	- imageRegion3.SetSize(2, imageRegion4.GetSize()[2]);
	-
	- // angular error image
	- typename OutputImageType::Pointer outputImage = OutputImageType::New();
	- outputImage->SetOrigin( origin3 );
	- outputImage->SetRegions( imageRegion3 );
	- outputImage->SetSpacing( spacing3 );
	- outputImage->SetDirection( direction3 );
	- outputImage->Allocate();
	- outputImage->FillBuffer(0.0);
	- this->SetNthOutput(0, outputImage);
	-
	- // length error image
	- outputImage = OutputImageType::New();
	- outputImage->SetOrigin( origin3 );
	- outputImage->SetRegions( imageRegion3 );
	- outputImage->SetSpacing( spacing3 );
	- outputImage->SetDirection( direction3 );
	- outputImage->Allocate();
	- outputImage->FillBuffer(0.0);
	- this->SetNthOutput(1, outputImage);
	-
	- if (m_MaskImage.IsNull())
	- {
	- m_MaskImage = UCharImageType::New();
	- m_MaskImage->SetOrigin( origin3 );
	- m_MaskImage->SetRegions( imageRegion3 );
	- m_MaskImage->SetSpacing( spacing3 );
	- m_MaskImage->SetDirection( direction3 );
	- m_MaskImage->Allocate();
	- m_MaskImage->FillBuffer(1);
	- }
	-
	- m_MeanAngularError = 0.0;
	- m_MedianAngularError = 0;
	- m_MaxAngularError = 0.0;
	- m_MinAngularError = itk::NumericTraits<float>::max();
	- m_VarAngularError = 0.0;
	- m_AngularErrorVector.clear();
	-
	- m_MeanLengthError = 0.0;
	- m_MedianLengthError = 0;
	- m_MaxLengthError = 0.0;
	- m_MinLengthError = itk::NumericTraits<float>::max();
	- m_VarLengthError = 0.0;
	- m_LengthErrorVector.clear();
	-
	- outputImage = static_cast< OutputImageType* >(this->ProcessObject::GetOutput(0));
	- typename OutputImageType::Pointer outputImage2 = static_cast< OutputImageType* >(this->ProcessObject::GetOutput(1));
	-
	- ImageRegionIterator< OutputImageType > oit(outputImage, outputImage->GetLargestPossibleRegion());
	- ImageRegionIterator< OutputImageType > oit2(outputImage2, outputImage2->GetLargestPossibleRegion());
	- ImageRegionIterator< UCharImageType > mit(m_MaskImage, m_MaskImage->GetLargestPossibleRegion());
	-
	-
	- boost::progress_display disp(outputImage->GetLargestPossibleRegion().GetSize()[0]outputImage->GetLargestPossibleRegion().GetSize()[1]outputImage->GetLargestPossibleRegion().GetSize()[2]);
	- while( !oit.IsAtEnd() )
	- {
	- ++disp;
	- if( mit.Get()!=1 )
	- {
	- ++oit;
	- ++oit2;
	- ++mit;
	- continue;
	- }
	- typename OutputImageType::IndexType index = oit.GetIndex();
	- itk::Index<4> idx4;
	- idx4[0] = index[0];
	- idx4[1] = index[1];
	- idx4[2] = index[2];
	-
	- std::vector< PixelType > ref_magnitudes;
	- std::vector< PeakType > ref_peaks;
	- for (unsigned int i=0; i<m_ReferenceImage->GetLargestPossibleRegion().GetSize()[3]/3; i++)
	- {
	- PeakType ref_peak;
	- idx4[3] = i*3;
	- ref_peak[0] = m_ReferenceImage->GetPixel(idx4);
	- idx4[3] = i*3 + 1;
	- ref_peak[1] = m_ReferenceImage->GetPixel(idx4);
	- idx4[3] = i*3 + 2;
	- ref_peak[2] = m_ReferenceImage->GetPixel(idx4);
	-
	- PixelType ref_mag = ref_peak.magnitude();
	- if (ref_mag > m_Eps )
	- {
	- ref_peak.normalize();
	- ref_peaks.push_back(ref_peak);
	- ref_magnitudes.push_back(ref_mag);
	- }
	- }
	-
	- std::vector< PixelType > test_magnitudes;
	- std::vector< PeakType > test_peaks;
	- for (unsigned int j=0; j<m_TestImage->GetLargestPossibleRegion().GetSize()[3]/3; j++)
	- {
	- PeakType test_peak;
	- idx4[3] = j*3;
	- test_peak[0] = m_TestImage->GetPixel(idx4);
	- idx4[3] = j*3 + 1;
	- test_peak[1] = m_TestImage->GetPixel(idx4);
	- idx4[3] = j*3 + 2;
	- test_peak[2] = m_TestImage->GetPixel(idx4);
	-
	- PixelType test_mag = test_peak.magnitude();
	- if (test_mag > m_Eps )
	- {
	- test_peak.normalize();
	- test_peaks.push_back(test_peak);
	- test_magnitudes.push_back(test_mag);
	- }
	- }
	-
	- if (test_peaks.empty() && ref_peaks.empty())
	- {
	- ++oit;
	- ++oit2;
	- ++mit;
	- continue;
	- }
	- else if (test_peaks.empty())
	- {
	- if (!m_IgnoreMissingTestDirections)
	- {
	- PixelType length_sum = 0;
	- for (auto l : ref_magnitudes)
	- {
	- length_sum += l;
	- m_AngularErrorVector.push_back(90);
	- m_LengthErrorVector.push_back(l);
	- m_MeanAngularError += m_AngularErrorVector.back();
	- m_MeanLengthError += m_LengthErrorVector.back();
	- }
	- oit2.Set(length_sum/ref_magnitudes.size());
	- oit.Set(90);
	- }
	- }
	- else if (ref_peaks.empty())
	- {
	- if (!m_IgnoreMissingRefDirections)
	- {
	- PixelType length_sum = 0;
	- for (auto l : test_magnitudes)
	- {
	- length_sum += l;
	- m_AngularErrorVector.push_back(90);
	- m_LengthErrorVector.push_back(length_sum);
	- m_MeanAngularError += m_AngularErrorVector.back();
	- m_MeanLengthError += m_LengthErrorVector.back();
	- }
	- oit2.Set(length_sum/test_magnitudes.size());
	- oit.Set(90);
	- }
	- }
	- else
	- {
	- PixelType error_a = 0;
	- PixelType error_l = 0;
	- for (unsigned int i=0; i<ref_peaks.size(); ++i)
	- {
	- PixelType max_a = 0;
	- PixelType max_l = 0;
	- for (unsigned int j=0; j<test_peaks.size(); ++j)
	- {
	- auto a = fabs(dot_product(test_peaks[j], ref_peaks[i]));
	- if (a>1.0)
	- a = 1.0;
	- if (a>max_a)
	- {
	- max_a = a;
	- max_l = fabs(ref_magnitudes[i]-test_magnitudes[j]);
	- }
	- }
	- m_LengthErrorVector.push_back( max_l );
	- m_AngularErrorVector.push_back( acos(max_a)*180.0/itk::Math::pi );
	- m_MeanAngularError += m_AngularErrorVector.back();
	- m_MeanLengthError += m_LengthErrorVector.back();
	- error_a += m_AngularErrorVector.back();
	- error_l += m_LengthErrorVector.back();
	- }
	-
	- for (unsigned int i=0; i<test_peaks.size(); ++i)
	- {
	- PixelType max_a = 0;
	- PixelType max_l = 0;
	- for (unsigned int j=0; j<ref_peaks.size(); ++j)
	- {
	- auto a = fabs(dot_product(test_peaks[i], ref_peaks[j]));
	- if (a>1.0)
	- a = 1.0;
	- if (a>max_a)
	- {
	- max_a = a;
	- max_l = fabs(ref_magnitudes[j]-test_magnitudes[i]);
	- }
	- }
	- m_LengthErrorVector.push_back( max_l );
	- m_AngularErrorVector.push_back( acos(max_a)*180.0/itk::Math::pi );
	- m_MeanAngularError += m_AngularErrorVector.back();
	- m_MeanLengthError += m_LengthErrorVector.back();
	- error_a += m_AngularErrorVector.back();
	- error_l += m_LengthErrorVector.back();
	- }
	-
	- error_a /= (test_peaks.size() + ref_peaks.size());
	- error_l /= (test_peaks.size() + ref_peaks.size());
	-
	- oit2.Set(error_l);
	- oit.Set(error_a);
	- }
	-
	- ++oit;
	- ++oit2;
	- ++mit;
	- }
	-
	- std::sort( m_AngularErrorVector.begin(), m_AngularErrorVector.end() );
	- if (!m_AngularErrorVector.empty())
	- m_MeanAngularError /= m_AngularErrorVector.size(); // mean
	-
	-
	- for (unsigned int i=0; i<m_AngularErrorVector.size(); i++)
	- {
	- float temp = m_AngularErrorVector.at(i) - m_MeanAngularError;
	- m_VarAngularError += temp*temp;
	-
	- if ( m_AngularErrorVector.at(i)>m_MaxAngularError )
	- m_MaxAngularError = m_AngularErrorVector.at(i);
	- if ( m_AngularErrorVector.at(i)<m_MinAngularError )
	- m_MinAngularError = m_AngularErrorVector.at(i);
	- }
	- if (m_AngularErrorVector.size()>1)
	- {
	- m_VarAngularError /= (m_AngularErrorVector.size()-1); // variance
	-
	- // median
	- if (m_AngularErrorVector.size()%2 == 0)
	- m_MedianAngularError = 0.5*( m_AngularErrorVector.at( m_AngularErrorVector.size()/2 ) + m_AngularErrorVector.at( m_AngularErrorVector.size()/2+1 ) );
	- else
	- m_MedianAngularError = m_AngularErrorVector.at( (m_AngularErrorVector.size()+1)/2 ) ;
	- }
	-
	- std::sort( m_LengthErrorVector.begin(), m_LengthErrorVector.end() );
	- m_MeanLengthError /= m_LengthErrorVector.size(); // mean
	- for (unsigned int i=0; i<m_LengthErrorVector.size(); i++)
	- {
	- float temp = m_LengthErrorVector.at(i) - m_MeanLengthError;
	- m_VarLengthError += temp*temp;
	-
	- if ( m_LengthErrorVector.at(i)>m_MaxLengthError )
	- m_MaxLengthError = m_LengthErrorVector.at(i);
	- if ( m_LengthErrorVector.at(i)<m_MinLengthError )
	- m_MinLengthError = m_LengthErrorVector.at(i);
	- }
	- if (m_LengthErrorVector.size()>1)
	- {
	- m_VarLengthError /= (m_LengthErrorVector.size()-1); // variance
	-
	- // median
	- if (m_LengthErrorVector.size()%2 == 0)
	- m_MedianLengthError = 0.5*( m_LengthErrorVector.at( m_LengthErrorVector.size()/2 ) + m_LengthErrorVector.at( m_LengthErrorVector.size()/2+1 ) );
	- else
	- m_MedianLengthError = m_LengthErrorVector.at( (m_LengthErrorVector.size()+1)/2 ) ;
	- }
	-}
	-
	-}
	-
	-#endif // __itkEvaluateDirectionImagesFilter_cpp
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkEvaluateDirectionImagesFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkEvaluateDirectionImagesFilter.h
	deleted file mode 100755
	index 561696edab..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkEvaluateDirectionImagesFilter.h
	+++ /dev/null
	@@ -1,115 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-/*===================================================================
	-
	-This file is based heavily on a corresponding ITK filter.
	-
	-===================================================================*/
	-#ifndef __itkEvaluateDirectionImagesFilter_h_
	-#define __itkEvaluateDirectionImagesFilter_h_
	-
	-#include <itkProcessObject.h>
	-#include <itkVectorContainer.h>
	-#include <itkImageSource.h>
	-#include <mitkPeakImage.h>
	-
	-namespace itk{
	-/** \brief Evaluates the voxel-wise angular error between two sets of peak images.
	- */
	-
	-template< class PixelType >
	-class ComparePeakImagesFilter : public ImageSource< Image< PixelType, 3 > >
	-{
	-
	-public:
	-
	- typedef ComparePeakImagesFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageSource< Image< PixelType, 3 > > Superclass;
	- typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
	- typedef typename Superclass::OutputImageType OutputImageType;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(EvaluateDirectionImagesFilter, ImageToImageFilter)
	-
	- typedef Image< float, 3 > FloatImageType;
	- typedef Image< bool, 3 > BoolImageType;
	- typedef Image< unsigned char, 3 > UCharImageType;
	- typedef mitk::PeakImage::ItkPeakImageType PeakImageType;
	- typedef vnl_vector_fixed< PixelType, 3 > PeakType;
	-
	- itkSetMacro( TestImage , PeakImageType::Pointer)
	- itkSetMacro( ReferenceImage , PeakImageType::Pointer)
	- itkSetMacro( MaskImage , UCharImageType::Pointer) ///< Calculation is only performed inside of the mask image.
	- itkSetMacro( IgnoreMissingTestDirections , bool)
	- itkSetMacro( IgnoreMissingRefDirections , bool)
	-
	- /** Output statistics of the measured angular errors. */
	- itkGetMacro( MeanAngularError, float)
	- itkGetMacro( MinAngularError, float)
	- itkGetMacro( MaxAngularError, float)
	- itkGetMacro( VarAngularError, float)
	- itkGetMacro( MedianAngularError, float)
	-
	- /** Output statistics of the measured peak length errors. */
	- itkGetMacro( MeanLengthError, float)
	- itkGetMacro( MinLengthError, float)
	- itkGetMacro( MaxLengthError, float)
	- itkGetMacro( VarLengthError, float)
	- itkGetMacro( MedianLengthError, float)
	-
	-protected:
	- ComparePeakImagesFilter();
	- ~ComparePeakImagesFilter() override {}
	-
	- void GenerateData() override;
	-
	- UCharImageType::Pointer m_MaskImage;
	- PeakImageType::Pointer m_TestImage;
	- PeakImageType::Pointer m_ReferenceImage;
	-
	- bool m_IgnoreMissingRefDirections;
	- bool m_IgnoreMissingTestDirections;
	- double m_MeanAngularError;
	- double m_MedianAngularError;
	- double m_MaxAngularError;
	- double m_MinAngularError;
	- double m_VarAngularError;
	- std::vector< double > m_AngularErrorVector;
	- double m_MeanLengthError;
	- double m_MedianLengthError;
	- double m_MaxLengthError;
	- double m_MinLengthError;
	- double m_VarLengthError;
	- std::vector< double > m_LengthErrorVector;
	-
	- double m_Eps;
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkEvaluateDirectionImagesFilter.cpp"
	-#endif
	-
	-#endif //__itkEvaluateDirectionImagesFilter_h_
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkEvaluateTractogramDirectionsFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkEvaluateTractogramDirectionsFilter.cpp
	deleted file mode 100755
	index 566334c1ad..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkEvaluateTractogramDirectionsFilter.cpp
	+++ /dev/null
	@@ -1,339 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkEvaluateTractogramDirectionsFilter_cpp
	-#define __itkEvaluateTractogramDirectionsFilter_cpp
	-
	-#include "itkEvaluateTractogramDirectionsFilter.h"
	-#include <itkImageRegionConstIterator.h>
	-#include <itkImageRegionIterator.h>
	-#include <itkImageDuplicator.h>
	-#include <boost/progress.hpp>
	-#include <mitkDiffusionFunctionCollection.h>
	-
	-namespace itk {
	-
	-template< class PixelType >
	-EvaluateTractogramDirectionsFilter< PixelType >
	-::EvaluateTractogramDirectionsFilter():
	- m_ReferenceImageSet(nullptr),
	- m_IgnoreMissingDirections(false),
	- m_Eps(0.0001),
	- m_UseInterpolation(false)
	-{
	- this->SetNumberOfOutputs(1);
	-}
	-
	-template< class PixelType >
	-itk::Vector<PixelType, 3> EvaluateTractogramDirectionsFilter< PixelType >::GetItkVector(double point[3])
	-{
	- itk::Vector<PixelType, 3> itkVector;
	- itkVector[0] = point[0];
	- itkVector[1] = point[1];
	- itkVector[2] = point[2];
	- return itkVector;
	-}
	-
	-template< class PixelType >
	-vnl_vector_fixed<PixelType, 3> EvaluateTractogramDirectionsFilter< PixelType >::GetVnlVector(double point[3])
	-{
	- vnl_vector_fixed<PixelType, 3> vnlVector;
	- vnlVector[0] = point[0];
	- vnlVector[1] = point[1];
	- vnlVector[2] = point[2];
	- return vnlVector;
	-}
	-
	-template< class PixelType >
	-vnl_vector_fixed<PixelType, 3> EvaluateTractogramDirectionsFilter< PixelType >::GetVnlVector(Vector<PixelType,3>& vector)
	-{
	- vnl_vector_fixed<PixelType, 3> vnlVector;
	- vnlVector[0] = vector[0];
	- vnlVector[1] = vector[1];
	- vnlVector[2] = vector[2];
	- return vnlVector;
	-}
	-
	-template< class PixelType >
	-void EvaluateTractogramDirectionsFilter< PixelType >::GenerateData()
	-{
	- if (m_Tractogram.IsNull() \|\| m_ReferenceImageSet.IsNull())
	- return;
	-
	- if (m_UseInterpolation)
	- MITK_INFO << "Using trilinear interpolation";
	- else
	- MITK_INFO << "Using nearest neighbor interpolation";
	-
	- if (m_IgnoreMissingDirections)
	- MITK_INFO << "Ignoring missing directions";
	- else
	- MITK_INFO << "Penalizing missing directions";
	-
	- // angular error image
	- typename OutputImageType::Pointer outputImage = OutputImageType::New();
	- outputImage->SetOrigin( m_ReferenceImageSet->GetElement(0)->GetOrigin() );
	- outputImage->SetRegions( m_ReferenceImageSet->GetElement(0)->GetLargestPossibleRegion() );
	- outputImage->SetSpacing( m_ReferenceImageSet->GetElement(0)->GetSpacing() );
	- outputImage->SetDirection( m_ReferenceImageSet->GetElement(0)->GetDirection() );
	- outputImage->Allocate();
	- outputImage->FillBuffer(0.0);
	-
	- DoubleImageType::Pointer counterImage = DoubleImageType::New();
	- counterImage->SetOrigin( m_ReferenceImageSet->GetElement(0)->GetOrigin() );
	- counterImage->SetRegions( m_ReferenceImageSet->GetElement(0)->GetLargestPossibleRegion() );
	- counterImage->SetSpacing( m_ReferenceImageSet->GetElement(0)->GetSpacing() );
	- counterImage->SetDirection( m_ReferenceImageSet->GetElement(0)->GetDirection() );
	- counterImage->Allocate();
	- counterImage->FillBuffer(0.0);
	-
	- std::vector< DoubleImageType::Pointer > directionFound;
	- for (int i=0; i<m_ReferenceImageSet->Size(); i++)
	- {
	- DoubleImageType::Pointer check = DoubleImageType::New();
	- check->SetOrigin( m_ReferenceImageSet->GetElement(0)->GetOrigin() );
	- check->SetRegions( m_ReferenceImageSet->GetElement(0)->GetLargestPossibleRegion() );
	- check->SetSpacing( m_ReferenceImageSet->GetElement(0)->GetSpacing() );
	- check->SetDirection( m_ReferenceImageSet->GetElement(0)->GetDirection() );
	- check->Allocate();
	- check->FillBuffer(90);
	- directionFound.push_back(check);
	- }
	-
	- if (m_MaskImage.IsNull())
	- {
	- m_MaskImage = UCharImageType::New();
	- m_MaskImage->SetOrigin( outputImage->GetOrigin() );
	- m_MaskImage->SetRegions( outputImage->GetLargestPossibleRegion() );
	- m_MaskImage->SetSpacing( outputImage->GetSpacing() );
	- m_MaskImage->SetDirection( outputImage->GetDirection() );
	- m_MaskImage->Allocate();
	- m_MaskImage->FillBuffer(1);
	- }
	-
	- m_MeanAngularError = 0.0;
	- m_MedianAngularError = 0;
	- m_MaxAngularError = 0.0;
	- m_MinAngularError = itk::NumericTraits<float>::max();
	- m_VarAngularError = 0.0;
	- m_AngularErrorVector.clear();
	-
	- float minSpacing = 1;
	- if(outputImage->GetSpacing()[0]<outputImage->GetSpacing()[1] && outputImage->GetSpacing()[0]<outputImage->GetSpacing()[2])
	- minSpacing = outputImage->GetSpacing()[0];
	- else if (outputImage->GetSpacing()[1] < outputImage->GetSpacing()[2])
	- minSpacing = outputImage->GetSpacing()[1];
	- else
	- minSpacing = outputImage->GetSpacing()[2];
	- FiberBundleType::Pointer fiberBundle = m_Tractogram->GetDeepCopy();
	- fiberBundle->ResampleFibers(minSpacing/10);
	-
	- MITK_INFO << "Evaluating tractogram";
	- vtkSmartPointer<vtkPolyData> fiberPolyData = fiberBundle->GetFiberPolyData();
	- boost::progress_display disp( fiberBundle->GetNumFibers() );
	- for( int i=0; i<fiberBundle->GetNumFibers(); i++ )
	- {
	- vtkCell* cell = fiberPolyData->GetCell(i);
	- int numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- if (numPoints<2)
	- continue;
	-
	- for( int j=0; j<numPoints; j++)
	- {
	- double* temp = points->GetPoint(j);
	- itk::Point<PixelType, 3> vertex = mitk::imv::GetItkPoint<PixelType>(temp);
	- itk::Vector<PixelType> v = GetItkVector(temp);
	-
	- itk::Vector<PixelType, 3> dir(3);
	- if (j<numPoints-1)
	- dir = GetItkVector(points->GetPoint(j+1))-v;
	- else
	- dir = v-GetItkVector(points->GetPoint(j-1));
	-
	- vnl_vector_fixed< PixelType, 3 > fiberDir = GetVnlVector(dir);
	- fiberDir.normalize();
	-
	- itk::Index<3> idx;
	- itk::ContinuousIndex<float, 3> contIndex;
	- m_MaskImage->TransformPhysicalPointToIndex(vertex, idx);
	- m_MaskImage->TransformPhysicalPointToContinuousIndex(vertex, contIndex);
	-
	- if (!m_UseInterpolation) // use nearest neighbour interpolation
	- {
	- if (!m_MaskImage->GetLargestPossibleRegion().IsInside(idx) \|\| m_MaskImage->GetPixel(idx)<=0)
	- continue;
	-
	- double angle = 90;
	- int usedIndex = -1;
	- for (int k=0; k<m_ReferenceImageSet->Size(); k++) // and each test direction
	- {
	- vnl_vector_fixed< PixelType, 3 > refDir = m_ReferenceImageSet->GetElement(k)->GetPixel(idx).GetVnlVector();
	- if (refDir.magnitude()>m_Eps) // normalize if not null
	- refDir.normalize();
	- else
	- continue;
	-
	- // calculate angle between directions
	- double tempAngle = acos(fabs(dot_product(refDir, fiberDir)))*180.0/itk::Math::pi;
	- directionFound.at(k)->SetPixel(idx, tempAngle);
	-
	- if (tempAngle < angle)
	- {
	- angle = tempAngle;
	- usedIndex = k;
	- }
	- }
	- if (usedIndex>=0)
	- directionFound.at(usedIndex)->SetPixel(idx, -1);
	- else if (m_IgnoreMissingDirections)
	- angle = 0;
	-
	- counterImage->SetPixel(idx, counterImage->GetPixel(idx)+1);
	- outputImage->SetPixel(idx, outputImage->GetPixel(idx)+angle);
	- continue;
	- }
	-
	- double frac_x = contIndex[0] - idx[0];
	- double frac_y = contIndex[1] - idx[1];
	- double frac_z = contIndex[2] - idx[2];
	- if (frac_x<0)
	- {
	- idx[0] -= 1;
	- frac_x += 1;
	- }
	- if (frac_y<0)
	- {
	- idx[1] -= 1;
	- frac_y += 1;
	- }
	- if (frac_z<0)
	- {
	- idx[2] -= 1;
	- frac_z += 1;
	- }
	-
	- // use trilinear interpolation
	- itk::Index<3> newIdx;
	- for (int x=0; x<2; x++)
	- {
	- frac_x = 1-frac_x;
	- for (int y=0; y<2; y++)
	- {
	- frac_y = 1-frac_y;
	- for (int z=0; z<2; z++)
	- {
	- frac_z = 1-frac_z;
	-
	- newIdx[0] = idx[0]+x;
	- newIdx[1] = idx[1]+y;
	- newIdx[2] = idx[2]+z;
	-
	- double frac = frac_xfrac_yfrac_z;
	-
	- // is position valid?
	- if (!m_MaskImage->GetLargestPossibleRegion().IsInside(newIdx) \|\| m_MaskImage->GetPixel(newIdx)<=0)
	- continue;
	-
	- double angle = 90;
	- int usedIndex = -1;
	- for (int k=0; k<m_ReferenceImageSet->Size(); k++) // and each test direction
	- {
	- vnl_vector_fixed< PixelType, 3 > refDir = m_ReferenceImageSet->GetElement(k)->GetPixel(newIdx).GetVnlVector();
	- if (refDir.magnitude()>m_Eps) // normalize if not null
	- refDir.normalize();
	- else
	- continue;
	-
	- // calculate angle between directions
	- double tempAngle = acos(fabs(dot_product(refDir, fiberDir)))*180.0/itk::Math::pi;
	- directionFound.at(k)->SetPixel(newIdx, tempAngle);
	-
	- if (tempAngle < angle)
	- {
	- angle = tempAngle;
	- usedIndex = k;
	- }
	- }
	- if (usedIndex>=0)
	- directionFound.at(usedIndex)->SetPixel(newIdx, -1);
	- else if (m_IgnoreMissingDirections)
	- angle = 0;
	-
	- counterImage->SetPixel(newIdx, counterImage->GetPixel(newIdx)+1);
	- outputImage->SetPixel(newIdx, outputImage->GetPixel(newIdx)+frac*angle);
	- }
	- }
	- }
	- }
	- ++disp;
	- }
	-
	- ImageRegionIterator< OutputImageType > oit(outputImage, outputImage->GetLargestPossibleRegion());
	- ImageRegionIterator< UCharImageType > mit(m_MaskImage, m_MaskImage->GetLargestPossibleRegion());
	- ImageRegionIterator< DoubleImageType > cit(counterImage, counterImage->GetLargestPossibleRegion());
	-
	-
	- if (!m_IgnoreMissingDirections)
	- MITK_INFO << "Creatings statistics and accounting for missing directions";
	- else
	- MITK_INFO << "Creatings statistics";
	- boost::progress_display disp2(outputImage->GetLargestPossibleRegion().GetNumberOfPixels());
	- while( !oit.IsAtEnd() )
	- {
	- if ( mit.Get()>0)
	- {
	- if ( cit.Get()>m_Eps )
	- oit.Set(oit.Get()/cit.Get());
	-
	- if (!m_IgnoreMissingDirections)
	- {
	- int missingCount = 0;
	-
	- if ( cit.Get()>m_Eps )
	- missingCount++;
	-
	- for (int i=0; i<directionFound.size(); i++)
	- {
	- if ( directionFound.at(i)->GetPixel(oit.GetIndex())>0 && m_ReferenceImageSet->GetElement(i)->GetPixel(oit.GetIndex()).GetVnlVector().magnitude()>m_Eps )
	- {
	- oit.Set(oit.Get()+directionFound.at(i)->GetPixel(oit.GetIndex()));
	- missingCount++;
	- }
	- }
	- if (missingCount>1)
	- oit.Set(oit.Get()/missingCount);
	- }
	-
	- if (oit.Get()>m_MaxAngularError)
	- m_MaxAngularError = oit.Get();
	- if (oit.Get()<m_MinAngularError)
	- m_MinAngularError = oit.Get();
	- }
	-
	- ++oit;
	- ++cit;
	- ++mit;
	- ++disp2;
	- }
	-
	- this->SetNthOutput(0, outputImage);
	-}
	-
	-}
	-
	-#endif // __itkEvaluateTractogramDirectionsFilter_cpp
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkEvaluateTractogramDirectionsFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkEvaluateTractogramDirectionsFilter.h
	deleted file mode 100755
	index de6c6e8873..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkEvaluateTractogramDirectionsFilter.h
	+++ /dev/null
	@@ -1,107 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-/*===================================================================
	-
	-This file is based heavily on a corresponding ITK filter.
	-
	-===================================================================*/
	-#ifndef __itkEvaluateTractogramDirectionsFilter_h_
	-#define __itkEvaluateTractogramDirectionsFilter_h_
	-
	-#include <itkProcessObject.h>
	-#include <itkVectorContainer.h>
	-#include <mitkFiberBundle.h>
	-#include <itkImageSource.h>
	-
	-namespace itk{
	-/** \brief Calculates the voxel-wise angular error of the input tractogram to a set of voxel-wise directions.
	- */
	-
	-template< class PixelType >
	-class EvaluateTractogramDirectionsFilter : public ImageSource< Image< PixelType, 3 > >
	-{
	-
	-public:
	-
	- typedef EvaluateTractogramDirectionsFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageSource< Image< PixelType, 3 > > Superclass;
	- typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
	- typedef typename Superclass::OutputImageType OutputImageType;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(EvaluateTractogramDirectionsFilter, ImageToImageFilter)
	-
	- typedef mitk::FiberBundle FiberBundleType;
	- typedef Vector< float, 3 > DirectionType;
	- typedef Image< DirectionType, 3 > DirectionImageType;
	- typedef VectorContainer< int, DirectionImageType::Pointer > DirectionImageContainerType;
	- typedef Image< float, 3 > FloatImageType;
	- typedef Image< bool, 3 > BoolImageType;
	- typedef Image< unsigned char, 3 > UCharImageType;
	- typedef Image< double, 3 > DoubleImageType;
	-
	- itkSetMacro( Tractogram, FiberBundleType::Pointer) ///< Input tractogram
	- itkSetMacro( ReferenceImageSet , DirectionImageContainerType::Pointer) ///< Input images containing one reference direction per voxel.
	- itkSetMacro( MaskImage , UCharImageType::Pointer) ///< Calculation is only performed inside of the mask image.
	- itkSetMacro( IgnoreMissingDirections , bool) ///< If in one voxel, the number of directions differs between the input tractogram and the reference, the excess directions are ignored. Otherwise, the error to the next closest direction is calculated.
	- itkSetMacro( UseInterpolation , bool) ///< Use trilinear interpolation.
	-
	- /** Output statistics. */
	- itkGetMacro( MeanAngularError, float)
	- itkGetMacro( MinAngularError, float)
	- itkGetMacro( MaxAngularError, float)
	- itkGetMacro( VarAngularError, float)
	- itkGetMacro( MedianAngularError, float)
	-
	-protected:
	- EvaluateTractogramDirectionsFilter();
	- ~EvaluateTractogramDirectionsFilter() {}
	-
	- void GenerateData();
	-
	- itk::Vector<PixelType, 3> GetItkVector(double point[3]);
	- vnl_vector_fixed<PixelType, 3> GetVnlVector(double point[3]);
	- vnl_vector_fixed<PixelType, 3> GetVnlVector(Vector< PixelType, 3 >& vector);
	-
	- UCharImageType::Pointer m_MaskImage;
	- DirectionImageContainerType::Pointer m_ReferenceImageSet;
	- bool m_IgnoreMissingDirections;
	- double m_MeanAngularError;
	- double m_MedianAngularError;
	- double m_MaxAngularError;
	- double m_MinAngularError;
	- double m_VarAngularError;
	- std::vector< double > m_AngularErrorVector;
	- double m_Eps;
	- FiberBundleType::Pointer m_Tractogram;
	- bool m_UseInterpolation;
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkEvaluateTractogramDirectionsFilter.cpp"
	-#endif
	-
	-#endif //__itkEvaluateTractogramDirectionsFilter_h_
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFiberCurvatureFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFiberCurvatureFilter.cpp
	deleted file mode 100644
	index 1437b8eddb..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFiberCurvatureFilter.cpp
	+++ /dev/null
	@@ -1,166 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#include "itkFiberCurvatureFilter.h"
	-
	-#include <vtkDoubleArray.h>
	-#include <vtkPointData.h>
	-#include <boost/progress.hpp>
	-
	-namespace itk{
	-
	-FiberCurvatureFilter::FiberCurvatureFilter()
	- : m_AngularDeviation(30)
	- , m_Distance(10.0)
	- , m_RemoveFibers(false)
	- , m_UseMedian(false)
	-{
	-
	-}
	-
	-FiberCurvatureFilter::~FiberCurvatureFilter()
	-{
	-
	-}
	-
	-void FiberCurvatureFilter::GenerateData()
	-{
	- vtkSmartPointer<vtkPolyData> inputPoly = m_InputFiberBundle->GetFiberPolyData();
	- vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
	- vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
	-
	- MITK_INFO << "Applying curvature threshold";
	- boost::progress_display disp(inputPoly->GetNumberOfCells());
	-#pragma omp parallel for
	- for (int i=0; i<inputPoly->GetNumberOfCells(); i++)
	- {
	- std::vector< vnl_vector_fixed< double, 3 > > vertices;
	-
	-#pragma omp critical
	- {
	- ++disp;
	- vtkCell* cell = inputPoly->GetCell(i);
	- int numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- for (int j=0; j<numPoints; j++)
	- {
	- double p[3];
	- points->GetPoint(j, p);
	- vnl_vector_fixed< double, 3 > p_vec;
	- p_vec[0]=p[0]; p_vec[1]=p[1]; p_vec[2]=p[2];
	- vertices.push_back(p_vec);
	- }
	- }
	-
	- // calculate curvatures
	- int numPoints = vertices.size();
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	- for (int j=0; j<numPoints; j++)
	- {
	- double dist = 0;
	- int c = j;
	- std::vector< vnl_vector_fixed< double, 3 > > vectors;
	- vnl_vector_fixed< double, 3 > meanV; meanV.fill(0.0);
	- while(dist<m_Distance/2 && c>1)
	- {
	- vnl_vector_fixed< double, 3 > p1 = vertices.at(c-1);
	- vnl_vector_fixed< double, 3 > p2 = vertices.at(c);
	-
	- vnl_vector_fixed< double, 3 > v = p2-p1;
	- dist += v.magnitude();
	- v.normalize();
	- vectors.push_back(v);
	- if (m_UseMedian && c==j)
	- meanV += v;
	- else if (!m_UseMedian)
	- meanV += v;
	- c--;
	- }
	- c = j;
	- dist = 0;
	- while(dist<m_Distance/2 && c<numPoints-1)
	- {
	- vnl_vector_fixed< double, 3 > p1 = vertices.at(c);
	- vnl_vector_fixed< double, 3 > p2 = vertices.at(c+1);
	-
	- vnl_vector_fixed< double, 3 > v = p2-p1;
	- dist += v.magnitude();
	- v.normalize();
	- vectors.push_back(v);
	- if (m_UseMedian && c==j)
	- meanV += v;
	- else if (!m_UseMedian)
	- meanV += v;
	- c++;
	- }
	- meanV.normalize();
	-
	- double dev = 0;
	- for (auto vec : vectors)
	- {
	- double angle = dot_product(meanV, vec);
	- if (angle>1.0)
	- angle = 1.0;
	- if (angle<-1.0)
	- angle = -1.0;
	- dev += acos(angle)*180/itk::Math::pi;
	- }
	- if (vectors.size()>0)
	- dev /= vectors.size();
	-
	- if (dev<m_AngularDeviation)
	- {
	-#pragma omp critical
	- {
	- vtkIdType id = vtkNewPoints->InsertNextPoint(vertices.at(j).data_block());
	- container->GetPointIds()->InsertNextId(id);
	- }
	- }
	- else
	- {
	- if (m_RemoveFibers)
	- {
	- container = vtkSmartPointer<vtkPolyLine>::New();
	- break;
	- }
	-
	- if (container->GetNumberOfPoints()>0)
	- {
	-#pragma omp critical
	- vtkNewCells->InsertNextCell(container);
	- }
	- container = vtkSmartPointer<vtkPolyLine>::New();
	- }
	- }
	-
	-#pragma omp critical
	- {
	- if (container->GetNumberOfPoints()>0)
	- vtkNewCells->InsertNextCell(container);
	- }
	- }
	-
	- vtkSmartPointer<vtkPolyData> outputPoly = vtkSmartPointer<vtkPolyData>::New();
	- outputPoly->SetPoints(vtkNewPoints);
	- outputPoly->SetLines(vtkNewCells);
	- m_OutputFiberBundle = FiberBundle::New(outputPoly);
	-}
	-
	-}
	-
	-
	-
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFiberCurvatureFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFiberCurvatureFilter.h
	deleted file mode 100644
	index c6c8ed9610..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFiberCurvatureFilter.h
	+++ /dev/null
	@@ -1,83 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef itkFiberCurvatureFilter_h
	-#define itkFiberCurvatureFilter_h
	-
	-// MITK
	-#include <mitkPlanarEllipse.h>
	-#include <mitkFiberBundle.h>
	-#include <mitkFiberfoxParameters.h>
	-
	-// ITK
	-#include <itkProcessObject.h>
	-
	-// VTK
	-#include <vtkSmartPointer.h>
	-#include <vtkPolyData.h>
	-#include <vtkCellArray.h>
	-#include <vtkPoints.h>
	-#include <vtkPolyLine.h>
	-
	-namespace itk{
	-
	-/**
	-* \brief */
	-
	-class FiberCurvatureFilter : public ProcessObject
	-{
	-public:
	-
	- typedef FiberCurvatureFilter Self;
	- typedef ProcessObject Superclass;
	- typedef SmartPointer< Self > Pointer;
	- typedef SmartPointer< const Self > ConstPointer;
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- itkTypeMacro( FiberCurvatureFilter, ProcessObject )
	-
	- void Update() override{
	- this->GenerateData();
	- }
	-
	- itkSetMacro( Distance, double )
	- itkSetMacro( AngularDeviation, double )
	- itkSetMacro( RemoveFibers, bool )
	- itkSetMacro( UseMedian, bool )
	- itkSetMacro( InputFiberBundle, FiberBundle::Pointer )
	- itkGetMacro( OutputFiberBundle, FiberBundle::Pointer )
	-
	-protected:
	-
	- void GenerateData() override;
	-
	- FiberCurvatureFilter();
	- ~FiberCurvatureFilter() override;
	-
	- FiberBundle::Pointer m_InputFiberBundle;
	- FiberBundle::Pointer m_OutputFiberBundle;
	- double m_AngularDeviation;
	- double m_Distance;
	- bool m_RemoveFibers;
	- bool m_UseMedian;
	-};
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkFiberCurvatureFilter.cpp"
	-#endif
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFiberExtractionFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFiberExtractionFilter.cpp
	deleted file mode 100644
	index 50ee12da4b..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFiberExtractionFilter.cpp
	+++ /dev/null
	@@ -1,500 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkFiberExtractionFilter_cpp
	-#define __itkFiberExtractionFilter_cpp
	-
	-#include "itkFiberExtractionFilter.h"
	-
	-#define _USE_MATH_DEFINES
	-#include <cmath>
	-#include <boost/progress.hpp>
	-#include <mitkDiffusionFunctionCollection.h>
	-#include <boost/lexical_cast.hpp>
	-
	-namespace itk{
	-
	-
	-template< class PixelType >
	-FiberExtractionFilter< PixelType >::FiberExtractionFilter()
	- : m_DontResampleFibers(false)
	- , m_Mode(MODE::OVERLAP)
	- , m_InputType(INPUT::SCALAR_MAP)
	- , m_BothEnds(true)
	- , m_OverlapFraction(0.8)
	- , m_NoNegatives(false)
	- , m_NoPositives(false)
	- , m_Interpolate(false)
	- , m_Threshold(0.5)
	- , m_Labels()
	- , m_SkipSelfConnections(false)
	- , m_OnlySelfConnections(false)
	- , m_SplitByRoi(false)
	- , m_SplitLabels(false)
	- , m_MinFibersPerTract(0)
	- , m_PairedStartEndLabels(false)
	-{
	- m_Interpolator = itk::LinearInterpolateImageFunction< itk::Image< PixelType, 3 >, float >::New();
	-}
	-
	-template< class PixelType >
	-FiberExtractionFilter< PixelType >::~FiberExtractionFilter()
	-{
	-
	-}
	-
	-template< class PixelType >
	-void FiberExtractionFilter< PixelType >::SetRoiImages(const std::vector<ItkInputImgType*> &rois)
	-{
	- for (auto roi : rois)
	- {
	- if (roi==nullptr)
	- {
	- MITK_INFO << "ROI image is NULL!";
	- return;
	- }
	- }
	- m_RoiImages = rois;
	-}
	-
	-template< class PixelType >
	-void FiberExtractionFilter< PixelType >::SetRoiImageNames(const std::vector< std::string > roi_names)
	-{
	- m_RoiImageNames = roi_names;
	-}
	-
	-template< class PixelType >
	-mitk::FiberBundle::Pointer FiberExtractionFilter< PixelType >::CreateFib(std::vector< unsigned int >& ids)
	-{
	- vtkSmartPointer<vtkFloatArray> weights = vtkSmartPointer<vtkFloatArray>::New();
	- vtkSmartPointer<vtkPolyData> pTmp = m_InputFiberBundle->GeneratePolyDataByIds(ids, weights);
	- mitk::FiberBundle::Pointer fib = mitk::FiberBundle::New(pTmp);
	- fib->SetFiberWeights(weights);
	- return fib;
	-}
	-
	-template< class PixelType >
	-bool FiberExtractionFilter< PixelType >::IsPositive(const itk::Point<float, 3>& itkP)
	-{
	- if( m_InputType == INPUT::SCALAR_MAP )
	- return mitk::imv::IsInsideMask<PixelType>(itkP, m_Interpolate, m_Interpolator, m_Threshold);
	- else if( m_InputType == INPUT::LABEL_MAP )
	- {
	- auto val = mitk::imv::GetImageValue<PixelType>(itkP, false, m_Interpolator);
	- for (auto l : m_Labels)
	- if (l==val)
	- return true;
	- }
	- else
	- mitkThrow() << "No valid input type selected!";
	- return false;
	-}
	-
	-template< class PixelType >
	-std::vector< std::string > FiberExtractionFilter< PixelType >::GetPositiveLabels() const
	-{
	- return m_PositiveLabels;
	-}
	-
	-template< class PixelType >
	-void FiberExtractionFilter< PixelType >::ExtractOverlap(mitk::FiberBundle::Pointer fib)
	-{
	- MITK_INFO << "Extracting fibers (min. overlap " << m_OverlapFraction << ")";
	- vtkSmartPointer<vtkPolyData> polydata = fib->GetFiberPolyData();
	-
	- std::vector< std::vector< unsigned int > > positive_ids; // one ID vector per ROI
	- positive_ids.resize(m_RoiImages.size());
	-
	- std::vector< unsigned int > negative_ids; // fibers not overlapping with ANY mask
	-
	- boost::progress_display disp(m_InputFiberBundle->GetNumFibers());
	- for (unsigned int i=0; i<m_InputFiberBundle->GetNumFibers(); i++)
	- {
	- ++disp;
	- vtkCell* cell = polydata->GetCell(i);
	- int numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- float best_ol = 0;
	- int best_ol_idx = -1;
	- for (unsigned int m=0; m<m_RoiImages.size(); ++m)
	- {
	- auto roi = m_RoiImages.at(m);
	- m_Interpolator->SetInputImage(roi);
	- PixelType inside = 0;
	- PixelType outside = 0;
	- for (int j=0; j<numPoints-1; j++)
	- {
	- itk::Point<float, 3> startVertex = mitk::imv::GetItkPoint(points->GetPoint(j));
	- itk::Index<3> startIndex;
	- itk::ContinuousIndex<float, 3> startIndexCont;
	- roi->TransformPhysicalPointToIndex(startVertex, startIndex);
	- roi->TransformPhysicalPointToContinuousIndex(startVertex, startIndexCont);
	-
	- itk::Point<float, 3> endVertex = mitk::imv::GetItkPoint(points->GetPoint(j + 1));
	- itk::Index<3> endIndex;
	- itk::ContinuousIndex<float, 3> endIndexCont;
	- roi->TransformPhysicalPointToIndex(endVertex, endIndex);
	- roi->TransformPhysicalPointToContinuousIndex(endVertex, endIndexCont);
	-
	- std::vector< std::pair< itk::Index<3>, double > > segments = mitk::imv::IntersectImage(roi->GetSpacing(), startIndex, endIndex, startIndexCont, endIndexCont);
	- for (std::pair< itk::Index<3>, double > segment : segments)
	- {
	- if (!roi->GetLargestPossibleRegion().IsInside(segment.first))
	- continue;
	- if (roi->GetPixel(segment.first)>=m_Threshold)
	- inside += segment.second;
	- else
	- outside += segment.second;
	- }
	- }
	-
	- float overlap = (float)inside/(inside+outside);
	- if (overlap > best_ol && overlap >= m_OverlapFraction)
	- {
	- best_ol_idx = m;
	- best_ol = overlap;
	- }
	- }
	- if (best_ol_idx<0)
	- negative_ids.push_back(i);
	- else
	- positive_ids.at(best_ol_idx).push_back(i);
	- }
	-
	- if (!m_NoNegatives)
	- m_Negatives.push_back(CreateFib(negative_ids));
	- if (!m_NoPositives)
	- {
	- for (unsigned int i=0; i<positive_ids.size(); ++i)
	- {
	- std::string name;
	- if (i<m_RoiImageNames.size())
	- name = m_RoiImageNames.at(i);
	- else
	- name = "Roi" + boost::lexical_cast<std::string>(i);
	-
	- if (positive_ids.at(i).size()>=m_MinFibersPerTract)
	- {
	- m_Positives.push_back(CreateFib(positive_ids.at(i)));
	- m_PositiveLabels.push_back(name);
	- }
	- }
	- if (!m_SplitByRoi)
	- {
	- mitk::FiberBundle::Pointer output = mitk::FiberBundle::New(nullptr);
	- output = output->AddBundles(m_Positives);
	- m_Positives.clear();
	- m_Positives.push_back(output);
	- m_PositiveLabels.clear();
	- m_PositiveLabels.push_back("");
	- }
	- }
	-}
	-
	-template< class PixelType >
	-void FiberExtractionFilter< PixelType >::ExtractEndpoints(mitk::FiberBundle::Pointer fib)
	-{
	- MITK_INFO << "Extracting fibers (endpoints in mask)";
	- vtkSmartPointer<vtkPolyData> polydata = fib->GetFiberPolyData();
	-
	- std::vector< std::vector< unsigned int > > positive_ids; // one ID vector per ROI
	- positive_ids.resize(m_RoiImages.size());
	-
	- std::vector< unsigned int > negative_ids; // fibers not overlapping with ANY mask
	-
	- boost::progress_display disp(m_InputFiberBundle->GetNumFibers());
	- for (unsigned int i=0; i<m_InputFiberBundle->GetNumFibers(); i++)
	- {
	- ++disp;
	- vtkCell* cell = polydata->GetCell(i);
	- int numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- bool positive = false;
	- if (numPoints>1)
	- for (unsigned int m=0; m<m_RoiImages.size(); ++m)
	- {
	- auto roi = m_RoiImages.at(m);
	- m_Interpolator->SetInputImage(roi);
	-
	- int inside = 0;
	-
	- // check first fiber point
	- {
	- double* p = points->GetPoint(0);
	- itk::Point<float, 3> itkP = mitk::imv::GetItkPoint(p);
	-
	- if ( IsPositive(itkP) )
	- inside++;
	- }
	-
	- // check second fiber point
	- {
	- double* p = points->GetPoint(numPoints-1);
	- itk::Point<float, 3> itkP = mitk::imv::GetItkPoint(p);
	-
	- if ( IsPositive(itkP) )
	- inside++;
	- }
	-
	- if (inside==2 \|\| (inside==1 && !m_BothEnds))
	- {
	- positive = true;
	- positive_ids[m].push_back(i);
	- }
	- }
	- if (!positive)
	- negative_ids.push_back(i);
	- }
	-
	- if (!m_NoNegatives)
	- m_Negatives.push_back(CreateFib(negative_ids));
	- if (!m_NoPositives)
	- {
	- for (unsigned int i=0; i<positive_ids.size(); ++i)
	- {
	- std::string name;
	- if (i<m_RoiImageNames.size())
	- name = m_RoiImageNames.at(i);
	- else
	- name = "Roi" + boost::lexical_cast<std::string>(i);
	-
	- if (positive_ids.at(i).size()>=m_MinFibersPerTract)
	- {
	- m_Positives.push_back(CreateFib(positive_ids.at(i)));
	- m_PositiveLabels.push_back(name);
	- }
	- }
	- if (!m_SplitByRoi)
	- {
	- mitk::FiberBundle::Pointer output = mitk::FiberBundle::New(nullptr);
	- output = output->AddBundles(m_Positives);
	- m_Positives.clear();
	- m_Positives.push_back(output);
	- m_PositiveLabels.clear();
	- m_PositiveLabels.push_back("");
	- }
	- }
	-}
	-
	-template< class PixelType >
	-void FiberExtractionFilter< PixelType >::ExtractLabels(mitk::FiberBundle::Pointer fib)
	-{
	- MITK_INFO << "Extracting fibers by labels";
	- vtkSmartPointer<vtkPolyData> polydata = fib->GetFiberPolyData();
	-
	- std::map< std::string, std::vector< unsigned int > > positive_ids;
	-
	- std::vector< unsigned int > negative_ids; // fibers not overlapping with ANY label
	-
	- boost::progress_display disp(m_InputFiberBundle->GetNumFibers());
	- for (unsigned int i=0; i<m_InputFiberBundle->GetNumFibers(); i++)
	- {
	- ++disp;
	- vtkCell* cell = polydata->GetCell(i);
	- int numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- bool positive = false;
	- if (numPoints>1)
	- for (unsigned int m=0; m<m_RoiImages.size(); ++m)
	- {
	- auto roi = m_RoiImages.at(m);
	- m_Interpolator->SetInputImage(roi);
	-
	- int inside = 0;
	-
	- double* p1 = points->GetPoint(0);
	- itk::Point<float, 3> itkP1 = mitk::imv::GetItkPoint(p1);
	- short label1 = mitk::imv::GetImageValue<PixelType>(itkP1, false, m_Interpolator);
	-
	- double* p2 = points->GetPoint(numPoints-1);
	- itk::Point<float, 3> itkP2 = mitk::imv::GetItkPoint(p2);
	- short label2 = mitk::imv::GetImageValue<PixelType>(itkP2, false, m_Interpolator);
	-
	- if (!m_Labels.empty()) // extract fibers from all pairwise label combinations
	- {
	- for (auto l : m_Labels)
	- {
	- if (l==label1)
	- inside++;
	- if (l==label2)
	- inside++;
	- if (inside==2)
	- break;
	- }
	- }
	- else if (!m_StartLabels.empty() \|\| !m_EndLabels.empty()) // extract fibers between start and end labels
	- {
	- if (!m_StartLabels.empty() && !m_EndLabels.empty())
	- m_BothEnds = true; // if we have start and end labels it does not make sense to not use both endpoints
	- if (m_PairedStartEndLabels)
	- {
	- if (m_StartLabels.size()!=m_EndLabels.size())
	- mitkThrow() << "Start and end label lists must have same size if paired labels are used";
	- for (unsigned int ii=0; ii<m_StartLabels.size(); ++ii)
	- if ( (m_StartLabels.at(ii)==label1 && m_EndLabels.at(ii)==label2) \|\| (m_StartLabels.at(ii)==label2 && m_EndLabels.at(ii)==label1) )
	- {
	- inside = 2;
	- break;
	- }
	- }
	- else
	- {
	- for (unsigned int ii=0; ii<m_StartLabels.size(); ++ii)
	- {
	- if ( m_StartLabels.at(ii)==label1 \|\| m_StartLabels.at(ii)==label2 )
	- {
	- ++inside;
	- break;
	- }
	- }
	- for (unsigned int jj=0; jj<m_EndLabels.size(); ++jj)
	- {
	- if ( m_EndLabels.at(jj)==label1 \|\| m_EndLabels.at(jj)==label2 )
	- {
	- ++inside;
	- break;
	- }
	- }
	- }
	- }
	- else // use all labels
	- {
	- if (label1!=0)
	- ++inside;
	- if (label2!=0)
	- ++inside;
	- }
	-
	- std::string key = "";
	-
	- if (m_SplitLabels)
	- {
	- if (label1<label2)
	- key = boost::lexical_cast<std::string>(label1) + "-" + boost::lexical_cast<std::string>(label2);
	- else
	- key = boost::lexical_cast<std::string>(label2) + "-" + boost::lexical_cast<std::string>(label1);
	- }
	-
	- if (m_SplitByRoi)
	- {
	- if (m<m_RoiImageNames.size())
	- key = m_RoiImageNames.at(m) + "_" + key;
	- else
	- key = "Roi" + boost::lexical_cast<std::string>(m) + "_" + key;
	- }
	-
	- if (m_BothEnds)
	- {
	- if ( (inside==2 && (!m_SkipSelfConnections \|\| label1!=label2)) \|\| (inside==2 && m_OnlySelfConnections && label1==label2) )
	- {
	- positive = true;
	- if ( positive_ids.count(key)==0 )
	- positive_ids.insert( std::pair< std::string, std::vector< unsigned int > >( key, {i}) );
	- else
	- positive_ids[key].push_back(i);
	- }
	- }
	- else
	- {
	- if ( (inside>=1 && (!m_SkipSelfConnections \|\| label1!=label2)) \|\| (inside==2 && m_OnlySelfConnections && label1==label2) )
	- {
	- positive = true;
	- if ( positive_ids.count(key)==0 )
	- positive_ids.insert( std::pair< std::string, std::vector< unsigned int > >( key, {i}) );
	- else
	- positive_ids[key].push_back(i);
	- }
	- }
	- }
	- if (!positive)
	- negative_ids.push_back(i);
	- }
	-
	- if (!m_NoNegatives)
	- m_Negatives.push_back(CreateFib(negative_ids));
	- if (!m_NoPositives)
	- {
	- for (auto label : positive_ids)
	- {
	- if (label.second.size()>=m_MinFibersPerTract)
	- {
	- m_Positives.push_back(CreateFib(label.second));
	- m_PositiveLabels.push_back(label.first);
	- }
	- }
	- }
	-}
	-
	-template< class PixelType >
	-void FiberExtractionFilter< PixelType >::SetLabels(const std::vector<unsigned short> &Labels)
	-{
	- m_Labels = Labels;
	-}
	-
	-template< class PixelType >
	-void FiberExtractionFilter< PixelType >::SetStartLabels(const std::vector<unsigned short> &Labels)
	-{
	- m_StartLabels = Labels;
	-}
	-
	-template< class PixelType >
	-void FiberExtractionFilter< PixelType >::SetEndLabels(const std::vector<unsigned short> &Labels)
	-{
	- m_EndLabels = Labels;
	-}
	-
	-template< class PixelType >
	-std::vector<mitk::FiberBundle::Pointer> FiberExtractionFilter< PixelType >::GetNegatives() const
	-{
	- return m_Negatives;
	-}
	-
	-template< class PixelType >
	-std::vector<mitk::FiberBundle::Pointer> FiberExtractionFilter< PixelType >::GetPositives() const
	-{
	- return m_Positives;
	-}
	-
	-template< class PixelType >
	-void FiberExtractionFilter< PixelType >::GenerateData()
	-{
	- mitk::FiberBundle::Pointer fib = m_InputFiberBundle;
	- if (fib->GetNumFibers()<=0)
	- {
	- MITK_INFO << "No fibers in tractogram!";
	- return;
	- }
	-
	- if (m_Mode == MODE::OVERLAP)
	- ExtractOverlap(fib);
	- else if (m_Mode == MODE::ENDPOINTS)
	- {
	- if (m_InputType==INPUT::LABEL_MAP)
	- ExtractLabels(fib);
	- else
	- ExtractEndpoints(fib);
	- }
	-}
	-
	-}
	-
	-#endif // __itkFiberExtractionFilter_cpp
	-
	-
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFiberExtractionFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFiberExtractionFilter.h
	deleted file mode 100644
	index dad095d1a3..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFiberExtractionFilter.h
	+++ /dev/null
	@@ -1,133 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef itkFiberExtractionFilter_h
	-#define itkFiberExtractionFilter_h
	-
	-// MITK
	-#include <mitkFiberBundle.h>
	-
	-// ITK
	-#include <itkProcessObject.h>
	-#include <itkLinearInterpolateImageFunction.h>
	-
	-namespace itk{
	-
	-/**
	-* \brief Extract streamlines from tractograms using ROI images */
	-
	-template< class PixelType >
	-class FiberExtractionFilter : public ProcessObject
	-{
	-public:
	-
	- enum MODE {
	- OVERLAP,
	- ENDPOINTS
	- };
	-
	- enum INPUT {
	- SCALAR_MAP, ///< In this case, positive means roi image vlaue > threshold
	- LABEL_MAP ///< In this case, positive means roi image value in labels vector
	- };
	-
	- typedef FiberExtractionFilter Self;
	- typedef ProcessObject Superclass;
	- typedef SmartPointer< Self > Pointer;
	- typedef SmartPointer< const Self > ConstPointer;
	- typedef itk::Image< PixelType , 3> ItkInputImgType;
	-
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- itkTypeMacro( FiberExtractionFilter, ProcessObject )
	-
	- void Update() override{
	- this->GenerateData();
	- }
	-
	- itkSetMacro( InputFiberBundle, mitk::FiberBundle::Pointer )
	- itkSetMacro( Mode, MODE ) ///< Overlap or endpoints
	- itkSetMacro( InputType, INPUT ) ///< Scalar map or label image
	- itkSetMacro( BothEnds, bool ) ///< Both streamline ends need to be inside of the ROI for the streamline to be considered positive
	- itkSetMacro( OverlapFraction, float ) ///< Necessary fraction of streamline points inside the ROI for the streamline to be considered positive
	- itkSetMacro( DontResampleFibers, bool ) ///< Don't resample input fibers to ensure coverage
	- itkSetMacro( NoNegatives, bool ) ///< Don't create output tractograms from negative streamlines (save the computation)
	- itkSetMacro( NoPositives, bool ) ///< Don't create output tractograms from positive streamlines (save the computation)
	- itkSetMacro( Interpolate, bool ) ///< Interpolate input ROI image (only relevant for ENDPOINTS mode
	- itkSetMacro( Threshold, float ) ///< Threshold on input ROI image value to determine positives/negatives
	- itkSetMacro( SkipSelfConnections, bool ) ///< Ignore streamlines between two identical labels
	- itkSetMacro( OnlySelfConnections, bool ) ///< Only keep streamlines between two identical labels
	- itkSetMacro( SplitLabels, bool ) ///< Output a separate tractogram for each label-->label tract
	- itkSetMacro( SplitByRoi, bool ) ///< Output a separate tractogram for each ROI image
	- itkSetMacro( MinFibersPerTract, unsigned int ) ///< Discard positives with less fibers
	- itkSetMacro( PairedStartEndLabels, bool )
	-
	- void SetRoiImages(const std::vector< ItkInputImgType* > &rois);
	- void SetRoiImageNames(const std::vector< std::string > roi_names);
	- void SetLabels(const std::vector<unsigned short> &Labels);
	- void SetStartLabels(const std::vector<unsigned short> &Labels);
	- void SetEndLabels(const std::vector<unsigned short> &Labels);
	-
	- std::vector<mitk::FiberBundle::Pointer> GetPositives() const; ///< Get positive tracts (filtered by the input ROIs)
	- std::vector<mitk::FiberBundle::Pointer> GetNegatives() const; ///< Get negative tracts (not filtered by the ROIs)
	- std::vector< std::string > GetPositiveLabels() const; ///< In case of label extraction, this vector contains the labels corresponding to the positive tracts
	-
	-protected:
	-
	- void GenerateData() override;
	-
	- FiberExtractionFilter();
	- ~FiberExtractionFilter() override;
	-
	- mitk::FiberBundle::Pointer CreateFib(std::vector< unsigned int >& ids);
	- void ExtractOverlap(mitk::FiberBundle::Pointer fib);
	- void ExtractEndpoints(mitk::FiberBundle::Pointer fib);
	- void ExtractLabels(mitk::FiberBundle::Pointer fib);
	- bool IsPositive(const itk::Point<float, 3>& itkP);
	-
	- mitk::FiberBundle::Pointer m_InputFiberBundle;
	- std::vector< mitk::FiberBundle::Pointer > m_Positives;
	- std::vector< mitk::FiberBundle::Pointer > m_Negatives;
	- std::vector< ItkInputImgType* > m_RoiImages;
	- std::vector< std::string > m_RoiImageNames;
	- bool m_DontResampleFibers;
	- MODE m_Mode;
	- INPUT m_InputType;
	- bool m_BothEnds;
	- float m_OverlapFraction;
	- bool m_NoNegatives;
	- bool m_NoPositives;
	- bool m_Interpolate;
	- float m_Threshold;
	- std::vector< unsigned short > m_Labels;
	- bool m_SkipSelfConnections;
	- bool m_OnlySelfConnections;
	- bool m_SplitByRoi;
	- bool m_SplitLabels;
	- unsigned int m_MinFibersPerTract;
	- std::vector< unsigned short > m_StartLabels;
	- std::vector< unsigned short > m_EndLabels;
	- bool m_PairedStartEndLabels;
	- std::vector< std::string > m_PositiveLabels;
	- typename itk::LinearInterpolateImageFunction< itk::Image< PixelType, 3 >, float >::Pointer m_Interpolator;
	-};
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkFiberExtractionFilter.cpp"
	-#endif
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFitFibersToImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFitFibersToImageFilter.cpp
	deleted file mode 100644
	index 011eeb3e49..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFitFibersToImageFilter.cpp
	+++ /dev/null
	@@ -1,985 +0,0 @@
	-#include "itkFitFibersToImageFilter.h"
	-
	-#include <boost/progress.hpp>
	-#include <mitkDiffusionFunctionCollection.h>
	-
	-namespace itk{
	-
	-FitFibersToImageFilter::FitFibersToImageFilter()
	- : m_PeakImage(nullptr)
	- , m_DiffImage(nullptr)
	- , m_ScalarImage(nullptr)
	- , m_MaskImage(nullptr)
	- , m_FitIndividualFibers(true)
	- , m_GradientTolerance(1e-5)
	- , m_Lambda(1.0)
	- , m_MaxIterations(20)
	- , m_Coverage(0)
	- , m_Overshoot(0)
	- , m_RMSE(0.0)
	- , m_FilterOutliers(false)
	- , m_MeanWeight(1.0)
	- , m_MedianWeight(1.0)
	- , m_MinWeight(1.0)
	- , m_MaxWeight(1.0)
	- , m_Verbose(true)
	- , m_NumUnknowns(0)
	- , m_NumResiduals(0)
	- , m_NumCoveredDirections(0)
	- , m_SignalModel(nullptr)
	- , sz_x(0)
	- , sz_y(0)
	- , sz_z(0)
	- , m_MeanTractDensity(0)
	- , m_MeanSignal(0)
	- , fiber_count(0)
	- , m_Regularization(VnlCostFunction::REGU::VOXEL_VARIANCE)
	-{
	- this->SetNumberOfRequiredOutputs(3);
	-}
	-
	-FitFibersToImageFilter::~FitFibersToImageFilter()
	-{
	-
	-}
	-
	-void FitFibersToImageFilter::CreateDiffSystem()
	-{
	- sz_x = m_DiffImage->GetLargestPossibleRegion().GetSize(0);
	- sz_y = m_DiffImage->GetLargestPossibleRegion().GetSize(1);
	- sz_z = m_DiffImage->GetLargestPossibleRegion().GetSize(2);
	- dim_four_size = m_DiffImage->GetVectorLength();
	- int num_voxels = sz_xsz_ysz_z;
	-
	- if (m_MaskImage.IsNotNull() &&
	- (m_MaskImage->GetLargestPossibleRegion().GetSize()[0]!=sz_x \|\|
	- m_MaskImage->GetLargestPossibleRegion().GetSize()[1]!=sz_y \|\|
	- m_MaskImage->GetLargestPossibleRegion().GetSize()[2]!=sz_z))
	- mitkThrow() << "Mask and peak image must have same size!";
	-
	- auto spacing = m_DiffImage->GetSpacing();
	-
	- m_NumResiduals = num_voxels * dim_four_size;
	-
	- MITK_INFO << "Num. unknowns: " << m_NumUnknowns;
	- MITK_INFO << "Num. residuals: " << m_NumResiduals;
	- MITK_INFO << "Creating system ...";
	-
	- A.set_size(m_NumResiduals, m_NumUnknowns);
	- b.set_size(m_NumResiduals); b.fill(0.0);
	-
	- m_MeanTractDensity = 0;
	- m_MeanSignal = 0;
	- m_NumCoveredDirections = 0;
	- fiber_count = 0;
	- vnl_vector<int> voxel_indicator; voxel_indicator.set_size(sz_xsz_ysz_z); voxel_indicator.fill(0);
	-
	- unsigned int numFibers = 0;
	- for (unsigned int bundle=0; bundle<m_Tractograms.size(); bundle++)
	- numFibers += m_Tractograms.at(bundle)->GetNumFibers();
	- boost::progress_display disp(numFibers);
	- m_GroupSizes.clear();
	- for (unsigned int bundle=0; bundle<m_Tractograms.size(); bundle++)
	- {
	- vtkSmartPointer<vtkPolyData> polydata = m_Tractograms.at(bundle)->GetFiberPolyData();
	- m_GroupSizes.push_back(m_Tractograms.at(bundle)->GetNumFibers());
	- for (unsigned int i=0; i<m_Tractograms.at(bundle)->GetNumFibers(); ++i)
	- {
	- ++disp;
	- vtkCell* cell = polydata->GetCell(i);
	- int numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- if (numPoints<2)
	- MITK_INFO << "FIBER WITH ONLY ONE POINT ENCOUNTERED!";
	-
	- for (int j=0; j<numPoints-1; ++j)
	- {
	- PointType3 startVertex = mitk::imv::GetItkPoint(points->GetPoint(j));
	- itk::Index<3> startIndex;
	- itk::ContinuousIndex<float, 3> startIndexCont;
	- m_DiffImage->TransformPhysicalPointToIndex(startVertex, startIndex);
	- m_DiffImage->TransformPhysicalPointToContinuousIndex(startVertex, startIndexCont);
	-
	- PointType3 endVertex = mitk::imv::GetItkPoint(points->GetPoint(j+1));
	- itk::Index<3> endIndex;
	- itk::ContinuousIndex<float, 3> endIndexCont;
	- m_DiffImage->TransformPhysicalPointToIndex(endVertex, endIndex);
	- m_DiffImage->TransformPhysicalPointToContinuousIndex(endVertex, endIndexCont);
	-
	- mitk::DiffusionSignalModel<>::GradientType fiber_dir;
	- fiber_dir[0] = endVertex[0]-startVertex[0];
	- fiber_dir[1] = endVertex[1]-startVertex[1];
	- fiber_dir[2] = endVertex[2]-startVertex[2];
	- fiber_dir.Normalize();
	-
	- std::vector< std::pair< itk::Index<3>, double > > segments = mitk::imv::IntersectImage(spacing, startIndex, endIndex, startIndexCont, endIndexCont);
	- for (std::pair< itk::Index<3>, double > seg : segments)
	- {
	- if (!m_DiffImage->GetLargestPossibleRegion().IsInside(seg.first) \|\| (m_MaskImage.IsNotNull() && m_MaskImage->GetPixel(seg.first)==0))
	- continue;
	-
	- int x = seg.first[0];
	- int y = seg.first[1];
	- int z = seg.first[2];
	-
	- mitk::DiffusionSignalModel<>::PixelType simulated_pixel = m_SignalModel->SimulateMeasurement(fiber_dir)*seg.second;
	- VectorImgType::PixelType measured_pixel = m_DiffImage->GetPixel(seg.first);
	-
	- double simulated_mean = 0;
	- double measured_mean = 0;
	- int num_nonzero_g = 0;
	- for (int g=0; g<dim_four_size; ++g)
	- {
	- if( m_SignalModel->GetGradientDirection(g).GetNorm()<mitk::eps )
	- continue;
	- simulated_mean += simulated_pixel[g];
	- measured_mean += (double)measured_pixel[g];
	- ++num_nonzero_g;
	- }
	- simulated_mean /= num_nonzero_g;
	- measured_mean /= num_nonzero_g;
	- simulated_pixel -= simulated_mean;
	-
	- if (voxel_indicator[x + sz_xy + sz_xsz_y*z]==0)
	- m_MeanSignal += measured_mean;
	- m_MeanTractDensity += simulated_mean;
	- voxel_indicator[x + sz_xy + sz_xsz_y*z] = 1;
	-
	- for (int g=0; g<dim_four_size; ++g)
	- {
	- unsigned int linear_index = x + sz_xy + sz_xsz_yz + sz_xsz_ysz_zg;
	-
	- if (m_FitIndividualFibers)
	- {
	- b[linear_index] = (double)measured_pixel[g] - measured_mean;
	- A.put(linear_index, fiber_count, A.get(linear_index, fiber_count) + simulated_pixel[g]);
	- }
	- else
	- {
	- b[linear_index] = (double)measured_pixel[g] - measured_mean;
	- A.put(linear_index, bundle, A.get(linear_index, bundle) + simulated_pixel[g]);
	- }
	- }
	- }
	-
	- }
	-
	- ++fiber_count;
	- }
	- }
	-
	- m_NumCoveredDirections = voxel_indicator.sum();
	- m_MeanTractDensity /= m_NumCoveredDirections;
	- m_MeanSignal /= m_NumCoveredDirections;
	- b /= m_MeanSignal;
	- b *= m_MeanTractDensity;
	-}
	-
	-void FitFibersToImageFilter::CreatePeakSystem()
	-{
	- sz_x = m_PeakImage->GetLargestPossibleRegion().GetSize(0);
	- sz_y = m_PeakImage->GetLargestPossibleRegion().GetSize(1);
	- sz_z = m_PeakImage->GetLargestPossibleRegion().GetSize(2);
	- dim_four_size = m_PeakImage->GetLargestPossibleRegion().GetSize(3)/3 + 1; // +1 for zero - peak
	- int num_voxels = sz_xsz_ysz_z;
	-
	- itk::Vector< double, 3 > spacing;
	- spacing[0] = m_PeakImage->GetSpacing()[0];
	- spacing[1] = m_PeakImage->GetSpacing()[1];
	- spacing[2] = m_PeakImage->GetSpacing()[2];
	-
	- PointType3 origin;
	- origin[0] = m_PeakImage->GetOrigin()[0];
	- origin[1] = m_PeakImage->GetOrigin()[1];
	- origin[2] = m_PeakImage->GetOrigin()[2];
	-
	- UcharImgType::RegionType::SizeType size;
	- size[0] = m_PeakImage->GetLargestPossibleRegion().GetSize()[0];
	- size[1] = m_PeakImage->GetLargestPossibleRegion().GetSize()[1];
	- size[2] = m_PeakImage->GetLargestPossibleRegion().GetSize()[2];
	- UcharImgType::RegionType imageRegion; imageRegion.SetSize(size);
	-
	- itk::Matrix<double, 3, 3> direction;
	- for (int r=0; r<3; r++)
	- for (int c=0; c<3; c++)
	- direction[r][c] = m_PeakImage->GetDirection()[r][c];
	-
	- if (m_MaskImage.IsNull())
	- {
	- m_MaskImage = UcharImgType::New();
	- m_MaskImage->SetSpacing( spacing );
	- m_MaskImage->SetOrigin( origin );
	- m_MaskImage->SetDirection( direction );
	- m_MaskImage->SetRegions( imageRegion );
	- m_MaskImage->Allocate();
	- m_MaskImage->FillBuffer(1);
	- }
	- else if (m_MaskImage->GetLargestPossibleRegion().GetSize()[0]!=sz_x \|\|
	- m_MaskImage->GetLargestPossibleRegion().GetSize()[1]!=sz_y \|\|
	- m_MaskImage->GetLargestPossibleRegion().GetSize()[2]!=sz_z)
	- mitkThrow() << "Mask and peak image must have same size!";
	-
	-
	- m_NumResiduals = num_voxels * dim_four_size;
	-
	- MITK_INFO << "Num. unknowns: " << m_NumUnknowns;
	- MITK_INFO << "Num. residuals: " << m_NumResiduals;
	- MITK_INFO << "Creating system ...";
	-
	- A.set_size(m_NumResiduals, m_NumUnknowns);
	- b.set_size(m_NumResiduals); b.fill(0.0);
	-
	- m_MeanTractDensity = 0;
	- m_MeanSignal = 0;
	- m_NumCoveredDirections = 0;
	- fiber_count = 0;
	-
	- m_GroupSizes.clear();
	-
	- int numFibers = 0;
	- for (unsigned int bundle=0; bundle<m_Tractograms.size(); bundle++)
	- numFibers += m_Tractograms.at(bundle)->GetNumFibers();
	- boost::progress_display disp(numFibers);
	- for (unsigned int bundle=0; bundle<m_Tractograms.size(); bundle++)
	- {
	- vtkSmartPointer<vtkPolyData> polydata = m_Tractograms.at(bundle)->GetFiberPolyData();
	-
	- m_GroupSizes.push_back(m_Tractograms.at(bundle)->GetNumFibers());
	- for (unsigned int i=0; i<m_Tractograms.at(bundle)->GetNumFibers(); ++i)
	- {
	- ++disp;
	- vtkCell* cell = polydata->GetCell(i);
	- int numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- if (numPoints<2)
	- MITK_INFO << "FIBER WITH ONLY ONE POINT ENCOUNTERED!";
	-
	- for (int j=0; j<numPoints-1; ++j)
	- {
	- PointType3 startVertex = mitk::imv::GetItkPoint(points->GetPoint(j));
	- itk::Index<3> startIndex;
	- itk::ContinuousIndex<float, 3> startIndexCont;
	- m_MaskImage->TransformPhysicalPointToIndex(startVertex, startIndex);
	- m_MaskImage->TransformPhysicalPointToContinuousIndex(startVertex, startIndexCont);
	-
	- PointType3 endVertex = mitk::imv::GetItkPoint(points->GetPoint(j+1));
	- itk::Index<3> endIndex;
	- itk::ContinuousIndex<float, 3> endIndexCont;
	- m_MaskImage->TransformPhysicalPointToIndex(endVertex, endIndex);
	- m_MaskImage->TransformPhysicalPointToContinuousIndex(endVertex, endIndexCont);
	-
	- vnl_vector_fixed<float,3> fiber_dir;
	- fiber_dir[0] = endVertex[0]-startVertex[0];
	- fiber_dir[1] = endVertex[1]-startVertex[1];
	- fiber_dir[2] = endVertex[2]-startVertex[2];
	- fiber_dir.normalize();
	-
	- std::vector< std::pair< itk::Index<3>, double > > segments = mitk::imv::IntersectImage(spacing, startIndex, endIndex, startIndexCont, endIndexCont);
	- for (std::pair< itk::Index<3>, double > seg : segments)
	- {
	- if (!m_MaskImage->GetLargestPossibleRegion().IsInside(seg.first) \|\| m_MaskImage->GetPixel(seg.first)==0)
	- continue;
	-
	- itk::Index<4> idx4;
	- idx4[0]=seg.first[0];
	- idx4[1]=seg.first[1];
	- idx4[2]=seg.first[2];
	- idx4[3]=0;
	-
	- double w = 1;
	- int peak_id = dim_four_size-1;
	-
	- double peak_mag = 0;
	- GetClosestPeak(idx4, m_PeakImage, fiber_dir, peak_id, w, peak_mag);
	- w *= seg.second;
	-
	- int x = idx4[0];
	- int y = idx4[1];
	- int z = idx4[2];
	-
	- unsigned int linear_index = x + sz_xy + sz_xsz_yz + sz_xsz_ysz_zpeak_id;
	-
	- if (b[linear_index] == 0 && peak_id<dim_four_size-1)
	- {
	- m_NumCoveredDirections++;
	- m_MeanSignal += peak_mag;
	- }
	- m_MeanTractDensity += w;
	-
	- if (m_FitIndividualFibers)
	- {
	- b[linear_index] = peak_mag;
	- A.put(linear_index, fiber_count, A.get(linear_index, fiber_count) + w);
	- }
	- else
	- {
	- b[linear_index] = peak_mag;
	- A.put(linear_index, bundle, A.get(linear_index, bundle) + w);
	- }
	- }
	- }
	-
	- ++fiber_count;
	- }
	- }
	-
	- m_MeanTractDensity /= m_NumCoveredDirections;
	- m_MeanSignal /= m_NumCoveredDirections;
	- b /= m_MeanSignal;
	- b *= m_MeanTractDensity;
	-}
	-
	-void FitFibersToImageFilter::CreateScalarSystem()
	-{
	- sz_x = m_ScalarImage->GetLargestPossibleRegion().GetSize(0);
	- sz_y = m_ScalarImage->GetLargestPossibleRegion().GetSize(1);
	- sz_z = m_ScalarImage->GetLargestPossibleRegion().GetSize(2);
	- int num_voxels = sz_xsz_ysz_z;
	-
	- if (m_MaskImage.IsNotNull() &&
	- (m_MaskImage->GetLargestPossibleRegion().GetSize()[0]!=sz_x \|\|
	- m_MaskImage->GetLargestPossibleRegion().GetSize()[1]!=sz_y \|\|
	- m_MaskImage->GetLargestPossibleRegion().GetSize()[2]!=sz_z))
	- mitkThrow() << "Mask and peak image must have same size!";
	-
	- auto spacing = m_ScalarImage->GetSpacing();
	- m_NumResiduals = num_voxels;
	-
	- MITK_INFO << "Num. unknowns: " << m_NumUnknowns;
	- MITK_INFO << "Num. residuals: " << m_NumResiduals;
	- MITK_INFO << "Creating system ...";
	-
	- A.set_size(m_NumResiduals, m_NumUnknowns);
	- b.set_size(m_NumResiduals); b.fill(0.0);
	-
	- m_MeanTractDensity = 0;
	- m_MeanSignal = 0;
	- int numCoveredVoxels = 0;
	- fiber_count = 0;
	-
	- int numFibers = 0;
	- for (unsigned int bundle=0; bundle<m_Tractograms.size(); bundle++)
	- numFibers += m_Tractograms.at(bundle)->GetNumFibers();
	- boost::progress_display disp(numFibers);
	- m_GroupSizes.clear();
	- for (unsigned int bundle=0; bundle<m_Tractograms.size(); bundle++)
	- {
	- vtkSmartPointer<vtkPolyData> polydata = m_Tractograms.at(bundle)->GetFiberPolyData();
	-
	- m_GroupSizes.push_back(m_Tractograms.at(bundle)->GetNumFibers());
	- for (unsigned int i=0; i<m_Tractograms.at(bundle)->GetNumFibers(); ++i)
	- {
	- ++disp;
	- vtkCell* cell = polydata->GetCell(i);
	- int numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- for (int j=0; j<numPoints-1; ++j)
	- {
	- PointType3 startVertex = mitk::imv::GetItkPoint(points->GetPoint(j));
	- itk::Index<3> startIndex;
	- itk::ContinuousIndex<float, 3> startIndexCont;
	- m_ScalarImage->TransformPhysicalPointToIndex(startVertex, startIndex);
	- m_ScalarImage->TransformPhysicalPointToContinuousIndex(startVertex, startIndexCont);
	-
	- PointType3 endVertex = mitk::imv::GetItkPoint(points->GetPoint(j+1));
	- itk::Index<3> endIndex;
	- itk::ContinuousIndex<float, 3> endIndexCont;
	- m_ScalarImage->TransformPhysicalPointToIndex(endVertex, endIndex);
	- m_ScalarImage->TransformPhysicalPointToContinuousIndex(endVertex, endIndexCont);
	-
	- std::vector< std::pair< itk::Index<3>, double > > segments = mitk::imv::IntersectImage(spacing, startIndex, endIndex, startIndexCont, endIndexCont);
	- for (std::pair< itk::Index<3>, double > seg : segments)
	- {
	- if (!m_ScalarImage->GetLargestPossibleRegion().IsInside(seg.first) \|\| (m_MaskImage.IsNotNull() && m_MaskImage->GetPixel(seg.first)==0))
	- continue;
	-
	- float image_value = m_ScalarImage->GetPixel(seg.first);
	- int x = seg.first[0];
	- int y = seg.first[1];
	- int z = seg.first[2];
	-
	- unsigned int linear_index = x + sz_xy + sz_xsz_y*z;
	-
	- if (b[linear_index] == 0)
	- {
	- numCoveredVoxels++;
	- m_MeanSignal += image_value;
	- }
	- m_MeanTractDensity += seg.second;
	-
	- if (m_FitIndividualFibers)
	- {
	- b[linear_index] = image_value;
	- A.put(linear_index, fiber_count, A.get(linear_index, fiber_count) + seg.second);
	- }
	- else
	- {
	- b[linear_index] = image_value;
	- A.put(linear_index, bundle, A.get(linear_index, bundle) + seg.second);
	- }
	- }
	- }
	-
	- ++fiber_count;
	- }
	- }
	-
	- m_MeanTractDensity /= numCoveredVoxels;
	- m_MeanSignal /= numCoveredVoxels;
	- b /= m_MeanSignal;
	- b *= m_MeanTractDensity;
	-}
	-
	-void FitFibersToImageFilter::GenerateData()
	-{
	- m_NumUnknowns = m_Tractograms.size();
	- if (m_FitIndividualFibers)
	- {
	- m_NumUnknowns = 0;
	- for (unsigned int bundle=0; bundle<m_Tractograms.size(); bundle++)
	- m_NumUnknowns += m_Tractograms.at(bundle)->GetNumFibers();
	- }
	- else
	- m_FilterOutliers = false;
	- if (m_NumUnknowns<1)
	- {
	- MITK_INFO << "No fibers in tractogram.";
	- return;
	- }
	-
	- fiber_count = 0;
	- sz_x = 0;
	- sz_y = 0;
	- sz_z = 0;
	- m_MeanTractDensity = 0;
	- m_MeanSignal = 0;
	- if (m_PeakImage.IsNotNull())
	- CreatePeakSystem();
	- else if (m_DiffImage.IsNotNull())
	- CreateDiffSystem();
	- else if (m_ScalarImage.IsNotNull())
	- CreateScalarSystem();
	- else
	- mitkThrow() << "No input image set!";
	-
	- MITK_INFO << "Initializing optimizer";
	- double init_lambda = fiber_count; // initialization for lambda estimation
	-
	- itk::TimeProbe clock;
	- clock.Start();
	-
	- cost = VnlCostFunction(m_NumUnknowns);
	- cost.SetProblem(A, b, init_lambda, m_Regularization);
	- cost.SetGroupSizes(m_GroupSizes);
	- m_Weights.set_size(m_NumUnknowns);
	- m_Weights.fill( 1.0/m_NumUnknowns );
	- vnl_lbfgsb minimizer(cost);
	- vnl_vector<double> l; l.set_size(m_NumUnknowns); l.fill(0);
	- vnl_vector<long> bound_selection; bound_selection.set_size(m_NumUnknowns); bound_selection.fill(1);
	- minimizer.set_bound_selection(bound_selection);
	- minimizer.set_lower_bound(l);
	- minimizer.set_projected_gradient_tolerance(m_GradientTolerance);
	-
	- if (m_Regularization==VnlCostFunction::REGU::MSM)
	- MITK_INFO << "Regularization type: MSM";
	- else if (m_Regularization==VnlCostFunction::REGU::VARIANCE)
	- MITK_INFO << "Regularization type: VARIANCE";
	- else if (m_Regularization==VnlCostFunction::REGU::LASSO)
	- MITK_INFO << "Regularization type: LASSO";
	- else if (m_Regularization==VnlCostFunction::REGU::VOXEL_VARIANCE)
	- MITK_INFO << "Regularization type: VOXEL_VARIANCE";
	- else if (m_Regularization==VnlCostFunction::REGU::GROUP_LASSO)
	- MITK_INFO << "Regularization type: GROUP_LASSO";
	- else if (m_Regularization==VnlCostFunction::REGU::GROUP_VARIANCE)
	- MITK_INFO << "Regularization type: GROUP_VARIANCE";
	- else if (m_Regularization==VnlCostFunction::REGU::NONE)
	- MITK_INFO << "Regularization type: NONE";
	-
	-// if (m_Regularization!=VnlCostFunction::REGU::NONE) // REMOVE FOR NEW FIT AND SET cost.m_Lambda = m_Lambda
	-// {
	-// MITK_INFO << "Estimating regularization";
	-// minimizer.set_trace(false);
	-// minimizer.set_max_function_evals(2);
	-// minimizer.minimize(m_Weights);
	-// vnl_vector<double> dx; dx.set_size(m_NumUnknowns); dx.fill(0.0);
	-// cost.calc_regularization_gradient(m_Weights, dx);
	-
	-// if (m_Weights.magnitude()==0)
	-// {
	-// MITK_INFO << "Regularization estimation failed. Using default value.";
	-// cost.m_Lambda = fiber_count*m_Lambda;
	-// }
	-// else
	-// {
	-// double r = dx.magnitude()/m_Weights.magnitude(); // wtf???
	-// cost.m_Lambda = m_Lambda55.0/r;
	-// MITK_INFO << r << " - " << m_Lambda*55.0/r;
	-// if (cost.m_Lambda>10e7)
	-// {
	-// MITK_INFO << "Regularization estimation failed. Using default value.";
	-// cost.m_Lambda = fiber_count*m_Lambda;
	-// }
	-// }
	-// }
	-// else
	-// cost.m_Lambda = 0;
	- cost.m_Lambda = m_Lambda;
	- MITK_INFO << "Using regularization factor of " << cost.m_Lambda << " (λ: " << m_Lambda << ")";
	-
	- MITK_INFO << "Fitting fibers";
	- minimizer.set_trace(m_Verbose);
	-
	- minimizer.set_max_function_evals(m_MaxIterations);
	- minimizer.minimize(m_Weights);
	-
	- std::vector< double > weights;
	- if (m_FilterOutliers)
	- {
	- for (auto w : m_Weights)
	- weights.push_back(w);
	- std::sort(weights.begin(), weights.end());
	- MITK_INFO << "Setting upper weight bound to " << weights.at(m_NumUnknowns*0.99);
	- vnl_vector<double> u; u.set_size(m_NumUnknowns); u.fill(weights.at(m_NumUnknowns*0.99));
	- minimizer.set_upper_bound(u);
	- bound_selection.fill(2);
	- minimizer.set_bound_selection(bound_selection);
	- minimizer.minimize(m_Weights);
	- weights.clear();
	- }
	-
	- for (auto w : m_Weights)
	- weights.push_back(w);
	- std::sort(weights.begin(), weights.end());
	-
	- m_MeanWeight = m_Weights.mean();
	- m_MedianWeight = weights.at(m_NumUnknowns*0.5);
	- m_MinWeight = weights.at(0);
	- m_MaxWeight = weights.at(m_NumUnknowns-1);
	-
	- MITK_INFO << "*************************";
	- MITK_INFO << "Weight statistics";
	- MITK_INFO << "Sum: " << m_Weights.sum();
	- MITK_INFO << "Mean: " << m_MeanWeight;
	- MITK_INFO << "1% quantile: " << weights.at(m_NumUnknowns*0.01);
	- MITK_INFO << "5% quantile: " << weights.at(m_NumUnknowns*0.05);
	- MITK_INFO << "25% quantile: " << weights.at(m_NumUnknowns*0.25);
	- MITK_INFO << "Median: " << m_MedianWeight;
	- MITK_INFO << "75% quantile: " << weights.at(m_NumUnknowns*0.75);
	- MITK_INFO << "95% quantile: " << weights.at(m_NumUnknowns*0.95);
	- MITK_INFO << "99% quantile: " << weights.at(m_NumUnknowns*0.99);
	- MITK_INFO << "Min: " << m_MinWeight;
	- MITK_INFO << "Max: " << m_MaxWeight;
	- MITK_INFO << "*************************";
	- MITK_INFO << "NumEvals: " << minimizer.get_num_evaluations();
	- MITK_INFO << "NumIterations: " << minimizer.get_num_iterations();
	- MITK_INFO << "Residual cost: " << minimizer.get_end_error();
	- m_RMSE = cost.S->get_rms_error(m_Weights);
	- MITK_INFO << "Final RMSE: " << m_RMSE;
	-
	- clock.Stop();
	- int h = clock.GetTotal()/3600;
	- int m = ((int)clock.GetTotal()%3600)/60;
	- int s = (int)clock.GetTotal()%60;
	- MITK_INFO << "Optimization took " << h << "h, " << m << "m and " << s << "s";
	-
	- MITK_INFO << "Weighting fibers";
	- m_RmsDiffPerBundle.set_size(m_Tractograms.size());
	- std::streambuf *old = cout.rdbuf(); // <-- save
	- std::stringstream ss;
	- std::cout.rdbuf (ss.rdbuf());
	- if (m_FitIndividualFibers)
	- {
	- unsigned int fiber_count = 0;
	- for (unsigned int bundle=0; bundle<m_Tractograms.size(); bundle++)
	- {
	- vnl_vector< double > temp_weights;
	- temp_weights.set_size(m_Weights.size());
	- temp_weights.copy_in(m_Weights.data_block());
	-
	- for (unsigned int i=0; i<m_Tractograms.at(bundle)->GetNumFibers(); i++)
	- {
	- m_Tractograms.at(bundle)->SetFiberWeight(i, m_Weights[fiber_count]);
	- temp_weights[fiber_count] = 0;
	-
	- ++fiber_count;
	- }
	- double d_rms = cost.S->get_rms_error(temp_weights) - m_RMSE;
	- m_RmsDiffPerBundle[bundle] = d_rms;
	- }
	- }
	- else
	- {
	- for (unsigned int i=0; i<m_Tractograms.size(); ++i)
	- {
	- vnl_vector< double > temp_weights;
	- temp_weights.set_size(m_Weights.size());
	- temp_weights.copy_in(m_Weights.data_block());
	- temp_weights[i] = 0;
	- double d_rms = cost.S->get_rms_error(temp_weights) - m_RMSE;
	- m_RmsDiffPerBundle[i] = d_rms;
	-
	- m_Tractograms.at(i)->SetFiberWeights(m_Weights[i]);
	- }
	- }
	- std::cout.rdbuf (old);
	-
	- // transform back
	- A *= m_MeanSignal/100.0;
	- b *= m_MeanSignal/100.0;
	-
	- MITK_INFO << "Generating output images ...";
	- if (m_PeakImage.IsNotNull())
	- GenerateOutputPeakImages();
	- else if (m_DiffImage.IsNotNull())
	- GenerateOutputDiffImages();
	- else if (m_ScalarImage.IsNotNull())
	- GenerateOutputScalarImages();
	-
	- m_Coverage = m_Coverage/m_MeanSignal;
	- m_Overshoot = m_Overshoot/m_MeanSignal;
	-
	- MITK_INFO << std::fixed << "Coverage: " << setprecision(2) << 100.0*m_Coverage << "%";
	- MITK_INFO << std::fixed << "Overshoot: " << setprecision(2) << 100.0*m_Overshoot << "%";
	-}
	-
	-void FitFibersToImageFilter::GenerateOutputDiffImages()
	-{
	- VectorImgType::PixelType pix; pix.SetSize(m_DiffImage->GetVectorLength()); pix.Fill(0);
	- itk::ImageDuplicator< VectorImgType >::Pointer duplicator = itk::ImageDuplicator< VectorImgType >::New();
	- duplicator->SetInputImage(m_DiffImage);
	- duplicator->Update();
	- m_UnderexplainedImageDiff = duplicator->GetOutput();
	- m_UnderexplainedImageDiff->FillBuffer(pix);
	-
	- duplicator->SetInputImage(m_UnderexplainedImageDiff);
	- duplicator->Update();
	- m_OverexplainedImageDiff = duplicator->GetOutput();
	- m_OverexplainedImageDiff->FillBuffer(pix);
	-
	- duplicator->SetInputImage(m_OverexplainedImageDiff);
	- duplicator->Update();
	- m_ResidualImageDiff = duplicator->GetOutput();
	- m_ResidualImageDiff->FillBuffer(pix);
	-
	- duplicator->SetInputImage(m_ResidualImageDiff);
	- duplicator->Update();
	- m_FittedImageDiff = duplicator->GetOutput();
	- m_FittedImageDiff->FillBuffer(pix);
	-
	- vnl_vector<double> fitted_b; fitted_b.set_size(b.size());
	- cost.S->multiply(m_Weights, fitted_b);
	-
	- itk::ImageRegionIterator<VectorImgType> it1 = itk::ImageRegionIterator<VectorImgType>(m_DiffImage, m_DiffImage->GetLargestPossibleRegion());
	- itk::ImageRegionIterator<VectorImgType> it2 = itk::ImageRegionIterator<VectorImgType>(m_FittedImageDiff, m_FittedImageDiff->GetLargestPossibleRegion());
	- itk::ImageRegionIterator<VectorImgType> it3 = itk::ImageRegionIterator<VectorImgType>(m_ResidualImageDiff, m_ResidualImageDiff->GetLargestPossibleRegion());
	- itk::ImageRegionIterator<VectorImgType> it4 = itk::ImageRegionIterator<VectorImgType>(m_UnderexplainedImageDiff, m_UnderexplainedImageDiff->GetLargestPossibleRegion());
	- itk::ImageRegionIterator<VectorImgType> it5 = itk::ImageRegionIterator<VectorImgType>(m_OverexplainedImageDiff, m_OverexplainedImageDiff->GetLargestPossibleRegion());
	-
	- m_MeanSignal = 0;
	- m_Coverage = 0;
	- m_Overshoot = 0;
	-
	- while( !it2.IsAtEnd() )
	- {
	- itk::Index<3> idx3 = it2.GetIndex();
	- VectorImgType::PixelType original_pix =it1.Get();
	- VectorImgType::PixelType fitted_pix =it2.Get();
	- VectorImgType::PixelType residual_pix =it3.Get();
	- VectorImgType::PixelType underexplained_pix =it4.Get();
	- VectorImgType::PixelType overexplained_pix =it5.Get();
	-
	- int num_nonzero_g = 0;
	- double original_mean = 0;
	- for (int g=0; g<dim_four_size; ++g)
	- {
	- if( m_SignalModel->GetGradientDirection(g).GetNorm()>=mitk::eps )
	- {
	- original_mean += original_pix[g];
	- ++num_nonzero_g;
	- }
	- }
	- original_mean /= num_nonzero_g;
	-
	- for (int g=0; g<dim_four_size; ++g)
	- {
	- unsigned int linear_index = idx3[0] + sz_xidx3[1] + sz_xsz_yidx3[2] + sz_xsz_ysz_zg;
	-
	- fitted_pix[g] = fitted_b[linear_index] + original_mean;
	- residual_pix[g] = original_pix[g] - fitted_b[linear_index] - original_mean;
	-
	- if (residual_pix[g]<0)
	- {
	- overexplained_pix[g] = residual_pix[g];
	- m_Coverage += b[linear_index] + original_mean;
	- m_Overshoot -= residual_pix[g];
	- }
	- else if (residual_pix[g]>=0)
	- {
	- underexplained_pix[g] = residual_pix[g];
	- m_Coverage += fitted_b[linear_index] + original_mean;
	- }
	- m_MeanSignal += b[linear_index] + original_mean;
	- }
	-
	- it2.Set(fitted_pix);
	- it3.Set(residual_pix);
	- it4.Set(underexplained_pix);
	- it5.Set(overexplained_pix);
	-
	- ++it1;
	- ++it2;
	- ++it3;
	- ++it4;
	- ++it5;
	- }
	-}
	-
	-void FitFibersToImageFilter::GenerateOutputScalarImages()
	-{
	- itk::ImageDuplicator< DoubleImgType >::Pointer duplicator = itk::ImageDuplicator< DoubleImgType >::New();
	- duplicator->SetInputImage(m_ScalarImage);
	- duplicator->Update();
	- m_UnderexplainedImageScalar = duplicator->GetOutput();
	- m_UnderexplainedImageScalar->FillBuffer(0);
	-
	- duplicator->SetInputImage(m_UnderexplainedImageScalar);
	- duplicator->Update();
	- m_OverexplainedImageScalar = duplicator->GetOutput();
	- m_OverexplainedImageScalar->FillBuffer(0);
	-
	- duplicator->SetInputImage(m_OverexplainedImageScalar);
	- duplicator->Update();
	- m_ResidualImageScalar = duplicator->GetOutput();
	- m_ResidualImageScalar->FillBuffer(0);
	-
	- duplicator->SetInputImage(m_ResidualImageScalar);
	- duplicator->Update();
	- m_FittedImageScalar = duplicator->GetOutput();
	- m_FittedImageScalar->FillBuffer(0);
	-
	- vnl_vector<double> fitted_b; fitted_b.set_size(b.size());
	- cost.S->multiply(m_Weights, fitted_b);
	-
	- itk::ImageRegionIterator<DoubleImgType> it1 = itk::ImageRegionIterator<DoubleImgType>(m_ScalarImage, m_ScalarImage->GetLargestPossibleRegion());
	- itk::ImageRegionIterator<DoubleImgType> it2 = itk::ImageRegionIterator<DoubleImgType>(m_FittedImageScalar, m_FittedImageScalar->GetLargestPossibleRegion());
	- itk::ImageRegionIterator<DoubleImgType> it3 = itk::ImageRegionIterator<DoubleImgType>(m_ResidualImageScalar, m_ResidualImageScalar->GetLargestPossibleRegion());
	- itk::ImageRegionIterator<DoubleImgType> it4 = itk::ImageRegionIterator<DoubleImgType>(m_UnderexplainedImageScalar, m_UnderexplainedImageScalar->GetLargestPossibleRegion());
	- itk::ImageRegionIterator<DoubleImgType> it5 = itk::ImageRegionIterator<DoubleImgType>(m_OverexplainedImageScalar, m_OverexplainedImageScalar->GetLargestPossibleRegion());
	-
	- m_MeanSignal = 0;
	- m_Coverage = 0;
	- m_Overshoot = 0;
	-
	- while( !it2.IsAtEnd() )
	- {
	- itk::Index<3> idx3 = it2.GetIndex();
	- DoubleImgType::PixelType original_pix =it1.Get();
	- DoubleImgType::PixelType fitted_pix =it2.Get();
	- DoubleImgType::PixelType residual_pix =it3.Get();
	- DoubleImgType::PixelType underexplained_pix =it4.Get();
	- DoubleImgType::PixelType overexplained_pix =it5.Get();
	-
	- unsigned int linear_index = idx3[0] + sz_xidx3[1] + sz_xsz_y*idx3[2];
	-
	- fitted_pix = fitted_b[linear_index];
	- residual_pix = original_pix - fitted_pix;
	-
	- if (residual_pix<0)
	- {
	- overexplained_pix = residual_pix;
	- m_Coverage += b[linear_index];
	- m_Overshoot -= residual_pix;
	- }
	- else if (residual_pix>=0)
	- {
	- underexplained_pix = residual_pix;
	- m_Coverage += fitted_b[linear_index];
	- }
	- m_MeanSignal += b[linear_index];
	-
	- it2.Set(fitted_pix);
	- it3.Set(residual_pix);
	- it4.Set(underexplained_pix);
	- it5.Set(overexplained_pix);
	-
	- ++it1;
	- ++it2;
	- ++it3;
	- ++it4;
	- ++it5;
	- }
	-}
	-
	-VnlCostFunction::REGU FitFibersToImageFilter::GetRegularization() const
	-{
	- return m_Regularization;
	-}
	-
	-void FitFibersToImageFilter::SetRegularization(const VnlCostFunction::REGU &Regularization)
	-{
	- m_Regularization = Regularization;
	-}
	-
	-void FitFibersToImageFilter::GenerateOutputPeakImages()
	-{
	- itk::ImageDuplicator< PeakImgType >::Pointer duplicator = itk::ImageDuplicator< PeakImgType >::New();
	- duplicator->SetInputImage(m_PeakImage);
	- duplicator->Update();
	- m_UnderexplainedImage = duplicator->GetOutput();
	- m_UnderexplainedImage->FillBuffer(0.0);
	-
	- duplicator->SetInputImage(m_UnderexplainedImage);
	- duplicator->Update();
	- m_OverexplainedImage = duplicator->GetOutput();
	- m_OverexplainedImage->FillBuffer(0.0);
	-
	- duplicator->SetInputImage(m_OverexplainedImage);
	- duplicator->Update();
	- m_ResidualImage = duplicator->GetOutput();
	- m_ResidualImage->FillBuffer(0.0);
	-
	- duplicator->SetInputImage(m_ResidualImage);
	- duplicator->Update();
	- m_FittedImage = duplicator->GetOutput();
	- m_FittedImage->FillBuffer(0.0);
	-
	- vnl_vector<double> fitted_b; fitted_b.set_size(b.size());
	- cost.S->multiply(m_Weights, fitted_b);
	-
	- for (unsigned int r=0; r<b.size(); r++)
	- {
	- itk::Index<4> idx4;
	- unsigned int linear_index = r;
	- idx4[0] = linear_index % sz_x; linear_index /= sz_x;
	- idx4[1] = linear_index % sz_y; linear_index /= sz_y;
	- idx4[2] = linear_index % sz_z; linear_index /= sz_z;
	- int peak_id = linear_index % dim_four_size;
	-
	- if (peak_id<dim_four_size-1)
	- {
	- vnl_vector_fixed<float,3> peak_dir;
	-
	- idx4[3] = peak_id*3;
	- peak_dir[0] = m_PeakImage->GetPixel(idx4);
	- idx4[3] += 1;
	- peak_dir[1] = m_PeakImage->GetPixel(idx4);
	- idx4[3] += 1;
	- peak_dir[2] = m_PeakImage->GetPixel(idx4);
	-
	- peak_dir.normalize();
	- peak_dir *= fitted_b[r];
	-
	- idx4[3] = peak_id*3;
	- m_FittedImage->SetPixel(idx4, peak_dir[0]);
	-
	- idx4[3] += 1;
	- m_FittedImage->SetPixel(idx4, peak_dir[1]);
	-
	- idx4[3] += 1;
	- m_FittedImage->SetPixel(idx4, peak_dir[2]);
	- }
	- }
	-
	- m_MeanSignal = 0;
	- m_Coverage = 0;
	- m_Overshoot = 0;
	-
	- itk::Index<4> idx4;
	- for (idx4[0]=0; idx4[0]<sz_x; ++idx4[0])
	- for (idx4[1]=0; idx4[1]<sz_y; ++idx4[1])
	- for (idx4[2]=0; idx4[2]<sz_z; ++idx4[2])
	- {
	- itk::Index<3> idx3; idx3[0] = idx4[0]; idx3[1] = idx4[1]; idx3[2] = idx4[2];
	- if (m_MaskImage.IsNotNull() && m_MaskImage->GetPixel(idx3)==0)
	- continue;
	-
	- vnl_vector_fixed<float,3> peak_dir;
	- vnl_vector_fixed<float,3> fitted_dir;
	- vnl_vector_fixed<float,3> overshoot_dir;
	- for (idx4[3]=0; idx4[3]<(itk::IndexValueType)m_PeakImage->GetLargestPossibleRegion().GetSize(3); ++idx4[3])
	- {
	- peak_dir[idx4[3]%3] = m_PeakImage->GetPixel(idx4);
	- fitted_dir[idx4[3]%3] = m_FittedImage->GetPixel(idx4);
	- m_ResidualImage->SetPixel(idx4, m_PeakImage->GetPixel(idx4) - m_FittedImage->GetPixel(idx4));
	-
	- if (idx4[3]%3==2)
	- {
	- m_MeanSignal += peak_dir.magnitude();
	-
	- itk::Index<4> tidx= idx4;
	- if (peak_dir.magnitude()>fitted_dir.magnitude())
	- {
	- m_Coverage += fitted_dir.magnitude();
	- m_UnderexplainedImage->SetPixel(tidx, peak_dir[2]-fitted_dir[2]); tidx[3]--;
	- m_UnderexplainedImage->SetPixel(tidx, peak_dir[1]-fitted_dir[1]); tidx[3]--;
	- m_UnderexplainedImage->SetPixel(tidx, peak_dir[0]-fitted_dir[0]);
	- }
	- else
	- {
	- overshoot_dir[0] = fitted_dir[0]-peak_dir[0];
	- overshoot_dir[1] = fitted_dir[1]-peak_dir[1];
	- overshoot_dir[2] = fitted_dir[2]-peak_dir[2];
	- m_Coverage += peak_dir.magnitude();
	- m_Overshoot += overshoot_dir.magnitude();
	- m_OverexplainedImage->SetPixel(tidx, overshoot_dir[2]); tidx[3]--;
	- m_OverexplainedImage->SetPixel(tidx, overshoot_dir[1]); tidx[3]--;
	- m_OverexplainedImage->SetPixel(tidx, overshoot_dir[0]);
	- }
	- }
	- }
	- }
	-}
	-
	-void FitFibersToImageFilter::GetClosestPeak(itk::Index<4> idx, PeakImgType::Pointer peak_image , vnl_vector_fixed<float,3> fiber_dir, int& id, double& w, double& peak_mag )
	-{
	- int m_NumDirs = peak_image->GetLargestPossibleRegion().GetSize()[3]/3;
	- vnl_vector_fixed<float,3> out_dir; out_dir.fill(0);
	- float angle = 0.9;
	-
	- for (int i=0; i<m_NumDirs; i++)
	- {
	- vnl_vector_fixed<float,3> dir;
	- idx[3] = i*3;
	- dir[0] = peak_image->GetPixel(idx);
	- idx[3] += 1;
	- dir[1] = peak_image->GetPixel(idx);
	- idx[3] += 1;
	- dir[2] = peak_image->GetPixel(idx);
	-
	- float mag = dir.magnitude();
	- if (mag<mitk::eps)
	- continue;
	-
	- float a = fabs(dot_product(dir, fiber_dir))/mag;
	- if (a>angle)
	- {
	- angle = a;
	- w = angle;
	- peak_mag = mag;
	- id = i;
	- }
	- }
	-}
	-
	-std::vector<mitk::FiberBundle::Pointer> FitFibersToImageFilter::GetTractograms() const
	-{
	- return m_Tractograms;
	-}
	-
	-void FitFibersToImageFilter::SetTractograms(const std::vector<mitk::FiberBundle::Pointer> &tractograms)
	-{
	- m_Tractograms = tractograms;
	-}
	-
	-void FitFibersToImageFilter::SetSignalModel(mitk::DiffusionSignalModel<> *SignalModel)
	-{
	- m_SignalModel = SignalModel;
	-}
	-
	-}
	-
	-
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFitFibersToImageFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFitFibersToImageFilter.h
	deleted file mode 100644
	index c897dd4839..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFitFibersToImageFilter.h
	+++ /dev/null
	@@ -1,474 +0,0 @@
	-#ifndef __itkFitFibersToImageFilter_h__
	-#define __itkFitFibersToImageFilter_h__
	-
	-// MITK
	-#include <mitkFiberBundle.h>
	-#include <itkImageSource.h>
	-#include <mitkPeakImage.h>
	-#include <vnl/algo/vnl_lbfgsb.h>
	-#include <vnl/vnl_sparse_matrix.h>
	-#include <vnl/vnl_sparse_matrix_linear_system.h>
	-#include <itkImageDuplicator.h>
	-#include <itkTimeProbe.h>
	-#include <itkMersenneTwisterRandomVariateGenerator.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <mitkDiffusionSignalModel.h>
	-
	-class VnlCostFunction : public vnl_cost_function
	-{
	-public:
	-
	- enum REGU
	- {
	- MSM,
	- VARIANCE,
	- LASSO,
	- VOXEL_VARIANCE,
	- GROUP_LASSO,
	- GROUP_VARIANCE,
	- NONE
	- };
	-
	- vnl_sparse_matrix_linear_system< double >* S;
	- vnl_sparse_matrix< double > m_A;
	- vnl_sparse_matrix< double > m_A_Ones; // matrix indicating active weights with 1
	- vnl_vector< double > m_b;
	- double m_Lambda; // regularization factor
	-
	- vnl_vector<double> row_sums; // number of active weights per row
	- vnl_vector<double> local_weight_means; // mean weight of each row
	- REGU regularization;
	- std::vector<unsigned int> group_sizes;
	-
	- void SetProblem(vnl_sparse_matrix< double >& A, vnl_vector<double>& b, double lambda, REGU regu)
	- {
	- S = new vnl_sparse_matrix_linear_system<double>(A, b);
	- m_A = A;
	- m_b = b;
	- m_Lambda = lambda;
	-
	- m_A_Ones.set_size(m_A.rows(), m_A.cols());
	- m_A.reset();
	- while (m_A.next())
	- m_A_Ones.put(m_A.getrow(), m_A.getcolumn(), 1);
	-
	- unsigned int N = m_b.size();
	- vnl_vector<double> ones; ones.set_size(dim); ones.fill(1.0);
	- row_sums.set_size(N);
	- m_A_Ones.mult(ones, row_sums);
	- local_weight_means.set_size(N);
	- regularization = regu;
	- }
	-
	- void SetGroupSizes(std::vector<unsigned int> sizes)
	- {
	- unsigned int sum = 0;
	- for (auto s : sizes)
	- sum += s;
	- if (sum!=m_A.cols())
	- {
	- MITK_INFO << "Group sizes do not match number of unknowns (" << sum << " vs. " << m_A.cols() << ")";
	- return;
	- }
	- group_sizes = sizes;
	- }
	-
	- VnlCostFunction(const int NumVars=0) : vnl_cost_function(NumVars)
	- {
	- }
	-
	- // Regularization: mean squared magnitude of weight vectors (small weights)
	- void regu_MSM(vnl_vector<double> const &x, double& cost)
	- {
	- cost += 10000.0m_Lambdax.squared_magnitude()/dim;
	- }
	-
	- // Regularization: mean squared deaviation of weights from mean weight (enforce uniform weights)
	- void regu_Variance(vnl_vector<double> const &x, double& cost)
	- {
	- double mean = x.mean();
	- vnl_vector<double> tx = x-mean;
	- cost += 10000.0m_Lambdatx.squared_magnitude()/dim;
	- }
	-
	- // Regularization: mean absolute magnitude of weight vectors (small weights) L1
	- void regu_Lasso(vnl_vector<double> const &x, double& cost)
	- {
	- cost += m_Lambda*x.one_norm()/dim;
	- }
	-
	- // Regularization: mean squared deaviation of weights from bundle mean weight (enforce uniform weights PER BUNDLE)
	- void regu_GroupVariance(vnl_vector<double> const &x, double& cost)
	- {
	- vnl_vector<double> tx(x);
	- unsigned int offset = 0;
	- for (auto g : group_sizes)
	- {
	- double group_mean = 0;
	- for (unsigned int i=0; i<g; ++i)
	- group_mean += x[offset+i];
	- group_mean /= g;
	-
	- for (unsigned int i=0; i<g; ++i)
	- tx[offset+i] -= group_mean;
	-
	- offset += g;
	- }
	-
	- cost += 10000.0m_Lambdatx.squared_magnitude()/dim;
	- }
	-
	- // Regularization: voxel-weise mean squared deaviation of weights from voxel-wise mean weight (enforce locally uniform weights)
	- void regu_VoxelVariance(vnl_vector<double> const &x, double& cost)
	- {
	- m_A_Ones.mult(x, local_weight_means);
	- local_weight_means = element_quotient(local_weight_means, row_sums);
	-
	- m_A_Ones.reset();
	- double regu = 0;
	- while (m_A_Ones.next())
	- {
	- double d = 0;
	- if (x[m_A_Ones.getcolumn()]>local_weight_means[m_A_Ones.getrow()])
	- d = std::exp(x[m_A_Ones.getcolumn()]) - std::exp(local_weight_means[m_A_Ones.getrow()]);
	- else
	- d = x[m_A_Ones.getcolumn()] - local_weight_means[m_A_Ones.getrow()];
	- regu += d*d;
	- }
	- cost += m_Lambda*regu/dim;
	- }
	-
	- // Regularization: group Lasso: sum_g(lambda_g * \|\|x_g\|\|_2)
	- void regu_GroupLasso(vnl_vector<double> const &x, double& cost)
	- {
	- unsigned int offset = 0;
	- for (auto g : group_sizes)
	- {
	- double group_cost = 0;
	- for (unsigned int i=0; i<g; ++i)
	- group_cost += x[offset+i]*x[offset+i];
	- cost += m_Lambdastd::sqrt(g)std::sqrt(group_cost)/dim;
	- offset += g;
	- }
	- }
	-
	- // gradients of regularization functions
	-
	- void grad_regu_MSM(vnl_vector<double> const &x, vnl_vector<double> &dx)
	- {
	- dx += 10000.0m_Lambda2.0*x/dim;
	- }
	-
	- void grad_regu_Variance(vnl_vector<double> const &x, vnl_vector<double> &dx)
	- {
	- double mean = x.mean();
	- vnl_vector<double> tx = x-mean; // difference to mean
	- dx += 10000.0tx(2.0-2.0/dim)/dim;
	- }
	-
	- void grad_regu_Lasso(vnl_vector<double> const &x, vnl_vector<double> &dx)
	- {
	- for (int i=0; i<dim; ++i)
	- if (x[i]>0)
	- dx[i] += m_Lambda/dim;
	- }
	-
	- void grad_regu_GroupVariance(vnl_vector<double> const &x, vnl_vector<double> &dx)
	- {
	- vnl_vector<double> tx(x);
	- unsigned int offset = 0;
	- for (auto g : group_sizes)
	- {
	- double group_mean = 0;
	- for (unsigned int i=0; i<g; ++i)
	- group_mean += x[offset+i];
	- group_mean /= g;
	-
	- for (unsigned int i=0; i<g; ++i)
	- tx[offset+i] -= group_mean;
	-
	- offset += g;
	- }
	-
	- dx += 10000.0tx(2.0-2.0/dim)/dim;
	- }
	-
	- void grad_regu_VoxelVariance(vnl_vector<double> const &x, vnl_vector<double> &dx)
	- {
	- m_A_Ones.mult(x, local_weight_means);
	- local_weight_means = element_quotient(local_weight_means, row_sums);
	-
	- vnl_vector<double> exp_x = x.apply(std::exp);
	- vnl_vector<double> exp_means = local_weight_means.apply(std::exp);
	-
	- vnl_vector<double> tdx(dim, 0);
	- m_A_Ones.reset();
	- while (m_A_Ones.next())
	- {
	- int c = m_A_Ones.getcolumn();
	- int r = m_A_Ones.getrow();
	-
	- if (x[c]>local_weight_means[r])
	- tdx[c] += exp_x[c] * ( exp_x[c] - exp_means[r] );
	- else
	- tdx[c] += x[c] - local_weight_means[r];
	- }
	- dx += tdx2.0m_Lambda/dim;
	- }
	-
	- void grad_regu_GroupLasso(vnl_vector<double> const &x, vnl_vector<double> &dx)
	- {
	- unsigned int offset = 0;
	- for (auto g : group_sizes)
	- {
	- double group_lambda = m_Lambda*std::sqrt(g)/dim;
	- double group_l2 = 0;
	- for (unsigned int i=0; i<g; ++i)
	- group_l2 += x[offset+i]*x[offset+i];
	- group_l2 = std::sqrt(group_l2);
	-
	- if (group_l2>0.0)
	- {
	- for (unsigned int i=0; i<g; ++i)
	- dx[offset+i] += x[offset+i]*group_lambda/group_l2;
	- }
	-
	- offset += g;
	- }
	- }
	-
	- void calc_regularization(vnl_vector<double> const &x, double& cost)
	- {
	- if (regularization==VOXEL_VARIANCE)
	- regu_VoxelVariance(x, cost);
	- else if (regularization==VARIANCE)
	- regu_Variance(x, cost);
	- else if (regularization==MSM)
	- regu_MSM(x, cost);
	- else if (regularization==LASSO)
	- regu_Lasso(x, cost);
	- else if (regularization==GROUP_LASSO)
	- regu_GroupLasso(x, cost);
	- else if (regularization==GROUP_VARIANCE)
	- regu_GroupVariance(x, cost);
	- }
	-
	- void calc_regularization_gradient(vnl_vector<double> const &x, vnl_vector<double> &dx)
	- {
	- if (regularization==VOXEL_VARIANCE)
	- grad_regu_VoxelVariance(x,dx);
	- else if (regularization==VARIANCE)
	- grad_regu_Variance(x,dx);
	- else if (regularization==MSM)
	- grad_regu_MSM(x,dx);
	- else if (regularization==LASSO)
	- grad_regu_Lasso(x,dx);
	- else if (regularization==GROUP_LASSO)
	- grad_regu_GroupLasso(x, dx);
	- else if (regularization==GROUP_VARIANCE)
	- grad_regu_GroupVariance(x, dx);
	- }
	-
	- // cost function
	- double f(vnl_vector<double> const &x)
	- {
	- // RMS error
	- unsigned int N = m_b.size();
	- vnl_vector<double> d; d.set_size(N);
	- S->multiply(x,d);
	- double cost = (d - m_b).squared_magnitude()/N;
	-
	- // regularize
	- calc_regularization(x, cost);
	-
	- return cost;
	- }
	-
	- // gradient of cost function
	- void gradf(vnl_vector<double> const &x, vnl_vector<double> &dx)
	- {
	- dx.fill(0.0);
	- unsigned int N = m_b.size();
	-
	- // calculate output difference d
	- vnl_vector<double> d; d.set_size(N);
	- S->multiply(x,d);
	- d -= m_b;
	-
	- // (f(u(x)))' = f'(u(x)) * u'(x)
	- // d/dx_j = 1/N * Sum_i A_i,j * 2(A_i,j x_j - b_i)
	- S->transpose_multiply(d, dx);
	- dx *= 2.0/N;
	-
	- calc_regularization_gradient(x,dx);
	- }
	-};
	-
	-namespace itk{
	-
	-/**
	-* \brief Fits the tractogram to the input image by assigning a weight to each fiber (similar to https://doi.org/10.1016/j.neuroimage.2015.06.092). */
	-
	-
	-class FitFibersToImageFilter : public ImageSource< mitk::PeakImage::ItkPeakImageType >
	-{
	-
	-public:
	-
	- typedef FitFibersToImageFilter Self;
	- typedef ProcessObject Superclass;
	- typedef SmartPointer< Self > Pointer;
	- typedef SmartPointer< const Self > ConstPointer;
	-
	- typedef itk::Point<float, 3> PointType3;
	- typedef itk::Point<float, 4> PointType4;
	- typedef mitk::DiffusionPropertyHelper::ImageType VectorImgType;
	- typedef mitk::PeakImage::ItkPeakImageType PeakImgType;
	- typedef itk::Image<unsigned char, 3> UcharImgType;
	- typedef itk::Image<double, 3> DoubleImgType;
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- itkTypeMacro( FitFibersToImageFilter, ImageSource )
	-
	- itkSetMacro( ScalarImage, DoubleImgType::Pointer)
	- itkGetMacro( ScalarImage, DoubleImgType::Pointer)
	- itkSetMacro( PeakImage, PeakImgType::Pointer)
	- itkGetMacro( PeakImage, PeakImgType::Pointer)
	- itkSetMacro( DiffImage, VectorImgType::Pointer)
	- itkGetMacro( DiffImage, VectorImgType::Pointer)
	- itkSetMacro( MaskImage, UcharImgType::Pointer)
	- itkGetMacro( MaskImage, UcharImgType::Pointer)
	- itkSetMacro( FitIndividualFibers, bool)
	- itkGetMacro( FitIndividualFibers, bool)
	- itkSetMacro( GradientTolerance, double)
	- itkGetMacro( GradientTolerance, double)
	- itkSetMacro( Lambda, double)
	- itkGetMacro( Lambda, double)
	- itkSetMacro( MaxIterations, int)
	- itkGetMacro( MaxIterations, int)
	- itkSetMacro( FilterOutliers, bool)
	- itkGetMacro( FilterOutliers, bool)
	- itkSetMacro( Verbose, bool)
	- itkGetMacro( Verbose, bool)
	-
	- itkGetMacro( Weights, vnl_vector<double>)
	- itkGetMacro( RmsDiffPerBundle, vnl_vector<double>)
	-
	- itkGetMacro( FittedImage, PeakImgType::Pointer)
	- itkGetMacro( ResidualImage, PeakImgType::Pointer)
	- itkGetMacro( OverexplainedImage, PeakImgType::Pointer)
	- itkGetMacro( UnderexplainedImage, PeakImgType::Pointer)
	-
	- itkGetMacro( FittedImageDiff, VectorImgType::Pointer)
	- itkGetMacro( ResidualImageDiff, VectorImgType::Pointer)
	- itkGetMacro( OverexplainedImageDiff, VectorImgType::Pointer)
	- itkGetMacro( UnderexplainedImageDiff, VectorImgType::Pointer)
	-
	- itkGetMacro( FittedImageScalar, DoubleImgType::Pointer)
	- itkGetMacro( ResidualImageScalar, DoubleImgType::Pointer)
	- itkGetMacro( OverexplainedImageScalar, DoubleImgType::Pointer)
	- itkGetMacro( UnderexplainedImageScalar, DoubleImgType::Pointer)
	-
	- itkGetMacro( Coverage, double)
	- itkGetMacro( Overshoot, double)
	- itkGetMacro( RMSE, double)
	- itkGetMacro( MeanWeight, double)
	- itkGetMacro( MedianWeight, double)
	- itkGetMacro( MinWeight, double)
	- itkGetMacro( MaxWeight, double)
	- itkGetMacro( NumUnknowns, unsigned int)
	- itkGetMacro( NumResiduals, unsigned int)
	- itkGetMacro( NumCoveredDirections, unsigned int)
	-
	- void SetTractograms(const std::vector<mitk::FiberBundle::Pointer> &tractograms);
	-
	- void GenerateData() override;
	-
	- std::vector<mitk::FiberBundle::Pointer> GetTractograms() const;
	-
	- void SetSignalModel(mitk::DiffusionSignalModel<> *SignalModel);
	-
	- VnlCostFunction::REGU GetRegularization() const;
	- void SetRegularization(const VnlCostFunction::REGU &GetRegularization);
	-
	-protected:
	-
	- FitFibersToImageFilter();
	- virtual ~FitFibersToImageFilter();
	-
	- void GetClosestPeak(itk::Index<4> idx, PeakImgType::Pointer m_PeakImage , vnl_vector_fixed<float,3> fiber_dir, int& id, double& w, double& peak_mag );
	-
	- void CreatePeakSystem();
	- void CreateDiffSystem();
	- void CreateScalarSystem();
	-
	- void GenerateOutputPeakImages();
	- void GenerateOutputDiffImages();
	- void GenerateOutputScalarImages();
	-
	- std::vector< mitk::FiberBundle::Pointer > m_Tractograms;
	- PeakImgType::Pointer m_PeakImage;
	- VectorImgType::Pointer m_DiffImage;
	- DoubleImgType::Pointer m_ScalarImage;
	- UcharImgType::Pointer m_MaskImage;
	- bool m_FitIndividualFibers;
	- double m_GradientTolerance;
	- double m_Lambda;
	- int m_MaxIterations;
	- double m_Coverage;
	- double m_Overshoot;
	- double m_RMSE;
	- bool m_FilterOutliers;
	- double m_MeanWeight;
	- double m_MedianWeight;
	- double m_MinWeight;
	- double m_MaxWeight;
	- bool m_Verbose;
	- unsigned int m_NumUnknowns;
	- unsigned int m_NumResiduals;
	- unsigned int m_NumCoveredDirections;
	-
	- // output
	- vnl_vector<double> m_RmsDiffPerBundle;
	- vnl_vector<double> m_Weights;
	-
	- PeakImgType::Pointer m_UnderexplainedImage;
	- PeakImgType::Pointer m_OverexplainedImage;
	- PeakImgType::Pointer m_ResidualImage;
	- PeakImgType::Pointer m_FittedImage;
	-
	- VectorImgType::Pointer m_UnderexplainedImageDiff;
	- VectorImgType::Pointer m_OverexplainedImageDiff;
	- VectorImgType::Pointer m_ResidualImageDiff;
	- VectorImgType::Pointer m_FittedImageDiff;
	-
	- DoubleImgType::Pointer m_UnderexplainedImageScalar;
	- DoubleImgType::Pointer m_OverexplainedImageScalar;
	- DoubleImgType::Pointer m_ResidualImageScalar;
	- DoubleImgType::Pointer m_FittedImageScalar;
	-
	- mitk::DiffusionSignalModel<>* m_SignalModel;
	-
	- vnl_sparse_matrix<double> A;
	- vnl_vector<double> b;
	- VnlCostFunction cost;
	- unsigned int sz_x;
	- unsigned int sz_y;
	- unsigned int sz_z;
	- int dim_four_size;
	- double m_MeanTractDensity;
	- double m_MeanSignal;
	- unsigned int fiber_count;
	-
	- VnlCostFunction::REGU m_Regularization;
	- std::vector<unsigned int> m_GroupSizes;
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkFitFibersToImageFilter.cpp"
	-#endif
	-
	-#endif // __itkFitFibersToImageFilter_h__
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkGibbsTrackingFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkGibbsTrackingFilter.cpp
	deleted file mode 100644
	index 413e4215b3..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkGibbsTrackingFilter.cpp
	+++ /dev/null
	@@ -1,515 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#include "itkGibbsTrackingFilter.h"
	-
	-// MITK
	-#include <itkOrientationDistributionFunction.h>
	-#include <itkDiffusionOdfGeneralizedFaImageFilter.h>
	-#include <mitkStandardFileLocations.h>
	-#include <mitkFiberBuilder.h>
	-#include <mitkMetropolisHastingsSampler.h>
	-//#include <mitkEnergyComputer.h>
	-#include <itkTensorImageToOdfImageFilter.h>
	-#include <mitkGibbsEnergyComputer.h>
	-
	-// ITK
	-#include <itkImageDuplicator.h>
	-#include <itkResampleImageFilter.h>
	-#include <itkTimeProbe.h>
	-
	-// MISC
	-#include <fstream>
	-// #include <QFile>
	-#include <tinyxml.h>
	-#include <boost/progress.hpp>
	-#include <mitkLexicalCast.h>
	-#include <boost/algorithm/string.hpp>
	-
	-namespace itk{
	-
	-template< class ItkOdfImageType >
	-GibbsTrackingFilter< ItkOdfImageType >::GibbsTrackingFilter():
	- m_StartTemperature(0.1),
	- m_EndTemperature(0.001),
	- m_Iterations(1e9),
	- m_CurrentIteration(0.0),
	- m_CurrentStep(0),
	- m_ParticleWeight(0),
	- m_ParticleWidth(0),
	- m_ParticleLength(0),
	- m_ConnectionPotential(10),
	- m_InexBalance(0),
	- m_ParticlePotential(0.2),
	- m_MinFiberLength(10),
	- m_AbortTracking(false),
	- m_NumAcceptedFibers(0),
	- m_BuildFibers(false),
	- m_ProposalAcceptance(0),
	- m_CurvatureThreshold(0.7),
	- m_DuplicateImage(true),
	- m_NumParticles(0),
	- m_NumConnections(0),
	- m_RandomSeed(-1),
	- m_LoadParameterFile(""),
	- m_LutPath(""),
	- m_IsInValidState(true)
	-{
	-
	-}
	-
	-template< class ItkOdfImageType >
	-GibbsTrackingFilter< ItkOdfImageType >::~GibbsTrackingFilter()
	-{
	-
	-}
	-
	-// fill output fiber bundle datastructure
	-template< class ItkOdfImageType >
	-typename GibbsTrackingFilter< ItkOdfImageType >::FiberPolyDataType GibbsTrackingFilter< ItkOdfImageType >::GetFiberBundle()
	-{
	- if (!m_AbortTracking)
	- {
	- m_BuildFibers = true;
	- while (m_BuildFibers){}
	- }
	-
	- return m_FiberPolyData;
	-}
	-
	-template< class ItkOdfImageType >
	-void
	-GibbsTrackingFilter< ItkOdfImageType >
	-::EstimateParticleWeight()
	-{
	- MITK_INFO << "GibbsTrackingFilter: estimating particle weight";
	-
	- float minSpacing;
	- if(m_OdfImage->GetSpacing()[0]<m_OdfImage->GetSpacing()[1] && m_OdfImage->GetSpacing()[0]<m_OdfImage->GetSpacing()[2])
	- minSpacing = m_OdfImage->GetSpacing()[0];
	- else if (m_OdfImage->GetSpacing()[1] < m_OdfImage->GetSpacing()[2])
	- minSpacing = m_OdfImage->GetSpacing()[1];
	- else
	- minSpacing = m_OdfImage->GetSpacing()[2];
	- float m_ParticleLength = 1.5*minSpacing;
	- float m_ParticleWidth = 0.5*minSpacing;
	-
	- // seed random generators
	- Statistics::MersenneTwisterRandomVariateGenerator::Pointer randGen = Statistics::MersenneTwisterRandomVariateGenerator::New();
	- if (m_RandomSeed>-1)
	- randGen->SetSeed(m_RandomSeed);
	- else
	- randGen->SetSeed();
	-
	- // instantiate all necessary components
	- SphereInterpolator* interpolator = new SphereInterpolator(m_LutPath);
	- // handle lookup table not found cases
	- if( !interpolator->IsInValidState() )
	- {
	- m_IsInValidState = false;
	- m_AbortTracking = true;
	- m_BuildFibers = false;
	- mitkThrow() << "Unable to load lookup tables.";
	- }
	- ParticleGrid* particleGrid = new ParticleGrid(m_MaskImage, m_ParticleLength, m_ParticleGridCellCapacity);
	- GibbsEnergyComputer* encomp = new GibbsEnergyComputer(m_OdfImage, m_MaskImage, particleGrid, interpolator, randGen);
	-
	- // EnergyComputer* encomp = new EnergyComputer(m_OdfImage, m_MaskImage, particleGrid, interpolator, randGen);
	- MetropolisHastingsSampler* sampler = new MetropolisHastingsSampler(particleGrid, encomp, randGen, m_CurvatureThreshold);
	-
	- float alpha = log(m_EndTemperature/m_StartTemperature);
	- m_ParticleWeight = 0.01;
	- int ppv = 0;
	- // main loop
	- int neededParts = 3000;
	- while (ppv<neededParts)
	- {
	- if (ppv<1000)
	- m_ParticleWeight /= 2;
	- else
	- m_ParticleWeight = ppv*m_ParticleWeight/neededParts;
	-
	- encomp->SetParameters(m_ParticleWeight,m_ParticleWidth,m_ConnectionPotentialm_ParticleLengthm_ParticleLength,m_CurvatureThreshold,m_InexBalance,m_ParticlePotential);
	- for( int step = 0; step < 10; step++ )
	- {
	- // update temperatur for simulated annealing process
	- float temperature = m_StartTemperature * exp(alpha(((1.0)step)/((1.0)*10)));
	- sampler->SetTemperature(temperature);
	-
	- for (unsigned long i=0; i<10000; i++)
	- sampler->MakeProposal();
	- }
	- ppv = particleGrid->m_NumParticles;
	- particleGrid->ResetGrid();
	- }
	- delete sampler;
	- delete encomp;
	- delete particleGrid;
	- delete interpolator;
	-
	- MITK_INFO << "GibbsTrackingFilter: finished estimating particle weight";
	-}
	-
	-// perform global tracking
	-template< class ItkOdfImageType >
	-void GibbsTrackingFilter< ItkOdfImageType >::GenerateData()
	-{
	- TimeProbe preClock; preClock.Start();
	- // check if input is Odf or tensor image and generate Odf if necessary
	- if (m_OdfImage.IsNull() && m_TensorImage.IsNotNull())
	- {
	- TensorImageToOdfImageFilter<float,float>::Pointer filter = TensorImageToOdfImageFilter<float,float>::New();
	- filter->SetInput( m_TensorImage );
	- filter->Update();
	- m_OdfImage = filter->GetOutput();
	- }
	- else if (m_DuplicateImage) // generate local working copy of Odf image (if not disabled)
	- {
	- typedef itk::ImageDuplicator< ItkOdfImageType > DuplicateFilterType;
	- typename DuplicateFilterType::Pointer duplicator = DuplicateFilterType::New();
	- duplicator->SetInputImage( m_OdfImage );
	- duplicator->Update();
	- m_OdfImage = duplicator->GetOutput();
	- }
	-
	- // perform mean subtraction on odfs
	- typedef ImageRegionIterator< ItkOdfImageType > InputIteratorType;
	- InputIteratorType it(m_OdfImage, m_OdfImage->GetLargestPossibleRegion() );
	- it.GoToBegin();
	- while (!it.IsAtEnd())
	- {
	- itk::OrientationDistributionFunction<float, ODF_SAMPLING_SIZE> odf(it.Get().GetDataPointer());
	- float mean = odf.GetMeanValue();
	- odf -= mean;
	- it.Set(odf.GetDataPointer());
	- ++it;
	- }
	-
	- // check if mask image is given if it needs resampling
	- PrepareMaskImage();
	-
	- // load parameter file
	- LoadParameters();
	-
	- // prepare parameters
	- float minSpacing;
	- if(m_OdfImage->GetSpacing()[0]<m_OdfImage->GetSpacing()[1] && m_OdfImage->GetSpacing()[0]<m_OdfImage->GetSpacing()[2])
	- minSpacing = m_OdfImage->GetSpacing()[0];
	- else if (m_OdfImage->GetSpacing()[1] < m_OdfImage->GetSpacing()[2])
	- minSpacing = m_OdfImage->GetSpacing()[1];
	- else
	- minSpacing = m_OdfImage->GetSpacing()[2];
	-
	- if(m_ParticleLength == 0)
	- m_ParticleLength = 1.5*minSpacing;
	- if(m_ParticleWidth == 0)
	- m_ParticleWidth = 0.5*minSpacing;
	-
	- if(m_ParticleWeight == 0)
	- EstimateParticleWeight();
	-
	- float alpha = log(m_EndTemperature/m_StartTemperature);
	-
	- if (m_CurvatureThreshold < mitk::eps)
	- m_CurvatureThreshold = 0;
	-
	- // seed random generators
	- Statistics::MersenneTwisterRandomVariateGenerator::Pointer randGen = Statistics::MersenneTwisterRandomVariateGenerator::New();
	- if (m_RandomSeed>-1)
	- randGen->SetSeed(m_RandomSeed);
	- else
	- randGen->SetSeed();
	-
	- // load sphere interpolator to evaluate the ODFs
	- SphereInterpolator* interpolator = new SphereInterpolator(m_LutPath);
	-
	- // handle lookup table not found cases
	- if( !interpolator->IsInValidState() )
	- {
	- m_IsInValidState = false;
	- m_AbortTracking = true;
	- m_BuildFibers = false;
	- mitkThrow() << "Unable to load lookup tables.";
	- }
	- // initialize the actual tracking components (ParticleGrid, Metropolis Hastings Sampler and Energy Computer)
	- ParticleGrid* particleGrid;
	- GibbsEnergyComputer* encomp;
	- MetropolisHastingsSampler* sampler;
	- try{
	- particleGrid = new ParticleGrid(m_MaskImage, m_ParticleLength, m_ParticleGridCellCapacity);
	- encomp = new GibbsEnergyComputer(m_OdfImage, m_MaskImage, particleGrid, interpolator, randGen);
	- encomp->SetParameters(m_ParticleWeight,m_ParticleWidth,m_ConnectionPotentialm_ParticleLengthm_ParticleLength,m_CurvatureThreshold,m_InexBalance,m_ParticlePotential);
	- sampler = new MetropolisHastingsSampler(particleGrid, encomp, randGen, m_CurvatureThreshold);
	- }
	- catch(...)
	- {
	- MITK_ERROR << "Particle grid allocation failed. Not enough memory? Try to increase the particle length.";
	- m_IsInValidState = false;
	- m_AbortTracking = true;
	- m_BuildFibers = false;
	- return;
	- }
	-
	- MITK_INFO << "----------------------------------------";
	- MITK_INFO << "Iterations: " << m_Iterations;
	- MITK_INFO << "Particle length: " << m_ParticleLength;
	- MITK_INFO << "Particle width: " << m_ParticleWidth;
	- MITK_INFO << "Particle weight: " << m_ParticleWeight;
	- MITK_INFO << "Start temperature: " << m_StartTemperature;
	- MITK_INFO << "End temperature: " << m_EndTemperature;
	- MITK_INFO << "In/Ex balance: " << m_InexBalance;
	- MITK_INFO << "Min. fiber length: " << m_MinFiberLength;
	- MITK_INFO << "Curvature threshold: " << m_CurvatureThreshold;
	- MITK_INFO << "Random seed: " << m_RandomSeed;
	- MITK_INFO << "----------------------------------------";
	-
	- // main loop
	- preClock.Stop();
	- TimeProbe clock; clock.Start();
	- m_NumAcceptedFibers = 0;
	- m_CurrentIteration = 0;
	- bool just_built_fibers = false;
	- boost::progress_display disp(m_Iterations);
	- if (!m_AbortTracking)
	- while (m_CurrentIteration<m_Iterations)
	- {
	- just_built_fibers = false;
	- ++disp;
	- m_CurrentIteration++;
	- if (m_AbortTracking)
	- break;
	-
	- // update temperatur for simulated annealing process
	- float temperature = m_StartTemperature * exp(alpha*m_CurrentIteration/m_Iterations);
	- sampler->SetTemperature(temperature);
	- sampler->MakeProposal();
	-
	- m_ProposalAcceptance = (float)sampler->GetNumAcceptedProposals()/m_CurrentIteration;
	- m_NumParticles = particleGrid->m_NumParticles;
	- m_NumConnections = particleGrid->m_NumConnections;
	-
	- if (m_AbortTracking)
	- break;
	-
	- if (m_BuildFibers)
	- {
	- FiberBuilder fiberBuilder(particleGrid, m_MaskImage);
	- m_FiberPolyData = fiberBuilder.iterate(m_MinFiberLength);
	- m_NumAcceptedFibers = m_FiberPolyData->GetNumberOfLines();
	- m_BuildFibers = false;
	- just_built_fibers = true;
	- }
	- }
	- if (!just_built_fibers)
	- {
	- FiberBuilder fiberBuilder(particleGrid, m_MaskImage);
	- m_FiberPolyData = fiberBuilder.iterate(m_MinFiberLength);
	- m_NumAcceptedFibers = m_FiberPolyData->GetNumberOfLines();
	- }
	- clock.Stop();
	-
	- delete sampler;
	- delete encomp;
	- delete interpolator;
	- delete particleGrid;
	- m_AbortTracking = true;
	- m_BuildFibers = false;
	-
	- int h = clock.GetTotal()/3600;
	- int m = ((int)clock.GetTotal()%3600)/60;
	- int s = (int)clock.GetTotal()%60;
	- MITK_INFO << "GibbsTrackingFilter: finished gibbs tracking in " << h << "h, " << m << "m and " << s << "s";
	- m = (int)preClock.GetTotal()/60;
	- s = (int)preClock.GetTotal()%60;
	- MITK_INFO << "GibbsTrackingFilter: preparation of the data took " << m << "m and " << s << "s";
	- MITK_INFO << "GibbsTrackingFilter: " << m_NumAcceptedFibers << " fibers accepted";
	-
	- // sampler->PrintProposalTimes();
	-
	- SaveParameters();
	-}
	-
	-template< class ItkOdfImageType >
	-void GibbsTrackingFilter< ItkOdfImageType >::PrepareMaskImage()
	-{
	- if(m_MaskImage.IsNull())
	- {
	- MITK_INFO << "GibbsTrackingFilter: generating default mask image";
	- m_MaskImage = ItkFloatImageType::New();
	- m_MaskImage->SetSpacing( m_OdfImage->GetSpacing() );
	- m_MaskImage->SetOrigin( m_OdfImage->GetOrigin() );
	- m_MaskImage->SetDirection( m_OdfImage->GetDirection() );
	- m_MaskImage->SetRegions( m_OdfImage->GetLargestPossibleRegion() );
	- m_MaskImage->Allocate();
	- m_MaskImage->FillBuffer(1.0);
	- }
	- else if ( m_MaskImage->GetLargestPossibleRegion().GetSize()[0]!=m_OdfImage->GetLargestPossibleRegion().GetSize()[0] \|\|
	- m_MaskImage->GetLargestPossibleRegion().GetSize()[1]!=m_OdfImage->GetLargestPossibleRegion().GetSize()[1] \|\|
	- m_MaskImage->GetLargestPossibleRegion().GetSize()[2]!=m_OdfImage->GetLargestPossibleRegion().GetSize()[2] \|\|
	- m_MaskImage->GetSpacing()[0]!=m_OdfImage->GetSpacing()[0] \|\|
	- m_MaskImage->GetSpacing()[1]!=m_OdfImage->GetSpacing()[1] \|\|
	- m_MaskImage->GetSpacing()[2]!=m_OdfImage->GetSpacing()[2] )
	- {
	- MITK_INFO << "GibbsTrackingFilter: resampling mask image";
	- typedef itk::ResampleImageFilter< ItkFloatImageType, ItkFloatImageType, float > ResamplerType;
	- ResamplerType::Pointer resampler = ResamplerType::New();
	- resampler->SetOutputSpacing( m_OdfImage->GetSpacing() );
	- resampler->SetOutputOrigin( m_OdfImage->GetOrigin() );
	- resampler->SetOutputDirection( m_OdfImage->GetDirection() );
	- resampler->SetSize( m_OdfImage->GetLargestPossibleRegion().GetSize() );
	-
	- resampler->SetInput( m_MaskImage );
	- resampler->SetDefaultPixelValue(0.0);
	- resampler->Update();
	- m_MaskImage = resampler->GetOutput();
	- MITK_INFO << "GibbsTrackingFilter: resampling finished";
	- }
	-}
	-
	-// load tracking paramters from xml file (.gtp)
	-template< class ItkOdfImageType >
	-bool GibbsTrackingFilter< ItkOdfImageType >::LoadParameters()
	-{
	- m_AbortTracking = true;
	- try
	- {
	- if( m_LoadParameterFile.length()==0 )
	- {
	- m_AbortTracking = false;
	- return true;
	- }
	-
	- MITK_INFO << "GibbsTrackingFilter: loading parameter file " << m_LoadParameterFile;
	-
	- TiXmlDocument doc( m_LoadParameterFile );
	- doc.LoadFile();
	-
	- TiXmlHandle hDoc(&doc);
	- TiXmlElement* pElem;
	- TiXmlHandle hRoot(nullptr);
	-
	- pElem = hDoc.FirstChildElement().Element();
	- hRoot = TiXmlHandle(pElem);
	- pElem = hRoot.FirstChildElement("parameter_set").Element();
	-
	- std::string iterations(pElem->Attribute("iterations"));
	- m_Iterations = boost::lexical_cast<double>(iterations);
	-
	- std::string particleLength(pElem->Attribute("particle_length"));
	- m_ParticleLength = boost::lexical_cast<float>(particleLength);
	-
	- std::string particleWidth(pElem->Attribute("particle_width"));
	- m_ParticleWidth = boost::lexical_cast<float>(particleWidth);
	-
	- std::string partWeight(pElem->Attribute("particle_weight"));
	- m_ParticleWeight = boost::lexical_cast<float>(partWeight);
	-
	- std::string startTemp(pElem->Attribute("temp_start"));
	- m_StartTemperature = boost::lexical_cast<float>(startTemp);
	-
	- std::string endTemp(pElem->Attribute("temp_end"));
	- m_EndTemperature = boost::lexical_cast<float>(endTemp);
	-
	- std::string inExBalance(pElem->Attribute("inexbalance"));
	- m_InexBalance = boost::lexical_cast<float>(inExBalance);
	-
	- std::string fiberLength(pElem->Attribute("fiber_length"));
	- m_MinFiberLength = boost::lexical_cast<float>(fiberLength);
	-
	- std::string curvThres(pElem->Attribute("curvature_threshold"));
	- m_CurvatureThreshold = cos(boost::lexical_cast<float>(curvThres)*itk::Math::pi/180);
	- m_AbortTracking = false;
	- MITK_INFO << "GibbsTrackingFilter: parameter file loaded successfully";
	- return true;
	- }
	- catch(...)
	- {
	- MITK_INFO << "GibbsTrackingFilter: could not load parameter file";
	- return false;
	- }
	-}
	-
	-// save current tracking paramters to xml file (.gtp)
	-template< class ItkOdfImageType >
	-bool GibbsTrackingFilter< ItkOdfImageType >::SaveParameters()
	-{
	- try
	- {
	- if( m_SaveParameterFile.length()==0 )
	- {
	- MITK_INFO << "GibbsTrackingFilter: no filename specified to save parameters";
	- return true;
	- }
	-
	- MITK_INFO << "GibbsTrackingFilter: saving parameter file " << m_SaveParameterFile;
	-
	- TiXmlDocument documentXML;
	- TiXmlDeclaration* declXML = new TiXmlDeclaration( "1.0", "", "" );
	- documentXML.LinkEndChild( declXML );
	-
	- TiXmlElement* mainXML = new TiXmlElement("global_tracking_parameter_file");
	- mainXML->SetAttribute("file_version", "0.1");
	- documentXML.LinkEndChild(mainXML);
	-
	- TiXmlElement* paramXML = new TiXmlElement("parameter_set");
	- paramXML->SetAttribute("iterations", boost::lexical_cast<std::string>(m_Iterations));
	- paramXML->SetAttribute("particle_length", boost::lexical_cast<std::string>(m_ParticleLength));
	- paramXML->SetAttribute("particle_width", boost::lexical_cast<std::string>(m_ParticleWidth));
	- paramXML->SetAttribute("particle_weight", boost::lexical_cast<std::string>(m_ParticleWeight));
	- paramXML->SetAttribute("temp_start", boost::lexical_cast<std::string>(m_StartTemperature));
	- paramXML->SetAttribute("temp_end", boost::lexical_cast<std::string>(m_EndTemperature));
	- paramXML->SetAttribute("inexbalance", boost::lexical_cast<std::string>(m_InexBalance));
	- paramXML->SetAttribute("fiber_length", boost::lexical_cast<std::string>(m_MinFiberLength));
	- paramXML->SetAttribute("curvature_threshold", boost::lexical_cast<std::string>(m_CurvatureThreshold));
	- mainXML->LinkEndChild(paramXML);
	-
	- if(!boost::algorithm::ends_with(m_SaveParameterFile, ".gtp"))
	- m_SaveParameterFile.append(".gtp");
	- documentXML.SaveFile( m_SaveParameterFile );
	-
	- MITK_INFO << "GibbsTrackingFilter: parameter file saved successfully";
	- return true;
	- }
	- catch(...)
	- {
	- MITK_INFO << "GibbsTrackingFilter: could not save parameter file";
	- return false;
	- }
	-}
	-
	-template< class ItkOdfImageType >
	-void GibbsTrackingFilter< ItkOdfImageType >::SetDicomProperties(mitk::FiberBundle::Pointer fib)
	-{
	- std::string model_code_value = "-";
	- std::string model_code_meaning = "-";
	- std::string algo_code_value = "sup181_ee03";
	- std::string algo_code_meaning = "Global";
	-
	-
	- fib->SetProperty("DICOM.anatomy.value", mitk::StringProperty::New("T-A0095"));
	- fib->SetProperty("DICOM.anatomy.meaning", mitk::StringProperty::New("White matter of brain and spinal cord"));
	-
	- fib->SetProperty("DICOM.algo_code.value", mitk::StringProperty::New(algo_code_value));
	- fib->SetProperty("DICOM.algo_code.meaning", mitk::StringProperty::New(algo_code_meaning));
	-
	- fib->SetProperty("DICOM.model_code.value", mitk::StringProperty::New(model_code_value));
	- fib->SetProperty("DICOM.model_code.meaning", mitk::StringProperty::New(model_code_meaning));
	-}
	-
	-}
	-
	-
	-
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkGibbsTrackingFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkGibbsTrackingFilter.h
	deleted file mode 100644
	index c733d4cd27..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkGibbsTrackingFilter.h
	+++ /dev/null
	@@ -1,156 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef itkGibbsTrackingFilter_h
	-#define itkGibbsTrackingFilter_h
	-
	-// MITK
	-#include <mitkSphereInterpolator.h>
	-#include <mitkFiberBundle.h>
	-
	-// ITK
	-#include <itkProcessObject.h>
	-#include <itkImage.h>
	-#include <itkDiffusionTensor3D.h>
	-#include <itkMersenneTwisterRandomVariateGenerator.h>
	-
	-// VTK
	-#include <vtkSmartPointer.h>
	-#include <vtkPolyData.h>
	-#include <vtkCellArray.h>
	-#include <vtkPoints.h>
	-#include <vtkPolyLine.h>
	-
	-namespace itk{
	-
	-/**
	-* \brief Performes global fiber tractography on the input ODF or tensor image (Gibbs tracking, Reisert 2010). */
	-
	-template< class ItkOdfImageType >
	-class GibbsTrackingFilter : public ProcessObject
	-{
	-public:
	- typedef GibbsTrackingFilter Self;
	- typedef ProcessObject Superclass;
	- typedef SmartPointer< Self > Pointer;
	- typedef SmartPointer< const Self > ConstPointer;
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- itkTypeMacro( GibbsTrackingFilter, ProcessObject )
	-
	- typedef Image< DiffusionTensor3D<float>, 3 > ItkTensorImage;
	- typedef typename ItkOdfImageType::Pointer ItkOdfImageTypePointer;
	- typedef Image< float, 3 > ItkFloatImageType;
	- typedef vtkSmartPointer< vtkPolyData > FiberPolyDataType;
	-
	- /** Setter. */
	- itkSetMacro( StartTemperature, float ) ///< Start temperature of simulated annealing process.
	- itkSetMacro( EndTemperature, float ) ///< End temperature of simulated annealing process.
	- itkSetMacro( Iterations, double ) ///< Number of iterations. More iterations usually mean better results.
	- itkSetMacro( ParticleWeight, float ) ///< Smaller particle weights result in a higher sensitivity if the method.
	- itkSetMacro( ParticleWidth, float ) ///< Thinner particles cause more reconstructed fibers.
	- itkSetMacro( ParticleLength, float )
	- itkSetMacro( ConnectionPotential, float )
	- itkSetMacro( InexBalance, float ) ///< Values < 0 result in a stronger weighting of the internal energy, values > 0 cause a stronger weighting of the external energy,
	- itkSetMacro( ParticlePotential, float )
	- itkSetMacro( MinFiberLength, int ) ///< Shorter fibers are discarded
	- itkSetMacro( AbortTracking, bool ) ///< Set flag to prematurely abort tracking.
	- itkSetMacro( CurvatureThreshold, float) ///< Absolute angular threshold between two particles (in radians).
	- itkSetMacro( DuplicateImage, bool ) ///< Work on copy of input image.
	- itkSetMacro( RandomSeed, int ) ///< Seed for random generator.
	- itkSetMacro( LoadParameterFile, std::string ) ///< Parameter file.
	- itkSetMacro( SaveParameterFile, std::string )
	- itkSetMacro( LutPath, std::string ) ///< Path to lookuptables. Default is binary directory.
	-
	- /** Getter. */
	- itkGetMacro( ParticleWeight, float )
	- itkGetMacro( ParticleWidth, float )
	- itkGetMacro( ParticleLength, float )
	- itkGetMacro( NumParticles, int )
	- itkGetMacro( NumConnections, int )
	- itkGetMacro( NumAcceptedFibers, int )
	- itkGetMacro( ProposalAcceptance, float )
	- itkGetMacro( CurrentIteration, double)
	- itkGetMacro( Iterations, double)
	- itkGetMacro( IsInValidState, bool)
	- FiberPolyDataType GetFiberBundle(); ///< Output fibers
	-
	- void SetDicomProperties(mitk::FiberBundle::Pointer fib);
	-
	- /** Input images. */
	- itkSetMacro(OdfImage, typename ItkOdfImageType::Pointer)
	- itkSetMacro(MaskImage, ItkFloatImageType::Pointer)
	- itkSetMacro(TensorImage, ItkTensorImage::Pointer)
	-
	- void Update() override{
	- this->GenerateData();
	- }
	-
	-protected:
	-
	- void GenerateData() override;
	-
	- GibbsTrackingFilter();
	- ~GibbsTrackingFilter() override;
	- void EstimateParticleWeight();
	- void PrepareMaskImage();
	- bool LoadParameters();
	- bool SaveParameters();
	-
	- // Input Images
	- typename ItkOdfImageType::Pointer m_OdfImage;
	- typename ItkFloatImageType::Pointer m_MaskImage;
	- typename ItkTensorImage::Pointer m_TensorImage;
	-
	- // Tracking parameters
	- float m_StartTemperature; ///< Start temperature
	- float m_EndTemperature; ///< End temperature
	- double m_Iterations; ///< Total number of iterations
	- double m_CurrentIteration; ///< Current iteration
	- unsigned long m_CurrentStep; ///< current tracking step
	- float m_ParticleWeight; ///< w (unitless)
	- float m_ParticleWidth; ///< sigma (mm)
	- float m_ParticleLength; ///< l (mm)
	- float m_ConnectionPotential; ///< gross L (chemisches potential, default 10)
	- float m_InexBalance; ///< gewichtung zwischen den lambdas; -5 ... 5 -> nur intern ... nur extern,default 0
	- float m_ParticlePotential; ///< default 0.2
	- int m_MinFiberLength; ///< discard all fibers shortan than the specified length in mm
	- bool m_AbortTracking; ///< set flag to abort tracking
	- int m_NumAcceptedFibers; ///< number of reconstructed fibers generated by the FiberBuilder
	- volatile bool m_BuildFibers; ///< set flag to generate fibers from particle grid
	- float m_ProposalAcceptance; ///< proposal acceptance rate (0-1)
	- float m_CurvatureThreshold; ///< curvature threshold in radians (1 -> no curvature is accepted, -1 all curvature angles are accepted)
	- bool m_DuplicateImage; ///< generates a working copy of the Odf image so that the original image won't be changed by the mean subtraction
	- int m_NumParticles; ///< current number of particles in grid
	- int m_NumConnections; ///< current number of connections between particles in grid
	- int m_RandomSeed; ///< seed value for random generator (-1 for standard seeding)
	- std::string m_LoadParameterFile; ///< filename of parameter file (reader)
	- std::string m_SaveParameterFile; ///< filename of parameter file (writer)
	- std::string m_LutPath; ///< path to lookuptables used by the sphere interpolator
	- bool m_IsInValidState; ///< Whether the filter is in a valid state, false if error occured
	-
	- FiberPolyDataType m_FiberPolyData; ///< container for reconstructed fibers
	-
	- //Constant values
	- static const int m_ParticleGridCellCapacity = 1024;
	-};
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkGibbsTrackingFilter.cpp"
	-#endif
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStochasticTractographyFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStochasticTractographyFilter.h
	deleted file mode 100644
	index 7b33763192..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStochasticTractographyFilter.h
	+++ /dev/null
	@@ -1,316 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef __itkStochasticTractographyFilter_h__
	-#define __itkStochasticTractographyFilter_h__
	-
	-#include "itkImageToImageFilter.h"
	-#include "vnl/vnl_random.h"
	-#include "vnl/vnl_vector_fixed.h"
	-#include "vnl/vnl_matrix.h"
	-#include "itkArray.h"
	-#include "itkVectorContainer.h"
	-#include "vnl/algo/vnl_qr.h"
	-#include "itkVariableLengthVector.h"
	-#include "StochasticTracking/itkSlowPolyLineParametricPath.h"
	-#include "itkSimpleFastMutexLock.h"
	-#include "itkRealTimeClock.h"
	-#include "itkDiffusionTensor3D.h"
	-#include <vector>
	-
	-namespace itk{
	-
	-/**
	-* \brief Performs probabilistic streamline tracking on the input dwi. */
	-
	-/Types for Probability Distribution /
	-typedef Image< Array< double >, 3 > ProbabilityDistributionImageType;
	-
	-template< class TInputDWIImage, class TInputWhiteMatterProbabilityImage,
	- class TOutputConnectivityImage >
	-class ITK_EXPORT StochasticTractographyFilter :
	- public ImageToImageFilter< TInputDWIImage,
	- TOutputConnectivityImage >{
	-public:
	- typedef StochasticTractographyFilter Self;
	- typedef ImageToImageFilter< TInputDWIImage,
	- TOutputConnectivityImage > Superclass;
	- typedef SmartPointer< Self > Pointer;
	- typedef SmartPointer< const Self > ConstPointer;
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- itkTypeMacro( StochasticTractographyFilter,
	- ImageToImageFilter )
	-
	- / Types for the DWI Input Image /
	- typedef TInputDWIImage InputDWIImageType;
	-
	- / Types for the Connectivity Output Image/
	- typedef TOutputConnectivityImage OutputConnectivityImageType;
	-
	- / Types for the Mask Image /
	- typedef TInputWhiteMatterProbabilityImage InputWhiteMatterProbabilityImageType;
	-
	- / Tract Types /
	- typedef SlowPolyLineParametricPath< 3 > TractType;
	-
	- / Types for the TractContainer /
	- typedef VectorContainer< unsigned int, typename TractType::Pointer >
	- TractContainerType;
	-
	- / Types for Tensor Output Image /
	- typedef Image< DiffusionTensor3D< double >, 3 > OutputTensorImageType;
	-
	- / Types for the Image-wide Magnetic Field Gradient Directions /
	- typedef VectorContainer< unsigned int, vnl_vector_fixed< double, 3 > >
	- GradientDirectionContainerType;
	-
	- / Types for the Image-wide bValues /
	- typedef double bValueType;
	- typedef VectorContainer< unsigned int, bValueType > bValueContainerType;
	-
	- / Types for the Measurement Frame of the Gradients /
	- typedef vnl_matrix_fixed< double, 3, 3 > MeasurementFrameType;
	-
	- / Type for the sample directions /
	- typedef VectorContainer< unsigned int, vnl_vector_fixed< double, 3 > >
	- TractOrientationContainerType;
	-
	- / the number of Tracts to generate /
	- itkSetMacro( TotalTracts, unsigned int)
	- itkGetMacro( TotalTracts, unsigned int)
	-
	- / the maximum length of Tract /
	- itkSetMacro( MaxTractLength, unsigned int )
	- itkGetMacro( MaxTractLength, unsigned int )
	-
	- / Set/Get bvalues /
	- itkSetConstObjectMacro( bValues, bValueContainerType )
	- itkGetConstObjectMacro( bValues, bValueContainerType )
	-
	- / Set/Get of gradient directions /
	- itkSetConstObjectMacro( Gradients, GradientDirectionContainerType )
	- itkGetConstObjectMacro( Gradients, GradientDirectionContainerType )
	-
	- / Set/Get the White Matter Probability Input image /
	- /* At each voxel specifies the probability of a mylinated fiber existing
	- at that location. This probability is interpreted to be the probability
	- that a fiber tract passes through that region.
	- */
	- itkSetInputMacro(WhiteMatterProbabilityImage, InputWhiteMatterProbabilityImageType)
	- itkGetInputMacro(WhiteMatterProbabilityImage, InputWhiteMatterProbabilityImageType)
	-
	- //overide the built in set input function
	- //we need to create a new cache everytime we change the input image
	- //but we need to preserve it when the input image is the same
	- void SetPrimaryInput(DataObject *input)
	- {
	- typename InputDWIImageType::Pointer dwiimagePtr;
	- try
	- {
	- dwiimagePtr = dynamic_cast<InputDWIImageType*>( input );
	- }
	- catch(itk::ExceptionObject &e)
	- {
	- MITK_INFO << "wrong image type: " << e.what();
	- throw;
	- }
	- Superclass::SetPrimaryInput( input );
	- //update the likelihood cache
	- this->m_LikelihoodCachePtr = ProbabilityDistributionImageType::New();
	- this->m_LikelihoodCachePtr->CopyInformation( this->GetInput() );
	- this->m_LikelihoodCachePtr->SetBufferedRegion( this->GetInput()->GetBufferedRegion() );
	- this->m_LikelihoodCachePtr->SetRequestedRegion( this->GetInput()->GetRequestedRegion() );
	- this->m_LikelihoodCachePtr->Allocate();
	- this->m_CurrentLikelihoodCacheElements = 0;
	- //update the likelihoodcache mutex image
	- this->m_LikelihoodCacheMutexImagePtr = LikelihoodCacheMutexImageType::New();
	- this->m_LikelihoodCacheMutexImagePtr->CopyInformation( this->GetInput() );
	- this->m_LikelihoodCacheMutexImagePtr->SetBufferedRegion( this->GetInput()->GetBufferedRegion() );
	- this->m_LikelihoodCacheMutexImagePtr->SetRequestedRegion( this->GetInput()->GetRequestedRegion() );
	- this->m_LikelihoodCacheMutexImagePtr->Allocate();
	- }
	-
	- / Set/Get the seed index /
	- itkSetMacro( SeedIndex, typename InputDWIImageType::IndexType )
	- itkGetMacro( SeedIndex, typename InputDWIImageType::IndexType )
	-
	- / Set/Get the list of directions to sample /
	- itkSetConstObjectMacro( SampleDirections, TractOrientationContainerType )
	- itkGetConstObjectMacro( SampleDirections, TractOrientationContainerType )
	-
	- / Set/Get the Measurement Frame /
	- itkSetMacro( MeasurementFrame, MeasurementFrameType )
	- itkGetMacro( MeasurementFrame, MeasurementFrameType )
	-
	- / Set/Get the Maximum Likelihood Cache Size, the max num. of cached voxels /
	- itkSetMacro( MaxLikelihoodCacheSize, unsigned int )
	- itkGetMacro( MaxLikelihoodCacheSize, unsigned int )
	-
	- / Get the Tracts that are generated /
	- itkGetObjectMacro( OutputTractContainer, TractContainerType )
	-
	- / Get TensorImage /
	- itkGetObjectMacro( OutputTensorImage, OutputTensorImageType )
	-
	- void GenerateData();
	- void GenerateTractContainerOutput( void );
	- void GenerateTensorImageOutput( void );
	-
	-protected:
	- / Convenience Types used only inside the filter /
	-
	- /Types for the parameters of the Tensor Model /
	- typedef vnl_vector_fixed< double, 7 > TensorModelParamType;
	-
	- /Types for the parameters of the Constrained Model /
	- typedef vnl_vector_fixed< double, 6 > ConstrainedModelParamType;
	-
	- /Type to hold generated DWI values/
	- typedef Image< VariableLengthVector< double >, 3 > DWIVectorImageType;
	-
	- /Types for Probability Distribution /
	- typedef Image< Array< double >, 3 > ProbabilityDistributionImageType;
	-
	- / Types for the Image of Mutexes of the Likelihood distribution /
	- typedef Image< SimpleFastMutexLock, 3 > LikelihoodCacheMutexImageType;
	-
	- StochasticTractographyFilter();
	- virtual ~StochasticTractographyFilter();
	-
	- / Load the default Sample Directions/
	- void LoadDefaultSampleDirections( void );
	-
	- / Randomly chose a neighboring pixel weighted on distance /
	- void ProbabilisticallyInterpolate( vnl_random& randomgenerator,
	- const TractType::ContinuousIndexType& cindex,
	- typename InputDWIImageType::IndexType& index);
	-
	- / Functions and data related to fitting the tensor model at each pixel /
	- void UpdateGradientDirections(void);
	- void UpdateTensorModelFittingMatrices( void );
	- void CalculateTensorModelParameters( const DWIVectorImageType::PixelType& dwivalues,
	- vnl_diag_matrix<double>& W,
	- TensorModelParamType& tensormodelparams);
	-
	- void CalculateConstrainedModelParameters( const TensorModelParamType& tensormodelparams,
	- ConstrainedModelParamType& constrainedmodelparams);
	-
	- void CalculateNoiseFreeDWIFromConstrainedModel( const ConstrainedModelParamType& constrainedmodelparams,
	- DWIVectorImageType::PixelType& noisefreedwi);
	-
	- void CalculateResidualVariance( const DWIVectorImageType::PixelType& noisydwi,
	- const DWIVectorImageType::PixelType& noisefreedwi,
	- const vnl_diag_matrix< double >& W,
	- const unsigned int numberofparameters,
	- double& residualvariance);
	-
	- void CalculateLikelihood( const DWIVectorImageType::PixelType &dwipixel,
	- TractOrientationContainerType::ConstPointer orientations,
	- ProbabilityDistributionImageType::PixelType& likelihood);
	-
	- void CalculatePrior( TractOrientationContainerType::Element v_prev,
	- TractOrientationContainerType::ConstPointer orientations,
	- ProbabilityDistributionImageType::PixelType& prior );
	-
	- void CalculatePosterior( const ProbabilityDistributionImageType::PixelType& likelihood,
	- const ProbabilityDistributionImageType::PixelType& prior,
	- ProbabilityDistributionImageType::PixelType& posterior);
	-
	- void SampleTractOrientation( vnl_random& randomgenerator,
	- const ProbabilityDistributionImageType::PixelType& posterior,
	- TractOrientationContainerType::ConstPointer orientations,
	- TractOrientationContainerType::Element& choosendirection );
	-
	- void StochasticTractGeneration( typename InputDWIImageType::ConstPointer dwiimagePtr,
	- typename InputWhiteMatterProbabilityImageType::ConstPointer maskimagePtr,
	- typename InputDWIImageType::IndexType seedindex,
	- unsigned long randomseed,
	- TractType::Pointer tract );
	-
	- /** Callback routine used by the threading library. This routine just calls
	- the ThreadedGenerateData method after setting the correct region for this
	- thread. **/
	- static ITK_THREAD_RETURN_TYPE StochasticTractGenerationCallback( void *arg );
	-
	- struct StochasticTractGenerationCallbackStruct{
	- Pointer Filter;
	- };
	-
	- / Thread Safe Function to check/update an entry in the likelihood cache /
	- ProbabilityDistributionImageType::PixelType&
	- AccessLikelihoodCache( typename InputDWIImageType::IndexType index );
	- / Thread Safe Function to delegate a tract and obtain a randomseed to start tracking /
	- bool DelegateTract(unsigned long& randomseed);
	- / Function to write a tract to the connectivity map /
	- void TractContainerToConnectivityMap(TractContainerType::Pointer tractcontainer);
	- / Thread Safe Function to store a tract to a TractContainer /
	- void StoreTract(TractType::Pointer tract);
	- / Randomly samples the existence of a fiber tract in the current voxel /
	- bool FiberExistenceTest( vnl_random& randomgenerator,
	- typename InputWhiteMatterProbabilityImageType::ConstPointer wmpimage,
	- typename InputWhiteMatterProbabilityImageType::IndexType index );
	-
	-
	-
	- MeasurementFrameType m_MeasurementFrame;
	-
	- LikelihoodCacheMutexImageType::Pointer m_LikelihoodCacheMutexImagePtr;
	- unsigned int m_TotalTracts;
	- unsigned int m_MaxTractLength;
	- GradientDirectionContainerType::ConstPointer m_Gradients;
	-
	- GradientDirectionContainerType::Pointer m_TransformedGradients;
	- bValueContainerType::ConstPointer m_bValues;
	-
	- typename InputDWIImageType::IndexType m_SeedIndex;
	- TractOrientationContainerType::ConstPointer m_SampleDirections;
	-
	- //these will be the same for every pixel in the image so
	- //go ahead and do a QR decomposition to optimize the
	- //LS fitting process for estimating the weighing matrix W
	- //in this case we solve instead:
	- //R*Beta = Q'logPhi
	- vnl_matrix< double >* m_A;
	- vnl_qr< double >* m_Aqr;
	- ProbabilityDistributionImageType::Pointer m_LikelihoodCachePtr;
	-
	- unsigned long m_MaxLikelihoodCacheSize; //in Megabytes
	- unsigned long m_MaxLikelihoodCacheElements; //in Elements (Voxels)
	- unsigned long m_CurrentLikelihoodCacheElements;
	- SimpleFastMutexLock m_LikelihoodCacheMutex;
	-
	- RealTimeClock::Pointer m_ClockPtr;
	- unsigned int m_TotalDelegatedTracts;
	- SimpleFastMutexLock m_TotalDelegatedTractsMutex;
	-
	- //unsigned long m_RandomSeed;
	- SimpleFastMutexLock m_OutputImageMutex;
	- TractContainerType::Pointer m_OutputTractContainer;
	- SimpleFastMutexLock m_OutputTractContainerMutex;
	-
	- OutputTensorImageType::Pointer m_OutputTensorImage;
	- vnl_random m_RandomGenerator;
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkStochasticTractographyFilter.txx"
	-#include "StochasticTracking/itkStochasticTractographyFilter_SD.txx"
	-#endif
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStochasticTractographyFilter.txx b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStochasticTractographyFilter.txx
	deleted file mode 100644
	index fd2b9670a9..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStochasticTractographyFilter.txx
	+++ /dev/null
	@@ -1,700 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#include "itkStochasticTractographyFilter.h"
	-#include "vnl/vnl_math.h"
	-#include "vnl/vnl_matrix_fixed.h"
	-#include "vnl/vnl_vector_fixed.h"
	-#include "vnl/vnl_matrix.h"
	-#include "vnl/vnl_sym_matrix.h"
	-#include "vnl/vnl_vector.h"
	-#include "vnl/vnl_diag_matrix.h"
	-#include "vnl/algo/vnl_qr.h"
	-//#include "vnl/algo/vnl_svd.h"
	-#include "vnl/algo/vnl_matrix_inverse.h"
	-//#include "vnl/algo/vnl_symmetric_eigensystem.h"
	-#include "itkSymmetricEigenAnalysis.h"
	-#include "vnl/vnl_transpose.h"
	-#include "itkVariableSizeMatrix.h"
	-#include "itkPathIterator.h"
	-#include "itkImageRegionIterator.h"
	-#include "itkImageRegionConstIterator.h"
	-#include "itkImageRegionConstIteratorWithIndex.h"
	-
	-namespace itk{
	-
	-template< class TInputDWIImage, class TInputWhiteMatterProbabilityImage, class TOutputConnectivityImage >
	-StochasticTractographyFilter< TInputDWIImage, TInputWhiteMatterProbabilityImage, TOutputConnectivityImage >
	-::StochasticTractographyFilter():
	- m_TotalTracts(0),m_MaxTractLength(0),m_Gradients(NULL), m_TransformedGradients(NULL),m_bValues(NULL),
	- m_SampleDirections(NULL), m_A(NULL), m_Aqr(NULL), m_LikelihoodCachePtr(NULL),
	- m_MaxLikelihoodCacheSize(0), m_CurrentLikelihoodCacheElements(0),
	- m_ClockPtr(NULL), m_TotalDelegatedTracts(0), m_OutputTractContainer(NULL){
	- this->m_SeedIndex[0]=0;
	- this->m_SeedIndex[1]=0;
	- this->m_SeedIndex[2]=0;
	- this->m_MeasurementFrame.set_identity();
	- this->SetNumberOfRequiredInputs(1); //Filter needs a DWI image and a Mask Image, but check will be outside itkProcessObject and inside GenerateData()
	-
	-
	- m_ClockPtr = RealTimeClock::New();
	- this->m_RandomGenerator.reseed( ((unsigned long) this->m_ClockPtr->GetTimeInSeconds()) );
	- //load in default sample directions
	- this->LoadDefaultSampleDirections();
	-}
	-
	-template< class TInputDWIImage, class TInputWhiteMatterProbabilityImage, class TOutputConnectivityImage >
	-StochasticTractographyFilter< TInputDWIImage, TInputWhiteMatterProbabilityImage, TOutputConnectivityImage >
	-::~StochasticTractographyFilter(){
	- delete this->m_A;
	- delete this->m_Aqr;
	-}
	-
	-template< class TInputDWIImage, class TInputWhiteMatterProbabilityImage, class TOutputConnectivityImage >
	-void
	-StochasticTractographyFilter< TInputDWIImage, TInputWhiteMatterProbabilityImage, TOutputConnectivityImage >
	-::ProbabilisticallyInterpolate( vnl_random& randomgenerator,
	- const TractType::ContinuousIndexType& cindex,
	- typename InputDWIImageType::IndexType& index){
	-
	- for(int i=0; i<3; i++){
	- if ((vcl_ceil(cindex[i]+vnl_math::eps)-cindex[i]) < randomgenerator.drand64())
	- index[i]=(int)vcl_ceil(cindex[i]);
	- else index[i]=(int)vcl_floor(cindex[i]);
	- }
	-}
	-
	-template< class TInputDWIImage, class TInputWhiteMatterProbabilityImage, class TOutputConnectivityImage >
	-void
	-StochasticTractographyFilter< TInputDWIImage, TInputWhiteMatterProbabilityImage, TOutputConnectivityImage >
	-::UpdateGradientDirections(void){
	- //the gradient direction is transformed into IJK space
	- //by moving into the image space and then to IJK space
	-
	- this->m_TransformedGradients = GradientDirectionContainerType::New();
	- unsigned int N = this->m_Gradients->Size();
	- for(unsigned int i=0; i<N; i++){
	- GradientDirectionContainerType::Element g_i =
	- this->m_MeasurementFrame *
	- this->m_Gradients->GetElement(i);
	-
	- / The correction to LPS space is not neccessary as of itk 3.2 /
	- //g_i[0] = -g_i[0];
	- //g_i[1] = -g_i[1];
	- g_i = this->GetInput()->GetDirection().GetInverse() * g_i;
	- this->m_TransformedGradients->InsertElement(i, g_i);
	- }
	-}
	-
	-template< class TInputDWIImage, class TInputWhiteMatterProbabilityImage, class TOutputConnectivityImage >
	-void
	-StochasticTractographyFilter< TInputDWIImage, TInputWhiteMatterProbabilityImage, TOutputConnectivityImage >
	-::UpdateTensorModelFittingMatrices( void ){
	- //std::cout<<"UpdateTensorFittingMatrix\n";
	- //estimate the parameters using linear LS estimation
	- //using convention specified by Salvador
	- //solve for Beta in: logPhi=X*Beta
	- //number of rows of the matrix depends on the number of inputs,
	- //i.e. the number of measurements of the voxel (n)
	- unsigned int N = this->m_TransformedGradients->Size();
	-
	- if(this->m_A!=NULL)
	- delete this->m_A;
	- this->m_A = new vnl_matrix< double >(N, 7); //potential memory leak here
	- vnl_matrix< double >& A = *(this->m_A);
	-
	- for(unsigned int j=0; j< N ; j++){
	- GradientDirectionContainerType::Element g = m_TransformedGradients->GetElement(j);
	- const bValueType& b_i = m_bValues->GetElement(j);
	-
	- A(j,0)=1.0;
	- A(j,1)=-1b_i(g[0]*g[0]);
	- A(j,2)=-1b_i(g[1]*g[1]);
	- A(j,3)=-1b_i(g[2]*g[2]);
	- A(j,4)=-1b_i(2g[0]g[1]);
	- A(j,5)=-1b_i(2g[0]g[2]);
	- A(j,6)=-1b_i(2g[1]g[2]);
	- }
	-
	- //Store a QR decomposition to quickly estimate
	- //the weighing matrix for each voxel
	- if(this->m_Aqr!=NULL)
	- delete this->m_Aqr;
	- this->m_Aqr = new vnl_qr< double >(A); //potential memory leak here
	-}
	-
	-template< class TInputDWIImage, class TInputWhiteMatterProbabilityImage, class TOutputConnectivityImage >
	-void
	-StochasticTractographyFilter< TInputDWIImage, TInputWhiteMatterProbabilityImage, TOutputConnectivityImage >
	-::CalculateTensorModelParameters( const DWIVectorImageType::PixelType& dwivalues,
	- vnl_diag_matrix<double>& W,
	- TensorModelParamType& tensormodelparams){
	-
	- unsigned int N = this->m_TransformedGradients->Size();
	-
	- //setup const references for code clarity
	- const vnl_matrix< double >& A = *(this->m_A);
	- const vnl_qr< double >& Aqr = *(this->m_Aqr);
	-
	- //vnl_vector is used because the itk vector is limited in its methods and does not
	- //contain an internal vnl class like VariableSizematrix
	- //also itk_matrix has methods which are compatible with vnl_vectors
	- vnl_vector< double > logPhi( N );
	-
	- for(unsigned int j=0; j< N ; j++){
	- //fill up the logPhi vector using log(dwi) values
	- logPhi.put(j, vcl_log(static_cast<double>(dwivalues[j]) + vnl_math::eps));
	- }
	-
	- / Find WLS estimate of the parameters of the Tensor model /
	-
	- // First estimate W by LS estimation of the intensities
	- //vnl_matrix< double > Q = Aqr.Q();
	- //vnl_vector< double > QtB = Aqr.Q().transpose()*logPhi;
	- //vnl_vector< double > QTB = Aqr.QtB(logPhi);
	- //vnl_matrix< double > R = Aqr.R();
	- W = A* vnl_qr< double >(Aqr.R()).solve(Aqr.QtB(logPhi));
	- //W = A * Aqr.solve(logPhi);
	- for(vnl_diag_matrix< double >::iterator i = W.begin();i!=W.end(); i++){
	- i = vcl_exp( i );
	- }
	-
	- // Now solve for parameters using the estimated weighing matrix
	- tensormodelparams = vnl_qr< double >((WA).transpose()W*A).solve(
	- (WA).transpose()W*logPhi);
	- //int a;
	- //tensormodelparams = vnl_qr< double >((WA)).solve(WlogPhi);
	-}
	-
	-template< class TInputDWIImage, class TInputWhiteMatterProbabilityImage, class TOutputConnectivityImage >
	-void
	-StochasticTractographyFilter< TInputDWIImage, TInputWhiteMatterProbabilityImage, TOutputConnectivityImage >
	-::CalculateConstrainedModelParameters( const TensorModelParamType& tensormodelparams,
	- ConstrainedModelParamType& constrainedmodelparams){
	-
	- vnl_sym_matrix< double > D( 3, 0 );
	- double alpha =0;
	- double beta=0;
	- //set the tensor model parameters into a Diffusion tensor
	- D(0,0) = tensormodelparams[1];
	- D(0,1) = tensormodelparams[4];
	- D(0,2) = tensormodelparams[5];
	- D(1,0) = tensormodelparams[4];
	- D(1,1) = tensormodelparams[2];
	- D(1,2) = tensormodelparams[6];
	- D(2,0) = tensormodelparams[5];
	- D(2,1) = tensormodelparams[6];
	- D(2,2) = tensormodelparams[3];
	-
	- //pass through the no gradient intensity Z_0 and
	- //calculate alpha, beta and v hat (the eigenvector
	- //associated with the largest eigenvalue)
	- vnl_matrix_fixed< double, 3, 3 > S(0.0);
	- vnl_vector_fixed< double, 3 > Lambda(0.0);
	- SymmetricEigenAnalysis< vnl_sym_matrix< double >,
	- vnl_vector_fixed< double, 3 >, vnl_matrix_fixed< double, 3, 3 > >
	- eigensystem( 3 );
	- eigensystem.ComputeEigenValuesAndVectors( D, Lambda, S );
	-
	- //need to take abs to get rid of negative eigenvalues
	- alpha = (vcl_abs(Lambda[0]) + vcl_abs(Lambda[1])) / 2;
	- beta = vcl_abs(Lambda[2]) - alpha;
	-
	- constrainedmodelparams[0] = tensormodelparams[0];
	- constrainedmodelparams[1] = alpha;
	- constrainedmodelparams[2] = beta;
	- constrainedmodelparams[3] = S[2][0];
	- constrainedmodelparams[4] = S[2][1];
	- constrainedmodelparams[5] = S[2][2];
	-}
	-
	-template< class TInputDWIImage, class TInputWhiteMatterProbabilityImage, class TOutputConnectivityImage >
	-void
	-StochasticTractographyFilter< TInputDWIImage, TInputWhiteMatterProbabilityImage, TOutputConnectivityImage >
	-::CalculateNoiseFreeDWIFromConstrainedModel( const ConstrainedModelParamType& constrainedmodelparams,
	- DWIVectorImageType::PixelType& noisefreedwi){
	-
	- unsigned int N = this->m_TransformedGradients->Size();
	- const double& z_0 = constrainedmodelparams[0];
	- const double& alpha = constrainedmodelparams[1];
	- const double& beta = constrainedmodelparams[2];
	- TractOrientationContainerType::Element v_hat( constrainedmodelparams[3],
	- constrainedmodelparams[4],
	- constrainedmodelparams[5]);
	-
	- for(unsigned int i=0; i < N ; i++ ){
	- const double& b_i = this->m_bValues->GetElement(i);
	- const GradientDirectionContainerType::Element& g_i =
	- this->m_TransformedGradients->GetElement(i);
	-
	- noisefreedwi.SetElement(i,
	- vcl_exp(z_0-(alphab_i+betab_i*vnl_math_sqr(dot_product(g_i, v_hat)))));
	- }
	-}
	-
	-template< class TInputDWIImage, class TInputWhiteMatterProbabilityImage, class TOutputConnectivityImage >
	-void
	-StochasticTractographyFilter< TInputDWIImage, TInputWhiteMatterProbabilityImage, TOutputConnectivityImage >
	-::CalculateResidualVariance( const DWIVectorImageType::PixelType& noisydwi,
	- const DWIVectorImageType::PixelType& noisefreedwi,
	- const vnl_diag_matrix< double >& W,
	- const unsigned int numberofparameters,
	- double& residualvariance){
	-
	- unsigned int N = this->m_TransformedGradients->Size();
	-
	- residualvariance=0;
	-
	- / Not sure if we should be taking difference of log or nonlog intensities /
	- / residual variance is too low if we take the difference of log intensities /
	- / perhaps using WLS will correct this problem /
	- for(unsigned int i=0; i<N; i++)
	- residualvariance+=vnl_math_sqr(W(i,i) * (vcl_log(noisydwi[i]/noisefreedwi[i])));
	- residualvariance/=(N-numberofparameters);
	-}
	-
	-template< class TInputDWIImage, class TInputWhiteMatterProbabilityImage, class TOutputConnectivityImage >
	-void
	-StochasticTractographyFilter< TInputDWIImage, TInputWhiteMatterProbabilityImage, TOutputConnectivityImage >
	-::CalculateLikelihood( const DWIVectorImageType::PixelType &dwipixel,
	- TractOrientationContainerType::ConstPointer orientations,
	- ProbabilityDistributionImageType::PixelType& likelihood){
	-
	- unsigned int N = this->m_TransformedGradients->Size();
	- TensorModelParamType tensorparams( 0.0 );
	- vnl_diag_matrix< double > W(N,0);
	- ConstrainedModelParamType constrainedparams( 0.0 );
	- DWIVectorImageType::PixelType noisefreedwi(N);
	- double residualvariance=0;
	- double jointlikelihood=1;
	-
	- CalculateTensorModelParameters( dwipixel, W, tensorparams );
	- CalculateConstrainedModelParameters( tensorparams, constrainedparams );
	- CalculateNoiseFreeDWIFromConstrainedModel( constrainedparams, noisefreedwi );
	- CalculateResidualVariance( dwipixel, noisefreedwi, W, 6, residualvariance );
	-
	- for(unsigned int i=0; i < orientations->Size(); i++){
	- /** Vary the entry corresponding to the estimated
	- Tract orientation over the selected sample directions,
	- while preserving the best estimate for the other parameters **/
	- TractOrientationContainerType::Element currentdir = orientations->GetElement(i);
	-
	- / Incorporate the current sample direction into the secondary parameters /
	- constrainedparams[3]=currentdir[0];
	- constrainedparams[4]=currentdir[1];
	- constrainedparams[5]=currentdir[2];
	-
	- /** Obtain the estimated
	- intensity for this choice of Tract direction **/
	- CalculateNoiseFreeDWIFromConstrainedModel(constrainedparams, noisefreedwi);
	-
	- jointlikelihood = 1.0;
	- for(unsigned int j=0; j<N; j++){
	- /** Calculate the likelihood given the residualvariance,
	- estimated intensity and the actual intensity (refer to Friman) **/
	- jointlikelihood *=
	- (noisefreedwi[j]/vcl_sqrt(2vnl_math::piresidualvariance))*
	- vcl_exp(-vnl_math_sqr(noisefreedwi[j]*vcl_log(dwipixel[j]/noisefreedwi[j]))/
	- (2*residualvariance));
	- }
	- likelihood[i]=jointlikelihood;
	- }
	-}
	-
	-template< class TInputDWIImage, class TInputWhiteMatterProbabilityImage, class TOutputConnectivityImage >
	-void
	-StochasticTractographyFilter< TInputDWIImage, TInputWhiteMatterProbabilityImage, TOutputConnectivityImage >
	-::CalculatePrior( TractOrientationContainerType::Element v_prev,
	- TractOrientationContainerType::ConstPointer orientations,
	- ProbabilityDistributionImageType::PixelType& prior ){
	-
	- const double gamma = 1;
	-
	- for(unsigned int i=0; i < orientations->Size(); i++){
	- if(v_prev.squared_magnitude()==0){
	- prior[i]=1.0;
	- }
	- else{
	- prior[i] = dot_product(orientations->GetElement(i),v_prev);;
	- if(prior[i]<0){
	- prior[i]=0;
	- }
	- else{
	- prior[i]=vcl_pow(prior[i],gamma);
	- }
	- }
	- }
	-}
	-
	-template< class TInputDWIImage, class TInputWhiteMatterProbabilityImage, class TOutputConnectivityImage >
	-void
	-StochasticTractographyFilter< TInputDWIImage, TInputWhiteMatterProbabilityImage, TOutputConnectivityImage >
	-::CalculatePosterior( const ProbabilityDistributionImageType::PixelType& likelihood,
	- const ProbabilityDistributionImageType::PixelType& prior,
	- ProbabilityDistributionImageType::PixelType& posterior){
	-
	- double sum=0;
	- for(unsigned int i=0; i<likelihood.Size(); i++){
	- sum+=likelihood[i]*prior[i];
	- }
	- for(unsigned int i=0; i<likelihood.Size(); i++){
	- posterior[i] = (likelihood[i]*prior[i])/sum;
	- }
	-}
	-
	-template< class TInputDWIImage, class TInputWhiteMatterProbabilityImage, class TOutputConnectivityImage >
	-void
	-StochasticTractographyFilter< TInputDWIImage, TInputWhiteMatterProbabilityImage, TOutputConnectivityImage >
	-::SampleTractOrientation( vnl_random& randomgenerator,
	- const ProbabilityDistributionImageType::PixelType& posterior,
	- TractOrientationContainerType::ConstPointer orientations,
	- TractOrientationContainerType::Element& choosendirection ){
	-
	- double randomnum = randomgenerator.drand64();
	- int i=0;
	- double cumsum=0;
	-
	- //will crash in the unlikely case that 0 was choosen as the randomnum
	- while(cumsum < randomnum){
	- cumsum+=posterior[i];
	- i++;
	- }
	- choosendirection = orientations->GetElement(i-1);
	-
	- //std::cout<< "cumsum: " << cumsum<<std::endl;
	- //std::cout<<"selected orientation:( " << (i-1)
	- // <<") "<<choosendirection<< std::endl;
	-}
	-template< class TInputDWIImage, class TInputWhiteMatterProbabilityImage, class TOutputConnectivityImage >
	-bool
	-StochasticTractographyFilter< TInputDWIImage, TInputWhiteMatterProbabilityImage, TOutputConnectivityImage >
	-::FiberExistenceTest( vnl_random& randomgenerator,
	- typename InputWhiteMatterProbabilityImageType::ConstPointer wmpimage,
	- typename InputWhiteMatterProbabilityImageType::IndexType index ){
	- double randomnum = randomgenerator.drand64();
	- if( randomnum < wmpimage->GetPixel( index ) )
	- return true;
	- else
	- return false;
	-}
	-//the seedindex is in continuous IJK coordinates
	-template< class TInputDWIImage, class TInputWhiteMatterProbabilityImage, class TOutputConnectivityImage >
	-void
	-StochasticTractographyFilter< TInputDWIImage, TInputWhiteMatterProbabilityImage, TOutputConnectivityImage >
	-::StochasticTractGeneration( typename InputDWIImageType::ConstPointer dwiimagePtr,
	- typename InputWhiteMatterProbabilityImageType::ConstPointer wmpimagePtr,
	- typename InputDWIImageType::IndexType seedindex,
	- unsigned long randomseed,
	- TractType::Pointer tract){
	-
	- TractType::ContinuousIndexType cindex_curr = seedindex;
	- typename InputDWIImageType::IndexType index_curr = {{0,0,0}};
	- ProbabilityDistributionImageType::PixelType
	- prior_curr(this->m_SampleDirections->Size());
	- ProbabilityDistributionImageType::PixelType
	- posterior_curr(this->m_SampleDirections->Size());
	- TractOrientationContainerType::Element v_curr(0,0,0);
	- TractOrientationContainerType::Element v_prev(0,0,0);
	-
	- tract->Initialize();
	- vnl_random randomgenerator(randomseed);
	- //std::cout<<randomseed<<std::endl;
	-
	- for(unsigned int j=0; j<this->m_MaxTractLength; j++){
	- this->ProbabilisticallyInterpolate( randomgenerator, cindex_curr, index_curr );
	-
	- if(!dwiimagePtr->GetLargestPossibleRegion().IsInside(index_curr)){
	- break;
	- }
	-
	- if( FiberExistenceTest( randomgenerator, wmpimagePtr, index_curr ) ){
	- tract->AddVertex(cindex_curr);
	-
	- this->CalculatePrior( v_prev, this->m_SampleDirections, prior_curr);
	-
	- const ProbabilityDistributionImageType::PixelType&
	- cachelikelihood_curr = this->AccessLikelihoodCache(index_curr);
	-
	- if( cachelikelihood_curr.GetSize() != 0){
	- //use the cached direction
	- this->CalculatePosterior( cachelikelihood_curr, prior_curr, posterior_curr);
	- }
	- else{
	- //do the likelihood calculation and discard
	- //std::cout<<"Cache Miss!\n";
	- ProbabilityDistributionImageType::PixelType
	- likelihood_curr_temp(this->m_SampleDirections->Size());
	-
	- this->CalculateLikelihood(static_cast< DWIVectorImageType::PixelType >(
	- dwiimagePtr->GetPixel(index_curr)),
	- this->m_SampleDirections,
	- likelihood_curr_temp);
	- this->CalculatePosterior( likelihood_curr_temp, prior_curr, posterior_curr);
	- }
	- this->SampleTractOrientation(randomgenerator, posterior_curr,
	- this->m_SampleDirections, v_curr);
	-
	- //takes into account voxels of different sizes
	- //converts from a step length of 1 mm to the corresponding length in IJK space
	- const typename InputDWIImageType::SpacingType& spacing = dwiimagePtr->GetSpacing();
	- cindex_curr[0]+=v_curr[0]/spacing[0];
	- cindex_curr[1]+=v_curr[1]/spacing[1];
	- cindex_curr[2]+=v_curr[2]/spacing[2];
	- v_prev=v_curr;
	- }
	- else{
	- //fiber doesn't exist in this voxel
	- //std::cout<<"Stopped Tracking: No Fiber in this Voxel\n";
	- break;
	- }
	- }
	-}
	-
	-template< class TInputDWIImage, class TInputWhiteMatterProbabilityImage, class TOutputConnectivityImage >
	-void
	-StochasticTractographyFilter< TInputDWIImage, TInputWhiteMatterProbabilityImage, TOutputConnectivityImage >
	-::GenerateTractContainerOutput(){
	- //allocate tractcontainer
	- this->m_OutputTractContainer = TractContainerType::New();
	-
	- this->UpdateGradientDirections();
	- this->UpdateTensorModelFittingMatrices();
	- this->m_TotalDelegatedTracts = 0;
	-
	- //calculate the number of voxels to cache from Megabyte memory size limit
	- ProbabilityDistributionImageType::PixelType
	- element(this->GetSampleDirections()->Size());
	- unsigned long elementsize = sizeof(ProbabilityDistributionImageType::PixelType) +
	- sizeof(double)*element.Size();
	- this->m_MaxLikelihoodCacheElements =
	- (this->m_MaxLikelihoodCacheSize*1048576)/elementsize;
	- std::cout << "MaxLikelhoodCacheElements: "
	- << this->m_MaxLikelihoodCacheElements
	- << std::endl;
	-
	- //setup the multithreader
	- StochasticTractGenerationCallbackStruct data;
	- data.Filter = this;
	- this->GetMultiThreader()->SetSingleMethod( StochasticTractGenerationCallback,
	- &data );
	- this->GetMultiThreader()->SetNumberOfThreads(this->GetNumberOfThreads());
	- std::cout<<"Number of Threads: " << this->GetMultiThreader()->GetNumberOfThreads() << std::endl;
	- //start the multithreaded execution
	- this->GetMultiThreader()->SingleMethodExecute();
	- std::cout<< "CurrentLikelihoodCacheElements: " <<
	- this->m_CurrentLikelihoodCacheElements << std::endl;
	-}
	-
	-template< class TInputDWIImage, class TInputWhiteMatterProbabilityImage, class TOutputConnectivityImage >
	-void
	-StochasticTractographyFilter< TInputDWIImage, TInputWhiteMatterProbabilityImage, TOutputConnectivityImage >
	-::GenerateData(){
	- //Generate the tracts
	- this->GenerateTractContainerOutput();
	-
	- //allocate outputs
	- this->AllocateOutputs();
	-
	- //write tracts to output image
	- this->TractContainerToConnectivityMap(this->m_OutputTractContainer);
	-
	-}
	-
	-template< class TInputDWIImage, class TInputWhiteMatterProbabilityImage, class TOutputConnectivityImage >
	-ITK_THREAD_RETURN_TYPE
	-StochasticTractographyFilter< TInputDWIImage, TInputWhiteMatterProbabilityImage, TOutputConnectivityImage >
	-::StochasticTractGenerationCallback( void *arg )
	-{
	- StochasticTractGenerationCallbackStruct* str=
	- (StochasticTractGenerationCallbackStruct *)
	- (((MultiThreader::ThreadInfoStruct *)(arg))->UserData);
	-
	- typename InputDWIImageType::ConstPointer inputDWIImagePtr = str->Filter->GetInput();
	- typename InputWhiteMatterProbabilityImageType::ConstPointer inputWMPImage =
	- str->Filter->GetWhiteMatterProbabilityImage();
	-
	- unsigned long randomseed=0;
	-
	- while(str->Filter->DelegateTract(randomseed)){
	- //std::cout<<randomseed<<std::endl;
	- //generate the tract
	- TractType::Pointer tract = TractType::New();
	-
	- str->Filter->StochasticTractGeneration( inputDWIImagePtr,
	- inputWMPImage,
	- str->Filter->GetSeedIndex(),
	- randomseed,
	- tract);
	-
	- //only store tract if it is of nonzero length
	- if( tract->GetVertexList()->Size() > 4 ){
	- //std::cout<<"Storing tract\n";
	- str->Filter->StoreTract(tract);
	- }
	- else{
	- //std::cout<<"Not Storing Tract\n";
	- }
	- }
	- return ITK_THREAD_RETURN_VALUE;
	-}
	-
	-template< class TInputDWIImage, class TInputWhiteMatterProbabilityImage, class TOutputConnectivityImage >
	-ProbabilityDistributionImageType::PixelType&
	-StochasticTractographyFilter< TInputDWIImage, TInputWhiteMatterProbabilityImage, TOutputConnectivityImage >
	-::AccessLikelihoodCache( typename InputDWIImageType::IndexType index )
	-{
	- this->m_LikelihoodCacheMutexImagePtr->GetPixel(index).Lock();
	-
	- ProbabilityDistributionImageType::PixelType& likelihood =
	- m_LikelihoodCachePtr->GetPixel( index );
	- typename InputDWIImageType::ConstPointer inputDWIImagePtr = this->GetInput();
	-
	- if( likelihood.GetSize() !=0){
	- //entry found in cache
	- this->m_LikelihoodCacheMutexImagePtr->GetPixel(index).Unlock();
	- return likelihood;
	- }
	- //we need to lock m_CurrentLikelihoodCacheElements as well but not crucial right now
	- else if( this->m_CurrentLikelihoodCacheElements < this->m_MaxLikelihoodCacheElements ){
	- //entry not found in cache but we have space to store it
	- likelihood.SetSize(this->m_SampleDirections->Size());
	-
	- this->CalculateLikelihood(static_cast< DWIVectorImageType::PixelType >(
	- inputDWIImagePtr->GetPixel(index)),
	- this->m_SampleDirections,
	- likelihood);
	- this->m_CurrentLikelihoodCacheElements++;
	-
	- this->m_LikelihoodCacheMutexImagePtr->GetPixel(index).Unlock();
	- return likelihood;
	- }
	- else{
	- //entry not found in cache and no space to store it
	- this->m_LikelihoodCacheMutexImagePtr->GetPixel(index).Unlock();
	- return likelihood;
	- }
	-
	-
	- this->m_LikelihoodCacheMutexImagePtr->GetPixel(index).Unlock();
	-
	- // dummy
	- return likelihood;
	-
	-}
	-
	-template< class TInputDWIImage, class TInputWhiteMatterProbabilityImage, class TOutputConnectivityImage >
	-bool
	-StochasticTractographyFilter< TInputDWIImage, TInputWhiteMatterProbabilityImage, TOutputConnectivityImage >
	-::DelegateTract(unsigned long& randomseed){
	- bool success = false;
	- this->m_TotalDelegatedTractsMutex.Lock();
	- if(this->m_TotalDelegatedTracts < this->m_TotalTracts){
	- randomseed = this->m_RandomGenerator.lrand32();
	- this->m_TotalDelegatedTracts++;
	- success = true;
	- //a tract was successfully delegated
	- }
	- else success = false; //all tracts have been delegated
	- this->m_TotalDelegatedTractsMutex.Unlock();
	-
	- return success;
	-}
	-
	-template< class TInputDWIImage, class TInputWhiteMatterProbabilityImage, class TOutputConnectivityImage >
	-void
	-StochasticTractographyFilter< TInputDWIImage, TInputWhiteMatterProbabilityImage, TOutputConnectivityImage >
	-::TractContainerToConnectivityMap(TractContainerType::Pointer tractcontainer){
	- //zero the output image
	- typename OutputConnectivityImageType::Pointer outputPtr = this->GetOutput();
	- outputPtr->FillBuffer(0);
	-
	- typedef PathIterator< OutputConnectivityImageType, TractType > OutputTractIteratorType;
	-
	- for(unsigned int i=0; i<tractcontainer->Size(); i++ ){
	- TractType::Pointer tract = tractcontainer->GetElement(i);
	- //std::cout<< tract->EndOfInput() <<std::endl;
	- OutputTractIteratorType outputtractIt( outputPtr,
	- tract );
	-
	- for(outputtractIt.GoToBegin(); !outputtractIt.IsAtEnd(); ++outputtractIt){
	- /* there is an issue using outputtractIt.Value() */
	-// outputtractIt.Set(outputtractIt.Get()+1);
	-
	-
	- }
	- }
	-}
	-
	-template< class TInputDWIImage, class TInputWhiteMatterProbabilityImage, class TOutputConnectivityImage >
	-void
	-StochasticTractographyFilter< TInputDWIImage, TInputWhiteMatterProbabilityImage, TOutputConnectivityImage >
	-::StoreTract(TractType::Pointer tract){
	- this->m_OutputTractContainerMutex.Lock();
	- this->m_OutputTractContainer->InsertElement(
	- this->m_OutputTractContainer->Size(),
	- tract);
	- this->m_OutputTractContainerMutex.Unlock();
	-}
	-
	-template< class TInputDWIImage, class TInputWhiteMatterProbabilityImage, class TOutputConnectivityImage >
	-void
	-StochasticTractographyFilter< TInputDWIImage, TInputWhiteMatterProbabilityImage, TOutputConnectivityImage >
	-::GenerateTensorImageOutput(void){
	- this->UpdateGradientDirections();
	- this->UpdateTensorModelFittingMatrices();
	-
	- //allocate the tensor image
	- this->m_OutputTensorImage = OutputTensorImageType::New();
	- m_OutputTensorImage->CopyInformation( this->GetInput() );
	- m_OutputTensorImage->SetBufferedRegion( this->GetInput()->GetBufferedRegion() );
	- m_OutputTensorImage->SetRequestedRegion( this->GetInput()->GetRequestedRegion() );
	- m_OutputTensorImage->Allocate();
	-
	- //define an iterator for the input and output images
	- typedef itk::ImageRegionConstIterator< InputDWIImageType > DWIImageIteratorType;
	- typedef itk::ImageRegionIterator< OutputTensorImageType > TensorImageIteratorType;
	-
	- DWIImageIteratorType
	- inputDWIit( this->GetInput(), m_OutputTensorImage->GetRequestedRegion() );
	-
	- TensorImageIteratorType outputtensorit
	- ( m_OutputTensorImage, m_OutputTensorImage->GetRequestedRegion() );
	-
	- unsigned int N = this->m_TransformedGradients->Size();
	- TensorModelParamType tensormodelparams( 0.0 );
	- vnl_diag_matrix< double > W(N,0);
	-
	- for(inputDWIit.GoToBegin(), outputtensorit.GoToBegin();
	- !outputtensorit.IsAtEnd(); ++inputDWIit, ++outputtensorit){
	- CalculateTensorModelParameters( inputDWIit.Get(),
	- W, tensormodelparams);
	-
	- OutputTensorImageType::PixelType& D = outputtensorit.Value();
	- //set the tensor model parameters into a Diffusion tensor
	- D(0,0) = tensormodelparams[1];
	- D(0,1) = tensormodelparams[4];
	- D(0,2) = tensormodelparams[5];
	- D(1,0) = tensormodelparams[4];
	- D(1,1) = tensormodelparams[2];
	- D(1,2) = tensormodelparams[6];
	- D(2,0) = tensormodelparams[5];
	- D(2,1) = tensormodelparams[6];
	- D(2,2) = tensormodelparams[3];
	-
	- //std::cout<<D;
	- }
	-}
	-
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.cpp
	deleted file mode 100644
	index ae79b0851f..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.cpp
	+++ /dev/null
	@@ -1,980 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <ctime>
	-#include <cstdio>
	-#include <cstdlib>
	-
	-#include <omp.h>
	-#include "itkStreamlineTrackingFilter.h"
	-#include <itkImageRegionConstIterator.h>
	-#include <itkImageRegionConstIteratorWithIndex.h>
	-#include <itkImageRegionIterator.h>
	-#include "itkPointShell.h"
	-#include <itkRescaleIntensityImageFilter.h>
	-#include <mitkLexicalCast.h>
	-#include <TrackingHandlers/mitkTrackingDataHandler.h>
	-#include <TrackingHandlers/mitkTrackingHandlerOdf.h>
	-#include <TrackingHandlers/mitkTrackingHandlerPeaks.h>
	-#include <TrackingHandlers/mitkTrackingHandlerTensor.h>
	-#include <TrackingHandlers/mitkTrackingHandlerRandomForest.h>
	-#include <mitkDiffusionFunctionCollection.h>
	-
	-namespace itk {
	-
	-
	-StreamlineTrackingFilter
	-::StreamlineTrackingFilter()
	- : m_PauseTracking(false)
	- , m_AbortTracking(false)
	- , m_BuildFibersFinished(false)
	- , m_BuildFibersReady(0)
	- , m_FiberPolyData(nullptr)
	- , m_Points(nullptr)
	- , m_Cells(nullptr)
	- , m_StoppingRegions(nullptr)
	- , m_TargetRegions(nullptr)
	- , m_SeedImage(nullptr)
	- , m_MaskImage(nullptr)
	- , m_ExclusionRegions(nullptr)
	- , m_OutputProbabilityMap(nullptr)
	- , m_Verbose(true)
	- , m_DemoMode(false)
	- , m_CurrentTracts(0)
	- , m_Progress(0)
	- , m_StopTracking(false)
	- , m_TrackingPriorHandler(nullptr)
	-{
	- this->SetNumberOfRequiredInputs(0);
	-}
	-
	-std::string StreamlineTrackingFilter::GetStatusText()
	-{
	- std::string status = "Seedpoints processed: " + boost::lexical_cast<std::string>(m_Progress) + "/" + boost::lexical_cast<std::string>(m_SeedPoints.size());
	- if (m_SeedPoints.size()>0)
	- status += " (" + boost::lexical_cast<std::string>(100*m_Progress/m_SeedPoints.size()) + "%)";
	- if (m_Parameters->m_MaxNumFibers>0)
	- status += "\nFibers accepted: " + boost::lexical_cast<std::string>(m_CurrentTracts) + "/" + boost::lexical_cast<std::string>(m_Parameters->m_MaxNumFibers);
	- else
	- status += "\nFibers accepted: " + boost::lexical_cast<std::string>(m_CurrentTracts);
	-
	- return status;
	-}
	-
	-void StreamlineTrackingFilter::BeforeTracking()
	-{
	- m_StopTracking = false;
	- m_TrackingHandler->SetParameters(m_Parameters);
	- m_TrackingHandler->InitForTracking();
	- m_FiberPolyData = PolyDataType::New();
	- m_Points = vtkSmartPointer< vtkPoints >::New();
	- m_Cells = vtkSmartPointer< vtkCellArray >::New();
	-
	- if (m_TrackingPriorHandler!=nullptr)
	- {
	- m_TrackingPriorHandler->InitForTracking();
	- }
	-
	- m_PolyDataContainer.clear();
	- for (unsigned int i=0; i<this->GetNumberOfThreads(); i++)
	- {
	- PolyDataType poly = PolyDataType::New();
	- m_PolyDataContainer.push_back(poly);
	- }
	-
	- auto imageSpacing = m_TrackingHandler->GetSpacing();
	- if (m_Parameters->m_OutputProbMap)
	- {
	- m_OutputProbabilityMap = ItkDoubleImgType::New();
	- m_OutputProbabilityMap->SetSpacing(imageSpacing);
	- m_OutputProbabilityMap->SetOrigin(m_TrackingHandler->GetOrigin());
	- m_OutputProbabilityMap->SetDirection(m_TrackingHandler->GetDirection());
	- m_OutputProbabilityMap->SetRegions(m_TrackingHandler->GetLargestPossibleRegion());
	- m_OutputProbabilityMap->Allocate();
	- m_OutputProbabilityMap->FillBuffer(0);
	- }
	-
	- m_MaskInterpolator = itk::LinearInterpolateImageFunction< ItkFloatImgType, float >::New();
	- m_StopInterpolator = itk::LinearInterpolateImageFunction< ItkFloatImgType, float >::New();
	- m_SeedInterpolator = itk::LinearInterpolateImageFunction< ItkFloatImgType, float >::New();
	- m_TargetInterpolator = itk::LinearInterpolateImageFunction< ItkFloatImgType, float >::New();
	- m_ExclusionInterpolator = itk::LinearInterpolateImageFunction< ItkFloatImgType, float >::New();
	-
	- if (m_StoppingRegions.IsNull())
	- {
	- m_StoppingRegions = ItkFloatImgType::New();
	- m_StoppingRegions->SetSpacing( imageSpacing );
	- m_StoppingRegions->SetOrigin( m_TrackingHandler->GetOrigin() );
	- m_StoppingRegions->SetDirection( m_TrackingHandler->GetDirection() );
	- m_StoppingRegions->SetRegions( m_TrackingHandler->GetLargestPossibleRegion() );
	- m_StoppingRegions->Allocate();
	- m_StoppingRegions->FillBuffer(0);
	- }
	- else
	- std::cout << "StreamlineTracking - Using stopping region image" << std::endl;
	- m_StopInterpolator->SetInputImage(m_StoppingRegions);
	-
	- if (m_ExclusionRegions.IsNotNull())
	- {
	- std::cout << "StreamlineTracking - Using exclusion region image" << std::endl;
	- m_ExclusionInterpolator->SetInputImage(m_ExclusionRegions);
	- }
	-
	- if (m_TargetRegions.IsNull())
	- {
	- m_TargetImageSet = false;
	- m_TargetRegions = ItkFloatImgType::New();
	- m_TargetRegions->SetSpacing( imageSpacing );
	- m_TargetRegions->SetOrigin( m_TrackingHandler->GetOrigin() );
	- m_TargetRegions->SetDirection( m_TrackingHandler->GetDirection() );
	- m_TargetRegions->SetRegions( m_TrackingHandler->GetLargestPossibleRegion() );
	- m_TargetRegions->Allocate();
	- m_TargetRegions->FillBuffer(1);
	- }
	- else
	- {
	- m_TargetImageSet = true;
	- m_TargetInterpolator->SetInputImage(m_TargetRegions);
	- std::cout << "StreamlineTracking - Using target region image" << std::endl;
	- }
	-
	- if (m_SeedImage.IsNull())
	- {
	- m_SeedImageSet = false;
	- m_SeedImage = ItkFloatImgType::New();
	- m_SeedImage->SetSpacing( imageSpacing );
	- m_SeedImage->SetOrigin( m_TrackingHandler->GetOrigin() );
	- m_SeedImage->SetDirection( m_TrackingHandler->GetDirection() );
	- m_SeedImage->SetRegions( m_TrackingHandler->GetLargestPossibleRegion() );
	- m_SeedImage->Allocate();
	- m_SeedImage->FillBuffer(1);
	- }
	- else
	- {
	- m_SeedImageSet = true;
	- std::cout << "StreamlineTracking - Using seed image" << std::endl;
	- }
	- m_SeedInterpolator->SetInputImage(m_SeedImage);
	-
	- if (m_MaskImage.IsNull())
	- {
	- // initialize mask image
	- m_MaskImage = ItkFloatImgType::New();
	- m_MaskImage->SetSpacing( imageSpacing );
	- m_MaskImage->SetOrigin( m_TrackingHandler->GetOrigin() );
	- m_MaskImage->SetDirection( m_TrackingHandler->GetDirection() );
	- m_MaskImage->SetRegions( m_TrackingHandler->GetLargestPossibleRegion() );
	- m_MaskImage->Allocate();
	- m_MaskImage->FillBuffer(1);
	- }
	- else
	- std::cout << "StreamlineTracking - Using mask image" << std::endl;
	- m_MaskInterpolator->SetInputImage(m_MaskImage);
	-
	- // Autosettings for endpoint constraints
	- if (m_Parameters->m_EpConstraints==EndpointConstraints::NONE && m_TargetImageSet && m_SeedImageSet)
	- {
	- MITK_INFO << "No endpoint constraint chosen but seed and target image set --> setting constraint to EPS_IN_SEED_AND_TARGET";
	- m_Parameters->m_EpConstraints = EndpointConstraints::EPS_IN_SEED_AND_TARGET;
	- }
	- else if (m_Parameters->m_EpConstraints==EndpointConstraints::NONE && m_TargetImageSet)
	- {
	- MITK_INFO << "No endpoint constraint chosen but target image set --> setting constraint to EPS_IN_TARGET";
	- m_Parameters->m_EpConstraints = EndpointConstraints::EPS_IN_TARGET;
	- }
	-
	- // Check if endpoint constraints are valid
	- FiberType test_fib; itk::Point<float> p; p.Fill(0);
	- test_fib.push_back(p); test_fib.push_back(p);
	- IsValidFiber(&test_fib);
	-
	- if (m_SeedPoints.empty())
	- GetSeedPointsFromSeedImage();
	-
	- m_BuildFibersReady = 0;
	- m_BuildFibersFinished = false;
	- m_Tractogram.clear();
	- m_SamplingPointset = mitk::PointSet::New();
	- m_AlternativePointset = mitk::PointSet::New();
	- m_StopVotePointset = mitk::PointSet::New();
	- m_StartTime = std::chrono::system_clock::now();
	-
	- if (m_DemoMode)
	- omp_set_num_threads(1);
	-
	- if (m_Parameters->m_Mode==mitk::TrackingDataHandler::MODE::DETERMINISTIC)
	- std::cout << "StreamlineTracking - Mode: deterministic" << std::endl;
	- else if(m_Parameters->m_Mode==mitk::TrackingDataHandler::MODE::PROBABILISTIC)
	- {
	- std::cout << "StreamlineTracking - Mode: probabilistic" << std::endl;
	- std::cout << "StreamlineTracking - Trials per seed: " << m_Parameters->m_TrialsPerSeed << std::endl;
	- }
	- else
	- std::cout << "StreamlineTracking - Mode: ???" << std::endl;
	-
	- if (m_Parameters->m_EpConstraints==EndpointConstraints::NONE)
	- std::cout << "StreamlineTracking - Endpoint constraint: NONE" << std::endl;
	- else if (m_Parameters->m_EpConstraints==EndpointConstraints::EPS_IN_TARGET)
	- std::cout << "StreamlineTracking - Endpoint constraint: EPS_IN_TARGET" << std::endl;
	- else if (m_Parameters->m_EpConstraints==EndpointConstraints::EPS_IN_TARGET_LABELDIFF)
	- std::cout << "StreamlineTracking - Endpoint constraint: EPS_IN_TARGET_LABELDIFF" << std::endl;
	- else if (m_Parameters->m_EpConstraints==EndpointConstraints::EPS_IN_SEED_AND_TARGET)
	- std::cout << "StreamlineTracking - Endpoint constraint: EPS_IN_SEED_AND_TARGET" << std::endl;
	- else if (m_Parameters->m_EpConstraints==EndpointConstraints::MIN_ONE_EP_IN_TARGET)
	- std::cout << "StreamlineTracking - Endpoint constraint: MIN_ONE_EP_IN_TARGET" << std::endl;
	- else if (m_Parameters->m_EpConstraints==EndpointConstraints::ONE_EP_IN_TARGET)
	- std::cout << "StreamlineTracking - Endpoint constraint: ONE_EP_IN_TARGET" << std::endl;
	- else if (m_Parameters->m_EpConstraints==EndpointConstraints::NO_EP_IN_TARGET)
	- std::cout << "StreamlineTracking - Endpoint constraint: NO_EP_IN_TARGET" << std::endl;
	-
	- std::cout << "StreamlineTracking - Angular threshold: " << m_Parameters->GetAngularThresholdDot() << "°" << std::endl;
	- std::cout << "StreamlineTracking - Stepsize: " << m_Parameters->GetStepSizeMm() << "mm (" << m_Parameters->GetStepSizeMm()/m_Parameters->GetMinVoxelSizeMm() << "*vox)" << std::endl;
	- std::cout << "StreamlineTracking - Seeds per voxel: " << m_Parameters->m_SeedsPerVoxel << std::endl;
	- std::cout << "StreamlineTracking - Max. tract length: " << m_Parameters->m_MaxTractLengthMm << "mm" << std::endl;
	- std::cout << "StreamlineTracking - Min. tract length: " << m_Parameters->m_MinTractLengthMm << "mm" << std::endl;
	- std::cout << "StreamlineTracking - Max. num. tracts: " << m_Parameters->m_MaxNumFibers << std::endl;
	- std::cout << "StreamlineTracking - Loop check: " << m_Parameters->GetLoopCheckDeg() << "°" << std::endl;
	-
	- std::cout << "StreamlineTracking - Num. neighborhood samples: " << m_Parameters->m_NumSamples << std::endl;
	- std::cout << "StreamlineTracking - Max. sampling distance: " << m_Parameters->GetSamplingDistanceMm() << "mm (" << m_Parameters->GetSamplingDistanceMm()/m_Parameters->GetMinVoxelSizeMm() << "*vox)" << std::endl;
	- std::cout << "StreamlineTracking - Deflection modifier: " << m_Parameters->m_DeflectionMod << std::endl;
	-
	- std::cout << "StreamlineTracking - Use stop votes: " << m_Parameters->m_StopVotes << std::endl;
	- std::cout << "StreamlineTracking - Only frontal samples: " << m_Parameters->m_OnlyForwardSamples << std::endl;
	-
	- if (m_TrackingPriorHandler!=nullptr)
	- std::cout << "StreamlineTracking - Using directional prior for tractography (w=" << m_Parameters->m_Weight << ")" << std::endl;
	-
	- if (m_DemoMode)
	- {
	- std::cout << "StreamlineTracking - Running in demo mode";
	- std::cout << "StreamlineTracking - Starting streamline tracking using 1 thread" << std::endl;
	- }
	- else
	- std::cout << "StreamlineTracking - Starting streamline tracking using " << omp_get_max_threads() << " threads" << std::endl;
	-}
	-
	-void StreamlineTrackingFilter::CalculateNewPosition(itk::Point<float, 3>& pos, vnl_vector_fixed<float, 3>& dir)
	-{
	- pos[0] += dir[0]*m_Parameters->GetStepSizeMm();
	- pos[1] += dir[1]*m_Parameters->GetStepSizeMm();
	- pos[2] += dir[2]*m_Parameters->GetStepSizeMm();
	-}
	-
	-std::vector< vnl_vector_fixed<float,3> > StreamlineTrackingFilter::CreateDirections(unsigned int NPoints)
	-{
	- std::vector< vnl_vector_fixed<float,3> > pointshell;
	-
	- if (NPoints<2)
	- return pointshell;
	-
	- std::vector< double > theta; theta.resize(NPoints);
	-
	- std::vector< double > phi; phi.resize(NPoints);
	-
	- auto C = sqrt(4*itk::Math::pi);
	-
	- phi[0] = 0.0;
	- phi[NPoints-1] = 0.0;
	-
	- for(unsigned int i=0; i<NPoints; i++)
	- {
	- theta[i] = acos(-1.0+2.0*i/(NPoints-1.0)) - itk::Math::pi / 2.0;
	- if( i>0 && i<NPoints-1)
	- {
	- phi[i] = (phi[i-1] + C / sqrt(NPoints(1-(-1.0+2.0i/(NPoints-1.0))(-1.0+2.0i/(NPoints-1.0)))));
	- // % (2*DIST_POINTSHELL_PI);
	- }
	- }
	-
	-
	- for(unsigned int i=0; i<NPoints; i++)
	- {
	- vnl_vector_fixed<float,3> d;
	- d[0] = static_cast<float>(cos(theta[i]) * cos(phi[i]));
	- d[1] = static_cast<float>(cos(theta[i]) * sin(phi[i]));
	- d[2] = static_cast<float>(sin(theta[i]));
	- pointshell.push_back(d);
	- }
	-
	- return pointshell;
	-}
	-
	-
	-vnl_vector_fixed<float,3> StreamlineTrackingFilter::GetNewDirection(const itk::Point<float, 3> &pos, std::deque<vnl_vector_fixed<float, 3> >& olddirs, itk::Index<3> &oldIndex)
	-{
	- if (m_DemoMode)
	- {
	- m_SamplingPointset->Clear();
	- m_AlternativePointset->Clear();
	- m_StopVotePointset->Clear();
	- }
	- vnl_vector_fixed<float,3> direction; direction.fill(0);
	-
	- if (mitk::imv::IsInsideMask<float>(pos, m_Parameters->m_InterpolateRoiImages, m_MaskInterpolator) && !mitk::imv::IsInsideMask<float>(pos, m_Parameters->m_InterpolateRoiImages, m_StopInterpolator))
	- direction = m_TrackingHandler->ProposeDirection(pos, olddirs, oldIndex); // get direction proposal at current streamline position
	- else
	- return direction;
	-
	- int stop_votes = 0;
	- int possible_stop_votes = 0;
	- if (!olddirs.empty())
	- {
	- vnl_vector_fixed<float,3> olddir = olddirs.back();
	- std::vector< vnl_vector_fixed<float,3> > probeVecs = CreateDirections(m_Parameters->m_NumSamples);
	- itk::Point<float, 3> sample_pos;
	- unsigned int alternatives = 1;
	- for (unsigned int i=0; i<probeVecs.size(); i++)
	- {
	- vnl_vector_fixed<float,3> d;
	- bool is_stop_voter = false;
	- if (!m_Parameters->m_FixRandomSeed && m_Parameters->m_RandomSampling)
	- {
	- d[0] = static_cast<float>(m_TrackingHandler->GetRandDouble(-0.5, 0.5));
	- d[1] = static_cast<float>(m_TrackingHandler->GetRandDouble(-0.5, 0.5));
	- d[2] = static_cast<float>(m_TrackingHandler->GetRandDouble(-0.5, 0.5));
	- d.normalize();
	- d *= static_cast<float>(m_TrackingHandler->GetRandDouble(0, static_cast<double>(m_Parameters->GetSamplingDistanceMm())));
	- }
	- else
	- {
	- d = probeVecs.at(i);
	- float dot = dot_product(d, olddir);
	- if (m_Parameters->m_StopVotes && dot>0.7f)
	- {
	- is_stop_voter = true;
	- possible_stop_votes++;
	- }
	- else if (m_Parameters->m_OnlyForwardSamples && dot<0)
	- continue;
	- d *= m_Parameters->GetSamplingDistanceMm();
	- }
	-
	- sample_pos[0] = pos[0] + d[0];
	- sample_pos[1] = pos[1] + d[1];
	- sample_pos[2] = pos[2] + d[2];
	-
	- vnl_vector_fixed<float,3> tempDir; tempDir.fill(0.0);
	- if (mitk::imv::IsInsideMask<float>(sample_pos, m_Parameters->m_InterpolateRoiImages, m_MaskInterpolator))
	- tempDir = m_TrackingHandler->ProposeDirection(sample_pos, olddirs, oldIndex); // sample neighborhood
	- if (tempDir.magnitude()>static_cast<float>(mitk::eps))
	- {
	- direction += tempDir;
	-
	- if(m_DemoMode)
	- m_SamplingPointset->InsertPoint(i, sample_pos);
	- }
	- else if (m_Parameters->m_AvoidStop && olddir.magnitude()>0.5f) // out of white matter
	- {
	- if (is_stop_voter)
	- stop_votes++;
	- if (m_DemoMode)
	- m_StopVotePointset->InsertPoint(i, sample_pos);
	-
	- float dot = dot_product(d, olddir);
	- if (dot >= 0.0f) // in front of plane defined by pos and olddir
	- d = -d + 2dotolddir; // reflect
	- else
	- d = -d; // invert
	-
	- // look a bit further into the other direction
	- sample_pos[0] = pos[0] + d[0];
	- sample_pos[1] = pos[1] + d[1];
	- sample_pos[2] = pos[2] + d[2];
	- alternatives++;
	- vnl_vector_fixed<float,3> tempDir; tempDir.fill(0.0);
	- if (mitk::imv::IsInsideMask<float>(sample_pos, m_Parameters->m_InterpolateRoiImages, m_MaskInterpolator))
	- tempDir = m_TrackingHandler->ProposeDirection(sample_pos, olddirs, oldIndex); // sample neighborhood
	-
	- if (tempDir.magnitude()>static_cast<float>(mitk::eps)) // are we back in the white matter?
	- {
	- direction += d * m_Parameters->m_DeflectionMod; // go into the direction of the white matter
	- direction += tempDir; // go into the direction of the white matter direction at this location
	-
	- if(m_DemoMode)
	- m_AlternativePointset->InsertPoint(alternatives, sample_pos);
	- }
	- else
	- {
	- if (m_DemoMode)
	- m_StopVotePointset->InsertPoint(i, sample_pos);
	- }
	- }
	- else
	- {
	- if (m_DemoMode)
	- m_StopVotePointset->InsertPoint(i, sample_pos);
	-
	- if (is_stop_voter)
	- stop_votes++;
	- }
	- }
	- }
	-
	- bool valid = false;
	- if (direction.magnitude()>0.001f && (possible_stop_votes==0 \|\| static_cast<float>(stop_votes)/possible_stop_votes<0.5f) )
	- {
	- direction.normalize();
	- valid = true;
	- }
	- else
	- direction.fill(0);
	-
	- if (m_TrackingPriorHandler!=nullptr && (m_Parameters->m_NewDirectionsFromPrior \|\| valid))
	- {
	- vnl_vector_fixed<float,3> prior = m_TrackingPriorHandler->ProposeDirection(pos, olddirs, oldIndex);
	- if (prior.magnitude()>0.001f)
	- {
	- prior.normalize();
	- if (dot_product(prior,direction)<0)
	- prior *= -1;
	- direction = (1.0f-m_Parameters->m_Weight) * direction + m_Parameters->m_Weight * prior;
	- direction.normalize();
	- }
	- else if (m_Parameters->m_RestrictToPrior)
	- direction.fill(0.0);
	- }
	-
	- return direction;
	-}
	-
	-
	-float StreamlineTrackingFilter::FollowStreamline(itk::Point<float, 3> pos, vnl_vector_fixed<float,3> dir, FiberType* fib, DirectionContainer* container, float tractLength, bool front, bool &exclude)
	-{
	- vnl_vector_fixed<float,3> zero_dir; zero_dir.fill(0.0);
	- std::deque< vnl_vector_fixed<float,3> > last_dirs;
	- for (unsigned int i=0; i<m_Parameters->m_NumPreviousDirections-1; i++)
	- last_dirs.push_back(zero_dir);
	-
	- for (int step=0; step< 5000; step++)
	- {
	- itk::Index<3> oldIndex;
	- m_TrackingHandler->WorldToIndex(pos, oldIndex);
	-
	- // get new position
	- CalculateNewPosition(pos, dir);
	-
	- if (m_ExclusionRegions.IsNotNull() && mitk::imv::IsInsideMask<float>(pos, m_Parameters->m_InterpolateRoiImages, m_ExclusionInterpolator))
	- {
	- exclude = true;
	- return tractLength;
	- }
	-
	- if (m_AbortTracking)
	- return tractLength;
	-
	- // if yes, add new point to streamline
	- dir.normalize();
	- if (front)
	- {
	- fib->push_front(pos);
	- container->push_front(dir);
	- }
	- else
	- {
	- fib->push_back(pos);
	- container->push_back(dir);
	- }
	- tractLength += m_Parameters->GetStepSizeMm();
	-
	- if (m_Parameters->GetLoopCheckDeg()>=0 && CheckCurvature(container, front)>m_Parameters->GetLoopCheckDeg())
	- return tractLength;
	-
	- if (tractLength>m_Parameters->m_MaxTractLengthMm)
	- return tractLength;
	-
	- if (m_DemoMode && !m_Parameters->m_OutputProbMap) // CHECK: warum sind die samplingpunkte der streamline in der visualisierung immer einen schritt voras?
	- {
	-#pragma omp critical
	- {
	- m_BuildFibersReady++;
	- m_Tractogram.push_back(*fib);
	- BuildFibers(true);
	- m_Stop = true;
	-
	- while (m_Stop){
	- }
	- }
	- }
	-
	- last_dirs.push_back(dir);
	- if (last_dirs.size()>m_Parameters->m_NumPreviousDirections)
	- last_dirs.pop_front();
	- dir = GetNewDirection(pos, last_dirs, oldIndex);
	-
	- while (m_PauseTracking){}
	-
	- if (dir.magnitude()<0.0001f)
	- return tractLength;
	- }
	- return tractLength;
	-}
	-
	-
	-float StreamlineTrackingFilter::CheckCurvature(DirectionContainer* fib, bool front)
	-{
	- if (fib->size()<8)
	- return 0;
	- float m_Distance = std::max(m_Parameters->GetMinVoxelSizeMm()4, m_Parameters->GetStepSizeMm()8);
	- float dist = 0;
	-
	- std::vector< vnl_vector_fixed< float, 3 > > vectors;
	- vnl_vector_fixed< float, 3 > meanV; meanV.fill(0);
	- float dev = 0;
	-
	- if (front)
	- {
	- int c = 0;
	- while(dist<m_Distance && c<static_cast<int>(fib->size())-1)
	- {
	- dist += m_Parameters->GetStepSizeMm();
	- vnl_vector_fixed< float, 3 > v = fib->at(static_cast<unsigned int>(c));
	- if (dot_product(v,meanV)<0)
	- v = -v;
	- vectors.push_back(v);
	- meanV += v;
	- c++;
	- }
	- }
	- else
	- {
	- int c = static_cast<int>(fib->size())-1;
	- while(dist<m_Distance && c>=0)
	- {
	- dist += m_Parameters->GetStepSizeMm();
	- vnl_vector_fixed< float, 3 > v = fib->at(static_cast<unsigned int>(c));
	- if (dot_product(v,meanV)<0)
	- v = -v;
	- vectors.push_back(v);
	- meanV += v;
	- c--;
	- }
	- }
	- meanV.normalize();
	-
	- for (unsigned int c=0; c<vectors.size(); c++)
	- {
	- float angle = std::fabs(dot_product(meanV, vectors.at(c)));
	- if (angle>1.0f)
	- angle = 1.0;
	- dev += acos(angle)*180.0f/static_cast<float>(itk::Math::pi);
	- }
	- if (vectors.size()>0)
	- dev /= vectors.size();
	-
	- return dev;
	-}
	-
	-std::shared_ptr<mitk::StreamlineTractographyParameters> StreamlineTrackingFilter::GetParameters() const
	-{
	- return m_Parameters;
	-}
	-
	-void StreamlineTrackingFilter::SetParameters(std::shared_ptr< mitk::StreamlineTractographyParameters > Parameters)
	-{
	- m_Parameters = Parameters;
	-}
	-
	-void StreamlineTrackingFilter::SetTrackingPriorHandler(mitk::TrackingDataHandler *TrackingPriorHandler)
	-{
	- m_TrackingPriorHandler = TrackingPriorHandler;
	-}
	-
	-void StreamlineTrackingFilter::GetSeedPointsFromSeedImage()
	-{
	- MITK_INFO << "StreamlineTracking - Calculating seed points.";
	- m_SeedPoints.clear();
	-
	- typedef ImageRegionConstIterator< ItkFloatImgType > MaskIteratorType;
	- MaskIteratorType sit(m_SeedImage, m_SeedImage->GetLargestPossibleRegion());
	- sit.GoToBegin();
	-
	- while (!sit.IsAtEnd())
	- {
	- if (sit.Value()>0)
	- {
	- ItkFloatImgType::IndexType index = sit.GetIndex();
	- itk::ContinuousIndex<float, 3> start;
	- start[0] = index[0];
	- start[1] = index[1];
	- start[2] = index[2];
	- itk::Point<float> worldPos;
	- m_SeedImage->TransformContinuousIndexToPhysicalPoint(start, worldPos);
	-
	- if ( mitk::imv::IsInsideMask<float>(worldPos, m_Parameters->m_InterpolateRoiImages, m_MaskInterpolator) )
	- {
	- m_SeedPoints.push_back(worldPos);
	- for (unsigned int s = 1; s < m_Parameters->m_SeedsPerVoxel; s++)
	- {
	- start[0] = index[0] + static_cast<float>(m_TrackingHandler->GetRandDouble(-0.5, 0.5));
	- start[1] = index[1] + static_cast<float>(m_TrackingHandler->GetRandDouble(-0.5, 0.5));
	- start[2] = index[2] + static_cast<float>(m_TrackingHandler->GetRandDouble(-0.5, 0.5));
	-
	- itk::Point<float> worldPos;
	- m_SeedImage->TransformContinuousIndexToPhysicalPoint(start, worldPos);
	- m_SeedPoints.push_back(worldPos);
	- }
	- }
	- }
	- ++sit;
	- }
	- if (m_SeedPoints.empty())
	- mitkThrow() << "No valid seed point in seed image! Is your seed image registered with the image you are tracking on?";
	-}
	-
	-void StreamlineTrackingFilter::GenerateData()
	-{
	- this->BeforeTracking();
	- if (!m_Parameters->m_FixRandomSeed)
	- std::random_shuffle(m_SeedPoints.begin(), m_SeedPoints.end());
	-
	- m_CurrentTracts = 0;
	- int num_seeds = static_cast<int>(m_SeedPoints.size());
	- itk::Index<3> zeroIndex; zeroIndex.Fill(0);
	- m_Progress = 0;
	- int i = 0;
	- int print_interval = num_seeds/100;
	- if (print_interval<100)
	- m_Verbose=false;
	-
	- unsigned int trials_per_seed = 1;
	- if(m_Parameters->m_Mode==mitk::TrackingDataHandler::MODE::PROBABILISTIC)
	- trials_per_seed = m_Parameters->m_TrialsPerSeed;
	-
	-#pragma omp parallel
	- while (i<num_seeds && !m_StopTracking)
	- {
	- int temp_i = 0;
	-#pragma omp critical
	- {
	- temp_i = i;
	- i++;
	- }
	-
	- if (temp_i>=num_seeds \|\| m_StopTracking)
	- continue;
	- else if (m_Verbose && i%print_interval==0)
	-#pragma omp critical
	- {
	- m_Progress += static_cast<unsigned int>(print_interval);
	- std::cout << " \r";
	- if (m_Parameters->m_MaxNumFibers>0)
	- std::cout << "Tried: " << m_Progress << "/" << num_seeds << " \| Accepted: " << m_CurrentTracts << "/" << m_Parameters->m_MaxNumFibers << '\r';
	- else
	- std::cout << "Tried: " << m_Progress << "/" << num_seeds << " \| Accepted: " << m_CurrentTracts << '\r';
	- cout.flush();
	- }
	-
	- const itk::Point<float> worldPos = m_SeedPoints.at(static_cast<unsigned int>(temp_i));
	-
	- for (unsigned int trials=0; trials<trials_per_seed; ++trials)
	- {
	- FiberType fib;
	- DirectionContainer direction_container;
	- float tractLength = 0;
	- unsigned long counter = 0;
	-
	- // get starting direction
	- vnl_vector_fixed<float,3> dir; dir.fill(0.0);
	- std::deque< vnl_vector_fixed<float,3> > olddirs;
	- dir = GetNewDirection(worldPos, olddirs, zeroIndex) * 0.5f;
	-
	- bool exclude = false;
	- if (m_ExclusionRegions.IsNotNull() && mitk::imv::IsInsideMask<float>(worldPos, m_Parameters->m_InterpolateRoiImages, m_ExclusionInterpolator))
	- exclude = true;
	-
	- bool success = false;
	- if (dir.magnitude()>0.0001f && !exclude)
	- {
	- // forward tracking
	- tractLength = FollowStreamline(worldPos, dir, &fib, &direction_container, 0, false, exclude);
	- fib.push_front(worldPos);
	-
	- // backward tracking
	- if (!exclude)
	- tractLength = FollowStreamline(worldPos, -dir, &fib, &direction_container, tractLength, true, exclude);
	-
	- counter = fib.size();
	-
	- if (tractLength>=m_Parameters->m_MinTractLengthMm && counter>=2 && !exclude)
	- {
	-#pragma omp critical
	- if ( IsValidFiber(&fib) )
	- {
	- if (!m_StopTracking)
	- {
	- if (!m_Parameters->m_OutputProbMap)
	- m_Tractogram.push_back(fib);
	- else
	- FiberToProbmap(&fib);
	- m_CurrentTracts++;
	- success = true;
	- }
	- if (m_Parameters->m_MaxNumFibers > 0 && m_CurrentTracts>=static_cast<unsigned int>(m_Parameters->m_MaxNumFibers))
	- {
	- if (!m_StopTracking)
	- {
	- std::cout << " \r";
	- MITK_INFO << "Reconstructed maximum number of tracts (" << m_CurrentTracts << "). Stopping tractography.";
	- }
	- m_StopTracking = true;
	- }
	- }
	- }
	- }
	-
	- if (success \|\| m_Parameters->m_Mode!=MODE::PROBABILISTIC)
	- break; // we only try one seed point multiple times if we use a probabilistic tracker and have not found a valid streamline yet
	-
	- }// trials per seed
	-
	- }// seed points
	-
	- this->AfterTracking();
	-}
	-
	-bool StreamlineTrackingFilter::IsValidFiber(FiberType* fib)
	-{
	- if (m_Parameters->m_EpConstraints==EndpointConstraints::NONE)
	- {
	- return true;
	- }
	- else if (m_Parameters->m_EpConstraints==EndpointConstraints::EPS_IN_TARGET)
	- {
	- if (m_TargetImageSet)
	- {
	- if ( mitk::imv::IsInsideMask<float>(fib->front(), m_Parameters->m_InterpolateRoiImages, m_TargetInterpolator)
	- && mitk::imv::IsInsideMask<float>(fib->back(), m_Parameters->m_InterpolateRoiImages, m_TargetInterpolator) )
	- return true;
	- return false;
	- }
	- else
	- mitkThrow() << "No target image set but endpoint constraint EPS_IN_TARGET chosen!";
	- }
	- else if (m_Parameters->m_EpConstraints==EndpointConstraints::EPS_IN_TARGET_LABELDIFF)
	- {
	- if (m_TargetImageSet)
	- {
	- float v1 = mitk::imv::GetImageValue<float>(fib->front(), false, m_TargetInterpolator);
	- float v2 = mitk::imv::GetImageValue<float>(fib->back(), false, m_TargetInterpolator);
	- if ( v1>0.0f && v2>0.0f && v1!=v2 )
	- return true;
	- return false;
	- }
	- else
	- mitkThrow() << "No target image set but endpoint constraint EPS_IN_TARGET_LABELDIFF chosen!";
	- }
	- else if (m_Parameters->m_EpConstraints==EndpointConstraints::EPS_IN_SEED_AND_TARGET)
	- {
	- if (m_TargetImageSet && m_SeedImageSet)
	- {
	- if ( mitk::imv::IsInsideMask<float>(fib->front(), m_Parameters->m_InterpolateRoiImages, m_SeedInterpolator)
	- && mitk::imv::IsInsideMask<float>(fib->back(), m_Parameters->m_InterpolateRoiImages, m_TargetInterpolator) )
	- return true;
	- if ( mitk::imv::IsInsideMask<float>(fib->back(), m_Parameters->m_InterpolateRoiImages, m_SeedInterpolator)
	- && mitk::imv::IsInsideMask<float>(fib->front(), m_Parameters->m_InterpolateRoiImages, m_TargetInterpolator) )
	- return true;
	- return false;
	- }
	- else
	- mitkThrow() << "No target or seed image set but endpoint constraint EPS_IN_SEED_AND_TARGET chosen!";
	- }
	- else if (m_Parameters->m_EpConstraints==EndpointConstraints::MIN_ONE_EP_IN_TARGET)
	- {
	- if (m_TargetImageSet)
	- {
	- if ( mitk::imv::IsInsideMask<float>(fib->front(), m_Parameters->m_InterpolateRoiImages, m_TargetInterpolator)
	- \|\| mitk::imv::IsInsideMask<float>(fib->back(), m_Parameters->m_InterpolateRoiImages, m_TargetInterpolator) )
	- return true;
	- return false;
	- }
	- else
	- mitkThrow() << "No target image set but endpoint constraint MIN_ONE_EP_IN_TARGET chosen!";
	- }
	- else if (m_Parameters->m_EpConstraints==EndpointConstraints::ONE_EP_IN_TARGET)
	- {
	- if (m_TargetImageSet)
	- {
	- if ( mitk::imv::IsInsideMask<float>(fib->front(), m_Parameters->m_InterpolateRoiImages, m_TargetInterpolator)
	- && !mitk::imv::IsInsideMask<float>(fib->back(), m_Parameters->m_InterpolateRoiImages, m_TargetInterpolator) )
	- return true;
	- if ( !mitk::imv::IsInsideMask<float>(fib->back(), m_Parameters->m_InterpolateRoiImages, m_TargetInterpolator)
	- && mitk::imv::IsInsideMask<float>(fib->front(), m_Parameters->m_InterpolateRoiImages, m_TargetInterpolator) )
	- return true;
	- return false;
	- }
	- else
	- mitkThrow() << "No target image set but endpoint constraint ONE_EP_IN_TARGET chosen!";
	- }
	- else if (m_Parameters->m_EpConstraints==EndpointConstraints::NO_EP_IN_TARGET)
	- {
	- if (m_TargetImageSet)
	- {
	- if ( mitk::imv::IsInsideMask<float>(fib->front(), m_Parameters->m_InterpolateRoiImages, m_TargetInterpolator)
	- \|\| mitk::imv::IsInsideMask<float>(fib->back(), m_Parameters->m_InterpolateRoiImages, m_TargetInterpolator) )
	- return false;
	- return true;
	- }
	- else
	- mitkThrow() << "No target image set but endpoint constraint NO_EP_IN_TARGET chosen!";
	- }
	-
	- return true;
	-}
	-
	-void StreamlineTrackingFilter::FiberToProbmap(FiberType* fib)
	-{
	- ItkDoubleImgType::IndexType last_idx; last_idx.Fill(0);
	- for (auto p : *fib)
	- {
	- ItkDoubleImgType::IndexType idx;
	- m_OutputProbabilityMap->TransformPhysicalPointToIndex(p, idx);
	-
	- if (idx != last_idx)
	- {
	- if (m_OutputProbabilityMap->GetLargestPossibleRegion().IsInside(idx))
	- m_OutputProbabilityMap->SetPixel(idx, m_OutputProbabilityMap->GetPixel(idx)+1);
	- last_idx = idx;
	- }
	- }
	-}
	-
	-void StreamlineTrackingFilter::BuildFibers(bool check)
	-{
	- if (m_BuildFibersReady<omp_get_num_threads() && check)
	- return;
	-
	- m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
	- vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
	- vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
	-
	- for (unsigned int i=0; i<m_Tractogram.size(); i++)
	- {
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	- FiberType fib = m_Tractogram.at(i);
	- for (FiberType::iterator it = fib.begin(); it!=fib.end(); ++it)
	- {
	- vtkIdType id = vNewPoints->InsertNextPoint((*it).GetDataPointer());
	- container->GetPointIds()->InsertNextId(id);
	- }
	- vNewLines->InsertNextCell(container);
	- }
	-
	- if (check)
	- for (int i=0; i<m_BuildFibersReady; i++)
	- m_Tractogram.pop_back();
	- m_BuildFibersReady = 0;
	-
	- m_FiberPolyData->SetPoints(vNewPoints);
	- m_FiberPolyData->SetLines(vNewLines);
	- m_BuildFibersFinished = true;
	-}
	-
	-void StreamlineTrackingFilter::AfterTracking()
	-{
	- if (m_Verbose)
	- std::cout << " \r";
	- if (!m_Parameters->m_OutputProbMap)
	- {
	- MITK_INFO << "Reconstructed " << m_Tractogram.size() << " fibers.";
	- MITK_INFO << "Generating polydata ";
	- BuildFibers(false);
	- }
	- else
	- {
	- itk::RescaleIntensityImageFilter< ItkDoubleImgType, ItkDoubleImgType >::Pointer filter = itk::RescaleIntensityImageFilter< ItkDoubleImgType, ItkDoubleImgType >::New();
	- filter->SetInput(m_OutputProbabilityMap);
	- filter->SetOutputMaximum(1.0);
	- filter->SetOutputMinimum(0.0);
	- filter->Update();
	- m_OutputProbabilityMap = filter->GetOutput();
	- }
	- MITK_INFO << "done";
	-
	- m_EndTime = std::chrono::system_clock::now();
	- std::chrono::hours hh = std::chrono::duration_cast<std::chrono::hours>(m_EndTime - m_StartTime);
	- std::chrono::minutes mm = std::chrono::duration_cast<std::chrono::minutes>(m_EndTime - m_StartTime);
	- std::chrono::seconds ss = std::chrono::duration_cast<std::chrono::seconds>(m_EndTime - m_StartTime);
	- mm %= 60;
	- ss %= 60;
	- MITK_INFO << "Tracking took " << hh.count() << "h, " << mm.count() << "m and " << ss.count() << "s";
	-
	- m_SeedPoints.clear();
	-}
	-
	-void StreamlineTrackingFilter::SetDicomProperties(mitk::FiberBundle::Pointer fib)
	-{
	- std::string model_code_value = "-";
	- std::string model_code_meaning = "-";
	- std::string algo_code_value = "-";
	- std::string algo_code_meaning = "-";
	-
	- if ( m_Parameters->m_Mode==MODE::DETERMINISTIC && dynamic_cast<mitk::TrackingHandlerTensor*>(m_TrackingHandler) && !m_Parameters->m_InterpolateTractographyData)
	- {
	- algo_code_value = "sup181_ee04";
	- algo_code_meaning = "FACT";
	- }
	- else if (m_Parameters->m_Mode==MODE::DETERMINISTIC)
	- {
	- algo_code_value = "sup181_ee01";
	- algo_code_meaning = "Deterministic";
	- }
	- else if (m_Parameters->m_Mode==MODE::PROBABILISTIC)
	- {
	- algo_code_value = "sup181_ee02";
	- algo_code_meaning = "Probabilistic";
	- }
	-
	- if (dynamic_cast<mitk::TrackingHandlerTensor>(m_TrackingHandler) \|\| (dynamic_cast<mitk::TrackingHandlerOdf>(m_TrackingHandler) && dynamic_cast<mitk::TrackingHandlerOdf*>(m_TrackingHandler)->GetIsOdfFromTensor() ) )
	- {
	- if ( dynamic_cast<mitk::TrackingHandlerTensor>(m_TrackingHandler) && dynamic_cast<mitk::TrackingHandlerTensor>(m_TrackingHandler)->GetNumTensorImages()>1 )
	- {
	- model_code_value = "sup181_bb02";
	- model_code_meaning = "Multi Tensor";
	- }
	- else
	- {
	- model_code_value = "sup181_bb01";
	- model_code_meaning = "Single Tensor";
	- }
	- }
	- else if (dynamic_cast<mitk::TrackingHandlerRandomForest<6, 28>>(m_TrackingHandler) \|\| dynamic_cast<mitk::TrackingHandlerRandomForest<6, 100>>(m_TrackingHandler))
	- {
	- model_code_value = "sup181_bb03";
	- model_code_meaning = "Model Free";
	- }
	- else if (dynamic_cast<mitk::TrackingHandlerOdf*>(m_TrackingHandler))
	- {
	- model_code_value = "-";
	- model_code_meaning = "ODF";
	- }
	- else if (dynamic_cast<mitk::TrackingHandlerPeaks*>(m_TrackingHandler))
	- {
	- model_code_value = "-";
	- model_code_meaning = "Peaks";
	- }
	-
	- fib->SetProperty("DICOM.anatomy.value", mitk::StringProperty::New("T-A0095"));
	- fib->SetProperty("DICOM.anatomy.meaning", mitk::StringProperty::New("White matter of brain and spinal cord"));
	-
	- fib->SetProperty("DICOM.algo_code.value", mitk::StringProperty::New(algo_code_value));
	- fib->SetProperty("DICOM.algo_code.meaning", mitk::StringProperty::New(algo_code_meaning));
	-
	- fib->SetProperty("DICOM.model_code.value", mitk::StringProperty::New(model_code_value));
	- fib->SetProperty("DICOM.model_code.meaning", mitk::StringProperty::New(model_code_meaning));
	-}
	-
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.h
	deleted file mode 100644
	index ef6c4f7adc..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.h
	+++ /dev/null
	@@ -1,195 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkMLBSTrackingFilter_h_
	-#define __itkMLBSTrackingFilter_h_
	-
	-#include <itkImageToImageFilter.h>
	-#include <itkVectorContainer.h>
	-#include <itkVectorImage.h>
	-#include <vtkSmartPointer.h>
	-#include <vtkPolyData.h>
	-#include <vtkCellArray.h>
	-#include <vtkPoints.h>
	-#include <vtkPolyLine.h>
	-#include <vtkCleanPolyData.h>
	-#include <itkOrientationDistributionFunction.h>
	-#include <itkMersenneTwisterRandomVariateGenerator.h>
	-#include <itkAnalyticalDiffusionQballReconstructionImageFilter.h>
	-#include <itkSimpleFastMutexLock.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <mitkPointSet.h>
	-#include <chrono>
	-#include <TrackingHandlers/mitkTrackingDataHandler.h>
	-#include <MitkFiberTrackingExports.h>
	-#include <mitkFiberBundle.h>
	-#include <mitkPeakImage.h>
	-#include <mitkStreamlineTractographyParameters.h>
	-
	-namespace itk{
	-
	-/**
	-* \brief Performs streamline tracking on the input image. Depending on the tracking handler this can be a tensor, peak or machine learning based tracking. */
	-
	-class MITKFIBERTRACKING_EXPORT StreamlineTrackingFilter : public ProcessObject
	-{
	-
	-public:
	-
	- typedef StreamlineTrackingFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ProcessObject Superclass;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(MLBSTrackingFilter, ImageToImageFilter)
	-
	- typedef itk::Image<unsigned char, 3> ItkUcharImgType;
	- typedef itk::Image<unsigned int, 3> ItkUintImgType;
	- typedef itk::Image<double, 3> ItkDoubleImgType;
	- typedef itk::Image<float, 3> ItkFloatImgType;
	- typedef vtkSmartPointer< vtkPolyData > PolyDataType;
	- typedef mitk::StreamlineTractographyParameters::EndpointConstraints EndpointConstraints;
	- typedef mitk::StreamlineTractographyParameters::MODE MODE;
	-
	- typedef std::deque< vnl_vector_fixed<float,3> > DirectionContainer;
	- typedef std::deque< itk::Point<float> > FiberType;
	- typedef std::vector< FiberType > BundleType;
	-
	- volatile bool m_PauseTracking;
	- bool m_AbortTracking;
	- bool m_BuildFibersFinished;
	- int m_BuildFibersReady;
	- volatile bool m_Stop;
	- mitk::PointSet::Pointer m_SamplingPointset;
	- mitk::PointSet::Pointer m_StopVotePointset;
	- mitk::PointSet::Pointer m_AlternativePointset;
	-
	- void SetDicomProperties(mitk::FiberBundle::Pointer fib);
	-
	- itkGetMacro( OutputProbabilityMap, ItkDoubleImgType::Pointer) ///< Output probability map
	- itkGetMacro( FiberPolyData, PolyDataType ) ///< Output fibers
	-
	- itkSetMacro( SeedImage, ItkFloatImgType::Pointer) ///< Seeds are only placed inside of this mask.
	- itkSetMacro( MaskImage, ItkFloatImgType::Pointer) ///< Tracking is only performed inside of this mask image.
	- itkSetMacro( ExclusionRegions, ItkFloatImgType::Pointer)///< Fibers passing any of the ROIs in this image are discarded.
	-
	- itkSetMacro( StoppingRegions, ItkFloatImgType::Pointer) ///< Streamlines entering a stopping region will stop immediately
	- itkSetMacro( TargetRegions, ItkFloatImgType::Pointer) ///< Only streamline starting and ending in this mask are retained
	- itkSetMacro( DemoMode, bool )
	- itkSetMacro( Verbose, bool ) ///< If true, output tracking progress (might be slower)
	- itkSetMacro( StopTracking, bool )
	-
	- ///< Use manually defined points in physical space as seed points instead of seed image
	- void SetSeedPoints( const std::vector< itk::Point<float> >& sP) {
	- m_SeedPoints = sP;
	- }
	-
	- void SetTrackingHandler( mitk::TrackingDataHandler* h ) ///<
	- {
	- m_TrackingHandler = h;
	- }
	-
	- void Update() override{
	- this->GenerateData();
	- }
	-
	- std::string GetStatusText();
	-
	- void SetTrackingPriorHandler(mitk::TrackingDataHandler *TrackingPriorHandler);
	-
	- std::shared_ptr< mitk::StreamlineTractographyParameters > GetParameters() const;
	- void SetParameters(std::shared_ptr< mitk::StreamlineTractographyParameters > Parameters);
	-
	-protected:
	-
	- void GenerateData() override;
	-
	- StreamlineTrackingFilter();
	- ~StreamlineTrackingFilter() override {}
	-
	- bool IsValidFiber(FiberType* fib); ///< Check endpoints
	- void FiberToProbmap(FiberType* fib);
	- void GetSeedPointsFromSeedImage();
	- void CalculateNewPosition(itk::Point<float, 3>& pos, vnl_vector_fixed<float,3>& dir); ///< Calculate next integration step.
	- float FollowStreamline(itk::Point<float, 3> start_pos, vnl_vector_fixed<float,3> dir, FiberType* fib, DirectionContainer* container, float tractLength, bool front, bool& exclude); ///< Start streamline in one direction.
	- vnl_vector_fixed<float,3> GetNewDirection(const itk::Point<float, 3>& pos, std::deque< vnl_vector_fixed<float,3> >& olddirs, itk::Index<3>& oldIndex); ///< Determine new direction by sample voting at the current position taking the last progression direction into account.
	-
	- std::vector< vnl_vector_fixed<float,3> > CreateDirections(unsigned int NPoints);
	-
	- void BeforeTracking();
	- void AfterTracking();
	-
	- PolyDataType m_FiberPolyData;
	- vtkSmartPointer<vtkPoints> m_Points;
	- vtkSmartPointer<vtkCellArray> m_Cells;
	- BundleType m_Tractogram;
	- BundleType m_GmStubs;
	-
	- ItkFloatImgType::Pointer m_StoppingRegions;
	- ItkFloatImgType::Pointer m_TargetRegions;
	- ItkFloatImgType::Pointer m_SeedImage;
	- ItkFloatImgType::Pointer m_MaskImage;
	- ItkFloatImgType::Pointer m_ExclusionRegions;
	- ItkDoubleImgType::Pointer m_OutputProbabilityMap;
	-
	- bool m_Verbose;
	- bool m_DemoMode;
	- std::vector< itk::Point<float> > m_SeedPoints;
	- unsigned int m_CurrentTracts;
	- unsigned int m_Progress;
	- bool m_StopTracking;
	-
	- void BuildFibers(bool check);
	- float CheckCurvature(DirectionContainer *fib, bool front);
	-
	- // decision forest
	- mitk::TrackingDataHandler* m_TrackingHandler;
	- std::vector< PolyDataType > m_PolyDataContainer;
	-
	- std::chrono::time_point<std::chrono::system_clock> m_StartTime;
	- std::chrono::time_point<std::chrono::system_clock> m_EndTime;
	-
	- itk::LinearInterpolateImageFunction< ItkFloatImgType, float >::Pointer m_MaskInterpolator;
	- itk::LinearInterpolateImageFunction< ItkFloatImgType, float >::Pointer m_StopInterpolator;
	- itk::LinearInterpolateImageFunction< ItkFloatImgType, float >::Pointer m_TargetInterpolator;
	- itk::LinearInterpolateImageFunction< ItkFloatImgType, float >::Pointer m_SeedInterpolator;
	- itk::LinearInterpolateImageFunction< ItkFloatImgType, float >::Pointer m_ExclusionInterpolator;
	- bool m_SeedImageSet;
	- bool m_TargetImageSet;
	-
	- std::shared_ptr< mitk::StreamlineTractographyParameters > m_Parameters;
	-
	-
	- // Directional priors
	- mitk::TrackingDataHandler* m_TrackingPriorHandler;
	-
	-private:
	-
	-};
	-
	-}
	-
	-//#ifndef ITK_MANUAL_INSTANTIATION
	-//#include "itkMLBSTrackingFilter.cpp"
	-//#endif
	-
	-#endif //__itkMLBSTrackingFilter_h_
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTdiToVolumeFractionFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTdiToVolumeFractionFilter.cpp
	deleted file mode 100644
	index 8c179673b2..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTdiToVolumeFractionFilter.cpp
	+++ /dev/null
	@@ -1,156 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkTdiToVolumeFractionFilter_txx
	-#define __itkTdiToVolumeFractionFilter_txx
	-
	-#include "itkTdiToVolumeFractionFilter.h"
	-#include <itkImageRegionConstIterator.h>
	-#include <itkImageRegionConstIteratorWithIndex.h>
	-#include <itkImageRegionIterator.h>
	-#include <math.h>
	-
	-namespace itk {
	-
	-template< class TPixelType >
	-TdiToVolumeFractionFilter< TPixelType >::TdiToVolumeFractionFilter()
	- : m_TdiThreshold(0.3)
	- , m_Sqrt(1.0)
	-{
	- this->SetNumberOfRequiredInputs(5);
	- this->SetNumberOfRequiredOutputs(4);
	-}
	-
	-template< class TPixelType >
	-void TdiToVolumeFractionFilter< TPixelType >::BeforeThreadedGenerateData()
	-{
	- typename InputImageType::Pointer input_tdi = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) );
	-
	- for (int i=0; i<4; ++i)
	- {
	- typename OutputImageType::Pointer outputImage = OutputImageType::New();
	- outputImage->SetOrigin( input_tdi->GetOrigin() );
	- outputImage->SetRegions( input_tdi->GetLargestPossibleRegion() );
	- outputImage->SetSpacing( input_tdi->GetSpacing() );
	- outputImage->SetDirection( input_tdi->GetDirection() );
	- outputImage->Allocate();
	- outputImage->FillBuffer(0.0);
	- this->SetNthOutput(i, outputImage);
	- }
	-}
	-
	-template< class TPixelType >
	-void TdiToVolumeFractionFilter< TPixelType >::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, ThreadIdType)
	-{
	- typename OutputImageType::Pointer o_intra_ax = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0));
	- typename OutputImageType::Pointer o_inter_ax = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(1));
	- typename OutputImageType::Pointer o_gray_matter = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(2));
	- typename OutputImageType::Pointer o_csf = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(3));
	-
	- ImageRegionIterator< OutputImageType > oit0(o_intra_ax, outputRegionForThread);
	- ImageRegionIterator< OutputImageType > oit1(o_inter_ax, outputRegionForThread);
	- ImageRegionIterator< OutputImageType > oit2(o_gray_matter, outputRegionForThread);
	- ImageRegionIterator< OutputImageType > oit3(o_csf, outputRegionForThread);
	-
	- typename InputImageType::Pointer i_wm = static_cast< InputImageType * >(this->ProcessObject::GetInput(1));
	- typename InputImageType::Pointer i_gm = static_cast< InputImageType * >(this->ProcessObject::GetInput(2));
	- typename InputImageType::Pointer i_dgm = static_cast< InputImageType * >(this->ProcessObject::GetInput(3));
	- typename InputImageType::Pointer i_csf = static_cast< InputImageType * >(this->ProcessObject::GetInput(4));
	-
	- ImageRegionIterator< OutputImageType > iit0(i_wm, outputRegionForThread);
	- ImageRegionIterator< OutputImageType > iit1(i_gm, outputRegionForThread);
	- ImageRegionIterator< OutputImageType > iit2(i_dgm, outputRegionForThread);
	- ImageRegionIterator< OutputImageType > iit3(i_csf, outputRegionForThread);
	-
	- typename InputImageType::Pointer input_tdi = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) );
	- ImageRegionConstIterator< InputImageType > tdi_it(input_tdi, outputRegionForThread);
	-
	- while( !tdi_it.IsAtEnd() )
	- {
	- TPixelType intra_ax_val = tdi_it.Get();
	- intra_ax_val = std::pow(intra_ax_val, 1.0/m_Sqrt);
	- if (intra_ax_val>m_TdiThreshold)
	- intra_ax_val = m_TdiThreshold;
	- intra_ax_val /= m_TdiThreshold;
	- if (intra_ax_val<0)
	- intra_ax_val = 0;
	-
	- TPixelType inter_ax_val = 0.0;
	- TPixelType wm_val = iit0.Get();
	- TPixelType gm_val = iit1.Get();
	- TPixelType dgm_val = iit2.Get();
	- TPixelType csf_val = iit3.Get();
	-
	- if (dgm_val>0)
	- {
	- TPixelType ex = 1.0 - intra_ax_val;
	- gm_val += dgm_val * ex;
	- }
	-
	- if (intra_ax_val < 0.0001 && wm_val > 0.0001)
	- {
	- if (csf_val+gm_val == 0 )
	- gm_val += wm_val;
	- else
	- {
	- if (csf_val>gm_val)
	- csf_val += wm_val;
	- else
	- gm_val += wm_val;
	- }
	- }
	- else if ( intra_ax_val>0.0001 )
	- {
	- auto comp_sum = csf_val+gm_val+intra_ax_val;
	- if (comp_sum<1.0)
	- inter_ax_val = 1.0 - comp_sum;
	- else if (comp_sum>1)
	- intra_ax_val = 1.0 - (csf_val+gm_val);
	- if (intra_ax_val<-0.01)
	- MITK_INFO << "Corrupted volume fraction. intra_ax_val=" << intra_ax_val;
	- if (intra_ax_val<0)
	- intra_ax_val = 0;
	- }
	- auto comp_sum = csf_val+gm_val+intra_ax_val+inter_ax_val;
	- if (std::fabs(comp_sum-1.0)>0.00001 && comp_sum > 0.0001)
	- {
	- csf_val /= comp_sum;
	- gm_val /= comp_sum;
	- intra_ax_val /= comp_sum;
	- inter_ax_val /= comp_sum;
	- }
	-
	- oit0.Set(intra_ax_val);
	- oit1.Set(inter_ax_val);
	- oit2.Set(gm_val);
	- oit3.Set(csf_val);
	-
	- ++tdi_it;
	-
	- ++iit0;
	- ++iit1;
	- ++iit2;
	- ++iit3;
	-
	- ++oit0;
	- ++oit1;
	- ++oit2;
	- ++oit3;
	- }
	-}
	-
	-}
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTdiToVolumeFractionFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTdiToVolumeFractionFilter.h
	deleted file mode 100644
	index b2c1caf944..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTdiToVolumeFractionFilter.h
	+++ /dev/null
	@@ -1,78 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-/*===================================================================
	-
	-This file is based heavily on a corresponding ITK filter.
	-
	-===================================================================*/
	-#ifndef __itkTdiToVolumeFractionFilter_h_
	-#define __itkTdiToVolumeFractionFilter_h_
	-
	-#include <MitkFiberTrackingExports.h>
	-#include <itkImageToImageFilter.h>
	-
	-namespace itk{
	-
	-/**
	-* \brief */
	-
	-template< class TPixelType >
	-class TdiToVolumeFractionFilter : public ImageToImageFilter< Image< TPixelType, 3 >, Image< TPixelType, 3 > >
	-{
	-
	-public:
	-
	- typedef TdiToVolumeFractionFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageToImageFilter< Image< TPixelType, 3 >, Image< TPixelType, 3 > > Superclass;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(TdiToVolumeFractionFilter, ImageToImageFilter)
	-
	- typedef typename Superclass::InputImageType InputImageType;
	- typedef typename Superclass::OutputImageType OutputImageType;
	- typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
	-
	- itkSetMacro( TdiThreshold, TPixelType )
	- itkSetMacro( Sqrt, TPixelType )
	-
	-protected:
	- TdiToVolumeFractionFilter();
	- ~TdiToVolumeFractionFilter() override {}
	-
	- void BeforeThreadedGenerateData() override;
	- void ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, ThreadIdType threadId) override;
	-
	-private:
	-
	- TPixelType m_TdiThreshold;
	- TPixelType m_Sqrt;
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkTdiToVolumeFractionFilter.cpp"
	-#endif
	-
	-#endif //__itkTdiToVolumeFractionFilter_h_
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractClusteringFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractClusteringFilter.cpp
	deleted file mode 100644
	index 68b555f8e3..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractClusteringFilter.cpp
	+++ /dev/null
	@@ -1,558 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#include "itkTractClusteringFilter.h"
	-
	-#define _USE_MATH_DEFINES
	-#include <math.h>
	-#include <boost/progress.hpp>
	-#include <vnl/vnl_sparse_matrix.h>
	-
	-namespace itk{
	-
	-TractClusteringFilter::TractClusteringFilter()
	- : m_NumPoints(12)
	- , m_InCentroids(nullptr)
	- , m_MinClusterSize(1)
	- , m_MaxClusters(0)
	- , m_MergeDuplicateThreshold(-1)
	- , m_DoResampling(true)
	- , m_FilterMask(nullptr)
	- , m_OverlapThreshold(0.0)
	-{
	-
	-}
	-
	-TractClusteringFilter::~TractClusteringFilter()
	-{
	- for (auto m : m_Metrics)
	- delete m;
	-}
	-
	-std::vector<std::vector<unsigned int> > TractClusteringFilter::GetOutFiberIndices() const
	-{
	- return m_OutFiberIndices;
	-}
	-
	-void TractClusteringFilter::SetMetrics(const std::vector<mitk::ClusteringMetric *> &Metrics)
	-{
	- m_Metrics = Metrics;
	-}
	-
	-std::vector<TractClusteringFilter::Cluster> TractClusteringFilter::GetOutClusters() const
	-{
	- return m_OutClusters;
	-}
	-
	-std::vector<mitk::FiberBundle::Pointer> TractClusteringFilter::GetOutCentroids() const
	-{
	- return m_OutCentroids;
	-}
	-
	-std::vector<mitk::FiberBundle::Pointer> TractClusteringFilter::GetOutTractograms() const
	-{
	- return m_OutTractograms;
	-}
	-
	-void TractClusteringFilter::SetDistances(const std::vector<float> &Distances)
	-{
	- m_Distances = Distances;
	-}
	-
	-float TractClusteringFilter::CalcOverlap(vnl_matrix<float>& t)
	-{
	- float overlap = 0;
	- if (m_FilterMask.IsNotNull())
	- {
	-
	- for (unsigned int i=0; i<m_NumPoints; ++i)
	- {
	- vnl_vector<float> p = t.get_column(i);
	- itk::Point<float,3> point;
	- point[0] = p[0];
	- point[1] = p[1];
	- point[2] = p[2];
	- itk::Index<3> idx;
	- m_FilterMask->TransformPhysicalPointToIndex(point, idx);
	- if (m_FilterMask->GetLargestPossibleRegion().IsInside(idx) && m_FilterMask->GetPixel(idx)>0)
	- overlap += 1;
	- }
	- overlap /= m_NumPoints;
	- }
	- else
	- return 1.0;
	-
	- return overlap;
	-}
	-
	-std::vector<vnl_matrix<float> > TractClusteringFilter::ResampleFibers(mitk::FiberBundle::Pointer tractogram)
	-{
	- mitk::FiberBundle::Pointer temp_fib = tractogram->GetDeepCopy();
	- if (m_DoResampling)
	- temp_fib->ResampleToNumPoints(m_NumPoints);
	-
	- std::vector< vnl_matrix<float> > out_fib;
	-
	- for (int i=0; i<temp_fib->GetFiberPolyData()->GetNumberOfCells(); i++)
	- {
	- vtkCell* cell = temp_fib->GetFiberPolyData()->GetCell(i);
	- int numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- vnl_matrix<float> streamline;
	- streamline.set_size(3, m_NumPoints);
	- streamline.fill(0.0);
	-
	- for (int j=0; j<numPoints; j++)
	- {
	- double cand[3];
	- points->GetPoint(j, cand);
	-
	- vnl_vector_fixed< float, 3 > candV;
	- candV[0]=cand[0]; candV[1]=cand[1]; candV[2]=cand[2];
	- streamline.set_column(j, candV);
	- }
	-
	- out_fib.push_back(streamline);
	- }
	-
	- return out_fib;
	-}
	-
	-std::vector< TractClusteringFilter::Cluster > TractClusteringFilter::ClusterStep(std::vector< unsigned int > f_indices, std::vector<float> distances)
	-{
	- float dist_thres = distances.back();
	- distances.pop_back();
	- std::vector< Cluster > C;
	-
	- int N = f_indices.size();
	-
	- Cluster c1;
	- c1.I.push_back(f_indices.at(0));
	- c1.h = T[f_indices.at(0)];
	- c1.n = 1;
	- C.push_back(c1);
	- if (f_indices.size()==1)
	- return C;
	-
	- for (int i=1; i<N; ++i)
	- {
	- vnl_matrix<float> t = T.at(f_indices.at(i));
	-
	- int min_cluster_index = -1;
	- float min_cluster_distance = 99999;
	- bool flip = false;
	-
	- for (unsigned int k=0; k<C.size(); ++k)
	- {
	- vnl_matrix<float> v = C.at(k).h / C.at(k).n;
	- bool f = false;
	- float d = 0;
	- for (auto m : m_Metrics)
	- d += m->CalculateDistance(t, v, f);
	- d /= m_Metrics.size();
	-
	- if (d<min_cluster_distance)
	- {
	- min_cluster_distance = d;
	- min_cluster_index = k;
	- flip = f;
	- }
	- }
	-
	- if (min_cluster_index>=0 && min_cluster_distance<dist_thres)
	- {
	- C[min_cluster_index].I.push_back(f_indices.at(i));
	- if (!flip)
	- C[min_cluster_index].h += t;
	- else
	- C[min_cluster_index].h += t.fliplr();
	- C[min_cluster_index].n += 1;
	- }
	- else
	- {
	- Cluster c;
	- c.I.push_back(f_indices.at(i));
	- c.h = t;
	- c.n = 1;
	- C.push_back(c);
	- }
	- }
	-
	- if (!distances.empty())
	- {
	- std::vector< Cluster > outC;
	-#pragma omp parallel for
	- for (int c=0; c<(int)C.size(); c++)
	- {
	-
	- std::vector< Cluster > tempC = ClusterStep(C.at(c).I, distances);
	-#pragma omp critical
	- AppendCluster(outC, tempC);
	- }
	- return outC;
	- }
	- else
	- return C;
	-}
	-
	-void TractClusteringFilter::AppendCluster(std::vector< Cluster >& a, std::vector< Cluster >&b)
	-{
	- for (auto c : b)
	- a.push_back(c);
	-}
	-
	-std::vector< TractClusteringFilter::Cluster > TractClusteringFilter::MergeDuplicateClusters2(std::vector< TractClusteringFilter::Cluster >& clusters)
	-{
	- if (m_MergeDuplicateThreshold<0)
	- m_MergeDuplicateThreshold = m_Distances.at(0)/2;
	- else if (m_MergeDuplicateThreshold==0)
	- return clusters;
	-
	- MITK_INFO << "Merging duplicate clusters with distance threshold " << m_MergeDuplicateThreshold;
	-
	- std::vector< TractClusteringFilter::Cluster > new_clusters;
	- for (Cluster c1 : clusters)
	- {
	- vnl_matrix<float> t = c1.h / c1.n;
	-
	- int min_idx = -1;
	- float min_d = 99999;
	- bool flip = false;
	-
	-#pragma omp parallel for
	- for (int k2=0; k2<(int)new_clusters.size(); ++k2)
	- {
	- Cluster c2 = new_clusters.at(k2);
	- vnl_matrix<float> v = c2.h / c2.n;
	-
	- bool f = false;
	- float d = 0;
	- for (auto m : m_Metrics)
	- d += m->CalculateDistance(t, v, f);
	- d /= m_Metrics.size();
	-
	-#pragma omp critical
	- if (d<min_d && d<m_MergeDuplicateThreshold)
	- {
	- min_d = d;
	- min_idx = k2;
	- flip = f;
	- }
	- }
	-
	- if (min_idx<0)
	- new_clusters.push_back(c1);
	- else
	- {
	- for (int i=0; i<c1.n; ++i)
	- {
	- new_clusters[min_idx].I.push_back(c1.I.at(i));
	- new_clusters[min_idx].n += 1;
	- }
	- if (!flip)
	- new_clusters[min_idx].h += c1.h;
	- else
	- new_clusters[min_idx].h += c1.h.fliplr();
	- }
	- }
	-
	- MITK_INFO << "\nNumber of clusters after merging duplicates: " << new_clusters.size();
	- return new_clusters;
	-}
	-
	-void TractClusteringFilter::MergeDuplicateClusters(std::vector< TractClusteringFilter::Cluster >& clusters)
	-{
	- if (m_MergeDuplicateThreshold<0)
	- m_MergeDuplicateThreshold = m_Distances.at(0)/2;
	- bool found = true;
	-
	-
	- MITK_INFO << "Merging duplicate clusters with distance threshold " << m_MergeDuplicateThreshold;
	- int start = 0;
	- while (found && m_MergeDuplicateThreshold>mitk::eps)
	- {
	- std::cout << " \r";
	- std::cout << "Number of clusters: " << clusters.size() << '\r';
	- cout.flush();
	-
	- found = false;
	- for (int k1=start; k1<(int)clusters.size(); ++k1)
	- {
	- Cluster c1 = clusters.at(k1);
	- vnl_matrix<float> t = c1.h / c1.n;
	-
	- std::vector< int > merge_indices;
	- std::vector< bool > flip_indices;
	-
	-#pragma omp parallel for
	- for (int k2=start+1; k2<(int)clusters.size(); ++k2)
	- {
	- if (k1!=k2)
	- {
	- Cluster c2 = clusters.at(k2);
	- vnl_matrix<float> v = c2.h / c2.n;
	- bool f = false;
	-
	- float d = 0;
	- for (auto m : m_Metrics)
	- d += m->CalculateDistance(t, v, f);
	- d /= m_Metrics.size();
	-
	-#pragma omp critical
	- if (d<m_MergeDuplicateThreshold)
	- {
	- merge_indices.push_back(k2);
	- flip_indices.push_back(f);
	- }
	- }
	- }
	-
	- for (unsigned int i=0; i<merge_indices.size(); ++i)
	- {
	- Cluster c2 = clusters.at(merge_indices.at(i));
	- for (int i=0; i<c2.n; ++i)
	- {
	- clusters[k1].I.push_back(c2.I.at(i));
	- clusters[k1].n += 1;
	- }
	- if (!flip_indices.at(i))
	- clusters[k1].h += c2.h;
	- else
	- clusters[k1].h += c2.h.fliplr();
	- }
	-
	- std::sort(merge_indices.begin(), merge_indices.end());
	- for (unsigned int i=0; i<merge_indices.size(); ++i)
	- {
	- clusters.erase (clusters.begin()+merge_indices.at(i)-i);
	- found = true;
	- }
	- if (found)
	- break;
	- }
	- ++start;
	- }
	- MITK_INFO << "\nNumber of clusters after merging duplicates: " << clusters.size();
	-}
	-
	-std::vector<TractClusteringFilter::Cluster> TractClusteringFilter::AddToKnownClusters(std::vector< unsigned int > f_indices, std::vector<vnl_matrix<float> >& centroids)
	-{
	- float dist_thres = m_Distances.at(0);
	- int N = f_indices.size();
	-
	- std::vector< Cluster > C;
	- vnl_matrix<float> zero_h; zero_h.set_size(T.at(0).rows(), T.at(0).cols()); zero_h.fill(0.0);
	- Cluster no_fit;
	- no_fit.h = zero_h;
	-
	- for (unsigned int i=0; i<centroids.size(); ++i)
	- {
	- Cluster c;
	- c.h.set_size(T.at(0).rows(), T.at(0).cols()); c.h.fill(0.0);
	- c.f_id = i;
	- C.push_back(c);
	- }
	-
	-#pragma omp parallel for
	- for (int i=0; i<N; ++i)
	- {
	- vnl_matrix<float> t = T.at(f_indices.at(i));
	-
	- int min_cluster_index = -1;
	- float min_cluster_distance = 99999;
	- bool flip = false;
	-
	- if (CalcOverlap(t)>=m_OverlapThreshold)
	- {
	- int c_idx = 0;
	- for (vnl_matrix<float> centroid : centroids)
	- {
	- bool f = false;
	- float d = 0;
	- for (auto m : m_Metrics)
	- d += m->CalculateDistance(t, centroid, f);
	- d /= m_Metrics.size();
	-
	- if (d<min_cluster_distance)
	- {
	- min_cluster_distance = d;
	- min_cluster_index = c_idx;
	- flip = f;
	- }
	- ++c_idx;
	- }
	- }
	-
	- if (min_cluster_index>=0 && min_cluster_distance<dist_thres)
	- {
	-#pragma omp critical
	- {
	- C[min_cluster_index].I.push_back(f_indices.at(i));
	- if (!flip)
	- C[min_cluster_index].h += t;
	- else
	- C[min_cluster_index].h += t.fliplr();
	- C[min_cluster_index].n += 1;
	- }
	- }
	- else
	- {
	-#pragma omp critical
	- {
	- no_fit.I.push_back(f_indices.at(i));
	- no_fit.n++;
	- }
	- }
	- }
	- C.push_back(no_fit);
	- return C;
	-}
	-
	-
	-
	-void TractClusteringFilter::GenerateData()
	-{
	- m_OutTractograms.clear();
	- m_OutCentroids.clear();
	- m_OutClusters.clear();
	-
	- if (m_Metrics.empty())
	- {
	- mitkThrow() << "No metric selected!";
	- return;
	- }
	-
	- T = ResampleFibers(m_Tractogram);
	- if (T.empty())
	- {
	- MITK_INFO << "No fibers in tractogram!";
	- return;
	- }
	-
	- std::vector< unsigned int > f_indices;
	- for (unsigned int i=0; i<T.size(); ++i)
	- f_indices.push_back(i);
	- // std::random_shuffle(f_indices.begin(), f_indices.end());
	-
	- Cluster no_match;
	- std::vector< Cluster > clusters;
	- if (m_InCentroids.IsNull())
	- {
	- MITK_INFO << "Clustering fibers";
	- clusters = ClusterStep(f_indices, m_Distances);
	- MITK_INFO << "Number of clusters: " << clusters.size();
	- clusters = MergeDuplicateClusters2(clusters);
	- std::sort(clusters.begin(),clusters.end());
	- }
	- else
	- {
	- std::vector<vnl_matrix<float> > centroids = ResampleFibers(m_InCentroids);
	- if (centroids.empty())
	- {
	- MITK_INFO << "No fibers in centroid tractogram!";
	- return;
	- }
	- MITK_INFO << "Clustering with input centroids";
	- clusters = AddToKnownClusters(f_indices, centroids);
	- no_match = clusters.back();
	- clusters.pop_back();
	- MITK_INFO << "Number of clusters: " << clusters.size();
	- clusters = MergeDuplicateClusters2(clusters);
	- }
	-
	- MITK_INFO << "Clustering finished";
	- int max = clusters.size()-1;
	- if (m_MaxClusters>0 && clusters.size()-1>m_MaxClusters)
	- max = m_MaxClusters;
	- int skipped = 0;
	- for (int i=clusters.size()-1; i>=0; --i)
	- {
	- Cluster c = clusters.at(i);
	- if ( c.n>=(int)m_MinClusterSize && !(m_MaxClusters>0 && clusters.size()-i>m_MaxClusters) )
	- {
	- m_OutClusters.push_back(c);
	-
	- vtkSmartPointer<vtkFloatArray> weights = vtkSmartPointer<vtkFloatArray>::New();
	- vtkSmartPointer<vtkPolyData> pTmp = m_Tractogram->GeneratePolyDataByIds(c.I, weights);
	- mitk::FiberBundle::Pointer fib = mitk::FiberBundle::New(pTmp);
	- if (max>0)
	- fib->SetFiberWeights((float)i/max);
	- m_OutTractograms.push_back(fib);
	- m_OutFiberIndices.push_back(c.I);
	-
	- // create centroid
	- vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
	- vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
	- vtkSmartPointer<vtkPolyData> polyData = vtkSmartPointer<vtkPolyData>::New();
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	- vnl_matrix<float> centroid_points = c.h / c.n;
	- for (unsigned int j=0; j<centroid_points.cols(); j++)
	- {
	- double p[3];
	- p[0] = centroid_points.get(0,j);
	- p[1] = centroid_points.get(1,j);
	- p[2] = centroid_points.get(2,j);
	-
	- vtkIdType id = vtkNewPoints->InsertNextPoint(p);
	- container->GetPointIds()->InsertNextId(id);
	- }
	- vtkNewCells->InsertNextCell(container);
	- polyData->SetPoints(vtkNewPoints);
	- polyData->SetLines(vtkNewCells);
	- mitk::FiberBundle::Pointer centroid = mitk::FiberBundle::New(polyData);
	- centroid->SetFiberColors(255, 255, 255);
	- m_OutCentroids.push_back(centroid);
	- }
	- else
	- {
	- skipped++;
	- }
	- }
	- MITK_INFO << "Final number of clusters: " << m_OutTractograms.size() << " (discarded " << skipped << " clusters)";
	-
	- int w = 0;
	- for (auto fib : m_OutTractograms)
	- {
	- if (m_OutTractograms.size()>1)
	- {
	- fib->SetFiberWeights((float)w/(m_OutTractograms.size()-1));
	- m_OutCentroids.at(w)->SetFiberWeights((float)w/(m_OutTractograms.size()-1));
	- }
	- else
	- {
	- fib->SetFiberWeights(1);
	- m_OutCentroids.at(w)->SetFiberWeights(1);
	- }
	- fib->ColorFibersByFiberWeights(false, false);
	- ++w;
	- }
	-
	- if (no_match.n>0)
	- {
	- vtkSmartPointer<vtkFloatArray> weights = vtkSmartPointer<vtkFloatArray>::New();
	- vtkSmartPointer<vtkPolyData> pTmp = m_Tractogram->GeneratePolyDataByIds(no_match.I, weights);
	- mitk::FiberBundle::Pointer fib = mitk::FiberBundle::New(pTmp);
	- fib->SetFiberColors(0, 0, 0);
	- m_OutFiberIndices.push_back(no_match.I);
	- m_OutTractograms.push_back(fib);
	- }
	-}
	-
	-}
	-
	-
	-
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractClusteringFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractClusteringFilter.h
	deleted file mode 100644
	index 308c4f493f..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractClusteringFilter.h
	+++ /dev/null
	@@ -1,140 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef itkTractClusteringFilter_h
	-#define itkTractClusteringFilter_h
	-
	-// MITK
	-#include <mitkPlanarEllipse.h>
	-#include <mitkFiberBundle.h>
	-#include <mitkFiberfoxParameters.h>
	-#include <mitkClusteringMetric.h>
	-
	-// ITK
	-#include <itkProcessObject.h>
	-
	-// VTK
	-#include <vtkSmartPointer.h>
	-#include <vtkPolyData.h>
	-#include <vtkCellArray.h>
	-#include <vtkPoints.h>
	-#include <vtkPolyLine.h>
	-
	-namespace itk{
	-
	-/**
	-* \brief */
	-
	-class TractClusteringFilter : public ProcessObject
	-{
	-public:
	-
	- struct Cluster
	- {
	- Cluster() : n(0), f_id(-1) {}
	-
	- vnl_matrix<float> h;
	- std::vector< unsigned int > I;
	- int n;
	- int f_id;
	-
	- bool operator <(Cluster const& b) const
	- {
	- return this->n < b.n;
	- }
	- };
	-
	- typedef TractClusteringFilter Self;
	- typedef ProcessObject Superclass;
	- typedef SmartPointer< Self > Pointer;
	- typedef SmartPointer< const Self > ConstPointer;
	- typedef itk::Image< float, 3 > FloatImageType;
	- typedef itk::Image< unsigned char, 3 > UcharImageType;
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- itkTypeMacro( TractClusteringFilter, ProcessObject )
	-
	- itkSetMacro(NumPoints, unsigned int) ///< Fibers are resampled to the specified number of points. If scalar maps are used, a larger number of points is recommended.
	- itkGetMacro(NumPoints, unsigned int) ///< Fibers are resampled to the specified number of points. If scalar maps are used, a larger number of points is recommended.
	- itkSetMacro(MinClusterSize, unsigned int) ///< Clusters with too few fibers are discarded
	- itkGetMacro(MinClusterSize, unsigned int) ///< Clusters with too few fibers are discarded
	- itkSetMacro(MaxClusters, unsigned int) ///< Only the N largest clusters are kept
	- itkGetMacro(MaxClusters, unsigned int) ///< Only the N largest clusters are kept
	- itkSetMacro(MergeDuplicateThreshold, float) ///< Clusters with centroids very close to each other are merged. Set to 0 to avoid merging and to -1 to use the original cluster size.
	- itkGetMacro(MergeDuplicateThreshold, float) ///< Clusters with centroids very close to each other are merged. Set to 0 to avoid merging and to -1 to use the original cluster size.
	- itkSetMacro(DoResampling, bool) ///< Resample fibers to equal number of points. This is mandatory, but can be performed outside of the filter if desired.
	- itkGetMacro(DoResampling, bool) ///< Resample fibers to equal number of points. This is mandatory, but can be performed outside of the filter if desired.
	- itkSetMacro(OverlapThreshold, float) ///< Overlap threshold used in conjunction with the filter mask when clustering around known centroids.
	- itkGetMacro(OverlapThreshold, float) ///< Overlap threshold used in conjunction with the filter mask when clustering around known centroids.
	-
	- itkSetMacro(Tractogram, mitk::FiberBundle::Pointer) ///< The streamlines to be clustered
	- itkSetMacro(InCentroids, mitk::FiberBundle::Pointer) ///< If a tractogram containing known tract centroids is set, the input fibers are assigned to the closest centroid. If no centroid is found within the specified smallest clustering distance, the fiber is assigned to the no-fit cluster.
	- itkSetMacro(FilterMask, UcharImageType::Pointer) ///< If fibers are clustered around the nearest input centroids (see SetInCentroids), the complete input tractogram can additionally be pre-filtered with this binary mask and a given overlap threshold (see SetOverlapThreshold).
	-
	- virtual void Update() override{
	- this->GenerateData();
	- }
	-
	- void SetDistances(const std::vector<float> &Distances); ///< Set clustering distances that are traversed recoursively. The distances have to be sorted in an ascending manner. The actual cluster size is determined by the smallest entry in the distance-list (index 0).
	-
	- std::vector<mitk::FiberBundle::Pointer> GetOutTractograms() const;
	- std::vector<mitk::FiberBundle::Pointer> GetOutCentroids() const;
	- std::vector<Cluster> GetOutClusters() const;
	-
	- void SetMetrics(const std::vector<mitk::ClusteringMetric *> &Metrics);
	-
	- std::vector<std::vector<unsigned int> > GetOutFiberIndices() const;
	-
	-protected:
	-
	- void GenerateData() override;
	- std::vector< vnl_matrix<float> > ResampleFibers(FiberBundle::Pointer tractogram);
	- float CalcOverlap(vnl_matrix<float>& t);
	-
	- std::vector< Cluster > ClusterStep(std::vector< unsigned int > f_indices, std::vector< float > distances);
	-
	- std::vector< TractClusteringFilter::Cluster > MergeDuplicateClusters2(std::vector< TractClusteringFilter::Cluster >& clusters);
	- void MergeDuplicateClusters(std::vector< TractClusteringFilter::Cluster >& clusters);
	- std::vector< Cluster > AddToKnownClusters(std::vector< unsigned int > f_indices, std::vector<vnl_matrix<float> > &centroids);
	- void AppendCluster(std::vector< Cluster >& a, std::vector< Cluster >&b);
	-
	- TractClusteringFilter();
	- virtual ~TractClusteringFilter();
	-
	- unsigned int m_NumPoints;
	- std::vector< float > m_Distances;
	- mitk::FiberBundle::Pointer m_Tractogram;
	- mitk::FiberBundle::Pointer m_InCentroids;
	- std::vector< mitk::FiberBundle::Pointer > m_OutTractograms;
	- std::vector< mitk::FiberBundle::Pointer > m_OutCentroids;
	- std::vector<vnl_matrix<float> > T;
	- unsigned int m_MinClusterSize;
	- unsigned int m_MaxClusters;
	- float m_MergeDuplicateThreshold;
	- std::vector< Cluster > m_OutClusters;
	- bool m_DoResampling;
	- UcharImageType::Pointer m_FilterMask;
	- float m_OverlapThreshold;
	- std::vector< mitk::ClusteringMetric* > m_Metrics;
	- std::vector< std::vector< unsigned int > > m_OutFiberIndices;
	-};
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkTractClusteringFilter.cpp"
	-#endif
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractDensityImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractDensityImageFilter.cpp
	deleted file mode 100644
	index d529eeefed..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractDensityImageFilter.cpp
	+++ /dev/null
	@@ -1,179 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Coindex[1]right (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#include "itkTractDensityImageFilter.h"
	-
	-// VTK
	-#include <vtkPolyLine.h>
	-#include <vtkCellArray.h>
	-#include <vtkCellData.h>
	-#include <vtkCell.h>
	-
	-// misc
	-#include <cmath>
	-#include <boost/progress.hpp>
	-#include <vtkBox.h>
	-#include <mitkDiffusionFunctionCollection.h>
	-
	-namespace itk{
	-
	-template< class OutputImageType >
	-TractDensityImageFilter< OutputImageType >::TractDensityImageFilter()
	- : m_UpsamplingFactor(1)
	- , m_InvertImage(false)
	- , m_BinaryOutput(false)
	- , m_UseImageGeometry(false)
	- , m_OutputAbsoluteValues(false)
	- , m_MaxDensity(0)
	- , m_NumCoveredVoxels(0)
	-{
	-}
	-
	-template< class OutputImageType >
	-TractDensityImageFilter< OutputImageType >::~TractDensityImageFilter()
	-{
	-}
	-
	-template< class OutputImageType >
	-void TractDensityImageFilter< OutputImageType >::GenerateData()
	-{
	- // generate upsampled image
	- mitk::BaseGeometry::Pointer geometry = m_FiberBundle->GetGeometry();
	- typename OutputImageType::Pointer outImage = this->GetOutput();
	-
	- // calculate new image parameters
	- itk::Vector<double,3> newSpacing;
	- mitk::Point3D newOrigin;
	- itk::Matrix<double, 3, 3> newDirection;
	- ImageRegion<3> upsampledRegion;
	- if (m_UseImageGeometry && !m_InputImage.IsNull())
	- {
	- MITK_INFO << "TractDensityImageFilter: using image geometry";
	- newSpacing = m_InputImage->GetSpacing()/m_UpsamplingFactor;
	- upsampledRegion = m_InputImage->GetLargestPossibleRegion();
	- newOrigin = m_InputImage->GetOrigin();
	- typename OutputImageType::RegionType::SizeType size = upsampledRegion.GetSize();
	- size[0] *= m_UpsamplingFactor;
	- size[1] *= m_UpsamplingFactor;
	- size[2] *= m_UpsamplingFactor;
	- upsampledRegion.SetSize(size);
	- newDirection = m_InputImage->GetDirection();
	- }
	- else
	- {
	- MITK_INFO << "TractDensityImageFilter: using fiber bundle geometry";
	- newSpacing = geometry->GetSpacing()/m_UpsamplingFactor;
	- newOrigin = geometry->GetOrigin();
	- mitk::Geometry3D::BoundsArrayType bounds = geometry->GetBounds();
	-
	- // we retrieve the origin from a vtk-polydata (corner-based) and hance have to translate it to an image geometry
	- // i.e. center-based
	- newOrigin[0] += bounds.GetElement(0) + 0.5 * newSpacing[0];
	- newOrigin[1] += bounds.GetElement(2) + 0.5 * newSpacing[1];
	- newOrigin[2] += bounds.GetElement(4) + 0.5 * newSpacing[2];
	-
	- for (int i=0; i<3; i++)
	- for (int j=0; j<3; j++)
	- newDirection[j][i] = geometry->GetMatrixColumn(i)[j];
	- upsampledRegion.SetSize(0, ceil( geometry->GetExtent(0)*m_UpsamplingFactor ) );
	- upsampledRegion.SetSize(1, ceil( geometry->GetExtent(1)*m_UpsamplingFactor ) );
	- upsampledRegion.SetSize(2, ceil( geometry->GetExtent(2)*m_UpsamplingFactor ) );
	- }
	- typename OutputImageType::RegionType::SizeType upsampledSize = upsampledRegion.GetSize();
	-
	- // apply new image parameters
	- outImage->SetSpacing( newSpacing );
	- outImage->SetOrigin( newOrigin );
	- outImage->SetDirection( newDirection );
	- outImage->SetLargestPossibleRegion( upsampledRegion );
	- outImage->SetBufferedRegion( upsampledRegion );
	- outImage->SetRequestedRegion( upsampledRegion );
	- outImage->Allocate();
	- outImage->FillBuffer(0.0);
	-
	- int w = upsampledSize[0];
	- int h = upsampledSize[1];
	- int d = upsampledSize[2];
	-
	- // set/initialize output
	- OutPixelType* outImageBufferPointer = (OutPixelType*)outImage->GetBufferPointer();
	-
	- MITK_INFO << "TractDensityImageFilter: starting image generation";
	- vtkSmartPointer<vtkPolyData> fiberPolyData = m_FiberBundle->GetFiberPolyData();
	-
	- int numFibers = m_FiberBundle->GetNumFibers();
	- boost::progress_display disp(numFibers);
	- for( int i=0; i<numFibers; i++ )
	- {
	- ++disp;
	- vtkCell* cell = fiberPolyData->GetCell(i);
	- int numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- float weight = m_FiberBundle->GetFiberWeight(i);
	-
	- // fill output image
	- for( int j=0; j<numPoints-1; j++)
	- {
	- itk::Point<float, 3> startVertex = mitk::imv::GetItkPoint(points->GetPoint(j));
	- itk::Index<3> startIndex;
	- itk::ContinuousIndex<float, 3> startIndexCont;
	- outImage->TransformPhysicalPointToIndex(startVertex, startIndex);
	- outImage->TransformPhysicalPointToContinuousIndex(startVertex, startIndexCont);
	-
	- itk::Point<float, 3> endVertex = mitk::imv::GetItkPoint(points->GetPoint(j + 1));
	- itk::Index<3> endIndex;
	- itk::ContinuousIndex<float, 3> endIndexCont;
	- outImage->TransformPhysicalPointToIndex(endVertex, endIndex);
	- outImage->TransformPhysicalPointToContinuousIndex(endVertex, endIndexCont);
	-
	- std::vector< std::pair< itk::Index<3>, double > > segments = mitk::imv::IntersectImage(newSpacing, startIndex, endIndex, startIndexCont, endIndexCont);
	- for (std::pair< itk::Index<3>, double > segment : segments)
	- {
	- if (!outImage->GetLargestPossibleRegion().IsInside(segment.first))
	- continue;
	- if (outImage->GetPixel(segment.first)==0)
	- m_NumCoveredVoxels++;
	-
	- if (m_BinaryOutput)
	- outImage->SetPixel(segment.first, 1);
	- else
	- outImage->SetPixel(segment.first, outImage->GetPixel(segment.first)+segment.second * weight);
	- }
	- }
	- }
	-
	- m_MaxDensity = 0;
	- for (int i=0; i<whd; i++)
	- if (m_MaxDensity < outImageBufferPointer[i])
	- m_MaxDensity = outImageBufferPointer[i];
	- if (!m_OutputAbsoluteValues && !m_BinaryOutput)
	- {
	- MITK_INFO << "TractDensityImageFilter: max-normalizing output image";
	- if (m_MaxDensity>0)
	- for (int i=0; i<whd; i++)
	- {
	- outImageBufferPointer[i] /= m_MaxDensity;
	- }
	- }
	- if (m_InvertImage)
	- {
	- MITK_INFO << "TractDensityImageFilter: inverting image";
	- for (int i=0; i<whd; i++)
	- outImageBufferPointer[i] = 1-outImageBufferPointer[i];
	- }
	- MITK_INFO << "TractDensityImageFilter: finished processing";
	-}
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractDensityImageFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractDensityImageFilter.h
	deleted file mode 100644
	index 1f28bc95e3..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractDensityImageFilter.h
	+++ /dev/null
	@@ -1,88 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef __itkTractDensityImageFilter_h__
	-#define __itkTractDensityImageFilter_h__
	-
	-#include <itkImageSource.h>
	-#include <itkImage.h>
	-#include <itkVectorContainer.h>
	-#include <itkRGBAPixel.h>
	-#include <mitkFiberBundle.h>
	-
	-namespace itk{
	-
	-/**
	-* \brief Generates tract density images from input fiberbundles (Calamante 2010). */
	-
	-template< class OutputImageType >
	-class TractDensityImageFilter : public ImageSource< OutputImageType >
	-{
	-
	-public:
	- typedef TractDensityImageFilter Self;
	- typedef ProcessObject Superclass;
	- typedef SmartPointer< Self > Pointer;
	- typedef SmartPointer< const Self > ConstPointer;
	-
	- typedef typename OutputImageType::PixelType OutPixelType;
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- itkTypeMacro( TractDensityImageFilter, ImageSource )
	-
	- itkSetMacro( UpsamplingFactor, float) ///< use higher resolution for ouput image
	- itkGetMacro( UpsamplingFactor, float) ///< use higher resolution for ouput image
	- itkSetMacro( InvertImage, bool) ///< voxelvalue = 1-voxelvalue
	- itkGetMacro( InvertImage, bool) ///< voxelvalue = 1-voxelvalue
	- itkSetMacro( BinaryOutput, bool) ///< generate binary fiber envelope
	- itkGetMacro( BinaryOutput, bool) ///< generate binary fiber envelope
	- itkSetMacro( OutputAbsoluteValues, bool) ///< output absolute values of the number of fibers per voxel
	- itkGetMacro( OutputAbsoluteValues, bool) ///< output absolute values of the number of fibers per voxel
	- itkSetMacro( UseImageGeometry, bool) ///< use input image geometry to initialize output image
	- itkGetMacro( UseImageGeometry, bool) ///< use input image geometry to initialize output image
	- itkSetMacro( FiberBundle, mitk::FiberBundle::Pointer) ///< input fiber bundle
	- itkSetMacro( InputImage, typename OutputImageType::Pointer) ///< use input image geometry to initialize output image
	- itkGetMacro( MaxDensity, OutPixelType)
	- itkGetMacro( NumCoveredVoxels, unsigned int)
	-
	- void GenerateData() override;
	-
	-protected:
	-
	- TractDensityImageFilter();
	- ~TractDensityImageFilter() override;
	-
	- typename OutputImageType::Pointer m_InputImage; ///< use input image geometry to initialize output image
	- mitk::FiberBundle::Pointer m_FiberBundle; ///< input fiber bundle
	- float m_UpsamplingFactor; ///< use higher resolution for ouput image
	- bool m_InvertImage; ///< voxelvalue = 1-voxelvalue
	- bool m_BinaryOutput; ///< generate binary fiber envelope
	- bool m_UseImageGeometry; ///< use input image geometry to initialize output image
	- bool m_OutputAbsoluteValues; ///< do not normalize image values to 0-1
	- bool m_UseTrilinearInterpolation;
	- bool m_DoFiberResampling;
	- bool m_WorkOnFiberCopy;
	- OutPixelType m_MaxDensity;
	- unsigned int m_NumCoveredVoxels;
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkTractDensityImageFilter.cpp"
	-#endif
	-
	-#endif // __itkTractDensityImageFilter_h__
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractDistanceFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractDistanceFilter.cpp
	deleted file mode 100644
	index f86b915e05..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractDistanceFilter.cpp
	+++ /dev/null
	@@ -1,189 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#include "itkTractDistanceFilter.h"
	-
	-#define _USE_MATH_DEFINES
	-#include <math.h>
	-#include <vnl/vnl_sparse_matrix.h>
	-
	-namespace itk{
	-
	-TractDistanceFilter::TractDistanceFilter()
	- : m_NumPoints(12)
	- , disp(0)
	-{
	-
	-}
	-
	-TractDistanceFilter::~TractDistanceFilter()
	-{
	- for (auto m : m_Metrics)
	- delete m;
	-}
	-
	-vnl_matrix<float> TractDistanceFilter::GetAllDistances() const
	-{
	- return m_AllDistances;
	-}
	-
	-vnl_vector<int> TractDistanceFilter::GetMinIndices() const
	-{
	- return m_MinIndices;
	-}
	-
	-vnl_vector<float> TractDistanceFilter::GetMinDistances() const
	-{
	- return m_MinDistances;
	-}
	-
	-void TractDistanceFilter::SetTracts2(const std::vector<FiberBundle::Pointer> &Tracts2)
	-{
	- m_Tracts2 = Tracts2;
	-}
	-
	-void TractDistanceFilter::SetTracts1(const std::vector<FiberBundle::Pointer> &Tracts1)
	-{
	- m_Tracts1 = Tracts1;
	-}
	-
	-void TractDistanceFilter::SetMetrics(const std::vector<mitk::ClusteringMetric *> &Metrics)
	-{
	- m_Metrics = Metrics;
	-}
	-
	-std::vector<vnl_matrix<float> > TractDistanceFilter::ResampleFibers(mitk::FiberBundle::Pointer tractogram)
	-{
	- std::streambuf *old = cout.rdbuf(); // <-- save
	- std::stringstream ss;
	- std::cout.rdbuf (ss.rdbuf()); // <-- redirect
	- mitk::FiberBundle::Pointer temp_fib = tractogram->GetDeepCopy();
	- temp_fib->ResampleToNumPoints(m_NumPoints);
	-
	- std::vector< vnl_matrix<float> > out_fib;
	-
	- for (int i=0; i<temp_fib->GetFiberPolyData()->GetNumberOfCells(); i++)
	- {
	- vtkCell* cell = temp_fib->GetFiberPolyData()->GetCell(i);
	- int numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- vnl_matrix<float> streamline;
	- streamline.set_size(3, m_NumPoints);
	- streamline.fill(0.0);
	-
	- for (int j=0; j<numPoints; j++)
	- {
	- double cand[3];
	- points->GetPoint(j, cand);
	-
	- vnl_vector_fixed< float, 3 > candV;
	- candV[0]=cand[0]; candV[1]=cand[1]; candV[2]=cand[2];
	- streamline.set_column(j, candV);
	- }
	-
	- out_fib.push_back(streamline);
	- }
	-
	- std::cout.rdbuf (old); // <-- restore
	- return out_fib;
	-}
	-
	-float TractDistanceFilter::calc_distance(const std::vector<vnl_matrix<float> >& T1, const std::vector<vnl_matrix<float> >& T2)
	-{
	- float distance = 0;
	- for (auto metric : m_Metrics)
	- {
	- unsigned int r = 0;
	- for (auto f1 : T1)
	- {
	- unsigned int c = 0;
	- float min_d = 99999;
	- for (auto f2 : T2)
	- {
	-#pragma omp critical
	- ++disp;
	- bool flipped = false;
	- float d = metric->CalculateDistance(f1, f2, flipped);
	- if (d < min_d)
	- min_d = d;
	- ++c;
	- }
	- distance += min_d;
	- ++r;
	- }
	- }
	- distance /= (T1.size() * m_Metrics.size());
	- return distance;
	-}
	-
	-void TractDistanceFilter::GenerateData()
	-{
	- if (m_Metrics.empty())
	- {
	- mitkThrow() << "No metric selected!";
	- return;
	- }
	-
	- m_MinIndices.clear();
	- m_MinDistances.clear();
	- std::vector<std::vector<vnl_matrix<float>>> T1;
	- std::vector<std::vector<vnl_matrix<float>>> T2;
	-
	- unsigned int num_fibs1 = 0;
	- unsigned int num_fibs2 = 0;
	- for (auto t : m_Tracts1)
	- {
	- T1.push_back(ResampleFibers(t));
	- num_fibs1 += T1.back().size();
	- }
	- for (auto t : m_Tracts2)
	- {
	- T2.push_back(ResampleFibers(t));
	- num_fibs2 += T2.back().size();
	- }
	-
	- disp.restart(m_Metrics.size() * num_fibs1 * num_fibs2);
	-
	- m_AllDistances.set_size(T1.size(), T2.size());
	-
	- m_MinIndices.set_size(T1.size());
	- m_MinDistances.set_size(T1.size());
	-
	-#pragma omp parallel for
	- for (int i=0; i<(int)T1.size(); ++i)
	- {
	- auto tracto1 = T1.at(i);
	- m_MinDistances[i] = 99999;
	- for (unsigned int j=0; j<T2.size(); ++j)
	- {
	- auto tracto2 = T2.at(j);
	- float d = calc_distance(tracto1, tracto2);
	- m_AllDistances[i][j] = d;
	-
	- if (d < m_MinDistances[i])
	- {
	- m_MinDistances[i] = d;
	- m_MinIndices[i] = j;
	- }
	- }
	- }
	-}
	-
	-}
	-
	-
	-
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractDistanceFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractDistanceFilter.h
	deleted file mode 100644
	index cb8218306c..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractDistanceFilter.h
	+++ /dev/null
	@@ -1,93 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef itkTractDistanceFilter_h
	-#define itkTractDistanceFilter_h
	-
	-#include <mitkPlanarEllipse.h>
	-#include <mitkFiberBundle.h>
	-#include <mitkFiberfoxParameters.h>
	-#include <mitkClusteringMetric.h>
	-#include <itkProcessObject.h>
	-#include <vtkSmartPointer.h>
	-#include <vtkPolyData.h>
	-#include <vtkCellArray.h>
	-#include <vtkPoints.h>
	-#include <vtkPolyLine.h>
	-#include <boost/progress.hpp>
	-
	-namespace itk{
	-
	-/**
	-* \brief */
	-
	-class TractDistanceFilter : public ProcessObject
	-{
	-public:
	-
	- typedef TractDistanceFilter Self;
	- typedef ProcessObject Superclass;
	- typedef SmartPointer< Self > Pointer;
	- typedef SmartPointer< const Self > ConstPointer;
	- typedef itk::Image< float, 3 > FloatImageType;
	- typedef itk::Image< unsigned char, 3 > UcharImageType;
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- itkTypeMacro( TractDistanceFilter, ProcessObject )
	-
	- itkSetMacro(NumPoints, unsigned int) ///< Fibers are resampled to the specified number of points. If scalar maps are used, a larger number of points is recommended.
	-
	- virtual void Update() override{
	- this->GenerateData();
	- }
	-
	- void SetMetrics(const std::vector<mitk::ClusteringMetric *> &Metrics);
	-
	- void SetTracts1(const std::vector<FiberBundle::Pointer> &Tracts1);
	-
	- void SetTracts2(const std::vector<FiberBundle::Pointer> &Tracts2);
	-
	- vnl_vector<float> GetMinDistances() const;
	-
	- vnl_vector<int> GetMinIndices() const;
	-
	- vnl_matrix<float> GetAllDistances() const;
	-
	-protected:
	-
	- void GenerateData() override;
	- std::vector< vnl_matrix<float> > ResampleFibers(FiberBundle::Pointer tractogram);
	- float calc_distance(const std::vector<vnl_matrix<float> > &T1, const std::vector<vnl_matrix<float> > &T2);
	-
	- TractDistanceFilter();
	- virtual ~TractDistanceFilter();
	-
	- std::vector<FiberBundle::Pointer> m_Tracts1;
	- std::vector<FiberBundle::Pointer> m_Tracts2;
	- unsigned int m_NumPoints;
	- std::vector<mitk::ClusteringMetric*> m_Metrics;
	- vnl_vector<float> m_MinDistances;
	- vnl_vector<int> m_MinIndices;
	- vnl_matrix<float> m_AllDistances;
	- boost::progress_display disp;
	-};
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkTractDistanceFilter.cpp"
	-#endif
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToFiberEndingsImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToFiberEndingsImageFilter.cpp
	deleted file mode 100644
	index b79d9e65ae..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToFiberEndingsImageFilter.cpp
	+++ /dev/null
	@@ -1,155 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#include "itkTractsToFiberEndingsImageFilter.h"
	-
	-// VTK
	-#include <vtkPolyLine.h>
	-#include <vtkCellArray.h>
	-#include <vtkCellData.h>
	-#include <boost/progress.hpp>
	-#include <mitkDiffusionFunctionCollection.h>
	-
	-namespace itk{
	-
	- template< class OutputImageType >
	- TractsToFiberEndingsImageFilter< OutputImageType >::TractsToFiberEndingsImageFilter()
	- : m_UpsamplingFactor(1)
	- , m_InvertImage(false)
	- , m_UseImageGeometry(false)
	- , m_BinaryOutput(false)
	- , m_InputImage(nullptr)
	- {
	-
	- }
	-
	- template< class OutputImageType >
	- TractsToFiberEndingsImageFilter< OutputImageType >::~TractsToFiberEndingsImageFilter()
	- {
	- }
	-
	- template< class OutputImageType >
	- void TractsToFiberEndingsImageFilter< OutputImageType >::GenerateData()
	- {
	- // generate upsampled image
	- mitk::BaseGeometry::Pointer geometry = m_FiberBundle->GetGeometry();
	- typename OutputImageType::Pointer outImage = this->GetOutput();
	-
	- // calculate new image parameters
	- itk::Vector<double, 3> newSpacing;
	- mitk::Point3D newOrigin;
	- itk::Matrix<double, 3, 3> newDirection;
	- ImageRegion<3> upsampledRegion;
	- if (m_UseImageGeometry && !m_InputImage.IsNull())
	- {
	- newSpacing = m_InputImage->GetSpacing()/m_UpsamplingFactor;
	- upsampledRegion = m_InputImage->GetLargestPossibleRegion();
	- newOrigin = m_InputImage->GetOrigin();
	- typename OutputImageType::RegionType::SizeType size = upsampledRegion.GetSize();
	- size[0] *= m_UpsamplingFactor;
	- size[1] *= m_UpsamplingFactor;
	- size[2] *= m_UpsamplingFactor;
	- upsampledRegion.SetSize(size);
	- newDirection = m_InputImage->GetDirection();
	- }
	- else
	- {
	- newSpacing = geometry->GetSpacing()/m_UpsamplingFactor;
	- newOrigin = geometry->GetOrigin();
	- mitk::Geometry3D::BoundsArrayType bounds = geometry->GetBounds();
	- newOrigin[0] += bounds.GetElement(0);
	- newOrigin[1] += bounds.GetElement(2);
	- newOrigin[2] += bounds.GetElement(4);
	-
	- for (int i=0; i<3; i++)
	- for (int j=0; j<3; j++)
	- newDirection[j][i] = geometry->GetMatrixColumn(i)[j];
	- upsampledRegion.SetSize(0, geometry->GetExtent(0)*m_UpsamplingFactor);
	- upsampledRegion.SetSize(1, geometry->GetExtent(1)*m_UpsamplingFactor);
	- upsampledRegion.SetSize(2, geometry->GetExtent(2)*m_UpsamplingFactor);
	- }
	- typename OutputImageType::RegionType::SizeType upsampledSize = upsampledRegion.GetSize();
	-
	- // apply new image parameters
	- outImage->SetSpacing( newSpacing );
	- outImage->SetOrigin( newOrigin );
	- outImage->SetDirection( newDirection );
	- outImage->SetRegions( upsampledRegion );
	- outImage->Allocate();
	-
	- int w = upsampledSize[0];
	- int h = upsampledSize[1];
	- int d = upsampledSize[2];
	-
	- // set/initialize output
	- OutPixelType* outImageBufferPointer = (OutPixelType*)outImage->GetBufferPointer();
	- for (int i=0; i<whd; i++)
	- outImageBufferPointer[i] = 0;
	-
	- // resample fiber bundle
	- vtkSmartPointer<vtkPolyData> fiberPolyData = m_FiberBundle->GetFiberPolyData();
	-
	- int numFibers = m_FiberBundle->GetNumFibers();
	- boost::progress_display disp(numFibers);
	- for( int i=0; i<numFibers; i++ )
	- {
	- ++disp;
	- vtkCell* cell = fiberPolyData->GetCell(i);
	- int numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- // fill output image
	- if (numPoints>0)
	- {
	- itk::Point<float, 3> vertex = mitk::imv::GetItkPoint(points->GetPoint(0));
	- itk::Index<3> index;
	- outImage->TransformPhysicalPointToIndex(vertex, index);
	- if (upsampledRegion.IsInside(index))
	- {
	- if (m_BinaryOutput)
	- {
	- outImage->SetPixel(index, 1);
	- }
	- else
	- {
	- outImage->SetPixel(index, outImage->GetPixel(index)+1);
	- }
	- }
	- }
	-
	- if (numPoints>=2)
	- {
	- itk::Point<float, 3> vertex = mitk::imv::GetItkPoint(points->GetPoint(numPoints-1));
	- itk::Index<3> index;
	- outImage->TransformPhysicalPointToIndex(vertex, index);
	- if (upsampledRegion.IsInside(index))
	- {
	- if (m_BinaryOutput)
	- {
	- outImage->SetPixel(index, 1);
	- }
	- else
	- {
	- outImage->SetPixel(index, outImage->GetPixel(index)+1);
	- }
	- }
	- }
	- }
	-
	- if (m_InvertImage)
	- for (int i=0; i<whd; i++)
	- outImageBufferPointer[i] = 1-outImageBufferPointer[i];
	- }
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToFiberEndingsImageFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToFiberEndingsImageFilter.h
	deleted file mode 100644
	index 7b9598daaa..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToFiberEndingsImageFilter.h
	+++ /dev/null
	@@ -1,84 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef __itkTractsToFiberEndingsImageFilter_h__
	-#define __itkTractsToFiberEndingsImageFilter_h__
	-
	-#include <itkImageSource.h>
	-#include <itkImage.h>
	-#include <itkVectorContainer.h>
	-#include <itkRGBAPixel.h>
	-#include <mitkFiberBundle.h>
	-
	-namespace itk{
	-
	-/**
	-* \brief Generates image where the pixel values are set according to the number of fibers ending in the voxel. */
	-
	-template< class OutputImageType >
	-class TractsToFiberEndingsImageFilter : public ImageSource< OutputImageType >
	-{
	-
	-public:
	- typedef TractsToFiberEndingsImageFilter Self;
	- typedef ProcessObject Superclass;
	- typedef SmartPointer< Self > Pointer;
	- typedef SmartPointer< const Self > ConstPointer;
	-
	- typedef typename OutputImageType::PixelType OutPixelType;
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- itkTypeMacro( TractsToFiberEndingsImageFilter, ImageSource )
	-
	- / Upsampling factor /
	- itkSetMacro( UpsamplingFactor, float)
	- itkGetMacro( UpsamplingFactor, float)
	-
	- / Invert Image /
	- itkSetMacro( InvertImage, bool)
	- itkGetMacro( InvertImage, bool)
	-
	- itkSetMacro( FiberBundle, mitk::FiberBundle::Pointer)
	- itkSetMacro( InputImage, typename OutputImageType::Pointer)
	-
	- / Use input image geometry to initialize output image /
	- itkSetMacro( UseImageGeometry, bool)
	- itkGetMacro( UseImageGeometry, bool)
	-
	- itkSetMacro( BinaryOutput, bool)
	-
	- void GenerateData() override;
	-
	-protected:
	-
	- TractsToFiberEndingsImageFilter();
	- virtual ~TractsToFiberEndingsImageFilter();
	-
	- mitk::FiberBundle::Pointer m_FiberBundle; ///< input fiber bundle
	- float m_UpsamplingFactor; ///< use higher resolution for ouput image
	- bool m_InvertImage; ///< voxelvalue = 1-voxelvalue
	- bool m_UseImageGeometry; ///< output image is given other geometry than fiberbundle (input image geometry)
	- bool m_BinaryOutput;
	- typename OutputImageType::Pointer m_InputImage;
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkTractsToFiberEndingsImageFilter.cpp"
	-#endif
	-
	-#endif // __itkTractsToFiberEndingsImageFilter_h__
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToRgbaImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToRgbaImageFilter.cpp
	deleted file mode 100644
	index cf55d71dcc..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToRgbaImageFilter.cpp
	+++ /dev/null
	@@ -1,187 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#include "itkTractsToRgbaImageFilter.h"
	-
	-// VTK
	-#include <vtkPolyLine.h>
	-#include <vtkCellArray.h>
	-#include <vtkCellData.h>
	-
	-// misc
	-#include <math.h>
	-#include <boost/progress.hpp>
	-#include <mitkDiffusionFunctionCollection.h>
	-
	-namespace itk{
	-
	-template< class OutputImageType >
	-TractsToRgbaImageFilter< OutputImageType >::TractsToRgbaImageFilter()
	- : m_UpsamplingFactor(1)
	- , m_UseImageGeometry(false)
	- , m_InputImage(nullptr)
	-{
	-
	-}
	-
	-template< class OutputImageType >
	-TractsToRgbaImageFilter< OutputImageType >::~TractsToRgbaImageFilter()
	-{
	-}
	-
	-template< class OutputImageType >
	-void TractsToRgbaImageFilter< OutputImageType >::GenerateData()
	-{
	- if(&typeid(OutPixelType) != &typeid(itk::RGBAPixel<unsigned char>))
	- return;
	-
	- // generate upsampled image
	- mitk::BaseGeometry::Pointer geometry = m_FiberBundle->GetGeometry();
	- typename OutputImageType::Pointer outImage = this->GetOutput();
	-
	- // calculate new image parameters
	- itk::Vector<double,3> newSpacing;
	- mitk::Point3D newOrigin;
	- itk::Matrix<double, 3, 3> newDirection;
	- ImageRegion<3> upsampledRegion;
	- if (m_UseImageGeometry && !m_InputImage.IsNull())
	- {
	- newSpacing = m_InputImage->GetSpacing()/m_UpsamplingFactor;
	- upsampledRegion = m_InputImage->GetLargestPossibleRegion();
	- newOrigin = m_InputImage->GetOrigin();
	- typename OutputImageType::RegionType::SizeType size = upsampledRegion.GetSize();
	- size[0] *= m_UpsamplingFactor;
	- size[1] *= m_UpsamplingFactor;
	- size[2] *= m_UpsamplingFactor;
	- upsampledRegion.SetSize(size);
	- newDirection = m_InputImage->GetDirection();
	- }
	- else
	- {
	- newSpacing = geometry->GetSpacing()/m_UpsamplingFactor;
	- newOrigin = geometry->GetOrigin();
	- mitk::Geometry3D::BoundsArrayType bounds = geometry->GetBounds();
	- newOrigin[0] += bounds.GetElement(0);
	- newOrigin[1] += bounds.GetElement(2);
	- newOrigin[2] += bounds.GetElement(4);
	-
	- for (int i=0; i<3; i++)
	- for (int j=0; j<3; j++)
	- newDirection[j][i] = geometry->GetMatrixColumn(i)[j];
	- upsampledRegion.SetSize(0, geometry->GetExtent(0)*m_UpsamplingFactor);
	- upsampledRegion.SetSize(1, geometry->GetExtent(1)*m_UpsamplingFactor);
	- upsampledRegion.SetSize(2, geometry->GetExtent(2)*m_UpsamplingFactor);
	- }
	- typename OutputImageType::RegionType::SizeType upsampledSize = upsampledRegion.GetSize();
	-
	- // apply new image parameters
	- outImage->SetSpacing( newSpacing );
	- outImage->SetOrigin( newOrigin );
	- outImage->SetDirection( newDirection );
	- outImage->SetRegions( upsampledRegion );
	- outImage->Allocate();
	- outImage->FillBuffer(0.0);
	-
	- itk::Image< itk::RGBAPixel<double>, 3 >::Pointer double_out = itk::Image< itk::RGBAPixel<double>, 3 >::New();
	- double_out->SetSpacing( newSpacing );
	- double_out->SetOrigin( newOrigin );
	- double_out->SetDirection( newDirection );
	- double_out->SetRegions( upsampledRegion );
	- double_out->Allocate();
	- double_out->FillBuffer(0.0);
	-
	- vtkSmartPointer<vtkPolyData> fiberPolyData = m_FiberBundle->GetFiberPolyData();
	- int numFibers = m_FiberBundle->GetNumFibers();
	-
	- float scale = 100 * pow((float)m_UpsamplingFactor,3);
	- boost::progress_display disp(numFibers);
	- for( int i=0; i<numFibers; ++i )
	- {
	- ++disp;
	- vtkCell* cell = fiberPolyData->GetCell(i);
	- int numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- for( int j=0; j<numPoints-1; ++j)
	- {
	- Point<float, 3> startVertex = mitk::imv::GetItkPoint(points->GetPoint(j));
	- Index<3> startIndex;
	- ContinuousIndex<float, 3> startIndexCont;
	- double_out->TransformPhysicalPointToIndex(startVertex, startIndex);
	- double_out->TransformPhysicalPointToContinuousIndex(startVertex, startIndexCont);
	-
	- Point<float, 3> endVertex = mitk::imv::GetItkPoint(points->GetPoint(j + 1));
	- Index<3> endIndex;
	- ContinuousIndex<float, 3> endIndexCont;
	- double_out->TransformPhysicalPointToIndex(endVertex, endIndex);
	- double_out->TransformPhysicalPointToContinuousIndex(endVertex, endIndexCont);
	-
	- Vector<float, 3> dir;
	- dir[0] = fabs(endVertex[0]-startVertex[0]);
	- dir[1] = fabs(endVertex[1]-startVertex[1]);
	- dir[2] = fabs(endVertex[2]-startVertex[2]);
	- dir.Normalize();
	-
	- std::vector< std::pair< itk::Index<3>, double > > segments = mitk::imv::IntersectImage(newSpacing, startIndex, endIndex, startIndexCont, endIndexCont);
	- for (std::pair< itk::Index<3>, double > segment : segments)
	- {
	- if (!double_out->GetLargestPossibleRegion().IsInside(segment.first))
	- continue;
	-
	- itk::RGBAPixel<double> pix = double_out->GetPixel(segment.first);
	- pix[0] += dir[0] * scale;
	- pix[1] += dir[1] * scale;
	- pix[2] += dir[2] * scale;
	- pix[3] += segment.second * scale;
	-
	- double_out->SetPixel(segment.first, pix);
	- }
	- }
	-
	- float maxRgb = 0.000000001;
	- float maxInt = 0.000000001;
	- int w = upsampledSize[0];
	- int h = upsampledSize[1];
	- int d = upsampledSize[2];
	- int numPix = whd*4;
	-
	- double* buffer = (double*)double_out->GetBufferPointer();
	- // calc maxima
	- for(int i=0; i<numPix; i++)
	- {
	- if((i-3)%4 != 0)
	- {
	- if(buffer[i] > maxRgb)
	- maxRgb = buffer[i];
	- }
	- else
	- {
	- if(buffer[i] > maxInt)
	- maxInt = buffer[i];
	- }
	- }
	-
	- // write output, normalized uchar 0..255
	- unsigned char* outImageBufferPointer = (unsigned char*)outImage->GetBufferPointer();
	- for(int i=0; i<numPix; i++)
	- {
	- if((i-3)%4 != 0)
	- outImageBufferPointer[i] = (unsigned char) (255.0 * buffer[i] / maxRgb);
	- else
	- outImageBufferPointer[i] = (unsigned char) (255.0 * buffer[i] / maxInt);
	- }
	- }
	-}
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToRgbaImageFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToRgbaImageFilter.h
	deleted file mode 100644
	index 78e6d1eac7..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToRgbaImageFilter.h
	+++ /dev/null
	@@ -1,78 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef __itkTractsToRgbaImageFilter_h__
	-#define __itkTractsToRgbaImageFilter_h__
	-
	-#include <itkImageSource.h>
	-#include <itkImage.h>
	-#include <itkVectorContainer.h>
	-#include <itkRGBAPixel.h>
	-#include <mitkFiberBundle.h>
	-
	-namespace itk{
	-
	-/**
	-* \brief Generates RGBA image from the input fibers where color values are set according to the local fiber directions. */
	-
	-template< class OutputImageType >
	-class TractsToRgbaImageFilter : public ImageSource< OutputImageType >
	-{
	-
	-public:
	- typedef TractsToRgbaImageFilter Self;
	- typedef ProcessObject Superclass;
	- typedef SmartPointer< Self > Pointer;
	- typedef SmartPointer< const Self > ConstPointer;
	-
	- typedef typename OutputImageType::PixelType OutPixelType;
	- typedef itk::Image<unsigned char, 3> InputImageType;
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- itkTypeMacro( TractsToRgbaImageFilter, ImageSource )
	-
	- / Upsampling factor /
	- itkSetMacro( UpsamplingFactor, float)
	- itkGetMacro( UpsamplingFactor, float)
	-
	- itkSetMacro( FiberBundle, mitk::FiberBundle::Pointer)
	- itkSetMacro( InputImage, typename InputImageType::Pointer)
	-
	- / Use input image geometry to initialize output image /
	- itkSetMacro( UseImageGeometry, bool)
	- itkGetMacro( UseImageGeometry, bool)
	-
	-
	- void GenerateData();
	-
	-protected:
	-
	- TractsToRgbaImageFilter();
	- virtual ~TractsToRgbaImageFilter();
	-
	- mitk::FiberBundle::Pointer m_FiberBundle; ///< input fiber bundle
	- float m_UpsamplingFactor; ///< use higher resolution for ouput image
	- bool m_UseImageGeometry; ///< output image is given other geometry than fiberbundle (input image geometry)
	- typename InputImageType::Pointer m_InputImage;
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkTractsToRgbaImageFilter.cpp"
	-#endif
	-
	-#endif // __itkTractsToRgbaImageFilter_h__
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.cpp
	deleted file mode 100644
	index 091edea234..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.cpp
	+++ /dev/null
	@@ -1,396 +0,0 @@
	-#include "itkTractsToVectorImageFilter.h"
	-
	-// VTK
	-#include <vtkPolyLine.h>
	-#include <vtkCellArray.h>
	-#include <vtkCellData.h>
	-
	-// ITK
	-#include <itkTimeProbe.h>
	-#include <itkImageRegionIterator.h>
	-
	-// misc
	-#define _USE_MATH_DEFINES
	-#include <cmath>
	-#include <boost/progress.hpp>
	-#include <mitkDiffusionFunctionCollection.h>
	-
	-namespace itk{
	-
	-static inline bool CompareVectorLengths(const vnl_vector_fixed< double, 3 >& v1, const vnl_vector_fixed< double, 3 >& v2)
	-{
	- return (v1.magnitude()>v2.magnitude());
	-}
	-
	-template< class PixelType >
	-TractsToVectorImageFilter< PixelType >::TractsToVectorImageFilter():
	- m_NormalizationMethod(GLOBAL_MAX),
	- m_AngularThreshold(0.7),
	- m_Epsilon(0.999),
	- m_MaxNumDirections(3),
	- m_SizeThreshold(0.3),
	- m_OnlyUseMaskGeometry(false)
	-{
	- this->SetNumberOfRequiredOutputs(1);
	-}
	-
	-
	-template< class PixelType >
	-TractsToVectorImageFilter< PixelType >::~TractsToVectorImageFilter()
	-{
	-}
	-
	-
	-template< class PixelType >
	-vnl_vector_fixed<double, 3> TractsToVectorImageFilter< PixelType >::GetVnlVector(double point[])
	-{
	- vnl_vector_fixed<double, 3> vnlVector;
	- vnlVector[0] = point[0];
	- vnlVector[1] = point[1];
	- vnlVector[2] = point[2];
	- return vnlVector;
	-}
	-
	-template< class PixelType >
	-void TractsToVectorImageFilter< PixelType >::GenerateData()
	-{
	- mitk::BaseGeometry::Pointer geometry = m_FiberBundle->GetGeometry();
	-
	- // calculate new image parameters
	- itk::Vector<double> spacing3;
	- itk::Point<double> origin3;
	- itk::Matrix<double, 3, 3> direction3;
	- ImageRegion<3> imageRegion3;
	- if (!m_MaskImage.IsNull())
	- {
	- spacing3 = m_MaskImage->GetSpacing();
	- imageRegion3 = m_MaskImage->GetLargestPossibleRegion();
	- origin3 = m_MaskImage->GetOrigin();
	- direction3 = m_MaskImage->GetDirection();
	- }
	- else
	- {
	- spacing3 = geometry->GetSpacing();
	- origin3 = geometry->GetOrigin();
	- mitk::BaseGeometry::BoundsArrayType bounds = geometry->GetBounds();
	- origin3[0] += bounds.GetElement(0);
	- origin3[1] += bounds.GetElement(2);
	- origin3[2] += bounds.GetElement(4);
	-
	- for (int i=0; i<3; i++)
	- for (int j=0; j<3; j++)
	- direction3[j][i] = geometry->GetMatrixColumn(i)[j];
	- imageRegion3.SetSize(0, geometry->GetExtent(0)+1);
	- imageRegion3.SetSize(1, geometry->GetExtent(1)+1);
	- imageRegion3.SetSize(2, geometry->GetExtent(2)+1);
	-
	-
	- m_MaskImage = ItkUcharImgType::New();
	- m_MaskImage->SetSpacing( spacing3 );
	- m_MaskImage->SetOrigin( origin3 );
	- m_MaskImage->SetDirection( direction3 );
	- m_MaskImage->SetRegions( imageRegion3 );
	- m_MaskImage->Allocate();
	- m_MaskImage->FillBuffer(1);
	- }
	- OutputImageType::RegionType::SizeType outImageSize = imageRegion3.GetSize();
	- m_OutImageSpacing = m_MaskImage->GetSpacing();
	- m_ClusteredDirectionsContainer = ContainerType::New();
	-
	- // initialize num directions image
	- m_NumDirectionsImage = ItkUcharImgType::New();
	- m_NumDirectionsImage->SetSpacing( spacing3 );
	- m_NumDirectionsImage->SetOrigin( origin3 );
	- m_NumDirectionsImage->SetDirection( direction3 );
	- m_NumDirectionsImage->SetRegions( imageRegion3 );
	- m_NumDirectionsImage->Allocate();
	- m_NumDirectionsImage->FillBuffer(0);
	-
	- itk::Vector<double, 4> spacing4;
	- itk::Point<float, 4> origin4;
	- itk::Matrix<double, 4, 4> direction4;
	- itk::ImageRegion<4> imageRegion4;
	-
	- spacing4[0] = spacing3[0]; spacing4[1] = spacing3[1]; spacing4[2] = spacing3[2]; spacing4[3] = 1;
	- origin4[0] = origin3[0]; origin4[1] = origin3[1]; origin4[2] = origin3[2]; origin3[3] = 0;
	- for (int r=0; r<3; r++)
	- for (int c=0; c<3; c++)
	- direction4[r][c] = direction3[r][c];
	- direction4[3][3] = 1;
	- imageRegion4.SetSize(0, imageRegion3.GetSize()[0]);
	- imageRegion4.SetSize(1, imageRegion3.GetSize()[1]);
	- imageRegion4.SetSize(2, imageRegion3.GetSize()[2]);
	- imageRegion4.SetSize(3, m_MaxNumDirections*3);
	-
	- m_DirectionImage = ItkDirectionImageType::New();
	- m_DirectionImage->SetSpacing( spacing4 );
	- m_DirectionImage->SetOrigin( origin4 );
	- m_DirectionImage->SetDirection( direction4 );
	- m_DirectionImage->SetRegions( imageRegion4 );
	- m_DirectionImage->Allocate();
	- m_DirectionImage->FillBuffer(0.0);
	-
	- // iterate over all fibers
	- vtkSmartPointer<vtkPolyData> fiberPolyData = m_FiberBundle->GetFiberPolyData();
	- int numFibers = m_FiberBundle->GetNumFibers();
	- m_DirectionsContainer = ContainerType::New();
	-
	- VectorContainer< unsigned int, std::vector< double > >::Pointer peakLengths = VectorContainer< unsigned int, std::vector< double > >::New();
	-
	- MITK_INFO << "Generating directions from tractogram";
	- boost::progress_display disp(numFibers);
	- for( int i=0; i<numFibers; i++ )
	- {
	- ++disp;
	- vtkCell* cell = fiberPolyData->GetCell(i);
	- int numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	- if (numPoints<2)
	- continue;
	-
	- vnl_vector_fixed<double, 3> dir;
	- vnl_vector<double> v;
	-
	- float fiberWeight = m_FiberBundle->GetFiberWeight(i);
	-
	- for( int j=0; j<numPoints-1; j++)
	- {
	- itk::Point<float, 3> startVertex = mitk::imv::GetItkPoint(points->GetPoint(j));
	- itk::Index<3> startIndex;
	- itk::ContinuousIndex<float, 3> startIndexCont;
	- m_MaskImage->TransformPhysicalPointToIndex(startVertex, startIndex);
	- m_MaskImage->TransformPhysicalPointToContinuousIndex(startVertex, startIndexCont);
	-
	- itk::Point<float, 3> endVertex = mitk::imv::GetItkPoint(points->GetPoint(j + 1));
	- itk::Index<3> endIndex;
	- itk::ContinuousIndex<float, 3> endIndexCont;
	- m_MaskImage->TransformPhysicalPointToIndex(endVertex, endIndex);
	- m_MaskImage->TransformPhysicalPointToContinuousIndex(endVertex, endIndexCont);
	-
	- dir[0] = endVertex[0]-startVertex[0];
	- dir[1] = endVertex[1]-startVertex[1];
	- dir[2] = endVertex[2]-startVertex[2];
	- if (dir.is_zero())
	- continue;
	- dir.normalize();
	-
	- std::vector< std::pair< itk::Index<3>, double > > segments = mitk::imv::IntersectImage(spacing3, startIndex, endIndex, startIndexCont, endIndexCont);
	- for (std::pair< itk::Index<3>, double > segment : segments)
	- {
	- if (!m_MaskImage->GetLargestPossibleRegion().IsInside(segment.first) \|\| (!m_OnlyUseMaskGeometry && m_MaskImage->GetPixel(segment.first)==0))
	- continue;
	-
	- // add direction to container
	- unsigned int idx = segment.first[0] + outImageSize[0](segment.first[1] + outImageSize[1]segment.first[2]);
	- DirectionContainerType::Pointer dirCont;
	- if (m_DirectionsContainer->IndexExists(idx))
	- {
	- peakLengths->ElementAt(idx).push_back(fiberWeight*segment.second);
	-
	- dirCont = m_DirectionsContainer->GetElement(idx);
	- if (dirCont.IsNull())
	- {
	- dirCont = DirectionContainerType::New();
	- dirCont->push_back(dir);
	- m_DirectionsContainer->InsertElement(idx, dirCont);
	- }
	- else
	- dirCont->push_back(dir);
	- }
	- else
	- {
	- dirCont = DirectionContainerType::New();
	- dirCont->push_back(dir);
	- m_DirectionsContainer->InsertElement(idx, dirCont);
	-
	- std::vector< double > lengths; lengths.push_back(fiberWeight*segment.second);
	- peakLengths->InsertElement(idx, lengths);
	- }
	- }
	-
	- }
	- }
	-
	- itk::ImageRegionIterator<ItkUcharImgType> dirIt(m_NumDirectionsImage, m_NumDirectionsImage->GetLargestPossibleRegion());
	-
	- MITK_INFO << "Clustering directions";
	- float max_dir_mag = 0;
	- boost::progress_display disp2(outImageSize[0]outImageSize[1]outImageSize[2]);
	- while(!dirIt.IsAtEnd())
	- {
	- ++disp2;
	- OutputImageType::IndexType idx3 = dirIt.GetIndex();
	- int idx_lin = idx3[0]+(idx3[1]+idx3[2]outImageSize[1])outImageSize[0];
	-
	- itk::Index<4> idx4; idx4[0] = idx3[0]; idx4[1] = idx3[1]; idx4[2] = idx3[2];
	-
	- if (!m_DirectionsContainer->IndexExists(idx_lin))
	- {
	- ++dirIt;
	- continue;
	- }
	- DirectionContainerType::Pointer dirCont = m_DirectionsContainer->GetElement(idx_lin);
	- if (dirCont.IsNull() \|\| dirCont->empty())
	- {
	- ++dirIt;
	- continue;
	- }
	-
	- DirectionContainerType::Pointer directions;
	- if (m_MaxNumDirections>0)
	- {
	- directions = FastClustering(dirCont, peakLengths->GetElement(idx_lin));
	- std::sort( directions->begin(), directions->end(), CompareVectorLengths );
	- }
	- else
	- directions = dirCont;
	-
	- unsigned int numDir = directions->size();
	- if (m_MaxNumDirections>0 && numDir>m_MaxNumDirections)
	- numDir = m_MaxNumDirections;
	-
	- float voxel_max_mag = 0;
	- for (unsigned int i=0; i<numDir; i++)
	- {
	- DirectionType dir = directions->at(i);
	- float mag = dir.magnitude();
	-
	- if (mag>voxel_max_mag)
	- voxel_max_mag = mag;
	- if (mag>max_dir_mag)
	- max_dir_mag = mag;
	- }
	-
	- int count = 0;
	- for (unsigned int i=0; i<numDir; i++)
	- {
	- DirectionType dir = directions->at(i);
	- count++;
	-
	- float mag = dir.magnitude();
	- if (m_NormalizationMethod==MAX_VEC_NORM && voxel_max_mag>mitk::eps)
	- dir /= voxel_max_mag;
	- else if (m_NormalizationMethod==SINGLE_VEC_NORM && mag>mitk::eps)
	- dir.normalize();
	-
	- for (unsigned int j = 0; j<3; j++)
	- {
	- idx4[3] = i*3 + j;
	- m_DirectionImage->SetPixel(idx4, dir[j]);
	- }
	- }
	- dirIt.Set(count);
	- ++dirIt;
	- }
	-
	- if (m_NormalizationMethod==GLOBAL_MAX && max_dir_mag>0)
	- {
	- itk::ImageRegionIterator<ItkDirectionImageType> dirImgIt(m_DirectionImage, m_DirectionImage->GetLargestPossibleRegion());
	- while(!dirImgIt.IsAtEnd())
	- {
	- dirImgIt.Set(dirImgIt.Get()/max_dir_mag);
	- ++dirImgIt;
	- }
	- }
	-}
	-
	-
	-template< class PixelType >
	-TractsToVectorImageFilter< PixelType >::DirectionContainerType::Pointer TractsToVectorImageFilter< PixelType >::FastClustering(DirectionContainerType::Pointer inDirs, std::vector< double > lengths)
	-{
	- DirectionContainerType::Pointer outDirs = DirectionContainerType::New();
	- if (inDirs->size()<2)
	- {
	- if (inDirs->size()==1)
	- inDirs->SetElement(0, inDirs->at(0)*lengths.at(0));
	- return inDirs;
	- }
	-
	- DirectionType oldMean, currentMean;
	- std::vector< int > touched;
	-
	- // initialize
	- touched.resize(inDirs->size(), 0);
	- bool free = true;
	- currentMean = inDirs->at(0); // initialize first seed
	- currentMean.normalize();
	- double length = lengths.at(0);
	- touched[0] = 1;
	- std::vector< double > newLengths;
	- bool meanChanged = false;
	-
	- double max = 0;
	- while (free)
	- {
	- oldMean.fill(0.0);
	-
	- // start mean-shift clustering
	- double angle = 0;
	-
	- while (fabs(dot_product(currentMean, oldMean))<0.99)
	- {
	- oldMean = currentMean;
	- currentMean.fill(0.0);
	- for (unsigned int i=0; i<inDirs->size(); i++)
	- {
	- angle = dot_product(oldMean, inDirs->at(i));
	- if (angle>=m_AngularThreshold)
	- {
	- currentMean += inDirs->at(i);
	- if (meanChanged)
	- length += lengths.at(i);
	- touched[i] = 1;
	- meanChanged = true;
	- }
	- else if (-angle>=m_AngularThreshold)
	- {
	- currentMean -= inDirs->at(i);
	- if (meanChanged)
	- length += lengths.at(i);
	- touched[i] = 1;
	- meanChanged = true;
	- }
	- }
	- if(!meanChanged)
	- currentMean = oldMean;
	- else
	- currentMean.normalize();
	- }
	-
	- // found stable mean
	- outDirs->push_back(currentMean);
	- newLengths.push_back(length);
	- if (length>max)
	- max = length;
	-
	- // find next unused seed
	- free = false;
	- for (unsigned int i=0; i<touched.size(); i++)
	- if (touched[i]==0)
	- {
	- currentMean = inDirs->at(i);
	- free = true;
	- meanChanged = false;
	- length = lengths.at(i);
	- touched[i] = 1;
	- break;
	- }
	- }
	-
	- if (inDirs->size()==outDirs->size())
	- {
	- if (max>0)
	- {
	- for (unsigned int i=0; i<outDirs->size(); i++)
	- outDirs->SetElement(i, outDirs->at(i)*newLengths.at(i));
	- }
	- return outDirs;
	- }
	- else
	- return FastClustering(outDirs, newLengths);
	-}
	-
	-}
	-
	-
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.h
	deleted file mode 100644
	index 18e494f856..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.h
	+++ /dev/null
	@@ -1,104 +0,0 @@
	-#ifndef __itkTractsToVectorImageFilter_h__
	-#define __itkTractsToVectorImageFilter_h__
	-
	-// MITK
	-#include <mitkFiberBundle.h>
	-
	-// ITK
	-#include <itkImageSource.h>
	-#include <itkVectorImage.h>
	-
	-// VTK
	-#include <vtkSmartPointer.h>
	-#include <vtkPolyData.h>
	-#include <vtkCellArray.h>
	-#include <vtkPoints.h>
	-#include <vtkPolyLine.h>
	-
	-namespace itk{
	-
	-/**
	-* \brief Extracts the voxel-wise main directions of the input fiber bundle. */
	-
	-template< class PixelType >
	-class TractsToVectorImageFilter : public ImageSource< Image< PixelType, 4 > >
	-{
	-
	-public:
	-
	- enum NormalizationMethods {
	- GLOBAL_MAX, ///< global maximum normalization
	- SINGLE_VEC_NORM, ///< normalize the single peaks to length 1
	- MAX_VEC_NORM ///< normalize all peaks according to their length in comparison to the largest peak in the voxel (0-1)
	- };
	-
	- typedef TractsToVectorImageFilter Self;
	- typedef ProcessObject Superclass;
	- typedef SmartPointer< Self > Pointer;
	- typedef SmartPointer< const Self > ConstPointer;
	-
	- typedef itk::Vector<float,3> OutputVectorType;
	- typedef itk::Image<OutputVectorType, 3> OutputImageType;
	- typedef std::vector< OutputImageType::Pointer > OutputImageContainerType;
	-
	- typedef vnl_vector_fixed< double, 3 > DirectionType;
	- typedef VectorContainer< unsigned int, DirectionType > DirectionContainerType;
	- typedef VectorContainer< unsigned int, DirectionContainerType::Pointer > ContainerType;
	- typedef Image< PixelType, 4 > ItkDirectionImageType;
	- typedef itk::Image<unsigned char, 3> ItkUcharImgType;
	- typedef itk::Image<double, 3> ItkDoubleImgType;
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- itkTypeMacro( TractsToVectorImageFilter, ImageSource )
	-
	- itkSetMacro( SizeThreshold, float)
	- itkGetMacro( SizeThreshold, float)
	- itkSetMacro( AngularThreshold, float) ///< cluster directions that are closer together than the specified threshold
	- itkGetMacro( AngularThreshold, float) ///< cluster directions that are closer together than the specified threshold
	- itkSetMacro( NormalizationMethod, NormalizationMethods) ///< normalization method of peaks
	- itkSetMacro( MaxNumDirections, unsigned long) ///< If more directions are extracted, only the largest are kept.
	- itkGetMacro( MaxNumDirections, unsigned long) ///< If more directions are extracted, only the largest are kept.
	- itkSetMacro( MaskImage, ItkUcharImgType::Pointer) ///< only process voxels inside mask
	- itkSetMacro( FiberBundle, mitk::FiberBundle::Pointer) ///< input fiber bundle
	- itkSetMacro( OnlyUseMaskGeometry, bool) ///< don't use content of mask image, only use it's geometry
	- itkGetMacro( ClusteredDirectionsContainer, ContainerType::Pointer) ///< output directions
	- itkGetMacro( NumDirectionsImage, ItkUcharImgType::Pointer) ///< number of directions per voxel
	- itkGetMacro( DirectionImage, typename ItkDirectionImageType::Pointer) ///< output directions
	-
	- void GenerateData() override;
	-
	-protected:
	-
	- DirectionContainerType::Pointer FastClustering(DirectionContainerType::Pointer inDirs, std::vector< double > lengths); ///< cluster fiber directions
	-
	- vnl_vector_fixed<double, 3> GetVnlVector(double point[3]);
	-
	-
	- TractsToVectorImageFilter();
	- ~TractsToVectorImageFilter() override;
	-
	- NormalizationMethods m_NormalizationMethod; ///< normalization method of peaks
	- mitk::FiberBundle::Pointer m_FiberBundle; ///< input fiber bundle
	- float m_AngularThreshold; ///< cluster directions that are closer together than the specified threshold
	- float m_Epsilon; ///< epsilon for vector equality check
	- ItkUcharImgType::Pointer m_MaskImage; ///< only voxels inside the binary mask are processed
	- itk::Vector<float> m_OutImageSpacing; ///< spacing of output image
	- ContainerType::Pointer m_DirectionsContainer; ///< container for fiber directions
	- unsigned long m_MaxNumDirections; ///< if more directions per voxel are extracted, only the largest are kept
	- float m_SizeThreshold;
	- bool m_OnlyUseMaskGeometry;
	-
	- // output datastructures
	- typename ItkDirectionImageType::Pointer m_DirectionImage;
	- ContainerType::Pointer m_ClusteredDirectionsContainer; ///< contains direction vectors for each voxel
	- ItkUcharImgType::Pointer m_NumDirectionsImage; ///< shows number of fibers per voxel
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkTractsToVectorImageFilter.cpp"
	-#endif
	-
	-#endif // __itkTractsToVectorImageFilter_h__
	diff --git a/Modules/DiffusionImaging/FiberTracking/CMakeLists.txt b/Modules/DiffusionImaging/FiberTracking/CMakeLists.txt
	deleted file mode 100644
	index 6907c24651..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/CMakeLists.txt
	+++ /dev/null
	@@ -1,47 +0,0 @@
	-
	-set(_module_deps MitkDiffusionCore MitkGraphAlgorithms MitkCLVigraRandomForest)
	-
	-mitk_check_module_dependencies(
	- MODULES ${_module_deps}
	- MISSING_DEPENDENCIES_VAR _missing_deps
	-)
	-
	-if(NOT _missing_deps)
	-
	- set(lut_url http://mitk.org/download/data/FibertrackingLUT.tar.gz)
	- set(lut_tarball ${CMAKE_CURRENT_BINARY_DIR}/FibertrackingLUT.tar.gz)
	- file(DOWNLOAD ${lut_url} ${lut_tarball}
	- EXPECTED_MD5 38ecb6d4a826c9ebb0f4965eb9aeee44
	- TIMEOUT 60
	- STATUS status
	- SHOW_PROGRESS
	- )
	-
	- list(GET status 0 status_code)
	- list(GET status 1 status_msg)
	-
	- if(NOT status_code EQUAL 0)
	- message(SEND_ERROR "${status_msg} (error code ${status_code})")
	- endif()
	-
	- file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/Resources)
	- execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf ../FibertrackingLUT.tar.gz
	- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/Resources
	- RESULT_VARIABLE result
	- ERROR_VARIABLE err_msg)
	- if(result)
	- message(SEND_ERROR "Unpacking FibertrackingLUT.tar.gz failed: ${err_msg}")
	- endif()
	-
	-endif()
	-
	-MITK_CREATE_MODULE(
	- SUBPROJECTS MITK-DTI
	- INCLUDE_DIRS Fiberfox Fiberfox/SignalModels Fiberfox/Sequences Algorithms Algorithms/TrackingHandlers Algorithms/ClusteringMetrics Algorithms/GibbsTracking Algorithms/StochasticTracking IODataStructures IODataStructures/FiberBundle IODataStructures/PlanarFigureComposite Rendering ${CMAKE_CURRENT_BINARY_DIR}
	- DEPENDS ${_module_deps}
	- PACKAGE_DEPENDS PUBLIC ITK\|ITKFFT ITK\|ITKDiffusionTensorImage Vigra HDF5 OpenMP\|OpenMP_CXX
	-)
	-
	-if(MODULE_IS_ENABLED)
	- add_subdirectory(Testing)
	-endif()
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/Sequences/mitkAcquisitionType.h b/Modules/DiffusionImaging/FiberTracking/Fiberfox/Sequences/mitkAcquisitionType.h
	deleted file mode 100644
	index 91551e4a30..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/Sequences/mitkAcquisitionType.h
	+++ /dev/null
	@@ -1,67 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_KspaceReadout_H
	-#define _MITK_KspaceReadout_H
	-
	-#include <mitkFiberfoxParameters.h>
	-#include <itkSize.h>
	-
	-namespace mitk {
	-
	-/**
	- * \brief Abstract class for k-space acquisiton type (k-space trajectory and echo placement)
	- *
	- */
	-class AcquisitionType
	-{
	-public:
	-
	- AcquisitionType(FiberfoxParameters* parameters)
	- {
	- m_Parameters = parameters;
	- kxMax = static_cast<int>(m_Parameters->m_SignalGen.m_CroppedRegion.GetSize(0));
	- kyMax = static_cast<int>(m_Parameters->m_SignalGen.m_CroppedRegion.GetSize(1));
	- }
	- virtual ~AcquisitionType(){}
	-
	- virtual float GetTimeFromMaxEcho(const int& tick) = 0; ///< Time from maximum echo intensity in milliseconds
	- virtual float GetTimeFromLastDiffusionGradient(const int& tick) = 0; ///< Time passed since readout started in milliseconds
	- virtual float GetTimeFromRf(const int& tick) = 0; ///< Time passed since RF pulse was applied in milliseconds
	- virtual itk::Index< 2 > GetActualKspaceIndex(const int& tick) = 0; ///< Transfer simple image iterator index to desired k-space index (depends on k-space readout scheme)
	- virtual void AdjustEchoTime() = 0; ///< Depending on the k-space readout scheme and acquisition parameters the minimum TE varies. This has to be checked and adjusted in this method.
	- itk::Index< 2 > GetSymmetricIndex(const itk::Index< 2 >& index)
	- {
	- itk::Index< 2 > sym;
	- sym[0] = (kxMax-kxMax%2-index[0])%kxMax;
	- sym[1] = (kyMax-kyMax%2-index[1])%kyMax;
	- return sym;
	- }
	-
	-protected:
	-
	- FiberfoxParameters* m_Parameters;
	- itk::Size< 2 > m_Size;
	-
	- float dt; // time to read one k-space voxe
	- int kxMax;
	- int kyMax;
	-};
	-
	-}
	-
	-#endif
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/Sequences/mitkConventionalSpinEcho.h b/Modules/DiffusionImaging/FiberTracking/Fiberfox/Sequences/mitkConventionalSpinEcho.h
	deleted file mode 100644
	index 9655853a44..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/Sequences/mitkConventionalSpinEcho.h
	+++ /dev/null
	@@ -1,90 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_ConventionalSpinEcho_H
	-#define _MITK_ConventionalSpinEcho_H
	-
	-#include <mitkAcquisitionType.h>
	-
	-namespace mitk {
	-
	-/**
	- * \brief Conventional spin echo sequence. Cartesian readout. One echo and one excitation per k-space line.
	- *
	- */
	-class ConventionalSpinEcho : public AcquisitionType
	-{
	-public:
	-
	- float half_read_time;
	- ConventionalSpinEcho(FiberfoxParameters* parameters) : AcquisitionType(parameters)
	- {
	- dt = m_Parameters->m_SignalGen.m_tLine/kxMax; // time to read one k-space voxel
	-
	- half_read_time = kxMax * dt/2;
	- }
	- ~ConventionalSpinEcho() override
	- {}
	-
	- // one echo per k-space line
	- float GetTimeFromMaxEcho(const int& tick) override
	- {
	- float t = dt*(tick % kxMax + 0.5f) - half_read_time;
	- return t;
	- }
	-
	- float GetTimeFromLastDiffusionGradient(const int& tick) override
	- {
	- return (tick % kxMax)*dt;
	- }
	-
	- // time from max-echo + TE
	- float GetTimeFromRf(const int& tick) override
	- {
	- return m_Parameters->m_SignalGen.m_tEcho + GetTimeFromMaxEcho(tick);
	- }
	-
	- itk::Index< 2 > GetActualKspaceIndex(const int& tick) override
	- {
	- itk::Index< 2 > out_idx;
	- out_idx[0] = tick % kxMax;
	- out_idx[1] = tick / kxMax;
	-
	- // reverse phase
	- if (!m_Parameters->m_SignalGen.m_ReversePhase)
	- out_idx[1] = kyMax-1-out_idx[1];
	-
	- return out_idx;
	- }
	-
	- void AdjustEchoTime() override
	- {
	- if ( m_Parameters->m_SignalGen.m_tEcho < m_Parameters->m_SignalGen.m_tLine )
	- {
	- m_Parameters->m_SignalGen.m_tEcho = m_Parameters->m_SignalGen.m_tLine;
	- MITK_WARN << "Echo time is too short! Time not sufficient to read slice. Automatically adjusted to " << m_Parameters->m_SignalGen.m_tEcho << " ms";
	- m_Parameters->m_Misc.m_AfterSimulationMessage += "Echo time was chosen too short! Time not sufficient to read slice. Internally adjusted to " + boost::lexical_cast<std::string>(m_Parameters->m_SignalGen.m_tEcho) + " ms\n";
	- }
	- }
	-
	-protected:
	-
	-};
	-
	-}
	-
	-#endif
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/Sequences/mitkFastSpinEcho.h b/Modules/DiffusionImaging/FiberTracking/Fiberfox/Sequences/mitkFastSpinEcho.h
	deleted file mode 100644
	index e631b1ab2e..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/Sequences/mitkFastSpinEcho.h
	+++ /dev/null
	@@ -1,96 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_FastSpinEcho_H
	-#define _MITK_FastSpinEcho_H
	-
	-#include <mitkAcquisitionType.h>
	-
	-namespace mitk {
	-
	-/**
	- * \brief Fast spin echo sequence. Cartesian readout.
	- * Echo spacing = TE
	- */
	-class FastSpinEcho : public AcquisitionType
	-{
	-public:
	-
	- unsigned int linesWithSameTime;
	- float half_read_time;
	- FastSpinEcho(FiberfoxParameters* parameters)
	- : AcquisitionType(parameters)
	- {
	- linesWithSameTime = static_cast<unsigned int>(std::ceil(static_cast<float>(kyMax)/m_Parameters->m_SignalGen.m_EchoTrainLength));
	-
	- dt = m_Parameters->m_SignalGen.m_tLine/kxMax; // time to read one k-space voxel
	-
	- half_read_time = kxMax * dt/2;
	- }
	- ~FastSpinEcho() override
	- {}
	-
	- // one echo per k-space line
	- float GetTimeFromMaxEcho(const int& tick) override
	- {
	- float t = dt*(tick % kxMax + 0.5f) - half_read_time;
	- return t;
	- }
	-
	- float GetTimeFromLastDiffusionGradient(const int& tick) override
	- {
	- return (tick % kxMax)*dt;
	- }
	-
	- // depends on ETL
	- float GetTimeFromRf(const int& tick) override
	- {
	- float echo_nr = std::ceil(static_cast<float>(tick/kxMax+1)/linesWithSameTime);
	- echo_nr -= std::ceil(static_cast<float>(m_Parameters->m_SignalGen.m_EchoTrainLength)/2);
	- return m_Parameters->m_SignalGen.m_tEcho + echo_nr*m_Parameters->m_SignalGen.m_tLine + GetTimeFromMaxEcho(tick);
	- }
	-
	- itk::Index< 2 > GetActualKspaceIndex(const int& tick) override
	- {
	- itk::Index< 2 > out_idx;
	- out_idx[0] = tick % kxMax;
	- out_idx[1] = tick / kxMax;
	-
	- // reverse phase
	- if (!m_Parameters->m_SignalGen.m_ReversePhase)
	- out_idx[1] = kyMax-1-out_idx[1];
	-
	- return out_idx;
	- }
	-
	- void AdjustEchoTime() override
	- {
	- if ( m_Parameters->m_SignalGen.m_tEcho < m_Parameters->m_SignalGen.m_EchoTrainLength*m_Parameters->m_SignalGen.m_tLine )
	- {
	- m_Parameters->m_SignalGen.m_tEcho = m_Parameters->m_SignalGen.m_EchoTrainLength*m_Parameters->m_SignalGen.m_tLine;
	- MITK_WARN << "Echo time is too short! Time not sufficient to read slice. Automatically adjusted to " << m_Parameters->m_SignalGen.m_tEcho << " ms";
	- m_Parameters->m_Misc.m_AfterSimulationMessage += "Echo time was chosen too short! Time not sufficient to read slice. Internally adjusted to " + boost::lexical_cast<std::string>(m_Parameters->m_SignalGen.m_tEcho) + " ms\n";
	- }
	- }
	-
	-protected:
	-
	-};
	-
	-}
	-
	-#endif
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/Sequences/mitkSingleShotEpi.h b/Modules/DiffusionImaging/FiberTracking/Fiberfox/Sequences/mitkSingleShotEpi.h
	deleted file mode 100644
	index 2203da4314..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/Sequences/mitkSingleShotEpi.h
	+++ /dev/null
	@@ -1,102 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_SingleShotEpi_H
	-#define _MITK_SingleShotEpi_H
	-
	-#include <mitkAcquisitionType.h>
	-
	-namespace mitk {
	-
	-/**
	- * \brief Realizes EPI readout: one echo, maximum intensity in the k-space center, zig-zag trajectory
	- *
	- */
	-class SingleShotEpi : public AcquisitionType
	-{
	-public:
	-
	- /*
	- TE
	- \| dt \| dt \| dt \| ... \|
	-
	- Total read time: Nvoxdt = kxMaxkyMax*dt
	-
	- */
	- float half_read_time;
	- SingleShotEpi(FiberfoxParameters* parameters) : AcquisitionType(parameters)
	- {
	- dt = m_Parameters->m_SignalGen.m_tLine/kxMax; // time to read one k-space voxel
	- half_read_time = (kxMaxkyMax) dt/2;
	- }
	- ~SingleShotEpi() override
	- {}
	-
	- // one echo per slice
	- float GetTimeFromMaxEcho(const int& tick) override
	- {
	- float t = dt*(static_cast<float>(tick) + 0.5f) - half_read_time;
	- return t;
	- }
	-
	- // we simply assume that readout starts directly after the last diffusion gradient
	- float GetTimeFromLastDiffusionGradient(const int& tick) override
	- {
	- return tick*dt + dt/2;
	- }
	-
	- float GetTimeFromRf(const int& tick) override
	- {
	- return m_Parameters->m_SignalGen.m_tEcho + GetTimeFromMaxEcho(tick);
	- }
	-
	- itk::Index< 2 > GetActualKspaceIndex(const int& tick) override
	- {
	- itk::Index< 2 > out_idx;
	- out_idx[0] = tick % kxMax;
	- out_idx[1] = tick / kxMax;
	-
	- if (!m_Parameters->m_SignalGen.m_ReversePhase)
	- {
	- out_idx[1] = kyMax-1-out_idx[1]; // in the not reversed case we start at the maximum k-space line
	-
	- if (out_idx[1]%2 == 1) // reverse frequency encoding direction
	- out_idx[0] = kxMax-out_idx[0]-1;
	- }
	- else if (out_idx[1]%2) // reverse frequency encoding direction
	- out_idx[0] = kxMax-out_idx[0]-1;
	-
	- return out_idx;
	- }
	-
	- void AdjustEchoTime() override
	- {
	- if ( m_Parameters->m_SignalGen.m_tEcho < kyMax*m_Parameters->m_SignalGen.m_tLine )
	- {
	- m_Parameters->m_SignalGen.m_tEcho = kyMax*m_Parameters->m_SignalGen.m_tLine;
	- MITK_WARN << "Echo time is too short! Time not sufficient to read slice. Automatically adjusted to " << m_Parameters->m_SignalGen.m_tEcho << " ms";
	- m_Parameters->m_Misc.m_AfterSimulationMessage += "Echo time was chosen too short! Time not sufficient to read slice. Internally adjusted to " + boost::lexical_cast<std::string>(m_Parameters->m_SignalGen.m_tEcho) + " ms\n";
	- }
	- }
	-
	-protected:
	-
	-};
	-
	-}
	-
	-#endif
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkAstroStickModel.cpp b/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkAstroStickModel.cpp
	deleted file mode 100644
	index 67b781173d..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkAstroStickModel.cpp
	+++ /dev/null
	@@ -1,122 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#include <vnl/vnl_cross.h>
	-#include <vnl/vnl_quaternion.h>
	-#include <mitkAstroStickModel.h>
	-
	-using namespace mitk;
	-
	-template< class ScalarType >
	-AstroStickModel< ScalarType >::AstroStickModel()
	- : m_Diffusivity(0.001)
	- , m_NumSticks(42)
	- , m_RandomizeSticks(false)
	-{
	- this->m_RandGen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New();
	- this->m_RandGen->SetSeed();
	-
	- vnl_matrix_fixed<double,3,42>* sticks = itk::PointShell<42, vnl_matrix_fixed<double, 3, 42> >::DistributePointShell();
	- for (unsigned int i=0; i<m_NumSticks; i++)
	- {
	- GradientType stick;
	- stick[0] = sticks->get(0,i); stick[1] = sticks->get(1,i); stick[2] = sticks->get(2,i);
	- stick.Normalize();
	- m_Sticks.push_back(stick);
	- }
	-}
	-
	-template< class ScalarType >
	-AstroStickModel< ScalarType >::~AstroStickModel()
	-{
	-
	-}
	-
	-template< class ScalarType >
	-ScalarType AstroStickModel< ScalarType >::SimulateMeasurement(unsigned int dir, GradientType& )
	-{
	- ScalarType signal = 0;
	-
	- if (dir>=this->m_GradientList.size())
	- return signal;
	-
	- ScalarType b = -this->m_BValue*m_Diffusivity;
	-
	- if (m_RandomizeSticks) // random number of sticks
	- m_NumSticks = 30 + this->m_RandGen->GetIntegerVariate()%31;
	-
	- GradientType g = this->m_GradientList[dir];
	- if (g.GetNorm()>0.0001) // is weighted direction
	- {
	- for (unsigned int j=0; j<m_NumSticks; j++)
	- {
	- ScalarType dot = 0;
	- if(m_RandomizeSticks)
	- dot = GetRandomDirection()*g;
	- else
	- dot = m_Sticks[j]*g;
	- signal += std::exp( (double)(bdotdot) ); // skip * bVal becaus bVal is already encoded in the dot product (norm of g encodes b-value relative to baseline b-value m_BValue)
	- }
	- signal /= m_NumSticks;
	- }
	- else // is baseline direction
	- signal = 1;
	-
	- return signal;
	-}
	-
	-template< class ScalarType >
	-typename AstroStickModel< ScalarType >::GradientType AstroStickModel< ScalarType >::GetRandomDirection()
	-{
	- GradientType vec;
	- vec[0] = this->m_RandGen->GetNormalVariate();
	- vec[1] = this->m_RandGen->GetNormalVariate();
	- vec[2] = this->m_RandGen->GetNormalVariate();
	- vec.Normalize();
	- return vec;
	-}
	-
	-template< class ScalarType >
	-typename AstroStickModel< ScalarType >::PixelType AstroStickModel< ScalarType >::SimulateMeasurement(GradientType& )
	-{
	- PixelType signal;
	- signal.SetSize(this->m_GradientList.size());
	- ScalarType b = -this->m_BValue*m_Diffusivity;
	-
	- if (m_RandomizeSticks)
	- m_NumSticks = 30 + this->m_RandGen->GetIntegerVariate()%31;
	-
	- for( unsigned int i=0; i<this->m_GradientList.size(); i++)
	- {
	- GradientType g = this->m_GradientList[i];
	- if (g.GetNorm()>0.0001)
	- {
	- for (unsigned int j=0; j<m_NumSticks; j++)
	- {
	- ScalarType dot = 0;
	- if(m_RandomizeSticks)
	- dot = GetRandomDirection()*g;
	- else
	- dot = m_Sticks[j]*g;
	- signal[i] += std::exp( (double)(bdotdot) ); // skip * bVal becaus bVal is already encoded in the dot product (norm of g encodes b-value relative to baseline b-value m_BValue)
	- }
	- signal[i] /= m_NumSticks;
	- }
	- else
	- signal[i] = 1;
	- }
	-
	- return signal;
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkAstroStickModel.h b/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkAstroStickModel.h
	deleted file mode 100644
	index 3e7fb2118a..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkAstroStickModel.h
	+++ /dev/null
	@@ -1,122 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_AstroStickModel_H
	-#define _MITK_AstroStickModel_H
	-
	-#include <mitkDiffusionSignalModel.h>
	-#include <itkPointShell.h>
	-
	-namespace mitk {
	-
	-/**
	- * \brief Generates the diffusion signal using a collection of idealised cylinder with zero radius: e^(-bd(ng)²)
	- *
	- */
	-
	-template< class ScalarType = double >
	-class AstroStickModel : public DiffusionSignalModel< ScalarType >
	-{
	-public:
	-
	- AstroStickModel();
	- template< class OtherType >AstroStickModel(AstroStickModel<OtherType>* model)
	- {
	- this->m_CompartmentId = model->m_CompartmentId;
	- this->m_T1 = model->GetT1();
	- this->m_T2 = model->GetT2();
	- this->m_GradientList = model->GetGradientList();
	- this->m_VolumeFractionImage = model->GetVolumeFractionImage();
	- this->m_RandGen = model->GetRandomGenerator();
	-
	- this->m_BValue = model->GetBvalue();
	- this->m_Diffusivity = model->GetDiffusivity();
	- this->m_Sticks = model->GetSticks();
	- this->m_NumSticks = model->GetNumSticks();
	- this->m_RandomizeSticks = model->GetRandomizeSticks();
	- }
	- ~AstroStickModel();
	-
	- typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType;
	- typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType;
	- typedef typename DiffusionSignalModel< ScalarType >::GradientListType GradientListType;
	-
	- / Actual signal generation /
	- PixelType SimulateMeasurement(GradientType& fiberDirection) override;
	- ScalarType SimulateMeasurement(unsigned int dir, GradientType& fiberDirection) override;
	-
	- void SetRandomizeSticks(bool randomize=true){ m_RandomizeSticks=randomize; } ///< Random stick configuration in each voxel
	- bool GetRandomizeSticks() { return m_RandomizeSticks; }
	-
	- void SetDiffusivity(double diffusivity) { m_Diffusivity = diffusivity; } ///< Scalar diffusion constant
	- double GetDiffusivity() { return m_Diffusivity; }
	-
	- void SetNumSticks(unsigned int order)
	- {
	- vnl_matrix<double> sticks;
	- switch (order)
	- {
	- case 1:
	- m_NumSticks = 12;
	- sticks = itk::PointShell<12, vnl_matrix_fixed<double, 3, 12> >::DistributePointShell()->as_matrix();
	- break;
	- case 2:
	- m_NumSticks = 42;
	- sticks = itk::PointShell<42, vnl_matrix_fixed<double, 3, 42> >::DistributePointShell()->as_matrix();
	- break;
	- case 3:
	- m_NumSticks = 92;
	- sticks = itk::PointShell<92, vnl_matrix_fixed<double, 3, 92> >::DistributePointShell()->as_matrix();
	- break;
	- case 4:
	- m_NumSticks = 162;
	- sticks = itk::PointShell<162, vnl_matrix_fixed<double, 3, 162> >::DistributePointShell()->as_matrix();
	- break;
	- case 5:
	- m_NumSticks = 252;
	- sticks = itk::PointShell<252, vnl_matrix_fixed<double, 3, 252> >::DistributePointShell()->as_matrix();
	- break;
	- default:
	- m_NumSticks = 42;
	- sticks = itk::PointShell<42, vnl_matrix_fixed<double, 3, 42> >::DistributePointShell()->as_matrix();
	- break;
	- }
	- for (int i=0; i<m_NumSticks; i++)
	- {
	- GradientType stick;
	- stick[0] = sticks.get(0,i); stick[1] = sticks.get(1,i); stick[2] = sticks.get(2,i);
	- stick.Normalize();
	- m_Sticks.push_back(stick);
	- }
	- }
	- unsigned int GetNumSticks(){ return m_NumSticks; }
	- GradientListType GetSticks(){ return m_Sticks; }
	-
	-protected:
	-
	- GradientType GetRandomDirection();
	- double m_Diffusivity; ///< Scalar diffusion constant
	- GradientListType m_Sticks; ///< Stick container
	- unsigned int m_NumSticks; ///< Number of sticks
	- bool m_RandomizeSticks;
	-};
	-
	-}
	-
	-#include "mitkAstroStickModel.cpp"
	-
	-#endif
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkBallModel.cpp b/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkBallModel.cpp
	deleted file mode 100644
	index 7255629a24..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkBallModel.cpp
	+++ /dev/null
	@@ -1,72 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#include <vnl/vnl_cross.h>
	-#include <vnl/vnl_quaternion.h>
	-#include <mitkBallModel.h>
	-
	-using namespace mitk;
	-
	-template< class ScalarType >
	-BallModel< ScalarType >::BallModel()
	- : m_Diffusivity(0.001)
	-{
	-
	-}
	-
	-template< class ScalarType >
	-BallModel< ScalarType >::~BallModel()
	-{
	-
	-}
	-
	-template< class ScalarType >
	-ScalarType BallModel< ScalarType >::SimulateMeasurement(unsigned int dir, GradientType& )
	-{
	- ScalarType signal = 0;
	-
	- if (dir>=this->m_GradientList.size())
	- return signal;
	-
	- GradientType g = this->m_GradientList[dir];
	- ScalarType bVal = g.GetNorm(); bVal *= bVal;
	-
	- if (bVal>0.0001)
	- signal = std::exp( -this->m_BValue * bVal * m_Diffusivity );
	- else
	- signal = 1;
	-
	- return signal;
	-}
	-
	-template< class ScalarType >
	-typename BallModel< ScalarType >::PixelType BallModel< ScalarType >::SimulateMeasurement(GradientType& )
	-{
	- PixelType signal;
	- signal.SetSize(this->m_GradientList.size());
	-
	- for( unsigned int i=0; i<this->m_GradientList.size(); i++)
	- {
	- GradientType g = this->m_GradientList[i];
	- ScalarType bVal = g.GetNorm(); bVal *= bVal;
	-
	- if (bVal>0.0001)
	- signal[i] = std::exp( -this->m_BValue * bVal * m_Diffusivity );
	- else
	- signal[i] = 1;
	- }
	-
	- return signal;
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkBallModel.h b/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkBallModel.h
	deleted file mode 100644
	index 2fb78b8eaa..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkBallModel.h
	+++ /dev/null
	@@ -1,71 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_BallModel_H
	-#define _MITK_BallModel_H
	-
	-#include <mitkDiffusionSignalModel.h>
	-
	-namespace mitk {
	-
	-/**
	- * \brief Generates direction independent diffusion measurement employing a scalar diffusion constant d: e^(-bd)
	- *
	- */
	-
	-template< class ScalarType = double >
	-class BallModel : public DiffusionSignalModel< ScalarType >
	-{
	-public:
	-
	- BallModel();
	- template< class OtherType >BallModel(BallModel<OtherType>* model)
	- {
	- this->m_CompartmentId = model->m_CompartmentId;
	- this->m_T1 = model->GetT1();
	- this->m_T2 = model->GetT2();
	- this->m_GradientList = model->GetGradientList();
	- this->m_VolumeFractionImage = model->GetVolumeFractionImage();
	- this->m_RandGen = model->GetRandomGenerator();
	-
	- this->m_BValue = model->GetBvalue();
	- this->m_Diffusivity = model->GetDiffusivity();
	- }
	- ~BallModel();
	-
	- typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType;
	- typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType;
	- typedef typename DiffusionSignalModel< ScalarType >::GradientListType GradientListType;
	-
	-
	- / Actual signal generation /
	- PixelType SimulateMeasurement(GradientType& fiberDirection) override;
	- ScalarType SimulateMeasurement(unsigned int dir, GradientType& fiberDirection) override;
	-
	- void SetDiffusivity(double D) { m_Diffusivity = D; }
	- double GetDiffusivity() { return m_Diffusivity; }
	-
	-protected:
	-
	- double m_Diffusivity; ///< Scalar diffusion constant
	-};
	-
	-}
	-
	-#include "mitkBallModel.cpp"
	-
	-#endif
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkChiSquareNoiseModel.cpp b/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkChiSquareNoiseModel.cpp
	deleted file mode 100644
	index f3bf77e2e7..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkChiSquareNoiseModel.cpp
	+++ /dev/null
	@@ -1,48 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#include <vnl/vnl_cross.h>
	-#include <vnl/vnl_quaternion.h>
	-#include <mitkChiSquareNoiseModel.h>
	-
	-using namespace mitk;
	-
	-template< class ScalarType >
	-ChiSquareNoiseModel< ScalarType >::ChiSquareNoiseModel()
	-{
	- m_RandGen.seed();
	-}
	-
	-template< class ScalarType >
	-ChiSquareNoiseModel< ScalarType >::~ChiSquareNoiseModel()
	-{
	-
	-}
	-
	-template< class ScalarType >
	-void ChiSquareNoiseModel< ScalarType >::SetSeed(int seed)
	-{
	- if (seed>=0)
	- m_RandGen.seed(seed);
	- else
	- m_RandGen.seed();
	-}
	-
	-template< class ScalarType >
	-void ChiSquareNoiseModel< ScalarType >::AddNoise(PixelType& pixel)
	-{
	- for( unsigned int i=0; i<pixel.Size(); i++)
	- pixel[i] += (ScalarType)(m_Distribution(m_RandGen)-m_Distribution.n());
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkChiSquareNoiseModel.h b/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkChiSquareNoiseModel.h
	deleted file mode 100644
	index 285f375860..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkChiSquareNoiseModel.h
	+++ /dev/null
	@@ -1,58 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_ChiSquareNoiseModel_H
	-#define _MITK_ChiSquareNoiseModel_H
	-
	-#include <mitkDiffusionNoiseModel.h>
	-#include <itkMersenneTwisterRandomVariateGenerator.h>
	-
	-namespace mitk {
	-
	-/**
	- * \brief Implementation of noise following a chi-squared distribution
	- *
	- */
	-
	-template< class ScalarType = double >
	-class ChiSquareNoiseModel : public DiffusionNoiseModel< ScalarType >
	-{
	-public:
	-
	- ChiSquareNoiseModel();
	- ~ChiSquareNoiseModel() override;
	-
	- typedef typename DiffusionNoiseModel< ScalarType >::PixelType PixelType;
	-
	- / Adds rician noise to the input pixel /
	- void AddNoise(PixelType& pixel) override;
	-
	- void SetNoiseVariance(double var) override{ m_Distribution = boost::random::chi_squared_distribution<double>(var/2); }
	- double GetNoiseVariance() override{ return m_Distribution.n()*2; }
	- void SetSeed(int seed) override; ///< seed for random number generator
	-
	-protected:
	-
	- boost::random::mt19937 m_RandGen;
	- boost::random::chi_squared_distribution<double> m_Distribution;
	-};
	-
	-}
	-
	-#include "mitkChiSquareNoiseModel.cpp"
	-
	-#endif
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkDiffusionNoiseModel.h b/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkDiffusionNoiseModel.h
	deleted file mode 100644
	index ae7ecd7f1a..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkDiffusionNoiseModel.h
	+++ /dev/null
	@@ -1,59 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_DiffusionNoiseModel_H
	-#define _MITK_DiffusionNoiseModel_H
	-
	-#include <MitkFiberTrackingExports.h>
	-#include <itkVariableLengthVector.h>
	-#include <itkVector.h>
	-#include <vnl/vnl_vector_fixed.h>
	-#include <boost/random.hpp>
	-
	-namespace mitk {
	-
	-/**
	- * \brief Abstract class for diffusion noise models
	- *
	- */
	-
	-template< class ScalarType = double >
	-class DiffusionNoiseModel
	-{
	-public:
	-
	- DiffusionNoiseModel(){}
	- virtual ~DiffusionNoiseModel(){}
	-
	- typedef itk::VariableLengthVector< ScalarType > PixelType;
	-
	- / Adds noise according to model to the input pixel. Has to be implemented in subclass. /
	- virtual void AddNoise(PixelType& pixel) = 0;
	-
	- / Seed for random generator. Has to be implemented in subclass. /
	- virtual void SetSeed(int seed) = 0;
	-
	- virtual double GetNoiseVariance() = 0;
	- virtual void SetNoiseVariance(double var) = 0;
	-
	-protected:
	-
	-};
	-
	-}
	-
	-#endif
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkDiffusionSignalModel.h b/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkDiffusionSignalModel.h
	deleted file mode 100644
	index c180960ec6..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkDiffusionSignalModel.h
	+++ /dev/null
	@@ -1,113 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_DiffusionSignalModel_H
	-#define _MITK_DiffusionSignalModel_H
	-
	-#include <MitkFiberTrackingExports.h>
	-#include <itkVariableLengthVector.h>
	-#include <itkVector.h>
	-#include <itkImage.h>
	-#include <itkMersenneTwisterRandomVariateGenerator.h>
	-#include <vnl/vnl_vector_fixed.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-
	-namespace mitk {
	-
	-/**
	- * \brief Abstract class for diffusion signal models
	- *
	- */
	-
	-template< class ScalarType = double >
	-class DiffusionSignalModel
	-{
	-public:
	-
	- DiffusionSignalModel()
	- : m_T2(100)
	- , m_T1(0)
	- , m_BValue(1000)
	- {}
	- ~DiffusionSignalModel(){}
	-
	- typedef itk::Image<double, 3> ItkDoubleImgType;
	- typedef itk::VariableLengthVector< ScalarType > PixelType;
	- typedef itk::Vector<double,3> GradientType;
	- typedef std::vector<GradientType> GradientListType;
	- typedef itk::Statistics::MersenneTwisterRandomVariateGenerator ItkRandGenType;
	- typedef mitk::DiffusionPropertyHelper DPH;
	-
	- / Realizes actual signal generation. Has to be implemented in subclass. /
	- virtual PixelType SimulateMeasurement(GradientType& fiberDirection) = 0;
	- virtual ScalarType SimulateMeasurement(unsigned int dir, GradientType& fiberDirection) = 0;
	-
	- void SetGradientList(DPH::GradientDirectionsContainerType* gradients)
	- {
	- m_GradientList.clear();
	- for ( unsigned int i=0; i<gradients->Size(); ++i )
	- {
	- DPH::GradientDirectionType g_vnl = gradients->GetElement(i);
	- GradientType g_itk;
	- g_itk[0] = g_vnl[0];
	- g_itk[1] = g_vnl[1];
	- g_itk[2] = g_vnl[2];
	- m_GradientList.push_back(g_itk);
	- }
	- }
	-
	- void SetGradientList(GradientListType gradientList) { this->m_GradientList = gradientList; }
	- GradientListType GetGradientList(){ return m_GradientList; }
	- GradientType GetGradientDirection(int i) { return m_GradientList.at(i); }
	-
	- void SetT2(double T2) { m_T2 = T2; }
	- double GetT2() { return m_T2; }
	-
	- void SetT1(double T1) { m_T1 = T1; }
	- double GetT1() { return m_T1; }
	-
	- void SetVolumeFractionImage(ItkDoubleImgType::Pointer img){ m_VolumeFractionImage = img; }
	- ItkDoubleImgType::Pointer GetVolumeFractionImage(){ return m_VolumeFractionImage; }
	-
	- void SetRandomGenerator(ItkRandGenType::Pointer randgen){ m_RandGen = randgen; }
	- ItkRandGenType::Pointer GetRandomGenerator(){ return m_RandGen; }
	-
	- void SetSeed(int s) ///< set seed for random generator
	- {
	- if (m_RandGen.IsNull())
	- m_RandGen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New();
	- m_RandGen->SetSeed(s);
	- }
	-
	- void SetBvalue(double bValue) { m_BValue = bValue; } ///< b-value used to generate the artificial signal
	- double GetBvalue() { return m_BValue; }
	-
	- unsigned int m_CompartmentId; ///< GUI flag. Which compartment is this model assigned to?
	-
	-protected:
	-
	- GradientListType m_GradientList; ///< Diffusion gradient direction container
	- double m_T2; ///< Tissue specific transversal relaxation time
	- double m_T1; ///< Tissue specific longitudinal relaxation time
	- ItkDoubleImgType::Pointer m_VolumeFractionImage; ///< Tissue specific volume fraction for each voxel (only relevant for non fiber compartments)
	- ItkRandGenType::Pointer m_RandGen; ///< Random number generator
	- double m_BValue;
	-};
	-
	-}
	-
	-#endif
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkDotModel.cpp b/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkDotModel.cpp
	deleted file mode 100644
	index 1eb8d4af29..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkDotModel.cpp
	+++ /dev/null
	@@ -1,47 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#include <vnl/vnl_cross.h>
	-#include <vnl/vnl_quaternion.h>
	-#include <mitkDotModel.h>
	-
	-using namespace mitk;
	-
	-template< class ScalarType >
	-DotModel< ScalarType >::DotModel()
	-{
	-
	-}
	-
	-template< class ScalarType >
	-DotModel< ScalarType >::~DotModel()
	-{
	-
	-}
	-
	-template< class ScalarType >
	-ScalarType DotModel< ScalarType >::SimulateMeasurement(unsigned int /dir/, GradientType& )
	-{
	- return 1;
	-}
	-
	-template< class ScalarType >
	-typename DotModel< ScalarType >::PixelType DotModel< ScalarType >::SimulateMeasurement(GradientType& )
	-{
	- PixelType signal;
	- signal.SetSize(this->m_GradientList.size());
	- signal.Fill(1);
	- return signal;
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkDotModel.h b/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkDotModel.h
	deleted file mode 100644
	index 09ff77acea..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkDotModel.h
	+++ /dev/null
	@@ -1,63 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_DotModel_H
	-#define _MITK_DotModel_H
	-
	-#include <mitkDiffusionSignalModel.h>
	-
	-namespace mitk {
	-
	-/**
	- * \brief Generates constant direction independent signal.
	- *
	- */
	-
	-template< class ScalarType = double >
	-class DotModel : public DiffusionSignalModel< ScalarType >
	-{
	-public:
	-
	- DotModel();
	- template< class OtherType >DotModel(DotModel<OtherType>* model)
	- {
	- this->m_CompartmentId = model->m_CompartmentId;
	- this->m_T1 = model->GetT1();
	- this->m_T2 = model->GetT2();
	- this->m_GradientList = model->GetGradientList();
	- this->m_VolumeFractionImage = model->GetVolumeFractionImage();
	- this->m_RandGen = model->GetRandomGenerator();
	- }
	- ~DotModel();
	-
	- typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType;
	- typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType;
	- typedef typename DiffusionSignalModel< ScalarType >::GradientListType GradientListType;
	-
	- / Actual signal generation /
	- PixelType SimulateMeasurement(GradientType& fiberDirection) override;
	- ScalarType SimulateMeasurement(unsigned int dir, GradientType& fiberDirection) override;
	-
	-protected:
	-
	-};
	-
	-}
	-
	-#include "mitkDotModel.cpp"
	-
	-#endif
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkRawShModel.cpp b/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkRawShModel.cpp
	deleted file mode 100644
	index d102967da0..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkRawShModel.cpp
	+++ /dev/null
	@@ -1,394 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#include <vnl/vnl_cross.h>
	-#include <vnl/vnl_quaternion.h>
	-#include <mitkRawShModel.h>
	-#include <boost/math/special_functions.hpp>
	-#include <itkOrientationDistributionFunction.h>
	-#include <mitkFiberfoxParameters.h>
	-#include <itkDiffusionTensor3DReconstructionImageFilter.h>
	-#include <itkAdcImageFilter.h>
	-#include <itkAnalyticalDiffusionQballReconstructionImageFilter.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <mitkImageCast.h>
	-#include <mitkProperties.h>
	-
	-using namespace mitk;
	-using namespace boost::math;
	-
	-template< class ScalarType >
	-RawShModel< ScalarType >::RawShModel()
	- : m_ShOrder(0)
	- , m_ModelIndex(-1)
	- , m_MaxNumKernels(1000)
	-{
	- this->m_RandGen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New();
	- this->m_RandGen->SetSeed();
	- m_AdcRange.first = 0;
	- m_AdcRange.second = 0.004;
	- m_FaRange.first = 0;
	- m_FaRange.second = 1;
	-}
	-
	-template< class ScalarType >
	-RawShModel< ScalarType >::~RawShModel()
	-{
	-
	-}
	-
	-template< class ScalarType >
	-void RawShModel< ScalarType >::Clear()
	-{
	- m_ShCoefficients.clear();
	- m_PrototypeMaxDirection.clear();
	- m_B0Signal.clear();
	-}
	-
	-template< class ScalarType >
	-void RawShModel< ScalarType >::RandomModel()
	-{
	- m_ModelIndex = this->m_RandGen->GetIntegerVariate(m_B0Signal.size()-1);
	-}
	-
	-template< class ScalarType >
	-unsigned int RawShModel< ScalarType >::GetNumberOfKernels()
	-{
	- return m_B0Signal.size();
	-}
	-
	-template< class ScalarType >
	-bool RawShModel< ScalarType >::SampleKernels(Image::Pointer diffImg, ItkUcharImageType::Pointer maskImage, TensorImageType::Pointer tensorImage, QballFilterType::CoefficientImageType::Pointer itkFeatureImage, ItkDoubleImageType::Pointer adcImage)
	-{
	- if (diffImg.IsNull())
	- return false;
	-
	- typedef itk::VectorImage<short, 3> ITKDiffusionImageType;
	- ITKDiffusionImageType::Pointer itkVectorImagePointer = ITKDiffusionImageType::New();
	- mitk::CastToItkImage(diffImg, itkVectorImagePointer);
	-
	- const int shOrder = 2;
	-
	- if (tensorImage.IsNull())
	- {
	- typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, double > TensorReconstructionImageFilterType;
	-
	- TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New();
	- filter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg));
	- filter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg), itkVectorImagePointer );
	- filter->Update();
	- tensorImage = filter->GetOutput();
	- }
	-
	- const int NumCoeffs = (shOrder*shOrder + shOrder + 2)/2 + shOrder;
	- if (itkFeatureImage.IsNull())
	- {
	- QballFilterType::Pointer qballfilter = QballFilterType::New();
	- qballfilter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg));
	- qballfilter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg), itkVectorImagePointer );
	- qballfilter->SetLambda(0.006);
	- qballfilter->SetNormalizationMethod(QballFilterType::QBAR_RAW_SIGNAL);
	- qballfilter->Update();
	- itkFeatureImage = qballfilter->GetCoefficientImage();
	- }
	-
	- if (adcImage.IsNull())
	- {
	- itk::AdcImageFilter< short, double >::Pointer adcFilter = itk::AdcImageFilter< short, double >::New();
	- adcFilter->SetInput(itkVectorImagePointer);
	- adcFilter->SetGradientDirections(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg));
	- adcFilter->SetB_value(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg));
	- adcFilter->Update();
	- adcImage = adcFilter->GetOutput();
	- }
	-
	- int b0Index = 0;
	- for (unsigned int i=0; i<mitk::DiffusionPropertyHelper::GetOriginalGradientContainer(diffImg)->Size(); i++)
	- if (mitk::DiffusionPropertyHelper::GetOriginalGradientContainer(diffImg)->GetElement(i).magnitude()<0.001 )
	- {
	- b0Index = i;
	- break;
	- }
	-
	- double max = 0;
	- {
	- itk::ImageRegionIterator< itk::VectorImage< short, 3 > > it(itkVectorImagePointer, itkVectorImagePointer->GetLargestPossibleRegion());
	- while(!it.IsAtEnd())
	- {
	- if (maskImage.IsNotNull() && maskImage->GetPixel(it.GetIndex())<=0)
	- {
	- ++it;
	- continue;
	- }
	- if (it.Get()[b0Index]>max)
	- max = it.Get()[b0Index];
	- ++it;
	- }
	- }
	-
	- MITK_INFO << "Sampling signal kernels.";
	- unsigned int count = 0;
	- itk::ImageRegionIterator< itk::Image< itk::DiffusionTensor3D< double >, 3 > > it(tensorImage, tensorImage->GetLargestPossibleRegion());
	- while(!it.IsAtEnd())
	- {
	- bool skipPixel = false;
	- if (maskImage.IsNotNull() && maskImage->GetPixel(it.GetIndex())<=0)
	- {
	- ++it;
	- continue;
	- }
	- for (unsigned int i=0; i<mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg)->Size(); i++)
	- {
	- if (itkVectorImagePointer->GetPixel(it.GetIndex())[i]!=itkVectorImagePointer->GetPixel(it.GetIndex())[i] \|\| itkVectorImagePointer->GetPixel(it.GetIndex())[i]<=0 \|\| itkVectorImagePointer->GetPixel(it.GetIndex())[i]>itkVectorImagePointer->GetPixel(it.GetIndex())[b0Index])
	- {
	- skipPixel = true;
	- break;
	- }
	- }
	- if (skipPixel)
	- {
	- ++it;
	- continue;
	- }
	-
	- typedef itk::DiffusionTensor3D<double> TensorType;
	- TensorType::EigenValuesArrayType eigenvalues;
	- TensorType::EigenVectorsMatrixType eigenvectors;
	- TensorType tensor = it.Get();
	- double FA = tensor.GetFractionalAnisotropy();
	- double ADC = adcImage->GetPixel(it.GetIndex());
	- QballFilterType::CoefficientImageType::PixelType itkv = itkFeatureImage->GetPixel(it.GetIndex());
	- vnl_vector_fixed< double, NumCoeffs > coeffs;
	- for (unsigned int c=0; c<itkv.Size(); c++)
	- coeffs[c] = itkv[c]/max;
	-
	- if ( this->GetMaxNumKernels()>this->GetNumberOfKernels() && FA>m_FaRange.first && FA<m_FaRange.second && ADC>m_AdcRange.first && ADC<m_AdcRange.second)
	- {
	- if (this->SetShCoefficients( coeffs, (double)itkVectorImagePointer->GetPixel(it.GetIndex())[b0Index]/max ))
	- {
	- tensor.ComputeEigenAnalysis(eigenvalues, eigenvectors);
	- itk::Vector<double,3> dir;
	- dir[0] = eigenvectors(2, 0);
	- dir[1] = eigenvectors(2, 1);
	- dir[2] = eigenvectors(2, 2);
	- m_PrototypeMaxDirection.push_back(dir);
	- count++;
	- MITK_INFO << "KERNEL: " << it.GetIndex() << " (" << count << ")";
	- }
	- }
	- ++it;
	- }
	-
	- if (m_ShCoefficients.size()>0)
	- return true;
	- return false;
	-}
	-
	-// convert cartesian to spherical coordinates
	-template< class ScalarType >
	-vnl_matrix<double> RawShModel<ScalarType>::Cart2Sph(GradientListType &gradients )
	-{
	- vnl_matrix<double> sphCoords;
	- sphCoords.set_size(gradients.size(), 2);
	- sphCoords.fill(0.0);
	-
	- for (unsigned int i=0; i<gradients.size(); i++)
	- {
	- GradientType g = gradients[i];
	- if( g.GetNorm() > 0.0001 )
	- {
	- gradients[i].Normalize();
	- sphCoords(i,0) = acos(gradients[i][2]); // theta
	- sphCoords(i,1) = atan2(gradients[i][1], gradients[i][0]); // phi
	- }
	- }
	-
	- return sphCoords;
	-}
	-
	-template< class ScalarType >
	-vnl_matrix<double> RawShModel< ScalarType >::SetFiberDirection(GradientType& fiberDirection)
	-{
	- RandomModel();
	- GradientType axis = itk::CrossProduct(fiberDirection, m_PrototypeMaxDirection.at(m_ModelIndex));
	- axis.Normalize();
	-
	- vnl_quaternion<double> rotation(axis.GetVnlVector(), acos(dot_product(fiberDirection.GetVnlVector(), m_PrototypeMaxDirection.at(m_ModelIndex).GetVnlVector())));
	- rotation.normalize();
	-
	- GradientListType gradients;
	- for (unsigned int i=0; i<this->m_GradientList.size(); i++)
	- {
	- GradientType dir = this->m_GradientList.at(i);
	- if( dir.GetNorm() > 0.0001 )
	- {
	- dir.Normalize();
	- vnl_vector_fixed< double, 3 > vnlDir = rotation.rotate(dir.GetVnlVector());
	- dir[0] = vnlDir[0]; dir[1] = vnlDir[1]; dir[2] = vnlDir[2];
	- dir.Normalize();
	- }
	- gradients.push_back(dir);
	- }
	-
	- return Cart2Sph( gradients );
	-}
	-
	-template< class ScalarType >
	-bool RawShModel< ScalarType >::SetShCoefficients(vnl_vector< double > shCoefficients, double b0 )
	-{
	- m_ShOrder = 2;
	- while ( (m_ShOrder*m_ShOrder + m_ShOrder + 2)/2 + m_ShOrder <= shCoefficients.size() )
	- m_ShOrder += 2;
	- m_ShOrder -= 2;
	-
	- m_ModelIndex = m_B0Signal.size();
	- m_B0Signal.push_back(b0);
	- m_ShCoefficients.push_back(shCoefficients);
	-
	- // itk::OrientationDistributionFunction<double, 10000> odf;
	- // GradientListType gradients;
	- // for (unsigned int i=0; i<odf.GetNumberOfComponents(); i++)
	- // {
	- // GradientType dir; dir[0]=odf.GetDirection(i)[0]; dir[1]=odf.GetDirection(i)[1]; dir[2]=odf.GetDirection(i)[2];
	- // dir.Normalize();
	- // gradients.push_back(dir);
	- // }
	- // Cart2Sph( this->m_GradientList );
	- // PixelType signal = SimulateMeasurement();
	-
	- // int minDirIdx = 0;
	- // double min = itk::NumericTraits<double>::max();
	- // for (unsigned int i=0; i<signal.GetSize(); i++)
	- // {
	- // if (signal[i]>b0 \|\| signal[i]<0)
	- // {
	- // MITK_INFO << "Corrupted signal value detected. Kernel rejected.";
	- // m_B0Signal.pop_back();
	- // m_ShCoefficients.pop_back();
	- // return false;
	- // }
	- // if (signal[i]<min)
	- // {
	- // min = signal[i];
	- // minDirIdx = i;
	- // }
	- // }
	- // GradientType maxDir = this->m_GradientList.at(minDirIdx);
	- // maxDir.Normalize();
	- // m_PrototypeMaxDirection.push_back(maxDir);
	-
	- Cart2Sph( this->m_GradientList );
	- m_ModelIndex = -1;
	-
	- return true;
	-}
	-
	-template< class ScalarType >
	-ScalarType RawShModel< ScalarType >::SimulateMeasurement(unsigned int dir, GradientType& fiberDirection)
	-{
	- ScalarType signal = 0;
	-
	- if (m_ModelIndex==-1)
	- RandomModel();
	-
	- vnl_matrix<double> sphCoords = this->SetFiberDirection(fiberDirection);
	-
	- if (dir>=this->m_GradientList.size())
	- return signal;
	-
	- int j, m; double mag, plm;
	-
	- if (this->m_GradientList[dir].GetNorm()>0.001)
	- {
	- j=0;
	- for (int l=0; l<=static_cast<int>(m_ShOrder); l=l+2)
	- for (m=-l; m<=l; m++)
	- {
	- plm = legendre_p<double>(l,abs(m),cos(sphCoords(dir,0)));
	- mag = sqrt((double)(2l+1)/(4.0itk::Math::pi)factorial<double>(l-abs(m))/factorial<double>(l+abs(m)))plm;
	- double basis;
	-
	- if (m<0)
	- basis = sqrt(2.0)magcos(fabs((double)m)*sphCoords(dir,1));
	- else if (m==0)
	- basis = mag;
	- else
	- basis = pow(-1.0, m)sqrt(2.0)magsin(msphCoords(dir,1));
	-
	- signal += m_ShCoefficients.at(m_ModelIndex)[j]*basis;
	- j++;
	- }
	- }
	- else
	- signal = m_B0Signal.at(m_ModelIndex);
	-
	- m_ModelIndex = -1;
	-
	- return signal;
	-}
	-
	-template< class ScalarType >
	-typename RawShModel< ScalarType >::PixelType RawShModel< ScalarType >::SimulateMeasurement(GradientType& fiberDirection)
	-{
	- if (m_ModelIndex==-1)
	- RandomModel();
	-
	- PixelType signal;
	- signal.SetSize(this->m_GradientList.size());
	-
	- int M = this->m_GradientList.size();
	- int j, m; double mag, plm;
	-
	- vnl_matrix< double > shBasis;
	- shBasis.set_size(M, m_ShCoefficients.at(m_ModelIndex).size());
	- shBasis.fill(0.0);
	-
	- vnl_matrix<double> sphCoords = this->SetFiberDirection(fiberDirection);
	-
	- for (int p=0; p<M; p++)
	- {
	- if (this->m_GradientList[p].GetNorm()>0.001)
	- {
	- j=0;
	- for (int l=0; l<=static_cast<int>(m_ShOrder); l=l+2)
	- for (m=-l; m<=l; m++)
	- {
	- plm = legendre_p<double>(l,abs(m),cos(sphCoords(p,0)));
	- mag = sqrt((double)(2l+1)/(4.0itk::Math::pi)factorial<double>(l-abs(m))/factorial<double>(l+abs(m)))plm;
	-
	- if (m<0)
	- shBasis(p,j) = sqrt(2.0)magcos(fabs((double)m)*sphCoords(p,1));
	- else if (m==0)
	- shBasis(p,j) = mag;
	- else
	- shBasis(p,j) = pow(-1.0, m)sqrt(2.0)magsin(msphCoords(p,1));
	-
	- j++;
	- }
	-
	-
	- double val = 0;
	- for (unsigned int cidx=0; cidx<m_ShCoefficients.at(m_ModelIndex).size(); cidx++)
	- val += m_ShCoefficients.at(m_ModelIndex)[cidx]*shBasis(p,cidx);
	- signal[p] = val;
	- }
	- else
	- signal[p] = m_B0Signal.at(m_ModelIndex);
	- }
	-
	- m_ModelIndex = -1;
	-
	- return signal;
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkRawShModel.h b/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkRawShModel.h
	deleted file mode 100644
	index cae30c69f9..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkRawShModel.h
	+++ /dev/null
	@@ -1,110 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_RawShModel_H
	-#define _MITK_RawShModel_H
	-
	-#include <mitkDiffusionSignalModel.h>
	-#include <mitkImage.h>
	-#include <itkAnalyticalDiffusionQballReconstructionImageFilter.h>
	-
	-namespace mitk {
	-
	-/**
	- * \brief The spherical harmonic representation of a prototype diffusion weighted MR signal is used to obtain the direction dependent signal.
	- *
	- */
	-
	-template< class ScalarType = double >
	-class RawShModel : public DiffusionSignalModel< ScalarType >
	-{
	-public:
	-
	- RawShModel();
	- template< class OtherType >RawShModel(RawShModel<OtherType>* model)
	- {
	- this->m_CompartmentId = model->m_CompartmentId;
	- this->m_T1 = model->GetT1();
	- this->m_T2 = model->GetT2();
	- this->m_GradientList = model->GetGradientList();
	- this->m_VolumeFractionImage = model->GetVolumeFractionImage();
	- this->m_RandGen = model->GetRandomGenerator();
	-
	- this->m_AdcRange = model->GetAdcRange();
	- this->m_FaRange = model->GetFaRange();
	- this->m_ShCoefficients = model->GetShCoefficients();
	- this->m_B0Signal = model->GetB0Signals();
	- this->m_ShOrder = model->GetShOrder();
	- this->m_ModelIndex = model->GetModelIndex();
	- this->m_MaxNumKernels = model->GetMaxNumKernels();
	- }
	- ~RawShModel();
	-
	- typedef itk::Image< double, 3 > ItkDoubleImageType;
	- typedef itk::Image< unsigned char, 3 > ItkUcharImageType;
	- typedef itk::Image< itk::DiffusionTensor3D< double >, 3 > TensorImageType;
	- typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,2,ODF_SAMPLING_SIZE> QballFilterType;
	- typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType;
	- typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType;
	- typedef typename DiffusionSignalModel< ScalarType >::GradientListType GradientListType;
	- typedef itk::Matrix< double, 3, 3 > MatrixType;
	-
	- / Actual signal generation /
	- PixelType SimulateMeasurement(GradientType& fiberDirection) override;
	- ScalarType SimulateMeasurement(unsigned int dir, GradientType& fiberDirection) override;
	-
	- bool SetShCoefficients(vnl_vector< double > shCoefficients, double b0);
	- vnl_matrix<double> SetFiberDirection(GradientType& fiberDirection);
	- void SetFaRange(double min, double max){ m_FaRange.first = min; m_FaRange.second = max; }
	- void SetAdcRange(double min, double max){ m_AdcRange.first = min; m_AdcRange.second = max; }
	- void SetMaxNumKernels(unsigned int max){ m_MaxNumKernels = max; }
	- unsigned int GetNumberOfKernels();
	- std::pair< double, double > GetFaRange(){ return m_FaRange; }
	- std::pair< double, double > GetAdcRange(){ return m_AdcRange; }
	- unsigned int GetMaxNumKernels(){ return m_MaxNumKernels; }
	- void Clear();
	-
	- std::vector< vnl_vector< double > > GetShCoefficients(){ return m_ShCoefficients; }
	- std::vector< double > GetB0Signals(){ return m_B0Signal; }
	- unsigned int GetShOrder(){ return m_ShOrder; }
	- int GetModelIndex(){ return m_ModelIndex; }
	-
	- double GetBaselineSignal(int index){ return m_B0Signal.at(index); }
	- vnl_vector< double > GetCoefficients(int listIndex){ return m_ShCoefficients.at(listIndex); }
	-
	- bool SampleKernels(Image::Pointer diffImg, ItkUcharImageType::Pointer maskImage, TensorImageType::Pointer tensorImage=nullptr, QballFilterType::CoefficientImageType::Pointer coeffImage=nullptr, ItkDoubleImageType::Pointer adcImage=nullptr);
	-
	-protected:
	-
	- vnl_matrix<double> Cart2Sph( GradientListType& gradients );
	- void RandomModel();
	-
	- std::vector< vnl_vector< double > > m_ShCoefficients;
	- std::vector< double > m_B0Signal;
	- std::vector< GradientType > m_PrototypeMaxDirection;
	- std::pair< double, double > m_AdcRange;
	- std::pair< double, double > m_FaRange;
	- unsigned int m_ShOrder;
	- int m_ModelIndex;
	- unsigned int m_MaxNumKernels;
	-};
	-
	-}
	-
	-#include "mitkRawShModel.cpp"
	-
	-#endif
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkRicianNoiseModel.cpp b/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkRicianNoiseModel.cpp
	deleted file mode 100644
	index 7bfb7c388f..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkRicianNoiseModel.cpp
	+++ /dev/null
	@@ -1,53 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#include <vnl/vnl_cross.h>
	-#include <vnl/vnl_quaternion.h>
	-#include <mitkRicianNoiseModel.h>
	-
	-using namespace mitk;
	-
	-template< class ScalarType >
	-RicianNoiseModel< ScalarType >::RicianNoiseModel()
	-{
	- m_RandGen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New();
	- m_RandGen->SetSeed();
	- this->m_NoiseVariance = 0;
	-}
	-
	-template< class ScalarType >
	-RicianNoiseModel< ScalarType >::~RicianNoiseModel()
	-{
	-
	-}
	-
	-template< class ScalarType >
	-void RicianNoiseModel< ScalarType >::SetSeed(int seed)
	-{
	- if (seed>=0)
	- m_RandGen->SetSeed(seed);
	- else
	- m_RandGen->SetSeed();
	-}
	-
	-template< class ScalarType >
	-void RicianNoiseModel< ScalarType >::AddNoise(PixelType& pixel)
	-{
	- for( unsigned int i=0; i<pixel.Size(); i++)
	- {
	- double signal = pixel[i];
	- pixel[i] = sqrt(pow(signal + m_RandGen->GetNormalVariate(0.0, this->m_NoiseVariance), 2) + pow(m_RandGen->GetNormalVariate(0.0, this->m_NoiseVariance),2));
	- }
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkRicianNoiseModel.h b/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkRicianNoiseModel.h
	deleted file mode 100644
	index aa75aa16ed..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkRicianNoiseModel.h
	+++ /dev/null
	@@ -1,59 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_RicianNoiseModel_H
	-#define _MITK_RicianNoiseModel_H
	-
	-#include <mitkDiffusionNoiseModel.h>
	-#include <itkMersenneTwisterRandomVariateGenerator.h>
	-
	-namespace mitk {
	-
	-/**
	- * \brief Implementation of noise following a rician distribution
	- *
	- */
	-
	-template< class ScalarType = double >
	-class RicianNoiseModel : public DiffusionNoiseModel< ScalarType >
	-{
	-public:
	-
	- RicianNoiseModel();
	- ~RicianNoiseModel() override;
	-
	- typedef typename DiffusionNoiseModel< ScalarType >::PixelType PixelType;
	-
	- / Adds rician noise to the input pixel /
	- void AddNoise(PixelType& pixel) override;
	-
	- void SetNoiseVariance(double var) override{ m_NoiseVariance = var; }
	- double GetNoiseVariance() override{ return m_NoiseVariance; }
	- void SetSeed(int seed) override; ///< Set seed for random number generator
	-
	-protected:
	-
	- itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer m_RandGen;
	- double m_NoiseVariance; ///< variance of underlying distribution
	-
	-};
	-
	-}
	-
	-#include "mitkRicianNoiseModel.cpp"
	-
	-#endif
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkStickModel.cpp b/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkStickModel.cpp
	deleted file mode 100644
	index e03559078c..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkStickModel.cpp
	+++ /dev/null
	@@ -1,74 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#include <vnl/vnl_cross.h>
	-#include <vnl/vnl_quaternion.h>
	-#include <mitkStickModel.h>
	-
	-using namespace mitk;
	-
	-template< class ScalarType >
	-StickModel< ScalarType >::StickModel()
	- : m_Diffusivity(0.001)
	-{
	-
	-}
	-
	-template< class ScalarType >
	-StickModel< ScalarType >::~StickModel()
	-{
	-
	-}
	-
	-template< class ScalarType >
	-ScalarType StickModel< ScalarType >::SimulateMeasurement(unsigned int dir, GradientType& fiberDirection)
	-{
	- ScalarType signal = 0;
	-
	- if (dir>=this->m_GradientList.size())
	- return signal;
	-
	- GradientType g = this->m_GradientList[dir];
	- if (g.GetNorm()>0.0001)
	- {
	- ScalarType dot = fiberDirection*g;
	- signal = std::exp( -this->m_BValuem_Diffusivitydotdot ); // skip bVal becaus bVal is already encoded in the dot product (norm of g encodes b-value relative to baseline b-value m_BValue)
	- }
	- else
	- signal = 1;
	-
	- return signal;
	-}
	-
	-template< class ScalarType >
	-typename StickModel< ScalarType >::PixelType StickModel< ScalarType >::SimulateMeasurement(GradientType &fiberDirection)
	-{
	- PixelType signal;
	- signal.SetSize(this->m_GradientList.size());
	-
	- for( unsigned int i=0; i<this->m_GradientList.size(); i++)
	- {
	- GradientType g = this->m_GradientList[i];
	- if (g.GetNorm()>0.0001)
	- {
	- ScalarType dot = fiberDirection*g;
	- signal[i] = std::exp( -this->m_BValuem_Diffusivitydotdot ); // skip bVal becaus bVal is already encoded in the dot product (norm of g encodes b-value relative to baseline b-value m_BValue)
	- }
	- else
	- signal[i] = 1;
	- }
	-
	- return signal;
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkStickModel.h b/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkStickModel.h
	deleted file mode 100644
	index adba40c938..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkStickModel.h
	+++ /dev/null
	@@ -1,70 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_StickModel_H
	-#define _MITK_StickModel_H
	-
	-#include <mitkDiffusionSignalModel.h>
	-
	-namespace mitk {
	-
	-/**
	- * \brief Generates the diffusion signal using an idealised cylinder with zero radius: e^(-bd(ng)²)
	- *
	- */
	-
	-template< class ScalarType = double >
	-class StickModel : public DiffusionSignalModel< ScalarType >
	-{
	-public:
	-
	- StickModel();
	- template< class OtherType >StickModel(StickModel<OtherType>* model)
	- {
	- this->m_CompartmentId = model->m_CompartmentId;
	- this->m_T1 = model->GetT1();
	- this->m_T2 = model->GetT2();
	- this->m_GradientList = model->GetGradientList();
	- this->m_VolumeFractionImage = model->GetVolumeFractionImage();
	- this->m_RandGen = model->GetRandomGenerator();
	-
	- this->m_BValue = model->GetBvalue();
	- this->m_Diffusivity = model->GetDiffusivity();
	- }
	- ~StickModel();
	-
	- typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType;
	- typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType;
	- typedef typename DiffusionSignalModel< ScalarType >::GradientListType GradientListType;
	-
	- / Actual signal generation /
	- PixelType SimulateMeasurement(GradientType& fiberDirection) override;
	- ScalarType SimulateMeasurement(unsigned int dir, GradientType& fiberDirection) override;
	-
	- void SetDiffusivity(double diffusivity) { m_Diffusivity = diffusivity; } ///< Scalar diffusion constant
	- double GetDiffusivity() { return m_Diffusivity; }
	-
	-protected:
	-
	- double m_Diffusivity; ///< Scalar diffusion constant
	-};
	-
	-}
	-
	-#include "mitkStickModel.cpp"
	-
	-#endif
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkTensorModel.cpp b/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkTensorModel.cpp
	deleted file mode 100644
	index fd93cafc71..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkTensorModel.cpp
	+++ /dev/null
	@@ -1,124 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#include <vnl/vnl_cross.h>
	-#include <vnl/vnl_quaternion.h>
	-#include <mitkTensorModel.h>
	-
	-using namespace mitk;
	-
	-template< class ScalarType >
	-TensorModel< ScalarType >::TensorModel()
	-{
	- m_KernelDirection[0]=1; m_KernelDirection[1]=0; m_KernelDirection[2]=0;
	- m_KernelTensorMatrix.fill(0.0);
	- m_KernelTensorMatrix[0][0] = 0.002;
	- m_KernelTensorMatrix[1][1] = 0.0005;
	- m_KernelTensorMatrix[2][2] = 0.0005;
	-}
	-
	-template< class ScalarType >
	-TensorModel< ScalarType >::~TensorModel()
	-{
	-
	-}
	-
	-template< class ScalarType >
	-ScalarType TensorModel< ScalarType >::SimulateMeasurement(unsigned int dir, GradientType &fiberDirection)
	-{
	- ScalarType signal = 0;
	-
	- if (dir>=this->m_GradientList.size())
	- return signal;
	-
	- ItkTensorType tensor; tensor.Fill(0.0);
	- vnl_vector_fixed<double, 3> axis = itk::CrossProduct(m_KernelDirection, fiberDirection).GetVnlVector(); axis.normalize();
	- vnl_quaternion<double> rotation(axis, acos(m_KernelDirection*fiberDirection));
	- rotation.normalize();
	- vnl_matrix_fixed<double, 3, 3> matrix = rotation.rotation_matrix_transpose();
	-
	- vnl_matrix_fixed<double, 3, 3> tensorMatrix = matrix.transpose()m_KernelTensorMatrixmatrix;
	- tensor[0] = tensorMatrix[0][0]; tensor[1] = tensorMatrix[0][1]; tensor[2] = tensorMatrix[0][2];
	- tensor[3] = tensorMatrix[1][1]; tensor[4] = tensorMatrix[1][2]; tensor[5] = tensorMatrix[2][2];
	-
	- GradientType g = this->m_GradientList[dir];
	- if (g.GetNorm()>0.0001)
	- {
	- // calc g^T * D * g
	- itk::DiffusionTensor3D< ScalarType > S;
	- S[0] = g[0]*g[0];
	- S[1] = g[1]*g[0];
	- S[2] = g[2]*g[0];
	- S[3] = g[1]*g[1];
	- S[4] = g[2]*g[1];
	- S[5] = g[2]*g[2];
	-
	- ScalarType D_scalar = tensor[0]S[0] + tensor[1]S[1] + tensor[2]*S[2] +
	- tensor[1]S[1] + tensor[3]S[3] + tensor[4]*S[4] +
	- tensor[2]S[2] + tensor[4]S[4] + tensor[5]*S[5];
	-
	- // check for corrupted tensor and generate signal
	- if (D_scalar>=0)
	- signal = std::exp ( -this->m_BValue * D_scalar ); // skip * bVal becaus bVal is already encoded in g^T*g (norm of g encodes b-value relative to baseline b-value m_BValue)
	- }
	- else
	- signal = 1;
	-
	- return signal;
	-}
	-
	-template< class ScalarType >
	-typename TensorModel< ScalarType >::PixelType TensorModel< ScalarType >::SimulateMeasurement(GradientType& fiberDirection)
	-{
	- PixelType signal; signal.SetSize(this->m_GradientList.size()); signal.Fill(0.0);
	-
	- ItkTensorType tensor; tensor.Fill(0.0);
	- vnl_vector_fixed<double, 3> axis = itk::CrossProduct(m_KernelDirection, fiberDirection).GetVnlVector(); axis.normalize();
	- vnl_quaternion<double> rotation(axis, acos(m_KernelDirection*fiberDirection));
	- rotation.normalize();
	- vnl_matrix_fixed<double, 3, 3> matrix = rotation.rotation_matrix_transpose();
	-
	- vnl_matrix_fixed<double, 3, 3> tensorMatrix = matrix.transpose()m_KernelTensorMatrixmatrix;
	- tensor[0] = tensorMatrix[0][0]; tensor[1] = tensorMatrix[0][1]; tensor[2] = tensorMatrix[0][2];
	- tensor[3] = tensorMatrix[1][1]; tensor[4] = tensorMatrix[1][2]; tensor[5] = tensorMatrix[2][2];
	-
	- for( unsigned int i=0; i<this->m_GradientList.size(); i++)
	- {
	- GradientType g = this->m_GradientList[i];
	- if (g.GetNorm()>0.0001)
	- {
	- // calc g^T * D * g
	- itk::DiffusionTensor3D< ScalarType > S;
	- S[0] = g[0]*g[0];
	- S[1] = g[1]*g[0];
	- S[2] = g[2]*g[0];
	- S[3] = g[1]*g[1];
	- S[4] = g[2]*g[1];
	- S[5] = g[2]*g[2];
	-
	- ScalarType D_scalar = tensor[0]S[0] + tensor[1]S[1] + tensor[2]*S[2] +
	- tensor[1]S[1] + tensor[3]S[3] + tensor[4]*S[4] +
	- tensor[2]S[2] + tensor[4]S[4] + tensor[5]*S[5];
	-
	- // check for corrupted tensor and generate signal
	- if (D_scalar>=0)
	- signal[i] = std::exp ( -this->m_BValue * D_scalar ); // skip * bVal becaus bVal is already encoded in g^T*g (norm of g encodes b-value relative to baseline b-value m_BValue)
	- }
	- else
	- signal[i] = 1;
	- }
	-
	- return signal;
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkTensorModel.h b/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkTensorModel.h
	deleted file mode 100644
	index 8657f9d26e..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/SignalModels/mitkTensorModel.h
	+++ /dev/null
	@@ -1,83 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_TensorModel_H
	-#define _MITK_TensorModel_H
	-
	-#include <mitkDiffusionSignalModel.h>
	-#include <itkDiffusionTensor3D.h>
	-
	-namespace mitk {
	-
	-/**
	- * \brief Generates diffusion measurement employing a second rank tensor model: e^(-bg^TDg)
	- *
	- */
	-
	-template< class ScalarType = double >
	-class TensorModel : public DiffusionSignalModel< ScalarType >
	-{
	-public:
	-
	- TensorModel();
	- template< class OtherType >TensorModel(TensorModel<OtherType>* model)
	- {
	- this->m_CompartmentId = model->m_CompartmentId;
	- this->m_T1 = model->GetT1();
	- this->m_T2 = model->GetT2();
	- this->m_GradientList = model->GetGradientList();
	- this->m_VolumeFractionImage = model->GetVolumeFractionImage();
	- this->m_RandGen = model->GetRandomGenerator();
	-
	- this->m_BValue = model->GetBvalue();
	- this->m_KernelDirection = model->GetKernelDirection();
	- this->m_KernelTensorMatrix = model->GetKernelTensorMatrix();
	- }
	- ~TensorModel();
	-
	- typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType;
	- typedef itk::DiffusionTensor3D< ScalarType > ItkTensorType;
	- typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType;
	- typedef typename DiffusionSignalModel< ScalarType >::GradientListType GradientListType;
	-
	- / Actual signal generation /
	- PixelType SimulateMeasurement(GradientType& fiberDirection) override;
	- ScalarType SimulateMeasurement(unsigned int dir, GradientType& fiberDirection) override;
	-
	- void SetDiffusivity1(double d1){ m_KernelTensorMatrix[0][0] = d1; }
	- void SetDiffusivity2(double d2){ m_KernelTensorMatrix[1][1] = d2; }
	- void SetDiffusivity3(double d3){ m_KernelTensorMatrix[2][2] = d3; }
	- double GetDiffusivity1() { return m_KernelTensorMatrix[0][0]; }
	- double GetDiffusivity2() { return m_KernelTensorMatrix[1][1]; }
	- double GetDiffusivity3() { return m_KernelTensorMatrix[2][2]; }
	-
	- GradientType GetKernelDirection(){ return m_KernelDirection; }
	- vnl_matrix_fixed<double, 3, 3> GetKernelTensorMatrix(){ return m_KernelTensorMatrix; }
	-
	-protected:
	-
	- / Calculates tensor matrix from FA and ADC /
	- void UpdateKernelTensor();
	- GradientType m_KernelDirection; ///< Direction of the kernel tensors principal eigenvector
	- vnl_matrix_fixed<double, 3, 3> m_KernelTensorMatrix; ///< 3x3 matrix containing the kernel tensor values
	-};
	-
	-}
	-
	-#include "mitkTensorModel.cpp"
	-
	-#endif
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkDftImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkDftImageFilter.cpp
	deleted file mode 100644
	index bc98defebd..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkDftImageFilter.cpp
	+++ /dev/null
	@@ -1,94 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkDftImageFilter_txx
	-#define __itkDftImageFilter_txx
	-
	-#include <ctime>
	-#include <cstdio>
	-#include <cstdlib>
	-
	-#include "itkDftImageFilter.h"
	-#include <itkImageRegionConstIterator.h>
	-#include <itkImageRegionConstIteratorWithIndex.h>
	-#include <itkImageRegionIterator.h>
	-
	-namespace itk {
	-
	-template< class TPixelType >
	-DftImageFilter< TPixelType >
	-::DftImageFilter()
	-{
	- this->SetNumberOfRequiredInputs( 1 );
	-}
	-
	-template< class TPixelType >
	-void DftImageFilter< TPixelType >
	-::BeforeThreadedGenerateData()
	-{
	-
	-}
	-
	-template< class TPixelType >
	-void DftImageFilter< TPixelType >
	-::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, ThreadIdType)
	-{
	- typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0));
	-
	- ImageRegionIterator< OutputImageType > oit(outputImage, outputRegionForThread);
	-
	- typedef ImageRegionConstIterator< InputImageType > InputIteratorType;
	- typename InputImageType::Pointer inputImage = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) );
	-
	- float szx = outputImage->GetLargestPossibleRegion().GetSize(0);
	- float szy = outputImage->GetLargestPossibleRegion().GetSize(1);
	-
	- float x_shift = 0;
	- float y_shift = 0;
	- if (static_cast<int>(szx)%2==1)
	- x_shift = (szx-1)/2;
	- else
	- x_shift = szx/2;
	- if (static_cast<int>(szy)%2==1)
	- y_shift = (szy-1)/2;
	- else
	- y_shift = szy/2;
	-
	- while( !oit.IsAtEnd() )
	- {
	- float kx = oit.GetIndex()[0] - x_shift;
	- float ky = oit.GetIndex()[1] - y_shift;
	- kx /= szx;
	- ky /= szy;
	-
	- vcl_complex<TPixelType> s(0,0);
	- InputIteratorType it(inputImage, inputImage->GetLargestPossibleRegion() );
	- while( !it.IsAtEnd() )
	- {
	- float x = it.GetIndex()[0] - x_shift;
	- float y = it.GetIndex()[1] - y_shift;
	-
	- s += it.Get() * exp( std::complex<TPixelType>(0, -itk::Math::twopi * (kxx + kyy) ) );
	- ++it;
	- }
	-
	- oit.Set(s);
	- ++oit;
	- }
	-}
	-
	-}
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkDftImageFilter.h b/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkDftImageFilter.h
	deleted file mode 100644
	index 2960a600e7..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkDftImageFilter.h
	+++ /dev/null
	@@ -1,80 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-/*===================================================================
	-
	-This file is based heavily on a corresponding ITK filter.
	-
	-===================================================================*/
	-#ifndef __itkDftImageFilter_h_
	-#define __itkDftImageFilter_h_
	-
	-#include <MitkFiberTrackingExports.h>
	-#include <itkImageToImageFilter.h>
	-#include <itkDiffusionTensor3D.h>
	-#include <vcl_complex.h>
	-#include <mitkFiberfoxParameters.h>
	-
	-namespace itk{
	-
	-/**
	-* \brief 2D Discrete Fourier Transform Filter (complex to real). Special issue for Fiberfox -> rearranges slice. */
	-
	-template< class TPixelType >
	-class DftImageFilter :
	- public ImageToImageFilter< Image< vcl_complex< TPixelType > >, Image< vcl_complex< TPixelType > > >
	-{
	-
	-public:
	-
	- typedef DftImageFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageToImageFilter< Image< vcl_complex< TPixelType > >, Image< vcl_complex< TPixelType > > > Superclass;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(DftImageFilter, ImageToImageFilter)
	-
	- typedef typename Superclass::InputImageType InputImageType;
	- typedef typename Superclass::OutputImageType OutputImageType;
	- typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
	-
	- void SetParameters( FiberfoxParameters& param ){ m_Parameters = param; }
	-
	-protected:
	- DftImageFilter();
	- ~DftImageFilter() override {}
	-
	- void BeforeThreadedGenerateData() override;
	- void ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, ThreadIdType threadId) override;
	-
	-private:
	-
	- FiberfoxParameters m_Parameters;
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkDftImageFilter.cpp"
	-#endif
	-
	-#endif //__itkDftImageFilter_h_
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkFibersFromPlanarFiguresFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkFibersFromPlanarFiguresFilter.cpp
	deleted file mode 100644
	index a96514f0ef..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkFibersFromPlanarFiguresFilter.cpp
	+++ /dev/null
	@@ -1,248 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkibersFromPlanarFiguresFilter_cpp
	-#define __itkibersFromPlanarFiguresFilter_cpp
	-
	-#include "itkFibersFromPlanarFiguresFilter.h"
	-
	-#include <itkOrientationDistributionFunction.h>
	-#include <itkDiffusionOdfGeneralizedFaImageFilter.h>
	-#include <mitkStandardFileLocations.h>
	-#include <mitkFiberBuilder.h>
	-#include <mitkMetropolisHastingsSampler.h>
	-#include <itkTensorImageToOdfImageFilter.h>
	-#include <mitkGibbsEnergyComputer.h>
	-#include <mitkRotationOperation.h>
	-#include <mitkInteractionConst.h>
	-
	-#include <itkImageDuplicator.h>
	-#include <itkResampleImageFilter.h>
	-#include <itkTimeProbe.h>
	-#include <itkMersenneTwisterRandomVariateGenerator.h>
	-
	-#include <cmath>
	-
	-namespace itk{
	-
	-FibersFromPlanarFiguresFilter::FibersFromPlanarFiguresFilter()
	- : m_FixSeed(false)
	-{
	-
	-}
	-
	-FibersFromPlanarFiguresFilter::~FibersFromPlanarFiguresFilter()
	-{
	-
	-}
	-
	-
	-void FibersFromPlanarFiguresFilter::GeneratePoints()
	-{
	- Statistics::MersenneTwisterRandomVariateGenerator::Pointer randGen = Statistics::MersenneTwisterRandomVariateGenerator::New();
	- if (m_FixSeed)
	- randGen->SetSeed(0);
	- else
	- randGen->SetSeed();
	- m_2DPoints.clear();
	- unsigned int count = 0;
	-
	- while (count < m_Parameters.m_Density)
	- {
	- mitk::Vector2D p;
	- switch (m_Parameters.m_Distribution) {
	- case FiberGenerationParameters::DISTRIBUTE_GAUSSIAN:
	- p[0] = randGen->GetNormalVariate(0, m_Parameters.m_Variance);
	- p[1] = randGen->GetNormalVariate(0, m_Parameters.m_Variance);
	- break;
	- default:
	- p[0] = randGen->GetUniformVariate(-1, 1);
	- p[1] = randGen->GetUniformVariate(-1, 1);
	- }
	-
	- if (sqrt(p[0]p[0]+p[1]p[1]) <= 1)
	- {
	- m_2DPoints.push_back(p);
	- count++;
	- }
	- }
	-}
	-
	-void FibersFromPlanarFiguresFilter::SetFixSeed(bool FixSeed)
	-{
	- m_FixSeed = FixSeed;
	-}
	-
	-void FibersFromPlanarFiguresFilter::GenerateData()
	-{
	- // check if enough fiducials are available
	- for (unsigned int i=0; i<m_Parameters.m_Fiducials.size(); i++)
	- if (m_Parameters.m_Fiducials.at(i).size()<2)
	- itkExceptionMacro("At least 2 fiducials needed per fiber bundle!");
	-
	- for (unsigned int i=0; i<m_Parameters.m_Fiducials.size(); i++)
	- {
	- vtkSmartPointer<vtkCellArray> m_VtkCellArray = vtkSmartPointer<vtkCellArray>::New();
	- vtkSmartPointer<vtkPoints> m_VtkPoints = vtkSmartPointer<vtkPoints>::New();
	-
	- std::vector< mitk::PlanarEllipse::Pointer > bundle = m_Parameters.m_Fiducials.at(i);
	-
	- std::vector< unsigned int > fliplist;
	- if (i<m_Parameters.m_FlipList.size())
	- fliplist = m_Parameters.m_FlipList.at(i);
	- else
	- fliplist.resize(bundle.size(), 0);
	- if (fliplist.size()<bundle.size())
	- fliplist.resize(bundle.size(), 0);
	-
	- GeneratePoints();
	- for (unsigned int j = 0; j < m_Parameters.m_Density; ++j)
	- {
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	-
	- mitk::PlanarEllipse::Pointer figure = bundle.at(0);
	- mitk::Point2D p0 = figure->GetControlPoint(0);
	- mitk::Point2D p1 = figure->GetControlPoint(1);
	- mitk::Point2D p2 = figure->GetControlPoint(2);
	- mitk::Point2D p3 = figure->GetControlPoint(3);
	- double r1 = p0.EuclideanDistanceTo(p1);
	- double r2 = p0.EuclideanDistanceTo(p2);
	- mitk::Vector2D eDir = p1-p0; eDir.Normalize();
	- mitk::Vector2D tDir = p3-p0; tDir.Normalize();
	-
	- // apply twist
	- vnl_matrix_fixed<double, 2, 2> tRot;
	- tRot[0][0] = tDir[0];
	- tRot[1][1] = tRot[0][0];
	- tRot[1][0] = sin(acos(tRot[0][0]));
	- tRot[0][1] = -tRot[1][0];
	- if (tDir[1]<0)
	- tRot.inplace_transpose();
	- m_2DPoints[j].SetVnlVector(tRot*m_2DPoints[j].GetVnlVector());
	-
	- // apply new ellipse shape
	- vnl_vector_fixed< double, 2 > newP;
	- newP[0] = m_2DPoints.at(j)[0];
	- newP[1] = m_2DPoints.at(j)[1];
	- double alpha = acos(eDir[0]);
	- if (eDir[1]>0)
	- alpha = 2*itk::Math::pi-alpha;
	- vnl_matrix_fixed<double, 2, 2> eRot;
	- eRot[0][0] = cos(alpha);
	- eRot[1][1] = eRot[0][0];
	- eRot[1][0] = sin(alpha);
	- eRot[0][1] = -eRot[1][0];
	- newP = eRot*newP;
	- newP[0] *= r1;
	- newP[1] *= r2;
	- newP = eRot.transpose()*newP;
	-
	- p0[0] += newP[0];
	- p0[1] += newP[1];
	-
	- const mitk::PlaneGeometry* planeGeo = figure->GetPlaneGeometry();
	-
	- mitk::Point3D w, wc;
	- planeGeo->Map(p0, w);
	-
	- wc = figure->GetWorldControlPoint(0);
	-
	- vtkIdType id = m_VtkPoints->InsertNextPoint(w.GetDataPointer());
	- container->GetPointIds()->InsertNextId(id);
	-
	- vnl_vector_fixed< double, 3 > n = planeGeo->GetNormalVnl();
	-
	- for (unsigned int k=1; k<bundle.size(); k++)
	- {
	- figure = bundle.at(k);
	- p0 = figure->GetControlPoint(0);
	- p1 = figure->GetControlPoint(1);
	- p2 = figure->GetControlPoint(2);
	- p3 = figure->GetControlPoint(3);
	- r1 = p0.EuclideanDistanceTo(p1);
	- r2 = p0.EuclideanDistanceTo(p2);
	-
	- eDir = p1-p0; eDir.Normalize();
	- mitk::Vector2D tDir2 = p3-p0; tDir2.Normalize();
	- mitk::Vector2D temp; temp.Fill(0);
	- temp.SetVnlVector(tRot.transpose() * tDir2.GetVnlVector());
	-
	- // apply twist
	- tRot[0][0] = tDir[0]tDir2[0] + tDir[1]tDir2[1];
	- if (tRot[0][0]>1.0)
	- tRot[0][0] = 1.0;
	- tRot[1][1] = tRot[0][0];
	- tRot[1][0] = sin(acos(tRot[0][0]));
	- tRot[0][1] = -tRot[1][0];
	- if (temp[1]<0)
	- tRot.inplace_transpose();
	- m_2DPoints[j].SetVnlVector(tRot*m_2DPoints[j].GetVnlVector());
	- tDir = tDir2;
	-
	- // apply new ellipse shape
	- newP[0] = m_2DPoints.at(j)[0];
	- newP[1] = m_2DPoints.at(j)[1];
	-
	- // calculate normal
	- mitk::PlaneGeometry* planeGeo = const_cast<mitk::PlaneGeometry*>(figure->GetPlaneGeometry());
	- mitk::Vector3D perp = wc-planeGeo->ProjectPointOntoPlane(wc); perp.Normalize();
	- vnl_vector_fixed< double, 3 > n2 = planeGeo->GetNormalVnl();
	- wc = figure->GetWorldControlPoint(0);
	-
	- // is flip needed?
	- if (dot_product(perp.GetVnlVector(),n2)>0 && dot_product(n,n2)<=0.00001)
	- newP[0] *= -1;
	- if (fliplist.at(k)>0)
	- newP[0] *= -1;
	- n = n2;
	-
	- alpha = acos(eDir[0]);
	- if (eDir[1]>0)
	- alpha = 2*itk::Math::pi-alpha;
	- eRot[0][0] = cos(alpha);
	- eRot[1][1] = eRot[0][0];
	- eRot[1][0] = sin(alpha);
	- eRot[0][1] = -eRot[1][0];
	- newP = eRot*newP;
	- newP[0] *= r1;
	- newP[1] *= r2;
	- newP = eRot.transpose()*newP;
	-
	- p0[0] += newP[0];
	- p0[1] += newP[1];
	-
	- mitk::Point3D w;
	- planeGeo->Map(p0, w);
	-
	- vtkIdType id = m_VtkPoints->InsertNextPoint(w.GetDataPointer());
	- container->GetPointIds()->InsertNextId(id);
	- }
	-
	- m_VtkCellArray->InsertNextCell(container);
	- }
	-
	- vtkSmartPointer<vtkPolyData> fiberPolyData = vtkSmartPointer<vtkPolyData>::New();
	- fiberPolyData->SetPoints(m_VtkPoints);
	- fiberPolyData->SetLines(m_VtkCellArray);
	- mitk::FiberBundle::Pointer mitkFiberBundle = mitk::FiberBundle::New(fiberPolyData);
	- mitkFiberBundle->ResampleSpline(m_Parameters.m_Sampling, m_Parameters.m_Tension, m_Parameters.m_Continuity, m_Parameters.m_Bias);
	- m_FiberBundles.push_back(mitkFiberBundle);
	- }
	-}
	-
	-}
	-#endif // __itkFibersFromPlanarFiguresFilter_cpp
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkFibersFromPlanarFiguresFilter.h b/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkFibersFromPlanarFiguresFilter.h
	deleted file mode 100644
	index ea1445b073..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkFibersFromPlanarFiguresFilter.h
	+++ /dev/null
	@@ -1,88 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef itkFibersFromPlanarFiguresFilter_h
	-#define itkFibersFromPlanarFiguresFilter_h
	-
	-// MITK
	-#include <mitkPlanarEllipse.h>
	-#include <mitkFiberBundle.h>
	-#include <mitkFiberfoxParameters.h>
	-
	-// ITK
	-#include <itkProcessObject.h>
	-
	-// VTK
	-#include <vtkSmartPointer.h>
	-#include <vtkPolyData.h>
	-#include <vtkCellArray.h>
	-#include <vtkPoints.h>
	-#include <vtkPolyLine.h>
	-
	-namespace itk{
	-
	-/**
	-* \brief Generates artificial fibers distributed in and interpolated between the input planar figures. */
	-
	-class FibersFromPlanarFiguresFilter : public ProcessObject
	-{
	-public:
	-
	- typedef FibersFromPlanarFiguresFilter Self;
	- typedef ProcessObject Superclass;
	- typedef SmartPointer< Self > Pointer;
	- typedef SmartPointer< const Self > ConstPointer;
	- typedef mitk::FiberBundle::Pointer FiberType;
	- typedef std::vector< mitk::FiberBundle::Pointer > FiberContainerType;
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- itkTypeMacro( FibersFromPlanarFiguresFilter, ProcessObject )
	-
	- void Update() override{
	- this->GenerateData();
	- }
	-
	- // input
	- void SetParameters( FiberGenerationParameters param ) ///< Simulation parameters.
	- {
	- m_Parameters = param;
	- }
	-
	- // output
	- FiberContainerType GetFiberBundles(){ return m_FiberBundles; }
	-
	- void SetFixSeed(bool FixSeed);
	-
	-protected:
	-
	- void GenerateData() override;
	-
	- FibersFromPlanarFiguresFilter();
	- ~FibersFromPlanarFiguresFilter() override;
	- void GeneratePoints();
	-
	- FiberContainerType m_FiberBundles; ///< container for the output fiber bundles
	- std::vector< mitk::Vector2D > m_2DPoints; ///< container for the 2D fiber waypoints
	- FiberGenerationParameters m_Parameters;
	- bool m_FixSeed;
	-};
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkFibersFromPlanarFiguresFilter.cpp"
	-#endif
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkFieldmapGeneratorFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkFieldmapGeneratorFilter.cpp
	deleted file mode 100644
	index c4ef958c38..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkFieldmapGeneratorFilter.cpp
	+++ /dev/null
	@@ -1,79 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Coindex[1]right (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#include "itkFieldmapGeneratorFilter.h"
	-
	-#include <itkImageRegionIterator.h>
	-#include <math.h>
	-#include <itkPoint.h>
	-
	-namespace itk{
	-
	-template< class OutputImageType >
	-FieldmapGeneratorFilter< OutputImageType >::FieldmapGeneratorFilter()
	-{
	- m_Gradient.fill(0.0);
	- m_Offset.fill(0.0);
	-}
	-
	-template< class OutputImageType >
	-FieldmapGeneratorFilter< OutputImageType >::~FieldmapGeneratorFilter()
	-{
	-}
	-
	-template< class OutputImageType >
	-void FieldmapGeneratorFilter< OutputImageType >::BeforeThreadedGenerateData()
	-{
	- typename OutputImageType::Pointer outImage = OutputImageType::New();
	- outImage->SetSpacing( m_Spacing );
	- outImage->SetOrigin( m_Origin );
	- outImage->SetDirection( m_DirectionMatrix );
	- outImage->SetLargestPossibleRegion( m_ImageRegion );
	- outImage->SetBufferedRegion( m_ImageRegion );
	- outImage->SetRequestedRegion( m_ImageRegion );
	- outImage->Allocate();
	- outImage->FillBuffer(0);
	- this->SetNthOutput(0, outImage);
	-}
	-
	-template< class OutputImageType >
	-void FieldmapGeneratorFilter< OutputImageType >::ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, ThreadIdType threadId)
	-{
	- typename OutputImageType::Pointer outImage = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0));
	- ImageRegionIterator< OutputImageType > oit(outImage, outputRegionForThread);
	-
	- while( !oit.IsAtEnd() )
	- {
	- double value = 0;
	- IndexType idx = oit.GetIndex();
	- for (int i=0; i<3; i++)
	- value += idx[i]*m_Gradient[i] + m_Offset[i];
	-
	- for (unsigned int i=0; i<m_WorldPositions.size(); i++)
	- {
	- mitk::Point3D c = m_WorldPositions.at(i);
	- itk::Point<double, 3> vertex;
	- outImage->TransformIndexToPhysicalPoint(idx, vertex);
	- double dist = c.EuclideanDistanceTo(vertex);
	- value += m_Heights.at(i)exp(-distdist/(2*m_Variances.at(i)));
	- }
	- oit.Set(value);
	- ++oit;
	- }
	-
	- MITK_INFO << "Thread " << threadId << "finished processing";
	-}
	-
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkFieldmapGeneratorFilter.h b/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkFieldmapGeneratorFilter.h
	deleted file mode 100644
	index 74e17eb311..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkFieldmapGeneratorFilter.h
	+++ /dev/null
	@@ -1,93 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef __itkFieldmapGeneratorFilter_h__
	-#define __itkFieldmapGeneratorFilter_h__
	-
	-#include <itkImageSource.h>
	-#include <itkImage.h>
	-#include <itkImageRegion.h>
	-#include <itkVector.h>
	-#include <mitkNumericTypes.h>
	-#include <itkMatrix.h>
	-#include <vector>
	-
	-namespace itk{
	-
	-/**
	-* \brief Generate float image with artificial frequency maps used by Fiberfox. Simulates additional frequencies at (possibly multiple) positions based on 3D gaussians with the specified variance and amplitude and/or as a linear gradient in the image.
	-* See "Fiberfox: Facilitating the creation of realistic white matter software phantoms" (DOI: 10.1002/mrm.25045) for details.
	-*/
	-
	-template< class OutputImageType >
	-class FieldmapGeneratorFilter : public ImageSource< OutputImageType >
	-{
	-
	-public:
	- typedef FieldmapGeneratorFilter Self;
	- typedef ProcessObject Superclass;
	- typedef SmartPointer< Self > Pointer;
	- typedef SmartPointer< const Self > ConstPointer;
	-
	- typedef typename OutputImageType::PixelType PixelType;
	- typedef typename OutputImageType::IndexType IndexType;
	- typedef itk::ImageRegion<3> OutputImageRegionType;
	- typedef itk::Matrix<double, 3, 3> MatrixType;
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- itkTypeMacro( FieldmapGeneratorFilter, ImageSource )
	-
	- /** Output image parameters. */
	- itkSetMacro( Spacing, itk::Vector<double> )
	- itkSetMacro( Origin, mitk::Point3D )
	- itkSetMacro( DirectionMatrix, MatrixType )
	- itkSetMacro( ImageRegion, OutputImageRegionType )
	-
	- /** Gradient direction and offset. */
	- void SetGradient( vnl_vector_fixed< double, 3 > gradient ) { m_Gradient=gradient; }
	- void SetOffset( vnl_vector_fixed< double, 3 > offset ) { m_Offset=offset; }
	-
	- /** Parameters of gaussian frequency sources. */
	- void SetVariances( std::vector< double > variances ) { m_Variances=variances; }
	- void SetHeights( std::vector< double > heights ) { m_Heights=heights; }
	- void SetWorldPositions( std::vector< mitk::Point3D > worldPositions ) { m_WorldPositions=worldPositions; }
	-
	-protected:
	-
	- void BeforeThreadedGenerateData();
	- void ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, ThreadIdType threadId);
	-
	- FieldmapGeneratorFilter();
	- virtual ~FieldmapGeneratorFilter();
	-
	- itk::Vector<double> m_Spacing; ///< output image spacing
	- mitk::Point3D m_Origin; ///< output image origin
	- MatrixType m_DirectionMatrix; ///< output image rotation
	- OutputImageRegionType m_ImageRegion; ///< output image size
	- std::vector< double > m_Variances;
	- std::vector< double > m_Heights;
	- std::vector< mitk::Point3D > m_WorldPositions;
	- vnl_vector_fixed< double, 3 > m_Gradient;
	- vnl_vector_fixed< double, 3 > m_Offset;
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkFieldmapGeneratorFilter.cpp"
	-#endif
	-
	-#endif // __itkFieldmapGeneratorFilter_h__
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkKspaceImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkKspaceImageFilter.cpp
	deleted file mode 100644
	index b736e30811..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkKspaceImageFilter.cpp
	+++ /dev/null
	@@ -1,512 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkKspaceImageFilter_txx
	-#define __itkKspaceImageFilter_txx
	-//#endif
	-
	-#include <ctime>
	-#include <cstdio>
	-#include <cstdlib>
	-#include <math.h>
	-
	-#include "itkKspaceImageFilter.h"
	-#include <itkImageRegionConstIterator.h>
	-#include <itkImageRegionConstIteratorWithIndex.h>
	-#include <itkImageRegionIterator.h>
	-#include <mitkSingleShotEpi.h>
	-#include <mitkConventionalSpinEcho.h>
	-#include <mitkFastSpinEcho.h>
	-#include <mitkDiffusionFunctionCollection.h>
	-#include <itkImageFileWriter.h>
	-
	-namespace itk {
	-
	- template< class ScalarType >
	- KspaceImageFilter< ScalarType >::KspaceImageFilter()
	- : m_Z(0)
	- , m_RandSeed(-1)
	- , m_SpikesPerSlice(0)
	- , m_IsBaseline(true)
	- , m_StoreTimings(false)
	- {
	- m_DiffusionGradientDirection.Fill(0.0);
	- m_CoilPosition.Fill(0.0);
	- }
	-
	- template< class ScalarType >
	- void KspaceImageFilter< ScalarType >
	- ::BeforeThreadedGenerateData()
	- {
	- m_Spike = vcl_complex<ScalarType>(0,0);
	- m_SpikeLog = "";
	- m_TransX = -m_Translation[0];
	- m_TransY = -m_Translation[1];
	- m_TransZ = -m_Translation[2];
	-
	- kxMax = m_Parameters->m_SignalGen.m_CroppedRegion.GetSize(0);
	- kyMax = m_Parameters->m_SignalGen.m_CroppedRegion.GetSize(1);
	- xMax = m_CompartmentImages.at(0)->GetLargestPossibleRegion().GetSize(0); // scanner coverage in x-direction
	- yMax = m_CompartmentImages.at(0)->GetLargestPossibleRegion().GetSize(1); // scanner coverage in y-direction
	- yMaxFov = yMax;
	- if (m_Parameters->m_Misc.m_DoAddAliasing)
	- {
	- // actual FOV in y-direction (in x-direction FOV=xMax)
	- yMaxFov = static_cast<int>(yMaxFov * m_Parameters->m_SignalGen.m_CroppingFactor);
	- }
	- yMaxFov_half = (yMaxFov-1)/2;
	- numPix = kxMax*kyMax;
	-
	- float ringing_factor = static_cast<float>(m_Parameters->m_SignalGen.m_ZeroRinging)/100.0;
	- ringing_lines_x = static_cast<int>(ceil(kxMax/2 * ringing_factor));
	- ringing_lines_y = static_cast<int>(ceil(kyMax/2 * ringing_factor));
	-
	- // Adjust noise variance since it is the intended variance in physical space and not in k-space:
	- float noiseVar = m_Parameters->m_SignalGen.m_PartialFourierm_Parameters->m_SignalGen.m_NoiseVariance/(kyMaxkxMax);
	-
	- m_RandGen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New();
	- if (m_RandSeed>=0) // always generate the same random numbers?
	- m_RandGen->SetSeed(m_RandSeed);
	- else
	- m_RandGen->SetSeed();
	-
	- typename OutputImageType::Pointer outputImage = OutputImageType::New();
	- itk::ImageRegion<2> region;
	- region.SetSize(0, m_Parameters->m_SignalGen.m_CroppedRegion.GetSize(0));
	- region.SetSize(1, m_Parameters->m_SignalGen.m_CroppedRegion.GetSize(1));
	- outputImage->SetLargestPossibleRegion( region );
	- outputImage->SetBufferedRegion( region );
	- outputImage->SetRequestedRegion( region );
	- outputImage->Allocate();
	- vcl_complex<ScalarType> zero = vcl_complex<ScalarType>(0, 0);
	- outputImage->FillBuffer(zero);
	- if (m_Parameters->m_SignalGen.m_NoiseVariance>0 && m_Parameters->m_Misc.m_DoAddNoise)
	- {
	- ImageRegionIterator< OutputImageType > oit(outputImage, outputImage->GetLargestPossibleRegion());
	- while( !oit.IsAtEnd() )
	- {
	- oit.Set(vcl_complex<ScalarType>(m_RandGen->GetNormalVariate(0, noiseVar), m_RandGen->GetNormalVariate(0, noiseVar)));
	- ++oit;
	- }
	- }
	-
	- m_KSpaceImage = InputImageType::New();
	- m_KSpaceImage->SetLargestPossibleRegion( region );
	- m_KSpaceImage->SetBufferedRegion( region );
	- m_KSpaceImage->SetRequestedRegion( region );
	- m_KSpaceImage->Allocate();
	- m_KSpaceImage->FillBuffer(0.0);
	-
	- if (m_StoreTimings)
	- {
	- m_TickImage = InputImageType::New();
	- m_TickImage->SetLargestPossibleRegion( region );
	- m_TickImage->SetBufferedRegion( region );
	- m_TickImage->SetRequestedRegion( region );
	- m_TickImage->Allocate();
	- m_TickImage->FillBuffer(-1.0);
	-
	- m_RfImage = InputImageType::New();
	- m_RfImage->SetLargestPossibleRegion( region );
	- m_RfImage->SetBufferedRegion( region );
	- m_RfImage->SetRequestedRegion( region );
	- m_RfImage->Allocate();
	- m_RfImage->FillBuffer(-1.0);
	- }
	- else
	- {
	- m_TickImage = nullptr;
	- m_RfImage = nullptr;
	- }
	-
	- m_Gamma = 42576000*itk::Math::twopi; // Gyromagnetic ratio in Hz/T
	- if ( m_Parameters->m_SignalGen.m_EddyStrength>0 && m_DiffusionGradientDirection.GetNorm()>0.001)
	- {
	- m_DiffusionGradientDirection = m_DiffusionGradientDirection * m_Parameters->m_SignalGen.m_EddyStrength/1000 * m_Gamma;
	- m_IsBaseline = false;
	- }
	- else {
	- m_IsBaseline = true;
	- }
	-
	- this->SetNthOutput(0, outputImage);
	-
	- for (int i=0; i<3; i++)
	- for (int j=0; j<3; j++)
	- m_Transform[i][j] = m_Parameters->m_SignalGen.m_ImageDirection[i][j] * m_Parameters->m_SignalGen.m_ImageSpacing[j]/1000;
	-
	- float a = m_Parameters->m_SignalGen.m_ImageRegion.GetSize(0)*m_Parameters->m_SignalGen.m_ImageSpacing[0];
	- float b = m_Parameters->m_SignalGen.m_ImageRegion.GetSize(1)*m_Parameters->m_SignalGen.m_ImageSpacing[1];
	- float diagonal = sqrt(aa+bb)/1000; // image diagonal in m
	-
	- switch (m_Parameters->m_SignalGen.m_CoilSensitivityProfile)
	- {
	- case SignalGenerationParameters::COIL_CONSTANT:
	- {
	- m_CoilSensitivityFactor = 1; // same signal everywhere
	- break;
	- }
	- case SignalGenerationParameters::COIL_LINEAR:
	- {
	- m_CoilSensitivityFactor = -1/diagonal; // about 50% of the signal in the image center remaining
	- break;
	- }
	- case SignalGenerationParameters::COIL_EXPONENTIAL:
	- {
	- m_CoilSensitivityFactor = -log(0.1)/diagonal; // about 32% of the signal in the image center remaining
	- break;
	- }
	- }
	-
	- switch (m_Parameters->m_SignalGen.m_AcquisitionType)
	- {
	- case SignalGenerationParameters::SingleShotEpi:
	- m_ReadoutScheme = new mitk::SingleShotEpi(m_Parameters);
	- break;
	- case SignalGenerationParameters::ConventionalSpinEcho:
	- m_ReadoutScheme = new mitk::ConventionalSpinEcho(m_Parameters);
	- break;
	- case SignalGenerationParameters::FastSpinEcho:
	- m_ReadoutScheme = new mitk::FastSpinEcho(m_Parameters);
	- break;
	- default:
	- m_ReadoutScheme = new mitk::SingleShotEpi(m_Parameters);
	- }
	-
	- m_ReadoutScheme->AdjustEchoTime();
	-
	- m_MovedFmap = nullptr;
	- if (m_Parameters->m_Misc.m_DoAddDistortions && m_Parameters->m_SignalGen.m_FrequencyMap.IsNotNull() && m_Parameters->m_SignalGen.m_DoAddMotion)
	- {
	- // we have to account for the head motion since this also moves our frequency map
	- itk::LinearInterpolateImageFunction< itk::Image< float, 3 >, float >::Pointer fmapInterpolator;
	- fmapInterpolator = itk::LinearInterpolateImageFunction< itk::Image< float, 3 >, float >::New();
	- fmapInterpolator->SetInputImage(m_Parameters->m_SignalGen.m_FrequencyMap);
	-
	- m_MovedFmap = itk::Image< ScalarType, 2 >::New();
	- m_MovedFmap->SetLargestPossibleRegion( m_CompartmentImages.at(0)->GetLargestPossibleRegion() );
	- m_MovedFmap->SetBufferedRegion( m_CompartmentImages.at(0)->GetLargestPossibleRegion() );
	- m_MovedFmap->SetRequestedRegion( m_CompartmentImages.at(0)->GetLargestPossibleRegion() );
	- m_MovedFmap->Allocate();
	- m_MovedFmap->FillBuffer(0);
	-
	- ImageRegionIterator< InputImageType > it(m_MovedFmap, m_MovedFmap->GetLargestPossibleRegion() );
	- while( !it.IsAtEnd() )
	- {
	- itk::Image<float, 3>::IndexType index;
	- index[0] = it.GetIndex()[0];
	- index[1] = it.GetIndex()[1];
	- index[2] = m_Zidx;
	-
	- itk::Point<float, 3> point3D;
	- m_Parameters->m_SignalGen.m_FrequencyMap->TransformIndexToPhysicalPoint(index, point3D);
	- m_FiberBundle->TransformPoint<float>( point3D, m_RotationMatrix, m_TransX, m_TransY, m_TransZ );
	- it.Set(mitk::imv::GetImageValue<float>(point3D, true, fmapInterpolator));
	- ++it;
	- }
	- }
	-
	- // calculate T1 relaxation (independent of actual readout)
	- m_T1Relax.clear();
	- if ( m_Parameters->m_SignalGen.m_DoSimulateRelaxation)
	- for (unsigned int i=0; i<m_CompartmentImages.size(); i++)
	- {
	- // account for T1 relaxation (how much magnetization is available since last excitation?)
	- float relaxation = (1.0-std::exp(-m_Parameters->m_SignalGen.m_tRep/m_T1[i]));
	-
	- // account for inversion pulse and TI
	- if (m_Parameters->m_SignalGen.m_tInv > 0)
	- relaxation *= (1.0-std::exp(std::log(2) - m_Parameters->m_SignalGen.m_tInv/m_T1[i]));
	-
	- m_T1Relax.push_back(relaxation);
	- }
	- }
	-
	- template< class ScalarType >
	- float KspaceImageFilter< ScalarType >::CoilSensitivity(VectorType& pos)
	- {
	- // *************************************************************************
	- // Coil ring is moving with excited slice (FIX THIS SOMETIME)
	- m_CoilPosition[2] = pos[2];
	- // *************************************************************************
	-
	- switch (m_Parameters->m_SignalGen.m_CoilSensitivityProfile)
	- {
	- case SignalGenerationParameters::COIL_CONSTANT:
	- return 1;
	- case SignalGenerationParameters::COIL_LINEAR:
	- {
	- VectorType diff = pos-m_CoilPosition;
	- float sens = diff.GetNorm()*m_CoilSensitivityFactor + 1;
	- if (sens<0)
	- sens = 0;
	- return sens;
	- }
	- case SignalGenerationParameters::COIL_EXPONENTIAL:
	- {
	- VectorType diff = pos-m_CoilPosition;
	- float dist = static_cast<float>(diff.GetNorm());
	- return std::exp(-dist*m_CoilSensitivityFactor);
	- }
	- default:
	- return 1;
	- }
	- }
	-
	- template< class ScalarType >
	- void KspaceImageFilter< ScalarType >
	- ::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, ThreadIdType )
	- {
	- typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0));
	- ImageRegionIterator< OutputImageType > oit(outputImage, outputRegionForThread);
	- typedef ImageRegionConstIterator< InputImageType > InputIteratorType;
	-
	- // precalculate shifts for DFT
	- float x_shift = 0;
	- float y_shift = 0;
	- if (static_cast<int>(xMax)%2==1)
	- x_shift = (xMax-1)/2;
	- else
	- x_shift = xMax/2;
	- if (static_cast<int>(yMax)%2==1)
	- y_shift = (yMax-1)/2;
	- else
	- y_shift = yMax/2;
	-
	- float kx_shift = 0;
	- float ky_shift = 0;
	- if (static_cast<int>(kxMax)%2==1)
	- kx_shift = (kxMax-1)/2;
	- else
	- kx_shift = kxMax/2;
	- if (static_cast<int>(kyMax)%2==1)
	- ky_shift = (kyMax-1)/2;
	- else
	- ky_shift = kyMax/2;
	-
	- vcl_complex<ScalarType> zero = vcl_complex<ScalarType>(0, 0);
	- while( !oit.IsAtEnd() )
	- {
	- int tick = oit.GetIndex()[1] * kxMax + oit.GetIndex()[0];
	-
	- // get current k-space index (depends on the chosen k-space readout scheme)
	- itk::Index< 2 > kIdx = m_ReadoutScheme->GetActualKspaceIndex(tick);
	-
	- // we have to adjust the ticks to obtain correct times since the DFT is not completely symmetric in the even number of lines case
	- if (static_cast<int>(kyMax)%2 == 0 && !m_Parameters->m_SignalGen.m_ReversePhase)
	- {
	- tick += kxMax;
	- tick %= static_cast<int>(numPix);
	- }
	-
	- // partial fourier
	- // two cases because we always want to skip the "later" parts of k-space
	- // in "normal" phase direction, the higher k-space indices are acquired first
	- // in reversed phase direction, the higher k-space indices are acquired later
	- // if the image has an even number of lines, never skip line zero since it is missing on the other side (DFT not completely syymetric in even case)
	- if ((m_Parameters->m_SignalGen.m_ReversePhase && kIdx[1]>std::ceil(kyMax*m_Parameters->m_SignalGen.m_PartialFourier)) \|\|
	- (!m_Parameters->m_SignalGen.m_ReversePhase && kIdx[1]<std::floor(kyMax*(1.0 - m_Parameters->m_SignalGen.m_PartialFourier)) &&
	- (kIdx[1]>0 \|\| static_cast<int>(kyMax)%2 == 1)))
	- {
	- outputImage->SetPixel(kIdx, zero);
	- ++oit;
	- continue;
	- }
	- if (m_StoreTimings)
	- m_TickImage->SetPixel(kIdx, tick);
	-
	- // gibbs ringing by setting high frequencies to zero (alternative to using smaller k-space than input image space)
	- if (m_Parameters->m_SignalGen.m_DoAddGibbsRinging && m_Parameters->m_SignalGen.m_ZeroRinging>0)
	- {
	- if (kIdx[0] < ringing_lines_x \|\| kIdx[1] < ringing_lines_y \|\|
	- kIdx[0] >= kxMax - ringing_lines_x \|\| kIdx[1] >= kyMax - ringing_lines_y)
	- {
	- outputImage->SetPixel(kIdx, zero);
	- ++oit;
	- continue;
	- }
	- }
	-
	- // time from maximum echo
	- float t = m_ReadoutScheme->GetTimeFromMaxEcho(tick);
	-
	- // calculate eddy current decay factor
	- float eddyDecay = 0;
	- if ( m_Parameters->m_Misc.m_DoAddEddyCurrents && m_Parameters->m_SignalGen.m_EddyStrength>0 && !m_IsBaseline)
	- {
	- // time passed since k-space readout started
	- float tRead = m_ReadoutScheme->GetTimeFromLastDiffusionGradient(tick);
	- eddyDecay = std::exp(-tRead/m_Parameters->m_SignalGen.m_Tau ) * t/1000; // time in seconds here
	- }
	-
	- // calcualte signal relaxation factors
	- std::vector< float > relaxFactor;
	- if ( m_Parameters->m_SignalGen.m_DoSimulateRelaxation)
	- {
	- // time passes since application of the RF pulse
	- float tRf = m_ReadoutScheme->GetTimeFromRf(tick);
	- if (m_StoreTimings)
	- m_RfImage->SetPixel(kIdx, tRf);
	-
	- for (unsigned int i=0; i<m_CompartmentImages.size(); i++)
	- {
	- // account for T2 relaxation (how much transverse magnetization is left since applicatiohn of RF pulse?)
	- relaxFactor.push_back(m_T1Relax[i] * std::exp(-tRf/m_T2[i] -fabs(t)/ m_Parameters->m_SignalGen.m_tInhom));
	- }
	- }
	-
	- // shift k for DFT: (0 -- N) --> (-N/2 -- N/2)
	- float kx = kIdx[0] - kx_shift;
	- float ky = kIdx[1] - ky_shift;
	-
	- // add ghosting by adding gradient delay induced offset
	- if (m_Parameters->m_Misc.m_DoAddGhosts)
	- {
	- if (kIdx[1]%2 == 1)
	- kx -= m_Parameters->m_SignalGen.m_KspaceLineOffset;
	- else
	- kx += m_Parameters->m_SignalGen.m_KspaceLineOffset;
	- }
	-
	- // pull stuff out of inner loop
	- t /= 1000; // time in seconds
	- kx /= xMax;
	- ky /= yMaxFov;
	-
	- // calculate signal s at k-space position (kx, ky)
	- vcl_complex<ScalarType> s(0,0);
	- InputIteratorType it(m_CompartmentImages[0], m_CompartmentImages[0]->GetLargestPossibleRegion() );
	- while( !it.IsAtEnd() )
	- {
	- typename InputImageType::IndexType input_idx = it.GetIndex();
	-
	- // shift x,y for DFT: (0 -- N) --> (-N/2 -- N/2)
	- float x = input_idx[0] - x_shift;
	- float y = input_idx[1] - y_shift;
	-
	- // sum compartment signals and simulate relaxation
	- ScalarType f_real = 0;
	- for (unsigned int i=0; i<m_CompartmentImages.size(); i++)
	- if ( m_Parameters->m_SignalGen.m_DoSimulateRelaxation)
	- f_real += m_CompartmentImages[i]->GetPixel(input_idx) * relaxFactor[i];
	- else
	- f_real += m_CompartmentImages[i]->GetPixel(input_idx);
	-
	- // vector from image center to current position (in meter)
	- // only necessary for eddy currents and non-constant coil sensitivity
	- VectorType pos;
	- if ((m_Parameters->m_Misc.m_DoAddEddyCurrents && m_Parameters->m_SignalGen.m_EddyStrength>0 && !m_IsBaseline) \|\|
	- m_Parameters->m_SignalGen.m_CoilSensitivityProfile!=SignalGenerationParameters::COIL_CONSTANT)
	- {
	- pos[0] = x; pos[1] = y; pos[2] = m_Z;
	- pos = m_Transform*pos;
	- }
	-
	- if (m_Parameters->m_SignalGen.m_CoilSensitivityProfile!=SignalGenerationParameters::COIL_CONSTANT)
	- f_real *= CoilSensitivity(pos);
	-
	- // simulate eddy currents and other distortions
	- float phi = 0; // phase shift
	- if ( m_Parameters->m_Misc.m_DoAddEddyCurrents && m_Parameters->m_SignalGen.m_EddyStrength>0 && !m_IsBaseline)
	- {
	- // duration (tRead) already included in "eddyDecay"
	- phi += (m_DiffusionGradientDirection[0]pos[0]+m_DiffusionGradientDirection[1]pos[1]+m_DiffusionGradientDirection[2]pos[2]) eddyDecay;
	- }
	-
	- // simulate distortions
	- if (m_Parameters->m_Misc.m_DoAddDistortions)
	- {
	- if (m_MovedFmap.IsNotNull()) // if we have headmotion, use moved map
	- phi += m_MovedFmap->GetPixel(input_idx) * t;
	- else if (m_Parameters->m_SignalGen.m_FrequencyMap.IsNotNull())
	- {
	- itk::Image<float, 3>::IndexType index; index[0] = input_idx[0]; index[1] = input_idx[1]; index[2] = m_Zidx;
	- phi += m_Parameters->m_SignalGen.m_FrequencyMap->GetPixel(index) * t;
	- }
	- }
	-
	- // if signal comes from outside FOV, mirror it back (wrap-around artifact - aliasing
	- if (m_Parameters->m_Misc.m_DoAddAliasing)
	- {
	- if (y<-yMaxFov_half)
	- y += yMaxFov;
	- else if (y>yMaxFov_half)
	- y -= yMaxFov;
	- }
	-
	- // actual DFT term
	- vcl_complex<ScalarType> f(f_real * m_Parameters->m_SignalGen.m_SignalScale, 0);
	- s += f * std::exp( std::complex<ScalarType>(0, itk::Math::twopi * (kxx + kyy + phi )) );
	-
	- ++it;
	- }
	- s /= numPix;
	-
	- if (m_SpikesPerSlice>0 && sqrt(s.imag()s.imag()+s.real()s.real()) > sqrt(m_Spike.imag()m_Spike.imag()+m_Spike.real()m_Spike.real()) )
	- m_Spike = s;
	-
	- s += outputImage->GetPixel(kIdx); // add precalculated noise
	- outputImage->SetPixel(kIdx, s);
	- m_KSpaceImage->SetPixel(kIdx, sqrt(s.imag()s.imag()+s.real()s.real()) );
	-
	- ++oit;
	- }
	- }
	-
	- template< class ScalarType >
	- void KspaceImageFilter< ScalarType >
	- ::AfterThreadedGenerateData()
	- {
	- typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0));
	- int kxMax = outputImage->GetLargestPossibleRegion().GetSize(0); // k-space size in x-direction
	- int kyMax = outputImage->GetLargestPossibleRegion().GetSize(1); // k-space size in y-direction
	-
	- ImageRegionIterator< OutputImageType > oit(outputImage, outputImage->GetLargestPossibleRegion());
	- while( !oit.IsAtEnd() ) // use hermitian k-space symmetry to fill empty k-space parts resulting from partial fourier acquisition
	- {
	- int tick = oit.GetIndex()[1] * kxMax + oit.GetIndex()[0];
	- auto kIdx = m_ReadoutScheme->GetActualKspaceIndex(tick);
	-
	- if ((m_Parameters->m_SignalGen.m_ReversePhase && kIdx[1]>std::ceil(kyMax*m_Parameters->m_SignalGen.m_PartialFourier)) \|\|
	- (!m_Parameters->m_SignalGen.m_ReversePhase && kIdx[1]<std::floor(kyMax*(1.0 - m_Parameters->m_SignalGen.m_PartialFourier)) &&
	- (kIdx[1]>0 \|\| static_cast<int>(kyMax)%2 == 1)))
	- {
	- // calculate symmetric index
	- auto sym = m_ReadoutScheme->GetSymmetricIndex(kIdx);
	-
	- // use complex conjugate of symmetric index value at current index
	- vcl_complex<ScalarType> s = outputImage->GetPixel(sym);
	- s = vcl_complex<ScalarType>(s.real(), -s.imag());
	- outputImage->SetPixel(kIdx, s);
	-
	- m_KSpaceImage->SetPixel(kIdx, sqrt(s.imag()s.imag()+s.real()s.real()) );
	- }
	- ++oit;
	- }
	-
	- m_Spike *= m_Parameters->m_SignalGen.m_SpikeAmplitude;
	- itk::Index< 2 > spikeIdx;
	- for (unsigned int i=0; i<m_SpikesPerSlice; i++)
	- {
	- spikeIdx[0] = m_RandGen->GetIntegerVariate()%kxMax;
	- spikeIdx[1] = m_RandGen->GetIntegerVariate()%kyMax;
	- outputImage->SetPixel(spikeIdx, m_Spike);
	- m_SpikeLog += "[" + boost::lexical_cast<std::string>(spikeIdx[0]) + "," + boost::lexical_cast<std::string>(spikeIdx[1]) + "," + boost::lexical_cast<std::string>(m_Zidx) + "] Magnitude: " + boost::lexical_cast<std::string>(m_Spike.real()) + "+" + boost::lexical_cast<std::string>(m_Spike.imag()) + "i\n";
	- }
	- delete m_ReadoutScheme;
	- }
	-}
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkKspaceImageFilter.h b/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkKspaceImageFilter.h
	deleted file mode 100644
	index 471eec3723..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkKspaceImageFilter.h
	+++ /dev/null
	@@ -1,161 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-/*===================================================================
	-
	-This file is based heavily on a corresponding ITK filter.
	-
	-===================================================================*/
	-#ifndef __itkKspaceImageFilter_h_
	-#define __itkKspaceImageFilter_h_
	-
	-#include <MitkFiberTrackingExports.h>
	-#include <itkImageSource.h>
	-#include <vcl_complex.h>
	-#include <vector>
	-#include <itkMersenneTwisterRandomVariateGenerator.h>
	-#include <mitkFiberfoxParameters.h>
	-#include <mitkFiberBundle.h>
	-#include <mitkAcquisitionType.h>
	-
	-namespace itk{
	-
	-/**
	-* \brief Simulates k-space acquisition of one slice with a single shot EPI sequence. Enables the simulation of various effects occuring during real MR acquisitions:
	-* - T2 signal relaxation
	-* - Spikes
	-* - N/2 Ghosts
	-* - Aliasing (wrap around)
	-* - Image distortions (off-frequency effects)
	-* - Gibbs ringing
	-* - Eddy current effects
	-* Based on a discrete fourier transformation.
	-* See "Fiberfox: Facilitating the creation of realistic white matter software phantoms" (DOI: 10.1002/mrm.25045) for details.
	-*/
	-
	- template< class ScalarType >
	- class KspaceImageFilter :
	- public ImageSource< Image< vcl_complex< ScalarType >, 2 > >
	- {
	-
	- public:
	-
	- typedef KspaceImageFilter Self;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	- typedef ImageSource< Image< vcl_complex< ScalarType >, 2 > > Superclass;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Runtime information support. */
	- itkTypeMacro(KspaceImageFilter, ImageToImageFilter)
	-
	- typedef typename itk::Image< ScalarType, 2 > InputImageType;
	- typedef typename InputImageType::Pointer InputImagePointerType;
	- typedef typename Superclass::OutputImageType OutputImageType;
	- typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
	- typedef itk::Matrix<float, 3, 3> MatrixType;
	- typedef itk::Point<float,2> Point2D;
	- typedef itk::Vector< float,3> VectorType;
	-
	- itkSetMacro( SpikesPerSlice, unsigned int ) ///< Number of spikes per slice. Corresponding parameter in fiberfox parameter object specifies the number of spikes for the whole image and can thus not be used here.
	- itkSetMacro( Z, double ) ///< Slice position, necessary for eddy current simulation.
	- itkSetMacro( RandSeed, int ) ///< Use constant seed for random generator for reproducible results.
	- itkSetMacro( Translation, VectorType )
	- itkSetMacro( RotationMatrix, MatrixType )
	- itkSetMacro( Zidx, int )
	- itkSetMacro( StoreTimings, bool )
	- itkSetMacro( FiberBundle, FiberBundle::Pointer )
	- itkSetMacro( CoilPosition, VectorType )
	- itkGetMacro( KSpaceImage, typename InputImageType::Pointer ) ///< k-space magnitude image
	- itkGetMacro( TickImage, typename InputImageType::Pointer ) ///< k-space readout ordering encoded in the voxels
	- itkGetMacro( RfImage, typename InputImageType::Pointer ) ///< time passed since last RF pulse encoded per voxel
	- itkGetMacro( SpikeLog, std::string )
	-
	- void SetParameters( FiberfoxParameters* param ){ m_Parameters = param; }
	-
	- void SetCompartmentImages( std::vector< InputImagePointerType > cImgs ) { m_CompartmentImages=cImgs; } ///< One signal image per compartment.
	- void SetT2( std::vector< float > t2Vector ) { m_T2=t2Vector; } ///< One T2 relaxation constant per compartment image.
	- void SetT1( std::vector< float > t1Vector ) { m_T1=t1Vector; } ///< One T1 relaxation constant per compartment image.
	- void SetDiffusionGradientDirection(itk::Vector<double,3> g) { m_DiffusionGradientDirection=g; } ///< Gradient direction is needed for eddy current simulation.
	-
	- protected:
	- KspaceImageFilter();
	- ~KspaceImageFilter() override {}
	-
	- float CoilSensitivity(VectorType& pos);
	-
	- void BeforeThreadedGenerateData() override;
	- void ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, ThreadIdType threadID) override;
	- void AfterThreadedGenerateData() override;
	-
	- VectorType m_CoilPosition;
	- FiberfoxParameters* m_Parameters;
	- std::vector< float > m_T2;
	- std::vector< float > m_T1;
	- std::vector< float > m_T1Relax;
	- std::vector< InputImagePointerType > m_CompartmentImages;
	- itk::Vector<double,3> m_DiffusionGradientDirection;
	- float m_Z;
	- int m_Zidx;
	- int m_RandSeed;
	- itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer m_RandGen;
	- unsigned int m_SpikesPerSlice;
	- FiberBundle::Pointer m_FiberBundle;
	- float m_Gamma;
	- VectorType m_Translation; ///< used to find correct point in frequency map (head motion)
	- MatrixType m_RotationMatrix;
	- float m_TransX;
	- float m_TransY;
	- float m_TransZ;
	-
	- bool m_IsBaseline;
	- vcl_complex<ScalarType> m_Spike;
	- MatrixType m_Transform;
	- std::string m_SpikeLog;
	-
	- float m_CoilSensitivityFactor;
	- typename InputImageType::Pointer m_KSpaceImage;
	- typename InputImageType::Pointer m_TickImage;
	- typename InputImageType::Pointer m_RfImage;
	- AcquisitionType* m_ReadoutScheme;
	-
	- typename itk::Image< ScalarType, 2 >::Pointer m_MovedFmap;
	- int ringing_lines_x;
	- int ringing_lines_y;
	- float kxMax;
	- float kyMax;
	- float xMax;
	- float yMax;
	- float yMaxFov;
	- float yMaxFov_half;
	- float numPix;
	- bool m_StoreTimings;
	-
	- private:
	-
	- };
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkKspaceImageFilter.cpp"
	-#endif
	-
	-#endif //__itkKspaceImageFilter_h_
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkRandomPhantomFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkRandomPhantomFilter.cpp
	deleted file mode 100644
	index 4a992d292d..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkRandomPhantomFilter.cpp
	+++ /dev/null
	@@ -1,457 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-//#ifndef __itkRandomPhantomFilter_cpp
	-//#define __itkRandomPhantomFilter_cpp
	-
	-#include "itkRandomPhantomFilter.h"
	-
	-#include <itkFibersFromPlanarFiguresFilter.h>
	-#include <cmath>
	-
	-namespace itk{
	-
	-RandomPhantomFilter::RandomPhantomFilter()
	- : m_NumTracts(1)
	- , m_MinStreamlineDensity(25)
	- , m_MaxStreamlineDensity(200)
	- , m_StartRadiusMin(5)
	- , m_StartRadiusMax(30)
	- , m_CurvynessMin(10)
	- , m_CurvynessMax(45)
	- , m_StepSizeMin(15)
	- , m_StepSizeMax(30)
	- , m_MinTwist(10)
	- , m_MaxTwist(30)
	- , m_FixSeed(-1)
	-{
	- m_VolumeSize[0] = 500;
	- m_VolumeSize[1] = 500;
	- m_VolumeSize[2] = 500;
	-}
	-
	-RandomPhantomFilter::~RandomPhantomFilter()
	-{
	-
	-}
	-
	-
	-void RandomPhantomFilter::TransformPlanarFigure(mitk::PlanarEllipse* pe, mitk::Vector3D translation, mitk::Vector3D rotation, double twistangle, double radius1, double radius2)
	-{
	- mitk::BaseGeometry* geom = pe->GetGeometry();
	-
	- // translate
	- geom->Translate(translation);
	-
	- // calculate rotation matrix
	- double x = rotation[0]*itk::Math::pi/180;
	- double y = rotation[1]*itk::Math::pi/180;
	- double z = rotation[2]*itk::Math::pi/180;
	-
	- itk::Matrix< double, 3, 3 > rotX; rotX.SetIdentity();
	- rotX[1][1] = cos(x);
	- rotX[2][2] = rotX[1][1];
	- rotX[1][2] = -sin(x);
	- rotX[2][1] = -rotX[1][2];
	-
	- itk::Matrix< double, 3, 3 > rotY; rotY.SetIdentity();
	- rotY[0][0] = cos(y);
	- rotY[2][2] = rotY[0][0];
	- rotY[0][2] = sin(y);
	- rotY[2][0] = -rotY[0][2];
	-
	- itk::Matrix< double, 3, 3 > rotZ; rotZ.SetIdentity();
	- rotZ[0][0] = cos(z);
	- rotZ[1][1] = rotZ[0][0];
	- rotZ[0][1] = -sin(z);
	- rotZ[1][0] = -rotZ[0][1];
	-
	- itk::Matrix< double, 3, 3 > rot = rotZrotYrotX;
	-
	- // rotate fiducial
	- geom->GetIndexToWorldTransform()->SetMatrix(rot*geom->GetIndexToWorldTransform()->GetMatrix());
	-
	- // adjust control points
	- auto p0 = pe->GetControlPoint(0);
	- auto p1 = pe->GetControlPoint(1);
	- auto p2 = pe->GetControlPoint(2);
	- auto p3 = pe->GetControlPoint(3);
	-
	- auto v1 = p1 - p0;
	- auto v2 = p2 - p0;
	- auto dot = std::cos(itk::Math::pi*twistangle/180.0);
	-
	- vnl_matrix_fixed<double, 2, 2> tRot;
	- tRot[0][0] = dot;
	- tRot[1][1] = tRot[0][0];
	- tRot[1][0] = sin(acos(tRot[0][0]));
	- tRot[0][1] = -tRot[1][0];
	- if (twistangle<0)
	- tRot = tRot.transpose();
	- vnl_vector_fixed<double, 2> vt; vt[0]=1; vt[1]=0;
	- vnl_vector_fixed<double, 2> v3 = tRot*vt;
	-
	- v1.Normalize();
	- v2.Normalize();
	-
	- p1 = p0 + radius1;
	- p2 = p0 + radius2;
	-
	- p3 = p0 + mitk::Vector2D(v3);
	- pe->SetControlPoint(1, p1);
	- pe->SetControlPoint(2, p2);
	- pe->SetControlPoint(3, p3);
	-
	-
	- pe->Modified();
	-}
	-
	-mitk::PlanarEllipse::Pointer RandomPhantomFilter::CreatePlanarFigure()
	-{
	- mitk::PlaneGeometry::Pointer pl = mitk::PlaneGeometry::New();
	- pl->SetIdentity();
	- // mitk::Point3D o; o.Fill(10.0);
	- // pl->SetOrigin(o);
	- mitk::PlanarEllipse::Pointer figure = mitk::PlanarEllipse::New();
	- figure->ResetNumberOfControlPoints(0);
	- figure->SetPlaneGeometry(pl);
	-
	- mitk::Point2D p0; p0.Fill(0.0);
	- mitk::Point2D p1; p1.Fill(0.0); p1[0] = 1;
	- mitk::Point2D p2; p2.Fill(0.0); p2[1] = 1;
	-
	- figure->PlaceFigure(p0);
	- figure->AddControlPoint(p0);
	- figure->AddControlPoint(p1);
	- figure->AddControlPoint(p2);
	- figure->AddControlPoint(p2);
	- figure->SetProperty("initiallyplaced", mitk::BoolProperty::New(true));
	- return figure;
	-}
	-
	-void RandomPhantomFilter::SetNumTracts(unsigned int NumTracts)
	-{
	- m_NumTracts = NumTracts;
	-}
	-
	-void RandomPhantomFilter::GetPfOnBoundingPlane(mitk::Vector3D& pos, mitk::Vector3D& rot)
	-{
	- auto plane = randGen->GetIntegerVariate(5) + 1;
	- MITK_INFO << "Plane: " << plane;
	- switch(plane)
	- {
	- case 1:
	- {
	- pos[0] = randGen->GetUniformVariate(0, m_VolumeSize[0]);
	- pos[1] = randGen->GetUniformVariate(0, m_VolumeSize[1]);
	- pos[2] = 0;
	-
	- rot[0] = 0;
	- rot[1] = 0;
	- rot[2] = 0;
	- break;
	- }
	- case 2:
	- {
	- pos[0] = 0;
	- pos[1] = randGen->GetUniformVariate(0, m_VolumeSize[1]);
	- pos[2] = randGen->GetUniformVariate(0, m_VolumeSize[2]);
	-
	- rot[0] = 0;
	- rot[1] = 90;
	- rot[2] = 0;
	- break;
	- }
	- case 3:
	- {
	- pos[0] = randGen->GetUniformVariate(0, m_VolumeSize[0]);
	- pos[1] = 0;
	- pos[2] = randGen->GetUniformVariate(0, m_VolumeSize[2]);
	-
	- rot[0] = -90;
	- rot[1] = 0;
	- rot[2] = 0;
	- break;
	- }
	- case 4:
	- {
	- pos[0] = randGen->GetUniformVariate(0, m_VolumeSize[0]);
	- pos[1] = m_VolumeSize[1];
	- pos[2] = randGen->GetUniformVariate(0, m_VolumeSize[2]);
	-
	- rot[0] = 90;
	- rot[1] = 0;
	- rot[2] = 0;
	- break;
	- }
	- case 5:
	- {
	- pos[0] = m_VolumeSize[0];
	- pos[1] = randGen->GetUniformVariate(0, m_VolumeSize[1]);
	- pos[2] = randGen->GetUniformVariate(0, m_VolumeSize[2]);
	-
	- rot[0] = 0;
	- rot[1] = -90;
	- rot[2] = 0;
	- break;
	- }
	- case 6:
	- {
	- pos[0] = randGen->GetUniformVariate(0, m_VolumeSize[0]);
	- pos[1] = randGen->GetUniformVariate(0, m_VolumeSize[1]);
	- pos[2] = m_VolumeSize[2];
	-
	- rot[0] = 180;
	- rot[1] = 0;
	- rot[2] = 0;
	- break;
	- }
	- }
	-}
	-
	-bool RandomPhantomFilter::IsInVolume(mitk::Vector3D pos)
	-{
	- if (pos[0]>=0 &&
	- pos[0]<=m_VolumeSize[0] &&
	- pos[1]>=0 &&
	- pos[1]<=m_VolumeSize[1] &&
	- pos[2]>=0 &&
	- pos[2]<=m_VolumeSize[2])
	- return true;
	- return false;
	-}
	-
	-void RandomPhantomFilter::SetFixSeed(int FixSeed)
	-{
	- m_FixSeed = FixSeed;
	-}
	-
	-void RandomPhantomFilter::SetMinTwist(unsigned int MinTwist)
	-{
	- m_MinTwist = MinTwist;
	-}
	-
	-void RandomPhantomFilter::SetMaxStreamlineDensity(unsigned int MaxStreamlineDensity)
	-{
	- m_MaxStreamlineDensity = MaxStreamlineDensity;
	-}
	-
	-void RandomPhantomFilter::SetMinStreamlineDensity(unsigned int MinStreamlinDensity)
	-{
	- m_MinStreamlineDensity = MinStreamlinDensity;
	-}
	-
	-void RandomPhantomFilter::SetMaxTwist(unsigned int MaxTwist)
	-{
	- m_MaxTwist = MaxTwist;
	-}
	-
	-void RandomPhantomFilter::SetVolumeSize(const mitk::Vector3D &VolumeSize)
	-{
	- m_VolumeSize = VolumeSize;
	-}
	-
	-void RandomPhantomFilter::SetStepSizeMax(unsigned int StepSizeMax)
	-{
	- m_StepSizeMax = StepSizeMax;
	-}
	-
	-void RandomPhantomFilter::SetStepSizeMin(unsigned int StepSizeMin)
	-{
	- m_StepSizeMin = StepSizeMin;
	-}
	-
	-void RandomPhantomFilter::SetCurvynessMax(unsigned int CurvynessMax)
	-{
	- m_CurvynessMax = CurvynessMax;
	-}
	-
	-void RandomPhantomFilter::SetCurvynessMin(unsigned int CurvynessMin)
	-{
	- m_CurvynessMin = CurvynessMin;
	-}
	-
	-void RandomPhantomFilter::SetStartRadiusMax(unsigned int StartRadiusMax)
	-{
	- m_StartRadiusMax = StartRadiusMax;
	-}
	-
	-void RandomPhantomFilter::SetStartRadiusMin(unsigned int StartRadiusMin)
	-{
	- m_StartRadiusMin = StartRadiusMin;
	-}
	-
	-void RandomPhantomFilter::GenerateData()
	-{
	- randGen = Statistics::MersenneTwisterRandomVariateGenerator::New();
	- if (m_FixSeed>=0)
	- randGen->SetSeed(m_FixSeed);
	- else
	- randGen->SetSeed();
	-
	- for (unsigned int i=0; i<m_NumTracts; ++i)
	- {
	- MITK_INFO << "Generating Bundle_" << i+1;
	- FiberGenerationParameters fiber_params;
	- std::vector< mitk::PlanarEllipse::Pointer > bundle_waypoints;
	-
	- double curvyness = randGen->GetUniformVariate(m_CurvynessMin, m_CurvynessMax);
	- int twistdir = static_cast<int>(randGen->GetIntegerVariate(2)) - 1;
	- double dtwist = randGen->GetUniformVariate(m_MinTwist, m_MaxTwist);
	-
	- mitk::Vector3D pos; pos.Fill(0.0);
	- mitk::Vector3D rot; rot.Fill(0.0);
	- double twist = 0;
	- double radius1 = randGen->GetUniformVariate(m_StartRadiusMin, m_StartRadiusMax);
	- double radius2 = randGen->GetUniformVariate(m_StartRadiusMin, m_StartRadiusMax);
	-
	- GetPfOnBoundingPlane(pos, rot);
	- rot[0] += randGen->GetUniformVariate(-curvyness, curvyness);
	- rot[1] += randGen->GetUniformVariate(-curvyness, curvyness);
	- rot[2] += randGen->GetUniformVariate(-curvyness, curvyness);
	-
	- mitk::PlanarEllipse::Pointer start = CreatePlanarFigure();
	- TransformPlanarFigure(start, pos, rot, twist, radius1, radius2);
	- bundle_waypoints.push_back(start);
	-
	- double c_area = itk::Math::piradius1radius2;
	-
	- int sizestrategy = static_cast<int>(randGen->GetIntegerVariate(2)) - 1;
	-
	- MITK_INFO << "Twist: " << dtwist;
	- MITK_INFO << "Twist direction: " << twistdir;
	- MITK_INFO << "Curvyness: " << curvyness;
	- MITK_INFO << "Size strategy: " << sizestrategy;
	-
	- int c = 1;
	- while(IsInVolume(pos))
	- {
	- pos += bundle_waypoints.at(c-1)->GetPlaneGeometry()->GetNormal() * randGen->GetUniformVariate(m_StepSizeMin, m_StepSizeMax);
	- rot[0] += randGen->GetUniformVariate(-curvyness, curvyness);
	- rot[1] += randGen->GetUniformVariate(-curvyness, curvyness);
	- rot[2] += randGen->GetUniformVariate(-curvyness, curvyness);
	-
	- twist += dtwist * twistdir;
	- if (randGen->GetUniformVariate(0.0, 1.0) < 0.25)
	- {
	- int temp = static_cast<int>(randGen->GetIntegerVariate(2)) - 1;
	- if (temp!=twistdir)
	- {
	- twistdir = temp;
	- MITK_INFO << "Twist direction change: " << twistdir;
	- }
	- }
	-
	- if (randGen->GetUniformVariate(0.0, 1.0) < 0.25)
	- {
	- int temp = static_cast<int>(randGen->GetIntegerVariate(2)) - 1;
	- if (temp!=sizestrategy)
	- {
	- sizestrategy = temp;
	- MITK_INFO << "Size strategy change: " << sizestrategy;
	- }
	- }
	-
	- double minradius = 0.5*static_cast<double>(m_StartRadiusMin);
	- double dsize = 0.5*minradius;
	- double maxradius = 2.0*static_cast<double>(m_StartRadiusMax);
	- if (sizestrategy==0)
	- {
	- radius1 += randGen->GetUniformVariate(-dsize, dsize);
	- radius2 += randGen->GetUniformVariate(-dsize, dsize);
	- while (radius1 < 5)
	- radius1 += randGen->GetUniformVariate(-dsize, dsize);
	- while (radius2 < 5)
	- radius2 += randGen->GetUniformVariate(-dsize, dsize);
	- }
	- else if (sizestrategy==1)
	- {
	- radius1 += randGen->GetUniformVariate(0, dsize);
	- radius2 += randGen->GetUniformVariate(0, dsize);
	- if (radius1 > maxradius)
	- {
	- radius1 = maxradius;
	- sizestrategy = static_cast<int>(randGen->GetIntegerVariate(1)) - 1;
	- }
	- if (radius2 > maxradius)
	- {
	- radius2 = maxradius;
	- sizestrategy = static_cast<int>(randGen->GetIntegerVariate(1)) - 1;
	- }
	- }
	- else if (sizestrategy==-1)
	- {
	- radius1 += randGen->GetUniformVariate(-dsize, 0);
	- radius2 += randGen->GetUniformVariate(-dsize, 0);
	- if (radius1 < minradius)
	- {
	- radius1 = minradius;
	- sizestrategy = static_cast<int>(randGen->GetIntegerVariate(1));
	- }
	- if (radius2 < minradius)
	- {
	- radius2 = minradius;
	- sizestrategy = static_cast<int>(randGen->GetIntegerVariate(1));
	- }
	- }
	-
	- c_area += itk::Math::piradius1radius2;
	-
	- mitk::PlanarEllipse::Pointer pf = CreatePlanarFigure();
	- TransformPlanarFigure(pf, pos, rot, twist, radius1, radius2);
	-
	- bundle_waypoints.push_back(pf);
	- ++c;
	- }
	- c_area /= c;
	- c_area /= 100;
	- MITK_INFO << "Average crossectional area: " << c_area << "cm²";
	-
	- fiber_params.m_Fiducials.push_back(bundle_waypoints);
	- auto density = randGen->GetUniformVariate(m_MinStreamlineDensity, m_MaxStreamlineDensity);
	- MITK_INFO << "Density: " << density;
	- MITK_INFO << "Num. fibers: " << fiber_params.m_Density;
	-
	- fiber_params.m_Density = static_cast<unsigned int>(std::ceil(c_area*density));
	- if (randGen->GetIntegerVariate(1)==0)
	- {
	- fiber_params.m_Distribution = FiberGenerationParameters::DISTRIBUTE_UNIFORM;
	- MITK_INFO << "Distribution: uniform";
	- }
	- else
	- {
	- fiber_params.m_Distribution = FiberGenerationParameters::DISTRIBUTE_GAUSSIAN;
	- MITK_INFO << "Distribution: Gaussian";
	- }
	-
	- MITK_INFO << "Num. fiducials: " << c;
	- MITK_INFO << "------------\n";
	-
	- std::streambuf *old = cout.rdbuf(); // <-- save
	- std::stringstream ss;
	- std::cout.rdbuf (ss.rdbuf()); // <-- redirect
	- itk::FibersFromPlanarFiguresFilter::Pointer filter = itk::FibersFromPlanarFiguresFilter::New();
	- filter->SetParameters(fiber_params);
	- filter->SetFixSeed(m_FixSeed);
	- filter->Update();
	- m_FiberBundles.push_back(filter->GetFiberBundles().at(0));
	- std::cout.rdbuf (old); // <-- restore
	- }
	-}
	-
	-}
	-//#endif // __itkRandomPhantomFilter_cpp
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkRandomPhantomFilter.h b/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkRandomPhantomFilter.h
	deleted file mode 100644
	index 5ae5bfea1b..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkRandomPhantomFilter.h
	+++ /dev/null
	@@ -1,114 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef itkRandomPhantomFilter_h
	-#define itkRandomPhantomFilter_h
	-
	-// MITK
	-#include <mitkPlanarEllipse.h>
	-#include <mitkFiberBundle.h>
	-#include <mitkFiberfoxParameters.h>
	-
	-// ITK
	-#include <itkProcessObject.h>
	-#include <itkMersenneTwisterRandomVariateGenerator.h>
	-
	-namespace itk{
	-
	-/**
	-* \brief */
	-
	-class RandomPhantomFilter : public ProcessObject
	-{
	-public:
	-
	- typedef RandomPhantomFilter Self;
	- typedef ProcessObject Superclass;
	- typedef SmartPointer< Self > Pointer;
	- typedef SmartPointer< const Self > ConstPointer;
	- typedef mitk::FiberBundle::Pointer FiberType;
	- typedef std::vector< mitk::FiberBundle::Pointer > FiberContainerType;
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- itkTypeMacro( RandomPhantomFilter, ProcessObject )
	-
	- void Update() override{
	- this->GenerateData();
	- }
	-
	- // output
	- FiberContainerType GetFiberBundles(){ return m_FiberBundles; }
	-
	- void SetNumTracts(unsigned int NumTracts);
	-
	- void SetStartRadiusMin(unsigned int StartRadiusMin);
	-
	- void SetStartRadiusMax(unsigned int StartRadiusMax);
	-
	- void SetCurvynessMin(unsigned int CurvynessMin);
	-
	- void SetCurvynessMax(unsigned int CurvynessMax);
	-
	- void SetStepSizeMin(unsigned int StepSizeMin);
	-
	- void SetStepSizeMax(unsigned int StepSizeMax);
	-
	- void SetVolumeSize(const mitk::Vector3D &VolumeSize);
	-
	- void SetMaxTwist(unsigned int MaxTwist);
	-
	- void SetMinStreamlineDensity(unsigned int MinStreamlinDensity);
	-
	- void SetMaxStreamlineDensity(unsigned int MaxStreamlineDensity);
	-
	- void SetMinTwist(unsigned int MinTwist);
	-
	- void SetFixSeed(int FixSeed);
	-
	-protected:
	-
	- void GenerateData() override;
	-
	- RandomPhantomFilter();
	- ~RandomPhantomFilter() override;
	- void TransformPlanarFigure(mitk::PlanarEllipse* pe, mitk::Vector3D translation, mitk::Vector3D rotation, double twistangle, double radius1, double radius2);
	- mitk::PlanarEllipse::Pointer CreatePlanarFigure();
	- void GetPfOnBoundingPlane(mitk::Vector3D& pos, mitk::Vector3D& rot);
	- bool IsInVolume(mitk::Vector3D pos);
	-
	- FiberContainerType m_FiberBundles; ///< container for the output fiber bundles
	- unsigned int m_NumTracts;
	- unsigned int m_MinStreamlineDensity;
	- unsigned int m_MaxStreamlineDensity;
	- unsigned int m_StartRadiusMin;
	- unsigned int m_StartRadiusMax;
	- unsigned int m_CurvynessMin;
	- unsigned int m_CurvynessMax;
	- unsigned int m_StepSizeMin;
	- unsigned int m_StepSizeMax;
	- unsigned int m_MinTwist;
	- unsigned int m_MaxTwist;
	- mitk::Vector3D m_VolumeSize;
	- int m_FixSeed;
	- Statistics::MersenneTwisterRandomVariateGenerator::Pointer randGen;
	-};
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkRandomPhantomFilter.cpp"
	-#endif
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkTractsToDWIImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkTractsToDWIImageFilter.cpp
	deleted file mode 100755
	index c3d3fcd928..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkTractsToDWIImageFilter.cpp
	+++ /dev/null
	@@ -1,1767 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "itkTractsToDWIImageFilter.h"
	-#include <boost/progress.hpp>
	-#include <vtkSmartPointer.h>
	-#include <vtkPolyData.h>
	-#include <vtkCellArray.h>
	-#include <vtkPoints.h>
	-#include <vtkPolyLine.h>
	-#include <itkImageRegionIteratorWithIndex.h>
	-#include <itkResampleImageFilter.h>
	-#include <itkNearestNeighborInterpolateImageFunction.h>
	-#include <itkBSplineInterpolateImageFunction.h>
	-#include <itkCastImageFilter.h>
	-#include <itkImageFileWriter.h>
	-#include <itkRescaleIntensityImageFilter.h>
	-#include <itkWindowedSincInterpolateImageFunction.h>
	-#include <itkResampleDwiImageFilter.h>
	-#include <itkKspaceImageFilter.h>
	-#include <itkDftImageFilter.h>
	-#include <itkAddImageFilter.h>
	-#include <itkConstantPadImageFilter.h>
	-#include <itkCropImageFilter.h>
	-#include <mitkAstroStickModel.h>
	-#include <vtkTransform.h>
	-#include <iostream>
	-#include <fstream>
	-#include <exception>
	-#include <itkImageDuplicator.h>
	-#include <itksys/SystemTools.hxx>
	-#include <mitkIOUtil.h>
	-#include <itkDiffusionTensor3DReconstructionImageFilter.h>
	-#include <itkDiffusionTensor3D.h>
	-#include <itkTractDensityImageFilter.h>
	-#include <mitkLexicalCast.h>
	-#include <itkTractsToVectorImageFilter.h>
	-#include <itkInvertIntensityImageFilter.h>
	-#include <itkShiftScaleImageFilter.h>
	-#include <itkExtractImageFilter.h>
	-#include <itkResampleDwiImageFilter.h>
	-#include <boost/algorithm/string/replace.hpp>
	-#include <omp.h>
	-#include <cmath>
	-#include <thread>
	-
	-namespace itk
	-{
	-
	-template< class PixelType >
	-TractsToDWIImageFilter< PixelType >::TractsToDWIImageFilter()
	- : m_StatusText("")
	- , m_UseConstantRandSeed(false)
	- , m_RandGen(itk::Statistics::MersenneTwisterRandomVariateGenerator::New())
	-{
	- m_DoubleInterpolator = itk::LinearInterpolateImageFunction< ItkDoubleImgType, float >::New();
	- m_NullDir.Fill(0);
	-}
	-
	-template< class PixelType >
	-TractsToDWIImageFilter< PixelType >::~TractsToDWIImageFilter()
	-{
	-
	-}
	-
	-template< class PixelType >
	-TractsToDWIImageFilter< PixelType >::DoubleDwiType::Pointer TractsToDWIImageFilter< PixelType >::
	-SimulateKspaceAcquisition( std::vector< DoubleDwiType::Pointer >& compartment_images )
	-{
	- unsigned int numFiberCompartments = m_Parameters.m_FiberModelList.size();
	- // create slice object
	- ImageRegion<2> sliceRegion;
	- sliceRegion.SetSize(0, m_WorkingImageRegion.GetSize()[0]);
	- sliceRegion.SetSize(1, m_WorkingImageRegion.GetSize()[1]);
	- Vector< double, 2 > sliceSpacing;
	- sliceSpacing[0] = m_WorkingSpacing[0];
	- sliceSpacing[1] = m_WorkingSpacing[1];
	-
	- DoubleDwiType::PixelType nullPix; nullPix.SetSize(compartment_images.at(0)->GetVectorLength()); nullPix.Fill(0.0);
	- auto magnitudeDwiImage = DoubleDwiType::New();
	- magnitudeDwiImage->SetSpacing( m_Parameters.m_SignalGen.m_ImageSpacing );
	- magnitudeDwiImage->SetOrigin( m_Parameters.m_SignalGen.m_ImageOrigin );
	- magnitudeDwiImage->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection );
	- magnitudeDwiImage->SetLargestPossibleRegion( m_Parameters.m_SignalGen.m_CroppedRegion );
	- magnitudeDwiImage->SetBufferedRegion( m_Parameters.m_SignalGen.m_CroppedRegion );
	- magnitudeDwiImage->SetRequestedRegion( m_Parameters.m_SignalGen.m_CroppedRegion );
	- magnitudeDwiImage->SetVectorLength( compartment_images.at(0)->GetVectorLength() );
	- magnitudeDwiImage->Allocate();
	- magnitudeDwiImage->FillBuffer(nullPix);
	-
	- m_PhaseImage = DoubleDwiType::New();
	- m_PhaseImage->SetSpacing( m_Parameters.m_SignalGen.m_ImageSpacing );
	- m_PhaseImage->SetOrigin( m_Parameters.m_SignalGen.m_ImageOrigin );
	- m_PhaseImage->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection );
	- m_PhaseImage->SetLargestPossibleRegion( m_Parameters.m_SignalGen.m_CroppedRegion );
	- m_PhaseImage->SetBufferedRegion( m_Parameters.m_SignalGen.m_CroppedRegion );
	- m_PhaseImage->SetRequestedRegion( m_Parameters.m_SignalGen.m_CroppedRegion );
	- m_PhaseImage->SetVectorLength( compartment_images.at(0)->GetVectorLength() );
	- m_PhaseImage->Allocate();
	- m_PhaseImage->FillBuffer(nullPix);
	-
	- m_KspaceImage = DoubleDwiType::New();
	- m_KspaceImage->SetSpacing( m_Parameters.m_SignalGen.m_ImageSpacing );
	- m_KspaceImage->SetOrigin( m_Parameters.m_SignalGen.m_ImageOrigin );
	- m_KspaceImage->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection );
	- m_KspaceImage->SetLargestPossibleRegion( m_Parameters.m_SignalGen.m_CroppedRegion );
	- m_KspaceImage->SetBufferedRegion( m_Parameters.m_SignalGen.m_CroppedRegion );
	- m_KspaceImage->SetRequestedRegion( m_Parameters.m_SignalGen.m_CroppedRegion );
	- m_KspaceImage->SetVectorLength( m_Parameters.m_SignalGen.m_NumberOfCoils );
	- m_KspaceImage->Allocate();
	- m_KspaceImage->FillBuffer(nullPix);
	-
	- // calculate coil positions
	- double a = m_Parameters.m_SignalGen.m_ImageRegion.GetSize(0)*m_Parameters.m_SignalGen.m_ImageSpacing[0];
	- double b = m_Parameters.m_SignalGen.m_ImageRegion.GetSize(1)*m_Parameters.m_SignalGen.m_ImageSpacing[1];
	- double c = m_Parameters.m_SignalGen.m_ImageRegion.GetSize(2)*m_Parameters.m_SignalGen.m_ImageSpacing[2];
	- double diagonal = sqrt(aa+bb)/1000; // image diagonal in m
	-
	- m_CoilPointset = mitk::PointSet::New();
	- std::vector< itk::Vector<double, 3> > coilPositions;
	- itk::Vector<double, 3> pos; pos.Fill(0.0); pos[1] = -diagonal/2;
	- itk::Vector<double, 3> center;
	- center[0] = a/2-m_Parameters.m_SignalGen.m_ImageSpacing[0]/2;
	- center[1] = b/2-m_Parameters.m_SignalGen.m_ImageSpacing[2]/2;
	- center[2] = c/2-m_Parameters.m_SignalGen.m_ImageSpacing[1]/2;
	- for (unsigned int c=0; c<m_Parameters.m_SignalGen.m_NumberOfCoils; c++)
	- {
	- coilPositions.push_back(pos);
	- m_CoilPointset->InsertPoint(c, pos*1000 + m_Parameters.m_SignalGen.m_ImageOrigin.GetVectorFromOrigin() + center );
	-
	- double rz = 360.0/m_Parameters.m_SignalGen.m_NumberOfCoils * itk::Math::pi/180;
	- vnl_matrix_fixed< double, 3, 3 > rotZ; rotZ.set_identity();
	- rotZ[0][0] = cos(rz);
	- rotZ[1][1] = rotZ[0][0];
	- rotZ[0][1] = -sin(rz);
	- rotZ[1][0] = -rotZ[0][1];
	-
	- pos.SetVnlVector(rotZ*pos.GetVnlVector());
	- }
	-
	- auto num_slices = compartment_images.at(0)->GetLargestPossibleRegion().GetSize(2);
	- auto num_gradient_volumes = static_cast<int>(compartment_images.at(0)->GetVectorLength());
	- auto max_threads = omp_get_max_threads();
	- int out_threads = Math::ceil(std::sqrt(max_threads));
	- int in_threads = Math::floor(std::sqrt(max_threads));
	- if (out_threads > num_gradient_volumes)
	- {
	- out_threads = num_gradient_volumes;
	- in_threads = Math::floor(static_cast<float>(max_threads/out_threads));
	- }
	- PrintToLog("Parallel volumes: " + boost::lexical_cast<std::string>(out_threads), false, true, true);
	- PrintToLog("Threads per slice: " + boost::lexical_cast<std::string>(in_threads), false, true, true);
	-
	- std::list< std::tuple<unsigned int, unsigned int, unsigned int> > spikes;
	- if (m_Parameters.m_Misc.m_DoAddSpikes)
	- for (unsigned int i=0; i<m_Parameters.m_SignalGen.m_Spikes; i++)
	- {
	- // gradient volume and slice index
	- auto spike = std::tuple<unsigned int, unsigned int, unsigned int>(
	- m_RandGen->GetIntegerVariate()%num_gradient_volumes,
	- m_RandGen->GetIntegerVariate()%num_slices,
	- m_RandGen->GetIntegerVariate()%m_Parameters.m_SignalGen.m_NumberOfCoils);
	- spikes.push_back(spike);
	- }
	-
	- bool output_timing = m_Parameters.m_Misc.m_OutputAdditionalImages;
	-
	- PrintToLog("0% 10 20 30 40 50 60 70 80 90 100%", false, true, false);
	- PrintToLog("\|----\|----\|----\|----\|----\|----\|----\|----\|----\|----\|\n*", false, false, false);
	- unsigned long lastTick = 0;
	-
	- boost::progress_display disp(static_cast<unsigned long>(num_gradient_volumes)*compartment_images.at(0)->GetLargestPossibleRegion().GetSize(2));
	-
	-#pragma omp parallel for num_threads(out_threads)
	- for (int g=0; g<num_gradient_volumes; g++)
	- {
	- if (this->GetAbortGenerateData())
	- continue;
	-
	- std::list< std::tuple<unsigned int, unsigned int> > spikeSlice;
	-#pragma omp critical
	- {
	-
	- for (auto spike : spikes)
	- if (std::get<0>(spike) == static_cast<unsigned int>(g))
	- spikeSlice.push_back(std::tuple<unsigned int, unsigned int>(std::get<1>(spike), std::get<2>(spike)));
	- }
	-
	- for (unsigned int z=0; z<num_slices; z++)
	- {
	- std::vector< Float2DImageType::Pointer > compartment_slices;
	- std::vector< float > t2Vector;
	- std::vector< float > t1Vector;
	-
	- for (unsigned int i=0; i<compartment_images.size(); i++)
	- {
	- DiffusionSignalModel<double>* signalModel;
	- if (i<numFiberCompartments)
	- signalModel = m_Parameters.m_FiberModelList.at(i);
	- else
	- signalModel = m_Parameters.m_NonFiberModelList.at(i-numFiberCompartments);
	-
	- auto slice = Float2DImageType::New();
	- slice->SetLargestPossibleRegion( sliceRegion );
	- slice->SetBufferedRegion( sliceRegion );
	- slice->SetRequestedRegion( sliceRegion );
	- slice->SetSpacing(sliceSpacing);
	- slice->Allocate();
	- slice->FillBuffer(0.0);
	-
	- // extract slice from channel g
	- for (unsigned int y=0; y<compartment_images.at(0)->GetLargestPossibleRegion().GetSize(1); y++)
	- for (unsigned int x=0; x<compartment_images.at(0)->GetLargestPossibleRegion().GetSize(0); x++)
	- {
	- Float2DImageType::IndexType index2D; index2D[0]=x; index2D[1]=y;
	- DoubleDwiType::IndexType index3D; index3D[0]=x; index3D[1]=y; index3D[2]=z;
	-
	- slice->SetPixel(index2D, compartment_images.at(i)->GetPixel(index3D)[g]);
	- }
	-
	- compartment_slices.push_back(slice);
	- t2Vector.push_back(signalModel->GetT2());
	- t1Vector.push_back(signalModel->GetT1());
	- }
	-
	- if (this->GetAbortGenerateData())
	- continue;
	-
	- for (unsigned int c=0; c<m_Parameters.m_SignalGen.m_NumberOfCoils; c++)
	- {
	- int numSpikes = 0;
	- for (auto ss : spikeSlice)
	- if (std::get<0>(ss) == z && std::get<1>(ss) == c)
	- ++numSpikes;
	-
	- // create k-sapce (inverse fourier transform slices)
	- auto idft = itk::KspaceImageFilter< Float2DImageType::PixelType >::New();
	- idft->SetCompartmentImages(compartment_slices);
	- idft->SetT2(t2Vector);
	- idft->SetT1(t1Vector);
	- if (m_UseConstantRandSeed)
	- {
	- int linear_seed = g + num_gradient_volumesz + num_gradient_volumescompartment_images.at(0)->GetLargestPossibleRegion().GetSize(2)*c;
	- idft->SetRandSeed(linear_seed);
	- }
	- idft->SetParameters(&m_Parameters);
	- idft->SetZ((float)z-(float)( compartment_images.at(0)->GetLargestPossibleRegion().GetSize(2)
	- -compartment_images.at(0)->GetLargestPossibleRegion().GetSize(2)%2 ) / 2.0);
	- idft->SetZidx(z);
	- idft->SetCoilPosition(coilPositions.at(c));
	- idft->SetFiberBundle(m_FiberBundle);
	- idft->SetTranslation(m_Translations.at(g));
	- idft->SetRotationMatrix(m_RotationsInv.at(g));
	- idft->SetDiffusionGradientDirection(m_Parameters.m_SignalGen.GetGradientDirection(g)*m_Parameters.m_SignalGen.GetBvalue()/1000.0);
	- idft->SetSpikesPerSlice(numSpikes);
	- idft->SetNumberOfThreads(in_threads);
	-#pragma omp critical
	- if (output_timing)
	- {
	- idft->SetStoreTimings(true);
	- output_timing = false;
	- }
	- idft->Update();
	-
	-#pragma omp critical
	- if (numSpikes>0)
	- {
	- m_SpikeLog += "Volume " + boost::lexical_cast<std::string>(g) + " Coil " + boost::lexical_cast<std::string>(c) + "\n";
	- m_SpikeLog += idft->GetSpikeLog();
	- }
	-
	- Complex2DImageType::Pointer fSlice;
	- fSlice = idft->GetOutput();
	-
	- if (idft->GetTickImage().IsNotNull())
	- m_TickImage = idft->GetTickImage();
	- if (idft->GetRfImage().IsNotNull())
	- m_RfImage = idft->GetRfImage();
	-
	- // fourier transform slice
	- Complex2DImageType::Pointer newSlice;
	- auto dft = itk::DftImageFilter< Float2DImageType::PixelType >::New();
	- dft->SetInput(fSlice);
	- dft->SetParameters(m_Parameters);
	- dft->SetNumberOfThreads(in_threads);
	- dft->Update();
	- newSlice = dft->GetOutput();
	-
	- // put slice back into channel g
	- for (unsigned int y=0; y<fSlice->GetLargestPossibleRegion().GetSize(1); y++)
	- for (unsigned int x=0; x<fSlice->GetLargestPossibleRegion().GetSize(0); x++)
	- {
	- DoubleDwiType::IndexType index3D; index3D[0]=x; index3D[1]=y; index3D[2]=z;
	- Complex2DImageType::IndexType index2D; index2D[0]=x; index2D[1]=y;
	-
	- Complex2DImageType::PixelType cPix = newSlice->GetPixel(index2D);
	- double magn = sqrt(cPix.real()cPix.real()+cPix.imag()cPix.imag());
	- double phase = 0;
	- if (cPix.real()!=0)
	- phase = atan( cPix.imag()/cPix.real() );
	-
	- DoubleDwiType::PixelType real_pix = m_OutputImagesReal.at(c)->GetPixel(index3D);
	- real_pix[g] = cPix.real();
	- m_OutputImagesReal.at(c)->SetPixel(index3D, real_pix);
	-
	- DoubleDwiType::PixelType imag_pix = m_OutputImagesImag.at(c)->GetPixel(index3D);
	- imag_pix[g] = cPix.imag();
	- m_OutputImagesImag.at(c)->SetPixel(index3D, imag_pix);
	-
	- DoubleDwiType::PixelType dwiPix = magnitudeDwiImage->GetPixel(index3D);
	- DoubleDwiType::PixelType phasePix = m_PhaseImage->GetPixel(index3D);
	-
	- if (m_Parameters.m_SignalGen.m_NumberOfCoils>1)
	- {
	- dwiPix[g] += magn*magn;
	- phasePix[g] += phase*phase;
	- }
	- else
	- {
	- dwiPix[g] = magn;
	- phasePix[g] = phase;
	- }
	-
	- //#pragma omp critical
	- {
	- magnitudeDwiImage->SetPixel(index3D, dwiPix);
	- m_PhaseImage->SetPixel(index3D, phasePix);
	-
	- // k-space image
	- if (g==0)
	- {
	- DoubleDwiType::PixelType kspacePix = m_KspaceImage->GetPixel(index3D);
	- kspacePix[c] = idft->GetKSpaceImage()->GetPixel(index2D);
	- m_KspaceImage->SetPixel(index3D, kspacePix);
	- }
	- }
	- }
	- }
	-
	- if (m_Parameters.m_SignalGen.m_NumberOfCoils>1)
	- {
	- for (int y=0; y<static_cast<int>(magnitudeDwiImage->GetLargestPossibleRegion().GetSize(1)); y++)
	- for (int x=0; x<static_cast<int>(magnitudeDwiImage->GetLargestPossibleRegion().GetSize(0)); x++)
	- {
	- DoubleDwiType::IndexType index3D; index3D[0]=x; index3D[1]=y; index3D[2]=z;
	- DoubleDwiType::PixelType magPix = magnitudeDwiImage->GetPixel(index3D);
	- magPix[g] = sqrt(magPix[g]/m_Parameters.m_SignalGen.m_NumberOfCoils);
	-
	- DoubleDwiType::PixelType phasePix = m_PhaseImage->GetPixel(index3D);
	- phasePix[g] = sqrt(phasePix[g]/m_Parameters.m_SignalGen.m_NumberOfCoils);
	-
	- //#pragma omp critical
	- {
	- magnitudeDwiImage->SetPixel(index3D, magPix);
	- m_PhaseImage->SetPixel(index3D, phasePix);
	- }
	- }
	- }
	-
	- ++disp;
	- unsigned long newTick = 50*disp.count()/disp.expected_count();
	- for (unsigned long tick = 0; tick<(newTick-lastTick); tick++)
	- PrintToLog("*", false, false, false);
	- lastTick = newTick;
	- }
	- }
	-
	-
	- PrintToLog("\n", false);
	- return magnitudeDwiImage;
	-}
	-
	-template< class PixelType >
	-TractsToDWIImageFilter< PixelType >::ItkDoubleImgType::Pointer TractsToDWIImageFilter< PixelType >::
	-NormalizeInsideMask(ItkDoubleImgType::Pointer image)
	-{
	- double max = itk::NumericTraits< double >::min();
	- double min = itk::NumericTraits< double >::max();
	-
	- itk::ImageRegionIterator< ItkDoubleImgType > it(image, image->GetLargestPossibleRegion());
	- while(!it.IsAtEnd())
	- {
	- if (m_Parameters.m_SignalGen.m_MaskImage.IsNotNull() && m_Parameters.m_SignalGen.m_MaskImage->GetPixel(it.GetIndex())<=0)
	- {
	- it.Set(0.0);
	- ++it;
	- continue;
	- }
	-
	- if (it.Get()>max)
	- max = it.Get();
	- if (it.Get()<min)
	- min = it.Get();
	- ++it;
	- }
	- auto scaler = itk::ShiftScaleImageFilter< ItkDoubleImgType, ItkDoubleImgType >::New();
	- scaler->SetInput(image);
	- scaler->SetShift(-min);
	- scaler->SetScale(1.0/(max-min));
	- scaler->Update();
	- return scaler->GetOutput();
	-}
	-
	-template< class PixelType >
	-void TractsToDWIImageFilter< PixelType >::CheckVolumeFractionImages()
	-{
	- m_UseRelativeNonFiberVolumeFractions = false;
	-
	- // check for fiber volume fraction maps
	- unsigned int fibVolImages = 0;
	- for (std::size_t i=0; i<m_Parameters.m_FiberModelList.size(); i++)
	- {
	- if (m_Parameters.m_FiberModelList[i]->GetVolumeFractionImage().IsNotNull())
	- {
	- PrintToLog("Using volume fraction map for fiber compartment " + boost::lexical_cast<std::string>(i+1), false);
	- fibVolImages++;
	- }
	- }
	-
	- // check for non-fiber volume fraction maps
	- unsigned int nonfibVolImages = 0;
	- for (std::size_t i=0; i<m_Parameters.m_NonFiberModelList.size(); i++)
	- {
	- if (m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage().IsNotNull())
	- {
	- PrintToLog("Using volume fraction map for non-fiber compartment " + boost::lexical_cast<std::string>(i+1), false);
	- nonfibVolImages++;
	- }
	- }
	-
	- // not all fiber compartments are using volume fraction maps
	- // --> non-fiber volume fractions are assumed to be relative to the
	- // non-fiber volume and not absolute voxel-volume fractions.
	- // this means if two non-fiber compartments are used but only one of them
	- // has an associated volume fraction map, the repesctive other volume fraction map
	- // can be determined as inverse (1-val) of the present volume fraction map-
	- if ( fibVolImages<m_Parameters.m_FiberModelList.size() && nonfibVolImages==1 && m_Parameters.m_NonFiberModelList.size()==2)
	- {
	- PrintToLog("Calculating missing non-fiber volume fraction image by inverting the other.\n"
	- "Assuming non-fiber volume fraction images to contain values relative to the"
	- " remaining non-fiber volume, not absolute values.", false);
	-
	- auto inverter = itk::InvertIntensityImageFilter< ItkDoubleImgType, ItkDoubleImgType >::New();
	- inverter->SetMaximum(1.0);
	- if ( m_Parameters.m_NonFiberModelList[0]->GetVolumeFractionImage().IsNull()
	- && m_Parameters.m_NonFiberModelList[1]->GetVolumeFractionImage().IsNotNull() )
	- {
	- // m_Parameters.m_NonFiberModelList[1]->SetVolumeFractionImage(
	- // NormalizeInsideMask( m_Parameters.m_NonFiberModelList[1]->GetVolumeFractionImage() ) );
	- inverter->SetInput( m_Parameters.m_NonFiberModelList[1]->GetVolumeFractionImage() );
	- inverter->Update();
	- m_Parameters.m_NonFiberModelList[0]->SetVolumeFractionImage(inverter->GetOutput());
	- }
	- else if ( m_Parameters.m_NonFiberModelList[1]->GetVolumeFractionImage().IsNull()
	- && m_Parameters.m_NonFiberModelList[0]->GetVolumeFractionImage().IsNotNull() )
	- {
	- // m_Parameters.m_NonFiberModelList[0]->SetVolumeFractionImage(
	- // NormalizeInsideMask( m_Parameters.m_NonFiberModelList[0]->GetVolumeFractionImage() ) );
	- inverter->SetInput( m_Parameters.m_NonFiberModelList[0]->GetVolumeFractionImage() );
	- inverter->Update();
	- m_Parameters.m_NonFiberModelList[1]->SetVolumeFractionImage(inverter->GetOutput());
	- }
	- else
	- {
	- itkExceptionMacro("Something went wrong in automatically calculating the missing non-fiber volume fraction image!"
	- " Did you use two non fiber compartments but only one volume fraction image?"
	- " Then it should work and this error is really strange.");
	- }
	- m_UseRelativeNonFiberVolumeFractions = true;
	-
	- nonfibVolImages++;
	- }
	-
	- // Up to two fiber compartments are allowed without volume fraction maps since the volume fractions can then be determined automatically
	- if (m_Parameters.m_FiberModelList.size()>2
	- && fibVolImages!=m_Parameters.m_FiberModelList.size())
	- itkExceptionMacro("More than two fiber compartment selected but no corresponding volume fraction maps set!");
	-
	- // One non-fiber compartment is allowed without volume fraction map since the volume fraction can then be determined automatically
	- if (m_Parameters.m_NonFiberModelList.size()>1
	- && nonfibVolImages!=m_Parameters.m_NonFiberModelList.size())
	- itkExceptionMacro("More than one non-fiber compartment selected but no volume fraction maps set!");
	-
	- if (fibVolImages<m_Parameters.m_FiberModelList.size() && nonfibVolImages>0)
	- {
	- PrintToLog("Not all fiber compartments are using an associated volume fraction image.\n"
	- "Assuming non-fiber volume fraction images to contain values relative to the"
	- " remaining non-fiber volume, not absolute values.", false);
	- m_UseRelativeNonFiberVolumeFractions = true;
	-
	-// mitk::LocaleSwitch localeSwitch("C");
	- // itk::ImageFileWriter<ItkDoubleImgType>::Pointer wr = itk::ImageFileWriter<ItkDoubleImgType>::New();
	- // wr->SetInput(m_Parameters.m_NonFiberModelList[1]->GetVolumeFractionImage());
	- // wr->SetFileName("/local/volumefraction.nrrd");
	- // wr->Update();
	- }
	-
	- // initialize the images that store the output volume fraction of each compartment
	- m_VolumeFractions.clear();
	- for (std::size_t i=0; i<m_Parameters.m_FiberModelList.size()+m_Parameters.m_NonFiberModelList.size(); i++)
	- {
	- auto doubleImg = ItkDoubleImgType::New();
	- doubleImg->SetSpacing( m_WorkingSpacing );
	- doubleImg->SetOrigin( m_WorkingOrigin );
	- doubleImg->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection );
	- doubleImg->SetLargestPossibleRegion( m_WorkingImageRegion );
	- doubleImg->SetBufferedRegion( m_WorkingImageRegion );
	- doubleImg->SetRequestedRegion( m_WorkingImageRegion );
	- doubleImg->Allocate();
	- doubleImg->FillBuffer(0);
	- m_VolumeFractions.push_back(doubleImg);
	- }
	-}
	-
	-template< class PixelType >
	-void TractsToDWIImageFilter< PixelType >::InitializeData()
	-{
	- m_Rotations.clear();
	- m_Translations.clear();
	- m_MotionLog = "";
	- m_SpikeLog = "";
	-
	- m_TickImage = nullptr;
	- m_RfImage = nullptr;
	-
	- // initialize output dwi image
	- m_Parameters.m_SignalGen.m_CroppedRegion = m_Parameters.m_SignalGen.m_ImageRegion;
	- if (m_Parameters.m_Misc.m_DoAddAliasing)
	- m_Parameters.m_SignalGen.m_CroppedRegion.SetSize( 1, m_Parameters.m_SignalGen.m_CroppedRegion.GetSize(1)
	- *m_Parameters.m_SignalGen.m_CroppingFactor);
	-
	- itk::Point<double,3> shiftedOrigin = m_Parameters.m_SignalGen.m_ImageOrigin;
	- shiftedOrigin[1] += (m_Parameters.m_SignalGen.m_ImageRegion.GetSize(1)
	- -m_Parameters.m_SignalGen.m_CroppedRegion.GetSize(1))*m_Parameters.m_SignalGen.m_ImageSpacing[1]/2;
	-
	- m_OutputImage = OutputImageType::New();
	- m_OutputImage->SetSpacing( m_Parameters.m_SignalGen.m_ImageSpacing );
	- m_OutputImage->SetOrigin( shiftedOrigin );
	- m_OutputImage->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection );
	- m_OutputImage->SetLargestPossibleRegion( m_Parameters.m_SignalGen.m_CroppedRegion );
	- m_OutputImage->SetBufferedRegion( m_Parameters.m_SignalGen.m_CroppedRegion );
	- m_OutputImage->SetRequestedRegion( m_Parameters.m_SignalGen.m_CroppedRegion );
	- m_OutputImage->SetVectorLength( m_Parameters.m_SignalGen.GetNumVolumes() );
	- m_OutputImage->Allocate();
	- typename OutputImageType::PixelType temp;
	- temp.SetSize(m_Parameters.m_SignalGen.GetNumVolumes());
	- temp.Fill(0.0);
	- m_OutputImage->FillBuffer(temp);
	-
	- PrintToLog("Output image spacing: [" + boost::lexical_cast<std::string>(m_Parameters.m_SignalGen.m_ImageSpacing[0]) + "," + boost::lexical_cast<std::string>(m_Parameters.m_SignalGen.m_ImageSpacing[1]) + "," + boost::lexical_cast<std::string>(m_Parameters.m_SignalGen.m_ImageSpacing[2]) + "]", false);
	- PrintToLog("Output image size: [" + boost::lexical_cast<std::string>(m_Parameters.m_SignalGen.m_CroppedRegion.GetSize(0)) + "," + boost::lexical_cast<std::string>(m_Parameters.m_SignalGen.m_CroppedRegion.GetSize(1)) + "," + boost::lexical_cast<std::string>(m_Parameters.m_SignalGen.m_CroppedRegion.GetSize(2)) + "]", false);
	-
	- // images containing real and imaginary part of the dMRI signal for each coil
	- m_OutputImagesReal.clear();
	- m_OutputImagesImag.clear();
	- for (unsigned int i=0; i<m_Parameters.m_SignalGen.m_NumberOfCoils; ++i)
	- {
	- typename DoubleDwiType::Pointer outputImageReal = DoubleDwiType::New();
	- outputImageReal->SetSpacing( m_Parameters.m_SignalGen.m_ImageSpacing );
	- outputImageReal->SetOrigin( shiftedOrigin );
	- outputImageReal->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection );
	- outputImageReal->SetLargestPossibleRegion( m_Parameters.m_SignalGen.m_CroppedRegion );
	- outputImageReal->SetBufferedRegion( m_Parameters.m_SignalGen.m_CroppedRegion );
	- outputImageReal->SetRequestedRegion( m_Parameters.m_SignalGen.m_CroppedRegion );
	- outputImageReal->SetVectorLength( m_Parameters.m_SignalGen.GetNumVolumes() );
	- outputImageReal->Allocate();
	- outputImageReal->FillBuffer(temp);
	- m_OutputImagesReal.push_back(outputImageReal);
	-
	- typename DoubleDwiType::Pointer outputImageImag = DoubleDwiType::New();
	- outputImageImag->SetSpacing( m_Parameters.m_SignalGen.m_ImageSpacing );
	- outputImageImag->SetOrigin( shiftedOrigin );
	- outputImageImag->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection );
	- outputImageImag->SetLargestPossibleRegion( m_Parameters.m_SignalGen.m_CroppedRegion );
	- outputImageImag->SetBufferedRegion( m_Parameters.m_SignalGen.m_CroppedRegion );
	- outputImageImag->SetRequestedRegion( m_Parameters.m_SignalGen.m_CroppedRegion );
	- outputImageImag->SetVectorLength( m_Parameters.m_SignalGen.GetNumVolumes() );
	- outputImageImag->Allocate();
	- outputImageImag->FillBuffer(temp);
	- m_OutputImagesImag.push_back(outputImageImag);
	- }
	-
	- // Apply in-plane upsampling for Gibbs ringing artifact
	- double upsampling = 1;
	- if (m_Parameters.m_SignalGen.m_DoAddGibbsRinging && m_Parameters.m_SignalGen.m_ZeroRinging==0)
	- upsampling = 2;
	- m_WorkingSpacing = m_Parameters.m_SignalGen.m_ImageSpacing;
	- m_WorkingSpacing[0] /= upsampling;
	- m_WorkingSpacing[1] /= upsampling;
	- m_WorkingImageRegion = m_Parameters.m_SignalGen.m_ImageRegion;
	- m_WorkingImageRegion.SetSize(0, m_Parameters.m_SignalGen.m_ImageRegion.GetSize()[0]*upsampling);
	- m_WorkingImageRegion.SetSize(1, m_Parameters.m_SignalGen.m_ImageRegion.GetSize()[1]*upsampling);
	- m_WorkingOrigin = m_Parameters.m_SignalGen.m_ImageOrigin;
	- m_WorkingOrigin[0] -= m_Parameters.m_SignalGen.m_ImageSpacing[0]/2;
	- m_WorkingOrigin[0] += m_WorkingSpacing[0]/2;
	- m_WorkingOrigin[1] -= m_Parameters.m_SignalGen.m_ImageSpacing[1]/2;
	- m_WorkingOrigin[1] += m_WorkingSpacing[1]/2;
	- m_WorkingOrigin[2] -= m_Parameters.m_SignalGen.m_ImageSpacing[2]/2;
	- m_WorkingOrigin[2] += m_WorkingSpacing[2]/2;
	- m_VoxelVolume = m_WorkingSpacing[0]m_WorkingSpacing[1]m_WorkingSpacing[2];
	-
	- PrintToLog("Working image spacing: [" + boost::lexical_cast<std::string>(m_WorkingSpacing[0]) + "," + boost::lexical_cast<std::string>(m_WorkingSpacing[1]) + "," + boost::lexical_cast<std::string>(m_WorkingSpacing[2]) + "]", false);
	- PrintToLog("Working image size: [" + boost::lexical_cast<std::string>(m_WorkingImageRegion.GetSize(0)) + "," + boost::lexical_cast<std::string>(m_WorkingImageRegion.GetSize(1)) + "," + boost::lexical_cast<std::string>(m_WorkingImageRegion.GetSize(2)) + "]", false);
	-
	- // generate double images to store the individual compartment signals
	- m_CompartmentImages.clear();
	- int numFiberCompartments = m_Parameters.m_FiberModelList.size();
	- int numNonFiberCompartments = m_Parameters.m_NonFiberModelList.size();
	- for (int i=0; i<numFiberCompartments+numNonFiberCompartments; i++)
	- {
	- auto doubleDwi = DoubleDwiType::New();
	- doubleDwi->SetSpacing( m_WorkingSpacing );
	- doubleDwi->SetOrigin( m_WorkingOrigin );
	- doubleDwi->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection );
	- doubleDwi->SetLargestPossibleRegion( m_WorkingImageRegion );
	- doubleDwi->SetBufferedRegion( m_WorkingImageRegion );
	- doubleDwi->SetRequestedRegion( m_WorkingImageRegion );
	- doubleDwi->SetVectorLength( m_Parameters.m_SignalGen.GetNumVolumes() );
	- doubleDwi->Allocate();
	- DoubleDwiType::PixelType pix;
	- pix.SetSize(m_Parameters.m_SignalGen.GetNumVolumes());
	- pix.Fill(0.0);
	- doubleDwi->FillBuffer(pix);
	- m_CompartmentImages.push_back(doubleDwi);
	- }
	-
	- if (m_FiberBundle.IsNull() && m_InputImage.IsNotNull())
	- {
	- m_CompartmentImages.clear();
	-
	- m_Parameters.m_SignalGen.m_DoAddMotion = false;
	- m_Parameters.m_SignalGen.m_DoSimulateRelaxation = false;
	-
	- PrintToLog("Simulating acquisition for input diffusion-weighted image.", false);
	- auto caster = itk::CastImageFilter< OutputImageType, DoubleDwiType >::New();
	- caster->SetInput(m_InputImage);
	- caster->Update();
	-
	- if (m_Parameters.m_SignalGen.m_DoAddGibbsRinging && m_Parameters.m_SignalGen.m_ZeroRinging==0)
	- {
	- PrintToLog("Upsampling input diffusion-weighted image for Gibbs ringing simulation.", false);
	-
	- auto resampler = itk::ResampleDwiImageFilter< double >::New();
	- resampler->SetInput(caster->GetOutput());
	- itk::Vector< double, 3 > samplingFactor;
	- samplingFactor[0] = upsampling;
	- samplingFactor[1] = upsampling;
	- samplingFactor[2] = 1;
	- resampler->SetSamplingFactor(samplingFactor);
	- resampler->SetInterpolation(itk::ResampleDwiImageFilter< double >::Interpolate_WindowedSinc);
	- resampler->Update();
	- m_CompartmentImages.push_back(resampler->GetOutput());
	- }
	- else
	- m_CompartmentImages.push_back(caster->GetOutput());
	-
	- VectorType translation; translation.Fill(0.0);
	- MatrixType rotation; rotation.SetIdentity();
	- for (unsigned int g=0; g<m_Parameters.m_SignalGen.GetNumVolumes(); g++)
	- {
	- m_Rotations.push_back(rotation);
	- m_RotationsInv.push_back(rotation);
	- m_Translations.push_back(translation);
	- }
	- }
	-
	- // resample mask image and frequency map to fit upsampled geometry
	- if (m_Parameters.m_SignalGen.m_MaskImage.IsNotNull() && m_Parameters.m_SignalGen.m_MaskImage->GetLargestPossibleRegion()!=m_WorkingImageRegion)
	- {
	- PrintToLog("Resampling tissue mask", false);
	- // rescale mask image (otherwise there are problems with the resampling)
	- auto rescaler = itk::RescaleIntensityImageFilter<ItkUcharImgType,ItkUcharImgType>::New();
	- rescaler->SetInput(0,m_Parameters.m_SignalGen.m_MaskImage);
	- rescaler->SetOutputMaximum(100);
	- rescaler->SetOutputMinimum(0);
	- rescaler->Update();
	-
	- // resample mask image
	- auto resampler = itk::ResampleImageFilter<ItkUcharImgType, ItkUcharImgType>::New();
	- resampler->SetInput(rescaler->GetOutput());
	- resampler->SetSize(m_WorkingImageRegion.GetSize());
	- resampler->SetOutputSpacing(m_WorkingSpacing);
	- resampler->SetOutputOrigin(m_WorkingOrigin);
	- resampler->SetOutputDirection(m_Parameters.m_SignalGen.m_ImageDirection);
	- resampler->SetOutputStartIndex ( m_WorkingImageRegion.GetIndex() );
	- auto nn_interpolator = itk::NearestNeighborInterpolateImageFunction<ItkUcharImgType, double>::New();
	- resampler->SetInterpolator(nn_interpolator);
	- resampler->Update();
	- m_Parameters.m_SignalGen.m_MaskImage = resampler->GetOutput();
	- }
	- // resample frequency map
	- if (m_Parameters.m_SignalGen.m_FrequencyMap.IsNotNull() && m_Parameters.m_SignalGen.m_FrequencyMap->GetLargestPossibleRegion()!=m_WorkingImageRegion)
	- {
	- PrintToLog("Resampling frequency map", false);
	- auto resampler = itk::ResampleImageFilter<ItkFloatImgType, ItkFloatImgType>::New();
	- resampler->SetInput(m_Parameters.m_SignalGen.m_FrequencyMap);
	- resampler->SetSize(m_WorkingImageRegion.GetSize());
	- resampler->SetOutputSpacing(m_WorkingSpacing);
	- resampler->SetOutputOrigin(m_WorkingOrigin);
	- resampler->SetOutputDirection(m_Parameters.m_SignalGen.m_ImageDirection);
	- resampler->SetOutputStartIndex ( m_WorkingImageRegion.GetIndex() );
	- auto nn_interpolator = itk::NearestNeighborInterpolateImageFunction<ItkFloatImgType, double>::New();
	- resampler->SetInterpolator(nn_interpolator);
	- resampler->Update();
	- m_Parameters.m_SignalGen.m_FrequencyMap = resampler->GetOutput();
	- }
	-
	- m_MaskImageSet = true;
	- if (m_Parameters.m_SignalGen.m_MaskImage.IsNull())
	- {
	- // no input tissue mask is set -> create default
	- PrintToLog("No tissue mask set", false);
	- m_Parameters.m_SignalGen.m_MaskImage = ItkUcharImgType::New();
	- m_Parameters.m_SignalGen.m_MaskImage->SetSpacing( m_WorkingSpacing );
	- m_Parameters.m_SignalGen.m_MaskImage->SetOrigin( m_WorkingOrigin );
	- m_Parameters.m_SignalGen.m_MaskImage->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection );
	- m_Parameters.m_SignalGen.m_MaskImage->SetLargestPossibleRegion( m_WorkingImageRegion );
	- m_Parameters.m_SignalGen.m_MaskImage->SetBufferedRegion( m_WorkingImageRegion );
	- m_Parameters.m_SignalGen.m_MaskImage->SetRequestedRegion( m_WorkingImageRegion );
	- m_Parameters.m_SignalGen.m_MaskImage->Allocate();
	- m_Parameters.m_SignalGen.m_MaskImage->FillBuffer(100);
	- m_MaskImageSet = false;
	- }
	- else
	- {
	- PrintToLog("Using tissue mask", false);
	- }
	-
	- if (m_Parameters.m_SignalGen.m_DoAddMotion)
	- {
	- if (m_Parameters.m_SignalGen.m_DoRandomizeMotion)
	- {
	- PrintToLog("Random motion artifacts:", false);
	- PrintToLog("Maximum rotation: +/-" + boost::lexical_cast<std::string>(m_Parameters.m_SignalGen.m_Rotation) + "°", false);
	- PrintToLog("Maximum translation: +/-" + boost::lexical_cast<std::string>(m_Parameters.m_SignalGen.m_Translation) + "mm", false);
	- }
	- else
	- {
	- PrintToLog("Linear motion artifacts:", false);
	- PrintToLog("Maximum rotation: " + boost::lexical_cast<std::string>(m_Parameters.m_SignalGen.m_Rotation) + "°", false);
	- PrintToLog("Maximum translation: " + boost::lexical_cast<std::string>(m_Parameters.m_SignalGen.m_Translation) + "mm", false);
	- }
	- }
	- if ( m_Parameters.m_SignalGen.m_MotionVolumes.empty() )
	- {
	- // no motion in first volume
	- m_Parameters.m_SignalGen.m_MotionVolumes.push_back(false);
	-
	- // motion in all other volumes
	- while ( m_Parameters.m_SignalGen.m_MotionVolumes.size() < m_Parameters.m_SignalGen.GetNumVolumes() )
	- {
	- m_Parameters.m_SignalGen.m_MotionVolumes.push_back(true);
	- }
	- }
	- // we need to know for every volume if there is motion. if this information is missing, then set corresponding fal to false
	- while ( m_Parameters.m_SignalGen.m_MotionVolumes.size()<m_Parameters.m_SignalGen.GetNumVolumes() )
	- {
	- m_Parameters.m_SignalGen.m_MotionVolumes.push_back(false);
	- }
	-
	- m_NumMotionVolumes = 0;
	- for (unsigned int i=0; i<m_Parameters.m_SignalGen.GetNumVolumes(); ++i)
	- {
	- if (m_Parameters.m_SignalGen.m_MotionVolumes[i])
	- ++m_NumMotionVolumes;
	- }
	- m_MotionCounter = 0;
	-
	- // creat image to hold transformed mask (motion artifact)
	- m_TransformedMaskImage = ItkUcharImgType::New();
	- auto duplicator = itk::ImageDuplicator<ItkUcharImgType>::New();
	- duplicator->SetInputImage(m_Parameters.m_SignalGen.m_MaskImage);
	- duplicator->Update();
	- m_TransformedMaskImage = duplicator->GetOutput();
	-
	- // second upsampling needed for motion artifacts
	- ImageRegion<3> upsampledImageRegion = m_WorkingImageRegion;
	- VectorType upsampledSpacing = m_WorkingSpacing;
	- upsampledSpacing[0] /= 4;
	- upsampledSpacing[1] /= 4;
	- upsampledSpacing[2] /= 4;
	- upsampledImageRegion.SetSize(0, m_WorkingImageRegion.GetSize()[0]*4);
	- upsampledImageRegion.SetSize(1, m_WorkingImageRegion.GetSize()[1]*4);
	- upsampledImageRegion.SetSize(2, m_WorkingImageRegion.GetSize()[2]*4);
	- itk::Point<double,3> upsampledOrigin = m_WorkingOrigin;
	- upsampledOrigin[0] -= m_WorkingSpacing[0]/2;
	- upsampledOrigin[0] += upsampledSpacing[0]/2;
	- upsampledOrigin[1] -= m_WorkingSpacing[1]/2;
	- upsampledOrigin[1] += upsampledSpacing[1]/2;
	- upsampledOrigin[2] -= m_WorkingSpacing[2]/2;
	- upsampledOrigin[2] += upsampledSpacing[2]/2;
	-
	- m_UpsampledMaskImage = ItkUcharImgType::New();
	- auto upsampler = itk::ResampleImageFilter<ItkUcharImgType, ItkUcharImgType>::New();
	- upsampler->SetInput(m_Parameters.m_SignalGen.m_MaskImage);
	- upsampler->SetOutputParametersFromImage(m_Parameters.m_SignalGen.m_MaskImage);
	- upsampler->SetSize(upsampledImageRegion.GetSize());
	- upsampler->SetOutputSpacing(upsampledSpacing);
	- upsampler->SetOutputOrigin(upsampledOrigin);
	-
	- auto nn_interpolator = itk::NearestNeighborInterpolateImageFunction<ItkUcharImgType, double>::New();
	- upsampler->SetInterpolator(nn_interpolator);
	- upsampler->Update();
	- m_UpsampledMaskImage = upsampler->GetOutput();
	-}
	-
	-template< class PixelType >
	-void TractsToDWIImageFilter< PixelType >::InitializeFiberData()
	-{
	- m_mmRadius = m_Parameters.m_SignalGen.m_AxonRadius/1000;
	-
	- auto caster = itk::CastImageFilter< itk::Image<unsigned char, 3>, itk::Image<double, 3> >::New();
	- caster->SetInput(m_TransformedMaskImage);
	- caster->Update();
	-
	- vtkSmartPointer<vtkFloatArray> weights = m_FiberBundle->GetFiberWeights();
	- float mean_weight = 0;
	- for (int i=0; i<weights->GetSize(); i++)
	- mean_weight += weights->GetValue(i);
	- mean_weight /= weights->GetSize();
	-
	- if (mean_weight>0.000001)
	- for (int i=0; i<weights->GetSize(); i++)
	- m_FiberBundle->SetFiberWeight(i, weights->GetValue(i)/mean_weight);
	- else
	- PrintToLog("\nWarning: streamlines have VERY low weights. Average weight: " + boost::lexical_cast<std::string>(mean_weight) + ". Possible source of calculation errors.", false, true, true);
	-
	-
	- auto density_calculator = itk::TractDensityImageFilter< itk::Image<double, 3> >::New();
	- density_calculator->SetFiberBundle(m_FiberBundle);
	- density_calculator->SetInputImage(caster->GetOutput());
	- density_calculator->SetBinaryOutput(false);
	- density_calculator->SetUseImageGeometry(true);
	- density_calculator->SetOutputAbsoluteValues(true);
	- density_calculator->Update();
	- double max_density = density_calculator->GetMaxDensity();
	-
	- double voxel_volume = m_WorkingSpacing[0]m_WorkingSpacing[1]m_WorkingSpacing[2];
	- if (m_mmRadius>0)
	- {
	- std::stringstream stream;
	- stream << std::fixed << setprecision(2) << itk::Math::pim_mmRadiusm_mmRadius*max_density;
	- std::string s = stream.str();
	- PrintToLog("\nMax. fiber volume: " + s + "mm².", false, true, true);
	-
	- {
	- double full_radius = 1000std::sqrt(voxel_volume/(max_densityitk::Math::pi));
	- std::stringstream stream;
	- stream << std::fixed << setprecision(2) << full_radius;
	- std::string s = stream.str();
	- PrintToLog("\nA full fiber voxel corresponds to a fiber radius of ~" + s + "µm, given the current fiber configuration.", false, true, true);
	- }
	- }
	- else
	- {
	- m_mmRadius = std::sqrt(voxel_volume/(max_density*itk::Math::pi));
	- std::stringstream stream;
	- stream << std::fixed << setprecision(2) << m_mmRadius*1000;
	- std::string s = stream.str();
	- PrintToLog("\nSetting fiber radius to " + s + "µm to obtain full voxel.", false, true, true);
	- }
	-
	- // a second fiber bundle is needed to store the transformed version of the m_FiberBundleWorkingCopy
	- m_FiberBundleTransformed = m_FiberBundle->GetDeepCopy();
	-}
	-
	-
	-template< class PixelType >
	-bool TractsToDWIImageFilter< PixelType >::PrepareLogFile()
	-{
	- if(m_Logfile.is_open())
	- m_Logfile.close();
	-
	- std::string filePath;
	- std::string fileName;
	-
	- // Get directory name:
	- if (m_Parameters.m_Misc.m_OutputPath.size() > 0)
	- {
	- filePath = m_Parameters.m_Misc.m_OutputPath;
	- if( *(--(filePath.cend())) != '/')
	- {
	- filePath.push_back('/');
	- }
	- }
	- else
	- return false;
	-
	- // Get file name:
	- if( ! m_Parameters.m_Misc.m_ResultNode->GetName().empty() )
	- {
	- fileName = m_Parameters.m_Misc.m_ResultNode->GetName();
	- }
	- else
	- {
	- fileName = "";
	- }
	-
	- if( ! m_Parameters.m_Misc.m_OutputPrefix.empty() )
	- {
	- fileName = m_Parameters.m_Misc.m_OutputPrefix + fileName;
	- }
	-
	- try
	- {
	- m_Logfile.open( ( filePath + '/' + fileName + ".log" ).c_str() );
	- }
	- catch (const std::ios_base::failure &fail)
	- {
	- MITK_ERROR << "itkTractsToDWIImageFilter.cpp: Exception " << fail.what()
	- << " while trying to open file" << filePath << '/' << fileName << ".log";
	- return false;
	- }
	-
	- if ( m_Logfile.is_open() )
	- {
	- PrintToLog( "Logfile: " + filePath + '/' + fileName + ".log", false );
	- return true;
	- }
	- else
	- return false;
	-}
	-
	-
	-template< class PixelType >
	-void TractsToDWIImageFilter< PixelType >::GenerateData()
	-{
	- PrintToLog("\n**********************************************", false);
	- // prepare logfile
	- PrepareLogFile();
	- PrintToLog("Starting Fiberfox dMRI simulation");
	-
	- m_TimeProbe.Start();
	-
	- // check input data
	- if (m_FiberBundle.IsNull() && m_InputImage.IsNull())
	- itkExceptionMacro("Input fiber bundle and input diffusion-weighted image is nullptr!");
	-
	- if (m_Parameters.m_FiberModelList.empty() && m_InputImage.IsNull())
	- itkExceptionMacro("No diffusion model for fiber compartments defined and input diffusion-weighted"
	- " image is nullptr! At least one fiber compartment is necessary to simulate diffusion.");
	-
	- if (m_Parameters.m_NonFiberModelList.empty() && m_InputImage.IsNull())
	- itkExceptionMacro("No diffusion model for non-fiber compartments defined and input diffusion-weighted"
	- " image is nullptr! At least one non-fiber compartment is necessary to simulate diffusion.");
	-
	- if (m_Parameters.m_SignalGen.m_DoDisablePartialVolume) // no partial volume? remove all but first fiber compartment
	- while (m_Parameters.m_FiberModelList.size()>1)
	- m_Parameters.m_FiberModelList.pop_back();
	-
	- if (!m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition) // No upsampling of input image needed if no k-space simulation is performed
	- m_Parameters.m_SignalGen.m_DoAddGibbsRinging = false;
	-
	- if (m_UseConstantRandSeed) // always generate the same random numbers?
	- m_RandGen->SetSeed(0);
	- else
	- m_RandGen->SetSeed();
	-
	- InitializeData();
	- if ( m_FiberBundle.IsNotNull() ) // if no fiber bundle is found, we directly proceed to the k-space acquisition simulation
	- {
	- CheckVolumeFractionImages();
	- InitializeFiberData();
	-
	- int numFiberCompartments = m_Parameters.m_FiberModelList.size();
	- int numNonFiberCompartments = m_Parameters.m_NonFiberModelList.size();
	-
	- double maxVolume = 0;
	- unsigned long lastTick = 0;
	- int signalModelSeed = m_RandGen->GetIntegerVariate();
	-
	- PrintToLog("\n", false, false);
	- PrintToLog("Generating " + boost::lexical_cast<std::string>(numFiberCompartments+numNonFiberCompartments)
	- + "-compartment diffusion-weighted signal.");
	-
	- std::vector< int > bVals = m_Parameters.m_SignalGen.GetBvalues();
	- PrintToLog("b-values: ", false, false, true);
	- for (auto v : bVals)
	- PrintToLog(boost::lexical_cast<std::string>(v) + " ", false, false, true);
	- PrintToLog("\nVolumes: " + boost::lexical_cast<std::string>(m_Parameters.m_SignalGen.GetNumVolumes()), false, true, true);
	-
	- PrintToLog("\n", false, false, true);
	- PrintToLog("\n", false, false, true);
	-
	- unsigned int image_size_x = m_WorkingImageRegion.GetSize(0);
	- unsigned int region_size_y = m_WorkingImageRegion.GetSize(1);
	- unsigned int num_gradients = m_Parameters.m_SignalGen.GetNumVolumes();
	- int numFibers = m_FiberBundle->GetNumFibers();
	- boost::progress_display disp(numFibers*num_gradients);
	-
	- if (m_FiberBundle->GetMeanFiberLength()<5.0)
	- omp_set_num_threads(2);
	-
	- PrintToLog("0% 10 20 30 40 50 60 70 80 90 100%", false, true, false);
	- PrintToLog("\|----\|----\|----\|----\|----\|----\|----\|----\|----\|----\|\n*", false, false, false);
	-
	- for (unsigned int g=0; g<num_gradients; ++g)
	- {
	- // move fibers
	- SimulateMotion(g);
	-
	- // Set signal model random generator seeds to get same configuration in each voxel
	- for (std::size_t i=0; i<m_Parameters.m_FiberModelList.size(); i++)
	- m_Parameters.m_FiberModelList.at(i)->SetSeed(signalModelSeed);
	- for (std::size_t i=0; i<m_Parameters.m_NonFiberModelList.size(); i++)
	- m_Parameters.m_NonFiberModelList.at(i)->SetSeed(signalModelSeed);
	-
	- // storing voxel-wise intra-axonal volume in mm³
	- auto intraAxonalVolumeImage = ItkDoubleImgType::New();
	- intraAxonalVolumeImage->SetSpacing( m_WorkingSpacing );
	- intraAxonalVolumeImage->SetOrigin( m_WorkingOrigin );
	- intraAxonalVolumeImage->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection );
	- intraAxonalVolumeImage->SetLargestPossibleRegion( m_WorkingImageRegion );
	- intraAxonalVolumeImage->SetBufferedRegion( m_WorkingImageRegion );
	- intraAxonalVolumeImage->SetRequestedRegion( m_WorkingImageRegion );
	- intraAxonalVolumeImage->Allocate();
	- intraAxonalVolumeImage->FillBuffer(0);
	- maxVolume = 0;
	- double* intraAxBuffer = intraAxonalVolumeImage->GetBufferPointer();
	-
	- if (this->GetAbortGenerateData())
	- continue;
	-
	- vtkPolyData* fiberPolyData = m_FiberBundleTransformed->GetFiberPolyData();
	- // generate fiber signal (if there are any fiber models present)
	- if (!m_Parameters.m_FiberModelList.empty())
	- {
	- std::vector< double* > buffers;
	- for (unsigned int i=0; i<m_CompartmentImages.size(); ++i)
	- buffers.push_back(m_CompartmentImages.at(i)->GetBufferPointer());
	-#pragma omp parallel for
	- for( int i=0; i<numFibers; ++i )
	- {
	- if (this->GetAbortGenerateData())
	- continue;
	-
	- float fiberWeight = m_FiberBundleTransformed->GetFiberWeight(i);
	- if (fiberWeight == 0)
	- continue;
	-
	- int numPoints = -1;
	- std::vector< itk::Vector<double, 3> > points_copy;
	-#pragma omp critical
	- {
	- vtkCell* cell = fiberPolyData->GetCell(i);
	- numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	- for (int j=0; j<numPoints; j++)
	- points_copy.push_back(GetItkVector(points->GetPoint(j)));
	- }
	-
	- if (numPoints<2)
	- continue;
	-
	- double seg_volume = fiberWeightitk::Math::pim_mmRadius*m_mmRadius;
	- for( int j=0; j<numPoints - 1; ++j)
	- {
	- if (this->GetAbortGenerateData())
	- {
	- j=numPoints;
	- continue;
	- }
	-
	- itk::Vector<double> v = points_copy.at(j);
	-
	- itk::Vector<double, 3> dir = points_copy.at(j+1)-v;
	- if ( dir.GetSquaredNorm()<0.0001 \|\| dir[0]!=dir[0] \|\| dir[1]!=dir[1] \|\| dir[2]!=dir[2] )
	- continue;
	- dir.Normalize();
	-
	- itk::Point<float, 3> startVertex = points_copy.at(j);
	- itk::Index<3> startIndex;
	- itk::ContinuousIndex<float, 3> startIndexCont;
	- m_TransformedMaskImage->TransformPhysicalPointToIndex(startVertex, startIndex);
	- m_TransformedMaskImage->TransformPhysicalPointToContinuousIndex(startVertex, startIndexCont);
	-
	- itk::Point<float, 3> endVertex = points_copy.at(j+1);
	- itk::Index<3> endIndex;
	- itk::ContinuousIndex<float, 3> endIndexCont;
	- m_TransformedMaskImage->TransformPhysicalPointToIndex(endVertex, endIndex);
	- m_TransformedMaskImage->TransformPhysicalPointToContinuousIndex(endVertex, endIndexCont);
	-
	- std::vector< std::pair< itk::Index<3>, double > > segments = mitk::imv::IntersectImage(m_WorkingSpacing, startIndex, endIndex, startIndexCont, endIndexCont);
	-
	- // generate signal for each fiber compartment
	- for (int k=0; k<numFiberCompartments; ++k)
	- {
	- double signal_add = m_Parameters.m_FiberModelList[k]->SimulateMeasurement(g, dir)*seg_volume;
	- for (std::pair< itk::Index<3>, double > seg : segments)
	- {
	- if (!m_TransformedMaskImage->GetLargestPossibleRegion().IsInside(seg.first) \|\| m_TransformedMaskImage->GetPixel(seg.first)<=0)
	- continue;
	-
	- double seg_signal = seg.second*signal_add;
	-
	- unsigned int linear_index = g + num_gradientsseg.first[0] + num_gradientsimage_size_xseg.first[1] + num_gradientsimage_size_xregion_size_yseg.first[2];
	-
	- // update dMRI volume
	-#pragma omp atomic
	- buffers[k][linear_index] += seg_signal;
	-
	- // update fiber volume image
	- if (k==0)
	- {
	- linear_index = seg.first[0] + image_size_xseg.first[1] + image_size_xregion_size_y*seg.first[2];
	-#pragma omp atomic
	- intraAxBuffer[linear_index] += seg.second*seg_volume;
	- double vol = intraAxBuffer[linear_index];
	- if (vol>maxVolume) { maxVolume = vol; }
	- }
	- }
	-
	- }
	- }
	-
	-#pragma omp critical
	- {
	- // progress report
	- ++disp;
	- unsigned long newTick = 50*disp.count()/disp.expected_count();
	- for (unsigned int tick = 0; tick<(newTick-lastTick); ++tick)
	- PrintToLog("*", false, false, false);
	- lastTick = newTick;
	- }
	- }
	- }
	-
	- // axon radius not manually defined --> set fullest voxel (maxVolume) to full fiber voxel
	- double density_correctiony_global = 1.0;
	- if (m_Parameters.m_SignalGen.m_AxonRadius<0.0001)
	- density_correctiony_global = m_VoxelVolume/maxVolume;
	-
	- // generate non-fiber signal
	- ImageRegionIterator<ItkUcharImgType> it3(m_TransformedMaskImage, m_TransformedMaskImage->GetLargestPossibleRegion());
	- while(!it3.IsAtEnd())
	- {
	- if (it3.Get()>0)
	- {
	- DoubleDwiType::IndexType index = it3.GetIndex();
	- double iAxVolume = intraAxonalVolumeImage->GetPixel(index);
	-
	- // get non-transformed point (remove headmotion tranformation)
	- // this point lives in the volume fraction image space
	- itk::Point<float, 3> volume_fraction_point;
	- if ( m_Parameters.m_SignalGen.m_DoAddMotion )
	- volume_fraction_point = GetMovedPoint(index, false);
	- else
	- m_TransformedMaskImage->TransformIndexToPhysicalPoint(index, volume_fraction_point);
	-
	- if (m_Parameters.m_SignalGen.m_DoDisablePartialVolume)
	- {
	- if (iAxVolume>0.0001) // scale fiber compartment to voxel
	- {
	- DoubleDwiType::PixelType pix = m_CompartmentImages.at(0)->GetPixel(index);
	- pix[g] *= m_VoxelVolume/iAxVolume;
	- m_CompartmentImages.at(0)->SetPixel(index, pix);
	-
	- if (g==0)
	- m_VolumeFractions.at(0)->SetPixel(index, 1);
	- }
	- else
	- {
	- DoubleDwiType::PixelType pix = m_CompartmentImages.at(0)->GetPixel(index);
	- pix[g] = 0;
	- m_CompartmentImages.at(0)->SetPixel(index, pix);
	- SimulateExtraAxonalSignal(index, volume_fraction_point, 0, g);
	- }
	- }
	- else
	- {
	- // manually defined axon radius and voxel overflow --> rescale to voxel volume
	- if ( m_Parameters.m_SignalGen.m_AxonRadius>=0.0001 && iAxVolume>m_VoxelVolume )
	- {
	- for (int i=0; i<numFiberCompartments; ++i)
	- {
	- DoubleDwiType::PixelType pix = m_CompartmentImages.at(i)->GetPixel(index);
	- pix[g] *= m_VoxelVolume/iAxVolume;
	- m_CompartmentImages.at(i)->SetPixel(index, pix);
	- }
	- iAxVolume = m_VoxelVolume;
	- }
	-
	- // if volume fraction image is set use it, otherwise use global scaling factor
	- double density_correction_voxel = density_correctiony_global;
	- if ( m_Parameters.m_FiberModelList[0]->GetVolumeFractionImage()!=nullptr && iAxVolume>0.0001 )
	- {
	- m_DoubleInterpolator->SetInputImage(m_Parameters.m_FiberModelList[0]->GetVolumeFractionImage());
	- double volume_fraction = mitk::imv::GetImageValue<double>(volume_fraction_point, true, m_DoubleInterpolator);
	- if (volume_fraction<0)
	- mitkThrow() << "Volume fraction image (index 1) contains negative values (intra-axonal compartment)!";
	- density_correction_voxel = m_VoxelVolume*volume_fraction/iAxVolume; // remove iAxVolume sclaing and scale to volume_fraction
	- }
	- else if (m_Parameters.m_FiberModelList[0]->GetVolumeFractionImage()!=nullptr)
	- density_correction_voxel = 0.0;
	-
	- // adjust intra-axonal compartment volume by density correction factor
	- DoubleDwiType::PixelType pix = m_CompartmentImages.at(0)->GetPixel(index);
	- pix[g] *= density_correction_voxel;
	- m_CompartmentImages.at(0)->SetPixel(index, pix);
	-
	- // normalize remaining fiber volume fractions (they are rescaled in SimulateExtraAxonalSignal)
	- if (iAxVolume>0.0001)
	- {
	- for (int i=1; i<numFiberCompartments; i++)
	- {
	- DoubleDwiType::PixelType pix = m_CompartmentImages.at(i)->GetPixel(index);
	- pix[g] /= iAxVolume;
	- m_CompartmentImages.at(i)->SetPixel(index, pix);
	- }
	- }
	- else
	- {
	- for (int i=1; i<numFiberCompartments; i++)
	- {
	- DoubleDwiType::PixelType pix = m_CompartmentImages.at(i)->GetPixel(index);
	- pix[g] = 0;
	- m_CompartmentImages.at(i)->SetPixel(index, pix);
	- }
	- }
	-
	- iAxVolume = density_correction_voxeliAxVolume; // new intra-axonal volume = old intra-axonal volume correction factor
	-
	- // simulate other compartments
	- SimulateExtraAxonalSignal(index, volume_fraction_point, iAxVolume, g);
	- }
	- }
	- ++it3;
	- }
	- }
	-
	- PrintToLog("\n", false);
	- }
	-
	- if (this->GetAbortGenerateData())
	- {
	- PrintToLog("\n", false, false);
	- PrintToLog("Simulation aborted");
	- return;
	- }
	-
	- DoubleDwiType::Pointer doubleOutImage;
	- double signalScale = m_Parameters.m_SignalGen.m_SignalScale;
	- if ( m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition ) // do k-space stuff
	- {
	- PrintToLog("\n", false, false);
	- PrintToLog("Simulating k-space acquisition using "
	- +boost::lexical_cast<std::string>(m_Parameters.m_SignalGen.m_NumberOfCoils)
	- +" coil(s)");
	-
	- switch (m_Parameters.m_SignalGen.m_AcquisitionType)
	- {
	- case SignalGenerationParameters::SingleShotEpi:
	- {
	- PrintToLog("Acquisition type: single shot EPI", false);
	- break;
	- }
	- case SignalGenerationParameters::ConventionalSpinEcho:
	- {
	- PrintToLog("Acquisition type: conventional spin echo (one RF pulse per line) with cartesian k-space trajectory", false);
	- break;
	- }
	- case SignalGenerationParameters::FastSpinEcho:
	- {
	- PrintToLog("Acquisition type: fast spin echo (one RF pulse per ETL lines) with cartesian k-space trajectory (ETL: " + boost::lexical_cast<std::string>(m_Parameters.m_SignalGen.m_EchoTrainLength) + ")", false);
	- break;
	- }
	- default:
	- {
	- PrintToLog("Acquisition type: single shot EPI", false);
	- break;
	- }
	- }
	- if(m_Parameters.m_SignalGen.m_tInv>0)
	- PrintToLog("Using inversion pulse with TI " + boost::lexical_cast<std::string>(m_Parameters.m_SignalGen.m_tInv) + "ms", false);
	-
	- if (m_Parameters.m_SignalGen.m_DoSimulateRelaxation)
	- PrintToLog("Simulating signal relaxation", false);
	- if (m_Parameters.m_SignalGen.m_NoiseVariance>0 && m_Parameters.m_Misc.m_DoAddNoise)
	- PrintToLog("Simulating complex Gaussian noise: " + boost::lexical_cast<std::string>(m_Parameters.m_SignalGen.m_NoiseVariance), false);
	- if (m_Parameters.m_SignalGen.m_FrequencyMap.IsNotNull() && m_Parameters.m_Misc.m_DoAddDistortions)
	- PrintToLog("Simulating distortions", false);
	- if (m_Parameters.m_SignalGen.m_DoAddGibbsRinging)
	- {
	- if (m_Parameters.m_SignalGen.m_ZeroRinging > 0)
	- PrintToLog("Simulating ringing artifacts by zeroing " + boost::lexical_cast<std::string>(m_Parameters.m_SignalGen.m_ZeroRinging) + "% of k-space frequencies", false);
	- else
	- PrintToLog("Simulating ringing artifacts by cropping high resolution inputs during k-space simulation", false);
	- }
	- if (m_Parameters.m_Misc.m_DoAddEddyCurrents && m_Parameters.m_SignalGen.m_EddyStrength>0)
	- PrintToLog("Simulating eddy currents: " + boost::lexical_cast<std::string>(m_Parameters.m_SignalGen.m_EddyStrength), false);
	- if (m_Parameters.m_Misc.m_DoAddSpikes && m_Parameters.m_SignalGen.m_Spikes>0)
	- PrintToLog("Simulating spikes: " + boost::lexical_cast<std::string>(m_Parameters.m_SignalGen.m_Spikes), false);
	- if (m_Parameters.m_Misc.m_DoAddAliasing && m_Parameters.m_SignalGen.m_CroppingFactor<1.0)
	- PrintToLog("Simulating aliasing: " + boost::lexical_cast<std::string>(m_Parameters.m_SignalGen.m_CroppingFactor), false);
	- if (m_Parameters.m_Misc.m_DoAddGhosts && m_Parameters.m_SignalGen.m_KspaceLineOffset>0)
	- PrintToLog("Simulating ghosts: " + boost::lexical_cast<std::string>(m_Parameters.m_SignalGen.m_KspaceLineOffset), false);
	-
	- doubleOutImage = SimulateKspaceAcquisition(m_CompartmentImages);
	- signalScale = 1; // already scaled in SimulateKspaceAcquisition()
	- }
	- else // don't do k-space stuff, just sum compartments
	- {
	- PrintToLog("Summing compartments");
	- doubleOutImage = m_CompartmentImages.at(0);
	-
	- for (unsigned int i=1; i<m_CompartmentImages.size(); i++)
	- {
	- auto adder = itk::AddImageFilter< DoubleDwiType, DoubleDwiType, DoubleDwiType>::New();
	- adder->SetInput1(doubleOutImage);
	- adder->SetInput2(m_CompartmentImages.at(i));
	- adder->Update();
	- doubleOutImage = adder->GetOutput();
	- }
	- }
	- if (this->GetAbortGenerateData())
	- {
	- PrintToLog("\n", false, false);
	- PrintToLog("Simulation aborted");
	- return;
	- }
	-
	- PrintToLog("Finalizing image");
	- if (m_Parameters.m_SignalGen.m_DoAddDrift && m_Parameters.m_SignalGen.m_Drift>0.0)
	- PrintToLog("Adding signal drift: " + boost::lexical_cast<std::string>(m_Parameters.m_SignalGen.m_Drift), false);
	- if (signalScale>1)
	- PrintToLog("Scaling signal", false);
	- if (m_Parameters.m_NoiseModel)
	- PrintToLog("Adding noise: " + boost::lexical_cast<std::string>(m_Parameters.m_SignalGen.m_NoiseVariance), false);
	- ImageRegionIterator<OutputImageType> it4 (m_OutputImage, m_OutputImage->GetLargestPossibleRegion());
	- DoubleDwiType::PixelType signal; signal.SetSize(m_Parameters.m_SignalGen.GetNumVolumes());
	- boost::progress_display disp2(m_OutputImage->GetLargestPossibleRegion().GetNumberOfPixels());
	-
	- PrintToLog("0% 10 20 30 40 50 60 70 80 90 100%", false, true, false);
	- PrintToLog("\|----\|----\|----\|----\|----\|----\|----\|----\|----\|----\|\n*", false, false, false);
	- int lastTick = 0;
	-
	- while(!it4.IsAtEnd())
	- {
	- if (this->GetAbortGenerateData())
	- {
	- PrintToLog("\n", false, false);
	- PrintToLog("Simulation aborted");
	- return;
	- }
	-
	- ++disp2;
	- unsigned long newTick = 50*disp2.count()/disp2.expected_count();
	- for (unsigned long tick = 0; tick<(newTick-lastTick); tick++)
	- PrintToLog("*", false, false, false);
	- lastTick = newTick;
	-
	- typename OutputImageType::IndexType index = it4.GetIndex();
	- signal = doubleOutImage->GetPixel(index)*signalScale;
	-
	- for (unsigned int i=0; i<signal.Size(); i++)
	- {
	- if (m_Parameters.m_SignalGen.m_DoAddDrift)
	- {
	- double df = -m_Parameters.m_SignalGen.m_Drift/(signal.Size()*signal.Size());
	- signal[i] += signal[i]dfi*i;
	- }
	- }
	-
	- if (m_Parameters.m_NoiseModel)
	- m_Parameters.m_NoiseModel->AddNoise(signal);
	-
	- for (unsigned int i=0; i<signal.Size(); i++)
	- {
	- if (signal[i]>0)
	- signal[i] = floor(signal[i]+0.5);
	- else
	- signal[i] = ceil(signal[i]-0.5);
	- }
	- it4.Set(signal);
	- ++it4;
	- }
	- this->SetNthOutput(0, m_OutputImage);
	-
	- PrintToLog("\n", false);
	- PrintToLog("Finished simulation");
	- m_TimeProbe.Stop();
	-
	- if (m_Parameters.m_SignalGen.m_DoAddMotion)
	- {
	- PrintToLog("\nHead motion log:", false);
	- PrintToLog(m_MotionLog, false, false);
	- }
	-
	- if (m_Parameters.m_Misc.m_DoAddSpikes && m_Parameters.m_SignalGen.m_Spikes>0)
	- {
	- PrintToLog("\nSpike log:", false);
	- PrintToLog(m_SpikeLog, false, false);
	- }
	-
	- if (m_Logfile.is_open())
	- m_Logfile.close();
	-}
	-
	-
	-template< class PixelType >
	-void TractsToDWIImageFilter< PixelType >::PrintToLog(std::string m, bool addTime, bool linebreak, bool stdOut)
	-{
	- // timestamp
	- if (addTime)
	- {
	- if ( m_Logfile.is_open() )
	- m_Logfile << this->GetTime() << " > ";
	- m_StatusText += this->GetTime() + " > ";
	- if (stdOut)
	- std::cout << this->GetTime() << " > ";
	- }
	-
	- // message
	- if (m_Logfile.is_open())
	- m_Logfile << m;
	- m_StatusText += m;
	- if (stdOut)
	- std::cout << m;
	-
	- // new line
	- if (linebreak)
	- {
	- if (m_Logfile.is_open())
	- m_Logfile << "\n";
	- m_StatusText += "\n";
	- if (stdOut)
	- std::cout << "\n";
	- }
	- if ( m_Logfile.is_open() )
	- m_Logfile.flush();
	-}
	-
	-template< class PixelType >
	-void TractsToDWIImageFilter< PixelType >::SimulateMotion(int g)
	-{
	- if ( m_Parameters.m_SignalGen.m_DoAddMotion &&
	- m_Parameters.m_SignalGen.m_DoRandomizeMotion &&
	- g>0 &&
	- m_Parameters.m_SignalGen.m_MotionVolumes[g-1])
	- {
	- // The last volume was randomly moved, so we have to reset to fiberbundle and the mask.
	- // Without motion or with linear motion, we keep the last position --> no reset.
	- m_FiberBundleTransformed = m_FiberBundle->GetDeepCopy();
	-
	- if (m_MaskImageSet)
	- {
	- auto duplicator = itk::ImageDuplicator<ItkUcharImgType>::New();
	- duplicator->SetInputImage(m_Parameters.m_SignalGen.m_MaskImage);
	- duplicator->Update();
	- m_TransformedMaskImage = duplicator->GetOutput();
	- }
	- }
	-
	- VectorType rotation;
	- VectorType translation;
	-
	- // is motion artifact enabled?
	- // is the current volume g affected by motion?
	- if ( m_Parameters.m_SignalGen.m_DoAddMotion
	- && m_Parameters.m_SignalGen.m_MotionVolumes[g]
	- && g<static_cast<int>(m_Parameters.m_SignalGen.GetNumVolumes()) )
	- {
	- // adjust motion transforms
	- if ( m_Parameters.m_SignalGen.m_DoRandomizeMotion )
	- {
	- // randomly
	- rotation[0] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_SignalGen.m_Rotation[0]*2)
	- -m_Parameters.m_SignalGen.m_Rotation[0];
	- rotation[1] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_SignalGen.m_Rotation[1]*2)
	- -m_Parameters.m_SignalGen.m_Rotation[1];
	- rotation[2] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_SignalGen.m_Rotation[2]*2)
	- -m_Parameters.m_SignalGen.m_Rotation[2];
	-
	- translation[0] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_SignalGen.m_Translation[0]*2)
	- -m_Parameters.m_SignalGen.m_Translation[0];
	- translation[1] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_SignalGen.m_Translation[1]*2)
	- -m_Parameters.m_SignalGen.m_Translation[1];
	- translation[2] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_SignalGen.m_Translation[2]*2)
	- -m_Parameters.m_SignalGen.m_Translation[2];
	-
	- m_FiberBundleTransformed->TransformFibers(rotation[0], rotation[1], rotation[2], translation[0], translation[1], translation[2]);
	-
	- }
	- else
	- {
	- // linearly
	- rotation = m_Parameters.m_SignalGen.m_Rotation / m_NumMotionVolumes;
	- translation = m_Parameters.m_SignalGen.m_Translation / m_NumMotionVolumes;
	- m_MotionCounter++;
	-
	- m_FiberBundleTransformed->TransformFibers(rotation[0], rotation[1], rotation[2], translation[0], translation[1], translation[2]);
	-
	- rotation *= m_MotionCounter;
	- translation *= m_MotionCounter;
	- }
	- MatrixType rotationMatrix = mitk::imv::GetRotationMatrixItk(rotation[0], rotation[1], rotation[2]);
	- MatrixType rotationMatrixInv = mitk::imv::GetRotationMatrixItk(-rotation[0], -rotation[1], -rotation[2]);
	-
	- m_Rotations.push_back(rotationMatrix);
	- m_RotationsInv.push_back(rotationMatrixInv);
	- m_Translations.push_back(translation);
	-
	- // move mask image accoring to new transform
	- if (m_MaskImageSet)
	- {
	- ImageRegionIterator<ItkUcharImgType> maskIt(m_UpsampledMaskImage, m_UpsampledMaskImage->GetLargestPossibleRegion());
	- m_TransformedMaskImage->FillBuffer(0);
	-
	- while(!maskIt.IsAtEnd())
	- {
	- if (maskIt.Get()<=0)
	- {
	- ++maskIt;
	- continue;
	- }
	-
	- DoubleDwiType::IndexType index = maskIt.GetIndex();
	- m_TransformedMaskImage->TransformPhysicalPointToIndex(GetMovedPoint(index, true), index);
	-
	- if (m_TransformedMaskImage->GetLargestPossibleRegion().IsInside(index))
	- m_TransformedMaskImage->SetPixel(index, 100);
	- ++maskIt;
	- }
	- }
	- }
	- else
	- {
	- if (m_Parameters.m_SignalGen.m_DoAddMotion && !m_Parameters.m_SignalGen.m_DoRandomizeMotion && g>0)
	- {
	- rotation = m_Parameters.m_SignalGen.m_Rotation / m_NumMotionVolumes;
	- rotation *= m_MotionCounter;
	- m_Rotations.push_back(m_Rotations.back());
	- m_RotationsInv.push_back(m_RotationsInv.back());
	- m_Translations.push_back(m_Translations.back());
	- }
	- else
	- {
	- rotation.Fill(0.0);
	- VectorType translation; translation.Fill(0.0);
	- MatrixType rotation_matrix; rotation_matrix.SetIdentity();
	-
	- m_Rotations.push_back(rotation_matrix);
	- m_RotationsInv.push_back(rotation_matrix);
	- m_Translations.push_back(translation);
	- }
	- }
	-
	- if (m_Parameters.m_SignalGen.m_DoAddMotion)
	- {
	- m_MotionLog += boost::lexical_cast<std::string>(g) + " rotation: " + boost::lexical_cast<std::string>(rotation[0])
	- + "," + boost::lexical_cast<std::string>(rotation[1])
	- + "," + boost::lexical_cast<std::string>(rotation[2]) + ";";
	-
	- m_MotionLog += " translation: " + boost::lexical_cast<std::string>(m_Translations.back()[0])
	- + "," + boost::lexical_cast<std::string>(m_Translations.back()[1])
	- + "," + boost::lexical_cast<std::string>(m_Translations.back()[2]) + "\n";
	- }
	-}
	-
	-template< class PixelType >
	-itk::Point<float, 3> TractsToDWIImageFilter< PixelType >::GetMovedPoint(itk::Index<3>& index, bool forward)
	-{
	- itk::Point<float, 3> transformed_point;
	- float tx = m_Translations.back()[0];
	- float ty = m_Translations.back()[1];
	- float tz = m_Translations.back()[2];
	-
	- if (forward)
	- {
	- m_UpsampledMaskImage->TransformIndexToPhysicalPoint(index, transformed_point);
	- m_FiberBundle->TransformPoint<>(transformed_point, m_Rotations.back(), tx, ty, tz);
	- }
	- else
	- {
	- tx = -1; ty = -1; tz *= -1;
	- m_TransformedMaskImage->TransformIndexToPhysicalPoint(index, transformed_point);
	- m_FiberBundle->TransformPoint<>(transformed_point, m_RotationsInv.back(), tx, ty, tz);
	- }
	- return transformed_point;
	-}
	-
	-template< class PixelType >
	-void TractsToDWIImageFilter< PixelType >::
	-SimulateExtraAxonalSignal(ItkUcharImgType::IndexType& index, itk::Point<float, 3>& volume_fraction_point, double intraAxonalVolume, int g)
	-{
	- int numFiberCompartments = m_Parameters.m_FiberModelList.size();
	- int numNonFiberCompartments = m_Parameters.m_NonFiberModelList.size();
	-
	- if (m_Parameters.m_SignalGen.m_DoDisablePartialVolume)
	- {
	- // simulate signal for largest non-fiber compartment
	- int max_compartment_index = 0;
	- double max_fraction = 0;
	- if (numNonFiberCompartments>1)
	- {
	- for (int i=0; i<numNonFiberCompartments; ++i)
	- {
	- m_DoubleInterpolator->SetInputImage(m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage());
	- double compartment_fraction = mitk::imv::GetImageValue<double>(volume_fraction_point, true, m_DoubleInterpolator);
	- if (compartment_fraction<0)
	- mitkThrow() << "Volume fraction image (index " << i << ") contains values less than zero!";
	-
	- if (compartment_fraction>max_fraction)
	- {
	- max_fraction = compartment_fraction;
	- max_compartment_index = i;
	- }
	- }
	- }
	-
	- DoubleDwiType::Pointer doubleDwi = m_CompartmentImages.at(max_compartment_index+numFiberCompartments);
	- DoubleDwiType::PixelType pix = doubleDwi->GetPixel(index);
	- pix[g] += m_Parameters.m_NonFiberModelList[max_compartment_index]->SimulateMeasurement(g, m_NullDir)*m_VoxelVolume;
	- doubleDwi->SetPixel(index, pix);
	-
	- if (g==0)
	- m_VolumeFractions.at(max_compartment_index+numFiberCompartments)->SetPixel(index, 1);
	- }
	- else
	- {
	- std::vector< double > fractions;
	- if (g==0)
	- m_VolumeFractions.at(0)->SetPixel(index, intraAxonalVolume/m_VoxelVolume);
	-
	- double extraAxonalVolume = m_VoxelVolume-intraAxonalVolume; // non-fiber volume
	- if (extraAxonalVolume<0)
	- {
	- if (extraAxonalVolume<-0.001)
	- MITK_ERROR << "Corrupted intra-axonal signal voxel detected. Fiber volume larger voxel volume! " << m_VoxelVolume << "<" << intraAxonalVolume;
	- extraAxonalVolume = 0;
	- }
	- double interAxonalVolume = 0;
	- if (numFiberCompartments>1)
	- interAxonalVolume = extraAxonalVolume * intraAxonalVolume/m_VoxelVolume; // inter-axonal fraction of non fiber compartment
	- double nonFiberVolume = extraAxonalVolume - interAxonalVolume; // rest of compartment
	- if (nonFiberVolume<0)
	- {
	- if (nonFiberVolume<-0.001)
	- MITK_ERROR << "Corrupted signal voxel detected. Fiber volume larger voxel volume!";
	- nonFiberVolume = 0;
	- interAxonalVolume = extraAxonalVolume;
	- }
	-
	- double compartmentSum = intraAxonalVolume;
	- fractions.push_back(intraAxonalVolume/m_VoxelVolume);
	-
	- // rescale extra-axonal fiber signal
	- for (int i=1; i<numFiberCompartments; ++i)
	- {
	- if (m_Parameters.m_FiberModelList[i]->GetVolumeFractionImage()!=nullptr)
	- {
	- m_DoubleInterpolator->SetInputImage(m_Parameters.m_FiberModelList[i]->GetVolumeFractionImage());
	- interAxonalVolume = mitk::imv::GetImageValue<double>(volume_fraction_point, true, m_DoubleInterpolator)*m_VoxelVolume;
	- if (interAxonalVolume<0)
	- mitkThrow() << "Volume fraction image (index " << i+1 << ") contains negative values!";
	- }
	-
	- DoubleDwiType::PixelType pix = m_CompartmentImages.at(i)->GetPixel(index);
	- pix[g] *= interAxonalVolume;
	- m_CompartmentImages.at(i)->SetPixel(index, pix);
	-
	- compartmentSum += interAxonalVolume;
	- fractions.push_back(interAxonalVolume/m_VoxelVolume);
	- if (g==0)
	- m_VolumeFractions.at(i)->SetPixel(index, interAxonalVolume/m_VoxelVolume);
	- }
	-
	- for (int i=0; i<numNonFiberCompartments; ++i)
	- {
	- double volume = nonFiberVolume;
	- if (m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()!=nullptr)
	- {
	- m_DoubleInterpolator->SetInputImage(m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage());
	- volume = mitk::imv::GetImageValue<double>(volume_fraction_point, true, m_DoubleInterpolator)*m_VoxelVolume;
	- if (volume<0)
	- mitkThrow() << "Volume fraction image (index " << numFiberCompartments+i+1 << ") contains negative values (non-fiber compartment)!";
	-
	- if (m_UseRelativeNonFiberVolumeFractions)
	- volume *= nonFiberVolume/m_VoxelVolume;
	- }
	-
	- DoubleDwiType::PixelType pix = m_CompartmentImages.at(i+numFiberCompartments)->GetPixel(index);
	- pix[g] += m_Parameters.m_NonFiberModelList[i]->SimulateMeasurement(g, m_NullDir)*volume;
	- m_CompartmentImages.at(i+numFiberCompartments)->SetPixel(index, pix);
	-
	- compartmentSum += volume;
	- fractions.push_back(volume/m_VoxelVolume);
	- if (g==0)
	- m_VolumeFractions.at(i+numFiberCompartments)->SetPixel(index, volume/m_VoxelVolume);
	- }
	-
	- if (compartmentSum/m_VoxelVolume>1.05)
	- {
	- MITK_ERROR << "Compartments do not sum to 1 in voxel " << index << " (" << compartmentSum/m_VoxelVolume << ")";
	- for (auto val : fractions)
	- MITK_ERROR << val;
	- }
	- }
	-}
	-
	-template< class PixelType >
	-itk::Vector<double, 3> TractsToDWIImageFilter< PixelType >::GetItkVector(double point[3])
	-{
	- itk::Vector<double, 3> itkVector;
	- itkVector[0] = point[0];
	- itkVector[1] = point[1];
	- itkVector[2] = point[2];
	- return itkVector;
	-}
	-
	-template< class PixelType >
	-vnl_vector_fixed<double, 3> TractsToDWIImageFilter< PixelType >::GetVnlVector(double point[3])
	-{
	- vnl_vector_fixed<double, 3> vnlVector;
	- vnlVector[0] = point[0];
	- vnlVector[1] = point[1];
	- vnlVector[2] = point[2];
	- return vnlVector;
	-}
	-
	-template< class PixelType >
	-vnl_vector_fixed<double, 3> TractsToDWIImageFilter< PixelType >::GetVnlVector(Vector<float,3>& vector)
	-{
	- vnl_vector_fixed<double, 3> vnlVector;
	- vnlVector[0] = vector[0];
	- vnlVector[1] = vector[1];
	- vnlVector[2] = vector[2];
	- return vnlVector;
	-}
	-
	-template< class PixelType >
	-double TractsToDWIImageFilter< PixelType >::RoundToNearest(double num) {
	- return (num > 0.0) ? floor(num + 0.5) : ceil(num - 0.5);
	-}
	-
	-template< class PixelType >
	-std::string TractsToDWIImageFilter< PixelType >::GetTime()
	-{
	- m_TimeProbe.Stop();
	- unsigned long total = RoundToNearest(m_TimeProbe.GetTotal());
	- unsigned long hours = total/3600;
	- unsigned long minutes = (total%3600)/60;
	- unsigned long seconds = total%60;
	- std::string out = "";
	- out.append(boost::lexical_cast<std::string>(hours));
	- out.append(":");
	- out.append(boost::lexical_cast<std::string>(minutes));
	- out.append(":");
	- out.append(boost::lexical_cast<std::string>(seconds));
	- m_TimeProbe.Start();
	- return out;
	-}
	-
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkTractsToDWIImageFilter.h b/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkTractsToDWIImageFilter.h
	deleted file mode 100755
	index cefcee8683..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkTractsToDWIImageFilter.h
	+++ /dev/null
	@@ -1,177 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef __itkTractsToDWIImageFilter_h__
	-#define __itkTractsToDWIImageFilter_h__
	-
	-#include <mitkFiberBundle.h>
	-#include <itkVnlForwardFFTImageFilter.h>
	-#include <itkVectorImage.h>
	-#include <cmath>
	-#include <mitkFiberfoxParameters.h>
	-#include <itkTimeProbe.h>
	-#include <mitkRawShModel.h>
	-#include <itkAnalyticalDiffusionQballReconstructionImageFilter.h>
	-#include <mitkPointSet.h>
	-#include <itkLinearInterpolateImageFunction.h>
	-
	-namespace itk
	-{
	-
	-/**
	-* \brief Generates artificial diffusion weighted image volume from the input fiberbundle using a generic multicompartment model.
	-* See "Fiberfox: Facilitating the creation of realistic white matter software phantoms" (DOI: 10.1002/mrm.25045) for details.
	-*/
	-
	-template< class PixelType >
	-class TractsToDWIImageFilter : public ImageSource< itk::VectorImage< PixelType, 3 > >
	-{
	-
	-public:
	-
	- typedef TractsToDWIImageFilter Self;
	- typedef ImageSource< itk::VectorImage< PixelType, 3 > > Superclass;
	- typedef SmartPointer< Self > Pointer;
	- typedef SmartPointer< const Self > ConstPointer;
	-
	- typedef typename Superclass::OutputImageType OutputImageType;
	- typedef itk::Image<double, 4> ItkDoubleImgType4D;
	- typedef itk::Image<double, 3> ItkDoubleImgType;
	- typedef itk::Image<float, 3> ItkFloatImgType;
	- typedef itk::Image<unsigned char, 3> ItkUcharImgType;
	- typedef mitk::FiberBundle::Pointer FiberBundleType;
	- typedef itk::VectorImage< double, 3 > DoubleDwiType;
	- typedef itk::Matrix<float, 3, 3> MatrixType;
	- typedef itk::Image< float, 2 > Float2DImageType;
	- typedef itk::Image< vcl_complex< float >, 2 > Complex2DImageType;
	- typedef itk::Vector< float, 3> VectorType;
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- itkTypeMacro( TractsToDWIImageFilter, ImageSource )
	-
	- /** Input */
	- itkSetMacro( FiberBundle, FiberBundleType ) ///< Input fiber bundle
	- itkSetMacro( InputImage, typename OutputImageType::Pointer ) ///< Input diffusion-weighted image. If no fiber bundle is set, then the acquisition is simulated for this image without a new diffusion simulation.
	- itkSetMacro( UseConstantRandSeed, bool ) ///< Seed for random generator.
	- void SetParameters( FiberfoxParameters param ) ///< Simulation parameters.
	- { m_Parameters = param; }
	-
	- /** Output */
	- FiberfoxParameters GetParameters(){ return m_Parameters; }
	- std::vector< ItkDoubleImgType::Pointer > GetVolumeFractions() ///< one double image for each compartment containing the corresponding volume fraction per voxel
	- { return m_VolumeFractions; }
	- itkGetMacro( StatusText, std::string )
	- itkGetMacro( PhaseImage, DoubleDwiType::Pointer )
	- itkGetMacro( KspaceImage, DoubleDwiType::Pointer )
	- itkGetMacro( CoilPointset, mitk::PointSet::Pointer )
	- itkGetMacro( TickImage, typename Float2DImageType::Pointer ) ///< k-space readout ordering encoded in the voxels
	- itkGetMacro( RfImage, typename Float2DImageType::Pointer ) ///< time passed since last RF pulse encoded per voxel
	-
	- void GenerateData() override;
	-
	- std::vector<DoubleDwiType::Pointer> GetOutputImagesReal() const
	- {
	- return m_OutputImagesReal;
	- }
	-
	- std::vector<DoubleDwiType::Pointer> GetOutputImagesImag() const
	- {
	- return m_OutputImagesImag;
	- }
	-
	-protected:
	-
	- TractsToDWIImageFilter();
	- ~TractsToDWIImageFilter() override;
	- itk::Vector<double, 3> GetItkVector(double point[3]);
	- vnl_vector_fixed<double, 3> GetVnlVector(double point[3]);
	- vnl_vector_fixed<double, 3> GetVnlVector(Vector< float, 3 >& vector);
	- double RoundToNearest(double num);
	- std::string GetTime();
	- bool PrepareLogFile(); /** Prepares the log file and returns true if successful or false if failed. */
	- void PrintToLog(std::string m, bool addTime=true, bool linebreak=true, bool stdOut=true);
	-
	- /** Transform generated image compartment by compartment, channel by channel and slice by slice using DFT and add k-space artifacts/effects. */
	- DoubleDwiType::Pointer SimulateKspaceAcquisition(std::vector< DoubleDwiType::Pointer >& images);
	-
	- /** Generate signal of non-fiber compartments. */
	- void SimulateExtraAxonalSignal(ItkUcharImgType::IndexType& index, itk::Point<float, 3>& volume_fraction_point, double intraAxonalVolume, int g);
	-
	- /** Move fibers to simulate headmotion */
	- void SimulateMotion(int g=-1);
	-
	- void CheckVolumeFractionImages();
	- ItkDoubleImgType::Pointer NormalizeInsideMask(ItkDoubleImgType::Pointer image);
	- void InitializeData();
	- void InitializeFiberData();
	-
	- itk::Point<float, 3> GetMovedPoint(itk::Index<3>& index, bool forward);
	-
	- // input
	- mitk::FiberfoxParameters m_Parameters;
	- FiberBundleType m_FiberBundle;
	- typename OutputImageType::Pointer m_InputImage;
	-
	- // output
	- typename OutputImageType::Pointer m_OutputImage;
	- typename DoubleDwiType::Pointer m_PhaseImage;
	- typename DoubleDwiType::Pointer m_KspaceImage;
	- std::vector < typename DoubleDwiType::Pointer > m_OutputImagesReal;
	- std::vector < typename DoubleDwiType::Pointer > m_OutputImagesImag;
	- std::vector< ItkDoubleImgType::Pointer > m_VolumeFractions;
	- std::string m_StatusText;
	-
	- // MISC
	- itk::TimeProbe m_TimeProbe;
	- bool m_UseConstantRandSeed;
	- bool m_MaskImageSet;
	- ofstream m_Logfile;
	- std::string m_MotionLog;
	- std::string m_SpikeLog;
	-
	- // signal generation
	- FiberBundleType m_FiberBundleTransformed; ///< transformed bundle simulating headmotion
	- itk::Vector<double,3> m_WorkingSpacing;
	- itk::Point<double,3> m_WorkingOrigin;
	- ImageRegion<3> m_WorkingImageRegion;
	- double m_VoxelVolume;
	- std::vector< DoubleDwiType::Pointer > m_CompartmentImages;
	- ItkUcharImgType::Pointer m_TransformedMaskImage; ///< copy of mask image (changes for each motion step)
	- ItkUcharImgType::Pointer m_UpsampledMaskImage; ///< helper image for motion simulation
	- std::vector< MatrixType > m_RotationsInv;
	- std::vector< MatrixType > m_Rotations; ///<stores the individual rotation of each volume (needed for k-space simulation to obtain correct frequency map position)
	- std::vector< VectorType > m_Translations; ///<stores the individual translation of each volume (needed for k-space simulation to obtain correct frequency map position)
	- double m_mmRadius;
	- double m_SegmentVolume;
	- bool m_UseRelativeNonFiberVolumeFractions;
	- mitk::PointSet::Pointer m_CoilPointset;
	- int m_MotionCounter;
	- int m_NumMotionVolumes;
	-
	- itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer m_RandGen;
	- itk::LinearInterpolateImageFunction< ItkDoubleImgType, float >::Pointer m_DoubleInterpolator;
	- itk::Vector<double,3> m_NullDir;
	-
	- Float2DImageType::Pointer m_TickImage;
	- Float2DImageType::Pointer m_RfImage;
	-};
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkTractsToDWIImageFilter.cpp"
	-#endif
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundle.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundle.cpp
	deleted file mode 100755
	index 8c2ae3a975..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundle.cpp
	+++ /dev/null
	@@ -1,2683 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkFiberBundle.h"
	-
	-#include <mitkPlanarCircle.h>
	-#include <mitkPlanarPolygon.h>
	-#include <mitkPlanarFigureComposite.h>
	-#include "mitkImagePixelReadAccessor.h"
	-#include <mitkPixelTypeMultiplex.h>
	-
	-#include <vtkPointData.h>
	-#include <vtkDataArray.h>
	-#include <vtkUnsignedCharArray.h>
	-#include <vtkPolyLine.h>
	-#include <vtkCellArray.h>
	-#include <vtkCellData.h>
	-#include <vtkIdFilter.h>
	-#include <vtkClipPolyData.h>
	-#include <vtkPlane.h>
	-#include <vtkDoubleArray.h>
	-#include <vtkKochanekSpline.h>
	-#include <vtkParametricFunctionSource.h>
	-#include <vtkParametricSpline.h>
	-#include <vtkPolygon.h>
	-#include <vtkCleanPolyData.h>
	-#include <boost/progress.hpp>
	-#include <vtkTransformPolyDataFilter.h>
	-#include <mitkTransferFunction.h>
	-#include <vtkLookupTable.h>
	-#include <mitkLookupTable.h>
	-#include <vtkCardinalSpline.h>
	-#include <vtkAppendPolyData.h>
	-
	-const char* mitk::FiberBundle::FIBER_ID_ARRAY = "Fiber_IDs";
	-
	-mitk::FiberBundle::FiberBundle( vtkPolyData* fiberPolyData )
	- : m_NumFibers(0)
	-{
	- m_FiberWeights = vtkSmartPointer<vtkFloatArray>::New();
	- m_FiberWeights->SetName("FIBER_WEIGHTS");
	-
	- m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
	- if (fiberPolyData != nullptr)
	- m_FiberPolyData = fiberPolyData;
	- else
	- {
	- this->m_FiberPolyData->SetPoints(vtkSmartPointer<vtkPoints>::New());
	- this->m_FiberPolyData->SetLines(vtkSmartPointer<vtkCellArray>::New());
	- }
	-
	- this->UpdateFiberGeometry();
	- this->GenerateFiberIds();
	- this->ColorFibersByOrientation();
	-}
	-
	-mitk::FiberBundle::~FiberBundle()
	-{
	-
	-}
	-
	-mitk::FiberBundle::Pointer mitk::FiberBundle::GetDeepCopy()
	-{
	- mitk::FiberBundle::Pointer newFib = mitk::FiberBundle::New(m_FiberPolyData);
	- newFib->SetFiberColors(this->m_FiberColors);
	- newFib->SetFiberWeights(this->m_FiberWeights);
	- return newFib;
	-}
	-
	-vtkSmartPointer<vtkPolyData> mitk::FiberBundle::GeneratePolyDataByIds(std::vector<unsigned int> fiberIds, vtkSmartPointer<vtkFloatArray> weights)
	-{
	- vtkSmartPointer<vtkPolyData> newFiberPolyData = vtkSmartPointer<vtkPolyData>::New();
	- vtkSmartPointer<vtkCellArray> newLineSet = vtkSmartPointer<vtkCellArray>::New();
	- vtkSmartPointer<vtkPoints> newPointSet = vtkSmartPointer<vtkPoints>::New();
	- weights->SetNumberOfValues(fiberIds.size());
	-
	- int counter = 0;
	- auto finIt = fiberIds.begin();
	- while ( finIt != fiberIds.end() )
	- {
	- if (*finIt>GetNumFibers()){
	- MITK_INFO << "FiberID can not be negative or >NumFibers!!! check id Extraction!" << *finIt;
	- break;
	- }
	-
	- vtkSmartPointer<vtkCell> fiber = m_FiberIdDataSet->GetCell(*finIt);//->DeepCopy(fiber);
	- vtkSmartPointer<vtkPoints> fibPoints = fiber->GetPoints();
	- vtkSmartPointer<vtkPolyLine> newFiber = vtkSmartPointer<vtkPolyLine>::New();
	- newFiber->GetPointIds()->SetNumberOfIds( fibPoints->GetNumberOfPoints() );
	-
	- for(int i=0; i<fibPoints->GetNumberOfPoints(); i++)
	- {
	- newFiber->GetPointIds()->SetId(i, newPointSet->GetNumberOfPoints());
	- newPointSet->InsertNextPoint(fibPoints->GetPoint(i)[0], fibPoints->GetPoint(i)[1], fibPoints->GetPoint(i)[2]);
	- }
	-
	- weights->InsertValue(counter, this->GetFiberWeight(*finIt));
	- newLineSet->InsertNextCell(newFiber);
	- ++finIt;
	- ++counter;
	- }
	-
	- newFiberPolyData->SetPoints(newPointSet);
	- newFiberPolyData->SetLines(newLineSet);
	- return newFiberPolyData;
	-}
	-
	-// merge two fiber bundles
	-mitk::FiberBundle::Pointer mitk::FiberBundle::AddBundles(std::vector< mitk::FiberBundle::Pointer > fibs)
	-{
	- vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
	- vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
	- vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
	-
	- // add current fiber bundle
	- vtkSmartPointer<vtkFloatArray> weights = vtkSmartPointer<vtkFloatArray>::New();
	-
	- auto num_weights = this->GetNumFibers();
	- for (auto fib : fibs)
	- num_weights += fib->GetNumFibers();
	- weights->SetNumberOfValues(num_weights);
	-
	- unsigned int counter = 0;
	- for (unsigned int i=0; i<m_FiberPolyData->GetNumberOfCells(); ++i)
	- {
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	- for (unsigned int j=0; j<numPoints; ++j)
	- {
	- double p[3];
	- points->GetPoint(j, p);
	-
	- vtkIdType id = vNewPoints->InsertNextPoint(p);
	- container->GetPointIds()->InsertNextId(id);
	- }
	- weights->InsertValue(counter, this->GetFiberWeight(i));
	- vNewLines->InsertNextCell(container);
	- counter++;
	- }
	-
	- for (auto fib : fibs)
	- {
	- // add new fiber bundle
	- for (unsigned int i=0; i<fib->GetFiberPolyData()->GetNumberOfCells(); i++)
	- {
	- vtkCell* cell = fib->GetFiberPolyData()->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	- for (unsigned int j=0; j<numPoints; j++)
	- {
	- double p[3];
	- points->GetPoint(j, p);
	-
	- vtkIdType id = vNewPoints->InsertNextPoint(p);
	- container->GetPointIds()->InsertNextId(id);
	- }
	- weights->InsertValue(counter, fib->GetFiberWeight(i));
	- vNewLines->InsertNextCell(container);
	- counter++;
	- }
	- }
	-
	- // initialize PolyData
	- vNewPolyData->SetPoints(vNewPoints);
	- vNewPolyData->SetLines(vNewLines);
	-
	- // initialize fiber bundle
	- mitk::FiberBundle::Pointer newFib = mitk::FiberBundle::New(vNewPolyData);
	- newFib->SetFiberWeights(weights);
	- return newFib;
	-}
	-
	-// merge two fiber bundles
	-mitk::FiberBundle::Pointer mitk::FiberBundle::AddBundle(mitk::FiberBundle* fib)
	-{
	- if (fib==nullptr)
	- return this->GetDeepCopy();
	-
	- MITK_INFO << "Adding fibers";
	-
	- vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
	- vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
	- vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
	-
	- // add current fiber bundle
	- vtkSmartPointer<vtkFloatArray> weights = vtkSmartPointer<vtkFloatArray>::New();
	- weights->SetNumberOfValues(this->GetNumFibers()+fib->GetNumFibers());
	-
	- unsigned int counter = 0;
	- for (unsigned int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
	- {
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	- for (unsigned int j=0; j<numPoints; j++)
	- {
	- double p[3];
	- points->GetPoint(j, p);
	-
	- vtkIdType id = vNewPoints->InsertNextPoint(p);
	- container->GetPointIds()->InsertNextId(id);
	- }
	- weights->InsertValue(counter, this->GetFiberWeight(i));
	- vNewLines->InsertNextCell(container);
	- counter++;
	- }
	-
	- // add new fiber bundle
	- for (unsigned int i=0; i<fib->GetFiberPolyData()->GetNumberOfCells(); i++)
	- {
	- vtkCell* cell = fib->GetFiberPolyData()->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	- for (unsigned int j=0; j<numPoints; j++)
	- {
	- double p[3];
	- points->GetPoint(j, p);
	-
	- vtkIdType id = vNewPoints->InsertNextPoint(p);
	- container->GetPointIds()->InsertNextId(id);
	- }
	- weights->InsertValue(counter, fib->GetFiberWeight(i));
	- vNewLines->InsertNextCell(container);
	- counter++;
	- }
	-
	- // initialize PolyData
	- vNewPolyData->SetPoints(vNewPoints);
	- vNewPolyData->SetLines(vNewLines);
	-
	- // initialize fiber bundle
	- mitk::FiberBundle::Pointer newFib = mitk::FiberBundle::New(vNewPolyData);
	- newFib->SetFiberWeights(weights);
	- return newFib;
	-}
	-
	-// Only retain fibers with a weight larger than the specified threshold
	-mitk::FiberBundle::Pointer mitk::FiberBundle::FilterByWeights(float weight_thr, bool invert)
	-{
	- vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
	- vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
	- vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
	-
	- std::vector<float> weights;
	-
	- for (unsigned int i=0; i<this->GetNumFibers(); i++)
	- {
	- if ( (invert && this->GetFiberWeight(i)>weight_thr) \|\| (!invert && this->GetFiberWeight(i)<=weight_thr))
	- continue;
	-
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	- for (int j=0; j<numPoints; j++)
	- {
	- double p[3];
	- points->GetPoint(j, p);
	-
	- vtkIdType id = vNewPoints->InsertNextPoint(p);
	- container->GetPointIds()->InsertNextId(id);
	- }
	- vNewLines->InsertNextCell(container);
	- weights.push_back(this->GetFiberWeight(i));
	- }
	-
	- // initialize PolyData
	- vNewPolyData->SetPoints(vNewPoints);
	- vNewPolyData->SetLines(vNewLines);
	-
	- // initialize fiber bundle
	- mitk::FiberBundle::Pointer newFib = mitk::FiberBundle::New(vNewPolyData);
	- for (unsigned int i=0; i<weights.size(); ++i)
	- newFib->SetFiberWeight(i, weights.at(i));
	- return newFib;
	-}
	-
	-// Only retain a subsample of the fibers
	-mitk::FiberBundle::Pointer mitk::FiberBundle::SubsampleFibers(float factor, bool random_seed)
	-{
	- vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
	- vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
	- vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
	-
	- unsigned int new_num_fibs = static_cast<unsigned int>(std::round(this->GetNumFibers()*factor));
	- MITK_INFO << "Subsampling fibers with factor " << factor << "(" << new_num_fibs << "/" << this->GetNumFibers() << ")";
	-
	- // add current fiber bundle
	- vtkSmartPointer<vtkFloatArray> weights = vtkSmartPointer<vtkFloatArray>::New();
	- weights->SetNumberOfValues(new_num_fibs);
	-
	- std::vector< unsigned int > ids;
	- for (unsigned int i=0; i<this->GetNumFibers(); i++)
	- ids.push_back(i);
	- if (random_seed)
	- std::srand(static_cast<unsigned int>(std::time(nullptr)));
	- else
	- std::srand(0);
	- std::random_shuffle(ids.begin(), ids.end());
	-
	- unsigned int counter = 0;
	- for (unsigned int i=0; i<new_num_fibs; i++)
	- {
	- vtkCell* cell = m_FiberPolyData->GetCell(ids.at(i));
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	- for (int j=0; j<numPoints; j++)
	- {
	- double p[3];
	- points->GetPoint(j, p);
	-
	- vtkIdType id = vNewPoints->InsertNextPoint(p);
	- container->GetPointIds()->InsertNextId(id);
	- }
	- weights->InsertValue(counter, this->GetFiberWeight(ids.at(i)));
	- vNewLines->InsertNextCell(container);
	- counter++;
	- }
	-
	- // initialize PolyData
	- vNewPolyData->SetPoints(vNewPoints);
	- vNewPolyData->SetLines(vNewLines);
	-
	- // initialize fiber bundle
	- mitk::FiberBundle::Pointer newFib = mitk::FiberBundle::New(vNewPolyData);
	- newFib->SetFiberWeights(weights);
	- return newFib;
	-}
	-
	-// subtract two fiber bundles
	-mitk::FiberBundle::Pointer mitk::FiberBundle::SubtractBundle(mitk::FiberBundle* fib)
	-{
	- if (fib==nullptr)
	- return this->GetDeepCopy();
	-
	- MITK_INFO << "Subtracting fibers";
	- vtkSmartPointer<vtkPolyData> vNewPolyData = vtkSmartPointer<vtkPolyData>::New();
	- vtkSmartPointer<vtkCellArray> vNewLines = vtkSmartPointer<vtkCellArray>::New();
	- vtkSmartPointer<vtkPoints> vNewPoints = vtkSmartPointer<vtkPoints>::New();
	-
	- std::vector< std::vector< itk::Point<float, 3> > > points1;
	- for(unsigned int i=0; i<m_NumFibers; i++ )
	- {
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- if (points==nullptr \|\| numPoints<=0)
	- continue;
	-
	- itk::Point<float, 3> start = mitk::imv::GetItkPoint(points->GetPoint(0));
	- itk::Point<float, 3> end = mitk::imv::GetItkPoint(points->GetPoint(numPoints-1));
	-
	- points1.push_back( {start, end} );
	- }
	-
	- std::vector< std::vector< itk::Point<float, 3> > > points2;
	- for(unsigned int i=0; i<fib->GetNumFibers(); i++ )
	- {
	- vtkCell* cell = fib->GetFiberPolyData()->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- if (points==nullptr \|\| numPoints<=0)
	- continue;
	-
	- itk::Point<float, 3> start =mitk::imv::GetItkPoint(points->GetPoint(0));
	- itk::Point<float, 3> end =mitk::imv::GetItkPoint(points->GetPoint(numPoints-1));
	-
	- points2.push_back( {start, end} );
	- }
	-
	- // int progress = 0;
	- std::vector< int > ids;
	-#pragma omp parallel for
	- for (int i=0; i<static_cast<int>(points1.size()); i++)
	- {
	- bool match = false;
	- for (unsigned int j=0; j<points2.size(); j++)
	- {
	- auto v1 = points1.at(static_cast<unsigned int>(i));
	- auto v2 = points2.at(j);
	-
	- float dist=0;
	- for (unsigned int c=0; c<v1.size(); c++)
	- {
	- float d = v1[c][0]-v2[c][0];
	- dist += d*d;
	-
	- d = v1[c][1]-v2[c][1];
	- dist += d*d;
	-
	- d = v1[c][2]-v2[c][2];
	- dist += d*d;
	- }
	- dist /= v1.size();
	-
	- if (dist<0.000001f)
	- {
	- match = true;
	- break;
	- }
	-
	- dist=0;
	- for (unsigned int c=0; c<v1.size(); c++)
	- {
	- float d = v1[v1.size()-1-c][0]-v2[c][0];
	- dist += d*d;
	-
	- d = v1[v1.size()-1-c][1]-v2[c][1];
	- dist += d*d;
	-
	- d = v1[v1.size()-1-c][2]-v2[c][2];
	- dist += d*d;
	- }
	- dist /= v1.size();
	-
	- if (dist<0.000001f)
	- {
	- match = true;
	- break;
	- }
	- }
	-
	-#pragma omp critical
	- if (!match)
	- ids.push_back(i);
	- }
	-
	- for( int i : ids )
	- {
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- if (points==nullptr \|\| numPoints<=0)
	- continue;
	-
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	- for( int j=0; j<numPoints; j++)
	- {
	- vtkIdType id = vNewPoints->InsertNextPoint(points->GetPoint(j));
	- container->GetPointIds()->InsertNextId(id);
	- }
	- vNewLines->InsertNextCell(container);
	- }
	- if(vNewLines->GetNumberOfCells()==0)
	- return mitk::FiberBundle::New();
	- // initialize PolyData
	- vNewPolyData->SetPoints(vNewPoints);
	- vNewPolyData->SetLines(vNewLines);
	-
	- // initialize fiber bundle
	- return mitk::FiberBundle::New(vNewPolyData);
	-}
	-
	-/*
	- * set PolyData (additional flag to recompute fiber geometry, default = true)
	- */
	-void mitk::FiberBundle::SetFiberPolyData(vtkSmartPointer<vtkPolyData> fiberPD, bool updateGeometry)
	-{
	- if (fiberPD == nullptr)
	- this->m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
	- else
	- m_FiberPolyData->DeepCopy(fiberPD);
	-
	- m_NumFibers = static_cast<unsigned int>(m_FiberPolyData->GetNumberOfLines());
	-
	- if (updateGeometry)
	- UpdateFiberGeometry();
	- GenerateFiberIds();
	- ColorFibersByOrientation();
	-}
	-
	-/*
	- * return vtkPolyData
	- */
	-vtkSmartPointer<vtkPolyData> mitk::FiberBundle::GetFiberPolyData() const
	-{
	- return m_FiberPolyData;
	-}
	-
	-void mitk::FiberBundle::ColorFibersByLength(bool opacity, bool normalize)
	-{
	- if (m_MaxFiberLength<=0)
	- return;
	-
	- auto numOfPoints = this->GetNumberOfPoints();
	-
	- //colors and alpha value for each single point, RGBA = 4 components
	- unsigned char rgba[4] = {0,0,0,0};
	- m_FiberColors = vtkSmartPointer<vtkUnsignedCharArray>::New();
	- m_FiberColors->Allocate(numOfPoints * 4);
	- m_FiberColors->SetNumberOfComponents(4);
	- m_FiberColors->SetName("FIBER_COLORS");
	-
	- auto numOfFibers = m_FiberPolyData->GetNumberOfLines();
	- if (numOfFibers < 1)
	- return;
	-
	- mitk::LookupTable::Pointer mitkLookup = mitk::LookupTable::New();
	- vtkSmartPointer<vtkLookupTable> lookupTable = vtkSmartPointer<vtkLookupTable>::New();
	- lookupTable->SetTableRange(0.0, 0.8);
	- lookupTable->Build();
	- mitkLookup->SetVtkLookupTable(lookupTable);
	- mitkLookup->SetType(mitk::LookupTable::JET);
	-
	- unsigned int count = 0;
	- for (unsigned int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
	- {
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	-
	- float l = m_FiberLengths.at(i)/m_MaxFiberLength;
	- if (!normalize)
	- {
	- l = m_FiberLengths.at(i)/255.0f;
	- if (l > 1.0f)
	- l = 1.0;
	- }
	- for (int j=0; j<numPoints; j++)
	- {
	- double color[3];
	- lookupTable->GetColor(1.0 - static_cast<double>(l), color);
	-
	- rgba[0] = static_cast<unsigned char>(255.0 * color[0]);
	- rgba[1] = static_cast<unsigned char>(255.0 * color[1]);
	- rgba[2] = static_cast<unsigned char>(255.0 * color[2]);
	- if (opacity)
	- rgba[3] = static_cast<unsigned char>(255.0f * l);
	- else
	- rgba[3] = static_cast<unsigned char>(255.0);
	- m_FiberColors->InsertTypedTuple(cell->GetPointId(j), rgba);
	- count++;
	- }
	- }
	- m_UpdateTime3D.Modified();
	- m_UpdateTime2D.Modified();
	-}
	-
	-void mitk::FiberBundle::ColorFibersByOrientation()
	-{
	- //===== FOR WRITING A TEST ========================
	- // colorT size == tupelComponents * tupelElements
	- // compare color results
	- // to cover this code 100% also PolyData needed, where colorarray already exists
	- // + one fiber with exactly 1 point
	- // + one fiber with 0 points
	- //=================================================
	-
	- vtkPoints* extrPoints = m_FiberPolyData->GetPoints();
	- vtkIdType numOfPoints = 0;
	- if (extrPoints!=nullptr)
	- numOfPoints = extrPoints->GetNumberOfPoints();
	-
	- //colors and alpha value for each single point, RGBA = 4 components
	- unsigned char rgba[4] = {0,0,0,0};
	- m_FiberColors = vtkSmartPointer<vtkUnsignedCharArray>::New();
	- m_FiberColors->Allocate(numOfPoints * 4);
	- m_FiberColors->SetNumberOfComponents(4);
	- m_FiberColors->SetName("FIBER_COLORS");
	-
	- auto numOfFibers = m_FiberPolyData->GetNumberOfLines();
	- if (numOfFibers < 1)
	- return;
	-
	- /* extract single fibers of fiberBundle */
	- vtkCellArray* fiberList = m_FiberPolyData->GetLines();
	- fiberList->InitTraversal();
	- for (int fi=0; fi<numOfFibers; ++fi) {
	-
	- vtkIdType* idList; // contains the point id's of the line
	- vtkIdType pointsPerFiber; // number of points for current line
	- fiberList->GetNextCell(pointsPerFiber, idList);
	-
	- /* single fiber checkpoints: is number of points valid */
	- if (pointsPerFiber > 1)
	- {
	- /* operate on points of single fiber */
	- for (int i=0; i <pointsPerFiber; ++i)
	- {
	- /* process all points elastV[0]ept starting and endpoint for calculating color value take current point, previous point and next point */
	- if (i<pointsPerFiber-1 && i > 0)
	- {
	- /* The color value of the current point is influenced by the previous point and next point. */
	- vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]);
	- vnl_vector_fixed< double, 3 > nextPntvtk(extrPoints->GetPoint(idList[i+1])[0], extrPoints->GetPoint(idList[i+1])[1], extrPoints->GetPoint(idList[i+1])[2]);
	- vnl_vector_fixed< double, 3 > prevPntvtk(extrPoints->GetPoint(idList[i-1])[0], extrPoints->GetPoint(idList[i-1])[1], extrPoints->GetPoint(idList[i-1])[2]);
	-
	- vnl_vector_fixed< double, 3 > diff1;
	- diff1 = currentPntvtk - nextPntvtk;
	-
	- vnl_vector_fixed< double, 3 > diff2;
	- diff2 = currentPntvtk - prevPntvtk;
	-
	- vnl_vector_fixed< double, 3 > diff;
	- diff = (diff1 - diff2) / 2.0;
	- diff.normalize();
	-
	- rgba[0] = static_cast<unsigned char>(255.0 * std::fabs(diff[0]));
	- rgba[1] = static_cast<unsigned char>(255.0 * std::fabs(diff[1]));
	- rgba[2] = static_cast<unsigned char>(255.0 * std::fabs(diff[2]));
	- rgba[3] = static_cast<unsigned char>(255.0);
	- }
	- else if (i==0)
	- {
	- /* First point has no previous point, therefore only diff1 is taken */
	-
	- vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]);
	- vnl_vector_fixed< double, 3 > nextPntvtk(extrPoints->GetPoint(idList[i+1])[0], extrPoints->GetPoint(idList[i+1])[1], extrPoints->GetPoint(idList[i+1])[2]);
	-
	- vnl_vector_fixed< double, 3 > diff1;
	- diff1 = currentPntvtk - nextPntvtk;
	- diff1.normalize();
	-
	- rgba[0] = static_cast<unsigned char>(255.0 * std::fabs(diff1[0]));
	- rgba[1] = static_cast<unsigned char>(255.0 * std::fabs(diff1[1]));
	- rgba[2] = static_cast<unsigned char>(255.0 * std::fabs(diff1[2]));
	- rgba[3] = static_cast<unsigned char>(255.0);
	- }
	- else if (i==pointsPerFiber-1)
	- {
	- /* Last point has no next point, therefore only diff2 is taken */
	- vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]);
	- vnl_vector_fixed< double, 3 > prevPntvtk(extrPoints->GetPoint(idList[i-1])[0], extrPoints->GetPoint(idList[i-1])[1], extrPoints->GetPoint(idList[i-1])[2]);
	-
	- vnl_vector_fixed< double, 3 > diff2;
	- diff2 = currentPntvtk - prevPntvtk;
	- diff2.normalize();
	-
	- rgba[0] = static_cast<unsigned char>(255.0 * std::fabs(diff2[0]));
	- rgba[1] = static_cast<unsigned char>(255.0 * std::fabs(diff2[1]));
	- rgba[2] = static_cast<unsigned char>(255.0 * std::fabs(diff2[2]));
	- rgba[3] = static_cast<unsigned char>(255.0);
	- }
	- m_FiberColors->InsertTypedTuple(idList[i], rgba);
	- }
	- }
	- else if (pointsPerFiber == 1)
	- {
	- /* a single point does not define a fiber (use vertex mechanisms instead */
	- continue;
	- }
	- else
	- {
	- MITK_DEBUG << "Fiber with 0 points detected... please check your tractography algorithm!" ;
	- continue;
	- }
	- }
	- m_UpdateTime3D.Modified();
	- m_UpdateTime2D.Modified();
	-}
	-
	-void mitk::FiberBundle::ColorFibersByCurvature(bool, bool normalize)
	-{
	- double window = 5;
	-
	- //colors and alpha value for each single point, RGBA = 4 components
	- unsigned char rgba[4] = {0,0,0,0};
	- m_FiberColors = vtkSmartPointer<vtkUnsignedCharArray>::New();
	- m_FiberColors->Allocate(m_FiberPolyData->GetNumberOfPoints() * 4);
	- m_FiberColors->SetNumberOfComponents(4);
	- m_FiberColors->SetName("FIBER_COLORS");
	-
	- mitk::LookupTable::Pointer mitkLookup = mitk::LookupTable::New();
	- vtkSmartPointer<vtkLookupTable> lookupTable = vtkSmartPointer<vtkLookupTable>::New();
	- lookupTable->SetTableRange(0.0, 0.8);
	- lookupTable->Build();
	- mitkLookup->SetVtkLookupTable(lookupTable);
	- mitkLookup->SetType(mitk::LookupTable::JET);
	-
	- std::vector< double > values;
	- double min = 1;
	- double max = 0;
	- MITK_INFO << "Coloring fibers by curvature";
	- boost::progress_display disp(static_cast<unsigned long>(m_FiberPolyData->GetNumberOfCells()));
	- for (int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
	- {
	- ++disp;
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- // calculate curvatures
	- for (int j=0; j<numPoints; j++)
	- {
	- double dist = 0;
	- int c = j;
	- std::vector< vnl_vector_fixed< double, 3 > > vectors;
	- vnl_vector_fixed< double, 3 > meanV; meanV.fill(0.0);
	- while(dist<window/2 && c>1)
	- {
	- double p1[3];
	- points->GetPoint(c-1, p1);
	- double p2[3];
	- points->GetPoint(c, p2);
	-
	- vnl_vector_fixed< double, 3 > v;
	- v[0] = p2[0]-p1[0];
	- v[1] = p2[1]-p1[1];
	- v[2] = p2[2]-p1[2];
	- dist += v.magnitude();
	- v.normalize();
	- vectors.push_back(v);
	- meanV += v;
	- c--;
	- }
	- c = j;
	- dist = 0;
	- while(dist<window/2 && c<numPoints-1)
	- {
	- double p1[3];
	- points->GetPoint(c, p1);
	- double p2[3];
	- points->GetPoint(c+1, p2);
	-
	- vnl_vector_fixed< double, 3 > v;
	- v[0] = p2[0]-p1[0];
	- v[1] = p2[1]-p1[1];
	- v[2] = p2[2]-p1[2];
	- dist += v.magnitude();
	- v.normalize();
	- vectors.push_back(v);
	- meanV += v;
	- c++;
	- }
	- meanV.normalize();
	-
	- double dev = 0;
	- for (unsigned int c=0; c<vectors.size(); c++)
	- {
	- double angle = dot_product(meanV, vectors.at(c));
	- if (angle>1.0)
	- angle = 1.0;
	- if (angle<-1.0)
	- angle = -1.0;
	- dev += acos(angle)*180/itk::Math::pi;
	- }
	- if (vectors.size()>0)
	- dev /= vectors.size();
	-
	- dev = 1.0-dev/180.0;
	- values.push_back(dev);
	- if (dev<min)
	- min = dev;
	- if (dev>max)
	- max = dev;
	- }
	- }
	- unsigned int count = 0;
	- for (int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
	- {
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- for (int j=0; j<numPoints; j++)
	- {
	- double color[3];
	- double dev = values.at(count);
	- if (normalize)
	- dev = (dev-min)/(max-min);
	- else if (dev>1)
	- dev = 1;
	- lookupTable->GetColor(dev, color);
	-
	- rgba[0] = static_cast<unsigned char>(255.0 * color[0]);
	- rgba[1] = static_cast<unsigned char>(255.0 * color[1]);
	- rgba[2] = static_cast<unsigned char>(255.0 * color[2]);
	- rgba[3] = static_cast<unsigned char>(255.0);
	- m_FiberColors->InsertTypedTuple(cell->GetPointId(j), rgba);
	- count++;
	- }
	- }
	- m_UpdateTime3D.Modified();
	- m_UpdateTime2D.Modified();
	-}
	-
	-void mitk::FiberBundle::SetFiberOpacity(vtkDoubleArray* FAValArray)
	-{
	- for(long i=0; i<m_FiberColors->GetNumberOfTuples(); i++)
	- {
	- double faValue = FAValArray->GetValue(i);
	- faValue = faValue * 255.0;
	- m_FiberColors->SetComponent(i,3, static_cast<unsigned char>(faValue) );
	- }
	- m_UpdateTime3D.Modified();
	- m_UpdateTime2D.Modified();
	-}
	-
	-void mitk::FiberBundle::ResetFiberOpacity()
	-{
	- for(long i=0; i<m_FiberColors->GetNumberOfTuples(); i++)
	- m_FiberColors->SetComponent(i,3, 255.0 );
	- m_UpdateTime3D.Modified();
	- m_UpdateTime2D.Modified();
	-}
	-
	-void mitk::FiberBundle::ColorFibersByScalarMap(mitk::Image::Pointer FAimage, bool opacity, bool normalize)
	-{
	- mitkPixelTypeMultiplex3( ColorFibersByScalarMap, FAimage->GetPixelType(), FAimage, opacity, normalize );
	- m_UpdateTime3D.Modified();
	- m_UpdateTime2D.Modified();
	-}
	-
	-template <typename TPixel>
	-void mitk::FiberBundle::ColorFibersByScalarMap(const mitk::PixelType, mitk::Image::Pointer image, bool opacity, bool normalize)
	-{
	- m_FiberColors = vtkSmartPointer<vtkUnsignedCharArray>::New();
	- m_FiberColors->Allocate(m_FiberPolyData->GetNumberOfPoints() * 4);
	- m_FiberColors->SetNumberOfComponents(4);
	- m_FiberColors->SetName("FIBER_COLORS");
	-
	- mitk::ImagePixelReadAccessor<TPixel,3> readimage(image, image->GetVolumeData(0));
	-
	- unsigned char rgba[4] = {0,0,0,0};
	- vtkPoints* pointSet = m_FiberPolyData->GetPoints();
	-
	- mitk::LookupTable::Pointer mitkLookup = mitk::LookupTable::New();
	- vtkSmartPointer<vtkLookupTable> lookupTable = vtkSmartPointer<vtkLookupTable>::New();
	- lookupTable->SetTableRange(0.0, 0.8);
	- lookupTable->Build();
	- mitkLookup->SetVtkLookupTable(lookupTable);
	- mitkLookup->SetType(mitk::LookupTable::JET);
	-
	- double min = 999999;
	- double max = -999999;
	- for(long i=0; i<m_FiberPolyData->GetNumberOfPoints(); ++i)
	- {
	- Point3D px;
	- px[0] = pointSet->GetPoint(i)[0];
	- px[1] = pointSet->GetPoint(i)[1];
	- px[2] = pointSet->GetPoint(i)[2];
	- auto pixelValue = static_cast<double>(readimage.GetPixelByWorldCoordinates(px));
	- if (pixelValue>max)
	- max = pixelValue;
	- if (pixelValue<min)
	- min = pixelValue;
	- }
	-
	- for(long i=0; i<m_FiberPolyData->GetNumberOfPoints(); ++i)
	- {
	- Point3D px;
	- px[0] = pointSet->GetPoint(i)[0];
	- px[1] = pointSet->GetPoint(i)[1];
	- px[2] = pointSet->GetPoint(i)[2];
	- auto pixelValue = static_cast<double>(readimage.GetPixelByWorldCoordinates(px));
	-
	- if (normalize)
	- pixelValue = (pixelValue-min)/(max-min);
	- else if (pixelValue>1)
	- pixelValue = 1;
	-
	- double color[3];
	- lookupTable->GetColor(1-pixelValue, color);
	-
	- rgba[0] = static_cast<unsigned char>(255.0 * color[0]);
	- rgba[1] = static_cast<unsigned char>(255.0 * color[1]);
	- rgba[2] = static_cast<unsigned char>(255.0 * color[2]);
	- if (opacity)
	- rgba[3] = static_cast<unsigned char>(255.0 * pixelValue);
	- else
	- rgba[3] = static_cast<unsigned char>(255.0);
	- m_FiberColors->InsertTypedTuple(i, rgba);
	- }
	- m_UpdateTime3D.Modified();
	- m_UpdateTime2D.Modified();
	-}
	-
	-
	-void mitk::FiberBundle::ColorFibersByFiberWeights(bool opacity, bool normalize)
	-{
	- m_FiberColors = vtkSmartPointer<vtkUnsignedCharArray>::New();
	- m_FiberColors->Allocate(m_FiberPolyData->GetNumberOfPoints() * 4);
	- m_FiberColors->SetNumberOfComponents(4);
	- m_FiberColors->SetName("FIBER_COLORS");
	-
	- mitk::LookupTable::Pointer mitkLookup = mitk::LookupTable::New();
	- vtkSmartPointer<vtkLookupTable> lookupTable = vtkSmartPointer<vtkLookupTable>::New();
	- lookupTable->SetTableRange(0.0, 0.8);
	- lookupTable->Build();
	- mitkLookup->SetVtkLookupTable(lookupTable);
	- mitkLookup->SetType(mitk::LookupTable::JET);
	-
	- unsigned char rgba[4] = {0,0,0,0};
	- unsigned int counter = 0;
	-
	- float max = -999999;
	- float min = 999999;
	- for (unsigned int i=0; i<m_NumFibers; i++)
	- {
	- float weight = this->GetFiberWeight(i);
	- if (weight>max)
	- max = weight;
	- if (weight<min)
	- min = weight;
	- }
	- if (fabs(max-min)<0.00001f)
	- {
	- max = 1;
	- min = 0;
	- }
	-
	- for (unsigned int i=0; i<m_NumFibers; i++)
	- {
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- auto weight = this->GetFiberWeight(i);
	-
	- for (int j=0; j<numPoints; j++)
	- {
	- float v = weight;
	- if (normalize)
	- v = (v-min)/(max-min);
	- else if (v>1)
	- v = 1;
	- double color[3];
	- lookupTable->GetColor(static_cast<double>(1-v), color);
	-
	- rgba[0] = static_cast<unsigned char>(255.0 * color[0]);
	- rgba[1] = static_cast<unsigned char>(255.0 * color[1]);
	- rgba[2] = static_cast<unsigned char>(255.0 * color[2]);
	- if (opacity)
	- rgba[3] = static_cast<unsigned char>(255.0f * v);
	- else
	- rgba[3] = static_cast<unsigned char>(255.0);
	-
	- m_FiberColors->InsertTypedTuple(counter, rgba);
	- counter++;
	- }
	- }
	-
	- m_UpdateTime3D.Modified();
	- m_UpdateTime2D.Modified();
	-}
	-
	-void mitk::FiberBundle::SetFiberColors(float r, float g, float b, float alpha)
	-{
	- m_FiberColors = vtkSmartPointer<vtkUnsignedCharArray>::New();
	- m_FiberColors->Allocate(m_FiberPolyData->GetNumberOfPoints() * 4);
	- m_FiberColors->SetNumberOfComponents(4);
	- m_FiberColors->SetName("FIBER_COLORS");
	-
	- unsigned char rgba[4] = {0,0,0,0};
	- for(long i=0; i<m_FiberPolyData->GetNumberOfPoints(); ++i)
	- {
	- rgba[0] = static_cast<unsigned char>(r);
	- rgba[1] = static_cast<unsigned char>(g);
	- rgba[2] = static_cast<unsigned char>(b);
	- rgba[3] = static_cast<unsigned char>(alpha);
	- m_FiberColors->InsertTypedTuple(i, rgba);
	- }
	- m_UpdateTime3D.Modified();
	- m_UpdateTime2D.Modified();
	-}
	-
	-void mitk::FiberBundle::GenerateFiberIds()
	-{
	- if (m_FiberPolyData == nullptr)
	- return;
	-
	- vtkSmartPointer<vtkIdFilter> idFiberFilter = vtkSmartPointer<vtkIdFilter>::New();
	- idFiberFilter->SetInputData(m_FiberPolyData);
	- idFiberFilter->CellIdsOn();
	- // idFiberFilter->PointIdsOn(); // point id's are not needed
	- idFiberFilter->SetIdsArrayName(FIBER_ID_ARRAY);
	- idFiberFilter->FieldDataOn();
	- idFiberFilter->Update();
	-
	- m_FiberIdDataSet = idFiberFilter->GetOutput();
	-
	-}
	-
	-float mitk::FiberBundle::GetNumEpFractionInMask(ItkUcharImgType* mask, bool different_label)
	-{
	- vtkSmartPointer<vtkPolyData> PolyData = m_FiberPolyData;
	-
	- MITK_INFO << "Calculating EP-Fraction";
	-
	- boost::progress_display disp(m_NumFibers);
	- unsigned int in_mask = 0;
	-
	- for (unsigned int i=0; i<m_NumFibers; i++)
	- {
	- ++disp;
	- vtkCell* cell = PolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- itk::Point<float, 3> startVertex =mitk::imv::GetItkPoint(points->GetPoint(0));
	- itk::Index<3> startIndex;
	- mask->TransformPhysicalPointToIndex(startVertex, startIndex);
	-
	- itk::Point<float, 3> endVertex =mitk::imv::GetItkPoint(points->GetPoint(numPoints-1));
	- itk::Index<3> endIndex;
	- mask->TransformPhysicalPointToIndex(endVertex, endIndex);
	-
	- if (mask->GetLargestPossibleRegion().IsInside(startIndex) && mask->GetLargestPossibleRegion().IsInside(endIndex))
	- {
	- float v1 = mask->GetPixel(startIndex);
	- if (v1 < 0.5f)
	- continue;
	- float v2 = mask->GetPixel(startIndex);
	- if (v2 < 0.5f)
	- continue;
	-
	- if (!different_label)
	- ++in_mask;
	- else if (fabs(v1-v2)>0.00001f)
	- ++in_mask;
	- }
	- }
	- return float(in_mask)/m_NumFibers;
	-}
	-
	-std::tuple<float, float> mitk::FiberBundle::GetDirectionalOverlap(ItkUcharImgType* mask, mitk::PeakImage::ItkPeakImageType* peak_image)
	-{
	- vtkSmartPointer<vtkPolyData> PolyData = m_FiberPolyData;
	-
	- MITK_INFO << "Calculating overlap";
	- auto spacing = mask->GetSpacing();
	- boost::progress_display disp(m_NumFibers);
	- double length_sum = 0;
	- double in_mask_length = 0;
	- double aligned_length = 0;
	- for (unsigned int i=0; i<m_NumFibers; i++)
	- {
	- ++disp;
	- vtkCell* cell = PolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- for (int j=0; j<numPoints-1; j++)
	- {
	- itk::Point<float, 3> startVertex =mitk::imv::GetItkPoint(points->GetPoint(j));
	- itk::Index<3> startIndex;
	- itk::ContinuousIndex<float, 3> startIndexCont;
	- mask->TransformPhysicalPointToIndex(startVertex, startIndex);
	- mask->TransformPhysicalPointToContinuousIndex(startVertex, startIndexCont);
	-
	- itk::Point<float, 3> endVertex =mitk::imv::GetItkPoint(points->GetPoint(j + 1));
	- itk::Index<3> endIndex;
	- itk::ContinuousIndex<float, 3> endIndexCont;
	- mask->TransformPhysicalPointToIndex(endVertex, endIndex);
	- mask->TransformPhysicalPointToContinuousIndex(endVertex, endIndexCont);
	-
	- vnl_vector_fixed< float, 3 > fdir;
	- fdir[0] = endVertex[0] - startVertex[0];
	- fdir[1] = endVertex[1] - startVertex[1];
	- fdir[2] = endVertex[2] - startVertex[2];
	- fdir.normalize();
	-
	- std::vector< std::pair< itk::Index<3>, double > > segments = mitk::imv::IntersectImage(spacing, startIndex, endIndex, startIndexCont, endIndexCont);
	- for (std::pair< itk::Index<3>, double > segment : segments)
	- {
	- if ( mask->GetLargestPossibleRegion().IsInside(segment.first) && mask->GetPixel(segment.first) > 0 )
	- {
	- in_mask_length += segment.second;
	-
	- mitk::PeakImage::ItkPeakImageType::IndexType idx4;
	- idx4[0] = segment.first[0];
	- idx4[1] = segment.first[1];
	- idx4[2] = segment.first[2];
	-
	- vnl_vector_fixed< float, 3 > peak;
	- idx4[3] = 0;
	- peak[0] = peak_image->GetPixel(idx4);
	- idx4[3] = 1;
	- peak[1] = peak_image->GetPixel(idx4);
	- idx4[3] = 2;
	- peak[2] = peak_image->GetPixel(idx4);
	- if (std::isnan(peak[0]) \|\| std::isnan(peak[1]) \|\| std::isnan(peak[2]) \|\| peak.magnitude()<0.0001f)
	- continue;
	- peak.normalize();
	-
	- double f = 1.0 - std::acos(std::fabs(static_cast<double>(dot_product(fdir, peak)))) * 2.0/itk::Math::pi;
	- aligned_length += segment.second * f;
	- }
	- length_sum += segment.second;
	- }
	- }
	- }
	-
	- if (length_sum<=0.0001)
	- {
	- MITK_INFO << "Fiber length sum is zero!";
	- return std::make_tuple(0,0);
	- }
	- return std::make_tuple(aligned_length/length_sum, in_mask_length/length_sum);
	-}
	-
	-float mitk::FiberBundle::GetOverlap(ItkUcharImgType* mask)
	-{
	- vtkSmartPointer<vtkPolyData> PolyData = m_FiberPolyData;
	-
	- MITK_INFO << "Calculating overlap";
	- auto spacing = mask->GetSpacing();
	- boost::progress_display disp(m_NumFibers);
	- double length_sum = 0;
	- double in_mask_length = 0;
	- for (unsigned int i=0; i<m_NumFibers; i++)
	- {
	- ++disp;
	- vtkCell* cell = PolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- for (int j=0; j<numPoints-1; j++)
	- {
	- itk::Point<float, 3> startVertex =mitk::imv::GetItkPoint(points->GetPoint(j));
	- itk::Index<3> startIndex;
	- itk::ContinuousIndex<float, 3> startIndexCont;
	- mask->TransformPhysicalPointToIndex(startVertex, startIndex);
	- mask->TransformPhysicalPointToContinuousIndex(startVertex, startIndexCont);
	-
	- itk::Point<float, 3> endVertex =mitk::imv::GetItkPoint(points->GetPoint(j + 1));
	- itk::Index<3> endIndex;
	- itk::ContinuousIndex<float, 3> endIndexCont;
	- mask->TransformPhysicalPointToIndex(endVertex, endIndex);
	- mask->TransformPhysicalPointToContinuousIndex(endVertex, endIndexCont);
	-
	- std::vector< std::pair< itk::Index<3>, double > > segments = mitk::imv::IntersectImage(spacing, startIndex, endIndex, startIndexCont, endIndexCont);
	- for (std::pair< itk::Index<3>, double > segment : segments)
	- {
	- if ( mask->GetLargestPossibleRegion().IsInside(segment.first) && mask->GetPixel(segment.first) > 0 )
	- in_mask_length += segment.second;
	- length_sum += segment.second;
	- }
	- }
	- }
	-
	- if (length_sum<=0.000001)
	- {
	- MITK_INFO << "Fiber length sum is zero!";
	- return 0;
	- }
	- return static_cast<float>(in_mask_length/length_sum);
	-}
	-
	-mitk::FiberBundle::Pointer mitk::FiberBundle::RemoveFibersOutside(ItkUcharImgType* mask, bool invert)
	-{
	- vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
	- vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
	-
	- std::vector< float > fib_weights;
	-
	- MITK_INFO << "Cutting fibers";
	- boost::progress_display disp(m_NumFibers);
	- for (unsigned int i=0; i<m_NumFibers; i++)
	- {
	- ++disp;
	-
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	- int newNumPoints = 0;
	- if (numPoints>1)
	- {
	- for (int j=0; j<numPoints; j++)
	- {
	- itk::Point<float, 3> itkP =mitk::imv::GetItkPoint(points->GetPoint(j));
	- itk::Index<3> idx;
	- mask->TransformPhysicalPointToIndex(itkP, idx);
	-
	- bool inside = false;
	- if ( mask->GetLargestPossibleRegion().IsInside(idx) && mask->GetPixel(idx)!=0 )
	- inside = true;
	-
	- if (inside && !invert)
	- {
	- vtkIdType id = vtkNewPoints->InsertNextPoint(itkP.GetDataPointer());
	- container->GetPointIds()->InsertNextId(id);
	- newNumPoints++;
	- }
	- else if ( !inside && invert )
	- {
	- vtkIdType id = vtkNewPoints->InsertNextPoint(itkP.GetDataPointer());
	- container->GetPointIds()->InsertNextId(id);
	- newNumPoints++;
	- }
	- else if (newNumPoints>1)
	- {
	- fib_weights.push_back(this->GetFiberWeight(i));
	- vtkNewCells->InsertNextCell(container);
	- newNumPoints = 0;
	- container = vtkSmartPointer<vtkPolyLine>::New();
	- }
	- else
	- {
	- newNumPoints = 0;
	- container = vtkSmartPointer<vtkPolyLine>::New();
	- }
	- }
	-
	- if (newNumPoints>1)
	- {
	- fib_weights.push_back(this->GetFiberWeight(i));
	- vtkNewCells->InsertNextCell(container);
	- }
	- }
	-
	- }
	-
	- vtkSmartPointer<vtkFloatArray> newFiberWeights = vtkSmartPointer<vtkFloatArray>::New();
	- newFiberWeights->SetName("FIBER_WEIGHTS");
	- newFiberWeights->SetNumberOfValues(static_cast<vtkIdType>(fib_weights.size()));
	-
	- if (vtkNewCells->GetNumberOfCells()<=0)
	- return nullptr;
	-
	- for (unsigned int i=0; i<newFiberWeights->GetNumberOfValues(); i++)
	- newFiberWeights->SetValue(i, fib_weights.at(i));
	-
	-// vtkSmartPointer<vtkUnsignedCharArray> newFiberColors = vtkSmartPointer<vtkUnsignedCharArray>::New();
	-// newFiberColors->Allocate(m_FiberPolyData->GetNumberOfPoints() * 4);
	-// newFiberColors->SetNumberOfComponents(4);
	-// newFiberColors->SetName("FIBER_COLORS");
	-
	-// unsigned char rgba[4] = {0,0,0,0};
	-// for(long i=0; i<m_FiberPolyData->GetNumberOfPoints(); ++i)
	-// {
	-// rgba[0] = (unsigned char) r;
	-// rgba[1] = (unsigned char) g;
	-// rgba[2] = (unsigned char) b;
	-// rgba[3] = (unsigned char) alpha;
	-// m_FiberColors->InsertTypedTuple(i, rgba);
	-// }
	-
	- vtkSmartPointer<vtkPolyData> newPolyData = vtkSmartPointer<vtkPolyData>::New();
	- newPolyData->SetPoints(vtkNewPoints);
	- newPolyData->SetLines(vtkNewCells);
	- mitk::FiberBundle::Pointer newFib = mitk::FiberBundle::New(newPolyData);
	- newFib->SetFiberWeights(newFiberWeights);
	-// newFib->Compress(0.1);
	- return newFib;
	-}
	-
	-mitk::FiberBundle::Pointer mitk::FiberBundle::ExtractFiberSubset(DataNode* roi, DataStorage* storage)
	-{
	- if (roi==nullptr \|\| !(dynamic_cast<PlanarFigure>(roi->GetData()) \|\| dynamic_cast<PlanarFigureComposite>(roi->GetData())) )
	- return nullptr;
	-
	- std::vector<unsigned int> tmp = ExtractFiberIdSubset(roi, storage);
	-
	- if (tmp.size()<=0)
	- return mitk::FiberBundle::New();
	- vtkSmartPointer<vtkFloatArray> weights = vtkSmartPointer<vtkFloatArray>::New();
	- vtkSmartPointer<vtkPolyData> pTmp = GeneratePolyDataByIds(tmp, weights);
	- mitk::FiberBundle::Pointer fib = mitk::FiberBundle::New(pTmp);
	- fib->SetFiberWeights(weights);
	- return fib;
	-}
	-
	-std::vector<unsigned int> mitk::FiberBundle::ExtractFiberIdSubset(DataNode roi, DataStorage storage)
	-{
	- std::vector<unsigned int> result;
	- if (roi==nullptr \|\| roi->GetData()==nullptr)
	- return result;
	-
	- mitk::PlanarFigureComposite::Pointer pfc = dynamic_cast<mitk::PlanarFigureComposite*>(roi->GetData());
	- if (!pfc.IsNull()) // handle composite
	- {
	- DataStorage::SetOfObjects::ConstPointer children = storage->GetDerivations(roi);
	- if (children->size()==0)
	- return result;
	-
	- switch (pfc->getOperationType())
	- {
	- case 0: // AND
	- {
	- MITK_INFO << "AND";
	- result = this->ExtractFiberIdSubset(children->ElementAt(0), storage);
	- std::vector<unsigned int>::iterator it;
	- for (unsigned int i=1; i<children->Size(); ++i)
	- {
	- std::vector<unsigned int> inRoi = this->ExtractFiberIdSubset(children->ElementAt(i), storage);
	-
	- std::vector<unsigned int> rest(std::min(result.size(),inRoi.size()));
	- it = std::set_intersection(result.begin(), result.end(), inRoi.begin(), inRoi.end(), rest.begin() );
	- rest.resize( static_cast<unsigned int>(it - rest.begin()) );
	- result = rest;
	- }
	- break;
	- }
	- case 1: // OR
	- {
	- MITK_INFO << "OR";
	- result = ExtractFiberIdSubset(children->ElementAt(0), storage);
	- std::vector<unsigned int>::iterator it;
	- for (unsigned int i=1; i<children->Size(); ++i)
	- {
	- it = result.end();
	- std::vector<unsigned int> inRoi = ExtractFiberIdSubset(children->ElementAt(i), storage);
	- result.insert(it, inRoi.begin(), inRoi.end());
	- }
	-
	- // remove duplicates
	- sort(result.begin(), result.end());
	- it = unique(result.begin(), result.end());
	- result.resize( static_cast<unsigned int>(it - result.begin()) );
	- break;
	- }
	- case 2: // NOT
	- {
	- MITK_INFO << "NOT";
	- for(unsigned int i=0; i<this->GetNumFibers(); i++)
	- result.push_back(i);
	-
	- std::vector<unsigned int>::iterator it;
	- for (unsigned int i=0; i<children->Size(); ++i)
	- {
	- std::vector<unsigned int> inRoi = ExtractFiberIdSubset(children->ElementAt(i), storage);
	-
	- std::vector<unsigned int> rest(result.size()-inRoi.size());
	- it = std::set_difference(result.begin(), result.end(), inRoi.begin(), inRoi.end(), rest.begin() );
	- rest.resize( static_cast<unsigned int>(it - rest.begin()) );
	- result = rest;
	- }
	- break;
	- }
	- }
	- }
	- else if ( dynamic_cast<mitk::PlanarFigure*>(roi->GetData()) ) // actual extraction
	- {
	- if ( dynamic_cast<mitk::PlanarPolygon*>(roi->GetData()) )
	- {
	- mitk::PlanarFigure::Pointer planarPoly = dynamic_cast<mitk::PlanarFigure*>(roi->GetData());
	-
	- //create vtkPolygon using controlpoints from planarFigure polygon
	- vtkSmartPointer<vtkPolygon> polygonVtk = vtkSmartPointer<vtkPolygon>::New();
	- for (unsigned int i=0; i<planarPoly->GetNumberOfControlPoints(); ++i)
	- {
	- itk::Point<double,3> p = planarPoly->GetWorldControlPoint(i);
	- vtkIdType id = polygonVtk->GetPoints()->InsertNextPoint(p[0], p[1], p[2] );
	- polygonVtk->GetPointIds()->InsertNextId(id);
	- }
	-
	- MITK_INFO << "Extracting with polygon";
	- boost::progress_display disp(m_NumFibers);
	- for (unsigned int i=0; i<m_NumFibers; i++)
	- {
	- ++disp ;
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- for (int j=0; j<numPoints-1; j++)
	- {
	- // Inputs
	- double p1[3] = {0,0,0};
	- points->GetPoint(j, p1);
	- double p2[3] = {0,0,0};
	- points->GetPoint(j+1, p2);
	- double tolerance = 0.001;
	-
	- // Outputs
	- double t = 0; // Parametric coordinate of intersection (0 (corresponding to p1) to 1 (corresponding to p2))
	- double x[3] = {0,0,0}; // The coordinate of the intersection
	- double pcoords[3] = {0,0,0};
	- int subId = 0;
	-
	- int iD = polygonVtk->IntersectWithLine(p1, p2, tolerance, t, x, pcoords, subId);
	- if (iD!=0)
	- {
	- result.push_back(i);
	- break;
	- }
	- }
	- }
	- }
	- else if ( dynamic_cast<mitk::PlanarCircle*>(roi->GetData()) )
	- {
	- mitk::PlanarFigure::Pointer planarFigure = dynamic_cast<mitk::PlanarFigure*>(roi->GetData());
	- Vector3D planeNormal = planarFigure->GetPlaneGeometry()->GetNormal();
	- planeNormal.Normalize();
	-
	- //calculate circle radius
	- mitk::Point3D V1w = planarFigure->GetWorldControlPoint(0); //centerPoint
	- mitk::Point3D V2w = planarFigure->GetWorldControlPoint(1); //radiusPoint
	-
	- double radius = V1w.EuclideanDistanceTo(V2w);
	- radius *= radius;
	-
	- MITK_INFO << "Extracting with circle";
	- boost::progress_display disp(m_NumFibers);
	- for (unsigned int i=0; i<m_NumFibers; i++)
	- {
	- ++disp ;
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- for (int j=0; j<numPoints-1; j++)
	- {
	- // Inputs
	- double p1[3] = {0,0,0};
	- points->GetPoint(j, p1);
	- double p2[3] = {0,0,0};
	- points->GetPoint(j+1, p2);
	-
	- // Outputs
	- double t = 0; // Parametric coordinate of intersection (0 (corresponding to p1) to 1 (corresponding to p2))
	- double x[3] = {0,0,0}; // The coordinate of the intersection
	-
	- int iD = vtkPlane::IntersectWithLine(p1,p2,planeNormal.GetDataPointer(),V1w.GetDataPointer(),t,x);
	-
	- if (iD!=0)
	- {
	- double dist = (x[0]-V1w[0])(x[0]-V1w[0])+(x[1]-V1w[1])(x[1]-V1w[1])+(x[2]-V1w[2])*(x[2]-V1w[2]);
	- if( dist <= radius)
	- {
	- result.push_back(i);
	- break;
	- }
	- }
	- }
	- }
	- }
	- return result;
	- }
	-
	- return result;
	-}
	-
	-void mitk::FiberBundle::UpdateFiberGeometry()
	-{
	- vtkSmartPointer<vtkCleanPolyData> cleaner = vtkSmartPointer<vtkCleanPolyData>::New();
	- cleaner->SetInputData(m_FiberPolyData);
	- cleaner->PointMergingOff();
	- cleaner->Update();
	- m_FiberPolyData = cleaner->GetOutput();
	-
	- m_FiberLengths.clear();
	- m_MeanFiberLength = 0;
	- m_MedianFiberLength = 0;
	- m_LengthStDev = 0;
	- m_NumFibers = static_cast<unsigned int>(m_FiberPolyData->GetNumberOfCells());
	-
	- if (m_FiberColors==nullptr \|\| m_FiberColors->GetNumberOfTuples()!=m_FiberPolyData->GetNumberOfPoints())
	- this->ColorFibersByOrientation();
	-
	- if (m_FiberWeights->GetNumberOfValues()!=m_NumFibers)
	- {
	- m_FiberWeights = vtkSmartPointer<vtkFloatArray>::New();
	- m_FiberWeights->SetName("FIBER_WEIGHTS");
	- m_FiberWeights->SetNumberOfValues(m_NumFibers);
	- this->SetFiberWeights(1);
	- }
	-
	- if (m_NumFibers<=0) // no fibers present; apply default geometry
	- {
	- m_MinFiberLength = 0;
	- m_MaxFiberLength = 0;
	- mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New();
	- geometry->SetImageGeometry(false);
	- float b[] = {0, 1, 0, 1, 0, 1};
	- geometry->SetFloatBounds(b);
	- SetGeometry(geometry);
	- return;
	- }
	- double b[6];
	- m_FiberPolyData->GetBounds(b);
	-
	- // calculate statistics
	- for (int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
	- {
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- auto p = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	- float length = 0;
	- for (int j=0; j<p-1; j++)
	- {
	- double p1[3];
	- points->GetPoint(j, p1);
	- double p2[3];
	- points->GetPoint(j+1, p2);
	-
	- double dist = std::sqrt((p1[0]-p2[0])(p1[0]-p2[0])+(p1[1]-p2[1])(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
	- length += static_cast<float>(dist);
	- }
	- m_FiberLengths.push_back(length);
	- m_MeanFiberLength += length;
	- if (i==0)
	- {
	- m_MinFiberLength = length;
	- m_MaxFiberLength = length;
	- }
	- else
	- {
	- if (length<m_MinFiberLength)
	- m_MinFiberLength = length;
	- if (length>m_MaxFiberLength)
	- m_MaxFiberLength = length;
	- }
	- }
	- m_MeanFiberLength /= m_NumFibers;
	-
	- std::vector< float > sortedLengths = m_FiberLengths;
	- std::sort(sortedLengths.begin(), sortedLengths.end());
	- for (unsigned int i=0; i<m_NumFibers; i++)
	- m_LengthStDev += (m_MeanFiberLength-sortedLengths.at(i))*(m_MeanFiberLength-sortedLengths.at(i));
	- if (m_NumFibers>1)
	- m_LengthStDev /= (m_NumFibers-1);
	- else
	- m_LengthStDev = 0;
	- m_LengthStDev = std::sqrt(m_LengthStDev);
	- m_MedianFiberLength = sortedLengths.at(m_NumFibers/2);
	-
	- mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New();
	- geometry->SetFloatBounds(b);
	- this->SetGeometry(geometry);
	-
	- m_UpdateTime3D.Modified();
	- m_UpdateTime2D.Modified();
	-}
	-
	-float mitk::FiberBundle::GetFiberWeight(unsigned int fiber) const
	-{
	- return m_FiberWeights->GetValue(fiber);
	-}
	-
	-void mitk::FiberBundle::SetFiberWeights(float newWeight)
	-{
	- for (int i=0; i<m_FiberWeights->GetNumberOfValues(); i++)
	- m_FiberWeights->SetValue(i, newWeight);
	-}
	-
	-void mitk::FiberBundle::SetFiberWeights(vtkSmartPointer<vtkFloatArray> weights)
	-{
	- if (m_NumFibers!=weights->GetNumberOfValues())
	- {
	- MITK_INFO << "Weights array not equal to number of fibers! " << weights->GetNumberOfValues() << " vs " << m_NumFibers;
	- return;
	- }
	-
	- for (int i=0; i<weights->GetNumberOfValues(); i++)
	- m_FiberWeights->SetValue(i, weights->GetValue(i));
	-
	- m_FiberWeights->SetName("FIBER_WEIGHTS");
	-}
	-
	-void mitk::FiberBundle::SetFiberWeight(unsigned int fiber, float weight)
	-{
	- m_FiberWeights->SetValue(fiber, weight);
	-}
	-
	-void mitk::FiberBundle::SetFiberColors(vtkSmartPointer<vtkUnsignedCharArray> fiberColors)
	-{
	- for(long i=0; i<m_FiberPolyData->GetNumberOfPoints(); ++i)
	- {
	- unsigned char source[4] = {0,0,0,0};
	- fiberColors->GetTypedTuple(i, source);
	-
	- unsigned char target[4] = {0,0,0,0};
	- target[0] = source[0];
	- target[1] = source[1];
	- target[2] = source[2];
	- target[3] = source[3];
	- m_FiberColors->InsertTypedTuple(i, target);
	- }
	- m_UpdateTime3D.Modified();
	- m_UpdateTime2D.Modified();
	-}
	-
	-itk::Matrix< double, 3, 3 > mitk::FiberBundle::TransformMatrix(itk::Matrix< double, 3, 3 > m, double rx, double ry, double rz)
	-{
	- rx = rx*itk::Math::pi/180;
	- ry = ry*itk::Math::pi/180;
	- rz = rz*itk::Math::pi/180;
	-
	- itk::Matrix< double, 3, 3 > rotX; rotX.SetIdentity();
	- rotX[1][1] = cos(rx);
	- rotX[2][2] = rotX[1][1];
	- rotX[1][2] = -sin(rx);
	- rotX[2][1] = -rotX[1][2];
	-
	- itk::Matrix< double, 3, 3 > rotY; rotY.SetIdentity();
	- rotY[0][0] = cos(ry);
	- rotY[2][2] = rotY[0][0];
	- rotY[0][2] = sin(ry);
	- rotY[2][0] = -rotY[0][2];
	-
	- itk::Matrix< double, 3, 3 > rotZ; rotZ.SetIdentity();
	- rotZ[0][0] = cos(rz);
	- rotZ[1][1] = rotZ[0][0];
	- rotZ[0][1] = -sin(rz);
	- rotZ[1][0] = -rotZ[0][1];
	-
	- itk::Matrix< double, 3, 3 > rot = rotZrotYrotX;
	-
	- m = rot*m;
	-
	- return m;
	-}
	-
	-void mitk::FiberBundle::TransformFibers(itk::ScalableAffineTransform< mitk::ScalarType >::Pointer transform)
	-{
	- vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
	- vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
	-
	- for (unsigned int i=0; i<m_NumFibers; i++)
	- {
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	- for (int j=0; j<numPoints; j++)
	- {
	- itk::Point<float, 3> p =mitk::imv::GetItkPoint(points->GetPoint(j));
	- p = transform->TransformPoint(p);
	- vtkIdType id = vtkNewPoints->InsertNextPoint(p.GetDataPointer());
	- container->GetPointIds()->InsertNextId(id);
	- }
	- vtkNewCells->InsertNextCell(container);
	- }
	-
	- m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
	- m_FiberPolyData->SetPoints(vtkNewPoints);
	- m_FiberPolyData->SetLines(vtkNewCells);
	- this->SetFiberPolyData(m_FiberPolyData, true);
	-}
	-
	-void mitk::FiberBundle::TransformFibers(double rx, double ry, double rz, double tx, double ty, double tz)
	-{
	- vnl_matrix_fixed< double, 3, 3 > rot = mitk::imv::GetRotationMatrixVnl(rx, ry, rz);
	-
	- mitk::BaseGeometry::Pointer geom = this->GetGeometry();
	- mitk::Point3D center = geom->GetCenter();
	-
	- vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
	- vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
	-
	- for (unsigned int i=0; i<m_NumFibers; i++)
	- {
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	- for (int j=0; j<numPoints; j++)
	- {
	- double* p = points->GetPoint(j);
	- vnl_vector_fixed< double, 3 > dir;
	- dir[0] = p[0]-center[0];
	- dir[1] = p[1]-center[1];
	- dir[2] = p[2]-center[2];
	- dir = rot*dir;
	- dir[0] += center[0]+tx;
	- dir[1] += center[1]+ty;
	- dir[2] += center[2]+tz;
	- vtkIdType id = vtkNewPoints->InsertNextPoint(dir.data_block());
	- container->GetPointIds()->InsertNextId(id);
	- }
	- vtkNewCells->InsertNextCell(container);
	- }
	-
	- m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
	- m_FiberPolyData->SetPoints(vtkNewPoints);
	- m_FiberPolyData->SetLines(vtkNewCells);
	- this->SetFiberPolyData(m_FiberPolyData, true);
	-}
	-
	-void mitk::FiberBundle::RotateAroundAxis(double x, double y, double z)
	-{
	- x = x*itk::Math::pi/180;
	- y = y*itk::Math::pi/180;
	- z = z*itk::Math::pi/180;
	-
	- vnl_matrix_fixed< double, 3, 3 > rotX; rotX.set_identity();
	- rotX[1][1] = cos(x);
	- rotX[2][2] = rotX[1][1];
	- rotX[1][2] = -sin(x);
	- rotX[2][1] = -rotX[1][2];
	-
	- vnl_matrix_fixed< double, 3, 3 > rotY; rotY.set_identity();
	- rotY[0][0] = cos(y);
	- rotY[2][2] = rotY[0][0];
	- rotY[0][2] = sin(y);
	- rotY[2][0] = -rotY[0][2];
	-
	- vnl_matrix_fixed< double, 3, 3 > rotZ; rotZ.set_identity();
	- rotZ[0][0] = cos(z);
	- rotZ[1][1] = rotZ[0][0];
	- rotZ[0][1] = -sin(z);
	- rotZ[1][0] = -rotZ[0][1];
	-
	- mitk::BaseGeometry::Pointer geom = this->GetGeometry();
	- mitk::Point3D center = geom->GetCenter();
	-
	- vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
	- vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
	-
	- for (unsigned int i=0; i<m_NumFibers; i++)
	- {
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	- for (int j=0; j<numPoints; j++)
	- {
	- double* p = points->GetPoint(j);
	- vnl_vector_fixed< double, 3 > dir;
	- dir[0] = p[0]-center[0];
	- dir[1] = p[1]-center[1];
	- dir[2] = p[2]-center[2];
	- dir = rotZrotYrotX*dir;
	- dir[0] += center[0];
	- dir[1] += center[1];
	- dir[2] += center[2];
	- vtkIdType id = vtkNewPoints->InsertNextPoint(dir.data_block());
	- container->GetPointIds()->InsertNextId(id);
	- }
	- vtkNewCells->InsertNextCell(container);
	- }
	-
	- m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
	- m_FiberPolyData->SetPoints(vtkNewPoints);
	- m_FiberPolyData->SetLines(vtkNewCells);
	- this->SetFiberPolyData(m_FiberPolyData, true);
	-}
	-
	-void mitk::FiberBundle::ScaleFibers(double x, double y, double z, bool subtractCenter)
	-{
	- MITK_INFO << "Scaling fibers";
	- boost::progress_display disp(m_NumFibers);
	-
	- mitk::BaseGeometry* geom = this->GetGeometry();
	- mitk::Point3D c = geom->GetCenter();
	-
	- vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
	- vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
	-
	- for (unsigned int i=0; i<m_NumFibers; i++)
	- {
	- ++disp ;
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	- for (int j=0; j<numPoints; j++)
	- {
	- double* p = points->GetPoint(j);
	- if (subtractCenter)
	- {
	- p[0] -= c[0]; p[1] -= c[1]; p[2] -= c[2];
	- }
	- p[0] *= x;
	- p[1] *= y;
	- p[2] *= z;
	- if (subtractCenter)
	- {
	- p[0] += c[0]; p[1] += c[1]; p[2] += c[2];
	- }
	- vtkIdType id = vtkNewPoints->InsertNextPoint(p);
	- container->GetPointIds()->InsertNextId(id);
	- }
	- vtkNewCells->InsertNextCell(container);
	- }
	-
	- m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
	- m_FiberPolyData->SetPoints(vtkNewPoints);
	- m_FiberPolyData->SetLines(vtkNewCells);
	- this->SetFiberPolyData(m_FiberPolyData, true);
	-}
	-
	-void mitk::FiberBundle::TranslateFibers(double x, double y, double z)
	-{
	- vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
	- vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
	-
	- for (unsigned int i=0; i<m_NumFibers; i++)
	- {
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	- for (int j=0; j<numPoints; j++)
	- {
	- double* p = points->GetPoint(j);
	- p[0] += x;
	- p[1] += y;
	- p[2] += z;
	- vtkIdType id = vtkNewPoints->InsertNextPoint(p);
	- container->GetPointIds()->InsertNextId(id);
	- }
	- vtkNewCells->InsertNextCell(container);
	- }
	-
	- m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
	- m_FiberPolyData->SetPoints(vtkNewPoints);
	- m_FiberPolyData->SetLines(vtkNewCells);
	- this->SetFiberPolyData(m_FiberPolyData, true);
	-}
	-
	-void mitk::FiberBundle::MirrorFibers(unsigned int axis)
	-{
	- if (axis>2)
	- return;
	-
	- MITK_INFO << "Mirroring fibers";
	- boost::progress_display disp(m_NumFibers);
	-
	- vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
	- vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
	-
	- for (unsigned int i=0; i<m_NumFibers; i++)
	- {
	- ++disp;
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	- for (int j=0; j<numPoints; j++)
	- {
	- double* p = points->GetPoint(j);
	- p[axis] = -p[axis];
	- vtkIdType id = vtkNewPoints->InsertNextPoint(p);
	- container->GetPointIds()->InsertNextId(id);
	- }
	- vtkNewCells->InsertNextCell(container);
	- }
	-
	- m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
	- m_FiberPolyData->SetPoints(vtkNewPoints);
	- m_FiberPolyData->SetLines(vtkNewCells);
	- this->SetFiberPolyData(m_FiberPolyData, true);
	-}
	-
	-void mitk::FiberBundle::RemoveDir(vnl_vector_fixed<double,3> dir, double threshold)
	-{
	- dir.normalize();
	- vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
	- vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
	-
	- boost::progress_display disp(static_cast<unsigned long>(m_FiberPolyData->GetNumberOfCells()));
	- for (int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
	- {
	- ++disp ;
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- // calculate curvatures
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	- bool discard = false;
	- for (int j=0; j<numPoints-1; j++)
	- {
	- double p1[3];
	- points->GetPoint(j, p1);
	- double p2[3];
	- points->GetPoint(j+1, p2);
	-
	- vnl_vector_fixed< double, 3 > v1;
	- v1[0] = p2[0]-p1[0];
	- v1[1] = p2[1]-p1[1];
	- v1[2] = p2[2]-p1[2];
	- if (v1.magnitude()>0.001)
	- {
	- v1.normalize();
	-
	- if (fabs(dot_product(v1,dir))>threshold)
	- {
	- discard = true;
	- break;
	- }
	- }
	- }
	- if (!discard)
	- {
	- for (int j=0; j<numPoints; j++)
	- {
	- double p1[3];
	- points->GetPoint(j, p1);
	-
	- vtkIdType id = vtkNewPoints->InsertNextPoint(p1);
	- container->GetPointIds()->InsertNextId(id);
	- }
	- vtkNewCells->InsertNextCell(container);
	- }
	- }
	-
	- m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
	- m_FiberPolyData->SetPoints(vtkNewPoints);
	- m_FiberPolyData->SetLines(vtkNewCells);
	-
	- this->SetFiberPolyData(m_FiberPolyData, true);
	-
	- // UpdateColorCoding();
	- // UpdateFiberGeometry();
	-}
	-
	-bool mitk::FiberBundle::ApplyCurvatureThreshold(float minRadius, bool deleteFibers)
	-{
	- if (minRadius<0)
	- return true;
	-
	- vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
	- vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
	-
	- MITK_INFO << "Applying curvature threshold";
	- boost::progress_display disp(static_cast<unsigned long>(m_FiberPolyData->GetNumberOfCells()));
	- for (int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
	- {
	- ++disp ;
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- // calculate curvatures
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	- for (int j=0; j<numPoints-2; j++)
	- {
	- double p1[3];
	- points->GetPoint(j, p1);
	- double p2[3];
	- points->GetPoint(j+1, p2);
	- double p3[3];
	- points->GetPoint(j+2, p3);
	-
	- vnl_vector_fixed< float, 3 > v1, v2, v3;
	-
	- v1[0] = static_cast<float>(p2[0]-p1[0]);
	- v1[1] = static_cast<float>(p2[1]-p1[1]);
	- v1[2] = static_cast<float>(p2[2]-p1[2]);
	-
	- v2[0] = static_cast<float>(p3[0]-p2[0]);
	- v2[1] = static_cast<float>(p3[1]-p2[1]);
	- v2[2] = static_cast<float>(p3[2]-p2[2]);
	-
	- v3[0] = static_cast<float>(p1[0]-p3[0]);
	- v3[1] = static_cast<float>(p1[1]-p3[1]);
	- v3[2] = static_cast<float>(p1[2]-p3[2]);
	-
	- float a = v1.magnitude();
	- float b = v2.magnitude();
	- float c = v3.magnitude();
	- float r = abc/std::sqrt((a+b+c)(a+b-c)(b+c-a)*(a-b+c)); // radius of triangle via Heron's formula (area of triangle)
	-
	- vtkIdType id = vtkNewPoints->InsertNextPoint(p1);
	- container->GetPointIds()->InsertNextId(id);
	-
	- if (deleteFibers && r<minRadius)
	- break;
	-
	- if (r<minRadius)
	- {
	- j += 2;
	- vtkNewCells->InsertNextCell(container);
	- container = vtkSmartPointer<vtkPolyLine>::New();
	- }
	- else if (j==numPoints-3)
	- {
	- id = vtkNewPoints->InsertNextPoint(p2);
	- container->GetPointIds()->InsertNextId(id);
	- id = vtkNewPoints->InsertNextPoint(p3);
	- container->GetPointIds()->InsertNextId(id);
	- vtkNewCells->InsertNextCell(container);
	- }
	- }
	- }
	-
	- if (vtkNewCells->GetNumberOfCells()<=0)
	- return false;
	-
	- m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
	- m_FiberPolyData->SetPoints(vtkNewPoints);
	- m_FiberPolyData->SetLines(vtkNewCells);
	- this->SetFiberPolyData(m_FiberPolyData, true);
	- return true;
	-}
	-
	-bool mitk::FiberBundle::RemoveShortFibers(float lengthInMM)
	-{
	- MITK_INFO << "Removing short fibers";
	- if (lengthInMM<=0 \|\| lengthInMM<m_MinFiberLength)
	- {
	- MITK_INFO << "No fibers shorter than " << lengthInMM << " mm found!";
	- return true;
	- }
	-
	- if (lengthInMM>m_MaxFiberLength) // can't remove all fibers
	- {
	- MITK_WARN << "Process aborted. No fibers would be left!";
	- return false;
	- }
	-
	- vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
	- vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
	- float min = m_MaxFiberLength;
	-
	- boost::progress_display disp(m_NumFibers);
	- for (unsigned int i=0; i<m_NumFibers; i++)
	- {
	- ++disp;
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- if (m_FiberLengths.at(i)>=lengthInMM)
	- {
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	- for (int j=0; j<numPoints; j++)
	- {
	- double* p = points->GetPoint(j);
	- vtkIdType id = vtkNewPoints->InsertNextPoint(p);
	- container->GetPointIds()->InsertNextId(id);
	- }
	- vtkNewCells->InsertNextCell(container);
	- if (m_FiberLengths.at(i)<min)
	- min = m_FiberLengths.at(i);
	- }
	- }
	-
	- if (vtkNewCells->GetNumberOfCells()<=0)
	- return false;
	-
	- m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
	- m_FiberPolyData->SetPoints(vtkNewPoints);
	- m_FiberPolyData->SetLines(vtkNewCells);
	- this->SetFiberPolyData(m_FiberPolyData, true);
	- return true;
	-}
	-
	-bool mitk::FiberBundle::RemoveLongFibers(float lengthInMM)
	-{
	- if (lengthInMM<=0 \|\| lengthInMM>m_MaxFiberLength)
	- return true;
	-
	- if (lengthInMM<m_MinFiberLength) // can't remove all fibers
	- return false;
	-
	- vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
	- vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
	-
	- MITK_INFO << "Removing long fibers";
	- boost::progress_display disp(m_NumFibers);
	- for (unsigned int i=0; i<m_NumFibers; i++)
	- {
	- ++disp;
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- if (m_FiberLengths.at(i)<=lengthInMM)
	- {
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	- for (int j=0; j<numPoints; j++)
	- {
	- double* p = points->GetPoint(j);
	- vtkIdType id = vtkNewPoints->InsertNextPoint(p);
	- container->GetPointIds()->InsertNextId(id);
	- }
	- vtkNewCells->InsertNextCell(container);
	- }
	- }
	-
	- if (vtkNewCells->GetNumberOfCells()<=0)
	- return false;
	-
	- m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
	- m_FiberPolyData->SetPoints(vtkNewPoints);
	- m_FiberPolyData->SetLines(vtkNewCells);
	- this->SetFiberPolyData(m_FiberPolyData, true);
	- return true;
	-}
	-
	-void mitk::FiberBundle::ResampleSpline(float pointDistance, double tension, double continuity, double bias )
	-{
	- if (pointDistance<=0)
	- return;
	-
	- vtkSmartPointer<vtkPoints> vtkSmoothPoints = vtkSmartPointer<vtkPoints>::New(); //in smoothpoints the interpolated points representing a fiber are stored.
	-
	- //in vtkcells all polylines are stored, actually all id's of them are stored
	- vtkSmartPointer<vtkCellArray> vtkSmoothCells = vtkSmartPointer<vtkCellArray>::New(); //cellcontainer for smoothed lines
	-
	- MITK_INFO << "Smoothing fibers";
	- vtkSmartPointer<vtkFloatArray> newFiberWeights = vtkSmartPointer<vtkFloatArray>::New();
	- newFiberWeights->SetName("FIBER_WEIGHTS");
	- newFiberWeights->SetNumberOfValues(m_NumFibers);
	-
	- std::vector< vtkSmartPointer<vtkPolyLine> > resampled_streamlines;
	- resampled_streamlines.resize(m_NumFibers);
	-
	- boost::progress_display disp(m_NumFibers);
	-#pragma omp parallel for
	- for (int i=0; i<static_cast<int>(m_NumFibers); i++)
	- {
	- vtkSmartPointer<vtkPoints> newPoints = vtkSmartPointer<vtkPoints>::New();
	- float length = 0;
	-#pragma omp critical
	- {
	- length = m_FiberLengths.at(static_cast<unsigned int>(i));
	- ++disp;
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	- for (int j=0; j<numPoints; j++)
	- newPoints->InsertNextPoint(points->GetPoint(j));
	- }
	-
	- int sampling = static_cast<int>(std::ceil(length/pointDistance));
	-
	- vtkSmartPointer<vtkKochanekSpline> xSpline = vtkSmartPointer<vtkKochanekSpline>::New();
	- vtkSmartPointer<vtkKochanekSpline> ySpline = vtkSmartPointer<vtkKochanekSpline>::New();
	- vtkSmartPointer<vtkKochanekSpline> zSpline = vtkSmartPointer<vtkKochanekSpline>::New();
	- xSpline->SetDefaultBias(bias); xSpline->SetDefaultTension(tension); xSpline->SetDefaultContinuity(continuity);
	- ySpline->SetDefaultBias(bias); ySpline->SetDefaultTension(tension); ySpline->SetDefaultContinuity(continuity);
	- zSpline->SetDefaultBias(bias); zSpline->SetDefaultTension(tension); zSpline->SetDefaultContinuity(continuity);
	-
	- vtkSmartPointer<vtkParametricSpline> spline = vtkSmartPointer<vtkParametricSpline>::New();
	- spline->SetXSpline(xSpline);
	- spline->SetYSpline(ySpline);
	- spline->SetZSpline(zSpline);
	- spline->SetPoints(newPoints);
	-
	- vtkSmartPointer<vtkParametricFunctionSource> functionSource = vtkSmartPointer<vtkParametricFunctionSource>::New();
	- functionSource->SetParametricFunction(spline);
	- functionSource->SetUResolution(sampling);
	- functionSource->SetVResolution(sampling);
	- functionSource->SetWResolution(sampling);
	- functionSource->Update();
	-
	- vtkPolyData* outputFunction = functionSource->GetOutput();
	- vtkPoints* tmpSmoothPnts = outputFunction->GetPoints(); //smoothPoints of current fiber
	-
	- vtkSmartPointer<vtkPolyLine> smoothLine = vtkSmartPointer<vtkPolyLine>::New();
	-
	-#pragma omp critical
	- {
	- for (int j=0; j<tmpSmoothPnts->GetNumberOfPoints(); j++)
	- {
	- vtkIdType id = vtkSmoothPoints->InsertNextPoint(tmpSmoothPnts->GetPoint(j));
	- smoothLine->GetPointIds()->InsertNextId(id);
	- }
	-
	- resampled_streamlines[static_cast<unsigned long>(i)] = smoothLine;
	- }
	- }
	-
	- for (auto container : resampled_streamlines)
	- {
	- vtkSmoothCells->InsertNextCell(container);
	- }
	-
	- m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
	- m_FiberPolyData->SetPoints(vtkSmoothPoints);
	- m_FiberPolyData->SetLines(vtkSmoothCells);
	- this->SetFiberPolyData(m_FiberPolyData, true);
	-}
	-
	-void mitk::FiberBundle::ResampleSpline(float pointDistance)
	-{
	- ResampleSpline(pointDistance, 0, 0, 0 );
	-}
	-
	-unsigned int mitk::FiberBundle::GetNumberOfPoints() const
	-{
	- unsigned int points = 0;
	- for (int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
	- {
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- points += cell->GetNumberOfPoints();
	- }
	- return points;
	-}
	-
	-void mitk::FiberBundle::Compress(float error)
	-{
	- vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
	- vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
	-
	- MITK_INFO << "Compressing fibers";
	- unsigned int numRemovedPoints = 0;
	- boost::progress_display disp(static_cast<unsigned long>(m_FiberPolyData->GetNumberOfCells()));
	- vtkSmartPointer<vtkFloatArray> newFiberWeights = vtkSmartPointer<vtkFloatArray>::New();
	- newFiberWeights->SetName("FIBER_WEIGHTS");
	- newFiberWeights->SetNumberOfValues(m_NumFibers);
	-
	-#pragma omp parallel for
	- for (int i=0; i<static_cast<int>(m_FiberPolyData->GetNumberOfCells()); i++)
	- {
	-
	- std::vector< vnl_vector_fixed< double, 3 > > vertices;
	- float weight = 1;
	-
	-#pragma omp critical
	- {
	- ++disp;
	- weight = m_FiberWeights->GetValue(i);
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- for (int j=0; j<numPoints; j++)
	- {
	- double cand[3];
	- points->GetPoint(j, cand);
	- vnl_vector_fixed< double, 3 > candV;
	- candV[0]=cand[0]; candV[1]=cand[1]; candV[2]=cand[2];
	- vertices.push_back(candV);
	- }
	- }
	-
	- // calculate curvatures
	- auto numPoints = vertices.size();
	- std::vector< int > removedPoints; removedPoints.resize(numPoints, 0);
	- removedPoints[0]=-1; removedPoints[numPoints-1]=-1;
	-
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	- unsigned int remCounter = 0;
	-
	- bool pointFound = true;
	- while (pointFound)
	- {
	- pointFound = false;
	- double minError = static_cast<double>(error);
	- unsigned int removeIndex = 0;
	-
	- for (unsigned int j=0; j<vertices.size(); j++)
	- {
	- if (removedPoints[j]==0)
	- {
	- vnl_vector_fixed< double, 3 > candV = vertices.at(j);
	-
	- int validP = -1;
	- vnl_vector_fixed< double, 3 > pred;
	- for (int k=static_cast<int>(j)-1; k>=0; k--)
	- if (removedPoints[static_cast<unsigned int>(k)]<=0)
	- {
	- pred = vertices.at(static_cast<unsigned int>(k));
	- validP = k;
	- break;
	- }
	- int validS = -1;
	- vnl_vector_fixed< double, 3 > succ;
	- for (unsigned int k=j+1; k<numPoints; k++)
	- if (removedPoints[k]<=0)
	- {
	- succ = vertices.at(k);
	- validS = static_cast<int>(k);
	- break;
	- }
	-
	- if (validP>=0 && validS>=0)
	- {
	- double a = (candV-pred).magnitude();
	- double b = (candV-succ).magnitude();
	- double c = (pred-succ).magnitude();
	- double s=0.5*(a+b+c);
	- double hc=(2.0/c)sqrt(fabs(s(s-a)(s-b)(s-c)));
	-
	- if (hc<minError)
	- {
	- removeIndex = j;
	- minError = hc;
	- pointFound = true;
	- }
	- }
	- }
	- }
	-
	- if (pointFound)
	- {
	- removedPoints[removeIndex] = 1;
	- remCounter++;
	- }
	- }
	-
	- for (unsigned int j=0; j<numPoints; j++)
	- {
	- if (removedPoints[j]<=0)
	- {
	-#pragma omp critical
	- {
	- vtkIdType id = vtkNewPoints->InsertNextPoint(vertices.at(j).data_block());
	- container->GetPointIds()->InsertNextId(id);
	- }
	- }
	- }
	-
	-#pragma omp critical
	- {
	- newFiberWeights->SetValue(vtkNewCells->GetNumberOfCells(), weight);
	- numRemovedPoints += remCounter;
	- vtkNewCells->InsertNextCell(container);
	- }
	- }
	-
	- if (vtkNewCells->GetNumberOfCells()>0)
	- {
	- MITK_INFO << "Removed points: " << numRemovedPoints;
	- SetFiberWeights(newFiberWeights);
	- m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
	- m_FiberPolyData->SetPoints(vtkNewPoints);
	- m_FiberPolyData->SetLines(vtkNewCells);
	- this->SetFiberPolyData(m_FiberPolyData, true);
	- }
	-}
	-
	-void mitk::FiberBundle::ResampleToNumPoints(unsigned int targetPoints)
	-{
	- if (targetPoints<2)
	- mitkThrow() << "Minimum two points required for resampling!";
	-
	- MITK_INFO << "Resampling fibers (number of points " << targetPoints << ")";
	-
	- bool unequal_fibs = true;
	- while (unequal_fibs)
	- {
	- vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
	- vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
	-
	- vtkSmartPointer<vtkFloatArray> newFiberWeights = vtkSmartPointer<vtkFloatArray>::New();
	- newFiberWeights->SetName("FIBER_WEIGHTS");
	- newFiberWeights->SetNumberOfValues(m_NumFibers);
	-
	- unequal_fibs = false;
	- for (unsigned int i=0; i<m_FiberPolyData->GetNumberOfCells(); i++)
	- {
	-
	- std::vector< vnl_vector_fixed< double, 3 > > vertices;
	- float weight = 1;
	- double seg_len = 0;
	-
	- {
	- weight = m_FiberWeights->GetValue(i);
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- if (numPoints!=targetPoints)
	- seg_len = static_cast<double>(this->GetFiberLength(i)/(targetPoints-1));
	- vtkPoints* points = cell->GetPoints();
	-
	- for (int j=0; j<numPoints; j++)
	- {
	- double cand[3];
	- points->GetPoint(j, cand);
	- vnl_vector_fixed< double, 3 > candV;
	- candV[0]=cand[0]; candV[1]=cand[1]; candV[2]=cand[2];
	- vertices.push_back(candV);
	- }
	- }
	-
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	- vnl_vector_fixed< double, 3 > lastV = vertices.at(0);
	-
	- {
	- vtkIdType id = vtkNewPoints->InsertNextPoint(lastV.data_block());
	- container->GetPointIds()->InsertNextId(id);
	- }
	- for (unsigned int j=1; j<vertices.size(); j++)
	- {
	- vnl_vector_fixed< double, 3 > vec = vertices.at(j) - lastV;
	- double new_dist = vec.magnitude();
	-
	- if (new_dist >= seg_len && seg_len>0)
	- {
	- vnl_vector_fixed< double, 3 > newV = lastV;
	- if ( new_dist-seg_len <= mitk::eps )
	- {
	- vec.normalize();
	- newV += vec * seg_len;
	- }
	- else
	- {
	- // intersection between sphere (radius 'pointDistance', center 'lastV') and line (direction 'd' and point 'p')
	- vnl_vector_fixed< double, 3 > p = vertices.at(j-1);
	- vnl_vector_fixed< double, 3 > d = vertices.at(j) - p;
	-
	- double a = d[0]d[0] + d[1]d[1] + d[2]*d[2];
	- double b = 2 * (d[0] * (p[0] - lastV[0]) + d[1] * (p[1] - lastV[1]) + d[2] * (p[2] - lastV[2]));
	- double c = (p[0] - lastV[0])(p[0] - lastV[0]) + (p[1] - lastV[1])(p[1] - lastV[1]) + (p[2] - lastV[2])(p[2] - lastV[2]) - seg_lenseg_len;
	-
	- double v1 =(-b + std::sqrt(bb-4ac))/(2a);
	- double v2 =(-b - std::sqrt(bb-4ac))/(2a);
	-
	- if (v1>0)
	- newV = p + d * v1;
	- else if (v2>0)
	- newV = p + d * v2;
	- else
	- MITK_INFO << "ERROR1 - linear resampling";
	-
	- j--;
	- }
	-
	-//#pragma omp critical
	- {
	- vtkIdType id = vtkNewPoints->InsertNextPoint(newV.data_block());
	- container->GetPointIds()->InsertNextId(id);
	- }
	- lastV = newV;
	- }
	- else if ( (j==vertices.size()-1 && new_dist>0.0001) \|\| seg_len<=0.0000001)
	- {
	-//#pragma omp critical
	- {
	- vtkIdType id = vtkNewPoints->InsertNextPoint(vertices.at(j).data_block());
	- container->GetPointIds()->InsertNextId(id);
	- }
	- }
	- }
	-
	-//#pragma omp critical
	- {
	- newFiberWeights->SetValue(vtkNewCells->GetNumberOfCells(), weight);
	- vtkNewCells->InsertNextCell(container);
	- if (container->GetNumberOfPoints()!=targetPoints)
	- unequal_fibs = true;
	- }
	- }
	-
	- if (vtkNewCells->GetNumberOfCells()>0)
	- {
	- SetFiberWeights(newFiberWeights);
	- m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
	- m_FiberPolyData->SetPoints(vtkNewPoints);
	- m_FiberPolyData->SetLines(vtkNewCells);
	- this->SetFiberPolyData(m_FiberPolyData, true);
	- }
	- }
	-}
	-
	-void mitk::FiberBundle::ResampleLinear(double pointDistance)
	-{
	- vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
	- vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
	-
	- MITK_INFO << "Resampling fibers (linear)";
	- boost::progress_display disp(static_cast<unsigned long>(m_FiberPolyData->GetNumberOfCells()));
	- vtkSmartPointer<vtkFloatArray> newFiberWeights = vtkSmartPointer<vtkFloatArray>::New();
	- newFiberWeights->SetName("FIBER_WEIGHTS");
	- newFiberWeights->SetNumberOfValues(m_NumFibers);
	-
	- std::vector< vtkSmartPointer<vtkPolyLine> > resampled_streamlines;
	- resampled_streamlines.resize(static_cast<unsigned long>(m_FiberPolyData->GetNumberOfCells()));
	-
	-#pragma omp parallel for
	- for (int i=0; i<static_cast<int>(m_FiberPolyData->GetNumberOfCells()); i++)
	- {
	-
	- std::vector< vnl_vector_fixed< double, 3 > > vertices;
	-
	-#pragma omp critical
	- {
	- ++disp;
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- for (int j=0; j<numPoints; j++)
	- {
	- double cand[3];
	- points->GetPoint(j, cand);
	- vnl_vector_fixed< double, 3 > candV;
	- candV[0]=cand[0]; candV[1]=cand[1]; candV[2]=cand[2];
	- vertices.push_back(candV);
	- }
	- }
	-
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	- vnl_vector_fixed< double, 3 > lastV = vertices.at(0);
	-
	-#pragma omp critical
	- {
	- vtkIdType id = vtkNewPoints->InsertNextPoint(lastV.data_block());
	- container->GetPointIds()->InsertNextId(id);
	- }
	- for (unsigned int j=1; j<vertices.size(); j++)
	- {
	- vnl_vector_fixed< double, 3 > vec = vertices.at(j) - lastV;
	- double new_dist = vec.magnitude();
	-
	- if (new_dist >= pointDistance)
	- {
	- vnl_vector_fixed< double, 3 > newV = lastV;
	- if ( new_dist-pointDistance <= mitk::eps )
	- {
	- vec.normalize();
	- newV += vec * pointDistance;
	- }
	- else
	- {
	- // intersection between sphere (radius 'pointDistance', center 'lastV') and line (direction 'd' and point 'p')
	- vnl_vector_fixed< double, 3 > p = vertices.at(j-1);
	- vnl_vector_fixed< double, 3 > d = vertices.at(j) - p;
	-
	- double a = d[0]d[0] + d[1]d[1] + d[2]*d[2];
	- double b = 2 * (d[0] * (p[0] - lastV[0]) + d[1] * (p[1] - lastV[1]) + d[2] * (p[2] - lastV[2]));
	- double c = (p[0] - lastV[0])(p[0] - lastV[0]) + (p[1] - lastV[1])(p[1] - lastV[1]) + (p[2] - lastV[2])(p[2] - lastV[2]) - pointDistancepointDistance;
	-
	- double v1 =(-b + std::sqrt(bb-4ac))/(2a);
	- double v2 =(-b - std::sqrt(bb-4ac))/(2a);
	-
	- if (v1>0)
	- newV = p + d * v1;
	- else if (v2>0)
	- newV = p + d * v2;
	- else
	- MITK_INFO << "ERROR1 - linear resampling";
	-
	- j--;
	- }
	-
	-#pragma omp critical
	- {
	- vtkIdType id = vtkNewPoints->InsertNextPoint(newV.data_block());
	- container->GetPointIds()->InsertNextId(id);
	- }
	- lastV = newV;
	- }
	- else if (j==vertices.size()-1 && new_dist>0.0001)
	- {
	-#pragma omp critical
	- {
	- vtkIdType id = vtkNewPoints->InsertNextPoint(vertices.at(j).data_block());
	- container->GetPointIds()->InsertNextId(id);
	- }
	- }
	- }
	-
	-#pragma omp critical
	- {
	- resampled_streamlines[static_cast<unsigned int>(i)] = container;
	- }
	- }
	-
	- for (auto container : resampled_streamlines)
	- {
	- vtkNewCells->InsertNextCell(container);
	- }
	-
	- if (vtkNewCells->GetNumberOfCells()>0)
	- {
	- m_FiberPolyData = vtkSmartPointer<vtkPolyData>::New();
	- m_FiberPolyData->SetPoints(vtkNewPoints);
	- m_FiberPolyData->SetLines(vtkNewCells);
	- this->SetFiberPolyData(m_FiberPolyData, true);
	- }
	-}
	-
	-// reapply selected colorcoding in case PolyData structure has changed
	-bool mitk::FiberBundle::Equals(mitk::FiberBundle* fib, double eps)
	-{
	- if (fib==nullptr)
	- {
	- MITK_INFO << "Reference bundle is nullptr!";
	- return false;
	- }
	-
	- if (m_NumFibers!=fib->GetNumFibers())
	- {
	- MITK_INFO << "Unequal number of fibers!";
	- MITK_INFO << m_NumFibers << " vs. " << fib->GetNumFibers();
	- return false;
	- }
	-
	- for (unsigned int i=0; i<m_NumFibers; i++)
	- {
	- vtkCell* cell = m_FiberPolyData->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- vtkCell* cell2 = fib->GetFiberPolyData()->GetCell(i);
	- auto numPoints2 = cell2->GetNumberOfPoints();
	- vtkPoints* points2 = cell2->GetPoints();
	-
	- if (numPoints2!=numPoints)
	- {
	- MITK_INFO << "Unequal number of points in fiber " << i << "!";
	- MITK_INFO << numPoints2 << " vs. " << numPoints;
	- return false;
	- }
	-
	- for (int j=0; j<numPoints; j++)
	- {
	- double* p1 = points->GetPoint(j);
	- double* p2 = points2->GetPoint(j);
	- if (fabs(p1[0]-p2[0])>eps \|\| fabs(p1[1]-p2[1])>eps \|\| fabs(p1[2]-p2[2])>eps)
	- {
	- MITK_INFO << "Unequal points in fiber " << i << " at position " << j << "!";
	- MITK_INFO << "p1: " << p1[0] << ", " << p1[1] << ", " << p1[2];
	- MITK_INFO << "p2: " << p2[0] << ", " << p2[1] << ", " << p2[2];
	- return false;
	- }
	- }
	- }
	-
	- return true;
	-}
	-
	-void mitk::FiberBundle::PrintSelf(std::ostream &os, itk::Indent indent) const
	-{
	- os << this->GetNameOfClass() << ":\n";
	- os << indent << "Number of fibers: " << this->GetNumFibers() << std::endl;
	- os << indent << "Min. fiber length: " << this->GetMinFiberLength() << std::endl;
	- os << indent << "Max. fiber length: " << this->GetMaxFiberLength() << std::endl;
	- os << indent << "Mean fiber length: " << this->GetMeanFiberLength() << std::endl;
	- os << indent << "Median fiber length: " << this->GetMedianFiberLength() << std::endl;
	- os << indent << "STDEV fiber length: " << this->GetLengthStDev() << std::endl;
	- os << indent << "Number of points: " << this->GetNumberOfPoints() << std::endl;
	-
	- os << indent << "Extent x: " << this->GetGeometry()->GetExtentInMM(0) << "mm" << std::endl;
	- os << indent << "Extent y: " << this->GetGeometry()->GetExtentInMM(1) << "mm" << std::endl;
	- os << indent << "Extent z: " << this->GetGeometry()->GetExtentInMM(2) << "mm" << std::endl;
	- os << indent << "Diagonal: " << this->GetGeometry()->GetDiagonalLength() << "mm" << std::endl;
	-
	- if (m_FiberWeights!=nullptr)
	- {
	- std::vector< float > weights;
	- for (int i=0; i<m_FiberWeights->GetSize(); i++)
	- weights.push_back(m_FiberWeights->GetValue(i));
	-
	- std::sort(weights.begin(), weights.end());
	-
	- os << indent << "\nFiber weight statistics" << std::endl;
	- os << indent << "Min: " << weights.front() << std::endl;
	- os << indent << "1% quantile: " << weights.at(static_cast<unsigned long>(weights.size()*0.01)) << std::endl;
	- os << indent << "5% quantile: " << weights.at(static_cast<unsigned long>(weights.size()*0.05)) << std::endl;
	- os << indent << "25% quantile: " << weights.at(static_cast<unsigned long>(weights.size()*0.25)) << std::endl;
	- os << indent << "Median: " << weights.at(static_cast<unsigned long>(weights.size()*0.5)) << std::endl;
	- os << indent << "75% quantile: " << weights.at(static_cast<unsigned long>(weights.size()*0.75)) << std::endl;
	- os << indent << "95% quantile: " << weights.at(static_cast<unsigned long>(weights.size()*0.95)) << std::endl;
	- os << indent << "99% quantile: " << weights.at(static_cast<unsigned long>(weights.size()*0.99)) << std::endl;
	- os << indent << "Max: " << weights.back() << std::endl;
	- }
	- else
	- os << indent << "\n\nNo fiber weight array found." << std::endl;
	-
	- Superclass::PrintSelf(os, indent);
	-}
	-
	-/* ESSENTIAL IMPLEMENTATION OF SUPERCLASS METHODS */
	-void mitk::FiberBundle::UpdateOutputInformation()
	-{
	-
	-}
	-void mitk::FiberBundle::SetRequestedRegionToLargestPossibleRegion()
	-{
	-
	-}
	-bool mitk::FiberBundle::RequestedRegionIsOutsideOfTheBufferedRegion()
	-{
	- return false;
	-}
	-bool mitk::FiberBundle::VerifyRequestedRegion()
	-{
	- return true;
	-}
	-void mitk::FiberBundle::SetRequestedRegion(const itk::DataObject* )
	-{
	-
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundle.h b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundle.h
	deleted file mode 100644
	index 349c199781..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundle.h
	+++ /dev/null
	@@ -1,214 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef _MITK_FiberBundle_H
	-#define _MITK_FiberBundle_H
	-
	-//includes for MITK datastructure
	-#include <mitkBaseData.h>
	-#include <MitkFiberTrackingExports.h>
	-#include <mitkImage.h>
	-#include <mitkDataStorage.h>
	-#include <mitkPlanarFigure.h>
	-#include <mitkPixelTypeTraits.h>
	-#include <mitkPlanarFigureComposite.h>
	-#include <mitkPeakImage.h>
	-
	-//includes storing fiberdata
	-#include <vtkSmartPointer.h>
	-#include <vtkPolyData.h>
	-#include <vtkPoints.h>
	-#include <vtkDataSet.h>
	-#include <vtkTransform.h>
	-#include <vtkFloatArray.h>
	-#include <itkScalableAffineTransform.h>
	-#include <mitkDiffusionFunctionCollection.h>
	-
	-namespace mitk {
	-
	-/**
	- * \brief Base Class for Fiber Bundles; */
	-class MITKFIBERTRACKING_EXPORT FiberBundle : public BaseData
	-{
	-public:
	-
	- typedef itk::Image<unsigned char, 3> ItkUcharImgType;
	-
	- // fiber colorcodings
	- static const char* FIBER_ID_ARRAY;
	-
	- void UpdateOutputInformation() override;
	- void SetRequestedRegionToLargestPossibleRegion() override;
	- bool RequestedRegionIsOutsideOfTheBufferedRegion() override;
	- bool VerifyRequestedRegion() override;
	- void SetRequestedRegion(const itk::DataObject*) override;
	-
	- mitkClassMacro( FiberBundle, BaseData )
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- mitkNewMacro1Param(Self, vtkSmartPointer<vtkPolyData>) // custom constructor
	-
	- // colorcoding related methods
	- void ColorFibersByFiberWeights(bool opacity, bool normalize);
	- void ColorFibersByCurvature(bool opacity, bool normalize);
	- void ColorFibersByLength(bool opacity, bool normalize);
	- void ColorFibersByScalarMap(mitk::Image::Pointer, bool opacity, bool normalize);
	- template <typename TPixel>
	- void ColorFibersByScalarMap(const mitk::PixelType pixelType, mitk::Image::Pointer, bool opacity, bool normalize);
	- void ColorFibersByOrientation();
	- void SetFiberOpacity(vtkDoubleArray *FAValArray);
	- void ResetFiberOpacity();
	- void SetFiberColors(vtkSmartPointer<vtkUnsignedCharArray> fiberColors);
	- void SetFiberColors(float r, float g, float b, float alpha=255);
	- vtkSmartPointer<vtkUnsignedCharArray> GetFiberColors() const { return m_FiberColors; }
	-
	- // fiber compression
	- void Compress(float error = 0.0);
	-
	- // fiber resampling
	- void ResampleSpline(float pointDistance=1);
	- void ResampleSpline(float pointDistance, double tension, double continuity, double bias );
	- void ResampleLinear(double pointDistance=1);
	- void ResampleToNumPoints(unsigned int targetPoints);
	-
	- mitk::FiberBundle::Pointer FilterByWeights(float weight_thr, bool invert=false);
	- bool RemoveShortFibers(float lengthInMM);
	- bool RemoveLongFibers(float lengthInMM);
	- bool ApplyCurvatureThreshold(float minRadius, bool deleteFibers);
	- void MirrorFibers(unsigned int axis);
	- void RotateAroundAxis(double x, double y, double z);
	- void TranslateFibers(double x, double y, double z);
	- void ScaleFibers(double x, double y, double z, bool subtractCenter=true);
	- void TransformFibers(double rx, double ry, double rz, double tx, double ty, double tz);
	- void TransformFibers(itk::ScalableAffineTransform< mitk::ScalarType >::Pointer transform);
	- void RemoveDir(vnl_vector_fixed<double,3> dir, double threshold);
	-
	- template< class TType=float >
	- void TransformPoint(itk::Point<TType, 3>& point, itk::Matrix< TType, 3, 3>& rot, TType& tx, TType& ty, TType& tz)
	- {
	- mitk::Point3D center = this->GetGeometry()->GetCenter();
	-
	- point[0] -= center[0];
	- point[1] -= center[1];
	- point[2] -= center[2];
	- point = rot*point;
	- point[0] += center[0]+tx;
	- point[1] += center[1]+ty;
	- point[2] += center[2]+tz;
	- }
	-
	- template< class TType=float >
	- void TransformPoint(itk::Point<TType, 3>& point, TType rx, TType ry, TType rz, TType tx, TType ty, TType tz)
	- {
	- auto rot = mitk::imv::GetRotationMatrixItk<TType>(rx, ry, rz);
	- mitk::Point3D center = this->GetGeometry()->GetCenter();
	-
	- point[0] -= center[0];
	- point[1] -= center[1];
	- point[2] -= center[2];
	- point = rot*point;
	- point[0] += center[0]+tx;
	- point[1] += center[1]+ty;
	- point[2] += center[2]+tz;
	- }
	-
	- itk::Matrix< double, 3, 3 > TransformMatrix(itk::Matrix< double, 3, 3 > m, double rx, double ry, double rz);
	-
	- // add/subtract fibers
	- FiberBundle::Pointer AddBundle(FiberBundle* fib);
	- mitk::FiberBundle::Pointer AddBundles(std::vector< mitk::FiberBundle::Pointer > fibs);
	- FiberBundle::Pointer SubtractBundle(FiberBundle* fib);
	-
	- // fiber subset extraction
	- FiberBundle::Pointer ExtractFiberSubset(DataNode roi, DataStorage storage);
	- std::vector<unsigned int> ExtractFiberIdSubset(DataNode* roi, DataStorage* storage);
	- FiberBundle::Pointer RemoveFibersOutside(ItkUcharImgType* mask, bool invert=false);
	- float GetOverlap(ItkUcharImgType* mask);
	- std::tuple<float, float> GetDirectionalOverlap(ItkUcharImgType* mask, mitk::PeakImage::ItkPeakImageType* peak_image);
	- float GetNumEpFractionInMask(ItkUcharImgType* mask, bool different_label);
	- mitk::FiberBundle::Pointer SubsampleFibers(float factor, bool random_seed);
	-
	- // get/set data
	- float GetFiberLength(unsigned int index) const { return m_FiberLengths.at(index); }
	- vtkSmartPointer<vtkFloatArray> GetFiberWeights() const { return m_FiberWeights; }
	- float GetFiberWeight(unsigned int fiber) const;
	- void SetFiberWeights(float newWeight);
	- void SetFiberWeight(unsigned int fiber, float weight);
	- void SetFiberWeights(vtkSmartPointer<vtkFloatArray> weights);
	- void SetFiberPolyData(vtkSmartPointer<vtkPolyData>, bool updateGeometry = true);
	- vtkSmartPointer<vtkPolyData> GetFiberPolyData() const;
	- itkGetConstMacro( NumFibers, unsigned int)
	- //itkGetMacro( FiberSampling, int)
	- itkGetConstMacro( MinFiberLength, float )
	- itkGetConstMacro( MaxFiberLength, float )
	- itkGetConstMacro( MeanFiberLength, float )
	- itkGetConstMacro( MedianFiberLength, float )
	- itkGetConstMacro( LengthStDev, float )
	- itkGetConstMacro( UpdateTime2D, itk::TimeStamp )
	- itkGetConstMacro( UpdateTime3D, itk::TimeStamp )
	- void RequestUpdate2D(){ m_UpdateTime2D.Modified(); }
	- void RequestUpdate3D(){ m_UpdateTime3D.Modified(); }
	- void RequestUpdate(){ m_UpdateTime2D.Modified(); m_UpdateTime3D.Modified(); }
	-
	- unsigned int GetNumberOfPoints() const;
	-
	- // copy fiber bundle
	- mitk::FiberBundle::Pointer GetDeepCopy();
	-
	- // compare fiber bundles
	- bool Equals(FiberBundle* fib, double eps=0.01);
	-
	- itkSetMacro( ReferenceGeometry, mitk::BaseGeometry::Pointer )
	- itkGetConstMacro( ReferenceGeometry, mitk::BaseGeometry::Pointer )
	-
	- vtkSmartPointer<vtkPolyData> GeneratePolyDataByIds(std::vector<unsigned int> fiberIds, vtkSmartPointer<vtkFloatArray> weights);
	-
	-protected:
	-
	- FiberBundle( vtkPolyData* fiberPolyData = nullptr );
	- ~FiberBundle() override;
	-
	- void GenerateFiberIds();
	- void UpdateFiberGeometry();
	- void PrintSelf(std::ostream &os, itk::Indent indent) const override;
	-
	-private:
	-
	- // actual fiber container
	- vtkSmartPointer<vtkPolyData> m_FiberPolyData;
	-
	- // contains fiber ids
	- vtkSmartPointer<vtkDataSet> m_FiberIdDataSet;
	-
	- unsigned int m_NumFibers;
	-
	- vtkSmartPointer<vtkUnsignedCharArray> m_FiberColors;
	- vtkSmartPointer<vtkFloatArray> m_FiberWeights;
	- std::vector< float > m_FiberLengths;
	- float m_MinFiberLength;
	- float m_MaxFiberLength;
	- float m_MeanFiberLength;
	- float m_MedianFiberLength;
	- float m_LengthStDev;
	- itk::TimeStamp m_UpdateTime2D;
	- itk::TimeStamp m_UpdateTime3D;
	- mitk::BaseGeometry::Pointer m_ReferenceGeometry;
	-};
	-
	-} // namespace mitk
	-
	-#endif /* _MITK_FiberBundle_H */
	diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundleSource.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundleSource.cpp
	deleted file mode 100644
	index 15dbbee88a..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundleSource.cpp
	+++ /dev/null
	@@ -1,34 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#include "mitkOdfImageSource.h"
	-
	-
	-mitk::OdfImageSource::OdfImageSource()
	-{
	- // Create the output. We use static_cast<> here because we know the default
	- // output must be of type TOutputImage
	- OutputImageType::Pointer output
	- = static_cast<OutputImageType*>(this->MakeOutput(0).GetPointer());
	- Superclass::SetNumberOfRequiredOutputs(1);
	- Superclass::SetNthOutput(0, output.GetPointer());
	-}
	-
	-mitk::OdfImageSource::DataObjectPointer mitk::OdfImageSource::MakeOutput( unsigned int /idx/ )
	-{
	- return static_cast<itk::DataObject*>(OutputImageType::New().GetPointer());
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundleSource.h b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundleSource.h
	deleted file mode 100644
	index 7993aa54a2..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundleSource.h
	+++ /dev/null
	@@ -1,52 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef OdfImageSource_H_HEADER_INCLUDED_C1E7D6EC
	-#define OdfImageSource_H_HEADER_INCLUDED_C1E7D6EC
	-
	-#include "mitkImageSource.h"
	-#include "mitkOdfImage.h"
	-
	-//NOTE>umbenennen .. ableiten von DataSource
	-
	-
	-namespace mitk {
	-
	-class OdfImageSource : public ImageSource
	-{
	-public:
	-
	- typedef mitk::OdfImage OutputImageType;
	- typedef OutputImageType::Pointer OutputImagePointer;
	- typedef SlicedData::RegionType OutputImageRegionType;
	- typedef itk::DataObject::Pointer DataObjectPointer;
	-
	- mitkClassMacro(OdfImageSource,ImageSource);
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- virtual DataObjectPointer MakeOutput(DataObjectPointerArraySizeType idx);
	-
	-protected:
	- OdfImageSource();
	- virtual ~OdfImageSource() {}
	-
	-};
	-
	-} // namespace mitk
	-
	-#endif /* OdfImageSource_H_HEADER_INCLUDED_C1E7D6EC */
	diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundleThreadMonitor.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundleThreadMonitor.cpp
	deleted file mode 100644
	index 3aa3cbf85f..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundleThreadMonitor.cpp
	+++ /dev/null
	@@ -1,254 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#include "mitkFiberBundleThreadMonitor.h"
	-
	-
	-
	-mitk::FiberBundleThreadMonitor::FiberBundleThreadMonitor()
	-: m_monitorBracketOpen("[")
	-, m_monitorBracketClose("]")
	-, m_monitorHeading("Monitoring Fiberprocessing Threads")
	-, m_monitorMask("Thread Status:\nStarted: Finished: Terminated:")
	-, m_monitorStatus("_initialized")
	-, m_monitorStarted(0)
	-, m_monitorFinished(0)
	-, m_monitorTerminated(0)
	-{
	- m_monitorBracketOpenPosition[0] = 0;
	- m_monitorBracketOpenPosition[1] = 0;
	- m_monitorBracketClosePosition[0] = 0;
	- m_monitorBracketClosePosition[1] = 0;
	- m_monitorHeadingPosition[0] = 0;
	- m_monitorHeadingPosition[1] = 0;
	- m_monitorMaskPosition[0] = 0;
	- m_monitorMaskPosition[1] = 0;
	- m_monitorStatusPosition[0] = 0;
	- m_monitorStatusPosition[1] = 0;
	- m_monitorStartedPosition[0] = 0;
	- m_monitorStartedPosition[1] = 0;
	- m_monitorFinishedPosition[0] = 0;
	- m_monitorFinishedPosition[1] = 0;
	- m_monitorTerminatedPosition[0] = 0;
	- m_monitorTerminatedPosition[1] = 0;
	-
	-
	- m_monitorHeadingOpacity = 0;
	- m_monitorMaskOpacity = 0;
	- m_monitorTerminatedOpacity = 0;
	- m_monitorFinishedOpacity = 0;
	- m_monitorStartedOpacity = 0;
	- m_monitorStatusOpacity = 0;
	-}
	-
	-mitk::FiberBundleThreadMonitor::~FiberBundleThreadMonitor()
	-{
	-
	-}
	-
	-
	-QString mitk::FiberBundleThreadMonitor::getBracketOpen(){
	- return m_monitorBracketOpen;
	-}
	-mitk::Point2D mitk::FiberBundleThreadMonitor::getBracketOpenPosition(){
	- return m_monitorBracketOpenPosition;
	-}
	-void mitk::FiberBundleThreadMonitor::setBracketOpenPosition(mitk::Point2D pnt){
	- m_monitorBracketOpenPosition[0] = pnt[0];
	- m_monitorBracketOpenPosition[1] = pnt[1];
	-}
	-
	-
	-
	-
	-QString mitk::FiberBundleThreadMonitor::getBracketClose(){
	- return m_monitorBracketClose;
	-}
	-mitk::Point2D mitk::FiberBundleThreadMonitor::getBracketClosePosition(){
	- return m_monitorBracketClosePosition;
	-}
	-void mitk::FiberBundleThreadMonitor::setBracketClosePosition(mitk::Point2D pnt){
	- m_monitorBracketClosePosition[0] = pnt[0];
	- m_monitorBracketClosePosition[1] = pnt[1];
	-}
	-
	-
	-
	-QString mitk::FiberBundleThreadMonitor::getHeading(){
	- return m_monitorHeading;
	-}
	-mitk::Point2D mitk::FiberBundleThreadMonitor::getHeadingPosition(){
	- return m_monitorHeadingPosition;
	-}
	-void mitk::FiberBundleThreadMonitor::setHeadingPosition(mitk::Point2D pnt){
	- m_monitorHeadingPosition[0] = pnt[0];
	- m_monitorHeadingPosition[1] = pnt[1];
	-}
	-int mitk::FiberBundleThreadMonitor::getHeadingOpacity(){
	- return m_monitorHeadingOpacity;
	-}
	-void mitk::FiberBundleThreadMonitor::setHeadingOpacity(int opacity){
	- m_monitorHeadingOpacity = opacity;
	-}
	-
	-
	-
	-
	-QString mitk::FiberBundleThreadMonitor::getMask(){
	- return m_monitorMask;
	-}
	-mitk::Point2D mitk::FiberBundleThreadMonitor::getMaskPosition(){
	- return m_monitorMaskPosition;
	-}
	-void mitk::FiberBundleThreadMonitor::setMaskPosition(mitk::Point2D pnt){
	- m_monitorMaskPosition[0] = pnt[0];
	- m_monitorMaskPosition[1] = pnt[1];
	-}
	-int mitk::FiberBundleThreadMonitor::getMaskOpacity(){
	- return m_monitorMaskOpacity;
	-}
	-void mitk::FiberBundleThreadMonitor::setMaskOpacity(int opacity){
	- m_monitorMaskOpacity = opacity;
	-}
	-
	-
	-
	-
	-
	-QString mitk::FiberBundleThreadMonitor::getStatus(){
	- return m_monitorStatus;
	-}
	-void mitk::FiberBundleThreadMonitor::setStatus(QString status){
	- m_statusMutex.lock();
	- m_monitorStatus = status;
	- m_statusMutex.unlock();
	-}
	-mitk::Point2D mitk::FiberBundleThreadMonitor::getStatusPosition(){
	- return m_monitorStatusPosition;
	-}
	-void mitk::FiberBundleThreadMonitor::setStatusPosition(mitk::Point2D pnt){
	- m_monitorStatusPosition[0] = pnt[0];
	- m_monitorStatusPosition[1] = pnt[1];
	-}
	-int mitk::FiberBundleThreadMonitor::getStatusOpacity(){
	- return m_monitorStatusOpacity;
	-}
	-void mitk::FiberBundleThreadMonitor::setStatusOpacity(int opacity){
	- m_monitorStatusOpacity = opacity;
	-}
	-
	-
	-int mitk::FiberBundleThreadMonitor::getStarted(){
	- return m_monitorStarted;
	-}
	-/* is thread safe :) */
	-void mitk::FiberBundleThreadMonitor::setStarted(int val)
	-{
	- m_startedMutex.lock();
	- m_monitorStarted = val;
	- m_startedMutex.unlock();
	-}
	-mitk::Point2D mitk::FiberBundleThreadMonitor::getStartedPosition(){
	- return m_monitorStartedPosition;
	-}
	-void mitk::FiberBundleThreadMonitor::setStartedPosition(mitk::Point2D pnt){
	- m_monitorStartedPosition[0] = pnt[0];
	- m_monitorStartedPosition[1] = pnt[1];
	-}
	-int mitk::FiberBundleThreadMonitor::getStartedOpacity(){
	- return m_monitorStartedOpacity;
	-}
	-void mitk::FiberBundleThreadMonitor::setStartedOpacity(int opacity){
	- m_monitorStartedOpacity = opacity;
	-}
	-
	-
	-
	-
	-int mitk::FiberBundleThreadMonitor::getFinished(){
	- return m_monitorFinished;
	-}
	-void mitk::FiberBundleThreadMonitor::setFinished(int val)
	-{
	- m_finishedMutex.lock();
	- m_monitorFinished = val;
	- m_finishedMutex.unlock();
	-}
	-mitk::Point2D mitk::FiberBundleThreadMonitor::getFinishedPosition(){
	- return m_monitorFinishedPosition;
	-}
	-void mitk::FiberBundleThreadMonitor::setFinishedPosition(mitk::Point2D pnt){
	- m_monitorFinishedPosition[0] = pnt[0];
	- m_monitorFinishedPosition[1] = pnt[1];
	-}
	-int mitk::FiberBundleThreadMonitor::getFinishedOpacity(){
	- return m_monitorFinishedOpacity;
	-}
	-void mitk::FiberBundleThreadMonitor::setFinishedOpacity(int opacity){
	- m_monitorFinishedOpacity = opacity;
	-}
	-
	-
	-
	-
	-int mitk::FiberBundleThreadMonitor::getTerminated(){
	- return m_monitorTerminated;
	-}
	-void mitk::FiberBundleThreadMonitor::setTerminated(int val)
	-{
	- m_terminatedMutex.lock();
	- m_monitorTerminated = val;
	- m_terminatedMutex.unlock();
	-}
	-mitk::Point2D mitk::FiberBundleThreadMonitor::getTerminatedPosition(){
	- return m_monitorTerminatedPosition;
	-}
	-void mitk::FiberBundleThreadMonitor::setTerminatedPosition(mitk::Point2D pnt){
	- m_monitorTerminatedPosition[0] = pnt[0];
	- m_monitorTerminatedPosition[1] = pnt[1];
	-}
	-int mitk::FiberBundleThreadMonitor::getTerminatedOpacity(){
	- return m_monitorTerminatedOpacity;
	-}
	-void mitk::FiberBundleThreadMonitor::setTerminatedOpacity(int opacity){
	- m_monitorTerminatedOpacity = opacity;
	-}
	-
	-
	-
	-/* ESSENTIAL IMPLEMENTATION OF SUPERCLASS METHODS */
	-void mitk::FiberBundleThreadMonitor::UpdateOutputInformation()
	-{
	-
	-}
	-void mitk::FiberBundleThreadMonitor::SetRequestedRegionToLargestPossibleRegion()
	-{
	-
	-}
	-bool mitk::FiberBundleThreadMonitor::RequestedRegionIsOutsideOfTheBufferedRegion()
	-{
	- return false;
	-}
	-bool mitk::FiberBundleThreadMonitor::VerifyRequestedRegion()
	-{
	- return true;
	-}
	-void mitk::FiberBundleThreadMonitor::SetRequestedRegion(const itk::DataObject *data )
	-{
	-
	-}
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundleThreadMonitor.h b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundleThreadMonitor.h
	deleted file mode 100644
	index ba718a9ed9..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundleThreadMonitor.h
	+++ /dev/null
	@@ -1,154 +0,0 @@
	-
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_FiberBundleThreadMonitor_H
	-#define _MITK_FiberBundleThreadMonitor_H
	-
	-//includes for MITK datastructure
	-#include "mitkBaseData.h"
	-#include <MitkFiberTrackingExports.h>
	-#include <QString>
	-
	-#include <QMutex>
	-
	-
	-namespace mitk {
	-
	- /**
	- * \brief Base Class for Fiber Bundles; */
	- class MITKFIBERTRACKING_EXPORT FiberBundleThreadMonitor : public BaseData
	- {
	-
	- public:
	-
	- // ======virtual methods must have======
	- virtual void UpdateOutputInformation();
	- virtual void SetRequestedRegionToLargestPossibleRegion();
	- virtual bool RequestedRegionIsOutsideOfTheBufferedRegion();
	- virtual bool VerifyRequestedRegion();
	- virtual void SetRequestedRegion(const itk::DataObject *data );
	- //=======================================
	-
	- mitkClassMacro( FiberBundleThreadMonitor, BaseData );
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	-
	- void setTextL1(QString);
	- QString getTextL1();
	-
	- QString getBracketOpen();
	- mitk::Point2D getBracketOpenPosition();
	- void setBracketOpenPosition(mitk::Point2D);
	- int getBracketOpenOpacity(); // range 0 - 10, multiplicationfactor 0.1 (in mapper)
	-
	- QString getBracketClose();
	- mitk::Point2D getBracketClosePosition();
	- void setBracketClosePosition(mitk::Point2D);
	- int getBracketCloseOpacity(); // range 0 - 10, multiplicationfactor 0.1 (in mapper)
	-
	- QString getHeading();
	- mitk::Point2D getHeadingPosition();
	- void setHeadingPosition(mitk::Point2D);
	- int getHeadingOpacity(); // range 0 - 10, multiplicationfactor 0.1 (in mapper)
	- void setHeadingOpacity(int);
	-
	- QString getMask();
	- mitk::Point2D getMaskPosition();
	- void setMaskPosition(mitk::Point2D);
	- int getMaskOpacity(); // multiplicationfactor 0.1 (in mapper)
	- void setMaskOpacity(int);
	-
	- QString getStatus();
	- void setStatus(QString);
	- mitk::Point2D getStatusPosition();
	- void setStatusPosition(mitk::Point2D);
	- int getStatusOpacity(); // multiplicationfactor 0.1 (in mapper)
	- void setStatusOpacity(int);
	-
	- int getStarted();
	- void setStarted(int);
	- mitk::Point2D getStartedPosition();
	- void setStartedPosition(mitk::Point2D);
	- int getStartedOpacity(); // multiplicationfactor 0.1 (in mapper)
	- void setStartedOpacity(int);
	-
	- int getFinished();
	- void setFinished(int);
	- mitk::Point2D getFinishedPosition();
	- void setFinishedPosition(mitk::Point2D);
	- int getFinishedOpacity(); // multiplicationfactor 0.1 (in mapper)
	- void setFinishedOpacity(int);
	-
	- int getTerminated();
	- void setTerminated(int);
	- mitk::Point2D getTerminatedPosition();
	- void setTerminatedPosition(mitk::Point2D);
	- int getTerminatedOpacity(); // multiplicationfactor 0.1 (in mapper)
	- void setTerminatedOpacity(int);
	-
	-
	- protected:
	- FiberBundleThreadMonitor();
	- virtual ~FiberBundleThreadMonitor();
	-
	-
	- private:
	- QString m_monitorBracketOpen;
	- mitk::Point2D m_monitorBracketOpenPosition;
	-
	- QString m_monitorBracketClose;
	- mitk::Point2D m_monitorBracketClosePosition;
	-
	- QString m_monitorHeading;
	- mitk::Point2D m_monitorHeadingPosition;
	- int m_monitorHeadingOpacity;
	-
	- QString m_monitorMask;
	- mitk::Point2D m_monitorMaskPosition;
	- int m_monitorMaskOpacity;
	-
	- QString m_monitorStatus;
	- mitk::Point2D m_monitorStatusPosition;
	- int m_monitorStatusOpacity;
	-
	- int m_monitorStarted;
	- mitk::Point2D m_monitorStartedPosition;
	- int m_monitorStartedOpacity;
	-
	- int m_monitorFinished;
	- mitk::Point2D m_monitorFinishedPosition;
	- int m_monitorFinishedOpacity;
	-
	- int m_monitorTerminated;
	- mitk::Point2D m_monitorTerminatedPosition;
	- int m_monitorTerminatedOpacity;
	-
	- QMutex m_startedMutex;
	- QMutex m_finishedMutex;
	- QMutex m_terminatedMutex;
	- QMutex m_statusMutex;
	-
	-
	-
	-
	-
	- };
	-
	-} // namespace mitk
	-
	-#endif /* _MITK_FiberBundle_H */
	diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkTrackvis.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkTrackvis.cpp
	deleted file mode 100644
	index e659c92ee0..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkTrackvis.cpp
	+++ /dev/null
	@@ -1,241 +0,0 @@
	-#include <mitkTrackvis.h>
	-#include <vtkTransformPolyDataFilter.h>
	-
	-TrackVisFiberReader::TrackVisFiberReader() { m_Filename = ""; m_FilePointer = nullptr; }
	-
	-TrackVisFiberReader::~TrackVisFiberReader() { if (m_FilePointer) fclose( m_FilePointer ); }
	-
	-
	-// Create a TrackVis file and store standard metadata. The file is ready to append fibers.
	-// ---------------------------------------------------------------------------------------
	-short TrackVisFiberReader::create(std::string filename , const mitk::FiberBundle *fib, bool lps)
	-{
	- // prepare the header
	- for(int i=0; i<3 ;i++)
	- {
	- if (fib->GetReferenceGeometry().IsNotNull())
	- {
	- m_Header.dim[i] = fib->GetReferenceGeometry()->GetExtent(i);
	- m_Header.voxel_size[i] = fib->GetReferenceGeometry()->GetSpacing()[i];
	- m_Header.origin[i] = fib->GetReferenceGeometry()->GetOrigin()[i];
	- }
	- else
	- {
	- m_Header.dim[i] = fib->GetGeometry()->GetExtent(i);
	- m_Header.voxel_size[i] = fib->GetGeometry()->GetSpacing()[i];
	- m_Header.origin[i] = fib->GetGeometry()->GetOrigin()[i];
	- }
	- }
	- m_Header.n_scalars = 0;
	- m_Header.n_properties = 0;
	- if (lps)
	- sprintf(m_Header.voxel_order,"LPS");
	- else
	- sprintf(m_Header.voxel_order,"RAS");
	- m_Header.image_orientation_patient[0] = 1.0;
	- m_Header.image_orientation_patient[1] = 0.0;
	- m_Header.image_orientation_patient[2] = 0.0;
	- m_Header.image_orientation_patient[3] = 0.0;
	- m_Header.image_orientation_patient[4] = 1.0;
	- m_Header.image_orientation_patient[5] = 0.0;
	- m_Header.pad1[0] = 0;
	- m_Header.pad1[1] = 0;
	- m_Header.pad2[0] = 0;
	- m_Header.pad2[1] = 0;
	- m_Header.invert_x = 0;
	- m_Header.invert_y = 0;
	- m_Header.invert_z = 0;
	- m_Header.swap_xy = 0;
	- m_Header.swap_yz = 0;
	- m_Header.swap_zx = 0;
	- m_Header.n_count = 0;
	- m_Header.version = 1;
	- m_Header.hdr_size = 1000;
	-
	- // write the header to the file
	- m_FilePointer = fopen(filename.c_str(),"w+b");
	- if (m_FilePointer == nullptr)
	- {
	- printf("[ERROR] Unable to create file '%s'\n",filename.c_str());
	- return 0;
	- }
	- sprintf(m_Header.id_string,"TRACK");
	- if (fwrite((char*)&m_Header, 1, 1000, m_FilePointer) != 1000)
	- MITK_ERROR << "TrackVis::create : Error occurding during writing fiber.";
	-
	- this->m_Filename = filename;
	-
	- return 1;
	-}
	-
	-
	-// Open an existing TrackVis file and read metadata information.
	-// The file pointer is positiond at the beginning of fibers data
	-// -------------------------------------------------------------
	-short TrackVisFiberReader::open( std::string filename )
	-{
	- m_FilePointer = std::fopen(filename.c_str(), "rb");
	- if (m_FilePointer == nullptr)
	- {
	- printf("[ERROR] Unable to open file '%s'\n",filename.c_str());
	- return 0;
	- }
	- this->m_Filename = filename;
	-
	- return fread((char*)(&m_Header), 1, 1000, m_FilePointer);
	-}
	-
	-
	-
	-// Append a fiber to the file
	-// --------------------------
	-short TrackVisFiberReader::append(const mitk::FiberBundle *fib)
	-{
	- vtkPolyData* poly = fib->GetFiberPolyData();
	- for (unsigned int i=0; i<fib->GetNumFibers(); i++)
	- {
	- vtkCell* cell = poly->GetCell(i);
	- int numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- unsigned int numSaved, pos = 0;
	- //float* tmp = new float[3*maxSteps];
	- std::vector< float > tmp;
	- tmp.reserve(3*numPoints);
	-
	- numSaved = numPoints;
	- for(unsigned int i=0; i<numSaved ;i++)
	- {
	- double* p = points->GetPoint(i);
	-
	- tmp[pos++] = p[0];
	- tmp[pos++] = p[1];
	- tmp[pos++] = p[2];
	- }
	-
	- // write the coordinates to the file
	- if ( fwrite((char*)&numSaved, 1, 4, m_FilePointer) != 4 )
	- {
	- printf( "[ERROR] Problems saving the fiber!\n" );
	- return 1;
	- }
	- if ( fwrite((char)&(tmp.front()), 1, 4pos, m_FilePointer) != 4*pos )
	- {
	- printf( "[ERROR] Problems saving the fiber!\n" );
	- return 1;
	- }
	- }
	-
	- return 0;
	-}
	-
	-//// Read one fiber from the file
	-//// ----------------------------
	-short TrackVisFiberReader::read( mitk::FiberBundle* fib )
	-{
	- int numPoints;
	- vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
	- vtkSmartPointer<vtkCellArray> vtkNewCells = vtkSmartPointer<vtkCellArray>::New();
	-
	- while (fread((char*)&numPoints, 1, 4, m_FilePointer)==4)
	- {
	- if ( numPoints <= 0 )
	- {
	- printf( "[ERROR] Trying to read a fiber with %d points!\n", numPoints );
	- return -1;
	- }
	- vtkSmartPointer<vtkPolyLine> container = vtkSmartPointer<vtkPolyLine>::New();
	-
	- float tmp[3];
	- for(int i=0; i<numPoints; i++)
	- {
	- if (fread((char*)tmp, 1, 12, m_FilePointer) == 0)
	- MITK_ERROR << "TrackVis::read: Error during read.";
	-
	- vtkIdType id = vtkNewPoints->InsertNextPoint(tmp);
	- container->GetPointIds()->InsertNextId(id);
	- }
	- vtkNewCells->InsertNextCell(container);
	- }
	-
	- vtkSmartPointer<vtkPolyData> fiberPolyData = vtkSmartPointer<vtkPolyData>::New();
	- fiberPolyData->SetPoints(vtkNewPoints);
	- fiberPolyData->SetLines(vtkNewCells);
	-
	- // MITK_INFO << "Coordinate convention: " << m_Header.voxel_order;
	-
	- mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New();
	- vtkSmartPointer< vtkMatrix4x4 > matrix = vtkSmartPointer< vtkMatrix4x4 >::New();
	- matrix->Identity();
	-
	- if (m_Header.voxel_order[0]=='R')
	- matrix->SetElement(0,0,-matrix->GetElement(0,0));
	- if (m_Header.voxel_order[1]=='A')
	- matrix->SetElement(1,1,-matrix->GetElement(1,1));
	- if (m_Header.voxel_order[2]=='I')
	- matrix->SetElement(2,2,-matrix->GetElement(2,2));
	-
	- geometry->SetIndexToWorldTransformByVtkMatrix(matrix);
	-
	- vtkSmartPointer<vtkTransformPolyDataFilter> transformFilter = vtkSmartPointer<vtkTransformPolyDataFilter>::New();
	- transformFilter->SetInputData(fiberPolyData);
	- transformFilter->SetTransform(geometry->GetVtkTransform());
	- transformFilter->Update();
	- fib->SetFiberPolyData(transformFilter->GetOutput());
	-
	- mitk::Point3D origin;
	- origin[0]=m_Header.origin[0];
	- origin[1]=m_Header.origin[1];
	- origin[2]=m_Header.origin[2];
	- geometry->SetOrigin(origin);
	-
	- mitk::Vector3D spacing;
	- spacing[0]=m_Header.voxel_size[0];
	- spacing[1]=m_Header.voxel_size[1];
	- spacing[2]=m_Header.voxel_size[2];
	-
	- if (spacing[0]>0 && spacing[1]>0 && spacing[2]>0 && m_Header.dim[0]>0 && m_Header.dim[1]>0 && m_Header.dim[2]>0)
	- {
	- geometry->SetSpacing(spacing);
	- geometry->SetExtentInMM(0, m_Header.voxel_size[0]*m_Header.dim[0]);
	- geometry->SetExtentInMM(1, m_Header.voxel_size[1]*m_Header.dim[1]);
	- geometry->SetExtentInMM(2, m_Header.voxel_size[2]*m_Header.dim[2]);
	- fib->SetReferenceGeometry(dynamic_cast<mitk::BaseGeometry*>(geometry.GetPointer()));
	- }
	- return numPoints;
	-}
	-
	-
	-
	-// Update the field in the header to the new FIBER TOTAL.
	-// ------------------------------------------------------
	-void TrackVisFiberReader::updateTotal( int totFibers )
	-{
	- fseek(m_FilePointer, 1000-12, SEEK_SET);
	- if (fwrite((char*)&totFibers, 1, 4, m_FilePointer) != 4)
	- MITK_ERROR << "[ERROR] Problems saving the fiber!";
	-}
	-
	-
	-void TrackVisFiberReader::writeHdr()
	-{
	- fseek(m_FilePointer, 0, SEEK_SET);
	- if (fwrite((char*)&m_Header, 1, 1000, m_FilePointer) != 1000)
	- MITK_ERROR << "[ERROR] Problems saving the fiber!";
	-}
	-
	-
	-// Close the TrackVis file, but keep the metadata in the header.
	-// -------------------------------------------------------------
	-void TrackVisFiberReader::close()
	-{
	- fclose(m_FilePointer);
	- m_FilePointer = nullptr;
	-}
	-
	-bool TrackVisFiberReader::IsTransformValid()
	-{
	- if (fabs(m_Header.image_orientation_patient[0])<=0.001 \|\| fabs(m_Header.image_orientation_patient[3])<=0.001 \|\| fabs(m_Header.image_orientation_patient[5])<=0.001)
	- return false;
	- return true;
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkTrackvis.h b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkTrackvis.h
	deleted file mode 100644
	index 513b0a5ca5..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkTrackvis.h
	+++ /dev/null
	@@ -1,80 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef _TRACKVIS
	-#define _TRACKVIS
	-
	-#include <mitkCommon.h>
	-#include <mitkFiberBundle.h>
	-#include <vtkSmartPointer.h>
	-#include <vtkPolyData.h>
	-#include <vtkCellArray.h>
	-#include <vtkPoints.h>
	-#include <vtkPolyLine.h>
	-#include <itkSize.h>
	-
	-// Structure to hold metadata of a TrackVis file
	-// ---------------------------------------------
	-struct TrackVis_header
	-{
	- char id_string[6];
	- short int dim[3];
	- float voxel_size[3];
	- float origin[3];
	- short int n_scalars;
	- char scalar_name[10][20];
	- short int n_properties;
	- char property_name[10][20];
	- char reserved[508];
	- char voxel_order[4];
	- char pad2[4];
	- float image_orientation_patient[6];
	- char pad1[2];
	- unsigned char invert_x;
	- unsigned char invert_y;
	- unsigned char invert_z;
	- unsigned char swap_xy;
	- unsigned char swap_yz;
	- unsigned char swap_zx;
	- int n_count;
	- int version;
	- int hdr_size;
	-};
	-
	-// Class to handle TrackVis files.
	-// -------------------------------
	-class MITKFIBERTRACKING_EXPORT TrackVisFiberReader
	-{
	-private:
	- std::string m_Filename;
	- FILE* m_FilePointer;
	-
	-public:
	- TrackVis_header m_Header;
	-
	- short create(std::string m_Filename, const mitk::FiberBundle* fib, bool lps);
	- short open(std::string m_Filename );
	- short read( mitk::FiberBundle* fib );
	- short append(const mitk::FiberBundle* fib );
	- void writeHdr();
	- void updateTotal( int totFibers );
	- void close();
	- bool IsTransformValid();
	-
	- TrackVisFiberReader();
	- ~TrackVisFiberReader();
	-};
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/PlanarFigureComposite/mitkPlanarFigureComposite.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/PlanarFigureComposite/mitkPlanarFigureComposite.cpp
	deleted file mode 100644
	index 79e78f9927..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/PlanarFigureComposite/mitkPlanarFigureComposite.cpp
	+++ /dev/null
	@@ -1,60 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkPlanarFigureComposite.h"
	-
	-
	-mitk::PlanarFigureComposite::PlanarFigureComposite()
	-{
	- mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New();
	- this->SetGeometry(geometry);
	-}
	-
	-mitk::PlanarFigureComposite::~PlanarFigureComposite()
	-{
	-
	-}
	-
	-void mitk::PlanarFigureComposite::setOperationType(OperationType pfcOp)
	-{
	- this->m_compOperation = pfcOp;
	-}
	-
	-
	-mitk::PlanarFigureComposite::OperationType mitk::PlanarFigureComposite::getOperationType() const
	-{
	- return this->m_compOperation;
	-}
	-
	-/* ESSENTIAL IMPLEMENTATION OF SUPERCLASS METHODS */
	-
	-void mitk::PlanarFigureComposite::SetRequestedRegionToLargestPossibleRegion()
	-{
	-
	-}
	-bool mitk::PlanarFigureComposite::RequestedRegionIsOutsideOfTheBufferedRegion()
	-{
	- return false;
	-}
	-bool mitk::PlanarFigureComposite::VerifyRequestedRegion()
	-{
	- return true;
	-}
	-void mitk::PlanarFigureComposite::SetRequestedRegion(const itk::DataObject* )
	-{
	-
	-}
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/PlanarFigureComposite/mitkPlanarFigureComposite.h b/Modules/DiffusionImaging/FiberTracking/IODataStructures/PlanarFigureComposite/mitkPlanarFigureComposite.h
	deleted file mode 100644
	index 7487ab2d61..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/PlanarFigureComposite/mitkPlanarFigureComposite.h
	+++ /dev/null
	@@ -1,65 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_PLANARFIGURECOMPOSITE_H
	-#define _MITK_PLANARFIGURECOMPOSITE_H
	-
	-#include "mitkCommon.h"
	-#include "mitkBaseData.h"
	-#include <MitkFiberTrackingExports.h>
	-#include "mitkPlanarFigure.h"
	-#include "itkVectorContainer.h"
	-#include "mitkDataNode.h"
	-
	-
	-namespace mitk {
	-
	-class MITKFIBERTRACKING_EXPORT PlanarFigureComposite : public BaseData
	-{
	-
	-public:
	-
	- enum OperationType {
	- AND,
	- OR,
	- NOT
	- };
	-
	- mitkClassMacro(PlanarFigureComposite, BaseData)
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- void SetRequestedRegionToLargestPossibleRegion() override;
	- bool RequestedRegionIsOutsideOfTheBufferedRegion() override;
	- bool VerifyRequestedRegion() override;
	- void SetRequestedRegion(const itk::DataObject*) override;
	-
	- // set if this compsition is AND, OR, NOT
	- void setOperationType(OperationType);
	- OperationType getOperationType() const;
	-
	-protected:
	- PlanarFigureComposite();
	- ~PlanarFigureComposite() override;
	-
	- PlanarFigureComposite(const Self& other);
	-
	-private:
	- OperationType m_compOperation;
	-};
	-}
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp
	deleted file mode 100644
	index 07396322dd..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp
	+++ /dev/null
	@@ -1,1083 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#define RAPIDXML_NO_EXCEPTIONS
	-#include <boost/foreach.hpp>
	-#include <mitkLexicalCast.h>
	-#include <itkImageFileWriter.h>
	-#include <itkImageFileReader.h>
	-#include <mitkLog.h>
	-#include <algorithm>
	-#include <string>
	-#include <mitkFiberfoxParameters.h>
	-#include <mitkDiffusionFunctionCollection.h>
	-
	-mitk::FiberfoxParameters::FiberfoxParameters()
	- : m_NoiseModel(nullptr)
	-{
	- mitk::StickModel<ScalarType>* model_aniso = new mitk::StickModel<ScalarType>();
	- model_aniso->m_CompartmentId = 1;
	- m_FiberModelList.push_back(model_aniso);
	-
	- mitk::BallModel<ScalarType>* model_iso = new mitk::BallModel<ScalarType>();
	- model_iso->m_CompartmentId = 3;
	- m_NonFiberModelList.push_back(model_iso);
	-}
	-
	-mitk::FiberfoxParameters::FiberfoxParameters(const mitk::FiberfoxParameters& params)
	- : m_NoiseModel(nullptr)
	-{
	- m_FiberGen = params.m_FiberGen;
	- m_SignalGen = params.m_SignalGen;
	- m_Misc = params.m_Misc;
	-
	- if (params.m_NoiseModel!=nullptr)
	- {
	- if (dynamic_cast<mitk::RicianNoiseModel<>*>(params.m_NoiseModel.get()))
	- m_NoiseModel = std::make_shared< mitk::RicianNoiseModel<> >();
	- else if (dynamic_cast<mitk::ChiSquareNoiseModel<>*>(params.m_NoiseModel.get()))
	- m_NoiseModel = std::make_shared< mitk::ChiSquareNoiseModel<> >();
	- m_NoiseModel->SetNoiseVariance(params.m_NoiseModel->GetNoiseVariance());
	- }
	-
	- for (unsigned int i=0; i<params.m_FiberModelList.size()+params.m_NonFiberModelList.size(); i++)
	- {
	- mitk::DiffusionSignalModel<>* outModel = nullptr;
	- mitk::DiffusionSignalModel<>* signalModel = nullptr;
	- if (i<params.m_FiberModelList.size())
	- signalModel = params.m_FiberModelList.at(i);
	- else
	- signalModel = params.m_NonFiberModelList.at(i-params.m_FiberModelList.size());
	-
	- if (dynamic_cast<mitk::StickModel<>*>(signalModel))
	- outModel = new mitk::StickModel<>(dynamic_cast<mitk::StickModel<>*>(signalModel));
	- else if (dynamic_cast<mitk::TensorModel<>*>(signalModel))
	- outModel = new mitk::TensorModel<>(dynamic_cast<mitk::TensorModel<>*>(signalModel));
	- else if (dynamic_cast<mitk::RawShModel<>*>(signalModel))
	- outModel = new mitk::RawShModel<>(dynamic_cast<mitk::RawShModel<>*>(signalModel));
	- else if (dynamic_cast<mitk::BallModel<>*>(signalModel))
	- outModel = new mitk::BallModel<>(dynamic_cast<mitk::BallModel<>*>(signalModel));
	- else if (dynamic_cast<mitk::AstroStickModel<>*>(signalModel))
	- outModel = new mitk::AstroStickModel<>(dynamic_cast<mitk::AstroStickModel<>*>(signalModel));
	- else if (dynamic_cast<mitk::DotModel<>*>(signalModel))
	- outModel = new mitk::DotModel<>(dynamic_cast<mitk::DotModel<>*>(signalModel));
	-
	- if (i<params.m_FiberModelList.size())
	- m_FiberModelList.push_back(outModel);
	- else
	- m_NonFiberModelList.push_back(outModel);
	- }
	-}
	-
	-
	-void mitk::FiberfoxParameters::ClearFiberParameters()
	-{
	- m_Misc = MiscFiberfoxParameters();
	- m_FiberGen = FiberGenerationParameters();
	-}
	-
	-void mitk::FiberfoxParameters::ClearSignalParameters()
	-{
	- m_Misc = MiscFiberfoxParameters();
	- m_SignalGen = SignalGenerationParameters();
	-
	- m_FiberModelList.clear();
	- m_NonFiberModelList.clear();
	- m_NoiseModel = nullptr;
	- m_MissingTags = "";
	-}
	-
	-mitk::FiberfoxParameters::~FiberfoxParameters()
	-{
	-
	-}
	-
	-void mitk::SignalGenerationParameters::GenerateGradientHalfShell()
	-{
	- int NPoints = 2*m_NumGradients;
	- m_GradientDirections.clear();
	-
	- m_NumBaseline = NPoints/20;
	- if (m_NumBaseline==0)
	- m_NumBaseline=1;
	-
	- GradientType g;
	- g.Fill(0.0);
	- for (unsigned int i=0; i<m_NumBaseline; i++)
	- m_GradientDirections.push_back(g);
	-
	- if (NPoints==0)
	- return;
	-
	- vnl_vector<double> theta; theta.set_size(NPoints);
	- vnl_vector<double> phi; phi.set_size(NPoints);
	- double C = sqrt(4*itk::Math::pi);
	- phi(0) = 0.0;
	- phi(NPoints-1) = 0.0;
	- for(int i=0; i<NPoints; i++)
	- {
	- theta(i) = acos(-1.0+2.0*i/(NPoints-1.0)) - itk::Math::pi / 2.0;
	- if( i>0 && i<NPoints-1)
	- {
	- phi(i) = (phi(i-1) + C /
	- sqrt(NPoints(1-(-1.0+2.0i/(NPoints-1.0))(-1.0+2.0i/(NPoints-1.0)))));
	- }
	- }
	-
	- for(int i=0; i<NPoints; i++)
	- {
	- g[2] = sin(theta(i));
	- if (g[2]<0)
	- continue;
	- g[0] = cos(theta(i)) * cos(phi(i));
	- g[1] = cos(theta(i)) * sin(phi(i));
	- m_GradientDirections.push_back(g);
	- }
	-}
	-
	-std::vector< int > mitk::SignalGenerationParameters::GetBaselineIndices()
	-{
	- std::vector< int > result;
	- for( unsigned int i=0; i<this->m_GradientDirections.size(); i++)
	- if (m_GradientDirections.at(i).GetNorm()<0.0001)
	- result.push_back(i);
	- return result;
	-}
	-
	-unsigned int mitk::SignalGenerationParameters::GetFirstBaselineIndex()
	-{
	- for( unsigned int i=0; i<this->m_GradientDirections.size(); i++)
	- if (m_GradientDirections.at(i).GetNorm()<0.0001)
	- return i;
	- return -1;
	-}
	-
	-bool mitk::SignalGenerationParameters::IsBaselineIndex(unsigned int idx)
	-{
	- if (m_GradientDirections.size()>idx && m_GradientDirections.at(idx).GetNorm()<0.0001)
	- return true;
	- return false;
	-}
	-
	-unsigned int mitk::SignalGenerationParameters::GetNumWeightedVolumes()
	-{
	- return m_NumGradients;
	-}
	-
	-unsigned int mitk::SignalGenerationParameters::GetNumBaselineVolumes()
	-{
	- return m_NumBaseline;
	-}
	-
	-unsigned int mitk::SignalGenerationParameters::GetNumVolumes()
	-{
	- return m_GradientDirections.size();
	-}
	-
	-mitk::SignalGenerationParameters::GradientListType mitk::SignalGenerationParameters::GetGradientDirections()
	-{
	- return m_GradientDirections;
	-}
	-
	-mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer mitk::SignalGenerationParameters::GetItkGradientContainer()
	-{
	- int c = 0;
	- mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer out = mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::New();
	- for (auto g : m_GradientDirections)
	- {
	- mitk::DiffusionPropertyHelper::GradientDirectionType vnl_dir;
	- vnl_dir[0] = g[0];
	- vnl_dir[1] = g[1];
	- vnl_dir[2] = g[2];
	- out->InsertElement(c, vnl_dir);
	- ++c;
	- }
	- return out;
	-}
	-
	-mitk::SignalGenerationParameters::GradientType mitk::SignalGenerationParameters::GetGradientDirection(unsigned int i)
	-{
	- return m_GradientDirections.at(i);
	-}
	-
	-void mitk::SignalGenerationParameters::SetNumWeightedVolumes(int numGradients)
	-{
	- m_NumGradients = numGradients;
	- GenerateGradientHalfShell();
	-}
	-
	-std::vector< int > mitk::SignalGenerationParameters::GetBvalues()
	-{
	- std::vector< int > bVals;
	- for( GradientType g : m_GradientDirections)
	- {
	- float norm = g.GetNorm();
	- int bVal = std::round(normnormm_Bvalue);
	- if ( std::find(bVals.begin(), bVals.end(), bVal) == bVals.end() )
	- bVals.push_back(bVal);
	- }
	- return bVals;
	-}
	-
	-double mitk::SignalGenerationParameters::GetBvalue()
	-{
	- return m_Bvalue;
	-}
	-
	-void mitk::SignalGenerationParameters::SetGradienDirections(GradientListType gradientList)
	-{
	- m_GradientDirections = gradientList;
	- m_NumGradients = 0;
	- m_NumBaseline = 0;
	-
	- for( unsigned int i=0; i<this->m_GradientDirections.size(); i++)
	- {
	- float norm = m_GradientDirections.at(i).GetNorm();
	- if (norm>0.0001)
	- m_NumGradients++;
	- else
	- m_NumBaseline++;
	- }
	-}
	-
	-void mitk::SignalGenerationParameters::SetGradienDirections(mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer gradientList)
	-{
	- m_NumGradients = 0;
	- m_NumBaseline = 0;
	- m_GradientDirections.clear();
	-
	- for( unsigned int i=0; i<gradientList->Size(); i++)
	- {
	- GradientType g;
	- g[0] = gradientList->at(i)[0];
	- g[1] = gradientList->at(i)[1];
	- g[2] = gradientList->at(i)[2];
	- m_GradientDirections.push_back(g);
	-
	- float norm = m_GradientDirections.at(i).GetNorm();
	- if (norm>0.0001)
	- m_NumGradients++;
	- else
	- m_NumBaseline++;
	- }
	-}
	-
	-void mitk::SignalGenerationParameters::ApplyDirectionMatrix()
	-{
	- auto imageRotationMatrix = m_ImageDirection.GetVnlMatrix();
	-
	- GradientListType rotated_gradients;
	- for(auto g : m_GradientDirections)
	- {
	- vnl_vector<double> vec = g.GetVnlVector();
	- vec = vec.pre_multiply(imageRotationMatrix);
	-
	- GradientType g2;
	- g2[0] = vec[0];
	- g2[1] = vec[1];
	- g2[2] = vec[2];
	- rotated_gradients.push_back(g2);
	- }
	- m_GradientDirections = rotated_gradients;
	-}
	-
	-void mitk::FiberfoxParameters::ApplyDirectionMatrix()
	-{
	- m_SignalGen.ApplyDirectionMatrix();
	- UpdateSignalModels();
	-}
	-
	-void mitk::FiberfoxParameters::SaveParameters(std::string filename)
	-{
	- if(filename.empty())
	- return;
	- if(".ffp"!=filename.substr(filename.size()-4, 4))
	- filename += ".ffp";
	-
	- const std::string& locale = "C";
	- const std::string& currLocale = setlocale( LC_ALL, nullptr );
	-
	- if ( locale.compare(currLocale)!=0 )
	- {
	- try
	- {
	- setlocale(LC_ALL, locale.c_str());
	- }
	- catch(...)
	- {
	- MITK_INFO << "Could not set locale " << locale;
	- }
	- }
	-
	- boost::property_tree::ptree parameters;
	-
	- // fiber generation parameters
	- parameters.put("fiberfox.fibers.distribution", m_FiberGen.m_Distribution);
	- parameters.put("fiberfox.fibers.variance", m_FiberGen.m_Variance);
	- parameters.put("fiberfox.fibers.density", m_FiberGen.m_Density);
	- parameters.put("fiberfox.fibers.spline.sampling", m_FiberGen.m_Sampling);
	- parameters.put("fiberfox.fibers.spline.tension", m_FiberGen.m_Tension);
	- parameters.put("fiberfox.fibers.spline.continuity", m_FiberGen.m_Continuity);
	- parameters.put("fiberfox.fibers.spline.bias", m_FiberGen.m_Bias);
	- parameters.put("fiberfox.fibers.rotation.x", m_FiberGen.m_Rotation[0]);
	- parameters.put("fiberfox.fibers.rotation.y", m_FiberGen.m_Rotation[1]);
	- parameters.put("fiberfox.fibers.rotation.z", m_FiberGen.m_Rotation[2]);
	- parameters.put("fiberfox.fibers.translation.x", m_FiberGen.m_Translation[0]);
	- parameters.put("fiberfox.fibers.translation.y", m_FiberGen.m_Translation[1]);
	- parameters.put("fiberfox.fibers.translation.z", m_FiberGen.m_Translation[2]);
	- parameters.put("fiberfox.fibers.scale.x", m_FiberGen.m_Scale[0]);
	- parameters.put("fiberfox.fibers.scale.y", m_FiberGen.m_Scale[1]);
	- parameters.put("fiberfox.fibers.scale.z", m_FiberGen.m_Scale[2]);
	-
	- // image generation parameters
	- parameters.put("fiberfox.image.basic.size.x", m_SignalGen.m_ImageRegion.GetSize(0));
	- parameters.put("fiberfox.image.basic.size.y", m_SignalGen.m_ImageRegion.GetSize(1));
	- parameters.put("fiberfox.image.basic.size.z", m_SignalGen.m_ImageRegion.GetSize(2));
	- parameters.put("fiberfox.image.basic.spacing.x", m_SignalGen.m_ImageSpacing[0]);
	- parameters.put("fiberfox.image.basic.spacing.y", m_SignalGen.m_ImageSpacing[1]);
	- parameters.put("fiberfox.image.basic.spacing.z", m_SignalGen.m_ImageSpacing[2]);
	- parameters.put("fiberfox.image.basic.origin.x", m_SignalGen.m_ImageOrigin[0]);
	- parameters.put("fiberfox.image.basic.origin.y", m_SignalGen.m_ImageOrigin[1]);
	- parameters.put("fiberfox.image.basic.origin.z", m_SignalGen.m_ImageOrigin[2]);
	- parameters.put("fiberfox.image.basic.direction.d1", m_SignalGen.m_ImageDirection[0][0]);
	- parameters.put("fiberfox.image.basic.direction.d2", m_SignalGen.m_ImageDirection[0][1]);
	- parameters.put("fiberfox.image.basic.direction.d3", m_SignalGen.m_ImageDirection[0][2]);
	- parameters.put("fiberfox.image.basic.direction.d4", m_SignalGen.m_ImageDirection[1][0]);
	- parameters.put("fiberfox.image.basic.direction.d5", m_SignalGen.m_ImageDirection[1][1]);
	- parameters.put("fiberfox.image.basic.direction.d6", m_SignalGen.m_ImageDirection[1][2]);
	- parameters.put("fiberfox.image.basic.direction.d7", m_SignalGen.m_ImageDirection[2][0]);
	- parameters.put("fiberfox.image.basic.direction.d8", m_SignalGen.m_ImageDirection[2][1]);
	- parameters.put("fiberfox.image.basic.direction.d9", m_SignalGen.m_ImageDirection[2][2]);
	-
	- mitk::gradients::WriteBvalsBvecs(filename+".bvals", filename+".bvecs", m_SignalGen.GetItkGradientContainer(), m_SignalGen.m_Bvalue);
	-
	- parameters.put("fiberfox.image.acquisitiontype", m_SignalGen.m_AcquisitionType);
	- parameters.put("fiberfox.image.coilsensitivityprofile", m_SignalGen.m_CoilSensitivityProfile);
	- parameters.put("fiberfox.image.numberofcoils", m_SignalGen.m_NumberOfCoils);
	- parameters.put("fiberfox.image.reversephase", m_SignalGen.m_ReversePhase);
	- parameters.put("fiberfox.image.partialfourier", m_SignalGen.m_PartialFourier);
	- parameters.put("fiberfox.image.noisevariance", m_SignalGen.m_NoiseVariance);
	- parameters.put("fiberfox.image.trep", m_SignalGen.m_tRep);
	- parameters.put("fiberfox.image.tinv", m_SignalGen.m_tInv);
	- parameters.put("fiberfox.image.signalScale", m_SignalGen.m_SignalScale);
	- parameters.put("fiberfox.image.tEcho", m_SignalGen.m_tEcho);
	- parameters.put("fiberfox.image.tLine", m_SignalGen.m_tLine);
	- parameters.put("fiberfox.image.tInhom", m_SignalGen.m_tInhom);
	- parameters.put("fiberfox.image.echoTrainLength", m_SignalGen.m_EchoTrainLength);
	- parameters.put("fiberfox.image.simulatekspace", m_SignalGen.m_SimulateKspaceAcquisition);
	- parameters.put("fiberfox.image.axonRadius", m_SignalGen.m_AxonRadius);
	- parameters.put("fiberfox.image.doSimulateRelaxation", m_SignalGen.m_DoSimulateRelaxation);
	- parameters.put("fiberfox.image.doDisablePartialVolume", m_SignalGen.m_DoDisablePartialVolume);
	- parameters.put("fiberfox.image.artifacts.spikesnum", m_SignalGen.m_Spikes);
	- parameters.put("fiberfox.image.artifacts.spikesscale", m_SignalGen.m_SpikeAmplitude);
	- parameters.put("fiberfox.image.artifacts.kspaceLineOffset", m_SignalGen.m_KspaceLineOffset);
	- parameters.put("fiberfox.image.artifacts.eddyStrength", m_SignalGen.m_EddyStrength);
	- parameters.put("fiberfox.image.artifacts.eddyTau", m_SignalGen.m_Tau);
	- parameters.put("fiberfox.image.artifacts.aliasingfactor", m_SignalGen.m_CroppingFactor);
	- parameters.put("fiberfox.image.artifacts.drift", m_SignalGen.m_Drift);
	-
	- parameters.put("fiberfox.image.artifacts.doAddMotion", m_SignalGen.m_DoAddMotion);
	- parameters.put("fiberfox.image.artifacts.randomMotion", m_SignalGen.m_DoRandomizeMotion);
	- parameters.put("fiberfox.image.artifacts.translation0", m_SignalGen.m_Translation[0]);
	- parameters.put("fiberfox.image.artifacts.translation1", m_SignalGen.m_Translation[1]);
	- parameters.put("fiberfox.image.artifacts.translation2", m_SignalGen.m_Translation[2]);
	- parameters.put("fiberfox.image.artifacts.rotation0", m_SignalGen.m_Rotation[0]);
	- parameters.put("fiberfox.image.artifacts.rotation1", m_SignalGen.m_Rotation[1]);
	- parameters.put("fiberfox.image.artifacts.rotation2", m_SignalGen.m_Rotation[2]);
	- parameters.put("fiberfox.image.artifacts.motionvolumes", m_Misc.m_MotionVolumesBox);
	-
	- parameters.put("fiberfox.image.artifacts.addringing", m_SignalGen.m_DoAddGibbsRinging);
	- parameters.put("fiberfox.image.artifacts.zeroringing", m_SignalGen.m_ZeroRinging);
	- parameters.put("fiberfox.image.artifacts.addnoise", m_Misc.m_DoAddNoise);
	- parameters.put("fiberfox.image.artifacts.addghosts", m_Misc.m_DoAddGhosts);
	- parameters.put("fiberfox.image.artifacts.addaliasing", m_Misc.m_DoAddAliasing);
	- parameters.put("fiberfox.image.artifacts.addspikes", m_Misc.m_DoAddSpikes);
	- parameters.put("fiberfox.image.artifacts.addeddycurrents", m_Misc.m_DoAddEddyCurrents);
	- parameters.put("fiberfox.image.artifacts.doAddDistortions", m_Misc.m_DoAddDistortions);
	- parameters.put("fiberfox.image.artifacts.doAddDrift", m_SignalGen.m_DoAddDrift);
	-
	- parameters.put("fiberfox.image.outputvolumefractions", m_Misc.m_OutputAdditionalImages);
	- parameters.put("fiberfox.image.showadvanced", m_Misc.m_CheckAdvancedSignalOptionsBox);
	- parameters.put("fiberfox.image.signalmodelstring", m_Misc.m_SignalModelString);
	- parameters.put("fiberfox.image.artifactmodelstring", m_Misc.m_ArtifactModelString);
	- parameters.put("fiberfox.image.outpath", m_Misc.m_OutputPath);
	- parameters.put("fiberfox.fibers.realtime", m_Misc.m_CheckRealTimeFibersBox);
	- parameters.put("fiberfox.fibers.showadvanced", m_Misc.m_CheckAdvancedFiberOptionsBox);
	- parameters.put("fiberfox.fibers.constantradius", m_Misc.m_CheckConstantRadiusBox);
	- parameters.put("fiberfox.fibers.includeFiducials", m_Misc.m_CheckIncludeFiducialsBox);
	-
	- if (m_NoiseModel!=nullptr)
	- {
	- parameters.put("fiberfox.image.artifacts.noisevariance", m_NoiseModel->GetNoiseVariance());
	- if (dynamic_cast<mitk::RicianNoiseModel<>*>(m_NoiseModel.get()))
	- parameters.put("fiberfox.image.artifacts.noisetype", "rice");
	- else if (dynamic_cast<mitk::ChiSquareNoiseModel<>*>(m_NoiseModel.get()))
	- parameters.put("fiberfox.image.artifacts.noisetype", "chisquare");
	- }
	-
	- for (std::size_t i=0; i<m_FiberModelList.size()+m_NonFiberModelList.size(); i++)
	- {
	- mitk::DiffusionSignalModel<>* signalModel = nullptr;
	- if (i<m_FiberModelList.size())
	- {
	- signalModel = m_FiberModelList.at(i);
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".type", "fiber");
	- }
	- else
	- {
	- signalModel = m_NonFiberModelList.at(i-m_FiberModelList.size());
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".type", "non-fiber");
	- }
	-
	- if (dynamic_cast<mitk::StickModel<>*>(signalModel))
	- {
	- mitk::StickModel<>* model = dynamic_cast<mitk::StickModel<>*>(signalModel);
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".model", "stick");
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".d", model->GetDiffusivity());
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".t2", model->GetT2());
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".t1", model->GetT1());
	- }
	- else if (dynamic_cast<mitk::TensorModel<>*>(signalModel))
	- {
	- mitk::TensorModel<>* model = dynamic_cast<mitk::TensorModel<>*>(signalModel);
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".model", "tensor");
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".d1", model->GetDiffusivity1());
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".d2", model->GetDiffusivity2());
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".d3", model->GetDiffusivity3());
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".t2", model->GetT2());
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".t1", model->GetT1());
	- }
	- else if (dynamic_cast<mitk::RawShModel<>*>(signalModel))
	- {
	- mitk::RawShModel<>* model = dynamic_cast<mitk::RawShModel<>*>(signalModel);
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".model", "prototype");
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".minFA", model->GetFaRange().first);
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".maxFA", model->GetFaRange().second);
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".minADC", model->GetAdcRange().first);
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".maxADC", model->GetAdcRange().second);
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".maxNumSamples", model->GetMaxNumKernels());
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".numSamples", model->GetNumberOfKernels());
	- int shOrder = model->GetShOrder();
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".numCoeffs", (shOrder*shOrder + shOrder + 2)/2 + shOrder);
	-
	- for (unsigned int j=0; j<model->GetNumberOfKernels(); j++)
	- {
	- vnl_vector< double > coeffs = model->GetCoefficients(j);
	- for (unsigned int k=0; k<coeffs.size(); k++)
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".kernels."+boost::lexical_cast<std::string>(j)+".coeffs."+boost::lexical_cast<std::string>(k), coeffs[k]);
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".kernels."+boost::lexical_cast<std::string>(j)+".B0", model->GetBaselineSignal(j));
	- }
	- }
	- else if (dynamic_cast<mitk::BallModel<>*>(signalModel))
	- {
	- mitk::BallModel<>* model = dynamic_cast<mitk::BallModel<>*>(signalModel);
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".model", "ball");
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".d", model->GetDiffusivity());
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".t2", model->GetT2());
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".t1", model->GetT1());
	- }
	- else if (dynamic_cast<mitk::AstroStickModel<>*>(signalModel))
	- {
	- mitk::AstroStickModel<>* model = dynamic_cast<mitk::AstroStickModel<>*>(signalModel);
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".model", "astrosticks");
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".d", model->GetDiffusivity());
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".t2", model->GetT2());
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".t1", model->GetT1());
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".randomize", model->GetRandomizeSticks());
	- }
	- else if (dynamic_cast<mitk::DotModel<>*>(signalModel))
	- {
	- mitk::DotModel<>* model = dynamic_cast<mitk::DotModel<>*>(signalModel);
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".model", "dot");
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".t2", model->GetT2());
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".t1", model->GetT1());
	- }
	-
	- if (signalModel!=nullptr)
	- {
	- parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast<std::string>(i)+".ID", signalModel->m_CompartmentId);
	-
	- if (signalModel->GetVolumeFractionImage().IsNotNull())
	- {
	- try{
	- itk::ImageFileWriter<ItkDoubleImgType>::Pointer writer = itk::ImageFileWriter<ItkDoubleImgType>::New();
	- writer->SetFileName(filename+"_VOLUME"+boost::lexical_cast<std::string>(signalModel->m_CompartmentId)+".nii.gz");
	- writer->SetInput(signalModel->GetVolumeFractionImage());
	- writer->Update();
	- MITK_INFO << "Volume fraction image for compartment "+boost::lexical_cast<std::string>(signalModel->m_CompartmentId)+" saved.";
	- }
	- catch(...)
	- {
	- }
	- }
	- }
	- }
	-
	- boost::property_tree::xml_writer_settings<std::string> writerSettings(' ', 2);
	- boost::property_tree::xml_parser::write_xml(filename, parameters, std::locale(), writerSettings);
	-
	- try{
	- itk::ImageFileWriter<ItkFloatImgType>::Pointer writer = itk::ImageFileWriter<ItkFloatImgType>::New();
	- writer->SetFileName(filename+"_FMAP.nii.gz");
	- writer->SetInput(m_SignalGen.m_FrequencyMap);
	- writer->Update();
	- }
	- catch(...)
	- {
	- MITK_INFO << "No frequency map saved.";
	- }
	- try{
	- itk::ImageFileWriter<ItkUcharImgType>::Pointer writer = itk::ImageFileWriter<ItkUcharImgType>::New();
	- writer->SetFileName(filename+"_MASK.nii.gz");
	- writer->SetInput(m_SignalGen.m_MaskImage);
	- writer->Update();
	- }
	- catch(...)
	- {
	- MITK_INFO << "No mask image saved.";
	- }
	-
	- setlocale(LC_ALL, currLocale.c_str());
	-}
	-
	-
	-
	-template< class ParameterType >
	-ParameterType mitk::FiberfoxParameters::ReadVal(boost::property_tree::ptree::value_type const& v, std::string tag, ParameterType defaultValue, bool essential)
	-{
	- try
	- {
	- return v.second.get<ParameterType>(tag);
	- }
	- catch (...)
	- {
	- if (essential)
	- {
	- mitkThrow() << "Parameter file corrupted. Essential tag is missing: '" << tag << "'";
	- }
	- if (tag!="artifacts.noisetype")
	- {
	- MITK_INFO << "Tag '" << tag << "' not found. Using default value '" << defaultValue << "'.";
	- m_MissingTags += "\n- ";
	- m_MissingTags += tag;
	- }
	- return defaultValue;
	- }
	-}
	-
	-void mitk::FiberfoxParameters::UpdateSignalModels()
	-{
	- for (mitk::DiffusionSignalModel<>* m : m_FiberModelList)
	- {
	- m->SetGradientList(m_SignalGen.m_GradientDirections);
	- m->SetBvalue(m_SignalGen.m_Bvalue);
	- }
	- for (mitk::DiffusionSignalModel<>* m : m_NonFiberModelList)
	- {
	- m->SetGradientList(m_SignalGen.m_GradientDirections);
	- m->SetBvalue(m_SignalGen.m_Bvalue);
	- }
	-}
	-
	-void mitk::FiberfoxParameters::SetNumWeightedVolumes(int numGradients)
	-{
	- m_SignalGen.SetNumWeightedVolumes(numGradients);
	- UpdateSignalModels();
	-}
	-
	-void mitk::FiberfoxParameters::SetGradienDirections(mitk::SignalGenerationParameters::GradientListType gradientList)
	-{
	- m_SignalGen.SetGradienDirections(gradientList);
	- UpdateSignalModels();
	-}
	-
	-void mitk::FiberfoxParameters::SetGradienDirections(mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer gradientList)
	-{
	- m_SignalGen.SetGradienDirections(gradientList);
	- UpdateSignalModels();
	-}
	-
	-void mitk::FiberfoxParameters::SetBvalue(double Bvalue)
	-{
	- m_SignalGen.m_Bvalue = Bvalue;
	- UpdateSignalModels();
	-}
	-
	-void mitk::FiberfoxParameters::GenerateGradientHalfShell()
	-{
	- m_SignalGen.GenerateGradientHalfShell();
	- UpdateSignalModels();
	-}
	-
	-void mitk::FiberfoxParameters::LoadParameters(std::string filename, bool fix_seed)
	-{
	- itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer randgen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New();
	- if (fix_seed)
	- {
	- srand(0);
	- randgen->SetSeed(0);
	- }
	- else
	- {
	- srand(time(0));
	- randgen->SetSeed();
	- }
	- m_MissingTags = "";
	- if(filename.empty()) { return; }
	-
	- const std::string& locale = "C";
	- const std::string& currLocale = setlocale( LC_ALL, nullptr );
	-
	- if ( locale.compare(currLocale)!=0 )
	- {
	- try
	- {
	- setlocale(LC_ALL, locale.c_str());
	- }
	- catch(...)
	- {
	- MITK_INFO << "Could not set locale " << locale;
	- }
	- }
	-
	-
	- boost::property_tree::ptree parameterTree;
	- boost::property_tree::xml_parser::read_xml( filename, parameterTree );
	-
	-
	- m_FiberModelList.clear();
	- m_NonFiberModelList.clear();
	- if (m_NoiseModel) { m_NoiseModel = nullptr; }
	-
	- BOOST_FOREACH( boost::property_tree::ptree::value_type const& v1, parameterTree.get_child("fiberfox") )
	- {
	- if( v1.first == "fibers" )
	- {
	- m_Misc.m_CheckRealTimeFibersBox = ReadVal<bool>(v1,"realtime", m_Misc.m_CheckRealTimeFibersBox);
	- m_Misc.m_CheckAdvancedFiberOptionsBox = ReadVal<bool>(v1,"showadvanced", m_Misc.m_CheckAdvancedFiberOptionsBox);
	- m_Misc.m_CheckConstantRadiusBox = ReadVal<bool>(v1,"constantradius", m_Misc.m_CheckConstantRadiusBox);
	- m_Misc.m_CheckIncludeFiducialsBox = ReadVal<bool>(v1,"includeFiducials", m_Misc.m_CheckIncludeFiducialsBox);
	-
	- switch (ReadVal<unsigned int>(v1,"distribution", 0))
	- {
	- case 0:
	- m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_UNIFORM;
	- break;
	- case 1:
	- m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_GAUSSIAN;
	- break;
	- default:
	- m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_UNIFORM;
	- }
	- m_FiberGen.m_Variance = ReadVal<double>(v1,"variance", m_FiberGen.m_Variance);
	- m_FiberGen.m_Density = ReadVal<unsigned int>(v1,"density", m_FiberGen.m_Density);
	- m_FiberGen.m_Sampling = ReadVal<double>(v1,"spline.sampling", m_FiberGen.m_Sampling);
	- m_FiberGen.m_Tension = ReadVal<double>(v1,"spline.tension", m_FiberGen.m_Tension);
	- m_FiberGen.m_Continuity = ReadVal<double>(v1,"spline.continuity", m_FiberGen.m_Continuity);
	- m_FiberGen.m_Bias = ReadVal<double>(v1,"spline.bias", m_FiberGen.m_Bias);
	- m_FiberGen.m_Rotation[0] = ReadVal<double>(v1,"rotation.x", m_FiberGen.m_Rotation[0]);
	- m_FiberGen.m_Rotation[1] = ReadVal<double>(v1,"rotation.y", m_FiberGen.m_Rotation[1]);
	- m_FiberGen.m_Rotation[2] = ReadVal<double>(v1,"rotation.z", m_FiberGen.m_Rotation[2]);
	- m_FiberGen.m_Translation[0] = ReadVal<double>(v1,"translation.x", m_FiberGen.m_Translation[0]);
	- m_FiberGen.m_Translation[1] = ReadVal<double>(v1,"translation.y", m_FiberGen.m_Translation[1]);
	- m_FiberGen.m_Translation[2] = ReadVal<double>(v1,"translation.z", m_FiberGen.m_Translation[2]);
	- m_FiberGen.m_Scale[0] = ReadVal<double>(v1,"scale.x", m_FiberGen.m_Scale[0]);
	- m_FiberGen.m_Scale[1] = ReadVal<double>(v1,"scale.y", m_FiberGen.m_Scale[1]);
	- m_FiberGen.m_Scale[2] = ReadVal<double>(v1,"scale.z", m_FiberGen.m_Scale[2]);
	- }
	- else if ( v1.first == "image" )
	- {
	- m_Misc.m_SignalModelString = ReadVal<std::string>(v1,"signalmodelstring", m_Misc.m_SignalModelString);
	- m_Misc.m_ArtifactModelString = ReadVal<std::string>(v1,"artifactmodelstring", m_Misc.m_ArtifactModelString);
	- m_Misc.m_OutputPath = ReadVal<std::string>(v1,"outpath", m_Misc.m_OutputPath);
	- m_Misc.m_OutputAdditionalImages = ReadVal<bool>(v1,"outputvolumefractions", m_Misc.m_OutputAdditionalImages);
	- m_Misc.m_CheckAdvancedSignalOptionsBox = ReadVal<bool>(v1,"showadvanced", m_Misc.m_CheckAdvancedSignalOptionsBox);
	- m_Misc.m_DoAddDistortions = ReadVal<bool>(v1,"artifacts.doAddDistortions", m_Misc.m_DoAddDistortions);
	- m_Misc.m_DoAddNoise = ReadVal<bool>(v1,"artifacts.addnoise", m_Misc.m_DoAddNoise);
	- m_Misc.m_DoAddGhosts = ReadVal<bool>(v1,"artifacts.addghosts", m_Misc.m_DoAddGhosts);
	- m_Misc.m_DoAddAliasing = ReadVal<bool>(v1,"artifacts.addaliasing", m_Misc.m_DoAddAliasing);
	- m_Misc.m_DoAddSpikes = ReadVal<bool>(v1,"artifacts.addspikes", m_Misc.m_DoAddSpikes);
	- m_Misc.m_DoAddEddyCurrents = ReadVal<bool>(v1,"artifacts.addeddycurrents", m_Misc.m_DoAddEddyCurrents);
	-
	- m_SignalGen.m_ImageRegion.SetSize(0, ReadVal<int>(v1,"basic.size.x",m_SignalGen.m_ImageRegion.GetSize(0)));
	- m_SignalGen.m_ImageRegion.SetSize(1, ReadVal<int>(v1,"basic.size.y",m_SignalGen.m_ImageRegion.GetSize(1)));
	- m_SignalGen.m_ImageRegion.SetSize(2, ReadVal<int>(v1,"basic.size.z",m_SignalGen.m_ImageRegion.GetSize(2)));
	- m_SignalGen.m_ImageSpacing[0] = ReadVal<float>(v1,"basic.spacing.x",m_SignalGen.m_ImageSpacing[0]);
	- m_SignalGen.m_ImageSpacing[1] = ReadVal<float>(v1,"basic.spacing.y",m_SignalGen.m_ImageSpacing[1]);
	- m_SignalGen.m_ImageSpacing[2] = ReadVal<float>(v1,"basic.spacing.z",m_SignalGen.m_ImageSpacing[2]);
	- m_SignalGen.m_ImageOrigin[0] = ReadVal<float>(v1,"basic.origin.x",m_SignalGen.m_ImageOrigin[0]);
	- m_SignalGen.m_ImageOrigin[1] = ReadVal<float>(v1,"basic.origin.y",m_SignalGen.m_ImageOrigin[1]);
	- m_SignalGen.m_ImageOrigin[2] = ReadVal<float>(v1,"basic.origin.z",m_SignalGen.m_ImageOrigin[2]);
	-
	- int i = 0;
	- int j = 0;
	- for(auto v : v1.second.get_child("basic.direction"))
	- {
	- m_SignalGen.m_ImageDirection[i][j] = boost::lexical_cast<float>(v.second.data());
	- ++j;
	- if (j==3)
	- {
	- j = 0;
	- ++i;
	- }
	- }
	-
	- m_SignalGen.m_AcquisitionType = (SignalGenerationParameters::AcquisitionType)ReadVal<int>(v1,"acquisitiontype", m_SignalGen.m_AcquisitionType);
	- m_SignalGen.m_CoilSensitivityProfile = (SignalGenerationParameters::CoilSensitivityProfile)ReadVal<int>(v1,"coilsensitivityprofile", m_SignalGen.m_CoilSensitivityProfile);
	- m_SignalGen.m_NumberOfCoils = ReadVal<unsigned int>(v1,"numberofcoils", m_SignalGen.m_NumberOfCoils);
	- m_SignalGen.m_ReversePhase = ReadVal<bool>(v1,"reversephase", m_SignalGen.m_ReversePhase);
	- m_SignalGen.m_PartialFourier = ReadVal<float>(v1,"partialfourier", m_SignalGen.m_PartialFourier);
	- m_SignalGen.m_NoiseVariance = ReadVal<float>(v1,"noisevariance", m_SignalGen.m_NoiseVariance);
	- m_SignalGen.m_tRep = ReadVal<float>(v1,"trep", m_SignalGen.m_tRep);
	- m_SignalGen.m_tInv = ReadVal<float>(v1,"tinv", m_SignalGen.m_tInv);
	- m_SignalGen.m_SignalScale = ReadVal<float>(v1,"signalScale", m_SignalGen.m_SignalScale);
	- m_SignalGen.m_tEcho = ReadVal<float>(v1,"tEcho", m_SignalGen.m_tEcho);
	- m_SignalGen.m_tLine = ReadVal<float>(v1,"tLine", m_SignalGen.m_tLine);
	- m_SignalGen.m_tInhom = ReadVal<float>(v1,"tInhom", m_SignalGen.m_tInhom);
	- m_SignalGen.m_EchoTrainLength = ReadVal<unsigned int>(v1,"echoTrainLength", m_SignalGen.m_EchoTrainLength);
	- m_SignalGen.m_SimulateKspaceAcquisition = ReadVal<bool>(v1,"simulatekspace", m_SignalGen.m_SimulateKspaceAcquisition);
	-
	- m_SignalGen.m_AxonRadius = ReadVal<double>(v1,"axonRadius", m_SignalGen.m_AxonRadius);
	- m_SignalGen.m_Spikes = ReadVal<unsigned int>(v1,"artifacts.spikesnum", m_SignalGen.m_Spikes);
	- m_SignalGen.m_SpikeAmplitude = ReadVal<float>(v1,"artifacts.spikesscale", m_SignalGen.m_SpikeAmplitude);
	- m_SignalGen.m_KspaceLineOffset = ReadVal<float>(v1,"artifacts.kspaceLineOffset", m_SignalGen.m_KspaceLineOffset);
	- m_SignalGen.m_EddyStrength = ReadVal<float>(v1,"artifacts.eddyStrength", m_SignalGen.m_EddyStrength);
	- m_SignalGen.m_Tau = ReadVal<float>(v1,"artifacts.eddyTau", m_SignalGen.m_Tau);
	- m_SignalGen.m_CroppingFactor = ReadVal<float>(v1,"artifacts.aliasingfactor", m_SignalGen.m_CroppingFactor);
	- m_SignalGen.m_Drift = ReadVal<float>(v1,"artifacts.drift", m_SignalGen.m_Drift);
	- m_SignalGen.m_DoAddGibbsRinging = ReadVal<bool>(v1,"artifacts.addringing", m_SignalGen.m_DoAddGibbsRinging);
	- m_SignalGen.m_ZeroRinging = ReadVal<int>(v1,"artifacts.zeroringing", m_SignalGen.m_ZeroRinging);
	- m_SignalGen.m_DoSimulateRelaxation = ReadVal<bool>(v1,"doSimulateRelaxation", m_SignalGen.m_DoSimulateRelaxation);
	- m_SignalGen.m_DoDisablePartialVolume = ReadVal<bool>(v1,"doDisablePartialVolume", m_SignalGen.m_DoDisablePartialVolume);
	- m_SignalGen.m_DoAddMotion = ReadVal<bool>(v1,"artifacts.doAddMotion", m_SignalGen.m_DoAddMotion);
	- m_SignalGen.m_DoRandomizeMotion = ReadVal<bool>(v1,"artifacts.randomMotion", m_SignalGen.m_DoRandomizeMotion);
	- m_SignalGen.m_DoAddDrift = ReadVal<bool>(v1,"artifacts.doAddDrift", m_SignalGen.m_DoAddDrift);
	- m_SignalGen.m_Translation[0] = ReadVal<float>(v1,"artifacts.translation0", m_SignalGen.m_Translation[0]);
	- m_SignalGen.m_Translation[1] = ReadVal<float>(v1,"artifacts.translation1", m_SignalGen.m_Translation[1]);
	- m_SignalGen.m_Translation[2] = ReadVal<float>(v1,"artifacts.translation2", m_SignalGen.m_Translation[2]);
	- m_SignalGen.m_Rotation[0] = ReadVal<float>(v1,"artifacts.rotation0", m_SignalGen.m_Rotation[0]);
	- m_SignalGen.m_Rotation[1] = ReadVal<float>(v1,"artifacts.rotation1", m_SignalGen.m_Rotation[1]);
	- m_SignalGen.m_Rotation[2] = ReadVal<float>(v1,"artifacts.rotation2", m_SignalGen.m_Rotation[2]);
	-
	- if (itksys::SystemTools::FileExists(filename+".bvals") && itksys::SystemTools::FileExists(filename+".bvecs"))
	- {
	- m_Misc.m_BvalsFile = filename+".bvals";
	- m_Misc.m_BvecsFile = filename+".bvecs";
	- m_SignalGen.SetGradienDirections( mitk::gradients::ReadBvalsBvecs(m_Misc.m_BvalsFile, m_Misc.m_BvecsFile, m_SignalGen.m_Bvalue) );
	- }
	- else
	- {
	- m_SignalGen.m_Bvalue = ReadVal<double>(v1,"bvalue", m_SignalGen.m_Bvalue);
	- SignalGenerationParameters::GradientListType gradients;
	- try
	- {
	- BOOST_FOREACH( boost::property_tree::ptree::value_type const& v2, v1.second.get_child("gradients") )
	- {
	- SignalGenerationParameters::GradientType g;
	- g[0] = ReadVal<double>(v2,"x",0);
	- g[1] = ReadVal<double>(v2,"y",0);
	- g[2] = ReadVal<double>(v2,"z",0);
	- gradients.push_back(g);
	- }
	- }
	- catch(...)
	- {
	- MITK_INFO << "WARNING: Fiberfox parameters without any gradient directions loaded.";
	- }
	- m_SignalGen.SetGradienDirections(gradients);
	- }
	-
	- m_Misc.m_MotionVolumesBox = ReadVal<std::string>(v1,"artifacts.motionvolumes", m_Misc.m_MotionVolumesBox);
	- m_SignalGen.m_MotionVolumes.clear();
	-
	- if ( m_Misc.m_MotionVolumesBox == "random" )
	- {
	- m_SignalGen.m_MotionVolumes.push_back(0);
	- for ( size_t i=1; i < m_SignalGen.GetNumVolumes(); ++i )
	- {
	- m_SignalGen.m_MotionVolumes.push_back( bool( randgen->GetIntegerVariate()%2 ) );
	- }
	- MITK_DEBUG << "mitkFiberfoxParameters.cpp: Case m_Misc.m_MotionVolumesBox == \"random\".";
	- }
	- else if ( ! m_Misc.m_MotionVolumesBox.empty() )
	- {
	- std::stringstream stream( m_Misc.m_MotionVolumesBox );
	- std::vector<int> numbers;
	- int nummer = std::numeric_limits<int>::max();
	- while( stream >> nummer )
	- {
	- if( nummer < std::numeric_limits<int>::max() )
	- {
	- numbers.push_back( nummer );
	- }
	- }
	- // If a list of negative numbers is given:
	- if( *(std::min_element( numbers.begin(), numbers.end() )) < 0
	- && *(std::max_element( numbers.begin(), numbers.end() )) <= 0 ) // cave: -0 == +0
	- {
	- for ( size_t i=0; i<m_SignalGen.GetNumVolumes(); ++i )
	- {
	- m_SignalGen.m_MotionVolumes.push_back( true );
	- }
	- // set all true except those given.
	- for (auto number : numbers)
	- {
	- if (-number < static_cast<int>(m_SignalGen.GetNumVolumes()) && -number >= 0 )
	- m_SignalGen.m_MotionVolumes.at(-number) = false;
	- }
	- MITK_DEBUG << "mitkFiberfoxParameters.cpp: Case list of negative numbers.";
	- }
	- // If a list of positive numbers is given:
	- else if( *(std::min_element( numbers.begin(), numbers.end() )) >= 0
	- && *(std::max_element( numbers.begin(), numbers.end() )) >= 0 )
	- {
	- for ( size_t i=0; i<m_SignalGen.GetNumVolumes(); ++i )
	- {
	- m_SignalGen.m_MotionVolumes.push_back( false );
	- }
	- // set all false except those given.
	- for (auto number : numbers)
	- {
	- if (number < static_cast<int>(m_SignalGen.GetNumVolumes()) && number >= 0)
	- m_SignalGen.m_MotionVolumes.at(number) = true;
	- }
	- MITK_DEBUG << "mitkFiberfoxParameters.cpp: Case list of positive numbers.";
	- }
	- else
	- {
	- MITK_WARN << "mitkFiberfoxParameters.cpp: Inconsistent list of numbers in m_MotionVolumesBox.";
	- break;
	- }
	- }
	- else
	- {
	- MITK_WARN << "mitkFiberfoxParameters.cpp: Cannot make sense of string in m_MotionVolumesBox.";
	- break;
	- }
	-
	-
	- try
	- {
	- if (ReadVal<std::string>(v1,"artifacts.noisetype","")=="rice")
	- {
	- m_NoiseModel = std::make_shared< mitk::RicianNoiseModel<> >();
	- m_NoiseModel->SetNoiseVariance(ReadVal<float>(v1,"artifacts.noisevariance",m_NoiseModel->GetNoiseVariance()));
	- }
	- }
	- catch(...)
	- {
	- MITK_DEBUG << "mitkFiberfoxParameters.cpp: caught some error while trying m_NoiseModel->SetNoiseVariance()";
	- // throw;
	- }
	-
	- try
	- {
	- if (ReadVal<std::string>(v1,"artifacts.noisetype","")=="chisquare")
	- {
	- m_NoiseModel = std::make_shared< mitk::ChiSquareNoiseModel<> >();
	- m_NoiseModel->SetNoiseVariance(ReadVal<float>(v1,"artifacts.noisevariance",m_NoiseModel->GetNoiseVariance()));
	- }
	- }
	- catch(...)
	- {
	- MITK_DEBUG << "mitkFiberfoxParameters.cpp: caught some error while trying m_NoiseModel->SetNoiseVariance()";
	- // throw;
	- }
	-
	-
	- BOOST_FOREACH( boost::property_tree::ptree::value_type const& v2, v1.second.get_child("compartments") )
	- {
	- mitk::DiffusionSignalModel<>* signalModel = nullptr;
	-
	- std::string model = ReadVal<std::string>(v2,"model","",true);
	- if (model=="stick")
	- {
	- mitk::StickModel<>* model = new mitk::StickModel<>();
	- model->SetDiffusivity(ReadVal<double>(v2,"d",model->GetDiffusivity()));
	- model->SetT2(ReadVal<double>(v2,"t2",model->GetT2()));
	- model->SetT1(ReadVal<double>(v2,"t1",model->GetT1()));
	- model->SetBvalue(m_SignalGen.m_Bvalue);
	- model->m_CompartmentId = ReadVal<unsigned int>(v2,"ID",0,true);
	- if (ReadVal<std::string>(v2,"type","",true)=="fiber")
	- m_FiberModelList.push_back(model);
	- else if (ReadVal<std::string>(v2,"type","",true)=="non-fiber")
	- m_NonFiberModelList.push_back(model);
	- signalModel = model;
	- }
	- else if (model=="tensor")
	- {
	- mitk::TensorModel<>* model = new mitk::TensorModel<>();
	- model->SetDiffusivity1(ReadVal<double>(v2,"d1",model->GetDiffusivity1()));
	- model->SetDiffusivity2(ReadVal<double>(v2,"d2",model->GetDiffusivity2()));
	- model->SetDiffusivity3(ReadVal<double>(v2,"d3",model->GetDiffusivity3()));
	- model->SetT2(ReadVal<double>(v2,"t2",model->GetT2()));
	- model->SetT1(ReadVal<double>(v2,"t1",model->GetT1()));
	- model->SetBvalue(m_SignalGen.m_Bvalue);
	- model->m_CompartmentId = ReadVal<unsigned int>(v2,"ID",0,true);
	- if (ReadVal<std::string>(v2,"type","",true)=="fiber")
	- m_FiberModelList.push_back(model);
	- else if (ReadVal<std::string>(v2,"type","",true)=="non-fiber")
	- m_NonFiberModelList.push_back(model);
	- signalModel = model;
	- }
	- else if (model=="ball")
	- {
	- mitk::BallModel<>* model = new mitk::BallModel<>();
	- model->SetDiffusivity(ReadVal<double>(v2,"d",model->GetDiffusivity()));
	- model->SetT2(ReadVal<double>(v2,"t2",model->GetT2()));
	- model->SetT1(ReadVal<double>(v2,"t1",model->GetT1()));
	- model->SetBvalue(m_SignalGen.m_Bvalue);
	- model->m_CompartmentId = ReadVal<unsigned int>(v2,"ID",0,true);
	- if (ReadVal<std::string>(v2,"type","",true)=="fiber")
	- m_FiberModelList.push_back(model);
	- else if (ReadVal<std::string>(v2,"type","",true)=="non-fiber")
	- m_NonFiberModelList.push_back(model);
	- signalModel = model;
	- }
	- else if (model=="astrosticks")
	- {
	- mitk::AstroStickModel<>* model = new AstroStickModel<>();
	- model->SetDiffusivity(ReadVal<double>(v2,"d",model->GetDiffusivity()));
	- model->SetT2(ReadVal<double>(v2,"t2",model->GetT2()));
	- model->SetT1(ReadVal<double>(v2,"t1",model->GetT1()));
	- model->SetBvalue(m_SignalGen.m_Bvalue);
	- model->SetRandomizeSticks(ReadVal<bool>(v2,"randomize",model->GetRandomizeSticks()));
	- model->m_CompartmentId = ReadVal<unsigned int>(v2,"ID",0,true);
	- if (ReadVal<std::string>(v2,"type","",true)=="fiber")
	- m_FiberModelList.push_back(model);
	- else if (ReadVal<std::string>(v2,"type","",true)=="non-fiber")
	- m_NonFiberModelList.push_back(model);
	- signalModel = model;
	- }
	- else if (model=="dot")
	- {
	- mitk::DotModel<>* model = new mitk::DotModel<>();
	- model->SetT2(ReadVal<double>(v2,"t2",model->GetT2()));
	- model->SetT1(ReadVal<double>(v2,"t1",model->GetT1()));
	- model->m_CompartmentId = ReadVal<unsigned int>(v2,"ID",0,true);
	- if (ReadVal<std::string>(v2,"type","",true)=="fiber")
	- m_FiberModelList.push_back(model);
	- else if (ReadVal<std::string>(v2,"type","",true)=="non-fiber")
	- m_NonFiberModelList.push_back(model);
	- signalModel = model;
	- }
	- else if (model=="prototype")
	- {
	- mitk::RawShModel<>* model = new mitk::RawShModel<>();
	- model->SetMaxNumKernels(ReadVal<unsigned int>(v2,"maxNumSamples",model->GetMaxNumKernels()));
	- model->SetFaRange(ReadVal<double>(v2,"minFA",model->GetFaRange().first), ReadVal<double>(v2,"maxFA",model->GetFaRange().second));
	- model->SetAdcRange(ReadVal<double>(v2,"minADC",model->GetAdcRange().first), ReadVal<double>(v2,"maxADC",model->GetAdcRange().second));
	- model->m_CompartmentId = ReadVal<unsigned int>(v2,"ID",0,true);
	- unsigned int numCoeffs = ReadVal<unsigned int>(v2,"numCoeffs",0,true);
	- unsigned int numSamples = ReadVal<unsigned int>(v2,"numSamples",0,true);
	-
	- for (unsigned int j=0; j<numSamples; j++)
	- {
	- vnl_vector< double > coeffs(numCoeffs);
	- for (unsigned int k=0; k<numCoeffs; k++)
	- {
	- coeffs[k] = ReadVal<double>(v2,"kernels."+boost::lexical_cast<std::string>(j)+".coeffs."+boost::lexical_cast<std::string>(k),0,true);
	- }
	- model->SetShCoefficients( coeffs, ReadVal<double>(v2,"kernels."+boost::lexical_cast<std::string>(j)+".B0",0,true) );
	- }
	-
	- if (ReadVal<std::string>(v2,"type","",true)=="fiber")
	- { m_FiberModelList.push_back(model); }
	- else if (ReadVal<std::string>(v2,"type","",true)=="non-fiber")
	- { m_NonFiberModelList.push_back(model); }
	- // else ?
	- signalModel = model;
	- }
	-
	- if (signalModel!=nullptr)
	- {
	- try
	- {
	- itk::ImageFileReader<ItkDoubleImgType>::Pointer reader = itk::ImageFileReader<ItkDoubleImgType>::New();
	- if ( itksys::SystemTools::FileExists(filename+"_VOLUME"+ReadVal<std::string>(v2,"ID","")+".nii.gz") )
	- reader->SetFileName(filename+"_VOLUME"+ReadVal<std::string>(v2,"ID","")+".nii.gz");
	- else if ( itksys::SystemTools::FileExists(filename+"_VOLUME"+ReadVal<std::string>(v2,"ID","")+".nii") )
	- reader->SetFileName(filename+"_VOLUME"+ReadVal<std::string>(v2,"ID","")+".nii");
	- else
	- reader->SetFileName(filename+"_VOLUME"+ReadVal<std::string>(v2,"ID","")+".nrrd");
	- reader->Update();
	- signalModel->SetVolumeFractionImage(reader->GetOutput());
	- MITK_INFO << "Volume fraction image loaded for compartment " << signalModel->m_CompartmentId;
	- }
	- catch(...)
	- {
	- MITK_INFO << "No volume fraction image found for compartment " << signalModel->m_CompartmentId;
	- }
	- }
	- }
	- }
	- else
	- {
	-
	- }
	- }
	-
	- UpdateSignalModels();
	-
	- try
	- {
	- itk::ImageFileReader<ItkFloatImgType>::Pointer reader = itk::ImageFileReader<ItkFloatImgType>::New();
	- reader->SetFileName(filename+"_FMAP.nrrd");
	- if ( itksys::SystemTools::FileExists(filename+"_FMAP.nii.gz") )
	- reader->SetFileName(filename+"_FMAP.nii.gz");
	- else if ( itksys::SystemTools::FileExists(filename+"_FMAP.nii") )
	- reader->SetFileName(filename+"_FMAP.nii");
	- else
	- reader->SetFileName(filename+"_FMAP.nrrd");
	- reader->Update();
	- m_SignalGen.m_FrequencyMap = reader->GetOutput();
	- MITK_INFO << "Frequency map loaded.";
	- }
	- catch(...)
	- {
	- MITK_INFO << "No frequency map found.";
	- }
	-
	- try
	- {
	- itk::ImageFileReader<ItkUcharImgType>::Pointer reader = itk::ImageFileReader<ItkUcharImgType>::New();
	- if ( itksys::SystemTools::FileExists(filename+"_MASK.nii.gz") )
	- reader->SetFileName(filename+"_MASK.nii.gz");
	- else if ( itksys::SystemTools::FileExists(filename+"_MASK.nii") )
	- reader->SetFileName(filename+"_MASK.nii");
	- else
	- reader->SetFileName(filename+"_MASK.nrrd");
	- reader->Update();
	- m_SignalGen.m_MaskImage = reader->GetOutput();
	- m_SignalGen.m_ImageRegion = m_SignalGen.m_MaskImage->GetLargestPossibleRegion();
	- m_SignalGen.m_ImageSpacing = m_SignalGen.m_MaskImage->GetSpacing();
	- m_SignalGen.m_ImageOrigin = m_SignalGen.m_MaskImage->GetOrigin();
	- m_SignalGen.m_ImageDirection = m_SignalGen.m_MaskImage->GetDirection();
	- MITK_INFO << "Mask image loaded.";
	- }
	- catch(...)
	- {
	- MITK_INFO << "No mask image found.";
	- }
	-
	- setlocale(LC_ALL, currLocale.c_str());
	-}
	-
	-
	-void mitk::FiberfoxParameters::PrintSelf()
	-{
	- MITK_INFO << "Not implemented :(";
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.h b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.h
	deleted file mode 100644
	index 0aa0e29008..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.h
	+++ /dev/null
	@@ -1,339 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_FiberfoxParameters_H
	-#define _MITK_FiberfoxParameters_H
	-
	-#include <itkImageRegion.h>
	-#include <itkMatrix.h>
	-#include <mitkDiffusionNoiseModel.h>
	-#include <mitkDiffusionSignalModel.h>
	-#include <mitkDataNode.h>
	-#include <mitkRicianNoiseModel.h>
	-#include <mitkChiSquareNoiseModel.h>
	-#include <mitkImage.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <mitkPlanarEllipse.h>
	-#include <mitkStickModel.h>
	-#include <mitkTensorModel.h>
	-#include <mitkAstroStickModel.h>
	-#include <mitkBallModel.h>
	-#include <mitkDotModel.h>
	-#include <mitkRawShModel.h>
	-#include <boost/property_tree/ptree.hpp>
	-#include <boost/property_tree/xml_parser.hpp>
	-#include <boost/property_tree/json_parser.hpp>
	-#include <limits>
	-#include <MitkFiberTrackingExports.h>
	-#include <itkMersenneTwisterRandomVariateGenerator.h>
	-
	-namespace mitk
	-{
	- class MITKFIBERTRACKING_EXPORT FiberfoxParameters;
	-
	- /** Signal generation */
	- class MITKFIBERTRACKING_EXPORT SignalGenerationParameters
	- {
	- friend FiberfoxParameters;
	- public:
	- typedef itk::Image<float, 3> ItkFloatImgType;
	- typedef itk::Image<unsigned char, 3> ItkUcharImgType;
	- typedef itk::Vector<double,3> GradientType;
	- typedef std::vector<GradientType> GradientListType;
	-
	- enum CoilSensitivityProfile : int {
	- COIL_CONSTANT,
	- COIL_LINEAR,
	- COIL_EXPONENTIAL
	- };
	-
	- enum AcquisitionType : int
	- {
	- SingleShotEpi,
	- ConventionalSpinEcho,
	- FastSpinEcho,
	- };
	-
	- SignalGenerationParameters()
	- : m_AcquisitionType(SignalGenerationParameters::SingleShotEpi)
	- , m_SignalScale(100)
	- , m_tEcho(100)
	- , m_tRep(4000)
	- , m_tInv(0)
	- , m_tLine(1)
	- , m_tInhom(50)
	- , m_EchoTrainLength(8)
	- , m_ReversePhase(false)
	- , m_PartialFourier(1.0)
	- , m_NoiseVariance(0.001f)
	- , m_NumberOfCoils(1)
	- , m_CoilSensitivityProfile(SignalGenerationParameters::COIL_CONSTANT)
	- , m_CoilSensitivity(0.3f)
	- , m_SimulateKspaceAcquisition(false)
	- , m_AxonRadius(0)
	- , m_DoDisablePartialVolume(false)
	- , m_Spikes(0)
	- , m_SpikeAmplitude(1)
	- , m_KspaceLineOffset(0)
	- , m_EddyStrength(0.002f)
	- , m_Tau(70)
	- , m_CroppingFactor(1)
	- , m_Drift(0.06)
	- , m_DoAddGibbsRinging(false)
	- , m_ZeroRinging(0)
	- , m_DoSimulateRelaxation(true)
	- , m_DoAddMotion(false)
	- , m_DoRandomizeMotion(true)
	- , m_DoAddDrift(false)
	- , m_FrequencyMap(nullptr)
	- , m_MaskImage(nullptr)
	- , m_Bvalue(1000)
	- {
	- m_ImageRegion.SetSize(0, 12);
	- m_ImageRegion.SetSize(1, 12);
	- m_ImageRegion.SetSize(2, 3);
	- m_ImageSpacing.Fill(2.0);
	- m_ImageOrigin.Fill(0.0);
	- m_ImageDirection.SetIdentity();
	- m_Translation.Fill(0.0);
	- m_Rotation.Fill(0.0);
	- SetNumWeightedVolumes(6);
	- }
	-
	- /** input/output image specifications */
	- itk::ImageRegion<3> m_CroppedRegion; ///< Image size with reduced FOV.
	- itk::ImageRegion<3> m_ImageRegion; ///< Image size.
	- itk::Vector<float,3> m_ImageSpacing; ///< Image voxel size.
	- itk::Point<float,3> m_ImageOrigin; ///< Image origin.
	- itk::Matrix<double, 3, 3> m_ImageDirection; ///< Image rotation matrix.
	-
	- /** Other acquisitions parameters */
	- AcquisitionType m_AcquisitionType; ///< determines k-space trajectory and maximum echo position(s)
	- float m_SignalScale; ///< Scaling factor for output signal (before noise is added).
	- float m_tEcho; ///< Echo time TE.
	- float m_tRep; ///< Echo time TR.
	- float m_tInv; ///< Inversion time
	- float m_tLine; ///< k-space line readout time (dwell time).
	- float m_tInhom; ///< T2'
	- unsigned int m_EchoTrainLength; ///< Only relevant for Fast Spin Echo sequence (number of k-space lines acquired with one RF pulse)
	- bool m_ReversePhase; ///< If true, the phase readout direction will be inverted (-y instead of y)
	- float m_PartialFourier; ///< Partial fourier factor (0.5-1)
	- float m_NoiseVariance; ///< Variance of complex gaussian noise
	- unsigned int m_NumberOfCoils; ///< Number of coils in multi-coil acquisition
	- CoilSensitivityProfile m_CoilSensitivityProfile; ///< Choose between constant, linear or exponential sensitivity profile of the used coils
	- float m_CoilSensitivity; ///< signal remaining in slice center
	- bool m_SimulateKspaceAcquisition;///< Flag to enable/disable k-space acquisition simulation
	- double m_AxonRadius; ///< Determines compartment volume fractions (0 == automatic axon radius estimation)
	- bool m_DoDisablePartialVolume; ///< Disable partial volume effects. Each voxel is either all fiber or all non-fiber.
	-
	- /** Artifacts and other effects */
	- unsigned int m_Spikes; ///< Number of spikes randomly appearing in the image
	- float m_SpikeAmplitude; ///< amplitude of spikes relative to the largest signal intensity (magnitude of complex)
	- float m_KspaceLineOffset; ///< Causes N/2 ghosts. Larger offset means stronger ghost.
	- float m_EddyStrength; ///< Strength of eddy current induced gradients in mT/m.
	- float m_Tau; ///< Eddy current decay constant (in ms)
	- float m_CroppingFactor; ///< FOV size in y-direction is multiplied by this factor. Causes aliasing artifacts.
	- float m_Drift; ///< Global signal decrease by the end of the acquisition.
	- bool m_DoAddGibbsRinging; ///< Add Gibbs ringing artifact
	- int m_ZeroRinging; ///< If > 0, ringing is simulated by by setting the defined percentage of higher frequencies to 0 in k-space. Otherwise, the input to the k-space simulation is generated with twice the resolution and cropped during k-space simulation (much slower).
	- bool m_DoSimulateRelaxation; ///< Add T2 relaxation effects
	- bool m_DoAddMotion; ///< Enable motion artifacts.
	- bool m_DoRandomizeMotion; ///< Toggles between random and linear motion.
	- bool m_DoAddDrift; ///< Add quadratic signal drift.
	- std::vector< bool > m_MotionVolumes; ///< Indicates the image volumes that are affected by motion
	- ///< with positive numbers, inverted logic with negative numbers.
	- itk::Vector<float,3> m_Translation; ///< Maximum translational motion.
	- itk::Vector<float,3> m_Rotation; ///< Maximum rotational motion.
	- ItkFloatImgType::Pointer m_FrequencyMap; ///< If != nullptr, distortions are added to the image using this frequency map.
	- ItkUcharImgType::Pointer m_MaskImage; ///< Signal is only genrated inside of the mask image.
	-
	- std::vector< int > GetBaselineIndices(); ///< Returns list of nun-diffusion-weighted image volume indices
	- unsigned int GetFirstBaselineIndex(); ///< Returns index of first non-diffusion-weighted image volume
	- bool IsBaselineIndex(unsigned int idx); ///< Checks if image volume with given index is non-diffusion-weighted volume or not.
	- unsigned int GetNumWeightedVolumes(); ///< Get number of diffusion-weighted image volumes
	- unsigned int GetNumBaselineVolumes(); ///< Get number of non-diffusion-weighted image volumes
	- unsigned int GetNumVolumes(); ///< Get number of baseline and diffusion-weighted image volumes
	- GradientListType GetGradientDirections(); ///< Return gradient direction container
	- mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer GetItkGradientContainer();
	- GradientType GetGradientDirection(unsigned int i);
	- std::vector< int > GetBvalues(); ///< Returns a vector with all unique b-values (determined by the gradient magnitudes)
	- double GetBvalue();
	- void ApplyDirectionMatrix();
	-
	- protected:
	-
	- unsigned int m_NumGradients; ///< Number of diffusion-weighted image volumes.
	- unsigned int m_NumBaseline; ///< Number of non-diffusion-weighted image volumes.
	- GradientListType m_GradientDirections; ///< Total number of image volumes.
	- double m_Bvalue; ///< Acquisition b-value
	-
	- void SetNumWeightedVolumes(int numGradients); ///< Automaticall calls GenerateGradientHalfShell() afterwards.
	- void SetGradienDirections(GradientListType gradientList);
	- void SetGradienDirections(mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer gradientList);
	- void GenerateGradientHalfShell(); ///< Generates half shell of gradient directions (with m_NumGradients non-zero directions)
	- };
	-
	- /** Fiber generation */
	- class MITKFIBERTRACKING_EXPORT FiberGenerationParameters
	- {
	- public:
	-
	- enum FiberDistribution
	- {
	- DISTRIBUTE_UNIFORM, // distribute fibers uniformly in the ROIs
	- DISTRIBUTE_GAUSSIAN // distribute fibers using a 2D gaussian
	- };
	-
	- typedef std::vector< std::vector< mitk::PlanarEllipse::Pointer > > FiducialListType;
	- typedef std::vector< std::vector< unsigned int > > FlipListType;
	-
	- FiberGenerationParameters()
	- : m_Distribution(DISTRIBUTE_UNIFORM)
	- , m_Density(100)
	- , m_Variance(100)
	- , m_Sampling(1)
	- , m_Tension(0)
	- , m_Continuity(0)
	- , m_Bias(0)
	- {
	- m_Rotation.Fill(0.0);
	- m_Translation.Fill(0.0);
	- m_Scale.Fill(1.0);
	- }
	-
	- FiberDistribution m_Distribution;
	- unsigned int m_Density;
	- double m_Variance;
	- double m_Sampling;
	- double m_Tension;
	- double m_Continuity;
	- double m_Bias;
	- mitk::Vector3D m_Rotation;
	- mitk::Vector3D m_Translation;
	- mitk::Vector3D m_Scale;
	- FlipListType m_FlipList; ///< contains flags indicating a flip of the 2D fiber x-coordinates (needed to resolve some unwanted fiber twisting)
	- FiducialListType m_Fiducials; ///< container of the planar ellipses used as fiducials for the fiber generation process
	- };
	-
	- /** GUI persistence, input, output, ... */
	- class MITKFIBERTRACKING_EXPORT MiscFiberfoxParameters
	- {
	- public:
	- MiscFiberfoxParameters()
	- : m_ResultNode(DataNode::New())
	- , m_ParentNode(nullptr)
	- , m_SignalModelString("")
	- , m_ArtifactModelString("")
	- , m_OutputPath("/tmp/")
	- , m_OutputPrefix("fiberfox")
	- , m_AfterSimulationMessage("")
	- , m_BvalsFile("")
	- , m_BvecsFile("")
	- , m_OutputAdditionalImages(false)
	- , m_CheckAdvancedSignalOptionsBox(false)
	- , m_DoAddNoise(false)
	- , m_DoAddGhosts(false)
	- , m_DoAddAliasing(false)
	- , m_DoAddSpikes(false)
	- , m_DoAddEddyCurrents(false)
	- , m_DoAddDistortions(false)
	- , m_MotionVolumesBox("random")
	- , m_CheckRealTimeFibersBox(true)
	- , m_CheckAdvancedFiberOptionsBox(false)
	- , m_CheckConstantRadiusBox(false)
	- , m_CheckIncludeFiducialsBox(true)
	- {}
	-
	- DataNode::Pointer m_ResultNode; ///< Stores resulting image.
	- DataNode::Pointer m_ParentNode; ///< Parent node of result node.
	- std::string m_SignalModelString; ///< Appendet to the name of the result node
	- std::string m_ArtifactModelString; ///< Appendet to the name of the result node
	- std::string m_OutputPath; ///< Image is automatically saved to the specified folder after simulation is finished.
	- std::string m_OutputPrefix; /** Prefix for filename of output files and logfile. */
	- std::string m_AfterSimulationMessage; ///< Store messages that are displayed after the simulation has finished (e.g. warnings, automatic parameter adjustments etc.)
	- std::string m_BvalsFile;
	- std::string m_BvecsFile;
	-
	- /** member variables that store the check-state of GUI checkboxes */
	- // image generation
	- bool m_OutputAdditionalImages;
	- bool m_CheckAdvancedSignalOptionsBox;
	- bool m_DoAddNoise;
	- bool m_DoAddGhosts;
	- bool m_DoAddAliasing;
	- bool m_DoAddSpikes;
	- bool m_DoAddEddyCurrents;
	- bool m_DoAddDistortions;
	- std::string m_MotionVolumesBox;
	- // fiber generation
	- bool m_CheckRealTimeFibersBox;
	- bool m_CheckAdvancedFiberOptionsBox;
	- bool m_CheckConstantRadiusBox;
	- bool m_CheckIncludeFiducialsBox;
	- };
	-
	- /**
	- * \brief Datastructure to manage the Fiberfox signal generation parameters.
	- *
	- */
	- class MITKFIBERTRACKING_EXPORT FiberfoxParameters
	- {
	-
	- public:
	-
	-
	- typedef itk::Image<float, 3> ItkFloatImgType;
	- typedef itk::Image<double, 3> ItkDoubleImgType;
	- typedef itk::Image<unsigned char, 3> ItkUcharImgType;
	- typedef DiffusionSignalModel<double> DiffusionModelType;
	- typedef std::vector< DiffusionModelType* > DiffusionModelListType;
	- typedef DiffusionNoiseModel<double> NoiseModelType;
	-
	- FiberfoxParameters();
	- FiberfoxParameters(const FiberfoxParameters &params);
	- ~FiberfoxParameters();
	-
	- /** Not templated parameters */
	- FiberGenerationParameters m_FiberGen; ///< Fiber generation parameters
	- SignalGenerationParameters m_SignalGen; ///< Signal generation parameters
	- MiscFiberfoxParameters m_Misc; ///< GUI realted and I/O parameters
	-
	- /** Templated parameters */
	- DiffusionModelListType m_FiberModelList; ///< Intra- and inter-axonal compartments.
	- DiffusionModelListType m_NonFiberModelList; ///< Extra-axonal compartments.
	- std::shared_ptr< NoiseModelType > m_NoiseModel; ///< If != nullptr, noise is added to the image.
	-
	- void GenerateGradientHalfShell();
	- void SetNumWeightedVolumes(int numGradients); ///< Automaticall calls GenerateGradientHalfShell() afterwards.
	- void SetGradienDirections(mitk::SignalGenerationParameters::GradientListType gradientList);
	- void SetGradienDirections(mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer gradientList);
	- void SetBvalue(double Bvalue);
	- void UpdateSignalModels();
	- void ClearFiberParameters();
	- void ClearSignalParameters();
	- void ApplyDirectionMatrix();
	-
	- void PrintSelf(); ///< Print parameters to stdout.
	- void SaveParameters(std::string filename); ///< Save image generation parameters to .ffp file.
	- void LoadParameters(std::string filename, bool fix_seed=false); ///< Load image generation parameters from .ffp file.
	- template< class ParameterType >
	- ParameterType ReadVal(boost::property_tree::ptree::value_type const& v, std::string tag, ParameterType defaultValue, bool essential=false);
	- std::string m_MissingTags;
	- };
	-}
	-
	-#endif
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkStreamlineTractographyParameters.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkStreamlineTractographyParameters.cpp
	deleted file mode 100644
	index 9f704669d5..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkStreamlineTractographyParameters.cpp
	+++ /dev/null
	@@ -1,367 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <boost/foreach.hpp>
	-#include <mitkLexicalCast.h>
	-#include <itkImageFileWriter.h>
	-#include <itkImageFileReader.h>
	-#include <mitkLog.h>
	-#include <algorithm>
	-#include <string>
	-#include <mitkStreamlineTractographyParameters.h>
	-#include <mitkDiffusionFunctionCollection.h>
	-
	-mitk::StreamlineTractographyParameters::StreamlineTractographyParameters()
	-{
	- AutoAdjust();
	-}
	-
	-mitk::StreamlineTractographyParameters::~StreamlineTractographyParameters()
	-{
	-
	-}
	-
	-void mitk::StreamlineTractographyParameters::SaveParameters(std::string filename)
	-{
	- if(filename.empty())
	- return;
	- if(".stp"!=filename.substr(filename.size()-4, 4))
	- filename += ".stp";
	-
	- const std::string& locale = "C";
	- const std::string& currLocale = setlocale( LC_ALL, nullptr );
	-
	- if ( locale.compare(currLocale)!=0 )
	- {
	- try
	- {
	- setlocale(LC_ALL, locale.c_str());
	- }
	- catch(...)
	- {
	- MITK_INFO << "Could not set locale " << locale;
	- }
	- }
	-
	- boost::property_tree::ptree parameters;
	-
	- parameters.put("seeding.seeds_per_voxel", m_SeedsPerVoxel);
	- parameters.put("seeding.trials_per_seed", m_TrialsPerSeed);
	- parameters.put("seeding.max_num_fibers", m_MaxNumFibers);
	- parameters.put("seeding.interactive_radius_mm", m_InteractiveRadiusMm);
	- parameters.put("seeding.num_interactive_seeds", m_NumInteractiveSeeds);
	- parameters.put("seeding.enable_interactive", m_EnableInteractive);
	-
	- parameters.put("roi_constraints.ep_constraints", m_EpConstraints);
	-
	- parameters.put("tractography.mode", m_Mode);
	- parameters.put("tractography.sharpen_odfs", m_SharpenOdfs);
	- parameters.put("tractography.cutoff", m_Cutoff);
	- parameters.put("tractography.odf_cutoff", m_OdfCutoff);
	- parameters.put("tractography.step_size_vox", m_StepSizeVox);
	- parameters.put("tractography.min_tract_length_mm", m_MinTractLengthMm);
	- parameters.put("tractography.max_tract_length_mm", m_MaxTractLengthMm);
	- parameters.put("tractography.angluar_threshold_deg", m_AngularThresholdDeg);
	- parameters.put("tractography.loop_check_deg", m_LoopCheckDeg);
	- parameters.put("tractography.f", m_F);
	- parameters.put("tractography.g", m_G);
	- parameters.put("tractography.fix_seed", m_FixRandomSeed);
	- parameters.put("tractography.peak_jitter", m_PeakJitter);
	-
	- parameters.put("prior.weight", m_Weight);
	- parameters.put("prior.restrict_to_prior", m_RestrictToPrior);
	- parameters.put("prior.new_directions", m_NewDirectionsFromPrior);
	- parameters.put("prior.flip_x", m_PriorFlipX);
	- parameters.put("prior.flip_y", m_PriorFlipY);
	- parameters.put("prior.flip_z", m_PriorFlipZ);
	-
	- parameters.put("nsampling.num_samples", m_NumSamples);
	- parameters.put("nsampling.sampling_distance_vox", m_SamplingDistanceVox);
	- parameters.put("nsampling.only_frontal", m_OnlyForwardSamples);
	- parameters.put("nsampling.stop_votes", m_StopVotes);
	-
	- parameters.put("data_handling.flip_x", m_FlipX);
	- parameters.put("data_handling.flip_y", m_FlipY);
	- parameters.put("data_handling.flip_z", m_FlipZ);
	- parameters.put("data_handling.interpolate_tracto_data", m_InterpolateTractographyData);
	- parameters.put("data_handling.interpolate_roi_images", m_InterpolateRoiImages);
	-
	- parameters.put("output.compress", m_CompressFibers);
	- parameters.put("output.compression", m_Compression);
	- parameters.put("output.prob_map", m_OutputProbMap);
	-
	- boost::property_tree::json_parser::write_json(filename, parameters, std::locale(), true);
	-
	-// try{
	-// itk::ImageFileWriter<ItkFloatImgType>::Pointer writer = itk::ImageFileWriter<ItkFloatImgType>::New();
	-// writer->SetFileName(filename+"_FMAP.nii.gz");
	-// writer->SetInput(m_SignalGen.m_FrequencyMap);
	-// writer->Update();
	-// }
	-// catch(...)
	-// {
	-// MITK_INFO << "No frequency map saved.";
	-// }
	-
	- setlocale(LC_ALL, currLocale.c_str());
	-}
	-
	-
	-
	-template< class ParameterType >
	-ParameterType mitk::StreamlineTractographyParameters::ReadVal(boost::property_tree::ptree::value_type const& v, std::string tag, ParameterType defaultValue, bool essential)
	-{
	- try
	- {
	- return v.second.get<ParameterType>(tag);
	- }
	- catch (...)
	- {
	- if (essential)
	- {
	- mitkThrow() << "Parameter file corrupted. Essential tag is missing: '" << tag << "'";
	- }
	- MITK_INFO << "Tag '" << tag << "' not found. Using default value '" << defaultValue << "'.";
	- return defaultValue;
	- }
	-}
	-
	-void mitk::StreamlineTractographyParameters::LoadParameters(std::string filename)
	-{
	- if(filename.empty()) { return; }
	-
	- const std::string& locale = "C";
	- const std::string& currLocale = setlocale( LC_ALL, nullptr );
	-
	- if ( locale.compare(currLocale)!=0 )
	- {
	- try
	- {
	- setlocale(LC_ALL, locale.c_str());
	- }
	- catch(...)
	- {
	- MITK_INFO << "Could not set locale " << locale;
	- }
	- }
	-
	-
	- boost::property_tree::ptree parameterTree;
	- boost::property_tree::json_parser::read_json( filename, parameterTree );
	-
	- BOOST_FOREACH( boost::property_tree::ptree::value_type const& v1, parameterTree )
	- {
	- if( v1.first == "seeding" )
	- {
	- m_SeedsPerVoxel = ReadVal<unsigned int>(v1,"seeds_per_voxel", m_SeedsPerVoxel);
	- m_TrialsPerSeed = ReadVal<unsigned int>(v1,"trials_per_seed", m_TrialsPerSeed);
	- m_MaxNumFibers = ReadVal<int>(v1,"max_num_fibers", m_MaxNumFibers);
	- m_InteractiveRadiusMm = ReadVal<float>(v1,"interactive_radius_mm", m_InteractiveRadiusMm);
	- m_NumInteractiveSeeds = ReadVal<unsigned int>(v1,"num_interactive_seeds", m_NumInteractiveSeeds);
	- m_EnableInteractive = ReadVal<bool>(v1,"enable_interactive", m_EnableInteractive);
	- }
	- else if( v1.first == "roi_constraints" )
	- {
	- switch( ReadVal<int>(v1,"ep_constraints", 0) )
	- {
	- default:
	- m_EpConstraints = EndpointConstraints::NONE;
	- break;
	- case 1:
	- m_EpConstraints = EndpointConstraints::EPS_IN_TARGET;
	- break;
	- case 2:
	- m_EpConstraints = EndpointConstraints::EPS_IN_TARGET_LABELDIFF;
	- break;
	- case 3:
	- m_EpConstraints = EndpointConstraints::EPS_IN_SEED_AND_TARGET;
	- break;
	- case 4:
	- m_EpConstraints = EndpointConstraints::MIN_ONE_EP_IN_TARGET;
	- break;
	- case 5:
	- m_EpConstraints = EndpointConstraints::ONE_EP_IN_TARGET;
	- break;
	- case 6:
	- m_EpConstraints = EndpointConstraints::NO_EP_IN_TARGET;
	- break;
	- }
	- }
	- else if( v1.first == "tractography" )
	- {
	- if(ReadVal<int>(v1,"mode", 0) == 0)
	- m_Mode = MODE::DETERMINISTIC;
	- else
	- m_Mode = MODE::PROBABILISTIC;
	-
	- m_SharpenOdfs = ReadVal<bool>(v1,"sharpen_odfs", m_SharpenOdfs);
	- m_Cutoff = ReadVal<float>(v1,"cutoff", m_Cutoff);
	- m_OdfCutoff = ReadVal<float>(v1,"odf_cutoff", m_OdfCutoff);
	- SetStepSizeVox(ReadVal<float>(v1,"step_size_vox", m_StepSizeVox));
	- m_MinTractLengthMm = ReadVal<float>(v1,"min_tract_length_mm", m_MinTractLengthMm);
	- m_MaxTractLengthMm = ReadVal<float>(v1,"max_tract_length_mm", m_MaxTractLengthMm);
	- SetAngularThresholdDeg(ReadVal<float>(v1,"angluar_threshold_deg", m_AngularThresholdDeg));
	- SetLoopCheckDeg(ReadVal<float>(v1,"loop_check_deg", m_LoopCheckDeg));
	- m_F = ReadVal<float>(v1,"f", m_F);
	- m_G = ReadVal<float>(v1,"g", m_G);
	- m_FixRandomSeed = ReadVal<bool>(v1,"fix_seed", m_FixRandomSeed);
	- m_PeakJitter = ReadVal<float>(v1,"peak_jitter", m_PeakJitter);
	- }
	- else if( v1.first == "prior" )
	- {
	- m_Weight = ReadVal<float>(v1,"weight", m_Weight);
	- m_RestrictToPrior = ReadVal<bool>(v1,"restrict_to_prior", m_RestrictToPrior);
	- m_NewDirectionsFromPrior = ReadVal<bool>(v1,"new_directions", m_NewDirectionsFromPrior);
	- m_PriorFlipX = ReadVal<bool>(v1,"flip_x", m_PriorFlipX);
	- m_PriorFlipY = ReadVal<bool>(v1,"flip_y", m_PriorFlipY);
	- m_PriorFlipZ = ReadVal<bool>(v1,"flip_z", m_PriorFlipZ);
	- }
	- else if( v1.first == "nsampling" )
	- {
	- m_NumSamples = ReadVal<unsigned int>(v1,"num_samples", m_NumSamples);
	- m_SamplingDistanceVox = ReadVal<float>(v1,"sampling_distance_vox", m_SamplingDistanceVox);
	- m_OnlyForwardSamples = ReadVal<bool>(v1,"only_frontal", m_OnlyForwardSamples);
	- m_StopVotes = ReadVal<bool>(v1,"stop_votes", m_StopVotes);
	- }
	- else if( v1.first == "data_handling" )
	- {
	- m_FlipX = ReadVal<bool>(v1,"flip_x", m_FlipX);
	- m_FlipY = ReadVal<bool>(v1,"flip_y", m_FlipY);
	- m_FlipZ = ReadVal<bool>(v1,"flip_z", m_FlipZ);
	- m_InterpolateTractographyData = ReadVal<bool>(v1,"interpolate_tracto_data", m_InterpolateTractographyData);
	- m_InterpolateRoiImages = ReadVal<bool>(v1,"interpolate_roi_images", m_InterpolateRoiImages);
	- }
	- else if( v1.first == "output" )
	- {
	- m_CompressFibers = ReadVal<bool>(v1,"compress", m_CompressFibers);
	- m_Compression = ReadVal<float>(v1,"compression", m_Compression);
	- m_OutputProbMap = ReadVal<bool>(v1,"prob_map", m_OutputProbMap);
	- }
	- }
	-
	-// try
	-// {
	-// itk::ImageFileReader<ItkFloatImgType>::Pointer reader = itk::ImageFileReader<ItkFloatImgType>::New();
	-// reader->SetFileName(filename+"_FMAP.nrrd");
	-// if ( itksys::SystemTools::FileExists(filename+"_FMAP.nii.gz") )
	-// reader->SetFileName(filename+"_FMAP.nii.gz");
	-// else if ( itksys::SystemTools::FileExists(filename+"_FMAP.nii") )
	-// reader->SetFileName(filename+"_FMAP.nii");
	-// else
	-// reader->SetFileName(filename+"_FMAP.nrrd");
	-// reader->Update();
	-// m_SignalGen.m_FrequencyMap = reader->GetOutput();
	-// MITK_INFO << "Frequency map loaded.";
	-// }
	-// catch(...)
	-// {
	-// MITK_INFO << "No frequency map found.";
	-// }
	-
	- setlocale(LC_ALL, currLocale.c_str());
	-}
	-
	-float mitk::StreamlineTractographyParameters::GetSamplingDistanceMm() const
	-{
	- return m_SamplingDistanceMm;
	-}
	-
	-void mitk::StreamlineTractographyParameters::SetSamplingDistanceVox(float sampling_distance_vox)
	-{
	- m_SamplingDistanceVox = sampling_distance_vox;
	- AutoAdjust();
	-}
	-
	-void mitk::StreamlineTractographyParameters::AutoAdjust()
	-{
	- if (m_StepSizeVox<static_cast<float>(mitk::eps))
	- m_StepSizeVox = 0.5;
	- m_StepSizeMm = m_StepSizeVox*m_MinVoxelSizeMm;
	-
	- if (m_AngularThresholdDeg<0)
	- {
	- if (m_StepSizeMm/m_MinVoxelSizeMm<=0.966f) // minimum 15° for automatic estimation
	- m_AngularThresholdDot = static_cast<float>(std::cos( 0.5 * itk::Math::pi * static_cast<double>(m_StepSizeMm/m_MinVoxelSizeMm) ));
	- else
	- m_AngularThresholdDot = static_cast<float>(std::cos( 0.5 * itk::Math::pi * 0.966 ));
	-
	- m_AngularThresholdDeg = std::acos(m_AngularThresholdDot)*180.0/itk::Math::pi;
	- }
	- else
	- m_AngularThresholdDot = static_cast<float>(std::cos( static_cast<double>(m_AngularThresholdDeg)*itk::Math::pi/180.0 ));
	-
	- if (m_SamplingDistanceVox<static_cast<float>(mitk::eps))
	- m_SamplingDistanceVox = m_MinVoxelSizeMm*0.25f;
	- m_SamplingDistanceMm = m_SamplingDistanceVox*m_MinVoxelSizeMm;
	-}
	-
	-float mitk::StreamlineTractographyParameters::GetStepSizeVox() const
	-{
	- return m_StepSizeVox;
	-}
	-
	-float mitk::StreamlineTractographyParameters::GetAngularThresholdDeg() const
	-{
	- return m_AngularThresholdDeg;
	-}
	-
	-float mitk::StreamlineTractographyParameters::GetSamplingDistanceVox() const
	-{
	- return m_SamplingDistanceVox;
	-}
	-
	-float mitk::StreamlineTractographyParameters::GetMinVoxelSizeMm() const
	-{
	- return m_MinVoxelSizeMm;
	-}
	-
	-float mitk::StreamlineTractographyParameters::GetStepSizeMm() const
	-{
	- return m_StepSizeMm;
	-}
	-
	-void mitk::StreamlineTractographyParameters::SetMinVoxelSizeMm(float min_voxel_size_mm)
	-{
	- m_MinVoxelSizeMm = min_voxel_size_mm;
	- AutoAdjust();
	-}
	-
	-float mitk::StreamlineTractographyParameters::GetAngularThresholdDot() const
	-{
	- return m_AngularThresholdDot;
	-}
	-
	-void mitk::StreamlineTractographyParameters::SetStepSizeVox(float step_size_vox)
	-{
	- m_StepSizeVox = step_size_vox;
	- AutoAdjust();
	-}
	-
	-float mitk::StreamlineTractographyParameters::GetLoopCheckDeg() const
	-{
	- return m_LoopCheckDeg;
	-}
	-
	-void mitk::StreamlineTractographyParameters::SetLoopCheckDeg(float loop_check_deg)
	-{
	- m_LoopCheckDeg = loop_check_deg;
	-}
	-
	-void mitk::StreamlineTractographyParameters::SetAngularThresholdDeg(float angular_threshold_deg)
	-{
	- m_AngularThresholdDeg = angular_threshold_deg;
	- AutoAdjust();
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkStreamlineTractographyParameters.h b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkStreamlineTractographyParameters.h
	deleted file mode 100644
	index d85cd78644..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkStreamlineTractographyParameters.h
	+++ /dev/null
	@@ -1,163 +0,0 @@
	-#pragma once
	-
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkImage.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <boost/property_tree/ptree.hpp>
	-#include <boost/property_tree/json_parser.hpp>
	-#include <MitkFiberTrackingExports.h>
	-
	-namespace mitk
	-{
	- /**
	- * \brief Datastructure to manage streamline tractography parameters.
	- *
	- */
	- class MITKFIBERTRACKING_EXPORT StreamlineTractographyParameters
	- {
	-
	- public:
	-
	- enum EndpointConstraints {
	- NONE, ///< No constraints on endpoint locations
	- EPS_IN_TARGET, ///< Both EPs are required to be located in the target image
	- EPS_IN_TARGET_LABELDIFF, ///< Both EPs are required to be located in the target image and the image values at the respective position needs to be distinct
	- EPS_IN_SEED_AND_TARGET, ///< One EP is required to be located in the seed image and one in the target image
	- MIN_ONE_EP_IN_TARGET, ///< At least one EP is required to be located in the target image
	- ONE_EP_IN_TARGET, ///< Exactly one EP is required to be located in the target image
	- NO_EP_IN_TARGET ///< No EP is allowed to be located in the target image
	- };
	-
	- enum MODE {
	- DETERMINISTIC,
	- PROBABILISTIC
	- };
	-
	- typedef itk::Image<float, 3> ItkFloatImgType;
	- typedef itk::Image<double, 3> ItkDoubleImgType;
	- typedef itk::Image<unsigned char, 3> ItkUcharImgType;
	-
	- StreamlineTractographyParameters();
	- StreamlineTractographyParameters(const StreamlineTractographyParameters &params) = default;
	- ~StreamlineTractographyParameters();
	-
	- void SaveParameters(std::string filename); ///< Save image generation parameters to .stp file.
	- void LoadParameters(std::string filename); ///< Load image generation parameters from .stp file.
	-
	- template< class ParameterType >
	- ParameterType ReadVal(boost::property_tree::ptree::value_type const& v, std::string tag, ParameterType defaultValue, bool essential=false);
	-
	- // seeding
	- unsigned int m_SeedsPerVoxel = 1;
	- unsigned int m_TrialsPerSeed = 10;
	- int m_MaxNumFibers = -1;
	- // - seed image
	-
	- // interactive
	- float m_InteractiveRadiusMm = 2;
	- unsigned int m_NumInteractiveSeeds = 50;
	- bool m_EnableInteractive = false;
	-
	- // ROI constraints
	- EndpointConstraints m_EpConstraints;
	- // - mask image
	- // - stop image
	- // - exclusion image
	- // - target image
	-
	- // tractography
	- MODE m_Mode= MODE::DETERMINISTIC;
	- bool m_SharpenOdfs = false;
	- float m_Cutoff = 0.1;
	- // - fa/gfa image
	- float m_OdfCutoff = 0.00025;
	- float m_MinTractLengthMm = 20;
	- float m_MaxTractLengthMm = 400;
	- float m_F = 1;
	- float m_G = 0;
	- bool m_FixRandomSeed = false;
	- unsigned int m_NumPreviousDirections = 1;
	- float m_PeakJitter = 0.01; // actual jitter is drawn from a normal distribution with m_PeakJitter*fabs(direction_value) as standard deviation
	-
	- // prior
	- // - peak image
	- float m_Weight = 0.5;
	- bool m_RestrictToPrior = true;
	- bool m_NewDirectionsFromPrior = true;
	- bool m_PriorFlipX = false;
	- bool m_PriorFlipY = false;
	- bool m_PriorFlipZ = false;
	-
	- // neighborhood sampling
	- unsigned int m_NumSamples = 0;
	- bool m_OnlyForwardSamples = false;
	- bool m_StopVotes = false;
	- bool m_AvoidStop = true;
	- bool m_RandomSampling = false;
	- float m_DeflectionMod = 1.0;
	-
	- // data handling
	- bool m_FlipX = false;
	- bool m_FlipY = false;
	- bool m_FlipZ = false;
	- bool m_InterpolateTractographyData = true;
	- bool m_InterpolateRoiImages;
	- bool m_ApplyDirectionMatrix = false;
	-
	- // output and postprocessing
	- bool m_CompressFibers = true;
	- float m_Compression = 0.1;
	- bool m_OutputProbMap = false;
	-
	- float GetAngularThresholdDot() const;
	- float GetAngularThresholdDeg() const;
	- void SetAngularThresholdDeg(float angular_threshold_deg);
	-
	- float GetLoopCheckDeg() const;
	- void SetLoopCheckDeg(float loop_check_deg);
	-
	- float GetStepSizeMm() const;
	- float GetStepSizeVox() const;
	- void SetStepSizeVox(float step_size_vox);
	-
	- float GetSamplingDistanceMm() const;
	- float GetSamplingDistanceVox() const;
	- void SetSamplingDistanceVox(float sampling_distance_vox);
	-
	- void SetMinVoxelSizeMm(float min_voxel_size_mm);
	- float GetMinVoxelSizeMm() const;
	-
	- private:
	-
	- void AutoAdjust();
	-
	- float m_SamplingDistanceVox = -1;
	- float m_SamplingDistanceMm;
	-
	- float m_AngularThresholdDeg = -1;
	- float m_AngularThresholdDot;
	-
	- float m_LoopCheckDeg = -1;
	-
	- float m_StepSizeVox = -1;
	- float m_StepSizeMm;
	-
	- float m_MinVoxelSizeMm = 1.0;
	- };
	-}
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkTractographyForest.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkTractographyForest.cpp
	deleted file mode 100755
	index 9de8432872..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkTractographyForest.cpp
	+++ /dev/null
	@@ -1,117 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#define _USE_MATH_DEFINES
	-#include "mitkTractographyForest.h"
	-#include <mitkExceptionMacro.h>
	-#include <mitkGeometry3D.h>
	-
	-namespace mitk
	-{
	-
	-TractographyForest::TractographyForest( std::shared_ptr< vigra::RandomForest<int> > forest )
	-{
	- m_Forest = forest;
	- mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New();
	- SetGeometry(geometry);
	-}
	-
	-TractographyForest::~TractographyForest()
	-{
	-
	-}
	-
	-void TractographyForest::PredictProbabilities(vigra::MultiArray<2, float>& features, vigra::MultiArray<2, float>& probabilities) const
	-{
	- m_Forest->predictProbabilities(features, probabilities);
	-}
	-
	-int TractographyForest::GetNumFeatures() const
	-{
	- if (!HasForest())
	- mitkThrow() << "Forest is NULL";
	- return m_Forest->feature_count();
	-}
	-
	-int TractographyForest::GetNumTrees() const
	-{
	- if (!HasForest())
	- mitkThrow() << "Forest is NULL";
	- return m_Forest->tree_count();
	-}
	-
	-int TractographyForest::GetNumClasses() const
	-{
	- if (!HasForest())
	- mitkThrow() << "Forest is NULL";
	- return m_Forest->class_count();
	-}
	-
	-int TractographyForest::GetMaxTreeDepth() const
	-{
	- if (!HasForest())
	- mitkThrow() << "Forest is NULL";
	- return m_Forest->ext_param_.max_tree_depth;
	-}
	-
	-int TractographyForest::IndexToClassLabel(int idx) const
	-{
	- if (!HasForest())
	- mitkThrow() << "Forest is NULL";
	- unsigned int classLabel = 0;
	- m_Forest->ext_param_.to_classlabel(idx, classLabel);
	- return classLabel;
	-}
	-
	-bool TractographyForest::HasForest() const
	-{
	- return m_Forest!=nullptr;
	-}
	-
	-void TractographyForest::PrintSelf(std::ostream &os, itk::Indent indent) const
	-{
	-// Superclass::PrintSelf(os, indent);
	- os << indent << this->GetNameOfClass() << ":\n";
	- os << indent << "Number of features: " << GetNumFeatures() << std::endl;
	- os << indent << "Number of classes: " << GetNumClasses() << std::endl;
	- os << indent << "Number of trees: " << GetNumTrees() << std::endl;
	- os << indent << "Maximum tree depth: " << GetMaxTreeDepth() << std::endl;
	-}
	-
	-/* ESSENTIAL IMPLEMENTATION OF SUPERCLASS METHODS */
	-void TractographyForest::UpdateOutputInformation()
	-{
	-
	-}
	-void TractographyForest::SetRequestedRegionToLargestPossibleRegion()
	-{
	-
	-}
	-bool TractographyForest::RequestedRegionIsOutsideOfTheBufferedRegion()
	-{
	- return false;
	-}
	-bool TractographyForest::VerifyRequestedRegion()
	-{
	- return true;
	-}
	-void TractographyForest::SetRequestedRegion(const itk::DataObject* )
	-{
	-
	-}
	-
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkTractographyForest.h b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkTractographyForest.h
	deleted file mode 100644
	index e004f40ef5..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkTractographyForest.h
	+++ /dev/null
	@@ -1,72 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef _MITK_TractographyForest_H
	-#define _MITK_TractographyForest_H
	-
	-#include <mitkBaseData.h>
	-#include <MitkFiberTrackingExports.h>
	-
	-#undef DIFFERENCE
	-#define VIGRA_STATIC_LIB
	-#include <vigra/random_forest.hxx>
	-
	-namespace mitk {
	-
	-/**
	- * \brief Class containing random forest datastructures used for fiber tractography; */
	-class MITKFIBERTRACKING_EXPORT TractographyForest : public BaseData
	-{
	-public:
	-
	- void UpdateOutputInformation() override;
	- void SetRequestedRegionToLargestPossibleRegion() override;
	- bool RequestedRegionIsOutsideOfTheBufferedRegion() override;
	- bool VerifyRequestedRegion() override;
	- void SetRequestedRegion(const itk::DataObject*) override;
	-
	- mitkClassMacro( TractographyForest, BaseData )
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	- mitkNewMacro1Param(Self, std::shared_ptr< vigra::RandomForest<int> >) // custom constructor
	-
	- int GetNumFeatures() const;
	- int GetNumTrees() const;
	- int GetNumClasses() const;
	- int GetMaxTreeDepth() const;
	- int IndexToClassLabel(int idx) const;
	- bool HasForest() const;
	- void PredictProbabilities(vigra::MultiArray<2, float>& features, vigra::MultiArray<2, float>& probabilities) const;
	- std::shared_ptr< const vigra::RandomForest<int> > GetForest() const
	- { return m_Forest; }
	-
	-protected:
	-
	- TractographyForest( std::shared_ptr< vigra::RandomForest<int> > forest = nullptr );
	- ~TractographyForest() override;
	-
	- void PrintSelf(std::ostream &os, itk::Indent indent) const override;
	-
	-private:
	-
	- std::shared_ptr< vigra::RandomForest<int> > m_Forest; ///< random forest classifier
	-
	-};
	-
	-} // namespace mitk
	-
	-#endif /* _MITK_TractographyForest_H */
	diff --git a/Modules/DiffusionImaging/FiberTracking/Rendering/mitkFiberBundleThreadMonitorMapper3D.cpp b/Modules/DiffusionImaging/FiberTracking/Rendering/mitkFiberBundleThreadMonitorMapper3D.cpp
	deleted file mode 100644
	index 9dc5a40e1a..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Rendering/mitkFiberBundleThreadMonitorMapper3D.cpp
	+++ /dev/null
	@@ -1,196 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-
	-#include "mitkFiberBundleThreadMonitorMapper3D.h"
	-#include <mitkProperties.h>
	-#include <vtkPropAssembly.h>
	-//#include <vtkTextActor.h>
	-#include <vtkTextProperty.h>
	-
	-
	-
	-
	-mitk::FiberBundleThreadMonitorMapper3D::FiberBundleThreadMonitorMapper3D()
	-: m_FiberMonitorMapper(vtkSmartPointer<vtkPolyDataMapper>::New())
	-, m_TextActorClose(vtkSmartPointer<vtkTextActor>::New())
	-, m_TextActorOpen(vtkSmartPointer<vtkTextActor>::New())
	-, m_TextActorHeading(vtkSmartPointer<vtkTextActor>::New())
	-, m_TextActorMask(vtkSmartPointer<vtkTextActor>::New())
	-, m_TextActorStatus(vtkSmartPointer<vtkTextActor>::New())
	-, m_TextActorStarted(vtkSmartPointer<vtkTextActor>::New())
	-, m_TextActorFinished(vtkSmartPointer<vtkTextActor>::New())
	-, m_TextActorTerminated(vtkSmartPointer<vtkTextActor>::New())
	-, m_FiberAssembly(vtkPropAssembly::New())
	-, m_lastModifiedMonitorNodeTime(-1)
	-{
	- m_FiberAssembly->AddPart(m_TextActorClose);
	- m_FiberAssembly->AddPart(m_TextActorOpen);
	- m_FiberAssembly->AddPart(m_TextActorHeading);
	- m_FiberAssembly->AddPart(m_TextActorMask);
	- m_FiberAssembly->AddPart(m_TextActorStatus);
	- m_FiberAssembly->AddPart(m_TextActorStarted);
	- m_FiberAssembly->AddPart(m_TextActorFinished);
	- m_FiberAssembly->AddPart(m_TextActorTerminated);
	-
	-}
	-
	-
	-mitk::FiberBundleThreadMonitorMapper3D::~FiberBundleThreadMonitorMapper3D()
	-{
	- m_FiberAssembly->Delete();
	-}
	-
	-
	-const mitk::FiberBundleThreadMonitor* mitk::FiberBundleThreadMonitorMapper3D::GetInput()
	-{
	- return static_cast<const mitk::FiberBundleThreadMonitor * > ( GetDataNode()->GetData() );
	-}
	-
	-
	-/*
	- This method is called once the mapper gets new input,
	- for UI rotation or changes in colorcoding this method is NOT called
	- */
	-void mitk::FiberBundleThreadMonitorMapper3D::GenerateDataForRenderer( mitk::BaseRenderer *renderer )
	-{
	- bool visible = true;
	- GetDataNode()->GetVisibility(visible, renderer, "visible");
	-
	- if ( !visible ) return;
	-
	- const DataNode *node = this->GetDataNode();
	-
	- if (m_lastModifiedMonitorNodeTime >= node->GetMTime())
	- return;
	-
	- m_lastModifiedMonitorNodeTime = node->GetMTime();
	-
	- // MITK_INFO << m_LastUpdateTime;
	- FiberBundleThreadMonitor* monitor = dynamic_cast<FiberBundleThreadMonitor * > ( GetDataNode()->GetData() );
	-
	-// m_TextActor->SetInput( monitor->getTextL1().toStdString().c_str() );
	- m_TextActorClose->SetInput( monitor->getBracketClose().toStdString().c_str() );
	- vtkTextProperty* tpropClose = m_TextActorClose->GetTextProperty();
	- //tprop->SetFontFamilyToArial ();
	- //tprop->SetLineSpacing(1.0);
	- tpropClose->SetFontSize(16);
	- tpropClose->SetColor(0.85,0.8,0.8);
	- m_TextActorClose->SetDisplayPosition( monitor->getBracketClosePosition()[0], monitor->getBracketClosePosition()[1] );
	- //m_TextActorClose->Modified();
	-
	-
	- m_TextActorOpen->SetInput( monitor->getBracketOpen().toStdString().c_str() );
	- vtkTextProperty* tpropOpen = m_TextActorOpen->GetTextProperty();
	- //tprop->SetFontFamilyToArial ();
	- //tprop->SetLineSpacing(1.0);
	- tpropOpen->SetFontSize(16);
	- tpropOpen->SetColor(0.85,0.8,0.8);
	- m_TextActorOpen->SetDisplayPosition( monitor->getBracketOpenPosition()[0], monitor->getBracketOpenPosition()[1] );
	- //m_TextActorOpen->Modified();
	-
	-
	- m_TextActorHeading->SetInput( monitor->getHeading().toStdString().c_str() );
	- vtkTextProperty* tpropHeading = m_TextActorHeading->GetTextProperty();
	- tpropHeading->SetFontSize(12);
	- tpropHeading->SetOpacity( monitor->getHeadingOpacity() * 0.1 );
	- tpropHeading->SetColor(0.85,0.8,0.8);
	- m_TextActorHeading->SetDisplayPosition( monitor->getHeadingPosition()[0], monitor->getHeadingPosition()[1] );
	- //m_TextActorHeading->Modified();
	-
	-
	- m_TextActorMask->SetInput( monitor->getMask().toStdString().c_str() );
	- vtkTextProperty* tpropMask = m_TextActorMask->GetTextProperty();
	- tpropMask->SetFontSize(12);
	- tpropMask->SetOpacity( monitor->getMaskOpacity() * 0.1 );
	- tpropMask->SetColor(1.0,1.0,1.0);
	- m_TextActorMask->SetDisplayPosition( monitor->getMaskPosition()[0], monitor->getMaskPosition()[1] );
	- //m_TextActorHeading->Modified();
	-
	-
	- m_TextActorStatus->SetInput(monitor->getStatus().toStdString().c_str());
	- vtkTextProperty* tpropStatus = m_TextActorStatus->GetTextProperty();
	- tpropStatus->SetFontSize(10);
	- tpropStatus->SetOpacity( monitor->getStatusOpacity() * 0.1 );
	- tpropStatus->SetColor(0.85,0.8,0.8);
	- m_TextActorStatus->SetDisplayPosition( monitor->getStatusPosition()[0], monitor->getStatusPosition()[1] );
	- //m_TextActorStatus->Modified();
	-
	- m_TextActorStarted->SetInput(QString::number(monitor->getStarted()).toStdString().c_str());
	- vtkTextProperty* tpropStarted = m_TextActorStarted->GetTextProperty();
	- tpropStarted->SetFontSize(12);
	- tpropStarted->SetOpacity( monitor->getStartedOpacity() * 0.1 );
	- tpropStarted->SetColor(0.0,1.0,0.0);
	- m_TextActorStarted->SetDisplayPosition( monitor->getStartedPosition()[0], monitor->getStartedPosition()[1] );
	- //m_TextActorStarted->Modified();
	-
	- m_TextActorFinished->SetInput(QString::number(monitor->getFinished()).toStdString().c_str());
	- vtkTextProperty* tpropFinished = m_TextActorFinished->GetTextProperty();
	- tpropFinished->SetFontSize(12);
	- tpropFinished->SetOpacity( monitor->getFinishedOpacity() * 0.1 );
	- tpropFinished->SetColor(1.0,1.0,1.0);
	- m_TextActorFinished->SetDisplayPosition( monitor->getFinishedPosition()[0], monitor->getFinishedPosition()[1] );
	- //m_TextActorFinished->Modified();
	-
	- m_TextActorTerminated->SetInput(QString::number(monitor->getTerminated()).toStdString().c_str());
	- vtkTextProperty* tpropTerminated = m_TextActorTerminated->GetTextProperty();
	- tpropTerminated->SetFontSize(12);
	- tpropTerminated->SetOpacity( monitor->getTerminatedOpacity() * 0.1 );
	- tpropTerminated->SetColor(1.0,1.0,1.0);
	- m_TextActorTerminated->SetDisplayPosition( monitor->getTerminatedPosition()[0], monitor->getTerminatedPosition()[1] );
	- //m_TextActorTerminated->Modified();
	-
	-
	- // Calculate time step of the input data for the specified renderer (integer value)
	- // this method is implemented in mitkMapper
	-// this->CalculateTimeStep( renderer );
	-
	-
	-}
	-
	-
	-void mitk::FiberBundleThreadMonitorMapper3D::SetDefaultProperties(mitk::DataNode* node, mitk::BaseRenderer* renderer, bool overwrite)
	-{
	-
	-// MITK_INFO << "FiberBundlexXXMapper3D()SetDefaultProperties";
	-
	-
	- Superclass::SetDefaultProperties(node, renderer, overwrite);
	-
	-
	-
	-}
	-
	-vtkProp* mitk::FiberBundleThreadMonitorMapper3D::GetVtkProp(mitk::BaseRenderer *renderer)
	-{
	- //MITK_INFO << "FiberBundlexXXMapper3D()GetVTKProp";
	- //this->GenerateData();
	- return m_FiberAssembly;
	-
	-}
	-
	-void mitk::FiberBundleThreadMonitorMapper3D::ApplyProperties(mitk::BaseRenderer* renderer)
	-{
	-// MITK_INFO << "FiberBundleXXXMapper3D ApplyProperties(renderer)";
	-}
	-
	-void mitk::FiberBundleThreadMonitorMapper3D::UpdateVtkObjects()
	-{
	-// MITK_INFO << "FiberBundlexxXMapper3D UpdateVtkObjects()";
	-
	-
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/Rendering/mitkFiberBundleThreadMonitorMapper3D.h b/Modules/DiffusionImaging/FiberTracking/Rendering/mitkFiberBundleThreadMonitorMapper3D.h
	deleted file mode 100644
	index 9e4ed51f3e..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Rendering/mitkFiberBundleThreadMonitorMapper3D.h
	+++ /dev/null
	@@ -1,89 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef FiberBundleThreadMonitorMapper3D_H_HEADER_INCLUDED
	-#define FiberBundleThreadMonitorMapper3D_H_HEADER_INCLUDED
	-
	-//#include <mitkBaseData.h> //?? necessary
	-#include <MitkFiberTrackingExports.h>
	-#include <mitkVtkMapper.h>
	-#include <mitkFiberBundleThreadMonitor.h>
	-
	-#include <vtkSmartPointer.h>
	-#include <vtkPolyDataMapper.h>
	-#include <vtkTextActor.h>
	-
	-
	-
	-class vtkPropAssembly;
	-
	-
	-
	-
	-namespace mitk {
	-
	- //##Documentation
	- //## @brief Mapper for FiberBundle
	- //## @ingroup Mapper
	-
	- class MITKFIBERTRACKING_EXPORT FiberBundleThreadMonitorMapper3D : public VtkMapper
	- {
	- public:
	-
	- mitkClassMacro(FiberBundleThreadMonitorMapper3D, VtkMapper);
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- //========== essential implementation for 3D mapper ========
	- const FiberBundleThreadMonitor* GetInput();
	- virtual vtkProp GetVtkProp(mitk::BaseRenderer renderer); //looks like depricated.. should be replaced bz GetViewProp()
	- static void SetDefaultProperties(DataNode* node, BaseRenderer* renderer = nullptr, bool overwrite = false );
	- virtual void ApplyProperties(mitk::BaseRenderer* renderer);
	- virtual void GenerateDataForRenderer(mitk::BaseRenderer* renderer);
	- //=========================================================
	-
	- protected:
	-
	- FiberBundleThreadMonitorMapper3D();
	- virtual ~FiberBundleThreadMonitorMapper3D();
	-
	- void UpdateVtkObjects(); //??
	-
	-
	- vtkSmartPointer<vtkPolyDataMapper> m_FiberMonitorMapper;
	- vtkSmartPointer<vtkTextActor> m_TextActorClose;
	- vtkSmartPointer<vtkTextActor> m_TextActorOpen;
	- vtkSmartPointer<vtkTextActor> m_TextActorHeading;
	- vtkSmartPointer<vtkTextActor> m_TextActorMask;
	- vtkSmartPointer<vtkTextActor> m_TextActorStatus;
	- vtkSmartPointer<vtkTextActor> m_TextActorStarted;
	- vtkSmartPointer<vtkTextActor> m_TextActorFinished;
	- vtkSmartPointer<vtkTextActor> m_TextActorTerminated;
	- vtkPropAssembly* m_FiberAssembly;
	-
	- private:
	- double m_lastModifiedMonitorNodeTime;
	-
	- };
	-
	-} // end namespace mitk
	-
	-
	-
	-
	-#endif /* FiberBundleMapper3D_H_HEADER_INCLUDED */
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Resources/empty b/Modules/DiffusionImaging/FiberTracking/Resources/empty
	deleted file mode 100644
	index e69de29bb2..0000000000
	diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt b/Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt
	deleted file mode 100644
	index 28d176e5d9..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt
	+++ /dev/null
	@@ -1,25 +0,0 @@
	-MITK_CREATE_MODULE_TESTS()
	-
	-if("${CMAKE_SIZEOF_VOID_P}" EQUAL "8")
	-mitkAddCustomModuleTest(mitkFiberBundleReaderWriterTest mitkFiberBundleReaderWriterTest)
	-
	-# Temporarily disabled. Since method relies on random numbers, the behaviour is not consistent across different systems. Solution?
	-#mitkAddCustomModuleTest(mitkGibbsTrackingTest mitkGibbsTrackingTest ${MITK_DATA_DIR}/DiffusionImaging/qBallImage.qbi ${MITK_DATA_DIR}/DiffusionImaging/diffusionImageMask.nrrd ${MITK_DATA_DIR}/DiffusionImaging/gibbsTrackingParameters.gtp ${MITK_DATA_DIR}/DiffusionImaging/gibbsTractogram.fib)
	-
	-mitkAddCustomModuleTest(mitkFiberTransformationTest mitkFiberTransformationTest ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_transformed.fib)
	-mitkAddCustomModuleTest(mitkFiberExtractionTest mitkFiberExtractionTest ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_extracted.fib ${MITK_DATA_DIR}/DiffusionImaging/ROI1.pf ${MITK_DATA_DIR}/DiffusionImaging/ROI2.pf ${MITK_DATA_DIR}/DiffusionImaging/ROI3.pf ${MITK_DATA_DIR}/DiffusionImaging/ROIIMAGE.nrrd ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_inside.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_outside.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_passing-mask.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_ending-in-mask.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_subtracted.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_added.fib)
	-mitkAddCustomModuleTest(mitkFiberGenerationTest mitkFiberGenerationTest ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/Fiducial_0.pf ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/Fiducial_1.pf ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/Fiducial_2.pf ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/uniform.fib ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/gaussian.fib)
	-
	-mitkAddCustomModuleTest(mitkFiberfoxSignalGenerationBrainSliceTest mitkFiberfoxSignalGenerationBrainSliceTest)
	-mitkAddCustomModuleTest(mitkFiberfoxSignalGenerationTest mitkFiberfoxSignalGenerationTest)
	-mitkAddCustomModuleTest(mitkMachineLearningTrackingTest mitkMachineLearningTrackingTest)
	-mitkAddCustomModuleTest(mitkStreamlineTractographyTest mitkStreamlineTractographyTest)
	-mitkAddCustomModuleTest(mitkFiberProcessingTest mitkFiberProcessingTest)
	-mitkAddCustomModuleTest(mitkFiberFitTest mitkFiberFitTest)
	-mitkAddCustomModuleTest(mitkPeakShImageReaderTest mitkPeakShImageReaderTest)
	-
	-if(MITK_ENABLE_RENDERING_TESTING) # apparently does not work on ubuntu
	-mitkAddCustomModuleTest(mitkFiberMapper3DTest mitkFiberMapper3DTest)
	-ENDIF()
	-
	-ENDIF()
	diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/files.cmake b/Modules/DiffusionImaging/FiberTracking/Testing/files.cmake
	deleted file mode 100644
	index 3d06aa5391..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Testing/files.cmake
	+++ /dev/null
	@@ -1,17 +0,0 @@
	-SET(MODULE_CUSTOM_TESTS
	- mitkFiberBundleReaderWriterTest.cpp
	- mitkGibbsTrackingTest.cpp
	- mitkStreamlineTractographyTest.cpp
	- mitkFiberTransformationTest.cpp
	- mitkFiberExtractionTest.cpp
	- mitkFiberGenerationTest.cpp
	- mitkFiberfoxSignalGenerationTest.cpp
	- mitkFiberfoxSignalGenerationBrainSliceTest.cpp
	- mitkMachineLearningTrackingTest.cpp
	- mitkFiberProcessingTest.cpp
	- mitkFiberFitTest.cpp
	- mitkFiberMapper3DTest.cpp
	- mitkPeakShImageReaderTest.cpp
	-)
	-
	-
	diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberBundleReaderWriterTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberBundleReaderWriterTest.cpp
	deleted file mode 100644
	index ba435a1a45..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberBundleReaderWriterTest.cpp
	+++ /dev/null
	@@ -1,71 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkTestingMacros.h"
	-#include <mitkFiberBundle.h>
	-#include <mitkBaseData.h>
	-#include <itksys/SystemTools.hxx>
	-#include <mitkTestingConfig.h>
	-#include <mitkIOUtil.h>
	-
	-#include "mitkTestFixture.h"
	-
	-class mitkFiberBundleReaderWriterTestSuite : public mitk::TestFixture
	-{
	-
	- CPPUNIT_TEST_SUITE(mitkFiberBundleReaderWriterTestSuite);
	- MITK_TEST(Equal_SaveLoad_ReturnsTrue);
	- CPPUNIT_TEST_SUITE_END();
	-
	-private:
	-
	- /** Members used inside the different (sub-)tests. All members are initialized via setUp().*/
	- mitk::FiberBundle::Pointer fib1;
	- mitk::FiberBundle::Pointer fib2;
	-
	-public:
	-
	- void setUp() override
	- {
	- fib1 = nullptr;
	- fib2 = nullptr;
	-
	- std::string filename = GetTestDataFilePath("DiffusionImaging/fiberBundleX.fib");
	-
	- std::vector<mitk::BaseData::Pointer> fibInfile = mitk::IOUtil::Load( filename);
	- mitk::BaseData::Pointer baseData = fibInfile.at(0);
	-
	- fib1 = dynamic_cast<mitk::FiberBundle*>(baseData.GetPointer());
	- }
	-
	- void tearDown() override
	- {
	- fib1 = nullptr;
	- fib2 = nullptr;
	- }
	-
	- void Equal_SaveLoad_ReturnsTrue()
	- {
	- mitk::IOUtil::Save(fib1.GetPointer(), std::string(MITK_TEST_OUTPUT_DIR)+"/writerTest.fib");
	- std::vector<mitk::BaseData::Pointer> baseData = mitk::IOUtil::Load(std::string(MITK_TEST_OUTPUT_DIR)+"/writerTest.fib");
	- fib2 = dynamic_cast<mitk::FiberBundle*>(baseData[0].GetPointer());
	- CPPUNIT_ASSERT_MESSAGE("Should be equal", fib1->Equals(fib2));
	- //MITK_ASSERT_EQUAL(fib1, fib2, "A saved and re-loaded file should be equal");
	- }
	-
	-};
	-
	-MITK_TEST_SUITE_REGISTRATION(mitkFiberBundleReaderWriter)
	diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberExtractionTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberExtractionTest.cpp
	deleted file mode 100644
	index 32c3513861..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberExtractionTest.cpp
	+++ /dev/null
	@@ -1,143 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkTestingMacros.h>
	-#include <mitkIOUtil.h>
	-#include <mitkFiberBundle.h>
	-#include <mitkPlanarFigure.h>
	-#include <mitkPlanarFigureComposite.h>
	-#include <mitkImageCast.h>
	-#include <mitkStandaloneDataStorage.h>
	-#include <vtkDebugLeaks.h>
	-#include <omp.h>
	-#include <itkFiberExtractionFilter.h>
	-
	-/**Documentation
	- * Test if fiber transfortaiom methods work correctly
	- */
	-int mitkFiberExtractionTest(int argc, char* argv[])
	-{
	- MITK_TEST_BEGIN("mitkFiberExtractionTest");
	-
	- /// \todo Fix VTK memory leaks. Bug 18097.
	- vtkDebugLeaks::SetExitError(0);
	-
	- MITK_INFO << "argc: " << argc;
	- MITK_TEST_CONDITION_REQUIRED(argc==13,"check for input data");
	-
	- omp_set_num_threads(1);
	- try{
	- mitk::FiberBundle::Pointer groundTruthFibs = mitk::IOUtil::Load<mitk::FiberBundle>(argv[1]);
	- mitk::FiberBundle::Pointer testFibs = mitk::IOUtil::Load<mitk::FiberBundle>(argv[2]);
	-
	- // test planar figure based extraction
	- auto data = mitk::IOUtil::Load(argv[3])[0];
	- auto pf1 = mitk::DataNode::New();
	- pf1->SetData(data);
	-
	- data = mitk::IOUtil::Load(argv[4])[0];
	- auto pf2 = mitk::DataNode::New();
	- pf2->SetData(data);
	-
	- data = mitk::IOUtil::Load(argv[5])[0];
	- auto pf3 = mitk::DataNode::New();
	- pf3->SetData(data);
	-
	- mitk::StandaloneDataStorage::Pointer storage = mitk::StandaloneDataStorage::New();
	-
	- mitk::PlanarFigureComposite::Pointer pfc2 = mitk::PlanarFigureComposite::New();
	- pfc2->setOperationType(mitk::PlanarFigureComposite::OR);
	- mitk::DataNode::Pointer pfcNode2 = mitk::DataNode::New();
	- pfcNode2->SetData(pfc2);
	- mitk::DataStorage::SetOfObjects::Pointer set2 = mitk::DataStorage::SetOfObjects::New();
	- set2->push_back(pfcNode2);
	-
	- mitk::PlanarFigureComposite::Pointer pfc1 = mitk::PlanarFigureComposite::New();
	- pfc1->setOperationType(mitk::PlanarFigureComposite::AND);
	- mitk::DataNode::Pointer pfcNode1 = mitk::DataNode::New();
	- pfcNode1->SetData(pfc1);
	- mitk::DataStorage::SetOfObjects::Pointer set1 = mitk::DataStorage::SetOfObjects::New();
	- set1->push_back(pfcNode1);
	-
	- storage->Add(pfcNode2);
	- storage->Add(pf1, set2);
	- storage->Add(pfcNode1, set2);
	- storage->Add(pf2, set1);
	- storage->Add(pf3, set1);
	-
	- MITK_INFO << "TEST1";
	- mitk::FiberBundle::Pointer extractedFibs = groundTruthFibs->ExtractFiberSubset(pfcNode2, storage);
	- MITK_INFO << "TEST2";
	- MITK_TEST_CONDITION_REQUIRED(extractedFibs->Equals(testFibs),"check planar figure extraction");
	-
	- MITK_INFO << "TEST3";
	- // test subtraction and addition
	- mitk::FiberBundle::Pointer notExtractedFibs = groundTruthFibs->SubtractBundle(extractedFibs);
	-
	- MITK_INFO << argv[11];
	- testFibs = mitk::IOUtil::Load<mitk::FiberBundle>(argv[11]);
	- MITK_TEST_CONDITION_REQUIRED(notExtractedFibs->Equals(testFibs),"check bundle subtraction");
	-
	- mitk::FiberBundle::Pointer joinded = extractedFibs->AddBundle(notExtractedFibs);
	- testFibs = mitk::IOUtil::Load<mitk::FiberBundle>(argv[12]);
	- MITK_TEST_CONDITION_REQUIRED(joinded->Equals(testFibs),"check bundle addition");
	-
	- // test binary image based extraction
	- mitk::Image::Pointer mitkRoiImage = mitk::IOUtil::Load<mitk::Image>(argv[6]);
	- typedef itk::Image< unsigned char, 3 > itkUCharImageType;
	- itkUCharImageType::Pointer itkRoiImage = itkUCharImageType::New();
	- mitk::CastToItkImage(mitkRoiImage, itkRoiImage);
	-
	- {
	- testFibs = mitk::IOUtil::Load<mitk::FiberBundle>(argv[9]);
	- itk::FiberExtractionFilter<unsigned char>::Pointer extractor = itk::FiberExtractionFilter<unsigned char>::New();
	- extractor->SetInputFiberBundle(groundTruthFibs);
	- extractor->SetRoiImages({itkRoiImage});
	- extractor->SetOverlapFraction(0.0);
	- extractor->SetMode(itk::FiberExtractionFilter<unsigned char>::MODE::OVERLAP);
	- extractor->Update();
	- mitk::FiberBundle::Pointer passing = extractor->GetPositives().at(0);
	- bool ok = passing->Equals(testFibs);
	- if(!ok)
	- mitk::IOUtil::Save(passing, mitk::IOUtil::GetTempPath()+"passing_mask.fib");
	-
	- MITK_TEST_CONDITION_REQUIRED(ok,"check passing mask extraction");
	- }
	-
	- {
	- testFibs = mitk::IOUtil::Load<mitk::FiberBundle>(argv[10]);
	- itk::FiberExtractionFilter<unsigned char>::Pointer extractor = itk::FiberExtractionFilter<unsigned char>::New();
	- extractor->SetInputFiberBundle(groundTruthFibs);
	- extractor->SetRoiImages({itkRoiImage});
	- extractor->SetOverlapFraction(0.0);
	- extractor->SetBothEnds(true);
	- extractor->SetMode(itk::FiberExtractionFilter<unsigned char>::MODE::ENDPOINTS);
	- extractor->Update();
	- mitk::FiberBundle::Pointer ending = extractor->GetPositives().at(0);
	- bool ok = ending->Equals(testFibs);
	- if(!ok)
	- mitk::IOUtil::Save(ending, mitk::IOUtil::GetTempPath()+"ending_mask.fib");
	-
	- MITK_TEST_CONDITION_REQUIRED(ending->Equals(testFibs),"check ending in mask extraction");
	- }
	- }
	- catch(...) {
	- return EXIT_FAILURE;
	- }
	-
	- // always end with this!
	- MITK_TEST_END();
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberFitTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberFitTest.cpp
	deleted file mode 100644
	index d383efac16..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberFitTest.cpp
	+++ /dev/null
	@@ -1,277 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkTestingMacros.h"
	-#include <mitkFiberBundle.h>
	-#include <mitkBaseData.h>
	-#include <itksys/SystemTools.hxx>
	-#include <mitkTestingConfig.h>
	-#include <mitkIOUtil.h>
	-#include <omp.h>
	-#include <itkFitFibersToImageFilter.h>
	-#include <mitkTestFixture.h>
	-#include <mitkPeakImage.h>
	-#include <mitkPreferenceListReaderOptionsFunctor.h>
	-#include <mitkImageToItk.h>
	-#include <mitkImageCast.h>
	-#include <itkImageFileWriter.h>
	-#include <mitkLocaleSwitch.h>
	-
	-class mitkFiberFitTestSuite : public mitk::TestFixture
	-{
	-
	- CPPUNIT_TEST_SUITE(mitkFiberFitTestSuite);
	- MITK_TEST(Fit1);
	- MITK_TEST(Fit2);
	- MITK_TEST(Fit3);
	- MITK_TEST(Fit4);
	- MITK_TEST(Fit5);
	- MITK_TEST(Fit6);
	- CPPUNIT_TEST_SUITE_END();
	-
	- typedef itk::Image<float, 3> ItkFloatImgType;
	-
	-private:
	-
	- /** Members used inside the different (sub-)tests. All members are initialized via setUp().*/
	-
	- typedef itk::FitFibersToImageFilter FitterType;
	- FitterType::Pointer fitter;
	-
	-public:
	-
	- mitk::FiberBundle::Pointer LoadFib(std::string fib_name)
	- {
	- std::vector<mitk::BaseData::Pointer> fibInfile = mitk::IOUtil::Load(GetTestDataFilePath("DiffusionImaging/FiberFit/" + fib_name));
	- mitk::BaseData::Pointer baseData = fibInfile.at(0);
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(baseData.GetPointer());
	- return fib;
	- }
	-
	- void setUp() override
	- {
	- std::vector<mitk::FiberBundle::Pointer> tracts;
	- tracts.push_back(LoadFib("Cluster_0.fib"));
	- tracts.push_back(LoadFib("Cluster_1.fib"));
	- tracts.push_back(LoadFib("Cluster_2.fib"));
	- tracts.push_back(LoadFib("Cluster_3.fib"));
	- tracts.push_back(LoadFib("Cluster_4.fib"));
	-
	- mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Peak Image"}, {});
	- mitk::PeakImage::Pointer peaks = mitk::IOUtil::Load<mitk::PeakImage>(GetTestDataFilePath("DiffusionImaging/FiberFit/csd_peak_image.nii.gz"), &functor);
	-
	-
	- typedef mitk::ImageToItk< mitk::PeakImage::ItkPeakImageType > CasterType;
	- CasterType::Pointer caster = CasterType::New();
	- caster->SetInput(peaks);
	- caster->Update();
	- mitk::PeakImage::ItkPeakImageType::Pointer peak_image = caster->GetOutput();
	-
	- fitter = FitterType::New();
	- fitter->SetPeakImage(peak_image);
	- fitter->SetTractograms(tracts);
	- }
	-
	- void tearDown() override
	- {
	-
	- }
	-
	- void CompareFibs(mitk::FiberBundle::Pointer test, mitk::FiberBundle::Pointer ref, std::string out_name)
	- {
	- vtkSmartPointer<vtkFloatArray> weights = test->GetFiberWeights();
	- vtkSmartPointer<vtkFloatArray> ref_weights = ref->GetFiberWeights();
	-
	- CPPUNIT_ASSERT_MESSAGE("Number of weights should be equal", weights->GetSize()==ref_weights->GetSize());
	-
	- for (int i=0; i<weights->GetSize(); ++i)
	- {
	- if (ref_weights->GetValue(i)>0)
	- {
	- if (fabs( weights->GetValue(i)/ref_weights->GetValue(i)-1 )>0.01)
	- {
	- mitk::IOUtil::Save(test, mitk::IOUtil::GetTempPath()+out_name);
	- CPPUNIT_ASSERT_MESSAGE("Weights should be equal", false);
	- }
	- }
	- else if (weights->GetValue(i)>0)
	- {
	- mitk::IOUtil::Save(test, mitk::IOUtil::GetTempPath()+out_name);
	- CPPUNIT_ASSERT_MESSAGE("Weights should be equal", false);
	- }
	- }
	- }
	-
	- void CompareImages(mitk::PeakImage::ItkPeakImageType::Pointer testImage, std::string name)
	- {
	- mitk::LocaleSwitch localeSwitch("C");
	- typedef mitk::ImageToItk< mitk::PeakImage::ItkPeakImageType > CasterType;
	- CasterType::Pointer caster = CasterType::New();
	- caster->SetInput(mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/FiberFit/out/" + name)));
	- caster->Update();
	- mitk::PeakImage::ItkPeakImageType::Pointer refImage = caster->GetOutput();
	-
	-
	- itk::ImageRegionConstIterator< mitk::PeakImage::ItkPeakImageType > it1(testImage, testImage->GetLargestPossibleRegion());
	- itk::ImageRegionConstIterator< mitk::PeakImage::ItkPeakImageType > it2(refImage, refImage->GetLargestPossibleRegion());
	-
	- while(!it1.IsAtEnd())
	- {
	- if (it2.Get()>0.0001)
	- {
	- if (fabs( it1.Get()/it2.Get()-1 )>0.01)
	- {
	- itk::ImageFileWriter< mitk::PeakImage::ItkPeakImageType >::Pointer writer = itk::ImageFileWriter< mitk::PeakImage::ItkPeakImageType >::New();
	- writer->SetInput(testImage);
	- writer->SetFileName(mitk::IOUtil::GetTempPath()+name);
	- writer->Update();
	-
	- MITK_INFO << it1.Get() << " - " << it2.Get();
	-
	- CPPUNIT_ASSERT_MESSAGE("Peak images should be equal 1", false);
	- }
	- }
	- else if (it1.Get()>0.0001)
	- {
	- itk::ImageFileWriter< mitk::PeakImage::ItkPeakImageType >::Pointer writer = itk::ImageFileWriter< mitk::PeakImage::ItkPeakImageType >::New();
	- writer->SetInput(testImage);
	- writer->SetFileName(mitk::IOUtil::GetTempPath()+name);
	- writer->Update();
	-
	- CPPUNIT_ASSERT_MESSAGE("Peak images should be equal 2", false);
	- }
	-
	- ++it1;
	- ++it2;
	- }
	- }
	-
	- void Fit1()
	- {
	- omp_set_num_threads(1);
	-// fitter->SetLambda(0.1);
	- fitter->SetFilterOutliers(false);
	- fitter->SetRegularization(VnlCostFunction::NONE);
	- fitter->Update();
	-
	- std::vector< mitk::FiberBundle::Pointer > output_tracts = fitter->GetTractograms();
	- mitk::FiberBundle::Pointer test = mitk::FiberBundle::New();
	- test = test->AddBundles(output_tracts);
	- mitk::FiberBundle::Pointer ref = LoadFib("out/NONE_fitted.fib");
	- CompareFibs(test, ref, "NONE_fitted.fib");
	- CompareImages(fitter->GetFittedImage(), "NONE_fitted_image.nrrd");
	- CompareImages(fitter->GetResidualImage(), "NONE_residual_image.nrrd");
	- CompareImages(fitter->GetOverexplainedImage(), "NONE_underexplained_image.nrrd");
	- CompareImages(fitter->GetUnderexplainedImage(), "NONE_overexplained_image.nrrd");
	- }
	-
	- void Fit2()
	- {
	- omp_set_num_threads(1);
	-// fitter->SetLambda(0.1);
	- fitter->SetFilterOutliers(false);
	- fitter->SetRegularization(VnlCostFunction::MSM);
	- fitter->Update();
	-
	- std::vector< mitk::FiberBundle::Pointer > output_tracts = fitter->GetTractograms();
	- mitk::FiberBundle::Pointer test = mitk::FiberBundle::New();
	- test = test->AddBundles(output_tracts);
	- mitk::FiberBundle::Pointer ref = LoadFib("out/MSM_fitted.fib");
	- CompareFibs(test, ref, "MSM_fitted.fib");
	- CompareImages(fitter->GetFittedImage(), "MSM_fitted_image.nrrd");
	- CompareImages(fitter->GetResidualImage(), "MSM_residual_image.nrrd");
	- CompareImages(fitter->GetOverexplainedImage(), "MSM_underexplained_image.nrrd");
	- CompareImages(fitter->GetUnderexplainedImage(), "MSM_overexplained_image.nrrd");
	- }
	-
	- void Fit3()
	- {
	- omp_set_num_threads(1);
	-// fitter->SetLambda(0.1);
	- fitter->SetFilterOutliers(false);
	- fitter->SetRegularization(VnlCostFunction::VARIANCE);
	- fitter->Update();
	-
	- std::vector< mitk::FiberBundle::Pointer > output_tracts = fitter->GetTractograms();
	- mitk::FiberBundle::Pointer test = mitk::FiberBundle::New();
	- test = test->AddBundles(output_tracts);
	- mitk::FiberBundle::Pointer ref = LoadFib("out/MSE_fitted.fib");
	- CompareFibs(test, ref, "MSE_fitted.fib");
	- CompareImages(fitter->GetFittedImage(), "MSE_fitted_image.nrrd");
	- CompareImages(fitter->GetResidualImage(), "MSE_residual_image.nrrd");
	- CompareImages(fitter->GetOverexplainedImage(), "MSE_underexplained_image.nrrd");
	- CompareImages(fitter->GetUnderexplainedImage(), "MSE_overexplained_image.nrrd");
	- }
	-
	- void Fit4()
	- {
	- omp_set_num_threads(1);
	- fitter->SetLambda(100);
	- fitter->SetFilterOutliers(false);
	- fitter->SetRegularization(VnlCostFunction::VOXEL_VARIANCE);
	- fitter->Update();
	-
	- std::vector< mitk::FiberBundle::Pointer > output_tracts = fitter->GetTractograms();
	- mitk::FiberBundle::Pointer test = mitk::FiberBundle::New();
	- test = test->AddBundles(output_tracts);
	- mitk::FiberBundle::Pointer ref = LoadFib("out/LocalMSE_fitted.fib");
	- CompareFibs(test, ref, "LocalMSE_fitted.fib");
	- CompareImages(fitter->GetFittedImage(), "LocalMSE_fitted_image.nrrd");
	- CompareImages(fitter->GetResidualImage(), "LocalMSE_residual_image.nrrd");
	- CompareImages(fitter->GetOverexplainedImage(), "LocalMSE_underexplained_image.nrrd");
	- CompareImages(fitter->GetUnderexplainedImage(), "LocalMSE_overexplained_image.nrrd");
	- }
	-
	- void Fit5()
	- {
	- omp_set_num_threads(1);
	- fitter->SetFilterOutliers(false);
	- fitter->SetRegularization(VnlCostFunction::GROUP_VARIANCE);
	- fitter->Update();
	-
	- std::vector< mitk::FiberBundle::Pointer > output_tracts = fitter->GetTractograms();
	- mitk::FiberBundle::Pointer test = mitk::FiberBundle::New();
	- test = test->AddBundles(output_tracts);
	- mitk::FiberBundle::Pointer ref = LoadFib("out/GroupMSE_fitted.fib");
	- CompareFibs(test, ref, "GroupMSE_fitted.fib");
	- CompareImages(fitter->GetFittedImage(), "GroupMSE_fitted_image.nrrd");
	- CompareImages(fitter->GetResidualImage(), "GroupMSE_residual_image.nrrd");
	- CompareImages(fitter->GetOverexplainedImage(), "GroupMSE_underexplained_image.nrrd");
	- CompareImages(fitter->GetUnderexplainedImage(), "GroupMSE_overexplained_image.nrrd");
	- }
	-
	- void Fit6()
	- {
	- omp_set_num_threads(1);
	- fitter->SetLambda(1000);
	- fitter->SetFilterOutliers(false);
	- fitter->SetRegularization(VnlCostFunction::GROUP_LASSO);
	- fitter->Update();
	-
	- std::vector< mitk::FiberBundle::Pointer > output_tracts = fitter->GetTractograms();
	- mitk::FiberBundle::Pointer test = mitk::FiberBundle::New();
	- test = test->AddBundles(output_tracts);
	- mitk::FiberBundle::Pointer ref = LoadFib("out/GroupLasso_fitted.fib");
	- CompareFibs(test, ref, "GroupLasso_fitted.fib");
	- CompareImages(fitter->GetFittedImage(), "GroupLasso_fitted_image.nrrd");
	- CompareImages(fitter->GetResidualImage(), "GroupLasso_residual_image.nrrd");
	- CompareImages(fitter->GetOverexplainedImage(), "GroupLasso_underexplained_image.nrrd");
	- CompareImages(fitter->GetUnderexplainedImage(), "GroupLasso_overexplained_image.nrrd");
	- }
	-
	-};
	-
	-MITK_TEST_SUITE_REGISTRATION(mitkFiberFit)
	diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberGenerationTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberGenerationTest.cpp
	deleted file mode 100644
	index b754986684..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberGenerationTest.cpp
	+++ /dev/null
	@@ -1,81 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkTestingMacros.h>
	-#include <mitkIOUtil.h>
	-#include <mitkFiberBundle.h>
	-#include <mitkPlanarEllipse.h>
	-#include <itkFibersFromPlanarFiguresFilter.h>
	-#include <omp.h>
	-
	-/**Documentation
	- * Test if fiber transfortaiom methods work correctly
	- */
	-int mitkFiberGenerationTest(int argc, char* argv[])
	-{
	- omp_set_num_threads(1);
	- MITK_TEST_BEGIN("mitkFiberGenerationTest");
	-
	- MITK_TEST_CONDITION_REQUIRED(argc==6,"check for input data")
	-
	- try{
	-
	- mitk::PlanarEllipse::Pointer pf1 = mitk::IOUtil::Load<mitk::PlanarEllipse>(argv[1]);
	- mitk::PlanarEllipse::Pointer pf2 = mitk::IOUtil::Load<mitk::PlanarEllipse>(argv[2]);
	- mitk::PlanarEllipse::Pointer pf3 = mitk::IOUtil::Load<mitk::PlanarEllipse>(argv[3]);
	- mitk::FiberBundle::Pointer uniform = mitk::IOUtil::Load<mitk::FiberBundle>(argv[4]);
	- mitk::FiberBundle::Pointer gaussian = mitk::IOUtil::Load<mitk::FiberBundle>(argv[5]);
	-
	- FiberGenerationParameters parameters;
	- std::vector< mitk::PlanarEllipse::Pointer > fid; fid.push_back(pf1); fid.push_back(pf2); fid.push_back(pf3);
	- std::vector< unsigned int > flip; flip.push_back(0); flip.push_back(0); flip.push_back(0);
	- parameters.m_Fiducials.push_back(fid); parameters.m_FlipList.push_back(flip);
	- parameters.m_Density = 50;
	- parameters.m_Tension = 0;
	- parameters.m_Continuity = 0;
	- parameters.m_Bias = 0;
	- parameters.m_Sampling = 1;
	- parameters.m_Variance = 0.1;
	-
	- // check uniform fiber distribution
	- {
	- itk::FibersFromPlanarFiguresFilter::Pointer filter = itk::FibersFromPlanarFiguresFilter::New();
	- parameters.m_Distribution = FiberGenerationParameters::DISTRIBUTE_UNIFORM;
	- filter->SetParameters(parameters);
	- filter->SetFixSeed(true);
	- filter->Update();
	- std::vector< mitk::FiberBundle::Pointer > fiberBundles = filter->GetFiberBundles();
	- MITK_TEST_CONDITION_REQUIRED(uniform->Equals(fiberBundles.at(0)),"check uniform bundle")
	- }
	-
	- // check gaussian fiber distribution
	- {
	- itk::FibersFromPlanarFiguresFilter::Pointer filter = itk::FibersFromPlanarFiguresFilter::New();
	- parameters.m_Distribution = FiberGenerationParameters::DISTRIBUTE_GAUSSIAN;
	- filter->SetParameters(parameters);
	- filter->SetFixSeed(true);
	- filter->Update();
	- std::vector< mitk::FiberBundle::Pointer > fiberBundles = filter->GetFiberBundles();
	- MITK_TEST_CONDITION_REQUIRED(gaussian->Equals(fiberBundles.at(0)),"check gaussian bundle")
	- }
	- }
	- catch(...) {
	- return EXIT_FAILURE;
	- }
	-
	- // always end with this!
	- MITK_TEST_END();
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberMapper3DTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberMapper3DTest.cpp
	deleted file mode 100644
	index b14dc490f6..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberMapper3DTest.cpp
	+++ /dev/null
	@@ -1,165 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkNodePredicateDataType.h>
	-#include <mitkRenderingTestHelper.h>
	-#include <mitkSmartPointerProperty.h>
	-#include <mitkTestingMacros.h>
	-#include <vtkSmartPointer.h>
	-#include <vtkRenderLargeImage.h>
	-#include "mitkTestingMacros.h"
	-#include <mitkFiberBundle.h>
	-#include <itksys/SystemTools.hxx>
	-#include <mitkTestingConfig.h>
	-#include <mitkIOUtil.h>
	-#include <mitkTestFixture.h>
	-#include <vtkTesting.h>
	-#include <thread>
	-#include <chrono>
	-
	-class mitkFiberMapper3DTestSuite : public mitk::TestFixture
	-{
	-
	- CPPUNIT_TEST_SUITE(mitkFiberMapper3DTestSuite);
	- MITK_TEST(Default3D);
	- MITK_TEST(Color3D);
	- MITK_TEST(Ribbon3D);
	- MITK_TEST(Tubes3D);
	- MITK_TEST(Default2D);
	- CPPUNIT_TEST_SUITE_END();
	-
	- typedef itk::Image<float, 3> ItkFloatImgType;
	-
	-private:
	-
	- /** Members used inside the different (sub-)tests. All members are initialized via setUp().*/
	-
	- mitk::FiberBundle::Pointer fib;
	- mitk::DataNode::Pointer node;
	-
	-public:
	-
	- void setUp() override
	- {
	- fib = mitk::IOUtil::Load<mitk::FiberBundle>(GetTestDataFilePath("DiffusionImaging/Rendering/test_fibers.fib"));
	- MITK_INFO << fib->GetNumFibers();
	- node = mitk::DataNode::New();
	- node->SetData(fib);
	- }
	-
	- void tearDown() override
	- {
	-
	- }
	-
	- void AddGeneratedDataToStorage(mitk::DataStorage *dataStorage)
	- {
	- auto node = mitk::DataNode::New();
	- node->SetData(fib);
	-
	- dataStorage->Add(node);
	- }
	-
	- void Default2D()
	- {
	- mitk::RenderingTestHelper renderingHelper(640, 480);
	- renderingHelper.AddNodeToStorage(node);
	- renderingHelper.SetViewDirection(mitk::SliceNavigationController::Frontal);
	- renderingHelper.SetMapperIDToRender2D();
	-
	- std::this_thread::sleep_for(std::chrono::seconds(1));
	- renderingHelper.SaveReferenceScreenShot(mitk::IOUtil::GetTempPath()+"fib_2D.png");
	- mitk::Image::Pointer test_image = mitk::IOUtil::Load<mitk::Image>(mitk::IOUtil::GetTempPath()+"fib_2D.png");
	- mitk::Image::Pointer ref_image = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/Rendering/fib_2D.png"));
	- MITK_ASSERT_EQUAL(test_image, ref_image, "Check if images are equal.");
	- }
	-
	- void Default3D()
	- {
	- mitk::RenderingTestHelper renderingHelper(640, 480);
	- renderingHelper.AddNodeToStorage(node);
	- renderingHelper.SetMapperIDToRender3D();
	-
	- std::this_thread::sleep_for(std::chrono::seconds(1));
	- renderingHelper.SaveReferenceScreenShot(mitk::IOUtil::GetTempPath()+"fib_3D.png");
	- mitk::Image::Pointer test_image = mitk::IOUtil::Load<mitk::Image>(mitk::IOUtil::GetTempPath()+"fib_3D.png");
	- mitk::Image::Pointer ref_image = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/Rendering/fib_3D.png"));
	- MITK_ASSERT_EQUAL(test_image, ref_image, "Check if images are equal.");
	- }
	-
	- void Tubes3D()
	- {
	- node->SetFloatProperty("shape.tuberadius", 1);
	-
	- mitk::RenderingTestHelper renderingHelper(640, 480);
	- renderingHelper.AddNodeToStorage(node);
	- renderingHelper.SetMapperIDToRender3D();
	-
	- std::this_thread::sleep_for(std::chrono::seconds(1));
	- renderingHelper.SaveReferenceScreenShot(mitk::IOUtil::GetTempPath()+"fib_tubes_3D.png");
	- mitk::Image::Pointer test_image = mitk::IOUtil::Load<mitk::Image>(mitk::IOUtil::GetTempPath()+"fib_tubes_3D.png");
	- mitk::Image::Pointer ref_image = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/Rendering/fib_tubes_3D.png"));
	- MITK_ASSERT_EQUAL(test_image, ref_image, "Check if images are equal.");
	- }
	-
	- void Ribbon3D()
	- {
	- node->SetFloatProperty("shape.ribbonwidth", 1);
	-
	- mitk::RenderingTestHelper renderingHelper(640, 480);
	- renderingHelper.AddNodeToStorage(node);
	- renderingHelper.SetMapperIDToRender3D();
	-
	- std::this_thread::sleep_for(std::chrono::seconds(1));
	- renderingHelper.SaveReferenceScreenShot(mitk::IOUtil::GetTempPath()+"fib_ribbon_3D.png");
	- mitk::Image::Pointer test_image = mitk::IOUtil::Load<mitk::Image>(mitk::IOUtil::GetTempPath()+"fib_ribbon_3D.png");
	- mitk::Image::Pointer ref_image = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/Rendering/fib_ribbon_3D.png"));
	- MITK_ASSERT_EQUAL(test_image, ref_image, "Check if images are equal.");
	- }
	-
	- void Line3D()
	- {
	- node->SetFloatProperty("shape.linewidth", 1);
	-
	- mitk::RenderingTestHelper renderingHelper(640, 480);
	- renderingHelper.AddNodeToStorage(node);
	- renderingHelper.SetMapperIDToRender3D();
	-
	- std::this_thread::sleep_for(std::chrono::seconds(1));
	- renderingHelper.SaveReferenceScreenShot(mitk::IOUtil::GetTempPath()+"fib_line_3D.png");
	- mitk::Image::Pointer test_image = mitk::IOUtil::Load<mitk::Image>(mitk::IOUtil::GetTempPath()+"fib_line_3D.png");
	- mitk::Image::Pointer ref_image = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/Rendering/fib_line_3D.png"));
	- MITK_ASSERT_EQUAL(test_image, ref_image, "Check if images are equal.");
	- }
	-
	- void Color3D()
	- {
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
	- fib->SetFiberColors(255, 255, 255);
	-
	- mitk::RenderingTestHelper renderingHelper(640, 480);
	- renderingHelper.AddNodeToStorage(node);
	- renderingHelper.SetMapperIDToRender3D();
	-
	- std::this_thread::sleep_for(std::chrono::seconds(1));
	- renderingHelper.SaveReferenceScreenShot(mitk::IOUtil::GetTempPath()+"fib_color_3D.png");
	- mitk::Image::Pointer test_image = mitk::IOUtil::Load<mitk::Image>(mitk::IOUtil::GetTempPath()+"fib_color_3D.png");
	- mitk::Image::Pointer ref_image = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/Rendering/fib_color_3D.png"));
	- MITK_ASSERT_EQUAL(test_image, ref_image, "Check if images are equal.");
	- }
	-};
	-
	-MITK_TEST_SUITE_REGISTRATION(mitkFiberMapper3D)
	diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberProcessingTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberProcessingTest.cpp
	deleted file mode 100644
	index 5473cfdf41..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberProcessingTest.cpp
	+++ /dev/null
	@@ -1,304 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkTestingMacros.h"
	-#include <mitkFiberBundle.h>
	-#include <mitkBaseData.h>
	-#include <itksys/SystemTools.hxx>
	-#include <mitkTestingConfig.h>
	-#include <mitkIOUtil.h>
	-#include <itkFiberCurvatureFilter.h>
	-#include <omp.h>
	-#include "mitkTestFixture.h"
	-
	-class mitkFiberProcessingTestSuite : public mitk::TestFixture
	-{
	-
	- CPPUNIT_TEST_SUITE(mitkFiberProcessingTestSuite);
	- MITK_TEST(Test1);
	- MITK_TEST(Test2);
	- MITK_TEST(Test3);
	- MITK_TEST(Test4);
	- MITK_TEST(Test5);
	- MITK_TEST(Test6);
	- MITK_TEST(Test7);
	- MITK_TEST(Test8);
	- MITK_TEST(Test9);
	- MITK_TEST(Test10);
	- MITK_TEST(Test11);
	- MITK_TEST(Test12);
	- MITK_TEST(Test13);
	- MITK_TEST(Test14);
	- MITK_TEST(Test15);
	- MITK_TEST(Test16);
	- MITK_TEST(Test17);
	- MITK_TEST(Test18);
	- CPPUNIT_TEST_SUITE_END();
	-
	- typedef itk::Image<unsigned char, 3> ItkUcharImgType;
	-
	-private:
	-
	- /** Members used inside the different (sub-)tests. All members are initialized via setUp().*/
	- mitk::FiberBundle::Pointer original;
	- ItkUcharImgType::Pointer mask;
	-
	-public:
	-
	- void setUp() override
	- {
	- omp_set_num_threads(1);
	- original = nullptr;
	- original = mitk::IOUtil::Load<mitk::FiberBundle>(GetTestDataFilePath("DiffusionImaging/FiberProcessing/original.fib"));
	-
	- mitk::Image::Pointer img = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/FiberProcessing/MASK.nrrd"));
	- mask = ItkUcharImgType::New();
	- mitk::CastToItkImage(img, mask);
	- }
	-
	- void tearDown() override
	- {
	- original = nullptr;
	- }
	-
	- void Test1()
	- {
	- MITK_INFO << "TEST 1: Remove by direction";
	-
	- mitk::FiberBundle::Pointer fib = original->GetDeepCopy();
	- vnl_vector_fixed<double,3> dir;
	- dir[0] = 0;
	- dir[1] = 1;
	- dir[2] = 0;
	- fib->RemoveDir(dir,cos(5.0*itk::Math::pi/180));
	-
	- mitk::FiberBundle::Pointer ref = mitk::IOUtil::Load<mitk::FiberBundle>(GetTestDataFilePath("DiffusionImaging/FiberProcessing/remove_direction.fib"));
	-
	- CPPUNIT_ASSERT_MESSAGE("Should be equal", ref->Equals(fib));
	- }
	-
	- void Test2()
	- {
	- MITK_INFO << "TEST 2: Remove by length";
	-
	- mitk::FiberBundle::Pointer fib = original->GetDeepCopy();
	- fib->RemoveShortFibers(30);
	- fib->RemoveLongFibers(40);
	-
	- mitk::FiberBundle::Pointer ref = mitk::IOUtil::Load<mitk::FiberBundle>(GetTestDataFilePath("DiffusionImaging/FiberProcessing/remove_length.fib"));
	-
	- CPPUNIT_ASSERT_MESSAGE("Should be equal", ref->Equals(fib));
	- }
	-
	- void Test3()
	- {
	- MITK_INFO << "TEST 3: Remove by curvature 1";
	-
	- mitk::FiberBundle::Pointer fib = original->GetDeepCopy();
	- auto filter = itk::FiberCurvatureFilter::New();
	- filter->SetInputFiberBundle(fib);
	- filter->SetAngularDeviation(30);
	- filter->SetDistance(5);
	- filter->SetRemoveFibers(false);
	- filter->SetUseMedian(true);
	- filter->Update();
	- mitk::FiberBundle::Pointer ref = mitk::IOUtil::Load<mitk::FiberBundle>(GetTestDataFilePath("DiffusionImaging/FiberProcessing/remove_curvature1.fib"));
	- CPPUNIT_ASSERT_MESSAGE("Should be equal", ref->Equals(filter->GetOutputFiberBundle()));
	- }
	-
	- void Test4()
	- {
	- MITK_INFO << "TEST 4: Remove by curvature 2";
	-
	- mitk::FiberBundle::Pointer fib = original->GetDeepCopy();
	- auto filter = itk::FiberCurvatureFilter::New();
	- filter->SetInputFiberBundle(fib);
	- filter->SetAngularDeviation(30);
	- filter->SetDistance(5);
	- filter->SetRemoveFibers(true);
	- filter->SetUseMedian(true);
	- filter->Update();
	- mitk::FiberBundle::Pointer ref = mitk::IOUtil::Load<mitk::FiberBundle>(GetTestDataFilePath("DiffusionImaging/FiberProcessing/remove_curvature2.fib"));
	- CPPUNIT_ASSERT_MESSAGE("Should be equal", ref->Equals(filter->GetOutputFiberBundle()));
	- }
	-
	- void Test5()
	- {
	- MITK_INFO << "TEST 5: Remove outside mask";
	-
	- mitk::FiberBundle::Pointer fib = original->GetDeepCopy();
	- fib = fib->RemoveFibersOutside(mask);
	- mitk::FiberBundle::Pointer ref = mitk::IOUtil::Load<mitk::FiberBundle>(GetTestDataFilePath("DiffusionImaging/FiberProcessing/remove_outside.fib"));
	-// mitk::IOUtil::Save(fib, mitk::IOUtil::GetTempPath()+"remove_outside.fib");
	- CPPUNIT_ASSERT_MESSAGE("Should be equal", ref->Equals(fib));
	- }
	-
	- void Test6()
	- {
	- MITK_INFO << "TEST 6: Remove inside mask";
	-
	- mitk::FiberBundle::Pointer fib = original->GetDeepCopy();
	- fib = fib->RemoveFibersOutside(mask, true);
	- mitk::FiberBundle::Pointer ref = mitk::IOUtil::Load<mitk::FiberBundle>(GetTestDataFilePath("DiffusionImaging/FiberProcessing/remove_inside.fib"));
	- CPPUNIT_ASSERT_MESSAGE("Should be equal", ref->Equals(fib));
	- }
	-
	- void Test7()
	- {
	- MITK_INFO << "TEST 7: Modify resample spline";
	-
	- mitk::FiberBundle::Pointer fib = original->GetDeepCopy();
	- fib->ResampleSpline(5);
	- mitk::FiberBundle::Pointer ref = mitk::IOUtil::Load<mitk::FiberBundle>(GetTestDataFilePath("DiffusionImaging/FiberProcessing/modify_resample.fib"));
	- CPPUNIT_ASSERT_MESSAGE("Should be equal", ref->Equals(fib));
	- }
	-
	- void Test8()
	- {
	- MITK_INFO << "TEST 8: Modify compress";
	-
	- mitk::FiberBundle::Pointer fib = original->GetDeepCopy();
	- fib->Compress(0.1f);
	- mitk::FiberBundle::Pointer ref = mitk::IOUtil::Load<mitk::FiberBundle>(GetTestDataFilePath("DiffusionImaging/FiberProcessing/modify_compress.fib"));
	- CPPUNIT_ASSERT_MESSAGE("Should be equal", ref->Equals(fib));
	- }
	-
	- void Test9()
	- {
	- MITK_INFO << "TEST 9: Modify sagittal mirror";
	-
	- mitk::FiberBundle::Pointer fib = original->GetDeepCopy();
	- fib->MirrorFibers(0);
	- mitk::FiberBundle::Pointer ref = mitk::IOUtil::Load<mitk::FiberBundle>(GetTestDataFilePath("DiffusionImaging/FiberProcessing/modify_sagittal_mirror.fib"));
	- CPPUNIT_ASSERT_MESSAGE("Should be equal", ref->Equals(fib));
	- }
	-
	- void Test10()
	- {
	- MITK_INFO << "TEST 10: Modify coronal mirror";
	-
	- mitk::FiberBundle::Pointer fib = original->GetDeepCopy();
	- fib->MirrorFibers(1);
	- mitk::FiberBundle::Pointer ref = mitk::IOUtil::Load<mitk::FiberBundle>(GetTestDataFilePath("DiffusionImaging/FiberProcessing/modify_coronal_mirror.fib"));
	- CPPUNIT_ASSERT_MESSAGE("Should be equal", ref->Equals(fib));
	- }
	-
	- void Test11()
	- {
	- MITK_INFO << "TEST 11: Modify axial mirror";
	-
	- mitk::FiberBundle::Pointer fib = original->GetDeepCopy();
	- fib->MirrorFibers(2);
	- mitk::FiberBundle::Pointer ref = mitk::IOUtil::Load<mitk::FiberBundle>(GetTestDataFilePath("DiffusionImaging/FiberProcessing/modify_axial_mirror.fib"));
	- CPPUNIT_ASSERT_MESSAGE("Should be equal", ref->Equals(fib));
	- }
	-
	- void Test12()
	- {
	- MITK_INFO << "TEST 12: Weight and join";
	-
	- mitk::FiberBundle::Pointer fib = original->GetDeepCopy();
	- fib->SetFiberWeights(0.1f);
	-
	- mitk::FiberBundle::Pointer fib2 = original->GetDeepCopy();
	- fib2->SetFiberWeight(3, 0.5);
	-
	- fib = fib->AddBundle(fib2);
	-
	- mitk::FiberBundle::Pointer ref = mitk::IOUtil::Load<mitk::FiberBundle>(GetTestDataFilePath("DiffusionImaging/FiberProcessing/modify_weighted_joined.fib"));
	-
	- CPPUNIT_ASSERT_MESSAGE("Number of fibers", ref->GetNumFibers() == fib->GetNumFibers());
	-
	- for (unsigned int i=0; i<ref->GetNumFibers(); i++)
	- CPPUNIT_ASSERT_MESSAGE("Fiber weights", ref->GetFiberWeight(i) == fib->GetFiberWeight(i));
	- }
	-
	- void Test13()
	- {
	- MITK_INFO << "TEST 13: Subtract";
	-
	- mitk::FiberBundle::Pointer fib = original->GetDeepCopy();
	-
	- mitk::FiberBundle::Pointer fib2 = mitk::IOUtil::Load<mitk::FiberBundle>(GetTestDataFilePath("DiffusionImaging/FiberProcessing/remove_length.fib"));
	- fib = fib->SubtractBundle(fib2);
	-
	- mitk::FiberBundle::Pointer ref = mitk::IOUtil::Load<mitk::FiberBundle>(GetTestDataFilePath("DiffusionImaging/FiberProcessing/subtracted.fib"));
	-
	- CPPUNIT_ASSERT_MESSAGE("Should be equal", ref->Equals(fib));
	- }
	-
	- void Test14()
	- {
	- MITK_INFO << "TEST 14: rotate";
	-
	- mitk::FiberBundle::Pointer fib = original->GetDeepCopy();
	- fib->TransformFibers(1,2,3,0,0,0);
	-
	- mitk::FiberBundle::Pointer ref = mitk::IOUtil::Load<mitk::FiberBundle>(GetTestDataFilePath("DiffusionImaging/FiberProcessing/transform_rotate.fib"));
	-
	- CPPUNIT_ASSERT_MESSAGE("Should be equal", ref->Equals(fib));
	- }
	-
	- void Test15()
	- {
	- MITK_INFO << "TEST 15: translate";
	-
	- mitk::FiberBundle::Pointer fib = original->GetDeepCopy();
	- fib->TransformFibers(0,0,0,1,2,3);
	-
	- mitk::FiberBundle::Pointer ref = mitk::IOUtil::Load<mitk::FiberBundle>(GetTestDataFilePath("DiffusionImaging/FiberProcessing/transform_translate.fib"));
	-
	- CPPUNIT_ASSERT_MESSAGE("Should be equal", ref->Equals(fib));
	- }
	-
	- void Test16()
	- {
	- MITK_INFO << "TEST 16: scale 1";
	-
	- mitk::FiberBundle::Pointer fib = original->GetDeepCopy();
	- fib->ScaleFibers(0.1, 0.2, 0.3);
	-
	- mitk::FiberBundle::Pointer ref = mitk::IOUtil::Load<mitk::FiberBundle>(GetTestDataFilePath("DiffusionImaging/FiberProcessing/transform_scale1.fib"));
	-
	- CPPUNIT_ASSERT_MESSAGE("Should be equal", ref->Equals(fib));
	- }
	-
	- void Test17()
	- {
	- MITK_INFO << "TEST 17: scale 2";
	-
	- mitk::FiberBundle::Pointer fib = original->GetDeepCopy();
	- fib->ScaleFibers(0.1, 0.2, 0.3, false);
	-
	- mitk::FiberBundle::Pointer ref = mitk::IOUtil::Load<mitk::FiberBundle>(GetTestDataFilePath("DiffusionImaging/FiberProcessing/transform_scale2.fib"));
	-
	- CPPUNIT_ASSERT_MESSAGE("Should be equal", ref->Equals(fib));
	- }
	-
	- void Test18()
	- {
	- MITK_INFO << "TEST 18: Modify resample linear";
	-
	- mitk::FiberBundle::Pointer fib = original->GetDeepCopy();
	- fib->ResampleLinear();
	- mitk::FiberBundle::Pointer ref = mitk::IOUtil::Load<mitk::FiberBundle>(GetTestDataFilePath("DiffusionImaging/FiberProcessing/modify_resample_linear.fib"));
	-// mitk::IOUtil::Save(fib, mitk::IOUtil::GetTempPath()+"modify_resample_linear.fib");
	- CPPUNIT_ASSERT_MESSAGE("Should be equal", ref->Equals(fib));
	- }
	-
	-};
	-
	-MITK_TEST_SUITE_REGISTRATION(mitkFiberProcessing)
	diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberTransformationTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberTransformationTest.cpp
	deleted file mode 100644
	index 9f5e8e0f0d..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberTransformationTest.cpp
	+++ /dev/null
	@@ -1,55 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkTestingMacros.h>
	-#include <mitkIOUtil.h>
	-#include <mitkFiberBundle.h>
	-#include <omp.h>
	-
	-/**Documentation
	- * Test if fiber transfortaiom methods work correctly
	- */
	-int mitkFiberTransformationTest(int argc, char* argv[])
	-{
	- omp_set_num_threads(1);
	- MITK_TEST_BEGIN("mitkFiberTransformationTest");
	-
	- MITK_TEST_CONDITION_REQUIRED(argc==3,"check for input data")
	-
	- try{
	- mitk::FiberBundle::Pointer groundTruthFibs = mitk::IOUtil::Load<mitk::FiberBundle>(argv[1]);
	- mitk::FiberBundle::Pointer transformedFibs = mitk::IOUtil::Load<mitk::FiberBundle>(argv[2]);
	-
	- groundTruthFibs->RotateAroundAxis(90, 45, 10);
	- groundTruthFibs->TranslateFibers(2, 3, 5);
	- groundTruthFibs->ScaleFibers(1, 0.1, 1.3);
	- groundTruthFibs->RemoveLongFibers(150);
	- groundTruthFibs->RemoveShortFibers(20);
	- groundTruthFibs->ResampleSpline(1.0);
	- groundTruthFibs->ApplyCurvatureThreshold(3.0, true);
	- groundTruthFibs->MirrorFibers(0);
	- groundTruthFibs->MirrorFibers(1);
	- groundTruthFibs->MirrorFibers(2);
	-
	- MITK_TEST_CONDITION_REQUIRED(groundTruthFibs->Equals(transformedFibs),"check transformation")
	- }
	- catch(...) {
	- return EXIT_FAILURE;
	- }
	-
	- // always end with this!
	- MITK_TEST_END();
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxSignalGenerationBrainSliceTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxSignalGenerationBrainSliceTest.cpp
	deleted file mode 100644
	index f62e315cfd..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxSignalGenerationBrainSliceTest.cpp
	+++ /dev/null
	@@ -1,206 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkTestingMacros.h>
	-#include <mitkIOUtil.h>
	-#include <mitkFiberBundle.h>
	-#include <itkTractsToDWIImageFilter.h>
	-#include <mitkFiberfoxParameters.h>
	-#include <mitkStickModel.h>
	-#include <mitkTensorModel.h>
	-#include <mitkBallModel.h>
	-#include <mitkDotModel.h>
	-#include <mitkAstroStickModel.h>
	-#include <mitkImage.h>
	-#include <itkTestingComparisonImageFilter.h>
	-#include <itkImageRegionConstIterator.h>
	-#include <mitkRicianNoiseModel.h>
	-#include <mitkChiSquareNoiseModel.h>
	-#include <mitkIOUtil.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <mitkProperties.h>
	-#include <mitkITKImageImport.h>
	-#include <mitkImageCast.h>
	-#include <itkVectorImage.h>
	-
	-#include "mitkTestFixture.h"
	-
	-class mitkFiberfoxSignalGenerationBrainSliceTestSuite : public mitk::TestFixture
	-{
	-
	- CPPUNIT_TEST_SUITE(mitkFiberfoxSignalGenerationBrainSliceTestSuite);
	- MITK_TEST(Test1);
	- MITK_TEST(Test2);
	- MITK_TEST(Test3);
	- MITK_TEST(Test4);
	- MITK_TEST(Test5);
	- CPPUNIT_TEST_SUITE_END();
	-
	- typedef itk::VectorImage< short, 3> ItkDwiType;
	-
	-private:
	-
	-public:
	-
	- /** Members used inside the different (sub-)tests. All members are initialized via setUp().*/
	- FiberBundle::Pointer m_FiberBundle;
	- mitk::Image::Pointer m_Template;
	-
	- void setUp() override
	- {
	- m_FiberBundle = mitk::IOUtil::Load<FiberBundle>(GetTestDataFilePath("DiffusionImaging/Fiberfox/SignalGen_BrainSlice.fib"));
	- m_Template = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/Fiberfox/SignalGen_BrainSliceTemplate.nii.gz"));
	- }
	-
	- void adjust_to_template(mitk::FiberfoxParameters& parameters)
	- {
	- typedef itk::Image< short, 3 > ItkImageType;
	- ItkImageType::Pointer itkImagePointer = ItkImageType::New();
	- mitk::CastToItkImage(m_Template, itkImagePointer);
	- parameters.m_SignalGen.m_ImageRegion = itkImagePointer->GetLargestPossibleRegion();
	- parameters.m_SignalGen.m_ImageSpacing = itkImagePointer->GetSpacing();
	- parameters.m_SignalGen.m_ImageOrigin = itkImagePointer->GetOrigin();
	- parameters.m_SignalGen.m_ImageDirection = itkImagePointer->GetDirection();
	- }
	-
	- void tearDown() override
	- {
	-
	- }
	-
	- bool CompareDwi(itk::VectorImage< short, 3 >* dwi1, itk::VectorImage< short, 3 >* dwi2)
	- {
	- bool out = true;
	- typedef itk::VectorImage< short, 3 > DwiImageType;
	- try{
	- itk::ImageRegionIterator< DwiImageType > it1(dwi1, dwi1->GetLargestPossibleRegion());
	- itk::ImageRegionIterator< DwiImageType > it2(dwi2, dwi2->GetLargestPossibleRegion());
	- int count = 0;
	- while(!it1.IsAtEnd())
	- {
	- for (unsigned int i=0; i<dwi1->GetVectorLength(); ++i)
	- {
	- short d = abs(it1.Get()[i]-it2.Get()[i]);
	-
	- if (d>1)
	- {
	- if (count<10)
	- {
	- MITK_INFO << "**************************************";
	- MITK_INFO << "Test value: " << it1.GetIndex() << ":" << it1.Get()[i];
	- MITK_INFO << "Ref. value: " << it2.GetIndex() << ":" << it2.Get()[i];
	- }
	- out = false;
	- count++;
	- }
	- }
	- ++it1;
	- ++it2;
	- }
	- if (count>=10)
	- MITK_INFO << "Skipping errors.";
	- MITK_INFO << "Errors detected: " << count;
	- }
	- catch(...)
	- {
	- return false;
	- }
	- return out;
	- }
	-
	- void StartSimulation(FiberfoxParameters parameters, mitk::Image::Pointer refImage, std::string out)
	- {
	- itk::TractsToDWIImageFilter< short >::Pointer tractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New();
	- tractsToDwiFilter->SetUseConstantRandSeed(true);
	- tractsToDwiFilter->SetParameters(parameters);
	- tractsToDwiFilter->SetFiberBundle(m_FiberBundle);
	- tractsToDwiFilter->Update();
	-
	- mitk::Image::Pointer testImage = mitk::GrabItkImageMemory( tractsToDwiFilter->GetOutput() );
	- mitk::DiffusionPropertyHelper::SetGradientContainer(testImage, parameters.m_SignalGen.GetItkGradientContainer());
	- mitk::DiffusionPropertyHelper::SetReferenceBValue(testImage, parameters.m_SignalGen.GetBvalue());
	-
	- mitk::DiffusionPropertyHelper::InitializeImage( testImage );
	-
	- if (refImage.IsNotNull())
	- {
	- if(mitk::DiffusionPropertyHelper::GetGradientContainer(refImage).IsNotNull() )
	- {
	- ItkDwiType::Pointer itkTestImagePointer = ItkDwiType::New();
	- mitk::CastToItkImage(testImage, itkTestImagePointer);
	- ItkDwiType::Pointer itkRefImagePointer = ItkDwiType::New();
	- mitk::CastToItkImage(refImage, itkRefImagePointer);
	-
	- bool cond = CompareDwi(itkTestImagePointer, itkRefImagePointer);
	- if (!cond)
	- {
	- MITK_INFO << "Saving test image to " << mitk::IOUtil::GetTempPath()+out;
	- mitk::IOUtil::Save(testImage, "DWI_NIFTI", mitk::IOUtil::GetTempPath()+out);
	- mitk::IOUtil::Save(refImage, "DWI_NIFTI", mitk::IOUtil::GetTempPath()+ "REF_" + out);
	- }
	- CPPUNIT_ASSERT_MESSAGE("Simulated images should be equal", cond);
	- }
	- }
	- }
	-
	- void Test1()
	- {
	- FiberfoxParameters parameters;
	- parameters.LoadParameters(GetTestDataFilePath("DiffusionImaging/Fiberfox/params/BrainSlice_1.ffp"), true);
	- adjust_to_template(parameters);
	- mitk::Image::Pointer refImage = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/Fiberfox/params/BrainSlice_1_OUT.nii.gz"));
	- StartSimulation(parameters, refImage, "BrainSlice_1_OUT.nii.gz");
	- }
	-
	- void Test2()
	- {
	- FiberfoxParameters parameters;
	- parameters.LoadParameters(GetTestDataFilePath("DiffusionImaging/Fiberfox/params/BrainSlice_2.ffp"), true);
	- adjust_to_template(parameters);
	- mitk::Image::Pointer refImage = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/Fiberfox/params/BrainSlice_2_OUT.nii.gz"));
	- StartSimulation(parameters, refImage, "BrainSlice_2_OUT.nii.gz");
	- }
	-
	- void Test3()
	- {
	- FiberfoxParameters parameters;
	- parameters.LoadParameters(GetTestDataFilePath("DiffusionImaging/Fiberfox/params/BrainSlice_3.ffp"), true);
	- adjust_to_template(parameters);
	- mitk::Image::Pointer refImage = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/Fiberfox/params/BrainSlice_3_OUT.nii.gz"));
	- StartSimulation(parameters, refImage, "BrainSlice_3_OUT.nii.gz");
	- }
	-
	- void Test4()
	- {
	- FiberfoxParameters parameters;
	- parameters.LoadParameters(GetTestDataFilePath("DiffusionImaging/Fiberfox/params/BrainSlice_4.ffp"), true);
	- adjust_to_template(parameters);
	- mitk::Image::Pointer refImage = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/Fiberfox/params/BrainSlice_4_OUT.nii.gz"));
	- StartSimulation(parameters, refImage, "BrainSlice_4_OUT.nii.gz");
	- }
	-
	- void Test5()
	- {
	- FiberfoxParameters parameters;
	- parameters.LoadParameters(GetTestDataFilePath("DiffusionImaging/Fiberfox/params/BrainSlice_5.ffp"), true);
	- adjust_to_template(parameters);
	- mitk::Image::Pointer refImage = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/Fiberfox/params/BrainSlice_5_OUT.nii.gz"));
	- StartSimulation(parameters, refImage, "BrainSlice_5_OUT.nii.gz");
	- }
	-
	-};
	-
	-MITK_TEST_SUITE_REGISTRATION(mitkFiberfoxSignalGenerationBrainSlice)
	diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxSignalGenerationTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxSignalGenerationTest.cpp
	deleted file mode 100644
	index 1fd3ee00d5..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxSignalGenerationTest.cpp
	+++ /dev/null
	@@ -1,226 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkTestingMacros.h>
	-#include <mitkIOUtil.h>
	-#include <mitkFiberBundle.h>
	-#include <itkTractsToDWIImageFilter.h>
	-#include <mitkFiberfoxParameters.h>
	-#include <mitkStickModel.h>
	-#include <mitkTensorModel.h>
	-#include <mitkBallModel.h>
	-#include <mitkDotModel.h>
	-#include <mitkAstroStickModel.h>
	-#include <mitkImage.h>
	-#include <itkTestingComparisonImageFilter.h>
	-#include <itkImageRegionConstIterator.h>
	-#include <mitkRicianNoiseModel.h>
	-#include <mitkChiSquareNoiseModel.h>
	-#include <mitkIOUtil.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <mitkProperties.h>
	-#include <mitkITKImageImport.h>
	-#include <mitkImageCast.h>
	-
	-#include <itkVectorImage.h>
	-#include <omp.h>
	-
	-#include "mitkTestFixture.h"
	-
	-class mitkFiberfoxSignalGenerationTestSuite : public mitk::TestFixture
	-{
	-
	- CPPUNIT_TEST_SUITE(mitkFiberfoxSignalGenerationTestSuite);
	- MITK_TEST(Test1);
	- MITK_TEST(Test2);
	- MITK_TEST(Test3);
	- MITK_TEST(Test4);
	- MITK_TEST(Test5);
	- MITK_TEST(Test6);
	- MITK_TEST(Test7);
	- MITK_TEST(Test8);
	- MITK_TEST(Test9);
	- CPPUNIT_TEST_SUITE_END();
	-
	- typedef itk::VectorImage< short, 3> ItkDwiType;
	-
	-private:
	-
	-public:
	-
	- /** Members used inside the different (sub-)tests. All members are initialized via setUp().*/
	- FiberBundle::Pointer m_FiberBundle;
	-
	- void setUp() override
	- {
	- m_FiberBundle = mitk::IOUtil::Load<FiberBundle>(GetTestDataFilePath("DiffusionImaging/Fiberfox/Signalgen.fib"));
	- }
	-
	- void tearDown() override
	- {
	-
	- }
	-
	- bool CompareDwi(itk::VectorImage< short, 3 >* dwi1, itk::VectorImage< short, 3 >* dwi2)
	- {
	- bool out = true;
	- typedef itk::VectorImage< short, 3 > DwiImageType;
	- try{
	- itk::ImageRegionIterator< DwiImageType > it1(dwi1, dwi1->GetLargestPossibleRegion());
	- itk::ImageRegionIterator< DwiImageType > it2(dwi2, dwi2->GetLargestPossibleRegion());
	- int count = 0;
	- while(!it1.IsAtEnd())
	- {
	- for (unsigned int i=0; i<dwi1->GetVectorLength(); ++i)
	- {
	- short d = abs(it1.Get()[i]-it2.Get()[i]);
	-
	- if (d>1)
	- {
	- if (count<10)
	- {
	- MITK_INFO << "**************************************";
	- MITK_INFO << "Test value: " << it1.GetIndex() << ":" << it1.Get()[i];
	- MITK_INFO << "Ref. value: " << it2.GetIndex() << ":" << it2.Get()[i];
	- }
	- out = false;
	- count++;
	- }
	- }
	- ++it1;
	- ++it2;
	- }
	- if (count>=10)
	- MITK_INFO << "Skipping errors.";
	- MITK_INFO << "Errors detected: " << count;
	- }
	- catch(...)
	- {
	- return false;
	- }
	- return out;
	- }
	-
	- void StartSimulation(FiberfoxParameters parameters, mitk::Image::Pointer refImage, std::string out)
	- {
	- itk::TractsToDWIImageFilter< short >::Pointer tractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New();
	- tractsToDwiFilter->SetUseConstantRandSeed(true);
	- tractsToDwiFilter->SetParameters(parameters);
	- tractsToDwiFilter->SetFiberBundle(m_FiberBundle);
	- tractsToDwiFilter->Update();
	-
	- mitk::Image::Pointer testImage = mitk::GrabItkImageMemory( tractsToDwiFilter->GetOutput() );
	- mitk::DiffusionPropertyHelper::SetGradientContainer(testImage, parameters.m_SignalGen.GetItkGradientContainer());
	- mitk::DiffusionPropertyHelper::SetReferenceBValue(testImage, parameters.m_SignalGen.GetBvalue());
	-
	- mitk::DiffusionPropertyHelper::InitializeImage( testImage );
	-
	- if (refImage.IsNotNull())
	- {
	- if(mitk::DiffusionPropertyHelper::GetGradientContainer(refImage).IsNotNull() )
	- {
	- ItkDwiType::Pointer itkTestImagePointer = ItkDwiType::New();
	- mitk::CastToItkImage(testImage, itkTestImagePointer);
	- ItkDwiType::Pointer itkRefImagePointer = ItkDwiType::New();
	- mitk::CastToItkImage(refImage, itkRefImagePointer);
	-
	- bool cond = CompareDwi(itkTestImagePointer, itkRefImagePointer);
	- if (!cond)
	- {
	- MITK_INFO << "Saving test image to " << mitk::IOUtil::GetTempPath()+out;
	- mitk::IOUtil::Save(testImage, mitk::IOUtil::GetTempPath()+out);
	- mitk::IOUtil::Save(refImage, mitk::IOUtil::GetTempPath()+ "REF_" + out);
	- }
	- CPPUNIT_ASSERT_MESSAGE("Simulated images should be equal", cond);
	- }
	- }
	- }
	-
	- void Test1()
	- {
	- FiberfoxParameters parameters;
	- parameters.LoadParameters(GetTestDataFilePath("DiffusionImaging/Fiberfox/params/param1.ffp"), true);
	- mitk::Image::Pointer refImage = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/Fiberfox/params/param1.dwi"));
	- StartSimulation(parameters, refImage, "param1.dwi");
	- }
	-
	- void Test2()
	- {
	- FiberfoxParameters parameters;
	- parameters.LoadParameters(GetTestDataFilePath("DiffusionImaging/Fiberfox/params/param2.ffp"), true);
	- mitk::Image::Pointer refImage = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/Fiberfox/params/param2.dwi"));
	- StartSimulation(parameters, refImage, "param2.dwi");
	- }
	-
	- void Test3()
	- {
	- FiberfoxParameters parameters;
	- parameters.LoadParameters(GetTestDataFilePath("DiffusionImaging/Fiberfox/params/param3.ffp"), true);
	- mitk::Image::Pointer refImage = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/Fiberfox/params/param3.dwi"));
	- StartSimulation(parameters, refImage, "param3.dwi");
	- }
	-
	- void Test4()
	- {
	- FiberfoxParameters parameters;
	- parameters.LoadParameters(GetTestDataFilePath("DiffusionImaging/Fiberfox/params/param4.ffp"), true);
	- mitk::Image::Pointer refImage = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/Fiberfox/params/param4.dwi"));
	- StartSimulation(parameters, refImage, "param4.dwi");
	- }
	-
	- void Test5()
	- {
	- FiberfoxParameters parameters;
	- parameters.LoadParameters(GetTestDataFilePath("DiffusionImaging/Fiberfox/params/param5.ffp"), true);
	- mitk::Image::Pointer refImage = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/Fiberfox/params/param5.dwi"));
	- StartSimulation(parameters, refImage, "param5.dwi");
	- }
	-
	- void Test6()
	- {
	- FiberfoxParameters parameters;
	- parameters.LoadParameters(GetTestDataFilePath("DiffusionImaging/Fiberfox/params/param6.ffp"), true);
	- mitk::Image::Pointer refImage = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/Fiberfox/params/param6.dwi"));
	- StartSimulation(parameters, refImage, "param6.dwi");
	- }
	-
	- void Test7()
	- {
	- FiberfoxParameters parameters;
	- parameters.LoadParameters(GetTestDataFilePath("DiffusionImaging/Fiberfox/params/param7.ffp"), true);
	- mitk::Image::Pointer refImage = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/Fiberfox/params/param7.dwi"));
	- StartSimulation(parameters, refImage, "param7.dwi");
	- }
	-
	- void Test8()
	- {
	- FiberfoxParameters parameters;
	- parameters.LoadParameters(GetTestDataFilePath("DiffusionImaging/Fiberfox/params/param8.ffp"), true);
	- mitk::Image::Pointer refImage = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/Fiberfox/params/param8.dwi"));
	- StartSimulation(parameters, refImage, "param8.dwi");
	- }
	-
	- void Test9()
	- {
	- FiberfoxParameters parameters;
	- parameters.LoadParameters(GetTestDataFilePath("DiffusionImaging/Fiberfox/params/param9.ffp"), true);
	- mitk::Image::Pointer refImage = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/Fiberfox/params/param9.dwi"));
	- StartSimulation(parameters, refImage, "param9.dwi");
	- }
	-
	-};
	-
	-MITK_TEST_SUITE_REGISTRATION(mitkFiberfoxSignalGeneration)
	diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkGibbsTrackingTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkGibbsTrackingTest.cpp
	deleted file mode 100644
	index c1513d2410..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkGibbsTrackingTest.cpp
	+++ /dev/null
	@@ -1,92 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkTestingMacros.h>
	-#include <mitkImageCast.h>
	-#include <mitkOdfImage.h>
	-#include <itkGibbsTrackingFilter.h>
	-#include <mitkFiberBundle.h>
	-#include <mitkIOUtil.h>
	-
	-using namespace mitk;
	-
	-/**Documentation
	- * Test for gibbs tracking filter
	- */
	-int mitkGibbsTrackingTest(int argc, char* argv[])
	-{
	- MITK_TEST_BEGIN("mitkGibbsTrackingTest");
	-
	- MITK_TEST_CONDITION_REQUIRED(argc>4,"check for input data")
	-
	- OdfImage::Pointer mitkOdfImage;
	- Image::Pointer mitkMaskImage;
	- mitk::FiberBundle::Pointer fib1;
	-
	- try{
	-
	- MITK_INFO << "ODF image: " << argv[1];
	- MITK_INFO << "Mask image: " << argv[2];
	- MITK_INFO << "Parameter file: " << argv[3];
	- MITK_INFO << "Reference bundle: " << argv[4];
	-
	- std::vector<mitk::BaseData::Pointer> infile = mitk::IOUtil::Load( argv[1]);
	- mitkOdfImage = dynamic_cast<mitk::OdfImage*>(infile.at(0).GetPointer());
	- MITK_TEST_CONDITION_REQUIRED(mitkOdfImage.IsNotNull(),"check Odf image")
	-
	- infile = mitk::IOUtil::Load( argv[2] );
	- mitkMaskImage = dynamic_cast<mitk::Image*>(infile.at(0).GetPointer());
	- MITK_TEST_CONDITION_REQUIRED(mitkMaskImage.IsNotNull(),"check mask image")
	-
	- infile = mitk::IOUtil::Load( argv[4]);
	- fib1 = dynamic_cast<mitk::FiberBundle*>(infile.at(0).GetPointer());
	- MITK_TEST_CONDITION_REQUIRED(fib1.IsNotNull(),"check fiber bundle")
	-
	- typedef itk::Vector<float, ODF_SAMPLING_SIZE> OdfVectorType;
	- typedef itk::Image<OdfVectorType,3> OdfVectorImgType;
	- typedef itk::Image<float,3> MaskImgType;
	- typedef itk::GibbsTrackingFilter<OdfVectorImgType> GibbsTrackingFilterType;
	-
	- OdfVectorImgType::Pointer itk_odf = OdfVectorImgType::New();
	- mitk::CastToItkImage(mitkOdfImage, itk_odf);
	-
	- MaskImgType::Pointer itk_mask = MaskImgType::New();
	- mitk::CastToItkImage(mitkMaskImage, itk_mask);
	-
	- GibbsTrackingFilterType::Pointer gibbsTracker = GibbsTrackingFilterType::New();
	- gibbsTracker->SetOdfImage(itk_odf.GetPointer());
	- gibbsTracker->SetMaskImage(itk_mask);
	- gibbsTracker->SetDuplicateImage(false);
	- gibbsTracker->SetRandomSeed(1);
	- gibbsTracker->SetLoadParameterFile(argv[3]);
	- gibbsTracker->Update();
	-
	- mitk::FiberBundle::Pointer fib2 = mitk::FiberBundle::New(gibbsTracker->GetFiberBundle());
	- MITK_TEST_CONDITION_REQUIRED(fib1->Equals(fib2), "check if gibbs tracking has changed");
	-
	- gibbsTracker->SetRandomSeed(0);
	- gibbsTracker->Update();
	- fib2 = mitk::FiberBundle::New(gibbsTracker->GetFiberBundle());
	- MITK_TEST_CONDITION_REQUIRED(!fib1->Equals(fib2), "check if gibbs tracking has changed after wrong seed");
	- }
	- catch(...)
	- {
	- return EXIT_FAILURE;
	- }
	-
	- // always end with this!
	- MITK_TEST_END();
	-}
	diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkMachineLearningTrackingTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkMachineLearningTrackingTest.cpp
	deleted file mode 100644
	index a2d3d72928..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkMachineLearningTrackingTest.cpp
	+++ /dev/null
	@@ -1,110 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkTestingMacros.h"
	-#include <mitkFiberBundle.h>
	-#include <mitkBaseData.h>
	-#include <itksys/SystemTools.hxx>
	-#include <mitkTestingConfig.h>
	-#include <mitkIOUtil.h>
	-#include <itkStreamlineTrackingFilter.h>
	-#include <mitkTrackingHandlerRandomForest.h>
	-#include <mitkImageCast.h>
	-#include <mitkImageToItk.h>
	-#include <omp.h>
	-#include <mitkTractographyForest.h>
	-#include <mitkStreamlineTractographyParameters.h>
	-
	-#include "mitkTestFixture.h"
	-
	-class mitkMachineLearningTrackingTestSuite : public mitk::TestFixture
	-{
	-
	- CPPUNIT_TEST_SUITE(mitkMachineLearningTrackingTestSuite);
	- MITK_TEST(Track1);
	- CPPUNIT_TEST_SUITE_END();
	-
	- typedef itk::Image<float, 3> ItkFloatImgType;
	-
	-private:
	-
	- /** Members used inside the different (sub-)tests. All members are initialized via setUp().*/
	- mitk::FiberBundle::Pointer ref;
	- mitk::TrackingHandlerRandomForest<6, 100>* tfh;
	- mitk::Image::Pointer dwi;
	- ItkFloatImgType::Pointer seed;
	-
	-public:
	-
	- void setUp() override
	- {
	- ref = nullptr;
	- tfh = new mitk::TrackingHandlerRandomForest<6,100>();
	-
	- std::vector<mitk::BaseData::Pointer> fibInfile = mitk::IOUtil::Load(GetTestDataFilePath("DiffusionImaging/MachineLearningTracking/ReferenceTracts.fib"));
	- mitk::BaseData::Pointer baseData = fibInfile.at(0);
	- ref = dynamic_cast<mitk::FiberBundle*>(baseData.GetPointer());
	-
	- dwi = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/MachineLearningTracking/DiffusionImage.dwi"));
	-
	-
	- mitk::Image::Pointer img = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/MachineLearningTracking/seed.nrrd"));
	- seed = ItkFloatImgType::New();
	- mitk::CastToItkImage(img, seed);
	-
	- mitk::TractographyForest::Pointer forest = mitk::IOUtil::Load<mitk::TractographyForest>(GetTestDataFilePath("DiffusionImaging/MachineLearningTracking/forest.rf"));
	-
	- tfh->SetForest(forest);
	- tfh->AddDwi(dwi);
	- }
	-
	- void tearDown() override
	- {
	- delete tfh;
	- ref = nullptr;
	- }
	-
	- void Track1()
	- {
	- std::shared_ptr<mitk::StreamlineTractographyParameters> params = std::make_shared<mitk::StreamlineTractographyParameters>();
	- params->m_RandomSampling = false;
	- params->SetSamplingDistanceVox(0.5);
	- params->m_AvoidStop = true;
	- params->SetAngularThresholdDeg(45);
	- params->SetStepSizeVox(-1);
	- params->m_SeedsPerVoxel = 1;
	- params->m_InterpolateRoiImages = false;
	- omp_set_num_threads(1);
	- typedef itk::StreamlineTrackingFilter TrackerType;
	- TrackerType::Pointer tracker = TrackerType::New();
	- tracker->SetDemoMode(false);
	- tracker->SetSeedImage(seed);
	- tracker->SetTrackingHandler(tfh);
	- tracker->SetParameters(params);
	- tracker->Update();
	- vtkSmartPointer< vtkPolyData > poly = tracker->GetFiberPolyData();
	- mitk::FiberBundle::Pointer outFib = mitk::FiberBundle::New(poly);
	-
	- //MITK_INFO << mitk::IOUtil::GetTempPath() << "ReferenceTracts.fib";
	- if (!ref->Equals(outFib))
	- mitk::IOUtil::Save(outFib, mitk::IOUtil::GetTempPath()+"ML_Track1.fib");
	-
	- CPPUNIT_ASSERT_MESSAGE("Should be equal", ref->Equals(outFib));
	- }
	-
	-};
	-
	-MITK_TEST_SUITE_REGISTRATION(mitkMachineLearningTracking)
	diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkPeakShImageReaderTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkPeakShImageReaderTest.cpp
	deleted file mode 100644
	index 98d03dd875..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkPeakShImageReaderTest.cpp
	+++ /dev/null
	@@ -1,127 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkNodePredicateDataType.h>
	-#include <mitkRenderingTestHelper.h>
	-#include <mitkSmartPointerProperty.h>
	-#include <mitkTestingMacros.h>
	-#include <vtkSmartPointer.h>
	-#include "mitkTestingMacros.h"
	-#include <itksys/SystemTools.hxx>
	-#include <mitkTestingConfig.h>
	-#include <mitkIOUtil.h>
	-#include <mitkTestFixture.h>
	-#include <vtkTesting.h>
	-#include <mitkPeakImage.h>
	-#include <mitkShImage.h>
	-#include <mitkPreferenceListReaderOptionsFunctor.h>
	-#include <mitkImagePixelReadAccessor.h>
	-
	-
	-class mitkPeakShImageReaderTestSuite : public mitk::TestFixture
	-{
	-
	- CPPUNIT_TEST_SUITE(mitkPeakShImageReaderTestSuite);
	- MITK_TEST(PeakReader);
	- MITK_TEST(ShReader);
	- CPPUNIT_TEST_SUITE_END();
	-
	- typedef itk::Image<float, 3> ItkFloatImgType;
	-
	-private:
	-
	- /** Members used inside the different (sub-)tests. All members are initialized via setUp().*/
	-
	-public:
	-
	- void setUp() override
	- {
	-
	- }
	-
	- void tearDown() override
	- {
	-
	- }
	-
	- void PeakReader()
	- {
	- mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Peak Image"}, {});
	- auto inputData = mitk::IOUtil::Load<mitk::PeakImage>(GetTestDataFilePath("DiffusionImaging/peak_image_test.nii.gz"), &functor);
	- std::string class_name = "PeakImage";
	- bool ok = true;
	- if (class_name.compare(inputData->GetNameOfClass())!=0)
	- ok = false;
	- MITK_TEST_CONDITION_REQUIRED(ok, "Check class name = PeakImage");
	-
	- mitk::Vector3D sp;
	- sp[0] = 1.23;
	- sp[1] = 2.001;
	- sp[2] = 1.409;
	- MITK_TEST_CONDITION_REQUIRED(mitk::Equal(sp, inputData->GetGeometry()->GetSpacing(), 0.0001, true), "Check spacing ok");
	-
	- mitk::Point3D o;
	- o[0] = 0.615;
	- o[1] = 1.0005;
	- o[2] = 0.7045;
	- MITK_TEST_CONDITION_REQUIRED(mitk::Equal(o, inputData->GetGeometry()->GetOrigin(), 0.0001, true), "Check origin ok");
	-
	- mitk::ImagePixelReadAccessor<mitk::PeakImage::PixelType, 4> readAccess(inputData);
	- itk::Index<4> idx;
	- idx[0] = 5;
	- idx[1] = 4;
	- idx[2] = 1;
	- idx[3] = 0;
	- MITK_TEST_CONDITION_REQUIRED(fabs(-0.997147f-readAccess.GetPixelByIndex(idx))<0.0001f, "Check pixel value ok");
	- }
	-
	- void ShReader()
	- {
	- mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"SH Image"}, {});
	- auto inputData = mitk::IOUtil::Load<mitk::ShImage>(GetTestDataFilePath("DiffusionImaging/sh_image_test.nii.gz"), &functor);
	-
	- std::string class_name = "ShImage";
	- bool ok = true;
	- if (class_name.compare(inputData->GetNameOfClass())!=0)
	- ok = false;
	- MITK_TEST_CONDITION_REQUIRED(ok, "Check class name = ShImage");
	-
	- mitk::Vector3D sp;
	- sp[0] = 1.23;
	- sp[1] = 2.001;
	- sp[2] = 1.409;
	- MITK_TEST_CONDITION_REQUIRED(mitk::Equal(sp, inputData->GetGeometry()->GetSpacing(), 0.0001, true), "Check spacing ok");
	-
	- mitk::Point3D o;
	- o[0] = 0.615;
	- o[1] = 1.0005;
	- o[2] = 0.7045;
	- MITK_TEST_CONDITION_REQUIRED(mitk::Equal(o, inputData->GetGeometry()->GetOrigin(), 0.0001, true), "Check origin ok");
	-
	- mitk::ImagePixelReadAccessor<itk::Vector<float, 15>, 3> readAccess(inputData);
	- itk::Index<3> idx;
	- idx[0] = 5;
	- idx[1] = 4;
	- idx[2] = 1;
	- itk::Vector<float, 15> pixel = readAccess.GetPixelByIndex(idx);
	- MITK_TEST_CONDITION_REQUIRED(fabs(0.282095f-pixel[0])<0.000001f, "Check SH coeff value 0 ok");
	- MITK_TEST_CONDITION_REQUIRED(fabs(-0.00900571f-pixel[2])<0.000001f, "Check SH coeff value 2 ok");
	- MITK_TEST_CONDITION_REQUIRED(fabs(0.0513185f-pixel[6])<0.000001f, "Check SH coeff value 6 ok");
	- }
	-
	-};
	-
	-MITK_TEST_SUITE_REGISTRATION(mitkPeakShImageReader)
	diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkStreamlineTractographyTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkStreamlineTractographyTest.cpp
	deleted file mode 100755
	index edb22aadd7..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkStreamlineTractographyTest.cpp
	+++ /dev/null
	@@ -1,438 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkImageCast.h>
	-#include <mitkImageToItk.h>
	-#include <mitkTensorImage.h>
	-#include <mitkOdfImage.h>
	-#include <mitkIOUtil.h>
	-#include <mitkFiberBundle.h>
	-#include <itkStreamlineTrackingFilter.h>
	-#include <Algorithms/TrackingHandlers/mitkTrackingDataHandler.h>
	-#include <Algorithms/TrackingHandlers/mitkTrackingHandlerOdf.h>
	-#include <Algorithms/TrackingHandlers/mitkTrackingHandlerPeaks.h>
	-#include <Algorithms/TrackingHandlers/mitkTrackingHandlerTensor.h>
	-#include <itkDiffusionTensor3D.h>
	-#include <mitkTestingMacros.h>
	-#include <mitkTestFixture.h>
	-#include <mitkFiberBundle.h>
	-#include <omp.h>
	-#include <itksys/SystemTools.hxx>
	-#include <mitkEqual.h>
	-#include <mitkStreamlineTractographyParameters.h>
	-
	-class mitkStreamlineTractographyTestSuite : public mitk::TestFixture
	-{
	-
	- CPPUNIT_TEST_SUITE(mitkStreamlineTractographyTestSuite);
	- MITK_TEST(Test_Peak1);
	- MITK_TEST(Test_Peak2);
	- MITK_TEST(Test_Tensor1);
	- MITK_TEST(Test_Tensor2);
	- MITK_TEST(Test_Tensor3);
	- MITK_TEST(Test_Odf1);
	- MITK_TEST(Test_Odf2);
	- MITK_TEST(Test_Odf3);
	- MITK_TEST(Test_Odf4);
	- MITK_TEST(Test_Odf5);
	- MITK_TEST(Test_Odf6);
	- CPPUNIT_TEST_SUITE_END();
	-
	- typedef itk::VectorImage< short, 3> ItkDwiType;
	-
	-private:
	-
	-public:
	-
	- /** Members used inside the different (sub-)tests. All members are initialized via setUp().*/
	-
	- typedef itk::Image<float, 3> ItkFloatImgType;
	-
	- mitk::TrackingHandlerOdf::ItkOdfImageType::Pointer itk_odf_image;
	- mitk::TrackingHandlerTensor::ItkTensorImageType::ConstPointer itk_tensor_image;
	- mitk::TrackingHandlerPeaks::PeakImgType::Pointer itk_peak_image;
	- ItkFloatImgType::Pointer itk_seed_image;
	- ItkFloatImgType::Pointer itk_mask_image;
	- ItkFloatImgType::Pointer itk_gfa_image;
	-
	- float gfa_threshold;
	- float odf_threshold;
	- float peak_threshold;
	- std::shared_ptr<mitk::StreamlineTractographyParameters> params;
	-
	- itk::StreamlineTrackingFilter::Pointer tracker;
	-
	- void setUp() override
	- {
	- omp_set_num_threads(1);
	-
	- gfa_threshold = 0.2f;
	- odf_threshold = 0.1f;
	- peak_threshold = 0.1f;
	-
	- mitk::Image::Pointer odf_image = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/StreamlineTractography/qball_image.qbi"));
	- mitk::Image::Pointer tensor_image = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/StreamlineTractography/tensor_image.dti"));
	- mitk::Image::Pointer peak_image = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/StreamlineTractography/qball_peak_image.nii.gz"));
	- mitk::Image::Pointer seed_image = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/StreamlineTractography/seed_image.nii.gz"));
	- mitk::Image::Pointer mask_image = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/StreamlineTractography/mask_image.nii.gz"));
	- mitk::Image::Pointer gfa_image = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/StreamlineTractography/gfa_image.nii.gz"));
	-
	- params = std::make_shared<mitk::StreamlineTractographyParameters>();
	- params->m_FixRandomSeed = true;
	- params->m_InterpolateRoiImages = false;
	-
	- {
	- typedef mitk::ImageToItk< mitk::TrackingHandlerPeaks::PeakImgType > CasterType;
	- CasterType::Pointer caster = CasterType::New();
	- caster->SetInput(peak_image);
	- caster->Update();
	- itk_peak_image = caster->GetOutput();
	- }
	-
	- {
	- typedef mitk::ImageToItk< mitk::TrackingHandlerTensor::ItkTensorImageType > CasterType;
	- CasterType::Pointer caster = CasterType::New();
	- caster->SetInput(tensor_image);
	- caster->Update();
	- itk_tensor_image = caster->GetOutput();
	- }
	-
	- {
	- typedef mitk::ImageToItk< mitk::TrackingHandlerOdf::ItkOdfImageType > CasterType;
	- CasterType::Pointer caster = CasterType::New();
	- caster->SetInput(odf_image);
	- caster->Update();
	- itk_odf_image = caster->GetOutput();
	- }
	-
	- itk_gfa_image = ItkFloatImgType::New();
	- mitk::CastToItkImage(gfa_image, itk_gfa_image);
	-
	- itk_seed_image = ItkFloatImgType::New();
	- mitk::CastToItkImage(seed_image, itk_seed_image);
	-
	- itk_mask_image = ItkFloatImgType::New();
	- mitk::CastToItkImage(mask_image, itk_mask_image);
	- }
	-
	- mitk::FiberBundle::Pointer LoadReferenceFib(std::string filename)
	- {
	- mitk::FiberBundle::Pointer fib = nullptr;
	-
	- if (itksys::SystemTools::FileExists(GetTestDataFilePath("DiffusionImaging/StreamlineTractography/ReferenceFibs/" + filename)))
	- {
	- mitk::BaseData::Pointer baseData = mitk::IOUtil::Load(GetTestDataFilePath("DiffusionImaging/StreamlineTractography/ReferenceFibs/" + filename)).at(0);
	- fib = dynamic_cast<mitk::FiberBundle*>(baseData.GetPointer());
	- }
	- return fib;
	- }
	-
	- mitk::Image::Pointer LoadReferenceImage(std::string filename)
	- {
	- mitk::Image::Pointer img = nullptr;
	-
	- if (itksys::SystemTools::FileExists(GetTestDataFilePath("DiffusionImaging/StreamlineTractography/ReferenceFibs/" + filename)))
	- {
	- img = mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/StreamlineTractography/ReferenceFibs/" + filename));
	- }
	- return img;
	- }
	-
	- void SetupTracker(mitk::TrackingDataHandler* handler)
	- {
	-
	- tracker = itk::StreamlineTrackingFilter::New();
	-
	-// tracker->SetInterpolateMasks(false);
	-// tracker->SetNumberOfSamples(0);
	-// tracker->SetAngularThreshold(-1);
	- tracker->SetMaskImage(itk_mask_image);
	- tracker->SetSeedImage(itk_seed_image);
	- tracker->SetStoppingRegions(nullptr);
	-// tracker->SetSeedsPerVoxel(1);
	-// tracker->SetStepSize(0.5);
	-// tracker->SetSamplingDistance(0.25);
	-// tracker->SetUseStopVotes(true);
	-// tracker->SetOnlyForwardSamples(true);
	-// tracker->SetMinTractLength(20);
	-// tracker->SetMaxNumTracts(-1);
	- tracker->SetTrackingHandler(handler);
	-// tracker->SetUseOutputProbabilityMap(false);
	- tracker->SetParameters(params);
	- }
	-
	- void tearDown() override
	- {
	-
	- }
	-
	- void CheckFibResult(std::string ref_file, mitk::FiberBundle::Pointer test_fib)
	- {
	- mitk::FiberBundle::Pointer ref = LoadReferenceFib(ref_file);
	- if (ref.IsNull())
	- {
	- mitk::IOUtil::Save(test_fib, mitk::IOUtil::GetTempPath()+ref_file);
	- CPPUNIT_FAIL("Reference file not found. Saving test file to " + mitk::IOUtil::GetTempPath() + ref_file);
	- }
	- else
	- {
	- bool is_equal = ref->Equals(test_fib);
	- if (!is_equal)
	- {
	- mitk::IOUtil::Save(test_fib, mitk::IOUtil::GetTempPath()+ref_file);
	- CPPUNIT_FAIL("Tractograms are not equal! Saving test file to " + mitk::IOUtil::GetTempPath() + ref_file);
	- }
	- }
	- }
	-
	- void CheckImageResult(std::string ref_file, mitk::Image::Pointer test_img)
	- {
	- mitk::Image::Pointer ref = LoadReferenceImage(ref_file);
	- if (ref.IsNull())
	- {
	- mitk::IOUtil::Save(test_img, mitk::IOUtil::GetTempPath()+ref_file);
	- CPPUNIT_FAIL("Reference file not found. Saving test file to " + mitk::IOUtil::GetTempPath() + ref_file);
	- }
	- else
	- {
	- MITK_ASSERT_EQUAL(test_img, ref, "Images should be equal");
	- }
	- }
	-
	- void Test_Peak1()
	- {
	- mitk::TrackingHandlerPeaks* handler = new mitk::TrackingHandlerPeaks();
	- handler->SetPeakImage(itk_peak_image);
	- params->m_Cutoff = peak_threshold;
	-
	- SetupTracker(handler);
	- tracker->Update();
	-
	- vtkSmartPointer< vtkPolyData > poly = tracker->GetFiberPolyData();
	- mitk::FiberBundle::Pointer outFib = mitk::FiberBundle::New(poly);
	-
	- CheckFibResult("Test_Peak1.fib", outFib);
	-
	- delete handler;
	- }
	-
	- void Test_Peak2()
	- {
	- mitk::TrackingHandlerPeaks* handler = new mitk::TrackingHandlerPeaks();
	- handler->SetPeakImage(itk_peak_image);
	- params->m_Cutoff = peak_threshold;
	- params->m_InterpolateTractographyData = false;
	-
	- SetupTracker(handler);
	- tracker->Update();
	-
	- vtkSmartPointer< vtkPolyData > poly = tracker->GetFiberPolyData();
	- mitk::FiberBundle::Pointer outFib = mitk::FiberBundle::New(poly);
	-
	- CheckFibResult("Test_Peak2.fib", outFib);
	-
	- delete handler;
	- }
	-
	- void Test_Tensor1()
	- {
	- mitk::TrackingHandlerTensor* handler = new mitk::TrackingHandlerTensor();
	- handler->SetTensorImage(itk_tensor_image);
	- params->m_Cutoff = gfa_threshold;
	-
	- SetupTracker(handler);
	- tracker->Update();
	-
	- vtkSmartPointer< vtkPolyData > poly = tracker->GetFiberPolyData();
	- mitk::FiberBundle::Pointer outFib = mitk::FiberBundle::New(poly);
	-
	- CheckFibResult("Test_Tensor1.fib", outFib);
	-
	- delete handler;
	- }
	-
	- void Test_Tensor2()
	- {
	- mitk::TrackingHandlerTensor* handler = new mitk::TrackingHandlerTensor();
	- handler->SetTensorImage(itk_tensor_image);
	- params->m_Cutoff = gfa_threshold;
	- params->m_InterpolateTractographyData = false;
	-
	- SetupTracker(handler);
	- tracker->Update();
	-
	- vtkSmartPointer< vtkPolyData > poly = tracker->GetFiberPolyData();
	- mitk::FiberBundle::Pointer outFib = mitk::FiberBundle::New(poly);
	-
	- CheckFibResult("Test_Tensor2.fib", outFib);
	-
	- delete handler;
	- }
	-
	- void Test_Tensor3()
	- {
	- mitk::TrackingHandlerTensor* handler = new mitk::TrackingHandlerTensor();
	- handler->SetTensorImage(itk_tensor_image);
	- params->m_Cutoff = gfa_threshold;
	- params->m_InterpolateTractographyData = false;
	- params->m_F = 0;
	- params->m_G = 1;
	-
	- SetupTracker(handler);
	- tracker->Update();
	-
	- vtkSmartPointer< vtkPolyData > poly = tracker->GetFiberPolyData();
	- mitk::FiberBundle::Pointer outFib = mitk::FiberBundle::New(poly);
	-
	- CheckFibResult("Test_Tensor3.fib", outFib);
	-
	- delete handler;
	- }
	-
	- void Test_Odf1()
	- {
	- mitk::TrackingHandlerOdf* handler = new mitk::TrackingHandlerOdf();
	- handler->SetOdfImage(itk_odf_image);
	-
	- params->m_Cutoff = gfa_threshold;
	- params->m_OdfCutoff = 0;
	- params->m_SharpenOdfs = true;
	-
	- SetupTracker(handler);
	- tracker->Update();
	-
	- vtkSmartPointer< vtkPolyData > poly = tracker->GetFiberPolyData();
	- mitk::FiberBundle::Pointer outFib = mitk::FiberBundle::New(poly);
	-
	- CheckFibResult("Test_Odf1.fib", outFib);
	-
	- delete handler;
	- }
	-
	- void Test_Odf2()
	- {
	- mitk::TrackingHandlerOdf* handler = new mitk::TrackingHandlerOdf();
	- handler->SetOdfImage(itk_odf_image);
	-
	- params->m_Cutoff = gfa_threshold;
	- params->m_OdfCutoff = 0;
	- params->m_SharpenOdfs = false;
	-
	- SetupTracker(handler);
	- tracker->Update();
	-
	- vtkSmartPointer< vtkPolyData > poly = tracker->GetFiberPolyData();
	- mitk::FiberBundle::Pointer outFib = mitk::FiberBundle::New(poly);
	-
	- CheckFibResult("Test_Odf2.fib", outFib);
	-
	- delete handler;
	- }
	-
	-
	- void Test_Odf3()
	- {
	- mitk::TrackingHandlerOdf* handler = new mitk::TrackingHandlerOdf();
	- handler->SetOdfImage(itk_odf_image);
	-
	- params->m_Cutoff = gfa_threshold;
	- params->m_OdfCutoff = 0;
	- params->m_SharpenOdfs = true;
	- params->m_InterpolateTractographyData = false;
	-
	- SetupTracker(handler);
	- tracker->Update();
	-
	- vtkSmartPointer< vtkPolyData > poly = tracker->GetFiberPolyData();
	- mitk::FiberBundle::Pointer outFib = mitk::FiberBundle::New(poly);
	-
	- CheckFibResult("Test_Odf3.fib", outFib);
	-
	- delete handler;
	- }
	-
	- void Test_Odf4()
	- {
	- mitk::TrackingHandlerOdf* handler = new mitk::TrackingHandlerOdf();
	- handler->SetOdfImage(itk_odf_image);
	-
	- params->m_Cutoff = gfa_threshold;
	- params->m_OdfCutoff = 0;
	- params->m_SharpenOdfs = true;
	- params->m_SeedsPerVoxel = 3;
	-
	- SetupTracker(handler);
	- tracker->Update();
	-
	- vtkSmartPointer< vtkPolyData > poly = tracker->GetFiberPolyData();
	- mitk::FiberBundle::Pointer outFib = mitk::FiberBundle::New(poly);
	-
	- CheckFibResult("Test_Odf4.fib", outFib);
	-
	- delete handler;
	- }
	-
	- void Test_Odf5()
	- {
	- mitk::TrackingHandlerOdf* handler = new mitk::TrackingHandlerOdf();
	- handler->SetOdfImage(itk_odf_image);
	-
	- params->m_Cutoff = gfa_threshold;
	- params->m_OdfCutoff = 0;
	- params->m_SharpenOdfs = true;
	- params->m_SeedsPerVoxel = 3;
	- params->m_Mode = mitk::TrackingDataHandler::MODE::PROBABILISTIC;
	-
	- SetupTracker(handler);
	- tracker->Update();
	-
	- vtkSmartPointer< vtkPolyData > poly = tracker->GetFiberPolyData();
	- mitk::FiberBundle::Pointer outFib = mitk::FiberBundle::New(poly);
	-
	- CheckFibResult("Test_Odf5.fib", outFib);
	-
	- delete handler;
	- }
	-
	- void Test_Odf6()
	- {
	- mitk::TrackingHandlerOdf* handler = new mitk::TrackingHandlerOdf();
	- handler->SetOdfImage(itk_odf_image);
	-
	- params->m_Cutoff = gfa_threshold;
	- params->m_OdfCutoff = 0;
	- params->m_SharpenOdfs = true;
	- params->m_SeedsPerVoxel = 10;
	- params->m_Mode = mitk::TrackingDataHandler::MODE::PROBABILISTIC;
	- params->m_OutputProbMap = true;
	-
	- SetupTracker(handler);
	- tracker->Update();
	-
	- itk::StreamlineTrackingFilter::ItkDoubleImgType::Pointer outImg = tracker->GetOutputProbabilityMap();
	- mitk::Image::Pointer img = mitk::Image::New();
	- img->InitializeByItk(outImg.GetPointer());
	- img->SetVolume(outImg->GetBufferPointer());
	-
	- mitk::IOUtil::Save(img, mitk::IOUtil::GetTempPath()+"Test_Odf6.nrrd");
	- CheckImageResult("Test_Odf6.nrrd", img);
	-
	- delete handler;
	- }
	-
	-};
	-
	-MITK_TEST_SUITE_REGISTRATION(mitkStreamlineTractography)
	diff --git a/Modules/DiffusionImaging/FiberTracking/files.cmake b/Modules/DiffusionImaging/FiberTracking/files.cmake
	deleted file mode 100644
	index 39210be9cf..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/files.cmake
	+++ /dev/null
	@@ -1,111 +0,0 @@
	-set(CPP_FILES
	-
	- mitkFiberTrackingModuleActivator.cpp
	-
	- ## IO datastructures
	- IODataStructures/FiberBundle/mitkFiberBundle.cpp
	- IODataStructures/FiberBundle/mitkTrackvis.cpp
	- IODataStructures/PlanarFigureComposite/mitkPlanarFigureComposite.cpp
	- IODataStructures/mitkTractographyForest.cpp
	- IODataStructures/mitkFiberfoxParameters.cpp
	- IODataStructures/mitkStreamlineTractographyParameters.cpp
	-
	- # Interactions
	-
	- # Tractography
	- Algorithms/GibbsTracking/mitkParticleGrid.cpp
	- Algorithms/GibbsTracking/mitkMetropolisHastingsSampler.cpp
	- Algorithms/GibbsTracking/mitkEnergyComputer.cpp
	- Algorithms/GibbsTracking/mitkGibbsEnergyComputer.cpp
	- Algorithms/GibbsTracking/mitkFiberBuilder.cpp
	- Algorithms/GibbsTracking/mitkSphereInterpolator.cpp
	-
	- Algorithms/itkStreamlineTrackingFilter.cpp
	- Algorithms/TrackingHandlers/mitkTrackingDataHandler.cpp
	- Algorithms/TrackingHandlers/mitkTrackingHandlerTensor.cpp
	- Algorithms/TrackingHandlers/mitkTrackingHandlerPeaks.cpp
	- Algorithms/TrackingHandlers/mitkTrackingHandlerOdf.cpp
	-)
	-
	-set(H_FILES
	- # DataStructures -> FiberBundle
	- IODataStructures/FiberBundle/mitkFiberBundle.h
	- IODataStructures/FiberBundle/mitkTrackvis.h
	- IODataStructures/mitkFiberfoxParameters.h
	- IODataStructures/mitkTractographyForest.h
	- IODataStructures/mitkStreamlineTractographyParameters.h
	-
	- # Algorithms
	- Algorithms/itkTractDensityImageFilter.h
	- Algorithms/itkTractsToFiberEndingsImageFilter.h
	- Algorithms/itkTractsToRgbaImageFilter.h
	- Algorithms/itkTractsToVectorImageFilter.h
	- Algorithms/itkEvaluateDirectionImagesFilter.h
	- Algorithms/itkEvaluateTractogramDirectionsFilter.h
	- Algorithms/itkFiberCurvatureFilter.h
	- Algorithms/itkFitFibersToImageFilter.h
	- Algorithms/itkTractClusteringFilter.h
	- Algorithms/itkTractDistanceFilter.h
	- Algorithms/itkFiberExtractionFilter.h
	- Algorithms/itkTdiToVolumeFractionFilter.h
	-
	- # Tractography
	- Algorithms/TrackingHandlers/mitkTrackingDataHandler.h
	- Algorithms/TrackingHandlers/mitkTrackingHandlerRandomForest.h
	- Algorithms/TrackingHandlers/mitkTrackingHandlerTensor.h
	- Algorithms/TrackingHandlers/mitkTrackingHandlerPeaks.h
	- Algorithms/TrackingHandlers/mitkTrackingHandlerOdf.h
	-
	- Algorithms/itkGibbsTrackingFilter.h
	- Algorithms/itkStochasticTractographyFilter.h
	- Algorithms/GibbsTracking/mitkParticle.h
	- Algorithms/GibbsTracking/mitkParticleGrid.h
	- Algorithms/GibbsTracking/mitkMetropolisHastingsSampler.h
	- Algorithms/GibbsTracking/mitkSimpSamp.h
	- Algorithms/GibbsTracking/mitkEnergyComputer.h
	- Algorithms/GibbsTracking/mitkGibbsEnergyComputer.h
	- Algorithms/GibbsTracking/mitkSphereInterpolator.h
	- Algorithms/GibbsTracking/mitkFiberBuilder.h
	-
	- Algorithms/itkStreamlineTrackingFilter.h
	-
	- # Clustering
	- Algorithms/ClusteringMetrics/mitkClusteringMetric.h
	- Algorithms/ClusteringMetrics/mitkClusteringMetricEuclideanMean.h
	- Algorithms/ClusteringMetrics/mitkClusteringMetricEuclideanMax.h
	- Algorithms/ClusteringMetrics/mitkClusteringMetricEuclideanStd.h
	- Algorithms/ClusteringMetrics/mitkClusteringMetricAnatomic.h
	- Algorithms/ClusteringMetrics/mitkClusteringMetricScalarMap.h
	- Algorithms/ClusteringMetrics/mitkClusteringMetricInnerAngles.h
	- Algorithms/ClusteringMetrics/mitkClusteringMetricLength.h
	-
	- # Fiberfox
	- Fiberfox/itkFibersFromPlanarFiguresFilter.h
	- Fiberfox/itkTractsToDWIImageFilter.h
	- Fiberfox/itkKspaceImageFilter.h
	- Fiberfox/itkDftImageFilter.h
	- Fiberfox/itkFieldmapGeneratorFilter.h
	- Fiberfox/itkRandomPhantomFilter.h
	-
	- Fiberfox/SignalModels/mitkDiffusionSignalModel.h
	- Fiberfox/SignalModels/mitkTensorModel.h
	- Fiberfox/SignalModels/mitkBallModel.h
	- Fiberfox/SignalModels/mitkDotModel.h
	- Fiberfox/SignalModels/mitkAstroStickModel.h
	- Fiberfox/SignalModels/mitkStickModel.h
	- Fiberfox/SignalModels/mitkRawShModel.h
	- Fiberfox/SignalModels/mitkDiffusionNoiseModel.h
	- Fiberfox/SignalModels/mitkRicianNoiseModel.h
	- Fiberfox/SignalModels/mitkChiSquareNoiseModel.h
	-
	- Fiberfox/Sequences/mitkAcquisitionType.h
	- Fiberfox/Sequences/mitkSingleShotEpi.h
	- Fiberfox/Sequences/mitkConventionalSpinEcho.h
	- Fiberfox/Sequences/mitkFastSpinEcho.h
	-)
	-
	-set(RESOURCE_FILES
	- # Binary directory resources
	- FiberTrackingLUTBaryCoords.bin
	- FiberTrackingLUTIndices.bin
	-)
	diff --git a/Modules/DiffusionImaging/FiberTracking/mitkFiberTrackingModuleActivator.cpp b/Modules/DiffusionImaging/FiberTracking/mitkFiberTrackingModuleActivator.cpp
	deleted file mode 100644
	index 87579cf714..0000000000
	--- a/Modules/DiffusionImaging/FiberTracking/mitkFiberTrackingModuleActivator.cpp
	+++ /dev/null
	@@ -1,43 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#include <usModuleActivator.h>
	-
	-namespace mitk
	-{
	- /**
	- \brief Registers services for segmentation module.
	- */
	- class FiberTrackingModuleActivator : public us::ModuleActivator
	- {
	- public:
	-
	- void Load(us::ModuleContext* /context/) override
	- {
	-
	- }
	-
	- void Unload(us::ModuleContext*) override
	- {
	-
	- }
	-
	- private:
	-
	-
	- };
	-}
	-
	-US_EXPORT_MODULE_ACTIVATOR(mitk::FiberTrackingModuleActivator)
	diff --git a/Modules/DiffusionImaging/Quantification/Algorithms/itkRegularizedIVIMLocalVariationImageFilter.h b/Modules/DiffusionImaging/Quantification/Algorithms/itkRegularizedIVIMLocalVariationImageFilter.h
	deleted file mode 100644
	index 1b16a5d87a..0000000000
	--- a/Modules/DiffusionImaging/Quantification/Algorithms/itkRegularizedIVIMLocalVariationImageFilter.h
	+++ /dev/null
	@@ -1,152 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkRegularizedIVIMLocalVariationImageFilter_h
	-#define __itkRegularizedIVIMLocalVariationImageFilter_h
	-
	-#include "itkImageToImageFilter.h"
	-#include "itkImage.h"
	-
	-namespace itk
	-{
	-
	- template<class TPixelType>
	- class IVIMSquaredEuclideanMetric
	- {
	- public:
	- static double Calc(TPixelType p)
	- {
	- return p*p;
	- }
	- };
	-
	- template<>
	- class IVIMSquaredEuclideanMetric<itk::Vector<double,3> >
	- {
	- public:
	- static double Calc(itk::Vector<double,3> p)
	- {
	- return p[1]*p[1];
	- }
	- };
	-
	- template<>
	- class IVIMSquaredEuclideanMetric<itk::VariableLengthVector<float> >
	- {
	- public:
	- static double Calc(itk::VariableLengthVector<float> p)
	- {
	- return p.GetSquaredNorm();
	- }
	- };
	-
	- template<>
	- class IVIMSquaredEuclideanMetric<itk::VariableLengthVector<double> >
	- {
	- public:
	- static double Calc(itk::VariableLengthVector<double> p)
	- {
	- return p.GetSquaredNorm();
	- }
	- };
	-
	-/** \class RegularizedIVIMLocalVariationImageFilter
	- * \brief Calculates the local variation in each pixel
	- *
	- * Reference: Tony F. Chan et al., The digital TV filter and nonlinear denoising
	- *
	- * \sa Image
	- * \sa Neighborhood
	- * \sa NeighborhoodOperator
	- * \sa NeighborhoodIterator
	- *
	- * \ingroup IntensityImageFilters
	- */
	-template <class TInputImage, class TOutputImage>
	-class RegularizedIVIMLocalVariationImageFilter :
	- public ImageToImageFilter< TInputImage, TOutputImage >
	-{
	-public:
	- /** Extract dimension from input and output image. */
	- itkStaticConstMacro(InputImageDimension, unsigned int,
	- TInputImage::ImageDimension);
	- itkStaticConstMacro(OutputImageDimension, unsigned int,
	- TOutputImage::ImageDimension);
	-
	- /** Convenient typedefs for simplifying declarations. */
	- typedef TInputImage InputImageType;
	- typedef TOutputImage OutputImageType;
	-
	- /** Standard class typedefs. */
	- typedef RegularizedIVIMLocalVariationImageFilter Self;
	- typedef ImageToImageFilter< InputImageType, OutputImageType> Superclass;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Run-time type information (and related methods). */
	- itkTypeMacro(RegularizedIVIMLocalVariationImageFilter, ImageToImageFilter);
	-
	- /** Image typedef support. */
	- typedef typename InputImageType::PixelType InputPixelType;
	- typedef typename OutputImageType::PixelType OutputPixelType;
	-
	- typedef typename InputImageType::RegionType InputImageRegionType;
	- typedef typename OutputImageType::RegionType OutputImageRegionType;
	-
	- typedef typename InputImageType::SizeType InputSizeType;
	-
	- /** MedianImageFilter needs a larger input requested region than
	- * the output requested region. As such, MedianImageFilter needs
	- * to provide an implementation for GenerateInputRequestedRegion()
	- * in order to inform the pipeline execution model.
	- *
	- * \sa ImageToImageFilter::GenerateInputRequestedRegion() */
	- virtual void GenerateInputRequestedRegion();
	-
	-protected:
	- RegularizedIVIMLocalVariationImageFilter();
	- virtual ~RegularizedIVIMLocalVariationImageFilter() {}
	- void PrintSelf(std::ostream& os, Indent indent) const;
	-
	- /** MedianImageFilter can be implemented as a multithreaded filter.
	- * Therefore, this implementation provides a ThreadedGenerateData()
	- * routine which is called for each processing thread. The output
	- * image data is allocated automatically by the superclass prior to
	- * calling ThreadedGenerateData(). ThreadedGenerateData can only
	- * write to the portion of the output image specified by the
	- * parameter "outputRegionForThread"
	- *
	- * \sa ImageToImageFilter::ThreadedGenerateData(),
	- * ImageToImageFilter::GenerateData() */
	- void ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread,
	- ThreadIdType threadId );
	-
	-private:
	- RegularizedIVIMLocalVariationImageFilter(const Self&); //purposely not implemented
	- void operator=(const Self&); //purposely not implemented
	-};
	-
	-} // end namespace itk
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkRegularizedIVIMLocalVariationImageFilter.txx"
	-#endif
	-
	-#endif //RegularizedIVIMLocalVariationImageFilter
	diff --git a/Modules/DiffusionImaging/Quantification/Algorithms/itkRegularizedIVIMLocalVariationImageFilter.txx b/Modules/DiffusionImaging/Quantification/Algorithms/itkRegularizedIVIMLocalVariationImageFilter.txx
	deleted file mode 100644
	index 41e8b98647..0000000000
	--- a/Modules/DiffusionImaging/Quantification/Algorithms/itkRegularizedIVIMLocalVariationImageFilter.txx
	+++ /dev/null
	@@ -1,192 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef _itkRegularizedIVIMLocalVariationImageFilter_txx
	-#define _itkRegularizedIVIMLocalVariationImageFilter_txx
	-
	-#include "itkConstShapedNeighborhoodIterator.h"
	-#include "itkNeighborhoodInnerProduct.h"
	-#include "itkImageRegionIterator.h"
	-#include "itkNeighborhoodAlgorithm.h"
	-#include "itkZeroFluxNeumannBoundaryCondition.h"
	-#include "itkOffset.h"
	-#include "itkProgressReporter.h"
	-#include "itkVectorImage.h"
	-
	-#include <vector>
	-#include <algorithm>
	-
	-namespace itk
	-{
	-
	- template <class TInputImage, class TOutputImage>
	- RegularizedIVIMLocalVariationImageFilter<TInputImage, TOutputImage>
	- ::RegularizedIVIMLocalVariationImageFilter()
	- {}
	-
	- template <class TInputImage, class TOutputImage>
	- void
	- RegularizedIVIMLocalVariationImageFilter<TInputImage, TOutputImage>
	- ::GenerateInputRequestedRegion()
	- {
	- // call the superclass' implementation of this method
	- Superclass::GenerateInputRequestedRegion();
	-
	- // get pointers to the input and output
	- typename Superclass::InputImagePointer inputPtr =
	- const_cast< TInputImage * >( this->GetInput() );
	- typename Superclass::OutputImagePointer outputPtr = this->GetOutput();
	-
	- if ( !inputPtr \|\| !outputPtr )
	- {
	- return;
	- }
	-
	- // get a copy of the input requested region (should equal the output
	- // requested region)
	- typename TInputImage::RegionType inputRequestedRegion;
	- inputRequestedRegion = inputPtr->GetRequestedRegion();
	-
	- // pad the input requested region by 1
	- inputRequestedRegion.PadByRadius( 1 );
	-
	- // crop the input requested region at the input's largest possible region
	- if ( inputRequestedRegion.Crop(inputPtr->GetLargestPossibleRegion()) )
	- {
	- inputPtr->SetRequestedRegion( inputRequestedRegion );
	- return;
	- }
	- else
	- {
	- // Couldn't crop the region (requested region is outside the largest
	- // possible region). Throw an exception.
	-
	- // store what we tried to request (prior to trying to crop)
	- inputPtr->SetRequestedRegion( inputRequestedRegion );
	-
	- // build an exception
	- InvalidRequestedRegionError e(__FILE__, __LINE__);
	- e.SetLocation(ITK_LOCATION);
	- e.SetDescription("Requested region outside possible region.");
	- e.SetDataObject(inputPtr);
	- throw e;
	- }
	- }
	-
	- template< class TInputImage, class TOutputImage>
	- void
	- RegularizedIVIMLocalVariationImageFilter< TInputImage, TOutputImage>
	- ::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread,
	- ThreadIdType threadId)
	- {
	-
	- // Allocate output
	- typename OutputImageType::Pointer output = this->GetOutput();
	- typename InputImageType::ConstPointer input = this->GetInput();
	-
	- itk::Size<InputImageDimension> size;
	- for(unsigned int i=0; i<InputImageDimension; i++)
	- size[i] = 1;
	-
	- // Find the data-set boundary "faces"
	- NeighborhoodAlgorithm::ImageBoundaryFacesCalculator<InputImageType> bC;
	- typename NeighborhoodAlgorithm::
	- ImageBoundaryFacesCalculator<InputImageType>::FaceListType
	- faceList = bC(input, outputRegionForThread, size);
	-
	- // support progress methods/callbacks
	- ProgressReporter progress(
	- this, threadId, outputRegionForThread.GetNumberOfPixels());
	-
	- ZeroFluxNeumannBoundaryCondition<InputImageType> nbc;
	- std::vector<InputPixelType> pixels;
	-
	- // Process each of the boundary faces. These are N-d regions which border
	- // the edge of the buffer.
	- for ( typename NeighborhoodAlgorithm::
	- ImageBoundaryFacesCalculator<InputImageType>::FaceListType::iterator
	- fit=faceList.begin(); fit != faceList.end(); ++fit)
	- {
	-
	- // iterators over output and input
	- ImageRegionIterator<OutputImageType>
	- output_image_it(output, *fit);
	- ImageRegionConstIterator<InputImageType>
	- input_image_it(input.GetPointer(), *fit);
	-
	- // neighborhood iterator for input image
	- ConstShapedNeighborhoodIterator<InputImageType>
	- input_image_neighbors_it(size, input, *fit);
	- typename ConstShapedNeighborhoodIterator<InputImageType>::
	- OffsetType offset;
	- input_image_neighbors_it.OverrideBoundaryCondition(&nbc);
	- input_image_neighbors_it.ClearActiveList();
	- for(unsigned int i=0; i<InputImageDimension; i++)
	- {
	- offset.Fill(0);
	- offset[i] = -1;
	- input_image_neighbors_it.ActivateOffset(offset);
	- offset[i] = 1;
	- input_image_neighbors_it.ActivateOffset(offset);
	- }
	- input_image_neighbors_it.GoToBegin();
	- //const unsigned int neighborhoodSize = InputImageDimension*2;
	-
	- while ( ! input_image_neighbors_it.IsAtEnd() )
	- {
	- // collect all the pixels in the neighborhood, note that we use
	- // GetPixel on the NeighborhoodIterator to honor the boundary conditions
	- typename OutputImageType::PixelType locVariation = 0;
	- typename ConstShapedNeighborhoodIterator<InputImageType>::
	- ConstIterator input_neighbors_it;
	- for (input_neighbors_it = input_image_neighbors_it.Begin();
	- ! input_neighbors_it.IsAtEnd();
	- input_neighbors_it++)
	- {
	- typename TInputImage::PixelType diffVec =
	- input_neighbors_it.Get()-input_image_it.Get();
	- locVariation += IVIMSquaredEuclideanMetric
	- <typename TInputImage::PixelType>::Calc(diffVec);
	- }
	- locVariation = sqrt(locVariation + 0.0001);
	- output_image_it.Set(locVariation);
	-
	- // update iterators
	- ++input_image_neighbors_it;
	- ++output_image_it;
	- ++input_image_it;
	-
	- // report progress
	- progress.CompletedPixel();
	- }
	- }
	- }
	-
	- /**
	- * Standard "PrintSelf" method
	- */
	- template <class TInputImage, class TOutput>
	- void
	- RegularizedIVIMLocalVariationImageFilter<TInputImage, TOutput>
	- ::PrintSelf(
	- std::ostream& os,
	- Indent indent) const
	- {
	- Superclass::PrintSelf( os, indent );
	- }
	-
	-} // end namespace itk
	-
	-#endif //_itkRegularizedIVIMLocalVariationImageFilter_txx
	diff --git a/Modules/DiffusionImaging/Quantification/Algorithms/itkRegularizedIVIMReconstructionFilter.h b/Modules/DiffusionImaging/Quantification/Algorithms/itkRegularizedIVIMReconstructionFilter.h
	deleted file mode 100644
	index 3967c16c33..0000000000
	--- a/Modules/DiffusionImaging/Quantification/Algorithms/itkRegularizedIVIMReconstructionFilter.h
	+++ /dev/null
	@@ -1,132 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkRegularizedIVIMReconstructionFilter_h
	-#define __itkRegularizedIVIMReconstructionFilter_h
	-
	-#include "itkRegularizedIVIMReconstructionSingleIteration.h"
	-#include "itkImageToImageFilter.h"
	-#include "itkCastImageFilter.h"
	-#include "itkImage.h"
	-
	-namespace itk
	-{
	-/** \class RegularizedIVIMReconstructionFilter
	- * \brief Applies a total variation denoising filter to an image
	- *
	- * Reference: Tony F. Chan et al., The digital TV filter and nonlinear denoising
	- *
	- * \sa Image
	- * \sa Neighborhood
	- * \sa NeighborhoodOperator
	- * \sa NeighborhoodIterator
	- *
	- * \ingroup IntensityImageFilters
	- */
	-template <class TInputPixel, class TOutputPixel, class TRefPixelType>
	-class RegularizedIVIMReconstructionFilter :
	-public ImageToImageFilter< itk::Image<itk::Vector<TInputPixel,3>, 3>, itk::Image<itk::Vector<TOutputPixel,3>, 3> >
	-{
	-public:
	-
	- typedef TInputPixel InputPixelType;
	- typedef TOutputPixel OutputPixelType;
	- typedef TRefPixelType RefPixelType;
	-
	- /** Convenient typedefs for simplifying declarations. */
	- typedef itk::Image<itk::Vector<TInputPixel,3>, 3> InputImageType;
	- typedef itk::Image<itk::Vector<TOutputPixel,3>, 3> OutputImageType;
	- typedef itk::VectorImage<TRefPixelType,3> RefImageType;
	-
	- /** Image typedef support. */
	- typedef typename InputImageType::PixelType InputVectorType;
	- typedef typename OutputImageType::PixelType OutputVectorType;
	- typedef typename RefImageType::PixelType RefVectorType;
	-
	- /** Extract dimension from input and output image. */
	- itkStaticConstMacro(InputImageDimension, unsigned int,
	- InputImageType::ImageDimension);
	- itkStaticConstMacro(OutputImageDimension, unsigned int,
	- InputImageType::ImageDimension);
	-
	- /** Standard class typedefs. */
	- typedef RegularizedIVIMReconstructionFilter Self;
	- typedef ImageToImageFilter< InputImageType, OutputImageType> Superclass;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Run-time type information (and related methods). */
	- itkTypeMacro(RegularizedIVIMReconstructionFilter, ImageToImageFilter);
	-
	- typedef typename InputImageType::RegionType InputImageRegionType;
	- typedef typename OutputImageType::RegionType OutputImageRegionType;
	- typedef typename RefImageType::RegionType RefImageRegionType;
	-
	- typedef typename InputImageType::SizeType InputSizeType;
	-
	- typedef RegularizedIVIMReconstructionSingleIteration
	- <OutputPixelType, OutputPixelType, RefPixelType>
	- SingleIterationFilterType;
	-
	- typedef typename itk::CastImageFilter< InputImageType, OutputImageType > CastType;
	-
	- itkSetMacro(Lambda, double);
	- itkGetMacro(Lambda, double);
	-
	- itkSetMacro(NumberIterations, int);
	- itkGetMacro(NumberIterations, int);
	-
	- void SetBValues( vnl_vector<double> bvals )
	- { this->m_BValues = bvals; }
	- vnl_vector<double> GetBValues()
	- { return this->m_BValues; }
	-
	- void SetReferenceImage( typename RefImageType::Pointer refimg )
	- { this->m_ReferenceImage = refimg; }
	- typename RefImageType::Pointer GetReferenceImage()
	- { return this->m_ReferenceImage; }
	-
	-protected:
	- RegularizedIVIMReconstructionFilter();
	- virtual ~RegularizedIVIMReconstructionFilter() {}
	- void PrintSelf(std::ostream& os, Indent indent) const;
	-
	- void GenerateData();
	-
	- double m_Lambda;
	-
	- int m_NumberIterations;
	-
	- typename RefImageType::Pointer m_ReferenceImage;
	-
	- vnl_vector<double> m_BValues;
	-
	-private:
	- RegularizedIVIMReconstructionFilter(const Self&); //purposely not implemented
	- void operator=(const Self&); //purposely not implemented
	-};
	-
	-} // end namespace itk
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkRegularizedIVIMReconstructionFilter.txx"
	-#endif
	-
	-#endif //__itkRegularizedIVIMReconstructionFilter__
	diff --git a/Modules/DiffusionImaging/Quantification/Algorithms/itkRegularizedIVIMReconstructionFilter.txx b/Modules/DiffusionImaging/Quantification/Algorithms/itkRegularizedIVIMReconstructionFilter.txx
	deleted file mode 100644
	index 06dfaa8dfb..0000000000
	--- a/Modules/DiffusionImaging/Quantification/Algorithms/itkRegularizedIVIMReconstructionFilter.txx
	+++ /dev/null
	@@ -1,108 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef _itkRegularizedIVIMReconstructionFilter_txx
	-#define _itkRegularizedIVIMReconstructionFilter_txx
	-
	-#include "itkConstShapedNeighborhoodIterator.h"
	-#include "itkNeighborhoodInnerProduct.h"
	-#include "itkImageRegionIterator.h"
	-#include "itkImageRegionConstIterator.h"
	-#include "itkNeighborhoodAlgorithm.h"
	-#include "itkZeroFluxNeumannBoundaryCondition.h"
	-#include "itkOffset.h"
	-#include "itkProgressReporter.h"
	-
	-#include <vector>
	-#include <algorithm>
	-
	-namespace itk
	-{
	-
	- template <class TInputPixel, class TOutputPixel, class TRefPixelType>
	- RegularizedIVIMReconstructionFilter<TInputPixel, TOutputPixel, TRefPixelType>
	- ::RegularizedIVIMReconstructionFilter()
	- {
	- m_Lambda = 1.0;
	- }
	-
	-
	- template <class TInputPixel, class TOutputPixel, class TRefPixelType>
	- void
	- RegularizedIVIMReconstructionFilter<TInputPixel, TOutputPixel, TRefPixelType>
	- ::GenerateData()
	- {
	- // first we cast the input image to match output type
	- typename CastType::Pointer infilter = CastType::New();
	- infilter->SetInput(this->GetInput());
	- infilter->Update();
	- typename OutputImageType::Pointer image = infilter->GetOutput();
	-
	- typename SingleIterationFilterType::Pointer filter;
	- for(int i=0; i<m_NumberIterations; i++)
	- {
	- filter = SingleIterationFilterType::New();
	- filter->SetInput( image.GetPointer() );
	- filter->SetOriginalImage( m_ReferenceImage );
	- filter->SetBValues(m_BValues);
	- filter->SetLambda(m_Lambda);
	- filter->SetNumberOfThreads(this->GetNumberOfThreads());
	- filter->UpdateLargestPossibleRegion();
	- image = filter->GetOutput();
	- std::cout << "Iteration " << i+1 << "/" <<
	- m_NumberIterations << std::endl;
	- }
	-
	- typename OutputImageType::Pointer output = this->GetOutput();
	- output->SetOrigin( image->GetOrigin() ); // Set the image origin
	- output->SetDirection( image->GetDirection() ); // Set the image direction
	- output->SetSpacing(image->GetSpacing());
	- output->SetLargestPossibleRegion( image->GetLargestPossibleRegion() );
	- output->SetBufferedRegion( image->GetLargestPossibleRegion() );
	- output->Allocate();
	-
	- itk::ImageRegionIterator<OutputImageType> oit(
	- output, output->GetLargestPossibleRegion());
	- oit.GoToBegin();
	-
	- itk::ImageRegionConstIterator<OutputImageType> iit(
	- image, image->GetLargestPossibleRegion());
	- iit.GoToBegin();
	-
	- while(!oit.IsAtEnd())
	- {
	- oit.Set(iit.Get());
	- ++iit;
	- ++oit;
	- }
	- }
	-
	-
	- /**
	- * Standard "PrintSelf" method
	- */
	- template <class TInputPixel, class TOutputPixel, class TRefPixelType>
	- void
	- RegularizedIVIMReconstructionFilter<TInputPixel, TOutputPixel, TRefPixelType>
	- ::PrintSelf(
	- std::ostream& os,
	- Indent indent) const
	- {
	- Superclass::PrintSelf( os, indent );
	- }
	-
	-} // end namespace itk
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/Quantification/Algorithms/itkRegularizedIVIMReconstructionSingleIteration.h b/Modules/DiffusionImaging/Quantification/Algorithms/itkRegularizedIVIMReconstructionSingleIteration.h
	deleted file mode 100644
	index 96e01e8548..0000000000
	--- a/Modules/DiffusionImaging/Quantification/Algorithms/itkRegularizedIVIMReconstructionSingleIteration.h
	+++ /dev/null
	@@ -1,141 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __itkRegularizedIVIMReconstructionSingleIteration_h
	-#define __itkRegularizedIVIMReconstructionSingleIteration_h
	-
	-#include "itkImageToImageFilter.h"
	-#include "itkImage.h"
	-#include "itkVectorImage.h"
	-
	-namespace itk
	-{
	-/** \class RegularizedIVIMReconstructionSingleIteration
	- * \brief Applies a total variation denoising filter to an image
	- *
	- * Reference: Tony F. Chan et al., The digital TV filter and nonlinear denoising
	- *
	- * \sa Image
	- * \sa Neighborhood
	- * \sa NeighborhoodOperator
	- * \sa NeighborhoodIterator
	- *
	- * \ingroup IntensityImageFilters
	- */
	-template <class TInputPixel, class TOutputPixel, class TRefPixelType>
	-class RegularizedIVIMReconstructionSingleIteration :
	- public ImageToImageFilter< itk::Image<itk::Vector<TInputPixel,3>, 3>, itk::Image<itk::Vector<TOutputPixel,3>, 3> >
	-{
	-public:
	- /** Convenient typedefs for simplifying declarations. */
	- typedef itk::Image<itk::Vector<TInputPixel,3>, 3> InputImageType;
	- typedef itk::Image<itk::Vector<TOutputPixel,3>, 3> OutputImageType;
	- typedef itk::VectorImage<TRefPixelType,3> RefImageType;
	-
	- /** Extract dimension from input and output image. */
	- itkStaticConstMacro(InputImageDimension, unsigned int,
	- InputImageType::ImageDimension);
	- itkStaticConstMacro(OutputImageDimension, unsigned int,
	- OutputImageType::ImageDimension);
	-
	- typedef itk::Image<float,InputImageDimension> LocalVariationImageType;
	-
	- /** Standard class typedefs. */
	- typedef RegularizedIVIMReconstructionSingleIteration Self;
	- typedef ImageToImageFilter< InputImageType, OutputImageType> Superclass;
	- typedef SmartPointer<Self> Pointer;
	- typedef SmartPointer<const Self> ConstPointer;
	-
	- /** Method for creation through the object factory. */
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** Run-time type information (and related methods). */
	- itkTypeMacro(RegularizedIVIMReconstructionSingleIteration, ImageToImageFilter);
	-
	- /** Image typedef support. */
	- typedef typename InputImageType::PixelType InputPixelType;
	- typedef typename OutputImageType::PixelType OutputPixelType;
	-
	- typedef typename InputImageType::RegionType InputImageRegionType;
	- typedef typename OutputImageType::RegionType OutputImageRegionType;
	-
	- typedef typename InputImageType::SizeType InputSizeType;
	-
	- /** A larger input requested region than
	- * the output requested region is required.
	- * Therefore, an implementation for GenerateInputRequestedRegion()
	- * is provided.
	- *
	- * \sa ImageToImageFilter::GenerateInputRequestedRegion() */
	- virtual void GenerateInputRequestedRegion();
	-
	- itkSetMacro(Lambda, double);
	- itkGetMacro(Lambda, double);
	-
	- void SetBValues(vnl_vector<double> bvals)
	- { this->m_BValues = bvals; }
	- vnl_vector<double> GetBValues()
	- { return this->m_BValues; }
	-
	- void SetOriginalImage(RefImageType* in)
	- { this->m_OriginalImage = in; }
	- typename RefImageType::Pointer GetOriginialImage()
	- { return this->m_OriginalImage; }
	-
	-protected:
	- RegularizedIVIMReconstructionSingleIteration();
	- virtual ~RegularizedIVIMReconstructionSingleIteration() {}
	- void PrintSelf(std::ostream& os, Indent indent) const;
	-
	- /** MedianImageFilter can be implemented as a multithreaded filter.
	- * Therefore, this implementation provides a ThreadedGenerateData()
	- * routine which is called for each processing thread. The output
	- * image data is allocated automatically by the superclass prior to
	- * calling ThreadedGenerateData(). ThreadedGenerateData can only
	- * write to the portion of the output image specified by the
	- * parameter "outputRegionForThread"
	- *
	- * \sa ImageToImageFilter::ThreadedGenerateData(),
	- * ImageToImageFilter::GenerateData() */
	- void ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread,
	- ThreadIdType threadId );
	-
	- void BeforeThreadedGenerateData();
	-
	- typename LocalVariationImageType::Pointer m_LocalVariation;
	-
	- typename RefImageType::Pointer m_OriginalImage;
	-
	- double m_Lambda;
	-
	- vnl_vector<double> m_BValues;
	-
	-private:
	-
	- RegularizedIVIMReconstructionSingleIteration(const Self&);
	-
	- void operator=(const Self&);
	-
	-};
	-
	-} // end namespace itk
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkRegularizedIVIMReconstructionSingleIteration.txx"
	-#endif
	-
	-#endif //__itkRegularizedIVIMReconstructionSingleIteration__
	diff --git a/Modules/DiffusionImaging/Quantification/Algorithms/itkRegularizedIVIMReconstructionSingleIteration.txx b/Modules/DiffusionImaging/Quantification/Algorithms/itkRegularizedIVIMReconstructionSingleIteration.txx
	deleted file mode 100644
	index c9b2f4dad5..0000000000
	--- a/Modules/DiffusionImaging/Quantification/Algorithms/itkRegularizedIVIMReconstructionSingleIteration.txx
	+++ /dev/null
	@@ -1,310 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _itkRegularizedIVIMReconstructionSingleIteration_txx
	-#define _itkRegularizedIVIMReconstructionSingleIteration_txx
	-
	-// itk includes
	-#include "itkConstShapedNeighborhoodIterator.h"
	-#include "itkNeighborhoodInnerProduct.h"
	-#include "itkImageRegionIterator.h"
	-#include "itkNeighborhoodAlgorithm.h"
	-#include "itkZeroFluxNeumannBoundaryCondition.h"
	-#include "itkOffset.h"
	-#include "itkProgressReporter.h"
	-#include "itkRegularizedIVIMLocalVariationImageFilter.h"
	-
	-// other includes
	-#include <vector>
	-#include <algorithm>
	-
	-#define IVIM_FOO -100000
	-
	-namespace itk
	-{
	-
	- /**
	- * constructor
	- */
	- template <class TInputPixel, class TOutputPixel, class TRefPixelType>
	- RegularizedIVIMReconstructionSingleIteration<TInputPixel, TOutputPixel, TRefPixelType>
	- ::RegularizedIVIMReconstructionSingleIteration()
	- {
	- m_Lambda = 1.0;
	- m_LocalVariation = LocalVariationImageType::New();
	- }
	-
	- /**
	- * generate requested region
	- */
	- template <class TInputPixel, class TOutputPixel, class TRefPixelType>
	- void
	- RegularizedIVIMReconstructionSingleIteration<TInputPixel, TOutputPixel, TRefPixelType>
	- ::GenerateInputRequestedRegion()
	- {
	- // call the superclass' implementation of this method
	- Superclass::GenerateInputRequestedRegion();
	-
	- // get pointers to the input and output
	- typename Superclass::InputImagePointer inputPtr =
	- const_cast< InputImageType * >( this->GetInput() );
	- typename Superclass::OutputImagePointer outputPtr = this->GetOutput();
	-
	- if ( !inputPtr \|\| !outputPtr )
	- {
	- return;
	- }
	-
	- // get a copy of the input requested region (should equal the output
	- // requested region)
	- typename InputImageType::RegionType inputRequestedRegion;
	- inputRequestedRegion = inputPtr->GetRequestedRegion();
	-
	- // pad the input requested region by 1
	- inputRequestedRegion.PadByRadius( 1 );
	-
	- // crop the input requested region at the input's largest possible region
	- if ( inputRequestedRegion.Crop(inputPtr->GetLargestPossibleRegion()) )
	- {
	- inputPtr->SetRequestedRegion( inputRequestedRegion );
	- return;
	- }
	- else
	- {
	- // Couldn't crop the region (requested region is outside the largest
	- // possible region). Throw an exception.
	-
	- // store what we tried to request (prior to trying to crop)
	- inputPtr->SetRequestedRegion( inputRequestedRegion );
	-
	- // build an exception
	- InvalidRequestedRegionError e(__FILE__, __LINE__);
	- e.SetLocation(ITK_LOCATION);
	- e.SetDescription("Requested region outside possible region.");
	- e.SetDataObject(inputPtr);
	- throw e;
	- }
	- }
	-
	-
	- /**
	- * generate output
	- */
	- template <class TInputPixel, class TOutputPixel, class TRefPixelType>
	- void
	- RegularizedIVIMReconstructionSingleIteration<TInputPixel, TOutputPixel, TRefPixelType>
	- ::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread,
	- ThreadIdType)
	- {
	-
	- typename OutputImageType::Pointer output = this->GetOutput();
	- typename InputImageType::ConstPointer input = this->GetInput();
	-
	- // Find the data-set boundary "faces"
	- itk::Size<InputImageDimension> size;
	- for( unsigned int i=0; i<InputImageDimension; i++)
	- size[i] = 1;
	-
	- NeighborhoodAlgorithm::ImageBoundaryFacesCalculator<InputImageType> bC;
	- typename NeighborhoodAlgorithm::
	- ImageBoundaryFacesCalculator<InputImageType>::FaceListType
	- faceList = bC(input, outputRegionForThread, size);
	-
	- NeighborhoodAlgorithm::
	- ImageBoundaryFacesCalculator<LocalVariationImageType> lv_bC;
	- typename NeighborhoodAlgorithm::
	- ImageBoundaryFacesCalculator<LocalVariationImageType>::FaceListType
	- lv_faceList = lv_bC(m_LocalVariation, outputRegionForThread, size);
	-
	- ZeroFluxNeumannBoundaryCondition<InputImageType> nbc;
	- ZeroFluxNeumannBoundaryCondition<LocalVariationImageType> lv_nbc;
	- std::vector<double> ws;
	- std::vector<double> hs;
	-
	- typename NeighborhoodAlgorithm::
	- ImageBoundaryFacesCalculator<InputImageType>::FaceListType::iterator
	- lv_fit=lv_faceList.begin();
	-
	- // Process each of the boundary faces. These are N-d regions which border
	- // the edge of the buffer.
	- for ( typename NeighborhoodAlgorithm::
	- ImageBoundaryFacesCalculator<InputImageType>::FaceListType::iterator
	- fit=faceList.begin(); fit != faceList.end(); ++fit)
	- {
	-
	- // iterators over output, input, original and local variation image
	- ImageRegionIterator<OutputImageType> output_image_it =
	- ImageRegionIterator<OutputImageType>(output, *fit);
	- ImageRegionConstIterator<InputImageType> input_image_it =
	- ImageRegionConstIterator<InputImageType>(input, *fit);
	- ImageRegionConstIterator<RefImageType> orig_image_it =
	- ImageRegionConstIterator<RefImageType>(m_OriginalImage, *fit);
	- ImageRegionConstIterator<LocalVariationImageType> loc_var_image_it =
	- ImageRegionConstIterator<LocalVariationImageType>(
	- m_LocalVariation, *fit);
	-
	- // neighborhood in input image
	- ConstShapedNeighborhoodIterator<InputImageType>
	- input_image_neighbors_it(size, input, *fit);
	- typename ConstShapedNeighborhoodIterator<InputImageType>::
	- OffsetType offset;
	- input_image_neighbors_it.OverrideBoundaryCondition(&nbc);
	- input_image_neighbors_it.ClearActiveList();
	- for(unsigned int i=0; i<InputImageDimension; i++)
	- {
	- offset.Fill(0);
	- offset[i] = -1;
	- input_image_neighbors_it.ActivateOffset(offset);
	- offset[i] = 1;
	- input_image_neighbors_it.ActivateOffset(offset);
	- }
	- input_image_neighbors_it.GoToBegin();
	-
	- // neighborhood in local variation image
	- ConstShapedNeighborhoodIterator<LocalVariationImageType>
	- loc_var_image_neighbors_it(size, m_LocalVariation, *lv_fit);
	- loc_var_image_neighbors_it.OverrideBoundaryCondition(&lv_nbc);
	- loc_var_image_neighbors_it.ClearActiveList();
	- for(unsigned int i=0; i<InputImageDimension; i++)
	- {
	- offset.Fill(0);
	- offset[i] = -1;
	- loc_var_image_neighbors_it.ActivateOffset(offset);
	- offset[i] = 1;
	- loc_var_image_neighbors_it.ActivateOffset(offset);
	- }
	- loc_var_image_neighbors_it.GoToBegin();
	-
	- const unsigned int neighborhoodSize = InputImageDimension*2;
	- ws.resize(neighborhoodSize);
	-
	- while ( ! output_image_it.IsAtEnd() )
	- {
	-
	- //MITK_INFO << "looking at voxel " << output_image_it.GetIndex();
	-
	- // 1 / \|\|nabla_alpha(u)\|\|_a
	- double locvar_alpha_inv = 1.0/loc_var_image_it.Get();
	- //MITK_INFO << "locvar: " << loc_var_image_it.Get();
	- // compute w_alphabetas
	- int count = 0;
	- double wsum = 0;
	- typename ConstShapedNeighborhoodIterator<LocalVariationImageType>::
	- ConstIterator loc_var_neighbors_it;
	- for (loc_var_neighbors_it = loc_var_image_neighbors_it.Begin();
	- ! loc_var_neighbors_it.IsAtEnd();
	- loc_var_neighbors_it++)
	- {
	- // w_alphabeta(u) =
	- // 1 / \|\|nabla_alpha(u)\|\|_a + 1 / \|\|nabla_beta(u)\|\|_a
	- ws[count] =
	- locvar_alpha_inv + (1.0/(double)loc_var_neighbors_it.Get());
	- wsum += ws[count++];
	-
	- //MITK_INFO << "nb var: " << count << ": " << loc_var_neighbors_it.Get();
	- }
	- //MITK_INFO << "wsum: " << wsum;
	-
	- // h_alphaalpha * u_alpha^zero
	- typename RefImageType::PixelType orig = orig_image_it.Get();
	-// vnl_vector<double> estim(orig.GetSize());
	-// vnl_matrix<double> diff(orig.GetSize(),1);
	-// vnl_matrix<double> estimdash(orig.GetSize(),2);
	- vnl_vector_fixed<double,2> step;
	- step[0] = 0; step[1]=0;
	- for(size_t ind=0; ind<m_BValues.size(); ind++)
	- {
	- //MITK_INFO << "refval: " << orig[ind];
	- double estim = (1-input_image_it.Get()[0])exp(-m_BValues[ind]input_image_it.Get()[1]);
	- double estimdash1 = exp(-m_BValues[ind]*input_image_it.Get()[1]);
	- double estimdash2 = (-1.0) * (1.0-input_image_it.Get()[0]) * m_BValues[ind] * exp(-m_BValues[ind]*input_image_it.Get()[1]);
	- //MITK_INFO << "estimdash1: " << estimdash1 << "; estimdash2: " << estimdash2 << "; diff: " << (double) orig[ind] - estim;
	- if(orig[ind] != IVIM_FOO)
	- {
	- step[0] += ((double) orig[ind] - estim) * estimdash2;
	- step[1] += ((double) orig[ind] - estim) * estimdash1;
	- }
	- }
	-
	- step[1] *= m_Lambda / (m_Lambda+wsum);
	-
	- // add the different h_alphabeta * u_beta
	- count = 0;
	- typename ConstShapedNeighborhoodIterator<InputImageType>::
	- ConstIterator input_neighbors_it;
	- for (input_neighbors_it = input_image_neighbors_it.Begin();
	- ! input_neighbors_it.IsAtEnd();
	- input_neighbors_it++)
	- {
	- step[1] += (input_neighbors_it.Get()[1] - input_image_it.Get()[1]) * (ws[count++] / (m_Lambda+wsum));
	- }
	-
	- //MITK_INFO << "stepfinal: " << step[0] << "; " << step[1];
	-
	- // set output result
	- OutputPixelType out;
	- out[0] = input_image_it.Get()[0] + .001*step[0];
	- out[1] = input_image_it.Get()[1] + .00001*step[1];
	- output_image_it.Set( out );
	-
	- //MITK_INFO << "(" << input_image_it.Get()[0] << " ; " << input_image_it.Get()[1] << ") => (" << out[0] << " ; " << out[1] << ")";
	- // increment iterators
	- ++output_image_it;
	- ++input_image_it;
	- ++orig_image_it;
	- ++loc_var_image_it;
	- ++input_image_neighbors_it;
	- ++loc_var_image_neighbors_it;
	-
	- }
	-
	- ++lv_fit;
	- }
	- }
	-
	- /**
	- * first calculate local variation in the image
	- */
	- template <class TInputPixel, class TOutputPixel, class TRefPixelType>
	- void
	- RegularizedIVIMReconstructionSingleIteration<TInputPixel, TOutputPixel, TRefPixelType>
	- ::BeforeThreadedGenerateData()
	- {
	- typedef typename itk::RegularizedIVIMLocalVariationImageFilter
	- <InputImageType,LocalVariationImageType> FilterType;
	- typename FilterType::Pointer filter = FilterType::New();
	- filter->SetInput(this->GetInput(0));
	- filter->SetNumberOfThreads(this->GetNumberOfThreads());
	- filter->Update();
	- this->m_LocalVariation = filter->GetOutput();
	- }
	-
	- /**
	- * Standard "PrintSelf" method
	- */
	- template <class TInputPixel, class TOutputPixel, class TRefPixelType>
	- void
	- RegularizedIVIMReconstructionSingleIteration<TInputPixel, TOutputPixel, TRefPixelType>
	- ::PrintSelf(
	- std::ostream& os,
	- Indent indent) const
	- {
	- Superclass::PrintSelf( os, indent );
	- }
	-
	-} // end namespace itk
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/Quantification/Algorithms/itkSkeletonizationFilter.h b/Modules/DiffusionImaging/Quantification/Algorithms/itkSkeletonizationFilter.h
	deleted file mode 100644
	index 5b479f99da..0000000000
	--- a/Modules/DiffusionImaging/Quantification/Algorithms/itkSkeletonizationFilter.h
	+++ /dev/null
	@@ -1,119 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef ITKSKELETONIZATIONFILTER_H_
	-#define ITKSKELETONIZATIONFILTER_H_
	-
	-#include "itkImageToImageFilter.h"
	-#include "itkImage.h"
	-#include "mitkImage.h"
	-#include <itkVectorImage.h>
	-
	-namespace itk
	-{
	-
	-/**
	- * \brief Skeletonization part of the TBSS pipeline
	- *
	- * This class takes a 3D image which is typically the mean FA image that is calculated after registration by the FSL TBSS pipeline (see
	- * http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/tbss/index for the user manual) and performs the non-maximum-suppression to create a white matter skeleton.
	- *
	- *
	- * The skeletonization algorithm is described in Smith et al., 2009. http://dx.doi.org/10.1016/j.neuroimage.2006.02.024 )
	- */
	-
	-
	-template < class TInputImage, class TOutputImage >
	-class SkeletonizationFilter : public ImageToImageFilter<TInputImage, TOutputImage>
	-{
	-
	-
	-public:
	-
	- /** Typedef for input ImageType. */
	- typedef TInputImage InputImageType;
	-
	- typedef itk::CovariantVector<int,3> VectorType;
	-
	- typedef itk::Image<VectorType, 3> VectorImageType;
	-
	-
	- /** Typedef for output ImageType. */
	- typedef TOutputImage OutputImageType;
	-
	- typedef itk::VectorImage<int, 3> GradientImageType;
	-
	-
	- /** */
	- typedef SkeletonizationFilter Self;
	-
	- /** Superclass */
	- typedef ImageToImageFilter<InputImageType, OutputImageType> Superclass;
	-
	- typedef SmartPointer<Self> Pointer;
	-
	- typedef SmartPointer<const Self> ConstPointer;
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** \brief Performs the work */
	- void GenerateData() override;
	-
	-
	- /** \brief Output the gradient image as itkVectorImage
	- *
	- * Output the gradient image by first converting it to an itk vector image
	- */
	- GradientImageType::Pointer GetGradientImage();
	-
	- /** \brief Output the gradient image as an itkImage containing vector */
	- VectorImageType::Pointer GetVectorImage()
	- {
	- return m_DirectionImage;
	- }
	-
	-
	-
	-
	-protected:
	-
	- SkeletonizationFilter();
	-
	- ~SkeletonizationFilter() override;
	-
	- VectorImageType::Pointer m_DirectionImage;
	-
	- int round(float x)
	- {
	- if (x>0.0) return ((int) (x+0.5));
	- else return ((int) (x-0.5));
	- }
	-
	-
	-protected:
	-
	-
	-
	-};
	-
	-}
	-
	-#ifndef ITK_MANUAL_INSTANTIATION
	-#include "itkSkeletonizationFilter.txx"
	-#endif
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/Quantification/Algorithms/itkSkeletonizationFilter.txx b/Modules/DiffusionImaging/Quantification/Algorithms/itkSkeletonizationFilter.txx
	deleted file mode 100644
	index 1933a120aa..0000000000
	--- a/Modules/DiffusionImaging/Quantification/Algorithms/itkSkeletonizationFilter.txx
	+++ /dev/null
	@@ -1,306 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef _itkSkeletonizationFilter_txx
	-#define _itkSkeletonizationFilter_txx
	-
	-#include "itkSkeletonizationFilter.h"
	-#include "mitkProgressBar.h"
	-#include <limits>
	-#include <ctime>
	-
	-namespace itk
	-{
	-
	- template< class TInputImage, class TOutputImage >
	- SkeletonizationFilter<TInputImage, TOutputImage>::SkeletonizationFilter()
	- {
	- m_DirectionImage = VectorImageType::New();
	- }
	-
	- template< class TInputImage, class TOutputImage >
	- SkeletonizationFilter<TInputImage, TOutputImage>::~SkeletonizationFilter()
	- {
	-
	- }
	-
	-
	-
	-
	- template< class TInputImage, class TOutputImage >
	- void SkeletonizationFilter<TInputImage, TOutputImage>::GenerateData()
	- {
	- //----------------------------------------------------------------------//
	- // Progress bar //
	- //----------------------------------------------------------------------//
	- mitk::ProgressBar::GetInstance()->AddStepsToDo( 3 );
	-
	- std::cout << "Skeletonize" << std::endl;
	-
	-
	- const InputImageType* faImage = this->GetInput();
	- typename InputImageType::SizeType size = faImage->GetRequestedRegion().GetSize();
	-
	- //typename RealImageType::SizeType size = m_FaImage->GetRequestedRegion().GetSize();
	-
	- m_DirectionImage->SetRegions(faImage->GetRequestedRegion());
	- m_DirectionImage->SetDirection(faImage->GetDirection());
	- m_DirectionImage->SetSpacing(faImage->GetSpacing());
	- m_DirectionImage->SetOrigin(faImage->GetOrigin());
	- m_DirectionImage->Allocate();
	- m_DirectionImage->FillBuffer(0.0);
	-
	-
	- for(unsigned int z=1; z<size[2]-1; z++) for(unsigned int y=1; y<size[1]-1; y++) for(unsigned int x=1; x<size[0]-1; x++)
	- {
	- typename InputImageType::IndexType ix;
	- ix[0]=x; ix[1]=y; ix[2]=z;
	- float theval = faImage->GetPixel(ix);
	-
	- if(theval != 0)
	- {
	-
	- /* Calculate point of gravity. We will consider each 3x3x3 neighbourhood as a unit cube. The center
	- * point of each voxel will be a multiplicative of 1/6. The center of the unit cube is 3/6 = 1/2/
	- */
	-
	- float cogX = 0.0; float cogY = 0.0; float cogZ = 0.0; float sum = 0.0; float l;
	- int vecX = 0; int vecY = 0; int vecZ = 0;
	-
	- for(int dz=-1; dz<=1; dz++) for(int dy=-1; dy<=1; dy++) for(int dx=-1; dx<=1;dx++)
	- {
	- typename InputImageType::IndexType p;
	- p[0] = x+dx; p[1] = y+dy; p[2] = z+dz;
	- float mass = faImage->GetPixel(p);
	-
	- sum += mass;
	- cogX += (float)dxmass; cogY += (float)dymass; cogZ += (float)dz*mass;
	- }
	-
	- cogX /= sum; cogY /= sum; cogZ /= sum;
	- l = sqrt(cogXcogX + cogYcogY + cogZ*cogZ);
	-
	- if (l > 0.1) /* is CofG far enough away from centre voxel? */
	- {
	- vecX = std::max(std::min(round(cogX/l),1),-1);
	- vecY = std::max(std::min(round(cogY/l),1),-1);
	- vecZ = std::max(std::min(round(cogZ/l),1),-1);
	- }
	- else
	- // Find direction of max curvature
	- {
	-
	- float maxcost=0, centreval=2*theval;
	- for(int zz=0; zz<=1; zz++) // note - starts at zero as we're only searching half the voxels
	- {
	- for(int yy=-1; yy<=1; yy++)
	- {
	- for(int xx=-1; xx<=1; xx++)
	- {
	- if ( (zz==1) \|\| (yy==1) \|\| ((yy==0)&&(xx==1)) )
	- {
	- float weighting = pow( (float)(xxxx+yyyy+zz*zz) , (float)-0.7 ); // power is arbitrary: maybe test other functions here
	-
	-
	- typename InputImageType::IndexType i,j;
	- i[0] = x+xx; i[1] = y+yy; i[2] = z+zz;
	- j[0] = x-xx; j[1] = y-yy; j[2] = z-zz;
	- float cost = weighting * ( centreval
	- - (float)faImage->GetPixel(i)
	- - (float)faImage->GetPixel(j));
	-
	- if (cost>maxcost)
	- {
	- maxcost=cost;
	- vecX=xx;
	- vecY=yy;
	- vecZ=zz;
	- }
	- }
	- }
	- }
	- }
	- }
	-
	- VectorType vec;
	- vec[0] = vecX; vec[1] = vecY; vec[2]=vecZ;
	- m_DirectionImage->SetPixel(ix, vec);
	-
	- }
	- }
	-
	- mitk::ProgressBar::GetInstance()->Progress();
	-
	-
	- // Smooth m_DirectionImage and store in directionSmoothed by finding the
	- // mode in a 3*3 neighbourhoud
	- VectorImageType::Pointer directionSmoothed = VectorImageType::New();
	- directionSmoothed->SetRegions(faImage->GetRequestedRegion());
	- directionSmoothed->SetDirection(faImage->GetDirection());
	- directionSmoothed->SetSpacing(faImage->GetSpacing());
	- directionSmoothed->SetOrigin(faImage->GetOrigin());
	- directionSmoothed->Allocate();
	-
	- VectorImageType::PixelType p;
	- p[0]=0; p[1]=0; p[2]=0;
	- directionSmoothed->FillBuffer(p);
	-
	-
	-
	- for(unsigned int z=1; z<size[2]-1; z++) for(unsigned int y=1; y<size[1]-1; y++) for(unsigned int x=1; x<size[0]-1; x++)
	- {
	- VectorImageType::IndexType ix;
	- ix[0]=x; ix[1]=y; ix[2]=z;
	-
	- // Find the vector that occured most
	- auto localsum = new int[27];
	- int localmax=0, xxx, yyy, zzz;
	-
	- for(int zz=0; zz<27; zz++) localsum[zz]=0;
	-
	- for(int zz=-1; zz<=1; zz++) for(int yy=-1; yy<=1; yy++) for(int xx=-1; xx<=1; xx++)
	- {
	- VectorImageType::IndexType i;
	- i[0] = x+xx; i[1] = y+yy; i[2] = z+zz;
	- VectorType v = m_DirectionImage->GetPixel(i);
	- xxx = v[0];
	- yyy = v[1];
	- zzz = v[2];
	-
	- localsum[(1+zzz)9+(1+yyy)3+1+xxx]++;
	- localsum[(1-zzz)9+(1-yyy)3+1-xxx]++;
	- }
	-
	- for(int zz=-1; zz<=1; zz++) for(int yy=-1; yy<=1; yy++) for(int xx=-1; xx<=1; xx++)
	- {
	- if (localsum[(1+zz)9+(1+yy)3+1+xx]>localmax)
	- {
	- localmax=localsum[(1+zz)9+(1+yy)3+1+xx];
	- VectorType v;
	- v[0] = xx; v[1] = yy; v[2] = zz;
	- directionSmoothed->SetPixel(ix, v);
	- }
	- }
	-
	- delete[] localsum;
	-
	- }
	-
	- m_DirectionImage = directionSmoothed;
	-
	- mitk::ProgressBar::GetInstance()->Progress();
	-
	- // Do non-max-suppression in the direction of perp and set as output of the filter
	- typename OutputImageType::Pointer outputImg = OutputImageType::New();
	- outputImg->SetRegions(faImage->GetRequestedRegion());
	- outputImg->SetDirection(faImage->GetDirection());
	- outputImg->SetSpacing(faImage->GetSpacing());
	- outputImg->SetOrigin(faImage->GetOrigin());
	- outputImg->Allocate();
	- outputImg->FillBuffer(0.0);
	-
	- for(unsigned int z=1; z<size[2]-1; z++) for(unsigned int y=1; y<size[1]-1; y++) for(unsigned int x=1; x<size[0]-1; x++)
	- {
	-
	- typename InputImageType::IndexType ix;
	- ix[0]=x; ix[1]=y; ix[2]=z;
	-
	- float theval = faImage->GetPixel(ix);
	- VectorType v = directionSmoothed->GetPixel(ix);
	-
	- typename VectorImageType::IndexType i;
	-
	- i[0] = x-v[0]; i[1] = y-v[1]; i[2] = z-v[2];
	- float min = faImage->GetPixel(i);
	-
	- i[0] = x+v[0]; i[1] = y+v[1]; i[2] = z+v[2];
	- float plus = faImage->GetPixel(i);
	-
	- i[0] = x-2v[0]; i[1] = y-2v[1]; i[2] = z-2*v[2];
	- float minmin = faImage->GetPixel(i);
	-
	- i[0] = x+2v[0]; i[1] = y+2v[1]; i[2] = z+2*v[2];
	- float plusplus = faImage->GetPixel(i);
	-
	- if( ((v[0]!=0) \|\| (v[1]!=0) \|\| (v[2]!=0)) &&
	- theval >= plus && theval > min && theval >= plusplus && theval > minmin )
	- {
	- outputImg->SetPixel(ix, theval);
	- }
	-
	- }
	-
	-
	-
	- Superclass::SetNthOutput( 0, outputImg );
	- mitk::ProgressBar::GetInstance()->Progress();
	-
	- }
	-
	-
	-
	- // Can provide a vector image to visualize the gradient image used in the search for local maxima.
	- template< class TInputImage, class TOutputImage >
	- itk::VectorImage<int, 3>::Pointer SkeletonizationFilter<TInputImage, TOutputImage>::GetGradientImage()
	- {
	- GradientImageType::Pointer gradImg = GradientImageType::New();
	-
	- if(m_DirectionImage.IsNotNull())
	- {
	- gradImg->SetSpacing(m_DirectionImage->GetSpacing());
	- gradImg->SetOrigin(m_DirectionImage->GetOrigin());
	- gradImg->SetDirection(m_DirectionImage->GetDirection());
	- gradImg->SetRegions(m_DirectionImage->GetLargestPossibleRegion().GetSize());
	- gradImg->SetVectorLength(3);
	- gradImg->Allocate();
	-
	-
	- VectorImageType::SizeType size = m_DirectionImage->GetLargestPossibleRegion().GetSize();
	-
	- for(std::size_t i=0; i<size[0]; i++)
	- {
	- for(std::size_t j=0; j<size[1]; j++)
	- {
	- for(std::size_t k=0; k<size[2]; k++)
	- {
	- itk::Index<3> ix;
	- ix[0] = i;
	- ix[1] = j;
	- ix[2] = k;
	-
	- VectorType vec = m_DirectionImage->GetPixel(ix);
	-
	- itk::VariableLengthVector<int> pixel;
	- pixel.SetSize(3);
	- pixel.SetElement(0, vec.GetElement(0));
	- pixel.SetElement(1, vec.GetElement(1));
	- pixel.SetElement(2, vec.GetElement(2));
	-
	- gradImg->SetPixel(ix, pixel);
	-
	- }
	- }
	- }
	-
	- }
	-
	-
	-
	-
	- return gradImg;
	- }
	-
	-}
	-#endif // _itkSkeletonizationFilter_txx
	diff --git a/Modules/DiffusionImaging/Quantification/Algorithms/mitkTractAnalyzer.cpp b/Modules/DiffusionImaging/Quantification/Algorithms/mitkTractAnalyzer.cpp
	deleted file mode 100644
	index 7d0b7b9f16..0000000000
	--- a/Modules/DiffusionImaging/Quantification/Algorithms/mitkTractAnalyzer.cpp
	+++ /dev/null
	@@ -1,216 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkTractAnalyzer_cpp
	-#define __mitkTractAnalyzer_cpp
	-
	-
	-#include <mitkProgressBar.h>
	-#include <mitkLogMacros.h>
	-#include <mitkTractAnalyzer.h>
	-
	-#include <itkImageRegionIteratorWithIndex.h>
	-
	-
	-#include <itkShortestPathCostFunctionTbss.h>
	-#include <itkShortestPathImageFilter.h>
	-
	-#include <iostream>
	-#include <fstream>
	-
	-namespace mitk {
	-
	- TractAnalyzer::TractAnalyzer() { }
	-
	-
	- void TractAnalyzer::MakeRoi()
	- {
	-
	- m_CostSum = 0.0;
	-
	- int n = 0;
	- if(m_PointSetNode.IsNotNull())
	- {
	- n = m_PointSetNode->GetSize();
	- if(n==0)
	- {
	- mitkThrow() << "No points have been set yet.";
	- }
	- }
	- else{
	- mitkThrow() << "No points have been set yet.";
	- }
	-
	- std::string pathDescription = "";
	- std::vector< itk::Index<3> > totalPath;
	-
	- if(n>0)
	- {
	- for(int i=0; i<n-1; ++i)
	- {
	-
	- mitk::ProgressBar::GetInstance()->Progress();
	-
	- mitk::Point3D p = m_PointSetNode->GetPoint(i);
	- mitk::Point3D p2 = m_PointSetNode->GetPoint(i+1);
	-
	-
	- itk::Index<3> startPoint;
	- itk::Index<3> endPoint;
	-
	- m_InputImage->GetGeometry()->WorldToIndex(p,startPoint);
	- m_InputImage->GetGeometry()->WorldToIndex(p2,endPoint);
	-
	- MITK_INFO << "create roi";
	-
	- std::vector< itk::Index<3> > path = CreateSegment(startPoint, endPoint);
	-
	- for(auto it = path.begin();
	- it != path.end(); it++)
	- {
	- itk::Index<3> ix = *it;
	-
	- if (!(ix==endPoint))
	- {
	- mitk::ProgressBar::GetInstance()->Progress();
	-
	- totalPath.push_back(ix);
	- std::stringstream ss;
	- ss << ix[0] << " " << ix[1] << " " << ix[2] << "\n";
	- pathDescription += ss.str();
	- }
	- else
	- {
	- // Only when dealing with the last segment the last point should be added. This one will not occur
	- // as the first point of the next roi segment.
	- if(i == (n-2))
	- {
	- totalPath.push_back(endPoint);
	- std::stringstream ss;
	- ss << endPoint[0] << " " << endPoint[1] << " " << endPoint[2] << "\n";
	- pathDescription += ss.str();
	- }
	-
	- }
	-
	- }
	-
	- }
	-
	-
	- // save pathDescription to m_PathDescription
	- m_PathDescription = pathDescription;
	-
	- FloatImageType::Pointer itkImg = FloatImageType::New();
	- mitk::CastToItkImage(m_InputImage, itkImg);
	-
	- CharImageType::Pointer roiImg = CharImageType::New();
	- roiImg->SetRegions(itkImg->GetLargestPossibleRegion().GetSize());
	- roiImg->SetOrigin(itkImg->GetOrigin());
	- roiImg->SetSpacing(itkImg->GetSpacing());
	- roiImg->SetDirection(itkImg->GetDirection());
	- roiImg->Allocate();
	- roiImg->FillBuffer(0);
	-
	-
	- std::vector< itk::Index<3> > roi;
	-
	- std::vector< itk::Index<3> >::iterator it;
	- for(it = totalPath.begin();
	- it != totalPath.end();
	- it++)
	- {
	- itk::Index<3> ix = *it;
	- roiImg->SetPixel(ix, 1);
	- roi.push_back(ix);
	- }
	-
	-
	- m_TbssRoi = mitk::TbssRoiImage::New();
	-
	- m_TbssRoi->SetRoi(roi);
	-
	- m_TbssRoi->SetImage(roiImg);
	-
	- m_TbssRoi->InitializeFromImage();
	-
	-
	-
	- }
	-
	-
	-
	- }
	-
	-
	-
	- std::vector< itk::Index<3> > TractAnalyzer::CreateSegment(itk::Index<3> startPoint, itk::Index<3> endPoint)
	- {
	-
	- typedef itk::ShortestPathImageFilter<FloatImageType, CharImageType> ShortestPathFilterType;
	- typedef itk::ShortestPathCostFunctionTbss<FloatImageType> CostFunctionType;
	-
	-
	- FloatImageType::Pointer meanSkeleton;
	-
	- mitk::CastToItkImage(m_InputImage, meanSkeleton);
	-
	- // Only use the mitk image
	-
	-
	-
	- if(meanSkeleton)
	- {
	- CostFunctionType::Pointer costFunction = CostFunctionType::New();
	- costFunction->SetImage(meanSkeleton);
	- costFunction->SetStartIndex(startPoint);
	- costFunction->SetEndIndex(endPoint);
	- costFunction->SetThreshold(m_Threshold);
	-
	- ShortestPathFilterType::Pointer pathFinder = ShortestPathFilterType::New();
	- pathFinder->SetCostFunction(costFunction);
	- pathFinder->SetFullNeighborsMode(true);
	- pathFinder->SetGraph_fullNeighbors(true);
	- //pathFinder->SetCalcMode(ShortestPathFilterType::A_STAR);
	- pathFinder->SetInput(meanSkeleton);
	- pathFinder->SetStartIndex(startPoint);
	- pathFinder->SetEndIndex(endPoint);
	- pathFinder->Update();
	-
	- double segmentCost = 0.0;
	- std::vector< itk::Index<3> > path = pathFinder->GetVectorPath();
	-
	- for(unsigned int i=0; i<path.size()-1; i++)
	- {
	- itk::Index<3> ix1 = path[i];
	- itk::Index<3> ix2 = path[i+1];
	-
	- segmentCost += costFunction->GetCost(ix1, ix2);
	- }
	-
	- m_CostSum += segmentCost;
	-
	-
	- return pathFinder->GetVectorPath();
	-
	-
	- }
	- return std::vector< itk::Index<3> >();
	- }
	-
	-
	-}
	-#endif
	diff --git a/Modules/DiffusionImaging/Quantification/Algorithms/mitkTractAnalyzer.h b/Modules/DiffusionImaging/Quantification/Algorithms/mitkTractAnalyzer.h
	deleted file mode 100644
	index 6abdbeacb2..0000000000
	--- a/Modules/DiffusionImaging/Quantification/Algorithms/mitkTractAnalyzer.h
	+++ /dev/null
	@@ -1,155 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef __mitkTractAnalyzer_h_
	-#define __mitkTractAnalyzer_h_
	-
	-#include "MitkQuantificationExports.h"
	-#include <itkImage.h>
	-#include "mitkImage.h"
	-#include "mitkImageCast.h"
	-
	-#include <mitkTbssRoiImage.h>
	-#include <mitkPointSet.h>
	-
	-
	-namespace mitk{
	-/**
	- * \brief Creates a region of interest for tract-specific analysis of existing TBSS data
	- *
	- * This class needs a 3D image, which is the mean FA skeleton as produced by the standard TBSS pipeline of FSL.
	- * How this dataset can be obtained can be found in the TBSS user manual: http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/tbss/index
	- * Furthermore, this class requires a user-defined point set defining the points through which the region of interest should pass.
	- * The output is a TBSS roi image, which is a binary images defining the roi and metadata containing indices
	- * that can be used for plotting graphs using the QmitkTbssRoiAnalysisWidget
	- */
	-
	-
	-class MITKQUANTIFICATION_EXPORT TractAnalyzer
	-{
	-
	-public:
	-
	-
	- TractAnalyzer();
	- ~TractAnalyzer() {}
	-
	-
	- /** Image type definitions */
	- typedef itk::Image<unsigned char,3> CharImageType;
	- typedef itk::Image<float,3> FloatImageType;
	-
	-
	- /** \brief Main method for region of interest calculation
	- *
	- * A region of interest is calculated adding the segments between the points on the ROI
	- * that was specified by the user.
	- */
	- void MakeRoi();
	-
	-
	-
	- / \brief Returns the TbssRoiImage /
	- mitk::TbssRoiImage::Pointer GetRoiImage()
	- {
	- return m_TbssRoi;
	- }
	-
	-
	- /** \brief Sets the input image
	- *
	- * The region of interest is calculated on a 3D image. This is generally the mean FA skeleton as calculated
	- * in the standard TBSS pipeline (see http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS).
	- */
	- void SetInputImage(mitk::Image::Pointer inputImage)
	- {
	- m_InputImage = inputImage;
	- }
	-
	-
	- /** \brief Sets the user-defined point set
	- *
	- * Set the user-defined point sets. The region of interest must pass through these points.
	- */
	- void SetPointSet(mitk::PointSet::Pointer pointSet)
	- {
	- m_PointSetNode = pointSet;
	- }
	-
	-
	- /** \brief Sets a lower bound for the threshold.
	- *
	- * Low fractional anisotropy values can indicate partial volume of non white matter tissue.
	- * This thresholds limits the search for a region of interest to voxels with a minimum value.
	- */
	- void SetThreshold(double threshold)
	- {
	- m_Threshold = threshold;
	- }
	-
	-
	-
	- /** \brief Returns a string with the indices of points on the region of interest
	- *
	- * The region of interest calculated by the TractAnalyzer contains a list of ITK indices.
	- * This method returns a string containing these indices for display in the GUI
	- */
	- std::string GetPathDescription()
	- {
	- return m_PathDescription;
	- }
	-
	- itkGetMacro(CostSum, double)
	-
	-protected:
	-
	-
	-
	- /** \brief Calculates a segment of the region of interest
	- *
	- * The region of interest is calculated on a 3D image. This is generally the mean FA skeleton as calculated
	- * in the standard TBSS pipeline (see http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS).
	- */
	- std::vector< itk::Index<3> > CreateSegment(itk::Index<3> startPoint, itk::Index<3> endPoint);
	-
	-
	- /** \brief Output TbssRoiImage */
	- mitk::TbssRoiImage::Pointer m_TbssRoi;
	-
	- /** \brief Inputimage */
	- mitk::Image::Pointer m_InputImage;
	-
	- /** \brief Threshold for ROI search */
	- double m_Threshold;
	-
	- /** \brief User defined point set */
	- mitk::PointSet::Pointer m_PointSetNode;
	-
	- /** \brief Path description in as string for display in GUI */
	- std::string m_PathDescription;
	-
	- /** \brief Total cost of the path */
	- double m_CostSum;
	-
	-
	-private:
	-
	-};
	-
	-}
	-
	-#endif //__itkTractAnalyzer_h_
	diff --git a/Modules/DiffusionImaging/Quantification/CMakeLists.txt b/Modules/DiffusionImaging/Quantification/CMakeLists.txt
	deleted file mode 100644
	index d3b6e845cc..0000000000
	--- a/Modules/DiffusionImaging/Quantification/CMakeLists.txt
	+++ /dev/null
	@@ -1,14 +0,0 @@
	-# With apple gcc 4.2.1 the following waring leads to an build error if boost is enabled
	-if(APPLE)
	- mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=empty-body" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
	-endif()
	-
	-#DiffusionImaging/Quantification
	-MITK_CREATE_MODULE(
	- SUBPROJECTS MITK-DTI
	- INCLUDE_DIRS Algorithms IODataStructures IODataStructures/TbssImages Rendering ${CMAKE_CURRENT_BINARY_DIR}
	- DEPENDS MitkDiffusionCore MitkFiberTracking MitkGraphAlgorithms
	- PACKAGE_DEPENDS ITK\|ITKThresholding
	-)
	-
	-add_subdirectory(Testing)
	diff --git a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkNrrdTbssImageReader.cpp b/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkNrrdTbssImageReader.cpp
	deleted file mode 100644
	index e276c488e6..0000000000
	--- a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkNrrdTbssImageReader.cpp
	+++ /dev/null
	@@ -1,295 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkNrrdTbssImageReader_cpp
	-#define __mitkNrrdTbssImageReader_cpp
	-
	-#include "mitkNrrdTbssImageReader.h"
	-
	-#include "itkImageFileReader.h"
	-#include "itkMetaDataObject.h"
	-#include "itkNrrdImageIO.h"
	-#include "itkNiftiImageIO.h"
	-
	-#include <itkImageFileWriter.h>
	-
	-#include <iostream>
	-#include <fstream>
	-
	-#include "itksys/SystemTools.hxx"
	-
	-
	-namespace mitk
	-{
	- void NrrdTbssImageReader
	- ::GenerateData()
	- {
	-
	- // Since everything is completely read in GenerateOutputInformation() it is stored
	- // in a cache variable. A timestamp is associated.
	- // If the timestamp of the cache variable is newer than the MTime, we only need to
	- // assign the cache variable to the DataObject.
	- // Otherwise, the tree must be read again from the file and OuputInformation must
	- // be updated!
	- if ( ( ! m_OutputCache ) \|\| ( this->GetMTime( ) > m_CacheTime.GetMTime( ) ) )
	- {
	- this->GenerateOutputInformation();
	- itkWarningMacro("Cache regenerated!");
	- }
	-
	- if (!m_OutputCache)
	- {
	- itkWarningMacro("Tree cache is empty!")
	- }
	-
	-
	- static_cast<OutputType*>(this->GetPrimaryOutput())
	- ->SetImage(m_OutputCache->GetImage());
	- static_cast<OutputType*>(this->GetPrimaryOutput())
	- ->SetGroupInfo(m_OutputCache->GetGroupInfo());
	-
	- static_cast<OutputType*>(this->GetPrimaryOutput())
	- ->InitializeFromVectorImage();
	-
	- }
	-
	- void NrrdTbssImageReader
	- ::GenerateOutputInformation()
	- {
	- OutputType::Pointer outputForCache = OutputType::New();
	-
	- if ( m_FileName == "")
	- {
	- throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, the filename to be read is empty!");
	- }
	- else
	- {
	- try
	- {
	- const std::string& locale = "C";
	- const std::string& currLocale = setlocale( LC_ALL, nullptr );
	-
	- if ( locale.compare(currLocale)!=0 )
	- {
	- try
	- {
	- MITK_INFO << " ** Changing locale from " << setlocale(LC_ALL, nullptr) << " to '" << locale << "'";
	- setlocale(LC_ALL, locale.c_str());
	- }
	- catch(...)
	- {
	- MITK_INFO << "Could not set locale " << locale;
	- }
	- }
	-
	-
	- MITK_INFO << "NrrdTbssImageReader READING IMAGE INFORMATION";
	- ImageType::Pointer img;
	-
	- std::string ext = itksys::SystemTools::GetFilenameLastExtension(m_FileName);
	- ext = itksys::SystemTools::LowerCase(ext);
	- if (ext == ".tbss")
	- {
	- typedef itk::ImageFileReader<ImageType> FileReaderType;
	- FileReaderType::Pointer reader = FileReaderType::New();
	- reader->SetFileName(this->m_FileName);
	- itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
	- reader->SetImageIO(io);
	-
	- reader->Update();
	- img = reader->GetOutput();
	-
	-
	- MITK_INFO << "NrrdTbssImageReader READING HEADER INFORMATION";
	-
	-
	- itk::MetaDataDictionary imgMetaDictionary = img->GetMetaDataDictionary();
	- std::vector<std::string> imgMetaKeys = imgMetaDictionary.GetKeys();
	- std::vector<std::string>::const_iterator itKey = imgMetaKeys.begin();
	- std::string metaString;
	-
	-
	-
	- std::string measurementInfo;
	-
	-
	- std::vector< std::pair<std::string, int> > groups;
	-
	- for (; itKey != imgMetaKeys.end(); itKey ++)
	- {
	- itk::ExposeMetaData<std::string> (imgMetaDictionary, *itKey, metaString);
	-
	- MITK_INFO << *itKey << " ---> " << metaString;
	-
	- if (itKey->find("Group_index") != std::string::npos)
	- {
	-
	- std::vector<std::string> tokens;
	- this->Tokenize(metaString, tokens, " ");
	-
	-
	- std::pair< std::string, int > p;
	-
	- p.first="";
	- for (unsigned int i=0; i<tokens.size()-1;i++)
	- {
	- p.first.append(" ");
	- p.first.append(tokens.at(i));
	- }
	-
	- std::cout << p.first << std::endl;
	-
	- p.second = atoi(tokens.at(tokens.size()-1 ).c_str());
	- groups.push_back(p);
	-
	-
	-
	- }
	-
	- else if(itKey->find("Measurement info") != std::string::npos)
	- {
	- measurementInfo = metaString;
	- }
	-
	-
	-
	-
	- }
	-
	-
	- outputForCache->SetGroupInfo(groups);
	- outputForCache->SetMeasurementInfo(measurementInfo);
	-
	-
	- }
	-
	-
	-
	- // This call updates the output information of the associated VesselTreeData
	- outputForCache->SetImage(img);
	-
	-
	- // Since we have already read the tree, we can store it in a cache variable
	- // so that it can be assigned to the DataObject in GenerateData();
	- m_OutputCache = outputForCache;
	- m_CacheTime.Modified();
	-
	- try
	- {
	- MITK_INFO << " ** Changing locale back from " << setlocale(LC_ALL, nullptr) << " to '" << currLocale << "'";
	- setlocale(LC_ALL, currLocale.c_str());
	- }
	- catch(...)
	- {
	- MITK_INFO << "Could not reset locale " << currLocale;
	- }
	- }
	- catch(std::exception& e)
	- {
	- MITK_INFO << "Std::Exception while reading file!!";
	- MITK_INFO << e.what();
	- throw itk::ImageFileReaderException(__FILE__, __LINE__, e.what());
	- }
	- catch(...)
	- {
	- MITK_INFO << "Exception while reading file!!";
	- throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, an error occurred while reading the requested vessel tree file!");
	- }
	- }
	- }
	-
	-
	-
	- const char* NrrdTbssImageReader
	- ::GetFileName() const
	- {
	- return m_FileName.c_str();
	- }
	-
	- void NrrdTbssImageReader
	- ::SetFileName(const char* aFileName)
	- {
	- m_FileName = aFileName;
	- }
	-
	- const char* NrrdTbssImageReader
	- ::GetFilePrefix() const
	- {
	- return m_FilePrefix.c_str();
	- }
	-
	- void NrrdTbssImageReader
	- ::SetFilePrefix(const char* aFilePrefix)
	- {
	- m_FilePrefix = aFilePrefix;
	- }
	-
	- const char* NrrdTbssImageReader
	- ::GetFilePattern() const
	- {
	- return m_FilePattern.c_str();
	- }
	-
	- void NrrdTbssImageReader
	- ::SetFilePattern(const char* aFilePattern)
	- {
	- m_FilePattern = aFilePattern;
	- }
	-
	- bool NrrdTbssImageReader
	- ::CanReadFile(const std::string filename, const std::string filePrefix, const std::string filePattern)
	- {
	-
	- // First check the extension
	- if( filename == "" )
	- return false;
	-
	- // check if image is serie
	- if( filePattern != "" && filePrefix != "" )
	- return false;
	-
	-
	- std::string ext = itksys::SystemTools::GetFilenameLastExtension(filename);
	- ext = itksys::SystemTools::LowerCase(ext);
	-
	- if (ext == ".tbss")
	- {
	- itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
	-
	- typedef itk::ImageFileReader<ImageType> FileReaderType;
	- FileReaderType::Pointer reader = FileReaderType::New();
	- reader->SetImageIO(io);
	- reader->SetFileName(filename);
	-
	- try
	- {
	- reader->Update();
	- }
	- catch(itk::ExceptionObject e)
	- {
	- MITK_INFO << e.GetDescription();
	- return false;
	- }
	-
	-
	- return true;
	- }
	- return false;
	- }
	-
	-} //namespace MITK
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkNrrdTbssImageReader.h b/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkNrrdTbssImageReader.h
	deleted file mode 100644
	index 8198306b44..0000000000
	--- a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkNrrdTbssImageReader.h
	+++ /dev/null
	@@ -1,103 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkNrrdTbssImageReader_h
	-#define __mitkNrrdTbssImageReader_h
	-
	-#include "mitkCommon.h"
	-#include "mitkFileReader.h"
	-#include "mitkTbssImageSource.h"
	-#include "itkImage.h"
	-#include "itkVectorImage.h"
	-#include "mitkTbssImage.h"
	-
	-namespace mitk
	-{
	-
	- /** \brief
	- */
	-
	-
	- class MITKQUANTIFICATION_EXPORT NrrdTbssImageReader : public mitk::TbssImageSource, public FileReader
	- {
	- public:
	-
	- typedef mitk::TbssImage OutputType;
	- typedef itk::VectorImage<float,3> ImageType;
	- typedef TbssImageSource TbssVolSourceType;
	-
	-
	-
	- mitkClassMacro( NrrdTbssImageReader, TbssVolSourceType )
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- const char* GetFileName() const override;
	- void SetFileName(const char* aFileName) override;
	- const char* GetFilePrefix() const override;
	- void SetFilePrefix(const char* aFilePrefix) override;
	- const char* GetFilePattern() const override;
	- void SetFilePattern(const char* aFilePattern) override;
	-
	- static bool CanReadFile(const std::string filename, const std::string filePrefix, const std::string filePattern);
	-
	- protected:
	-
	- /** Does the real work. */
	- void GenerateData() override;
	- void GenerateOutputInformation() override;
	-
	-
	- std::string m_FileName;
	- std::string m_FilePrefix;
	- std::string m_FilePattern;
	-
	- std::vector< std::pair<std::string, int> > m_GroupInfo;
	-
	- OutputType::Pointer m_OutputCache;
	- itk::TimeStamp m_CacheTime;
	-
	-
	- void Tokenize(const std::string& str,
	- std::vector<std::string>& tokens,
	- const std::string& delimiters = " ")
	- {
	- // Skip delimiters at beginning.
	- std::string::size_type lastPos = str.find_first_not_of(delimiters, 0);
	- // Find first "non-delimiter".
	- std::string::size_type pos = str.find_first_of(delimiters, lastPos);
	-
	- while (std::string::npos != pos \|\| std::string::npos != lastPos)
	- {
	- // Found a token, add it to the vector.
	- tokens.push_back(str.substr(lastPos, pos - lastPos));
	- // Skip delimiters. Note the "not_of"
	- lastPos = str.find_first_not_of(delimiters, pos);
	- // Find next "non-delimiter"
	- pos = str.find_first_of(delimiters, lastPos);
	- }
	- }
	-
	-
	-
	- private:
	- void operator=(const Self&); //purposely not implemented
	- };
	-
	-} //namespace MITK
	-
	-
	-#endif // __mitkNrrdTbssImageReader_h
	diff --git a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkNrrdTbssImageWriter.cpp b/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkNrrdTbssImageWriter.cpp
	deleted file mode 100644
	index 0396e6a77c..0000000000
	--- a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkNrrdTbssImageWriter.cpp
	+++ /dev/null
	@@ -1,165 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkNrrdTbssImageWriter__cpp
	-#define __mitkNrrdTbssImageWriter__cpp
	-
	-#include "mitkNrrdTbssImageWriter.h"
	-#include "itkMetaDataDictionary.h"
	-#include "itkMetaDataObject.h"
	-#include "itkNrrdImageIO.h"
	-//#include "itkNiftiImageIO.h"
	-#include "itkImageFileWriter.h"
	-#include "itksys/SystemTools.hxx"
	-#include "mitkLexicalCast.h"
	-
	-#include <iostream>
	-#include <fstream>
	-
	-
	-mitk::NrrdTbssImageWriter::NrrdTbssImageWriter()
	- : m_FileName(""), m_FilePrefix(""), m_FilePattern(""), m_Success(false)
	-{
	- this->SetNumberOfRequiredInputs( 1 );
	-}
	-
	-mitk::NrrdTbssImageWriter::~NrrdTbssImageWriter()
	-{}
	-
	-
	-void mitk::NrrdTbssImageWriter::GenerateData()
	-{
	- m_Success = false;
	- InputType* input = this->GetInput();
	- if (input == nullptr)
	- {
	- itkWarningMacro(<<"Sorry, input to NrrdTbssImageWriter is nullptr!");
	- return;
	- }
	- if ( m_FileName == "" )
	- {
	- itkWarningMacro( << "Sorry, filename has not been set!" );
	- return ;
	- }
	-
	-
	-
	- itk::VectorImage<float, 3>::Pointer img = input->GetImage();
	-
	-
	-
	-
	- std::string key;
	- std::string val;
	-
	-
	- /* For the case of a tbss image containing data of the patients:
	- Save info about the groups and the type of measurement */
	-
	-
	-
	-
	- std::vector< std::pair <std::string, int> > groups = input->GetGroupInfo();
	- auto it = groups.begin();
	-
	- int i=0;
	- while(it != groups.end())
	- {
	- std::pair<std::string, int> p = *it;
	-
	- key = "Group_index_" + boost::lexical_cast<std::string>(i);
	- val = " " + p.first + " " + boost::lexical_cast<std::string>(p.second);
	- //sprintf( keybuffer, "Group_index_%04d", std::string(i) );
	- // sprintf( valbuffer, "%1d %1d", p.first, p.second);
	-
	- //std::cout << valbuffer << std::endl;
	-
	- //itk::EncapsulateMetaData< std::string >(input->GetImage()->GetMetaDataDictionary(),std::string(keybuffer),std::string(valbuffer));
	- itk::EncapsulateMetaData< std::string >(input->GetImage()->GetMetaDataDictionary(),key,val);
	- it++;
	- ++i;
	- }
	-
	- key = "Measurement info";
	- val = input->GetMeasurementInfo();
	- itk::EncapsulateMetaData< std::string >(input->GetImage()->GetMetaDataDictionary(),key,val);
	-
	-
	-
	-
	-
	- typedef itk::VectorImage<float,3> ImageType;
	-
	- itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
	- io->SetFileType( itk::ImageIOBase::Binary );
	- io->UseCompressionOn();
	-
	-
	- typedef itk::ImageFileWriter<ImageType> WriterType;
	- WriterType::Pointer nrrdWriter = WriterType::New();
	- nrrdWriter->UseInputMetaDataDictionaryOn();
	- nrrdWriter->SetInput( img );
	- nrrdWriter->SetImageIO(io);
	- nrrdWriter->SetFileName(m_FileName);
	- nrrdWriter->UseCompressionOn();
	- nrrdWriter->SetImageIO(io);
	- try
	- {
	- nrrdWriter->Update();
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.GetDescription() << std::endl;
	- }
	-
	- m_Success = true;
	-}
	-
	-
	-
	-
	-void mitk::NrrdTbssImageWriter::SetInput( InputType* tbssVol )
	-{
	- this->ProcessObject::SetNthInput( 0, tbssVol );
	-}
	-
	-
	-mitk::TbssImage* mitk::NrrdTbssImageWriter::GetInput()
	-{
	- if ( this->GetNumberOfInputs() < 1 )
	- {
	- return nullptr;
	- }
	- else
	- {
	- return dynamic_cast<InputType*> ( this->ProcessObject::GetInput( 0 ) );
	- }
	-}
	-
	-
	-std::vector<std::string> mitk::NrrdTbssImageWriter::GetPossibleFileExtensions()
	-{
	- std::vector<std::string> possibleFileExtensions;
	- possibleFileExtensions.push_back(".tbss");
	- return possibleFileExtensions;
	-}
	-
	-std::string mitk::NrrdTbssImageWriter::GetSupportedBaseData() const
	-{
	- return TbssImage::GetStaticNameOfClass();
	-}
	-
	-#endif //__mitkNrrdTbssImageWriter__cpp
	diff --git a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkNrrdTbssImageWriter.h b/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkNrrdTbssImageWriter.h
	deleted file mode 100644
	index fb5e950513..0000000000
	--- a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkNrrdTbssImageWriter.h
	+++ /dev/null
	@@ -1,143 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_NRRDTBSSVOL_WRITER__H_
	-#define _MITK_NRRDTBSSVOL_WRITER__H_
	-
	-#include <itkProcessObject.h>
	-#include <mitkFileWriterWithInformation.h>
	-#include <mitkTbssImage.h>
	-#include "MitkQuantificationExports.h"
	-
	-namespace mitk
	-{
	-
	-/**
	- * Writes diffusion volumes to a file
	- * @ingroup Process
	- */
	-
	-class MITKQUANTIFICATION_EXPORT NrrdTbssImageWriter : public mitk::FileWriterWithInformation
	-{
	-public:
	-
	- mitkClassMacro( NrrdTbssImageWriter, mitk::FileWriterWithInformation )
	-
	- mitkWriterMacro
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- typedef mitk::TbssImage InputType;
	-
	- /**
	- * Sets the filename of the file to write.
	- * @param FileName the nameInputType of the file to write.
	- */
	- itkSetStringMacro( FileName )
	-
	- /**
	- * @returns the name of the file to be written to disk.
	- */
	- itkGetStringMacro( FileName )
	-
	- /**
	- * @warning multiple write not (yet) supported
	- */
	- itkSetStringMacro( FilePrefix )
	-
	- /**
	- * @warning multiple write not (yet) supported
	- */
	- itkGetStringMacro( FilePrefix )
	-
	- /**
	- * @warning multiple write not (yet) supported
	- */
	- itkSetStringMacro( FilePattern )
	-
	- /**
	- * @warning multiple write not (yet) supported
	- */
	- itkGetStringMacro( FilePattern )
	-
	- /**image
	- * Sets the input object for the filter.
	- * @param input the diffusion volumes to write to file.
	- */
	- using ProcessObject::SetInput;
	- void SetInput( InputType* input );
	- /**itk::VectorImage<TPixelType, 3>
	- * @returns the 0'th input object of the filter.
	- */
	- InputType* GetInput();
	-
	- /**
	- * Returns false if an error happened during writing
	- */
	- itkGetMacro( Success, bool )
	-
	- /**
	- * @return possible file extensions for the data type associated with the writer
	- */
	- std::vector<std::string> GetPossibleFileExtensions() override;
	-
	- std::string GetSupportedBaseData() const override;
	-
	- // FileWriterWithInformation methods
	- const char * GetDefaultFilename() override { return "TbssImage.tbss"; }
	- const char * GetFileDialogPattern() override { return "Tbss Images (*.tbss)"; }
	- const char * GetDefaultExtension() override { return ".tbss"; }
	- bool CanWriteBaseDataType(BaseData::Pointer data) override
	- {
	- return (dynamic_cast<mitk::TbssImage*>(data.GetPointer()) != nullptr);
	- }
	-
	-
	- void DoWrite(BaseData::Pointer data) override {
	- if (CanWriteBaseDataType(data)) {
	- this->SetInput(dynamic_cast<mitk::TbssImage*>(data.GetPointer()));
	- this->Update();
	- }
	- }
	-
	-protected:
	-
	- NrrdTbssImageWriter();
	-
	- ~NrrdTbssImageWriter() override;
	-
	- void GenerateData() override;
	-
	- std::string m_FileName;
	-
	- std::string m_FilePrefix;
	-
	- std::string m_FilePattern;
	-
	- bool m_Success;
	-
	-
	-
	-
	-};
	-
	-
	-} // end of namespace mitk
	-
	-
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkNrrdTbssRoiImageReader.cpp b/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkNrrdTbssRoiImageReader.cpp
	deleted file mode 100644
	index f3ee7f3367..0000000000
	--- a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkNrrdTbssRoiImageReader.cpp
	+++ /dev/null
	@@ -1,356 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkNrrdTbssRoiReader_cpp
	-#define __mitkNrrdTbssRoiReader_cpp
	-
	-#include "mitkNrrdTbssRoiImageReader.h"
	-
	-#include "itkImageFileReader.h"
	-#include "itkMetaDataObject.h"
	-#include "itkNrrdImageIO.h"
	-#include "itkNiftiImageIO.h"
	-
	-#include <itkImageFileWriter.h>
	-
	-#include <iostream>
	-#include <fstream>
	-
	-#include "itksys/SystemTools.hxx"
	-
	-namespace mitk
	-{
	-
	-
	- void NrrdTbssRoiImageReader
	- ::GenerateData()
	- {
	-
	- try
	- {
	-
	- // Change locale if needed
	- const std::string& locale = "C";
	- const std::string& currLocale = setlocale( LC_ALL, nullptr );
	-
	- if ( locale.compare(currLocale)!=0 )
	- {
	- try
	- {
	- MITK_INFO << " ** Changing locale from " << setlocale(LC_ALL, nullptr) << " to '" << locale << "'";
	- setlocale(LC_ALL, locale.c_str());
	- }
	- catch(...)
	- {
	- MITK_INFO << "Could not set locale " << locale;
	- }
	- }
	-
	-
	-
	- // READ IMAGE INFORMATION
	- const unsigned int MINDIM = 3;
	- const unsigned int MAXDIM = 4;
	-
	- MITK_INFO << "loading " << m_FileName << " via mitk::NrrdTbssImageReader... " << std::endl;
	-
	- // Check to see if we can read the file given the name or prefix
	- if ( m_FileName == "" )
	- {
	- itkWarningMacro( << "Filename is empty!" )
	- return;
	- }
	-
	- itk::NrrdImageIO::Pointer imageIO = itk::NrrdImageIO::New();
	- imageIO->SetFileName( m_FileName.c_str() );
	- imageIO->ReadImageInformation();
	-
	- unsigned int ndim = imageIO->GetNumberOfDimensions();
	-
	- if ( ndim < MINDIM \|\| ndim > MAXDIM )
	- {
	- itkWarningMacro( << "Sorry, only dimensions 3 is supported. The given file has " << ndim << " dimensions!" )
	- return;
	- }
	-
	-
	- itk::ImageIORegion ioRegion( ndim );
	- itk::ImageIORegion::SizeType ioSize = ioRegion.GetSize();
	- itk::ImageIORegion::IndexType ioStart = ioRegion.GetIndex();
	-
	- unsigned int dimensions[ MAXDIM ];
	- dimensions[ 0 ] = 0;
	- dimensions[ 1 ] = 0;
	- dimensions[ 2 ] = 0;
	- dimensions[ 3 ] = 0;
	-
	- ScalarType spacing[ MAXDIM ];
	- spacing[ 0 ] = 1.0f;
	- spacing[ 1 ] = 1.0f;
	- spacing[ 2 ] = 1.0f;
	- spacing[ 3 ] = 1.0f;
	-
	-
	- Point3D origin;
	- origin.Fill(0);
	-
	- unsigned int i;
	- for ( i = 0; i < ndim ; ++i )
	- {
	- ioStart[ i ] = 0;
	- ioSize[ i ] = imageIO->GetDimensions( i );
	- if(i<MAXDIM)
	- {
	- dimensions[ i ] = imageIO->GetDimensions( i );
	- spacing[ i ] = imageIO->GetSpacing( i );
	- if(spacing[ i ] <= 0)
	- spacing[ i ] = 1.0f;
	- }
	- if(i<3)
	- {
	- origin[ i ] = imageIO->GetOrigin( i );
	- }
	- }
	-
	- ioRegion.SetSize( ioSize );
	- ioRegion.SetIndex( ioStart );
	-
	- MITK_INFO << "ioRegion: " << ioRegion << std::endl;
	- imageIO->SetIORegion( ioRegion );
	- void* buffer = new unsigned char[imageIO->GetImageSizeInBytes()];
	- imageIO->Read( buffer );
	- //mitk::Image::Pointer static_cast<OutputType*>(this->GetOutput())image = mitk::Image::New();
	- if((ndim==4) && (dimensions[3]<=1))
	- ndim = 3;
	- if((ndim==3) && (dimensions[2]<=1))
	- ndim = 2;
	-
	- static_cast<OutputType*>(this->GetPrimaryOutput())->Initialize( MakePixelType(imageIO), ndim, dimensions );
	- static_cast<OutputType*>(this->GetPrimaryOutput())->SetImportChannel( buffer, 0, Image::ManageMemory );
	-
	- // access direction of itk::Image and include spacing
	- mitk::Matrix3D matrix;
	- matrix.SetIdentity();
	- unsigned int j, itkDimMax3 = (ndim >= 3? 3 : ndim);
	- for ( i=0; i < itkDimMax3; ++i)
	- for( j=0; j < itkDimMax3; ++j )
	- matrix[i][j] = imageIO->GetDirection(j)[i];
	-
	- // re-initialize PlaneGeometry with origin and direction
	- PlaneGeometry* planeGeometry = static_cast<PlaneGeometry*>
	- (static_cast<OutputType*>
	- (this->GetPrimaryOutput())->GetSlicedGeometry(0)->GetPlaneGeometry(0));
	- planeGeometry->SetOrigin(origin);
	- planeGeometry->GetIndexToWorldTransform()->SetMatrix(matrix);
	-
	- // re-initialize SlicedGeometry3D
	- SlicedGeometry3D* slicedGeometry = static_cast<OutputType*>(this->GetPrimaryOutput())->GetSlicedGeometry(0);
	- slicedGeometry->InitializeEvenlySpaced(planeGeometry, static_cast<OutputType*>(this->GetPrimaryOutput())->GetDimension(2));
	- slicedGeometry->SetSpacing(spacing);
	-
	- // re-initialize TimeGeometry
	- dynamic_cast<ProportionalTimeGeometry >(static_cast<OutputType>(this->GetPrimaryOutput())->GetTimeGeometry())->Initialize(slicedGeometry, static_cast<OutputType*>(this->GetOutput(0))->GetDimension(3));
	-
	- buffer = nullptr;
	- MITK_INFO << "number of image components: "<< static_cast<OutputType*>(this->GetPrimaryOutput())->GetPixelType().GetNumberOfComponents() << std::endl;
	-
	-
	-
	- // READ TBSS HEADER INFORMATION
	- ImageType::Pointer img;
	-
	- std::string ext = itksys::SystemTools::GetFilenameLastExtension(m_FileName);
	- ext = itksys::SystemTools::LowerCase(ext);
	- if (ext == ".roi")
	- {
	- typedef itk::ImageFileReader<ImageType> FileReaderType;
	- FileReaderType::Pointer reader = FileReaderType::New();
	- reader->SetFileName(this->m_FileName);
	-
	- reader->SetImageIO(imageIO);
	- reader->Update();
	-
	- img = reader->GetOutput();
	-
	- static_cast<OutputType*>(this->GetPrimaryOutput())->SetImage(img);
	-
	- itk::MetaDataDictionary imgMetaDictionary = img->GetMetaDataDictionary();
	- ReadRoiInfo(imgMetaDictionary);
	-
	-
	-
	- }
	-
	-
	- // RESET LOCALE
	- try
	- {
	- MITK_INFO << " ** Changing locale back from " << setlocale(LC_ALL, nullptr) << " to '" << currLocale << "'";
	- setlocale(LC_ALL, currLocale.c_str());
	- }
	- catch(...)
	- {
	- MITK_INFO << "Could not reset locale " << currLocale;
	- }
	-
	- MITK_INFO << "...finished!" << std::endl;
	-
	- }
	- catch(std::exception& e)
	- {
	- MITK_INFO << "Std::Exception while reading file!!";
	- MITK_INFO << e.what();
	- throw itk::ImageFileReaderException(__FILE__, __LINE__, e.what());
	- }
	- catch(...)
	- {
	- MITK_INFO << "Exception while reading file!!";
	- throw itk::ImageFileReaderException(__FILE__, __LINE__, "Sorry, an error occurred while reading the requested vessel tree file!");
	- }
	-
	-
	- }
	-
	-
	-
	- void NrrdTbssRoiImageReader
	- ::ReadRoiInfo(itk::MetaDataDictionary dict)
	- {
	- std::vector<std::string> imgMetaKeys = dict.GetKeys();
	- std::vector<std::string>::const_iterator itKey = imgMetaKeys.begin();
	- std::string metaString;
	- std::vector< itk::Index<3> > roi;
	-
	- for (; itKey != imgMetaKeys.end(); itKey ++)
	- {
	- double x,y,z;
	- itk::Index<3> ix;
	- itk::ExposeMetaData<std::string> (dict, *itKey, metaString);
	-
	- if (itKey->find("ROI_index") != std::string::npos)
	- {
	- MITK_INFO << *itKey << " ---> " << metaString;
	- sscanf(metaString.c_str(), "%lf %lf %lf\n", &x, &y, &z);
	- ix[0] = x; ix[1] = y; ix[2] = z;
	- roi.push_back(ix);
	- }
	- else if(itKey->find("preprocessed FA") != std::string::npos)
	- {
	- MITK_INFO << *itKey << " ---> " << metaString;
	- static_cast<OutputType*>(this->GetPrimaryOutput())->SetPreprocessedFA(true);
	- static_cast<OutputType*>(this->GetPrimaryOutput())->SetPreprocessedFAFile(metaString);
	- }
	-
	- // Name of structure
	- if (itKey->find("structure") != std::string::npos)
	- {
	- MITK_INFO << *itKey << " ---> " << metaString;
	- static_cast<OutputType*>(this->GetPrimaryOutput())->SetStructure(metaString);
	- }
	- }
	- static_cast<OutputType*>(this->GetPrimaryOutput())->SetRoi(roi);
	-
	- }
	-
	-
	- const char* NrrdTbssRoiImageReader
	- ::GetFileName() const
	- {
	- return m_FileName.c_str();
	- }
	-
	-
	- void NrrdTbssRoiImageReader
	- ::SetFileName(const char* aFileName)
	- {
	- m_FileName = aFileName;
	- }
	-
	-
	- const char* NrrdTbssRoiImageReader
	- ::GetFilePrefix() const
	- {
	- return m_FilePrefix.c_str();
	- }
	-
	-
	- void NrrdTbssRoiImageReader
	- ::SetFilePrefix(const char* aFilePrefix)
	- {
	- m_FilePrefix = aFilePrefix;
	- }
	-
	-
	- const char* NrrdTbssRoiImageReader
	- ::GetFilePattern() const
	- {
	- return m_FilePattern.c_str();
	- }
	-
	-
	- void NrrdTbssRoiImageReader
	- ::SetFilePattern(const char* aFilePattern)
	- {
	- m_FilePattern = aFilePattern;
	- }
	-
	-
	- bool NrrdTbssRoiImageReader
	- ::CanReadFile(const std::string filename, const std::string filePrefix, const std::string filePattern)
	- {
	-
	- // First check the extension
	- if( filename == "" )
	- return false;
	-
	- // check if image is serie
	- if( filePattern != "" && filePrefix != "" )
	- return false;
	-
	-
	- std::string ext = itksys::SystemTools::GetFilenameLastExtension(filename);
	- ext = itksys::SystemTools::LowerCase(ext);
	-
	- if (ext == ".roi")
	- {
	- itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
	-
	- typedef itk::ImageFileReader<ImageType> FileReaderType;
	- FileReaderType::Pointer reader = FileReaderType::New();
	- reader->SetImageIO(io);
	- reader->SetFileName(filename);
	-
	- try
	- {
	- reader->Update();
	- }
	- catch(itk::ExceptionObject e)
	- {
	- MITK_INFO << e.GetDescription();
	- return false;
	- }
	-
	- return true;
	-
	-
	- }
	-
	- return false;
	- }
	-
	-} //namespace MITK
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkNrrdTbssRoiImageReader.h b/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkNrrdTbssRoiImageReader.h
	deleted file mode 100644
	index d2705ddd7a..0000000000
	--- a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkNrrdTbssRoiImageReader.h
	+++ /dev/null
	@@ -1,80 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkNrrdTbssRoiImageReader_h
	-#define __mitkNrrdTbssRoiImageReader_h
	-
	-#include "mitkCommon.h"
	-#include "mitkFileReader.h"
	-#include "mitkTbssRoiImageSource.h"
	-#include "itkImage.h"
	-#include "mitkTbssRoiImage.h"
	-
	-namespace mitk
	-{
	-
	- /** \brief
	- */
	-
	-
	- class MITKQUANTIFICATION_EXPORT NrrdTbssRoiImageReader : public mitk::TbssRoiImageSource, public FileReader
	- {
	- public:
	-
	- typedef mitk::TbssRoiImage OutputType;
	- typedef itk::Image<unsigned char,3> ImageType;
	- typedef TbssRoiImageSource TbssVolSourceType;
	-
	-
	-
	- mitkClassMacro( NrrdTbssRoiImageReader, TbssVolSourceType )
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- const char* GetFileName() const override;
	- void SetFileName(const char* aFileName) override;
	- const char* GetFilePrefix() const override;
	- void SetFilePrefix(const char* aFilePrefix) override;
	- const char* GetFilePattern() const override;
	- void SetFilePattern(const char* aFilePattern) override;
	-
	- static bool CanReadFile(const std::string filename, const std::string filePrefix, const std::string filePattern);
	-
	- protected:
	-
	- /** Does the real work. */
	- void GenerateData() override;
	-
	- void ReadRoiInfo(itk::MetaDataDictionary dict);
	-
	- std::string m_FileName;
	- std::string m_FilePrefix;
	- std::string m_FilePattern;
	-
	- OutputType::Pointer m_OutputCache;
	- itk::TimeStamp m_CacheTime;
	-
	-
	-
	- private:
	- void operator=(const Self&); //purposely not implemented
	- };
	-
	-} //namespace MITK
	-
	-//#include "mitkNrrdTbssRoiImageReader.cpp"
	-
	-#endif // __mitkNrrdTbssImageReader_h
	diff --git a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkNrrdTbssRoiImageWriter.cpp b/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkNrrdTbssRoiImageWriter.cpp
	deleted file mode 100644
	index 51ca9928d7..0000000000
	--- a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkNrrdTbssRoiImageWriter.cpp
	+++ /dev/null
	@@ -1,147 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkNrrdTbssRoiImageWriter__cpp
	-#define __mitkNrrdTbssRoiImageWriter__cpp
	-
	-#include "mitkNrrdTbssRoiImageWriter.h"
	-#include "itkMetaDataDictionary.h"
	-#include "itkMetaDataObject.h"
	-#include "itkNrrdImageIO.h"
	-//#include "itkNiftiImageIO.h"
	-#include "itkImageFileWriter.h"
	-#include "itksys/SystemTools.hxx"
	-
	-#include <iostream>
	-#include <fstream>
	-
	-
	-mitk::NrrdTbssRoiImageWriter::NrrdTbssRoiImageWriter()
	- : m_FileName(""), m_FilePrefix(""), m_FilePattern(""), m_Success(false)
	-{
	- this->SetNumberOfRequiredInputs( 1 );
	-}
	-
	-
	-mitk::NrrdTbssRoiImageWriter::~NrrdTbssRoiImageWriter()
	-{}
	-
	-void mitk::NrrdTbssRoiImageWriter::GenerateData()
	-{
	- m_Success = false;
	- InputType* input = this->GetInput();
	-
	- if (input == nullptr)
	- {
	- itkWarningMacro(<<"Sorry, input to NrrdTbssImageWriter is nullptr!")
	- return;
	- }
	- if ( m_FileName == "" )
	- {
	- itkWarningMacro( << "Sorry, filename has not been set!" )
	- return ;
	- }
	-
	-
	- char keybuffer[512];
	- std::stringstream valbuffer;
	-
	- std::vector< itk::Index<3> > roi = input->GetRoi();
	-
	- auto it = roi.begin();
	-
	- int i=0;
	- while(it != roi.end())
	- {
	- itk::Index<3> ix = *it;
	-
	- sprintf( keybuffer, "ROI_index_%04d", i );
	- valbuffer << ix[0] << " " << ix[1] << " " << ix[2];
	-
	- std::cout << valbuffer.str() << std::endl;
	-
	- //input->GetImage()->GetMetaDataDictionary();
	-
	- itk::EncapsulateMetaData< std::string >(input->GetImage()->GetMetaDataDictionary(), std::string(keybuffer), valbuffer.str());
	-
	- it++;
	- ++i;
	- }
	-
	- std::string structure = input->GetStructure();
	- itk::EncapsulateMetaData< std::string >(input->GetImage()->GetMetaDataDictionary(), "structure", structure);
	-
	- typedef itk::Image<unsigned char,3> ImageType;
	- ImageType::Pointer img = input->GetImage();
	-
	- itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
	- io->SetFileType( itk::ImageIOBase::Binary );
	- io->UseCompressionOn();
	-
	-
	- typedef itk::ImageFileWriter<ImageType> WriterType;
	- WriterType::Pointer nrrdWriter = WriterType::New();
	- nrrdWriter->UseInputMetaDataDictionaryOn();
	- nrrdWriter->SetInput( img );
	- nrrdWriter->SetImageIO(io);
	- nrrdWriter->SetFileName(m_FileName);
	- // nrrdWriter->UseCompressionOn();
	- nrrdWriter->SetImageIO(io);
	- try
	- {
	- nrrdWriter->Update();
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e.GetDescription() << std::endl;
	- }
	-
	- m_Success = true;
	-}
	-
	-
	-void mitk::NrrdTbssRoiImageWriter::SetInput( InputType* tbssVol )
	-{
	- this->ProcessObject::SetNthInput( 0, tbssVol );
	-}
	-
	-
	-mitk::TbssRoiImage* mitk::NrrdTbssRoiImageWriter::GetInput()
	-{
	- if ( this->GetNumberOfInputs() < 1 )
	- {
	- return nullptr;
	- }
	- else
	- {
	- return dynamic_cast<InputType*> ( this->ProcessObject::GetInput( 0 ) );
	- }
	-}
	-
	-
	-std::vector<std::string> mitk::NrrdTbssRoiImageWriter::GetPossibleFileExtensions()
	-{
	- std::vector<std::string> possibleFileExtensions;
	- possibleFileExtensions.push_back(".roi");
	- return possibleFileExtensions;
	-}
	-
	-std::string mitk::NrrdTbssRoiImageWriter::GetSupportedBaseData() const
	-{
	- return TbssRoiImage::GetStaticNameOfClass();
	-}
	-
	-#endif //__mitkNrrdTbssRoiImageWriter__cpp
	diff --git a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkNrrdTbssRoiImageWriter.h b/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkNrrdTbssRoiImageWriter.h
	deleted file mode 100644
	index f879e00eb9..0000000000
	--- a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkNrrdTbssRoiImageWriter.h
	+++ /dev/null
	@@ -1,141 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _MITK_NRRDTBSSROIVOL_WRITER__H_
	-#define _MITK_NRRDTBSSROIVOL_WRITER__H_
	-
	-#include <itkProcessObject.h>
	-#include <mitkFileWriterWithInformation.h>
	-#include <mitkTbssRoiImage.h>
	-#include "MitkQuantificationExports.h"
	-
	-namespace mitk
	-{
	-
	-/**
	- * Writes diffusion volumes to a file
	- * @ingroup Process
	- */
	-
	-class MITKQUANTIFICATION_EXPORT NrrdTbssRoiImageWriter : public mitk::FileWriterWithInformation
	-{
	-public:
	-
	- typedef itk::Image<unsigned char,3> ImageType;
	-
	- mitkClassMacro( NrrdTbssRoiImageWriter, mitk::FileWriterWithInformation )
	-
	- mitkWriterMacro
	-
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- typedef mitk::TbssRoiImage InputType;
	-
	- /**
	- * Sets the filename of the file to write.
	- * @param FileName the nameInputType of the file to write.
	- */
	- itkSetStringMacro( FileName );
	-
	- /**
	- * @returns the name of the file to be written to disk.
	- */
	- itkGetStringMacro( FileName );
	-
	- /**
	- * @warning multiple write not (yet) supported
	- */
	- itkSetStringMacro( FilePrefix );
	-
	- /**
	- * @warning multiple write not (yet) supported
	- */
	- itkGetStringMacro( FilePrefix );
	-
	- /**
	- * @warning multiple write not (yet) supported
	- */
	- itkSetStringMacro( FilePattern );
	-
	- /**
	- * @warning multiple write not (yet) supported
	- */
	- itkGetStringMacro( FilePattern );
	-
	- /**image
	- * Sets the input object for the filter.
	- * @param input the diffusion volumes to write to file.
	- */
	- using ProcessObject::SetInput;
	- void SetInput( InputType* input );
	-
	- /**
	- * @returns the 0'th input object of the filter.
	- */
	- InputType* GetInput();
	-
	- /**
	- * Returns false if an error happened during writing
	- */
	- itkGetMacro( Success, bool );
	-
	- /**
	- * @return possible file extensions for the data type associated with the writer
	- */
	- std::vector<std::string> GetPossibleFileExtensions() override;
	-
	- std::string GetSupportedBaseData() const override;
	-
	- // FileWriterWithInformation methods
	- const char * GetDefaultFilename() override { return "TbssRoiImage.roi"; }
	- const char * GetFileDialogPattern() override { return "Tbss Roi Images (*.roi)"; }
	- const char * GetDefaultExtension() override { return ".roi"; }
	- bool CanWriteBaseDataType(BaseData::Pointer data) override
	- {
	- return (dynamic_cast<mitk::TbssRoiImage*>(data.GetPointer()) != nullptr);
	- }
	-
	-
	- void DoWrite(BaseData::Pointer data) override {
	- if (CanWriteBaseDataType(data)) {
	- this->SetInput(dynamic_cast<mitk::TbssRoiImage*>(data.GetPointer()));
	- this->Update();
	- }
	- }
	-
	-protected:
	-
	- NrrdTbssRoiImageWriter();
	-
	- ~NrrdTbssRoiImageWriter() override;
	-
	- void GenerateData() override;
	-
	- std::string m_FileName;
	-
	- std::string m_FilePrefix;
	-
	- std::string m_FilePattern;
	-
	- bool m_Success;
	-
	-};
	-
	-
	-} // end of namespace mitk
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssImage.cpp b/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssImage.cpp
	deleted file mode 100644
	index 30a2d31584..0000000000
	--- a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssImage.cpp
	+++ /dev/null
	@@ -1,114 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkTbssImage__cpp
	-#define __mitkTbssImage__cpp
	-
	-
	-#include "mitkTbssImage.h"
	-#include "itkImageRegionIterator.h"
	-#include "itkImageRegionConstIterator.h"
	-#include "mitkImageCast.h"
	-
	-
	-
	-
	-mitk::TbssImage::TbssImage()
	-{
	-
	-}
	-
	-
	-void mitk::TbssImage::InitializeFromVectorImage()
	-{
	- if(!m_Image)
	- {
	- MITK_INFO << "TBSS Image could not be initialized. Set all members first!" << std::endl;
	- return;
	- }
	-
	-
	- typedef itk::Image<float,3> ImgType;
	- ImgType::Pointer img = ImgType::New();
	- img->SetSpacing( m_Image->GetSpacing() ); // Set the image spacing
	- img->SetOrigin( m_Image->GetOrigin() ); // Set the image origin
	- img->SetDirection( m_Image->GetDirection() ); // Set the image direction
	- img->SetLargestPossibleRegion( m_Image->GetLargestPossibleRegion());
	- img->SetBufferedRegion( m_Image->GetLargestPossibleRegion() );
	- img->Allocate();
	-
	- int vecLength = m_Image->GetVectorLength();
	- InitializeByItk( img.GetPointer(), 1, vecLength );
	-
	- //for(int i=0; i<vecLength; i++)
	- //{TbssImage();
	-
	-
	- itk::ImageRegionIterator<ImgType> itw (img, img->GetLargestPossibleRegion() );
	- itw.GoToBegin();
	-
	- itk::ImageRegionConstIterator<ImageType> itr (m_Image, m_Image->GetLargestPossibleRegion() );
	- itr.GoToBegin();
	-
	- while(!itr.IsAtEnd())
	- {
	- itw.Set(itr.Get().GetElement(0));
	- ++itr;
	- ++itw;
	- }
	-
	- // init
	- SetImportVolume(img->GetBufferPointer());//, 0, 0, CopyMemory);
	- //SetVolume( img->GetBufferPointer(), i );
	- //}::
	-
	- m_DisplayIndex = 0;
	- MITK_INFO << "Tbss-Image successfully initialized.";
	-
	-}
	-
	-void mitk::TbssImage::SetDisplayIndexForRendering(int displayIndex)
	-{
	- MITK_INFO << "displayindex: " << displayIndex;
	- int index = displayIndex;
	- int vecLength = m_Image->GetVectorLength();
	- index = index > vecLength-1 ? vecLength-1 : index;
	- if( m_DisplayIndex != index )
	- {
	- typedef itk::Image<float,3> ImgType;
	- ImgType::Pointer img = ImgType::New();
	- CastToItkImage(this, img);
	-
	- itk::ImageRegionIterator<ImgType> itw (img, img->GetLargestPossibleRegion() );
	- itw.GoToBegin();
	-
	- itk::ImageRegionConstIterator<ImageType> itr (m_Image, m_Image->GetLargestPossibleRegion() );
	- itr.GoToBegin();
	-
	- while(!itr.IsAtEnd())
	- {
	- itw.Set(itr.Get().GetElement(index));
	- ++itr;
	- ++itw;
	- }
	- }
	-
	- m_DisplayIndex = index;
	-}
	-
	-
	-
	-#endif /* __mitkTbssImage__cpp */
	diff --git a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssImage.h b/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssImage.h
	deleted file mode 100644
	index 571f8e8636..0000000000
	--- a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssImage.h
	+++ /dev/null
	@@ -1,117 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef __mitkTbssImage__h
	-#define __mitkTbssImage__h
	-
	-#include "mitkImage.h"
	-#include "itkVectorImage.h"
	-#include "mitkImageCast.h"
	-#include "MitkQuantificationExports.h"
	-
	-namespace mitk
	-{
	-
	- /**
	- * \brief this class encapsulates diffusion volumes (vectorimages not
	- * yet supported by mitkImage)
	- */
	-
	- class MITKQUANTIFICATION_EXPORT TbssImage : public Image
	- {
	-
	- public:
	-
	- typedef itk::VectorImage<float, 3> ImageType;
	-
	-
	- typedef itk::Index<3> IndexType;
	- //typedef typename std::vector <Index<3> > RoiType;
	-
	- mitkClassMacro( TbssImage, Image )
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	-
	- ImageType::Pointer GetImage()
	- {
	- return m_Image;
	- }
	- void SetImage(ImageType::Pointer image )
	- {
	- this->m_Image = image;
	- }
	-
	-
	- void InitializeFromImage()
	- {
	- MITK_INFO << "make an mitk image that can be shown by mitk";
	- this->InitializeByItk(m_Image.GetPointer(),1,1);
	- }
	-
	- void SetGroupInfo( std::vector< std::pair<std::string, int> > info)
	- {
	- m_GroupInfo = info;
	- }
	-
	- std::vector< std::pair<std::string, int> > GetGroupInfo()
	- {
	- return m_GroupInfo;
	- }
	-
	-
	- void SetMeasurementInfo(std::string s)
	- {
	- m_MeasurementInfo = s;
	- }
	-
	- std::string GetMeasurementInfo()
	- {
	- return m_MeasurementInfo;
	- }
	-
	- void InitializeFromVectorImage();
	-
	- void SetDisplayIndexForRendering(int displayIndex);
	-
	-
	-
	-
	-
	- protected:
	-
	- TbssImage();
	-
	- ~TbssImage() override{}
	-
	- ImageType::Pointer m_Image;
	-
	-
	- std::vector< std::pair<std::string, int> > m_GroupInfo;
	-
	- int m_DisplayIndex;
	-
	- std::string m_MeasurementInfo;
	-
	-
	-
	- };
	-
	-
	-} // namespace mitk
	-//#include "mitkTbssImage.cpp"
	-#endif /* __mitkTbssImage__h */
	diff --git a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssImageSource.cpp b/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssImageSource.cpp
	deleted file mode 100644
	index c428943138..0000000000
	--- a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssImageSource.cpp
	+++ /dev/null
	@@ -1,61 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __MITK_NRRD_TBSS_VOULMES_IO_FACTORY_CPP__
	-#define __MITK_NRRD_TBSS_VOULMES_IO_FACTORY_CPP__
	-
	-#include "mitkTbssImageSource.h"
	-#include "mitkTbssImage.h"
	-
	-
	-mitk::TbssImageSource::TbssImageSource()
	-{
	- // Create the output. We use static_cast<> here because we know the default
	- // output must be of type DiffusionImage
	- mitk::TbssImage::Pointer output
	- = static_cast<mitk::TbssImage*>(this->MakeOutput(0).GetPointer());
	-
	- Superclass::SetNumberOfRequiredOutputs(1);
	- Superclass::SetNthOutput(0, output.GetPointer());
	-}
	-
	-itk::DataObject::Pointer mitk::TbssImageSource::MakeOutput ( DataObjectPointerArraySizeType /idx/ )
	-{
	- return OutputType::New().GetPointer();
	-}
	-
	-
	-itk::DataObject::Pointer mitk::TbssImageSource::MakeOutput( const DataObjectIdentifierType & name )
	-{
	- itkDebugMacro("MakeOutput(" << name << ")");
	- if( this->IsIndexedOutputName(name) )
	- {
	- return this->MakeOutput( this->MakeIndexFromOutputName(name) );
	- }
	- return static_cast<itk::DataObject *>(OutputType::New().GetPointer());
	-}
	-
	-
	-
	-mitk::TbssImageSource::OutputType* mitk::TbssImageSource::GetOutput(unsigned int idx)
	-{
	- return static_cast<OutputType*>
	- (this->ProcessObject::GetOutput(idx));
	-}
	-
	-
	-
	-#endif //__MITK_NRRD_TBSS_VOULMES_IO_FACTORY_CPP__
	diff --git a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssImageSource.h b/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssImageSource.h
	deleted file mode 100644
	index d07f8d271d..0000000000
	--- a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssImageSource.h
	+++ /dev/null
	@@ -1,94 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef _MITK_TBSS_IMAGE_DATA_SOURCE_H_HEADER_
	-#define _MITK_TBSS_IMAGE_DATA_SOURCE_H_HEADER_
	-
	-
	-// Should be changed in a new type for TBSS
	-#include "mitkImageSource.h"
	-#include "MitkQuantificationExports.h"
	-
	-
	-namespace mitk {
	-
	-
	-
	- class TbssImage;
	-
	-
	-//##Documentation
	-//## @brief Superclass of all classes generating diffusion volumes (instances
	-//## of class DiffusionImage) as output.
	-//##
	-//## @ingroup Process
	-
	-class MITKQUANTIFICATION_EXPORT TbssImageSource : public ImageSource
	-{
	-public:
	- mitkClassMacro(TbssImageSource, BaseDataSource)
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- typedef TbssImage OutputType;
	- typedef itk::DataObject::Pointer DataObjectPointer;
	-
	- /**
	- * Allocates a new output object and returns it. Currently the
	- * index idx is not evaluated.
	- * @param idx the index of the output for which an object should be created
	- * @returns the new object
	- */
	- itk::DataObject::Pointer MakeOutput ( DataObjectPointerArraySizeType idx ) override;
	-
	- /**
	- * This is a default implementation to make sure we have something.
	- * Once all the subclasses of ProcessObject provide an appopriate
	- * MakeOutput(), then ProcessObject::MakeOutput() can be made pure
	- * virtual.
	- */
	- itk::DataObject::Pointer MakeOutput(const DataObjectIdentifierType &name) override;
	-
	- OutputType* GetOutput()
	- {
	- return itkDynamicCastInDebugMode<OutputType*>( this->GetPrimaryOutput() );
	- }
	-
	- //OutputType * GetOutput(unsigned int idx);
	-
	- //void SetOutput(OutputType* output);
	-
	- //{return Superclass::GetOutput();}
	-
	- OutputType* GetOutput(unsigned int idx);
	-
	- //virtual void GraftOutput(OutputType* graft);
	-
	- //virtual void GraftNthOutput(unsigned int idx, OutputType *graft);
	-
	-protected:
	- TbssImageSource();
	-
	- ~TbssImageSource() override{}
	-};
	-
	-} // namespace mitk
	-
	-//#include "mitkTbssImageSource.cpp"
	-
	-
	-#endif /* _MITK_DIFFUSION_IMAGE_DATA_SOURCE_H_HEADER_ */
	diff --git a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssImporter.cpp b/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssImporter.cpp
	deleted file mode 100644
	index 7fb007e593..0000000000
	--- a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssImporter.cpp
	+++ /dev/null
	@@ -1,137 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkTbssImporter_cpp
	-#define __mitkTbssImporter_cpp
	-
	-#include "mitkTbssImporter.h"
	-#include <mitkPixelTypeMultiplex.h>
	-#include "mitkImagePixelReadAccessor.h"
	-
	-namespace mitk
	-{
	-
	-TbssImage::Pointer TbssImporter::Import()
	-{
	- mitk::TbssImage::Pointer tbssImg = mitk::TbssImage::New();
	- mitkPixelTypeMultiplex1( Import, m_InputVolume->GetPixelType(), tbssImg);
	- return tbssImg;
	-}
	-
	-template <typename TPixel>
	-void TbssImporter::Import(const mitk::PixelType , mitk::TbssImage::Pointer tbssImg)
	-{
	- // read all images with all_*.nii.gz
	- MITK_INFO << "called import ...";
	- m_Data = DataImageType::New();
	-
	- mitk::BaseGeometry* geo = m_InputVolume->GetGeometry();
	- mitk::Vector3D spacing = geo->GetSpacing();
	- mitk::Point3D origin = geo->GetOrigin();
	-
	- //Size size
	- DataImageType::SizeType dataSize;
	- dataSize[0] = m_InputVolume->GetDimension(0);
	- dataSize[1] = m_InputVolume->GetDimension(1);
	- dataSize[2] = m_InputVolume->GetDimension(2);
	-
	- m_Data->SetRegions(dataSize);
	-
	- // Set spacing
	- DataImageType::SpacingType dataSpacing;
	- dataSpacing[0] = spacing[0];
	- dataSpacing[1] = spacing[1];
	- dataSpacing[2] = spacing[2];
	- m_Data->SetSpacing(dataSpacing);
	-
	- DataImageType::PointType dataOrigin;
	- dataOrigin[0] = origin[0];
	- dataOrigin[1] = origin[1];
	- dataOrigin[2] = origin[2];
	- m_Data->SetOrigin(dataOrigin);
	-
	- //Direction must be set
	- DataImageType::DirectionType dir;
	- const itk::Transform<ScalarType, 3, 3>* transform3D = geo->GetIndexToWorldTransform();
	- itk::Transform<ScalarType,3,3>::ParametersType p = transform3D->GetParameters();
	- int t=0;
	- for(int i=0; i<3; i++)
	- {
	- for(int j=0; j<3; j++)
	- {
	- dir[i][j] = p[t]; // row-major order (where the column index varies the fastest)
	- t++;
	- }
	- }
	-
	- m_Data->SetDirection(dir);
	-
	- // Set the length to one because otherwise allocate fails. Should be changed when groups/measurements are added
	- m_Data->SetVectorLength(m_InputVolume->GetDimension(3));
	- m_Data->Allocate();
	-
	- // Determine vector size of m_Data
	-
	- int vecSize = m_Data->GetVectorLength();
	-
	- MITK_INFO << "vecsize " <<vecSize;
	- try {
	- mitk::ImagePixelReadAccessor<TPixel,4> readTbss( m_InputVolume );
	-
	- for(unsigned int i=0; i<dataSize[0]; i++)
	- {
	- MITK_INFO << "i " << i << " / " << dataSize[0];
	- for(unsigned int j=0; j<dataSize[1]; j++)
	- {
	- for(unsigned int k=0; k<dataSize[2]; k++)
	- {
	- itk::VariableLengthVector<float> pixel;
	- itk::Index<3> id;
	- itk::Index<4> ix;
	-
	- ix[0] = id[0] = i;
	- ix[1] = id[1] = j;
	- ix[2] = id[2] = k;
	-
	- pixel = m_Data->GetPixel(id);
	-
	- for(int z=0; z<vecSize; z++)
	- {
	- ix[3] = z;
	- float value = readTbss.GetPixelByIndex(ix);
	- pixel.SetElement(z, value);
	- }
	- m_Data->SetPixel(id, pixel);
	- }
	- }
	- }
	- }
	- catch ( mitk::Exception& e )
	- {
	- MITK_ERROR << "TbssImporter::Import: No read access to tbss image: " << e.what() ;
	- }
	-
	- tbssImg->SetGroupInfo(m_Groups);
	- tbssImg->SetMeasurementInfo(m_MeasurementInfo);
	- tbssImg->SetImage(m_Data);
	-
	- tbssImg->InitializeFromVectorImage();
	-
	-}
	-
	-
	-}
	-#endif // __mitkTbssImporter_cpp
	diff --git a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssImporter.h b/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssImporter.h
	deleted file mode 100644
	index 1e183db01c..0000000000
	--- a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssImporter.h
	+++ /dev/null
	@@ -1,91 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkTbssImporter_h
	-#define __mitkTbssImporter_h
	-
	-#include "mitkCommon.h"
	-#include "mitkFileReader.h"
	-
	-#include "itkImage.h"
	-#include "itkVectorImage.h"
	-
	-#include "mitkTbssImage.h"
	-#include "MitkQuantificationExports.h"
	-
	-
	-namespace mitk
	-{
	-
	-/**
	- * \brief Converts FSL TBSS data (4D skeleton projection images) to a NRRD image with meta data.
	- *
	- * The TBSS pipeline of FSL produces a 4D image containing the 3D skeleton projections of all individuals.
	- * This class converts the FSL Nifty image to NRRD and adds information about the type of measurement and the study groups.
	- */
	-
	- class MITKQUANTIFICATION_EXPORT TbssImporter : public itk::Object {
	-
	- public:
	-
	- // type of the 3d vector image containing the skeletonized images
	- typedef itk::VectorImage<float,3> DataImageType;
	-
	- mitkClassMacroItkParent( TbssImporter, itk::Object )
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- /** \brief Converts the FSL Nifty to NRRD and adds the meta data */
	- mitk::TbssImage::Pointer Import();
	-
	- template <typename TPixel>
	- void Import(const mitk::PixelType pixelType, mitk::TbssImage::Pointer tbssImg);
	-
	- /** \brief Group info is set by providing a vector with pairs of group name and number*/
	- void SetGroupInfo(std::vector< std::pair<std::string, int> > groups)
	- {
	- m_Groups = groups;
	- }
	-
	- /** \brief Used to indicate the type of measurement */
	- void SetMeasurementInfo(std::string s)
	- {
	- m_MeasurementInfo = s;
	- }
	-
	- /** \brief Sets the FSL import volume */
	- void SetImportVolume(mitk::Image::Pointer inputVolume)
	- {
	- m_InputVolume = inputVolume;
	- }
	-
	- protected:
	-
	- TbssImporter(){}
	-
	- ~TbssImporter() override{}
	-
	- DataImageType::Pointer m_Data;
	-
	- std::vector< std::pair<std::string, int> > m_Groups;
	-
	- std::string m_MeasurementInfo;
	-
	- mitk::Image::Pointer m_InputVolume;
	-
	- };
	-}
	-#endif // __mitkTbssImporter_h
	diff --git a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssRoiImage.cpp b/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssRoiImage.cpp
	deleted file mode 100644
	index 1e42061c56..0000000000
	--- a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssRoiImage.cpp
	+++ /dev/null
	@@ -1,51 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __mitkTbssRoiImage__cpp
	-#define __mitkTbssRoiImage__cpp
	-
	-
	-#include "mitkTbssRoiImage.h"
	-#include "itkImageRegionIterator.h"
	-#include "itkImageRegionConstIterator.h"
	-#include "mitkImageCast.h"
	-
	-
	-
	-
	-mitk::TbssRoiImage::TbssRoiImage()
	-{
	- m_PreprocessedFA = false;
	-}
	-
	-
	-/*
	-
	-mitk::TbssRoiImage::~TbssImage()
	-{
	-
	-}
	-
	-
	-
	-void mitk::TbssRoiImage::InitializeFromImage()
	-{
	-
	-}
	-
	-*/
	-
	-#endif /* __mitkTbssImage__cpp */
	diff --git a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssRoiImage.h b/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssRoiImage.h
	deleted file mode 100644
	index 32617cf61f..0000000000
	--- a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssRoiImage.h
	+++ /dev/null
	@@ -1,133 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef __mitkTbssRoiImage__h
	-#define __mitkTbssRoiImage__h
	-
	-#include "mitkImage.h"
	-#include "itkImage.h"
	-#include "mitkImageCast.h"
	-#include "MitkQuantificationExports.h"
	-
	-namespace mitk
	-{
	-
	- /**
	- * \brief this class encapsulates diffusion volumes (vectorimages not
	- * yet supported by mitkImage)
	- */
	-
	- class MITKQUANTIFICATION_EXPORT TbssRoiImage : public Image
	- {
	-
	- public:
	-
	- typedef itk::Image<unsigned char, 3> ImageType;
	- typedef itk::Index<3> IndexType;
	- //typedef typename std::vector <Index<3> > RoiType;
	-
	- mitkClassMacro( TbssRoiImage, Image )
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	-
	- //void SetRequestedRegionToLargestPossibleRegion();
	- //bool RequestedRegionIsOutsideOfTheBufferedRegion();
	- //virtual bool VerifyRequestedRegion();
	- //void SetRequestedRegion( const itk::DataObject *data);
	-
	- ImageType::Pointer GetImage()
	- {
	- return m_Image;
	- }
	- void SetImage(ImageType::Pointer image )
	- {
	- this->m_Image = image;
	- }
	-
	- itkGetMacro(PreprocessedFA, bool)
	- itkSetMacro(PreprocessedFA, bool)
	- itkGetMacro(PreprocessedFAFile, std::string)
	- itkSetMacro(PreprocessedFAFile, std::string)
	- itkGetMacro(Structure, std::string)
	- itkSetMacro(Structure, std::string)
	-
	- void SetRoi(std::vector< itk::Index<3> > roi)
	- {
	- m_Roi = roi;
	- }
	-
	-
	- // depricated
	- std::vector< itk::Index<3> > GetRoi()
	- {
	- return m_Roi;
	- }
	-
	-
	- void InitializeFromImage()
	- {
	- MITK_INFO << "make an mitk image that can be shown by mitk";
	- this->InitializeByItk(m_Image.GetPointer());
	-
	- this->SetChannel(m_Image->GetBufferPointer());
	- }
	-
	-
	-
	-
	- protected:
	-
	- TbssRoiImage();
	-
	- ~TbssRoiImage() override{}
	-
	- ImageType::Pointer m_Image;
	-
	- std::vector< itk::Index<3> > m_Roi;
	-
	- bool m_PreprocessedFA;
	- std::string m_PreprocessedFAFile;
	-
	- std::string m_Structure;
	-
	-
	- };
	-
	-
	- // Does the same es the normal CastToMitkImage, but needed to reimplemented due to the templatet pixeltype
	- /*
	- template <typename ItkOutputImageType>
	- void CastToTbssImage(const ItkOutputImageType* itkimage, itk::SmartPointer< mitk::TbssRoiImage >& tbssoutputimage)
	- {
	- if(tbssoutputimage.IsNull())
	- {
	- tbssoutputimage = mitk::TbssRoiImage::New();
	- }
	- tbssoutputimage->InitializeByItk(itkimage);
	- tbssoutputimage->SetChannel(itkimage->GetBufferPointer());
	- }
	-*/
	-
	-
	-
	-
	-
	-} // namespace mitk
	-
	-//#include "mitkTbssRoiImage.cpp"
	-#endif /* __mitkTbssRoiImage__h */
	diff --git a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssRoiImageSource.cpp b/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssRoiImageSource.cpp
	deleted file mode 100644
	index 1b16532217..0000000000
	--- a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssRoiImageSource.cpp
	+++ /dev/null
	@@ -1,60 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef __MITK_NRRD_TBSSROI_VOLUMES_IO_FACTORY_CPP__
	-#define __MITK_NRRD_TBSSROI_VOLUMES_IO_FACTORY_CPP__
	-
	-#include "mitkTbssRoiImageSource.h"
	-#include "mitkTbssRoiImage.h"
	-
	-
	-mitk::TbssRoiImageSource::TbssRoiImageSource()
	-{
	- // Create the output. We use static_cast<> here because we know the default
	- // output must be of type DiffusionImage
	- mitk::TbssRoiImage::Pointer output
	- = static_cast<mitk::TbssRoiImage*>(this->MakeOutput(0).GetPointer());
	-
	- Superclass::SetNumberOfRequiredOutputs(1);
	- Superclass::SetNthOutput(0, output.GetPointer());
	-}
	-
	-
	-itk::DataObject::Pointer mitk::TbssRoiImageSource::MakeOutput ( DataObjectPointerArraySizeType /idx/ )
	-{
	- return OutputType::New().GetPointer();
	-}
	-
	-
	-itk::DataObject::Pointer mitk::TbssRoiImageSource::MakeOutput( const DataObjectIdentifierType & name )
	-{
	- itkDebugMacro("MakeOutput(" << name << ")");
	- if( this->IsIndexedOutputName(name) )
	- {
	- return this->MakeOutput( this->MakeIndexFromOutputName(name) );
	- }
	- return static_cast<itk::DataObject *>(OutputType::New().GetPointer());
	-}
	-
	-
	-
	-mitk::TbssRoiImageSource::OutputType* mitk::TbssRoiImageSource::GetOutput(unsigned int idx)
	-{
	- return static_cast<OutputType*>
	- (this->ProcessObject::GetOutput(idx));
	-}
	-
	-#endif //__MITK_NRRD_TBSS_VOULMES_IO_FACTORY_CPP__
	diff --git a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssRoiImageSource.h b/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssRoiImageSource.h
	deleted file mode 100644
	index 913073c9a4..0000000000
	--- a/Modules/DiffusionImaging/Quantification/IODataStructures/TbssImages/mitkTbssRoiImageSource.h
	+++ /dev/null
	@@ -1,77 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef _MITK_TBSS_ROI_IMAGE_DATA_SOURCE_H_HEADER_
	-#define _MITK_TBSS_ROI_IMAGE_DATA_SOURCE_H_HEADER_
	-
	-
	-// Should be changed in a new type for TBSS
	-#include "mitkImageSource.h"
	-#include "MitkQuantificationExports.h"
	-
	-
	-namespace mitk {
	-
	-
	-
	- class TbssRoiImage;
	-
	-
	-//##Documentation
	-//## @brief Superclass of all classes generating diffusion volumes (instances
	-//## of class DiffusionImage) as output.
	-//##
	-//## @ingroup Process
	-
	-class MITKQUANTIFICATION_EXPORT TbssRoiImageSource : public ImageSource
	-{
	-public:
	- mitkClassMacro(TbssRoiImageSource, BaseDataSource)
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- typedef TbssRoiImage OutputType;
	- typedef itk::DataObject::Pointer DataObjectPointer;
	-
	- /**
	- * Allocates a new output object and returns it. Currently the
	- * index idx is not evaluated.
	- * @param idx the index of the output for which an object should be created
	- * @returns the new object
	- */
	- itk::DataObject::Pointer MakeOutput ( DataObjectPointerArraySizeType idx ) override;
	-
	- /**
	- * This is a default implementation to make sure we have something.
	- * Once all the subclasses of ProcessObject provide an appopriate
	- * MakeOutput(), then ProcessObject::MakeOutput() can be made pure
	- * virtual.
	- */
	- itk::DataObject::Pointer MakeOutput(const DataObjectIdentifierType &name) override;
	-
	- OutputType* GetOutput(unsigned int idx);
	-
	-protected:
	- TbssRoiImageSource();
	-
	- ~TbssRoiImageSource() override{}
	-};
	-
	-} // namespace mitk
	-
	-
	-#endif /* _MITK_DIFFUSION_IMAGE_DATA_SOURCE_H_HEADER_ */
	diff --git a/Modules/DiffusionImaging/Quantification/Rendering/mitkTbssImageMapper.cpp b/Modules/DiffusionImaging/Quantification/Rendering/mitkTbssImageMapper.cpp
	deleted file mode 100644
	index 4e2bef926e..0000000000
	--- a/Modules/DiffusionImaging/Quantification/Rendering/mitkTbssImageMapper.cpp
	+++ /dev/null
	@@ -1,65 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef TbssImageMapper__cpp
	-#define TbssImageMapper__cpp
	-
	-#include "mitkTbssImageMapper.h"
	-
	-#include "mitkProperties.h"
	-#include "mitkTbssImage.h"
	-
	-
	-
	-mitk::TbssImageMapper::TbssImageMapper()
	-{
	-}
	-
	-
	-mitk::TbssImageMapper::~TbssImageMapper()
	-{
	-}
	-
	-
	-void mitk::TbssImageMapper::GenerateDataForRenderer( mitk::BaseRenderer *renderer )
	-{
	- int displayIndex(0);
	-
	-
	- this->GetDataNode()->GetIntProperty( "DisplayChannel", displayIndex, renderer );
	- mitk::Image input = const_cast< mitk::Image >(
	- this->GetInput()
	- );
	- mitk::TbssImage input2 = dynamic_cast< mitk::TbssImage >(
	- input
	- );
	-
	- MITK_INFO << "displayindex: " << displayIndex;
	-
	-
	- input2->SetDisplayIndexForRendering(displayIndex);
	- Superclass::GenerateDataForRenderer(renderer);
	-}
	-
	-
	-void mitk::TbssImageMapper::SetDefaultProperties(mitk::DataNode* node, mitk::BaseRenderer* renderer, bool overwrite)
	-{
	- node->AddProperty( "DisplayChannel", mitk::IntProperty::New( 0 ), renderer, overwrite );
	- Superclass::SetDefaultProperties(node, renderer, overwrite);
	-}
	-
	-#endif
	diff --git a/Modules/DiffusionImaging/Quantification/Rendering/mitkTbssImageMapper.h b/Modules/DiffusionImaging/Quantification/Rendering/mitkTbssImageMapper.h
	deleted file mode 100644
	index dd319e8206..0000000000
	--- a/Modules/DiffusionImaging/Quantification/Rendering/mitkTbssImageMapper.h
	+++ /dev/null
	@@ -1,55 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef TbssImageMapper_H_HEADER_INCLUDED
	-#define TbssImageMapper_H_HEADER_INCLUDED
	-
	-#include "mitkImageVtkMapper2D.h"
	-#include "MitkQuantificationExports.h"
	-
	-namespace mitk {
	-
	- //##Documentation
	- //## @brief Mapper for raw diffusion weighted images
	- //## @ingroup Mapper
	-
	- class MITKQUANTIFICATION_EXPORT TbssImageMapper : public ImageVtkMapper2D
	- {
	- public:
	-
	- mitkClassMacro(TbssImageMapper,ImageVtkMapper2D);
	- itkFactorylessNewMacro(Self)
	- itkCloneMacro(Self)
	-
	- void GenerateDataForRenderer( mitk::BaseRenderer *renderer ) override;
	-
	- static void SetDefaultProperties(DataNode* node, BaseRenderer* renderer = nullptr, bool overwrite = false );
	-
	- protected:
	-
	- TbssImageMapper();
	- ~TbssImageMapper() override;
	-
	- };
	-
	-} // namespace mitk
	-
	-//#include "mitkTbssImageMapper.cpp"
	-
	-
	-#endif /* TbssImageMapper_H_HEADER_INCLUDED */
	-
	diff --git a/Modules/DiffusionImaging/Quantification/Testing/CMakeLists.txt b/Modules/DiffusionImaging/Quantification/Testing/CMakeLists.txt
	deleted file mode 100644
	index a8460a241d..0000000000
	--- a/Modules/DiffusionImaging/Quantification/Testing/CMakeLists.txt
	+++ /dev/null
	@@ -1,15 +0,0 @@
	-MITK_CREATE_MODULE_TESTS()
	-
	-mitkAddCustomModuleTest(mitkTbssNrrdImageReaderTest mitkTbssNrrdImageReaderTest ${MITK_DATA_DIR}/DiffusionImaging/tbss.tbss)
	-#mitkAddCustomModuleTest(mitkTbssRoiNrrdImageReaderTest mitkTbssRoiNrrdImageReaderTest ${MITK_DATA_DIR}/DiffusionImaging/bodyfornix.roi)
	-mitkAddCustomModuleTest(mitkTbssNrrdImageWriterTest mitkTbssNrrdImageWriterTest ${MITK_DATA_DIR}/DiffusionImaging/tbss.tbss ${MITK_DATA_DIR}/DiffusionImaging/tbss2.tbss)
	-mitkAddCustomModuleTest(mitkTbssSkeletonizationTest mitkTbssSkeletonizationTest ${MITK_DATA_DIR}/DiffusionImaging/mean_FA.nii.gz
	- ${MITK_DATA_DIR}/DiffusionImaging/mean_FA_skeleton.nii.gz
	- ${MITK_DATA_DIR}/DiffusionImaging/LowerCingulum_1mm.nii.gz
	- ${MITK_DATA_DIR}/DiffusionImaging/single_subject4d.nhdr
	- ${MITK_DATA_DIR}/DiffusionImaging/single_subject_projected.nrrd)
	-
	-
	-mitkAddCustomModuleTest(mitkTractAnalyzerTest mitkTractAnalyzerTest ${MITK_DATA_DIR}/DiffusionImaging/mean_FA_skeleton.nii.gz
	- ${MITK_DATA_DIR}/DiffusionImaging/tbssRoiPointset.mps
	- ${MITK_DATA_DIR}/DiffusionImaging/roi_cc.roi)
	diff --git a/Modules/DiffusionImaging/Quantification/Testing/files.cmake b/Modules/DiffusionImaging/Quantification/Testing/files.cmake
	deleted file mode 100644
	index 18fe4baae5..0000000000
	--- a/Modules/DiffusionImaging/Quantification/Testing/files.cmake
	+++ /dev/null
	@@ -1,8 +0,0 @@
	-SET(MODULE_CUSTOM_TESTS
	- mitkTbssNrrdImageReaderTest.cpp
	- #mitkTbssRoiNrrdImageReaderTest.cpp
	- mitkTbssNrrdImageWriterTest.cpp
	- mitkTbssSkeletonizationTest.cpp
	- mitkTractAnalyzerTest.cpp
	-)
	-
	diff --git a/Modules/DiffusionImaging/Quantification/Testing/mitkTbssNrrdImageReaderTest.cpp b/Modules/DiffusionImaging/Quantification/Testing/mitkTbssNrrdImageReaderTest.cpp
	deleted file mode 100644
	index 9aa78a8b8d..0000000000
	--- a/Modules/DiffusionImaging/Quantification/Testing/mitkTbssNrrdImageReaderTest.cpp
	+++ /dev/null
	@@ -1,60 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkTestingMacros.h>
	-#include <mitkNrrdTbssImageReader.h>
	-#include "mitkCoreObjectFactory.h"
	-
	-
	-/**Documentation
	- * test for the class "mitkNrrdTbssImageReader".
	- */
	-int mitkTbssNrrdImageReaderTest(int , char* argv[])
	-{
	- MITK_TEST_BEGIN("TbssNrrdImageReaderTest");
	-
	- mitk::NrrdTbssImageReader::Pointer tbssNrrdReader = mitk::NrrdTbssImageReader::New();
	-
	- MITK_TEST_CONDITION_REQUIRED(tbssNrrdReader.GetPointer(), "Testing initialization of test object!");
	-
	- tbssNrrdReader->SetFileName(argv[1]);
	- MITK_TEST_CONDITION_REQUIRED( tbssNrrdReader->CanReadFile(argv[1], "", ""), "Testing CanReadFile() method with valid input file name!");
	- tbssNrrdReader->Update();
	-
	- mitk::TbssImage* tbssImg = tbssNrrdReader->GetOutput();
	-
	- MITK_TEST_CONDITION_REQUIRED(tbssImg != nullptr, "Testing that tbssImg is not null");
	-
	- mitk::TbssImage::SizeType size = tbssImg->GetLargestPossibleRegion().GetSize();
	-
	- MITK_TEST_CONDITION_REQUIRED(size[0]==2 && size[1]==2 && size[2]==2, "Test size of tbss image");
	-
	- // Test groups
	- std::vector< std::pair<std::string, int> > groups = tbssImg->GetGroupInfo();
	-
	- std::pair<std::string, int> group1 = groups.at(0);
	- std::pair<std::string, int> group2 = groups.at(1);
	-
	-
	-
	- MITK_TEST_CONDITION_REQUIRED(group1.first.compare("group1") && group1.second==1, "Test group 1 info");
	-
	- MITK_TEST_CONDITION_REQUIRED(group2.first.compare("group2") && group2.second==1, "Test group 2 info");
	-
	-
	-
	- MITK_TEST_END();
	-}
	diff --git a/Modules/DiffusionImaging/Quantification/Testing/mitkTbssNrrdImageWriterTest.cpp b/Modules/DiffusionImaging/Quantification/Testing/mitkTbssNrrdImageWriterTest.cpp
	deleted file mode 100644
	index 92b4d0526a..0000000000
	--- a/Modules/DiffusionImaging/Quantification/Testing/mitkTbssNrrdImageWriterTest.cpp
	+++ /dev/null
	@@ -1,76 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkTestingMacros.h>
	-#include <mitkNrrdTbssImageReader.h>
	-#include <mitkNrrdTbssImageWriter.h>
	-#include "mitkCoreObjectFactory.h"
	-
	-
	-/**Documentation
	- * test for the class "mitkNrrdTbssImageWriter".
	- */
	-int mitkTbssNrrdImageWriterTest(int, char* argv[])
	-{
	- MITK_TEST_BEGIN("TbssNrrdImageWriterTest");
	-
	- mitk::NrrdTbssImageReader::Pointer tbssNrrdReader = mitk::NrrdTbssImageReader::New();
	-
	- MITK_TEST_CONDITION_REQUIRED(tbssNrrdReader.GetPointer(), "Testing initialization of test object!");
	-
	- tbssNrrdReader->SetFileName(argv[1]);
	- MITK_TEST_CONDITION_REQUIRED( tbssNrrdReader->CanReadFile(argv[1], "", ""), "Testing CanReadFile() method with valid input file name!");
	- tbssNrrdReader->Update();
	-
	- mitk::TbssImage* tbssImg = tbssNrrdReader->GetOutput();
	-
	- MITK_TEST_CONDITION_REQUIRED(tbssImg != nullptr, "Testing that tbssImg is not null");
	-
	- mitk::NrrdTbssImageWriter::Pointer tbssNrrdWriter = mitk::NrrdTbssImageWriter::New();
	-
	-
	- try{
	- tbssNrrdWriter->SetFileName(argv[2]);
	- tbssNrrdWriter->SetInput(tbssImg);
	- tbssNrrdWriter->Update();
	- }
	- catch(...) {
	- std::cout << "Writing failed" << std::endl;
	- return EXIT_FAILURE;
	- }
	-
	- mitk::NrrdTbssImageReader::Pointer tbssNrrdReader2 = mitk::NrrdTbssImageReader::New();
	- tbssNrrdReader2->SetFileName(argv[1]);
	- MITK_TEST_CONDITION_REQUIRED( tbssNrrdReader2->CanReadFile(argv[1], "", ""), "Testing CanReadFile() method with previously saved file!");
	-
	- tbssNrrdReader2->Update();
	- mitk::TbssImage* tbssImg2 = tbssNrrdReader2->GetOutput();
	-
	-
	- std::vector< std::pair<std::string, int> > groups = tbssImg->GetGroupInfo();
	- std::vector< std::pair<std::string, int> > groups2 = tbssImg2->GetGroupInfo();
	-
	- MITK_TEST_CONDITION(groups == groups2, "Check that group information is identical");
	-
	-
	- mitk::TbssImage::SizeType size = tbssImg->GetLargestPossibleRegion().GetSize();
	- mitk::TbssImage::SizeType size2 = tbssImg2->GetLargestPossibleRegion().GetSize();
	-
	- MITK_TEST_CONDITION(size == size2, "Check that sizes are equal");
	-
	-
	- MITK_TEST_END();
	-}
	diff --git a/Modules/DiffusionImaging/Quantification/Testing/mitkTbssRoiNrrdImageReaderTest.cpp b/Modules/DiffusionImaging/Quantification/Testing/mitkTbssRoiNrrdImageReaderTest.cpp
	deleted file mode 100644
	index 55057f94ac..0000000000
	--- a/Modules/DiffusionImaging/Quantification/Testing/mitkTbssRoiNrrdImageReaderTest.cpp
	+++ /dev/null
	@@ -1,69 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkTestingMacros.h>
	-
	-#include <mitkNrrdTbssRoiImageReader.h>
	-#include "mitkDiffusionImagingObjectFactory.h"
	-#include "mitkCoreObjectFactory.h"
	-
	-
	-/**Documentation
	- * test for the class "mitkNrrdTbssImageReader".
	- */
	-int mitkTbssRoiNrrdImageReaderTest(int, char* argv[])
	-{
	- MITK_TEST_BEGIN("NrrdTbssRoiImageReaderTest");
	-
	-
	- mitk::NrrdTbssRoiImageReader::Pointer roiReader = mitk::NrrdTbssRoiImageReader::New();
	-
	- MITK_TEST_CONDITION_REQUIRED(roiReader.GetPointer(), "Testing initialization of test object!");
	-
	- RegisterDiffusionImagingObjectFactory();
	-
	-
	- roiReader->SetFileName(argv[1]);
	- MITK_TEST_CONDITION_REQUIRED( roiReader->CanReadFile(argv[1], "", ""), "Testing CanReadFile() method with valid input file name!");
	- roiReader->Update();
	-
	- mitk::TbssRoiImage* roiImg = roiReader->GetOutput();
	-
	- MITK_TEST_CONDITION_REQUIRED(roiImg != nullptr, "Testing that roiImg is not null");
	-
	- mitk::TbssRoiImage::SizeType size = roiImg->GetLargestPossibleRegion().GetSize();
	-
	- MITK_TEST_CONDITION_REQUIRED(size[0]==182 && size[1]==218 && size[2]==182, "Test size of ROI image");
	-
	-
	- // Test indices of the roi
	- std::vector< itk::Index<3> > indices = roiImg->GetRoi();
	-
	- MITK_TEST_CONDITION(indices.size() == 24, "Test the number of indices belonging to the Roi");
	-
	- itk::Index<3> ix = indices.at(0);
	-
	- MITK_TEST_CONDITION(ix[0]==90 && ix[1]==132 && ix[2]==74, "Test whether first index is correct");
	-
	- ix = indices.at(23);
	-
	- MITK_TEST_CONDITION(ix[0]==90 && ix[1]==117 && ix[2]==88, "Test whether last index is correct");
	-
	-
	-
	-
	- MITK_TEST_END();
	-}
	diff --git a/Modules/DiffusionImaging/Quantification/Testing/mitkTbssSkeletonizationTest.cpp b/Modules/DiffusionImaging/Quantification/Testing/mitkTbssSkeletonizationTest.cpp
	deleted file mode 100644
	index 51610a7e53..0000000000
	--- a/Modules/DiffusionImaging/Quantification/Testing/mitkTbssSkeletonizationTest.cpp
	+++ /dev/null
	@@ -1,167 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkTestingMacros.h>
	-#include <itkImageFileReader.h>
	-#include <itkSkeletonizationFilter.h>
	-#include <itkBinaryThresholdImageFilter.h>
	-#include <itkDistanceMapFilter.h>
	-#include <itkProjectionFilter.h>
	-#include <itkTestingComparisonImageFilter.h>
	-
	-/**Documentation
	- * test for the class "itkSkeletonizationFilter".
	- */
	-int mitkTbssSkeletonizationTest(int, char* argv[])
	-{
	-
	- MITK_TEST_BEGIN("TbssSkeletonizationTest");
	-
	-
	- // Load images
	- typedef itk::Image<float, 3> FloatImageType;
	- typedef itk::ImageFileReader<FloatImageType> ImageReaderType;
	-
	- ImageReaderType::Pointer reader = ImageReaderType::New();
	- reader->SetFileName(argv[1]);
	-
	- // Initialize skeletonization filter and feed it with the mean_FA.nii.gz
	-
	- typedef itk::SkeletonizationFilter<FloatImageType, FloatImageType> SkeletonisationFilterType;
	- SkeletonisationFilterType::Pointer skeletonizer = SkeletonisationFilterType::New();
	- skeletonizer->SetInput(reader->GetOutput());
	- skeletonizer->Update();
	-
	-
	- // Create a new image so the skeletonizaton won't be performed every time the skeleton is needed.
	- FloatImageType::Pointer skeleton = skeletonizer->GetOutput();
	-
	- // Check whether the skeleton is correct
	- reader->SetFileName(argv[2]);
	- reader->Update();
	-
	- FloatImageType::Pointer controlSkeleton = reader->GetOutput();
	-
	-
	- // Convert itk images to mitk images and use the mitk::Equal method to compare the result with the reference skeleton.
	-
	- mitk::Image::Pointer mitkSkeleton = mitk::Image::New();
	- mitkSkeleton->InitializeByItk(skeleton.GetPointer());
	-
	- mitk::Image::Pointer mitkRefSkeleton = mitk::Image::New();
	- mitkRefSkeleton->InitializeByItk(controlSkeleton.GetPointer());
	-
	-
	- MITK_TEST_CONDITION(mitk::Equal(mitkSkeleton, mitkRefSkeleton, 0.001, true), "Check correctness of the skeleton");
	-
	-
	- // Test the projection filter
	-
	- typedef itk::CovariantVector<int,3> VectorType;
	- typedef itk::Image<VectorType, 3> DirectionImageType;
	-
	- // Retrieve direction image needed later by the projection filter
	- DirectionImageType::Pointer directionImg = skeletonizer->GetVectorImage();
	-
	- // Define a distance map filter that creates a distance map to limit the projection search
	- typedef itk::DistanceMapFilter<FloatImageType, FloatImageType> DistanceMapFilterType;
	-
	- DistanceMapFilterType::Pointer distanceMapFilter = DistanceMapFilterType::New();
	- distanceMapFilter->SetInput(controlSkeleton); //use controlSkeleton to prevent updating the skeletonfilter, which is time consuming
	- distanceMapFilter->Update();
	-
	- FloatImageType::Pointer distanceMap = distanceMapFilter->GetOutput();
	-
	-
	-
	-
	- // Threshold the skeleton on FA=0.2 to create a binary skeleton mask
	- typedef itk::Image<char, 3> CharImageType;
	- typedef itk::BinaryThresholdImageFilter<FloatImageType, CharImageType> ThresholdFilterType;
	- ThresholdFilterType::Pointer thresholder = ThresholdFilterType::New();
	- thresholder->SetInput(controlSkeleton); //use controlSkeleton to prevent updating the skeletonfilter, which is time consuming
	- thresholder->SetLowerThreshold(0.2);
	- thresholder->SetUpperThreshold(std::numeric_limits<float>::max());
	- thresholder->SetOutsideValue(0);
	- thresholder->SetInsideValue(1);
	- thresholder->Update();
	-
	-
	- CharImageType::Pointer thresholdedImg = thresholder->GetOutput();
	-
	-
	- // Load the cingulum mask that defines the region where a tubular structure must be searched for
	- typedef itk::ImageFileReader< CharImageType > CharReaderType;
	- CharReaderType::Pointer charReader = CharReaderType::New();
	- charReader->SetFileName(argv[3]);
	- charReader->Update();
	- CharImageType::Pointer cingulum = charReader->GetOutput();
	-
	-
	-
	- // Define projection filter
	- typedef itk::ProjectionFilter ProjectionFilterType;
	-
	- // Read the 4d test image containing the registered FA data of one subject
	- typedef itk::Image<float, 4> Float4DImageType;
	- typedef itk::ImageFileReader<Float4DImageType> ImageReader4DType;
	-
	-
	-
	- ImageReader4DType::Pointer reader4d = ImageReader4DType::New();
	- reader4d->SetFileName(argv[4]);
	- reader4d->Update();
	-
	-
	-
	- ProjectionFilterType::Pointer projectionFilter = ProjectionFilterType::New();
	- projectionFilter->SetDistanceMap(distanceMap);
	- projectionFilter->SetDirections(directionImg);
	- projectionFilter->SetAllFA(reader4d->GetOutput());
	- projectionFilter->SetTube(cingulum);
	- projectionFilter->SetSkeleton(thresholdedImg);
	- projectionFilter->Project();
	-
	-
	-
	- Float4DImageType::Pointer projected = projectionFilter->GetProjections();
	-
	-
	-
	- // Open control projection image
	- reader4d->SetFileName(argv[5]);
	- reader4d->Update();
	- Float4DImageType::Pointer controlProjection = reader4d->GetOutput();
	-
	- // control dimensions
	- Float4DImageType::SizeType pSize = projected->GetLargestPossibleRegion().GetSize();
	- Float4DImageType::SizeType pControlSize = controlProjection->GetLargestPossibleRegion().GetSize();
	-
	- typedef itk::Testing::ComparisonImageFilter<Float4DImageType, Float4DImageType> ComparisonFilterType;
	- ComparisonFilterType::Pointer comparisonFilter = ComparisonFilterType::New();
	- comparisonFilter->SetTestInput(projected);
	- comparisonFilter->SetValidInput(controlProjection);
	- comparisonFilter->Update();
	- float diff = comparisonFilter->GetTotalDifference();
	-
	-
	- MITK_TEST_CONDITION(pSize == pControlSize, "Size of projection image and control projection image are the same");
	-
	- MITK_TEST_CONDITION(diff < 0.001, "Check correctness of the projections");
	-
	-
	- MITK_TEST_END();
	-}
	diff --git a/Modules/DiffusionImaging/Quantification/Testing/mitkTractAnalyzerTest.cpp b/Modules/DiffusionImaging/Quantification/Testing/mitkTractAnalyzerTest.cpp
	deleted file mode 100644
	index e913d84fe9..0000000000
	--- a/Modules/DiffusionImaging/Quantification/Testing/mitkTractAnalyzerTest.cpp
	+++ /dev/null
	@@ -1,82 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <mitkTestingMacros.h>
	-#include <mitkTractAnalyzer.h>
	-#include <itkImageFileReader.h>
	-#include <mitkNrrdTbssRoiImageReader.h>
	-#include <mitkIOUtil.h>
	-
	-/**Documentation
	- * test for the class "mitkTractAnalyzer".
	- */
	-int mitkTractAnalyzerTest(int, char* argv[])
	-{
	-
	- MITK_TEST_BEGIN("TractAnalyzer");
	-
	- // Load image
	- typedef itk::Image<float, 3> FloatImageType;
	- typedef itk::ImageFileReader<FloatImageType> ImageReaderType;
	-
	- ImageReaderType::Pointer reader = ImageReaderType::New();
	-
	- reader->SetFileName(argv[1]);
	- reader->Update();
	- FloatImageType::Pointer itkImage = reader->GetOutput();
	- mitk::Image::Pointer mitkImage = mitk::Image::New();
	-
	- mitk::CastToMitkImage(itkImage, mitkImage);
	-
	- // load point set
	- mitk::PointSet::Pointer pointSet = mitk::IOUtil::Load<mitk::PointSet>(argv[2]);
	-
	- mitk::TractAnalyzer analyzer;
	-
	- analyzer.SetInputImage(mitkImage);
	- analyzer.SetThreshold(0.2);
	- analyzer.SetPointSet(pointSet);
	- analyzer.MakeRoi();
	-
	- mitk::TbssRoiImage::Pointer tbssRoi = analyzer.GetRoiImage();
	-
	- std::vector< itk::Index<3> > roi = tbssRoi->GetRoi();
	-
	-
	-
	- // Output roi for debug purposes
	- std::cout << "ROI\n";
	- for(unsigned int t=0; t<roi.size(); t++)
	- {
	- itk::Index<3> ix = roi.at(t);
	- std::cout << ix[0] << ", " << ix[1] << ", " << ix[2] << "\n";
	- }
	-
	-
	- std::cout << std::endl;
	-
	- // check the cost of the roi
	- double cost = analyzer.GetCostSum();
	-
	- std::cout << "Cost: " << cost << std::endl;
	-
	- bool equal = mitk::Equal(cost, 5162.854, 0.001);
	-
	- MITK_TEST_CONDITION(equal, "Checking cost of found ROI");
	-
	-
	- MITK_TEST_END();
	-}
	diff --git a/Modules/DiffusionImaging/Quantification/files.cmake b/Modules/DiffusionImaging/Quantification/files.cmake
	deleted file mode 100644
	index 9477511ee7..0000000000
	--- a/Modules/DiffusionImaging/Quantification/files.cmake
	+++ /dev/null
	@@ -1,31 +0,0 @@
	-set(CPP_FILES
	-
	- # DataStructures -> Tbss
	- IODataStructures/TbssImages/mitkTbssImageSource.cpp
	- IODataStructures/TbssImages/mitkTbssRoiImageSource.cpp
	- IODataStructures/TbssImages/mitkNrrdTbssImageReader.cpp
	- IODataStructures/TbssImages/mitkNrrdTbssRoiImageReader.cpp
	- IODataStructures/TbssImages/mitkTbssImage.cpp
	- IODataStructures/TbssImages/mitkTbssRoiImage.cpp
	- IODataStructures/TbssImages/mitkNrrdTbssImageWriter.cpp
	- IODataStructures/TbssImages/mitkNrrdTbssRoiImageWriter.cpp
	- IODataStructures/TbssImages/mitkTbssImporter.cpp
	-
	- # Rendering
	- Rendering/mitkTbssImageMapper.cpp
	-
	- #Algorithms
	- Algorithms/mitkTractAnalyzer.cpp
	-)
	-
	-set(H_FILES
	- # DataStructures
	- IODataStructures/TbssImages/mitkTbssImporter.h
	-
	- # Rendering
	- Rendering/mitkTbssImageMapper.h
	-
	- Algorithms/itkRegularizedIVIMLocalVariationImageFilter.h
	- Algorithms/itkRegularizedIVIMReconstructionFilter.h
	- Algorithms/itkRegularizedIVIMReconstructionSingleIteration.h
	-)
	diff --git a/Modules/DiffusionImaging/mitkDiffusionImagingConfigure.h.in b/Modules/DiffusionImaging/mitkDiffusionImagingConfigure.h.in
	deleted file mode 100644
	index ef254c3c8f..0000000000
	--- a/Modules/DiffusionImaging/mitkDiffusionImagingConfigure.h.in
	+++ /dev/null
	@@ -1,4 +0,0 @@
	-#ifndef DIFFUSION_IMAGING_CONFIGURE
	-#define DIFFUSION_IMAGING_CONFIGURE
	-
	-#endif // DIFFUSION_IMAGING_CONFIGURE
	diff --git a/Modules/ModuleList.cmake b/Modules/ModuleList.cmake
	index 789023ab9c..a5e4263022 100644
	--- a/Modules/ModuleList.cmake
	+++ b/Modules/ModuleList.cmake
	@@ -1,89 +1,88 @@
	# The entries in the mitk_modules list must be
	# ordered according to their dependencies.

	set(MITK_MODULES
	Core
	CommandLine
	AppUtil
	RDF
	LegacyIO
	DataTypesExt
	Annotation
	LegacyGL
	AlgorithmsExt
	MapperExt
	DICOMReader
	DICOMReaderServices
	DICOMQI
	DICOMTesting
	SceneSerializationBase
	PlanarFigure
	ImageDenoising
	ImageExtraction
	SceneSerialization
	Gizmo
	GraphAlgorithms
	Multilabel
	Chart
	ImageStatistics
	ContourModel
	SurfaceInterpolation
	Segmentation
	PlanarFigureSegmentation
	QtWidgets
	QtWidgetsExt
	ImageStatisticsUI
	SegmentationUI
	MatchPointRegistration
	MatchPointRegistrationUI
	Classification
	GPGPU
	OpenIGTLink
	IGTBase
	IGT
	CameraCalibration
	OpenCL
	OpenCVVideoSupport
	QtOverlays
	ToFHardware
	ToFProcessing
	ToFUI
	PhotoacousticsHardware
	PhotoacousticsAlgorithms
	PhotoacousticsLib
	US
	USUI
	DicomUI
	Remeshing
	Python
	QtPython
	Persistence
	OpenIGTLinkUI
	IGTUI
	DicomRT
	RTUI
	IOExt
	XNAT
	TubeGraph
	BiophotonicsHardware
	- DiffusionImaging
	- TumorInvasionAnalysis
	+# TumorInvasionAnalysis
	BoundingShape
	RenderWindowManager
	RenderWindowManagerUI
	SemanticRelations
	SemanticRelationsUI
	CEST
	BasicImageProcessing
	ModelFit
	ModelFitUI
	Pharmacokinetics
	PharmacokineticsUI
	DICOMPM
	REST
	RESTService
	)

	if(MITK_ENABLE_PIC_READER)
	list(APPEND MITK_MODULES IpPicSupportIO)
	endif()
	diff --git a/Plugins/PluginList.cmake b/Plugins/PluginList.cmake
	index f874d7dd38..aeec51a9f9 100644
	--- a/Plugins/PluginList.cmake
	+++ b/Plugins/PluginList.cmake
	@@ -1,116 +1,102 @@

	# Plug-ins must be ordered according to their dependencies

	set(MITK_PLUGINS

	org.blueberry.core.runtime:ON
	org.blueberry.core.expressions:OFF
	org.blueberry.core.commands:OFF
	org.blueberry.core.jobs:OFF
	org.blueberry.ui.qt:OFF
	org.blueberry.ui.qt.help:ON
	org.blueberry.ui.qt.log:ON
	org.blueberry.ui.qt.objectinspector:OFF

	#org.blueberry.test:ON
	#org.blueberry.uitest:ON

	#Testing/org.blueberry.core.runtime.tests:ON
	#Testing/org.blueberry.osgi.tests:ON

	org.mitk.core.services:ON
	org.mitk.gui.common:ON
	org.mitk.planarfigure:ON
	org.mitk.core.ext:OFF
	org.mitk.core.jobs:OFF
	org.mitk.gui.qt.application:ON
	org.mitk.gui.qt.coreapplication:OFF
	org.mitk.gui.qt.ext:OFF
	org.mitk.gui.qt.extapplication:OFF
	org.mitk.gui.qt.common:ON
	org.mitk.gui.qt.stdmultiwidgeteditor:ON
	org.mitk.gui.qt.mxnmultiwidgeteditor:OFF
	org.mitk.gui.qt.common.legacy:OFF
	org.mitk.gui.qt.cmdlinemodules:OFF
	org.mitk.gui.qt.chartExample:OFF
	- org.mitk.gui.qt.diffusionimagingapp:OFF
	org.mitk.gui.qt.datamanager:ON
	org.mitk.gui.qt.datamanagerlight:OFF
	org.mitk.gui.qt.datastorageviewertest:OFF
	org.mitk.gui.qt.properties:ON
	org.mitk.gui.qt.basicimageprocessing:OFF
	org.mitk.gui.qt.dicom:OFF
	org.mitk.gui.qt.dicominspector:OFF
	- org.mitk.gui.qt.diffusionimaging:OFF
	- org.mitk.gui.qt.diffusionimaging.connectomics:OFF
	- org.mitk.gui.qt.diffusionimaging.denoising:OFF
	- org.mitk.gui.qt.diffusionimaging.fiberfox:OFF
	- org.mitk.gui.qt.diffusionimaging.fiberprocessing:OFF
	- org.mitk.gui.qt.diffusionimaging.ivim:OFF
	- org.mitk.gui.qt.diffusionimaging.odfpeaks:OFF
	- org.mitk.gui.qt.diffusionimaging.partialvolume:OFF
	- org.mitk.gui.qt.diffusionimaging.preprocessing:OFF
	- org.mitk.gui.qt.diffusionimaging.reconstruction:OFF
	- org.mitk.gui.qt.diffusionimaging.registration:OFF
	- org.mitk.gui.qt.diffusionimaging.tractography:OFF
	- org.mitk.gui.qt.diffusionimaging.python:OFF
	org.mitk.gui.qt.dosevisualization:OFF
	org.mitk.gui.qt.geometrytools:OFF
	org.mitk.gui.qt.igtexamples:OFF
	org.mitk.gui.qt.igttracking:OFF
	org.mitk.gui.qt.lasercontrol:OFF
	org.mitk.gui.qt.openigtlink:OFF
	org.mitk.gui.qt.imagecropper:OFF
	org.mitk.gui.qt.imagenavigator:ON
	org.mitk.gui.qt.viewnavigator:OFF
	org.mitk.gui.qt.materialeditor:OFF
	org.mitk.gui.qt.measurementtoolbox:OFF
	org.mitk.gui.qt.moviemaker:OFF
	org.mitk.gui.qt.pointsetinteraction:OFF
	org.mitk.gui.qt.pointsetinteractionmultispectrum:OFF
	org.mitk.gui.qt.python:OFF
	org.mitk.gui.qt.remeshing:OFF
	org.mitk.gui.qt.segmentation:OFF
	org.mitk.gui.qt.aicpregistration:OFF
	org.mitk.gui.qt.renderwindowmanager:OFF
	org.mitk.gui.qt.semanticrelations:OFF
	org.mitk.gui.qt.toftutorial:OFF
	org.mitk.gui.qt.tofutil:OFF
	org.mitk.gui.qt.tubegraph:OFF
	org.mitk.gui.qt.ugvisualization:OFF
	org.mitk.gui.qt.photoacoustics.pausviewer:OFF
	org.mitk.gui.qt.photoacoustics.pausmotioncompensation:OFF
	org.mitk.gui.qt.photoacoustics.imageprocessing:OFF
	org.mitk.gui.qt.photoacoustics.simulation:OFF
	org.mitk.gui.qt.photoacoustics.spectralunmixing:OFF
	org.mitk.gui.qt.ultrasound:OFF
	org.mitk.gui.qt.volumevisualization:OFF
	org.mitk.gui.qt.eventrecorder:OFF
	org.mitk.gui.qt.xnat:OFF
	org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation:OFF
	org.mitk.gui.qt.spectrocamrecorder:OFF
	org.mitk.gui.qt.classificationsegmentation:OFF
	org.mitk.gui.qt.overlaymanager:OFF
	org.mitk.gui.qt.igt.app.hummelprotocolmeasurements:OFF
	org.mitk.gui.qt.multilabelsegmentation:OFF
	org.mitk.matchpoint.core.helper:OFF
	org.mitk.gui.qt.matchpoint.algorithm.browser:OFF
	org.mitk.gui.qt.matchpoint.algorithm.control:OFF
	org.mitk.gui.qt.matchpoint.algorithm.batch:OFF
	org.mitk.gui.qt.matchpoint.mapper:OFF
	org.mitk.gui.qt.matchpoint.framereg:OFF
	org.mitk.gui.qt.matchpoint.visualizer:OFF
	org.mitk.gui.qt.matchpoint.evaluator:OFF
	org.mitk.gui.qt.matchpoint.manipulator:OFF
	org.mitk.gui.qt.preprocessing.resampling:OFF
	org.mitk.gui.qt.radiomics:OFF
	org.mitk.gui.qt.cest:OFF
	org.mitk.gui.qt.fit.demo:OFF
	org.mitk.gui.qt.fit.inspector:OFF
	org.mitk.gui.qt.fit.genericfitting:OFF
	org.mitk.gui.qt.pharmacokinetics.mri:OFF
	org.mitk.gui.qt.pharmacokinetics.pet:OFF
	org.mitk.gui.qt.pharmacokinetics.simulation:OFF
	org.mitk.gui.qt.pharmacokinetics.curvedescriptor:OFF
	org.mitk.gui.qt.pharmacokinetics.concentration.mri:OFF
	)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/CMakeLists.txt
	deleted file mode 100644
	index e440872661..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/CMakeLists.txt
	+++ /dev/null
	@@ -1,10 +0,0 @@
	-# The project name must correspond to the directory name of your plug-in
	-# and must not contain periods.
	-project(org_mitk_gui_qt_diffusionimaging_connectomics)
	-
	-mitk_create_plugin(
	- SUBPROJECTS MITK-DTI
	- EXPORT_DIRECTIVE DIFFUSIONIMAGING_CONNECTOMICS_EXPORT
	- EXPORTED_INCLUDE_SUFFIXES src
	- MODULE_DEPENDS MitkQtWidgetsExt MitkConnectomics
	-)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/documentation/UserManual/ConnectomicsManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/documentation/UserManual/ConnectomicsManual.dox
	deleted file mode 100644
	index ffeae7d831..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/documentation/UserManual/ConnectomicsManual.dox
	+++ /dev/null
	@@ -1,1421 +0,0 @@
	-/**
	-\page org_mitk_diffusionimagingapp_perspectives_connectomics The Connectomics Perspective
	-
	-\imageMacro{connectomics_perspective.png,"Icon of the Connectomics Perspective",2.00}
	-
	-The connectomics perspective is a collection of views which provide functionality for the work with brain connectivity networks. Currently there exist the following views:
	-
	-\subpage org_mitk_views_connectomicsdata provides network generation either from data or synthetically.
	-
	-\subpage org_mitk_views_connectomicsnetworkoperations provides functionalies to operate and process on networks and other data.
	-
	-\subpage org_mitk_views_connectomicsstatistics provides statistical measures for networks.
	-
	-\subpage org_mitk_views_randomparcellationview provides a method to randomly parcellate a segmentation using different criteria
	-
	-\section org_mitk_diffusionimagingapp_perspectives_connectomicsNetworkRenderingCustomization Network Rendering Customization
	-
	-The rendering of the connectomics networks can be customized by changing the associated properties using the property list. A selection of possible options are:
	-
	-<ul>
	- <li> Connectomics.Rendering.Edges.Filtering - Only render edges above a certain threshold
	- <li> Connectomics.Rendering.Edges.Gradient.Parameter - Color the edges according to certain parameters
	- <li> Connectomics.Rendering.Edges.Radius.Parameter - Change the radius of the edges according to certain parameters
	- <li> Connectomics.Rendering.Nodes.Filtering - Only render nodes above a certain threshold
	- <li> Connectomics.Rendering.Nodes.Gradient.Parameter - Color the nodes according to certain parameters
	- <li> Connectomics.Rendering.Nodes.Radius.Parameter - Change the radius of the nodes according to certain parameters
	- <li> Connectomics.Rendering.Scheme - Switch between the MITK rendering scheme using above properties and the very fast, but less customizable rendering scheme for VTK graphs
	-</ul>
	-
	-\section org_mitk_diffusionimagingapp_perspectives_connectomicsTrouble Troubleshooting
	-
	-No known problems.
	-
	-<B>All other problems.</B><BR>
	-Please report to the MITK mailing list.
	-See http://www.mitk.org/wiki/Mailinglist on how to do this.
	-
	-*/
	-
	-/**
	-\page org_mitk_views_connectomicsdata The Connectomics Network Data View
	-
	-\imageMacro{QmitkConnectomicsDataViewIcon_48.png,"Icon of the Connectomics Network Data View",2.00}
	-
	-This view can be used to create a network from a parcellation and a fiber image as well as to create synthetic networks.
	-
	-\imageMacro{dataview.png,"The user interface",4.85}
	-
	-To create a network select first a parcellation of the brain (e.g. as provided by <a href="http://surfer.nmr.mgh.harvard.edu/">freesurfer</a> ) by CTRL+Leftclick and secondly a fiber image ( as created using a tractography view). Then click on the "Create Network" button.
	-
	-<ul>
	- <li> "Use label of end position of fibers" will create a network containing a node for every label a fiber ends in
	- <li> "Extrapolate label" will avoid creating nodes using FreeSurfer white matter labels and instead extrapolate in which grey matter label the fiber would end
	-</ul>
	-
	-Additionally you have the option to create artificial networks, for testing purposes. Currently choices are:
	-<ul>
	- <li> A regular lattice, where each node is placed in a cubic pattern and only connected to its neighbours
	- <li> A heterogenic sphere, where one node is placed in the center and connected to all nodes on the shell
	- <li> A random network, where nodes are randomly placed on a spherical shell and randomly connected
	-</ul>
	-
	-Parcellation labels lookup table:
	-- 0 = "Unknown"
	-- 1 = "Left-Cerebral-Exterior"
	-- 2 = "Left-Cerebral-White-Matter"
	-- 3 = "Left-Cerebral-Cortex"
	-- 4 = "Left-Lateral-Ventricle"
	-- 5 = "Left-Inf-Lat-Vent"
	-- 6 = "Left-Cerebellum-Exterior"
	-- 7 = "Left-Cerebellum-White-Matter"
	-- 8 = "Left-Cerebellum-Cortex"
	-- 9 = "Left-Thalamus"
	-- 10 = "Left-Thalamus-Proper"
	-- 11 = "Left-Caudate"
	-- 12 = "Left-Putamen"
	-- 13 = "Left-Pallidum"
	-- 14 = "3rd-Ventricle"
	-- 15 = "4th-Ventricle"
	-- 16 = "Brain-Stem"
	-- 17 = "Left-Hippocampus"
	-- 18 = "Left-Amygdala"
	-- 19 = "Left-Insula"
	-- 20 = "Left-Operculum"
	-- 21 = "Line-1"
	-- 22 = "Line-2"
	-- 23 = "Line-3"
	-- 24 = "CSF"
	-- 25 = "Left-Lesion"
	-- 26 = "Left-Accumbens-area"
	-- 27 = "Left-Substancia-Nigra"
	-- 28 = "Left-VentralDC"
	-- 29 = "Left-undetermined"
	-- 30 = "Left-vessel"
	-- 31 = "Left-choroid-plexus"
	-- 32 = "Left-F3orb"
	-- 33 = "Left-lOg"
	-- 34 = "Left-aOg"
	-- 35 = "Left-mOg"
	-- 36 = "Left-pOg"
	-- 37 = "Left-Stellate"
	-- 38 = "Left-Porg"
	-- 39 = "Left-Aorg"
	-- 40 = "Right-Cerebral-Exterior"
	-- 41 = "Right-Cerebral-White-Matter"
	-- 42 = "Right-Cerebral-Cortex"
	-- 43 = "Right-Lateral-Ventricle"
	-- 44 = "Right-Inf-Lat-Vent"
	-- 45 = "Right-Cerebellum-Exterior"
	-- 46 = "Right-Cerebellum-White-Matter"
	-- 47 = "Right-Cerebellum-Cortex"
	-- 48 = "Right-Thalamus"
	-- 49 = "Right-Thalamus-Proper"
	-- 50 = "Right-Caudate"
	-- 51 = "Right-Putamen"
	-- 52 = "Right-Pallidum"
	-- 53 = "Right-Hippocampus"
	-- 54 = "Right-Amygdala"
	-- 55 = "Right-Insula"
	-- 56 = "Right-Operculum"
	-- 57 = "Right-Lesion"
	-- 58 = "Right-Accumbens-area"
	-- 59 = "Right-Substancia-Nigra"
	-- 60 = "Right-VentralDC"
	-- 61 = "Right-undetermined"
	-- 62 = "Right-vessel"
	-- 63 = "Right-choroid-plexus"
	-- 64 = "Right-F3orb"
	-- 65 = "Right-lOg"
	-- 66 = "Right-aOg"
	-- 67 = "Right-mOg"
	-- 68 = "Right-pOg"
	-- 69 = "Right-Stellate"
	-- 70 = "Right-Porg"
	-- 71 = "Right-Aorg"
	-- 72 = "5th-Ventricle"
	-- 73 = "Left-Interior"
	-- 74 = "Right-Interior"
	-- 77 = "WM-hypointensities"
	-- 78 = "Left-WM-hypointensities"
	-- 79 = "Right-WM-hypointensities"
	-- 80 = "non-WM-hypointensities"
	-- 81 = "Left-non-WM-hypointensities"
	-- 82 = "Right-non-WM-hypointensities"
	-- 83 = "Left-F1"
	-- 84 = "Right-F1"
	-- 85 = "Optic-Chiasm"
	-- 192 = "Corpus_Callosum"
	-- 86 = "Left_future_WMSA"
	-- 87 = "Right_future_WMSA"
	-- 88 = "future_WMSA"
	-- 96 = "Left-Amygdala-Anterior"
	-- 97 = "Right-Amygdala-Anterior"
	-- 98 = "Dura"
	-- 100 = "Left-wm-intensity-abnormality"
	-- 101 = "Left-caudate-intensity-abnormality"
	-- 102 = "Left-putamen-intensity-abnormality"
	-- 103 = "Left-accumbens-intensity-abnormality"
	-- 104 = "Left-pallidum-intensity-abnormality"
	-- 105 = "Left-amygdala-intensity-abnormality"
	-- 106 = "Left-hippocampus-intensity-abnormality"
	-- 107 = "Left-thalamus-intensity-abnormality"
	-- 108 = "Left-VDC-intensity-abnormality"
	-- 109 = "Right-wm-intensity-abnormality"
	-- 110 = "Right-caudate-intensity-abnormality"
	-- 111 = "Right-putamen-intensity-abnormality"
	-- 112 = "Right-accumbens-intensity-abnormality"
	-- 113 = "Right-pallidum-intensity-abnormality"
	-- 114 = "Right-amygdala-intensity-abnormality"
	-- 115 = "Right-hippocampus-intensity-abnormality"
	-- 116 = "Right-thalamus-intensity-abnormality"
	-- 117 = "Right-VDC-intensity-abnormality"
	-- 118 = "Epidermis"
	-- 119 = "Conn-Tissue"
	-- 120 = "SC-Fat-Muscle"
	-- 121 = "Cranium"
	-- 122 = "CSF-SA"
	-- 123 = "Muscle"
	-- 124 = "Ear"
	-- 125 = "Adipose"
	-- 126 = "Spinal-Cord"
	-- 127 = "Soft-Tissue"
	-- 128 = "Nerve"
	-- 129 = "Bone"
	-- 130 = "Air"
	-- 131 = "Orbital-Fat"
	-- 132 = "Tongue"
	-- 133 = "Nasal-Structures"
	-- 134 = "Globe"
	-- 135 = "Teeth"
	-- 136 = "Left-Caudate-Putamen"
	-- 137 = "Right-Caudate-Putamen"
	-- 138 = "Left-Claustrum"
	-- 139 = "Right-Claustrum"
	-- 140 = "Cornea"
	-- 142 = "Diploe"
	-- 143 = "Vitreous-Humor"
	-- 144 = "Lens"
	-- 145 = "Aqueous-Humor"
	-- 146 = "Outer-Table"
	-- 147 = "Inner-Table"
	-- 148 = "Periosteum"
	-- 149 = "Endosteum"
	-- 150 = "R-C-S"
	-- 151 = "Iris"
	-- 152 = "SC-Adipose-Muscle"
	-- 153 = "SC-Tissue"
	-- 154 = "Orbital-Adipose"
	-- 155 = "Left-IntCapsule-Ant"
	-- 156 = "Right-IntCapsule-Ant"
	-- 157 = "Left-IntCapsule-Pos"
	-- 158 = "Right-IntCapsule-Pos"
	-- 159 = "Left-Cerebral-WM-unmyelinated"
	-- 160 = "Right-Cerebral-WM-unmyelinated"
	-- 161 = "Left-Cerebral-WM-myelinated"
	-- 162 = "Right-Cerebral-WM-myelinated"
	-- 163 = "Left-Subcortical-Gray-Matter"
	-- 164 = "Right-Subcortical-Gray-Matter"
	-- 165 = "Skull"
	-- 166 = "Posterior-fossa"
	-- 167 = "Scalp"
	-- 168 = "Hematoma"
	-- 169 = "Left-Basal-Ganglia"
	-- 176 = "Right-Basal-Ganglia"
	-- 170 = "brainstem"
	-- 171 = "DCG"
	-- 172 = "Vermis"
	-- 173 = "Midbrain"
	-- 174 = "Pons"
	-- 175 = "Medulla"
	-- 180 = "Left-Cortical-Dysplasia"
	-- 181 = "Right-Cortical-Dysplasia"
	-- 193 = "Left-hippocampal_fissure"
	-- 194 = "Left-CADG-head"
	-- 195 = "Left-subiculum"
	-- 196 = "Left-fimbria"
	-- 197 = "Right-hippocampal_fissure"
	-- 198 = "Right-CADG-head"
	-- 199 = "Right-subiculum"
	-- 200 = "Right-fimbria"
	-- 201 = "alveus"
	-- 202 = "perforant_pathway"
	-- 203 = "parasubiculum"
	-- 204 = "presubiculum"
	-- 205 = "subiculum"
	-- 206 = "CA1"
	-- 207 = "CA2"
	-- 208 = "CA3"
	-- 209 = "CA4"
	-- 210 = "GC-ML-DG"
	-- 211 = "HATA"
	-- 212 = "fimbria"
	-- 213 = "lateral_ventricle"
	-- 214 = "molecular_layer_HP"
	-- 215 = "hippocampal_fissure"
	-- 216 = "entorhinal_cortex"
	-- 217 = "molecular_layer_subiculum"
	-- 218 = "Amygdala"
	-- 219 = "Cerebral_White_Matter"
	-- 220 = "Cerebral_Cortex"
	-- 221 = "Inf_Lat_Vent"
	-- 222 = "Perirhinal"
	-- 223 = "Cerebral_White_Matter_Edge"
	-- 224 = "Background"
	-- 225 = "Ectorhinal"
	-- 226 = "HP_tail"
	-- 250 = "Fornix"
	-- 251 = "CC_Posterior"
	-- 252 = "CC_Mid_Posterior"
	-- 253 = "CC_Central"
	-- 254 = "CC_Mid_Anterior"
	-- 255 = "CC_Anterior"
	-- 256 = "Voxel-Unchanged"
	-- 331 = "Aorta"
	-- 332 = "Left-Common-IliacA"
	-- 333 = "Right-Common-IliacA"
	-- 334 = "Left-External-IliacA"
	-- 335 = "Right-External-IliacA"
	-- 336 = "Left-Internal-IliacA"
	-- 337 = "Right-Internal-IliacA"
	-- 338 = "Left-Lateral-SacralA"
	-- 339 = "Right-Lateral-SacralA"
	-- 340 = "Left-ObturatorA"
	-- 341 = "Right-ObturatorA"
	-- 342 = "Left-Internal-PudendalA"
	-- 343 = "Right-Internal-PudendalA"
	-- 344 = "Left-UmbilicalA"
	-- 345 = "Right-UmbilicalA"
	-- 346 = "Left-Inf-RectalA"
	-- 347 = "Right-Inf-RectalA"
	-- 348 = "Left-Common-IliacV"
	-- 349 = "Right-Common-IliacV"
	-- 350 = "Left-External-IliacV"
	-- 351 = "Right-External-IliacV"
	-- 352 = "Left-Internal-IliacV"
	-- 353 = "Right-Internal-IliacV"
	-- 354 = "Left-ObturatorV"
	-- 355 = "Right-ObturatorV"
	-- 356 = "Left-Internal-PudendalV"
	-- 357 = "Right-Internal-PudendalV"
	-- 358 = "Pos-Lymph"
	-- 359 = "Neg-Lymph"
	-- 400 = "V1"
	-- 401 = "V2"
	-- 402 = "BA44"
	-- 403 = "BA45"
	-- 404 = "BA4a"
	-- 405 = "BA4p"
	-- 406 = "BA6"
	-- 407 = "BA2"
	-- 408 = "BA1_old"
	-- 409 = "BAun2"
	-- 410 = "BA1"
	-- 411 = "BA2b"
	-- 412 = "BA3a"
	-- 413 = "BA3b"
	-- 414 = "MT"
	-- 415 = "AIPS_AIP_l"
	-- 416 = "AIPS_AIP_r"
	-- 417 = "AIPS_VIP_l"
	-- 418 = "AIPS_VIP_r"
	-- 419 = "IPL_PFcm_l"
	-- 420 = "IPL_PFcm_r"
	-- 421 = "IPL_PF_l"
	-- 422 = "IPL_PFm_l"
	-- 423 = "IPL_PFm_r"
	-- 424 = "IPL_PFop_l"
	-- 425 = "IPL_PFop_r"
	-- 426 = "IPL_PF_r"
	-- 427 = "IPL_PFt_l"
	-- 428 = "IPL_PFt_r"
	-- 429 = "IPL_PGa_l"
	-- 430 = "IPL_PGa_r"
	-- 431 = "IPL_PGp_l"
	-- 432 = "IPL_PGp_r"
	-- 433 = "Visual_V3d_l"
	-- 434 = "Visual_V3d_r"
	-- 435 = "Visual_V4_l"
	-- 436 = "Visual_V4_r"
	-- 437 = "Visual_V5_b"
	-- 438 = "Visual_VP_l"
	-- 439 = "Visual_VP_r"
	-- 498 = "wmsa"
	-- 499 = "other_wmsa"
	-- 500 = "right_CA2_3"
	-- 501 = "right_alveus"
	-- 502 = "right_CA1"
	-- 503 = "right_fimbria"
	-- 504 = "right_presubiculum"
	-- 505 = "right_hippocampal_fissure"
	-- 506 = "right_CA4_DG"
	-- 507 = "right_subiculum"
	-- 508 = "right_fornix"
	-- 550 = "left_CA2_3"
	-- 551 = "left_alveus"
	-- 552 = "left_CA1"
	-- 553 = "left_fimbria"
	-- 554 = "left_presubiculum"
	-- 555 = "left_hippocampal_fissure"
	-- 556 = "left_CA4_DG"
	-- 557 = "left_subiculum"
	-- 558 = "left_fornix"
	-- 600 = "Tumor"
	-- 601 = "Cbm_Left_I_IV"
	-- 602 = "Cbm_Right_I_IV"
	-- 603 = "Cbm_Left_V"
	-- 604 = "Cbm_Right_V"
	-- 605 = "Cbm_Left_VI"
	-- 606 = "Cbm_Vermis_VI"
	-- 607 = "Cbm_Right_VI"
	-- 608 = "Cbm_Left_CrusI"
	-- 609 = "Cbm_Vermis_CrusI"
	-- 610 = "Cbm_Right_CrusI"
	-- 611 = "Cbm_Left_CrusII"
	-- 612 = "Cbm_Vermis_CrusII"
	-- 613 = "Cbm_Right_CrusII"
	-- 614 = "Cbm_Left_VIIb"
	-- 615 = "Cbm_Vermis_VIIb"
	-- 616 = "Cbm_Right_VIIb"
	-- 617 = "Cbm_Left_VIIIa"
	-- 618 = "Cbm_Vermis_VIIIa"
	-- 619 = "Cbm_Right_VIIIa"
	-- 620 = "Cbm_Left_VIIIb"
	-- 621 = "Cbm_Vermis_VIIIb"
	-- 622 = "Cbm_Right_VIIIb"
	-- 623 = "Cbm_Left_IX"
	-- 624 = "Cbm_Vermis_IX"
	-- 625 = "Cbm_Right_IX"
	-- 626 = "Cbm_Left_X"
	-- 627 = "Cbm_Vermis_X"
	-- 628 = "Cbm_Right_X"
	-- 640 = "Cbm_Right_I_V_med"
	-- 641 = "Cbm_Right_I_V_mid"
	-- 642 = "Cbm_Right_VI_med"
	-- 643 = "Cbm_Right_VI_mid"
	-- 644 = "Cbm_Right_VI_lat"
	-- 645 = "Cbm_Right_CrusI_med"
	-- 646 = "Cbm_Right_CrusI_mid"
	-- 647 = "Cbm_Right_CrusI_lat"
	-- 648 = "Cbm_Right_CrusII_med"
	-- 649 = "Cbm_Right_CrusII_mid"
	-- 650 = "Cbm_Right_CrusII_lat"
	-- 651 = "Cbm_Right_7med"
	-- 652 = "Cbm_Right_7mid"
	-- 653 = "Cbm_Right_7lat"
	-- 654 = "Cbm_Right_8med"
	-- 655 = "Cbm_Right_8mid"
	-- 656 = "Cbm_Right_8lat"
	-- 657 = "Cbm_Right_PUNs"
	-- 658 = "Cbm_Right_TONs"
	-- 659 = "Cbm_Right_FLOs"
	-- 660 = "Cbm_Left_I_V_med"
	-- 661 = "Cbm_Left_I_V_mid"
	-- 662 = "Cbm_Left_VI_med"
	-- 663 = "Cbm_Left_VI_mid"
	-- 664 = "Cbm_Left_VI_lat"
	-- 665 = "Cbm_Left_CrusI_med"
	-- 666 = "Cbm_Left_CrusI_mid"
	-- 667 = "Cbm_Left_CrusI_lat"
	-- 668 = "Cbm_Left_CrusII_med"
	-- 669 = "Cbm_Left_CrusII_mid"
	-- 670 = "Cbm_Left_CrusII_lat"
	-- 671 = "Cbm_Left_7med"
	-- 672 = "Cbm_Left_7mid"
	-- 673 = "Cbm_Left_7lat"
	-- 674 = "Cbm_Left_8med"
	-- 675 = "Cbm_Left_8mid"
	-- 676 = "Cbm_Left_8lat"
	-- 677 = "Cbm_Left_PUNs"
	-- 678 = "Cbm_Left_TONs"
	-- 679 = "Cbm_Left_FLOs"
	-- 701 = "CSF-FSL-FAST"
	-- 702 = "GrayMatter-FSL-FAST"
	-- 703 = "WhiteMatter-FSL-FAST"
	-- 999 = "SUSPICIOUS"
	-- 1000 = "ctx-lh-unknown"
	-- 1001 = "ctx-lh-bankssts"
	-- 1002 = "ctx-lh-caudalanteriorcingulate"
	-- 1003 = "ctx-lh-caudalmiddlefrontal"
	-- 1004 = "ctx-lh-corpuscallosum"
	-- 1005 = "ctx-lh-cuneus"
	-- 1006 = "ctx-lh-entorhinal"
	-- 1007 = "ctx-lh-fusiform"
	-- 1008 = "ctx-lh-inferiorparietal"
	-- 1009 = "ctx-lh-inferiortemporal"
	-- 1010 = "ctx-lh-isthmuscingulate"
	-- 1011 = "ctx-lh-lateraloccipital"
	-- 1012 = "ctx-lh-lateralorbitofrontal"
	-- 1013 = "ctx-lh-lingual"
	-- 1014 = "ctx-lh-medialorbitofrontal"
	-- 1015 = "ctx-lh-middletemporal"
	-- 1016 = "ctx-lh-parahippocampal"
	-- 1017 = "ctx-lh-paracentral"
	-- 1018 = "ctx-lh-parsopercularis"
	-- 1019 = "ctx-lh-parsorbitalis"
	-- 1020 = "ctx-lh-parstriangularis"
	-- 1021 = "ctx-lh-pericalcarine"
	-- 1022 = "ctx-lh-postcentral"
	-- 1023 = "ctx-lh-posteriorcingulate"
	-- 1024 = "ctx-lh-precentral"
	-- 1025 = "ctx-lh-precuneus"
	-- 1026 = "ctx-lh-rostralanteriorcingulate"
	-- 1027 = "ctx-lh-rostralmiddlefrontal"
	-- 1028 = "ctx-lh-superiorfrontal"
	-- 1029 = "ctx-lh-superiorparietal"
	-- 1030 = "ctx-lh-superiortemporal"
	-- 1031 = "ctx-lh-supramarginal"
	-- 1032 = "ctx-lh-frontalpole"
	-- 1033 = "ctx-lh-temporalpole"
	-- 1034 = "ctx-lh-transversetemporal"
	-- 1035 = "ctx-lh-insula"
	-- 2000 = "ctx-rh-unknown"
	-- 2001 = "ctx-rh-bankssts"
	-- 2002 = "ctx-rh-caudalanteriorcingulate"
	-- 2003 = "ctx-rh-caudalmiddlefrontal"
	-- 2004 = "ctx-rh-corpuscallosum"
	-- 2005 = "ctx-rh-cuneus"
	-- 2006 = "ctx-rh-entorhinal"
	-- 2007 = "ctx-rh-fusiform"
	-- 2008 = "ctx-rh-inferiorparietal"
	-- 2009 = "ctx-rh-inferiortemporal"
	-- 2010 = "ctx-rh-isthmuscingulate"
	-- 2011 = "ctx-rh-lateraloccipital"
	-- 2012 = "ctx-rh-lateralorbitofrontal"
	-- 2013 = "ctx-rh-lingual"
	-- 2014 = "ctx-rh-medialorbitofrontal"
	-- 2015 = "ctx-rh-middletemporal"
	-- 2016 = "ctx-rh-parahippocampal"
	-- 2017 = "ctx-rh-paracentral"
	-- 2018 = "ctx-rh-parsopercularis"
	-- 2019 = "ctx-rh-parsorbitalis"
	-- 2020 = "ctx-rh-parstriangularis"
	-- 2021 = "ctx-rh-pericalcarine"
	-- 2022 = "ctx-rh-postcentral"
	-- 2023 = "ctx-rh-posteriorcingulate"
	-- 2024 = "ctx-rh-precentral"
	-- 2025 = "ctx-rh-precuneus"
	-- 2026 = "ctx-rh-rostralanteriorcingulate"
	-- 2027 = "ctx-rh-rostralmiddlefrontal"
	-- 2028 = "ctx-rh-superiorfrontal"
	-- 2029 = "ctx-rh-superiorparietal"
	-- 2030 = "ctx-rh-superiortemporal"
	-- 2031 = "ctx-rh-supramarginal"
	-- 2032 = "ctx-rh-frontalpole"
	-- 2033 = "ctx-rh-temporalpole"
	-- 2034 = "ctx-rh-transversetemporal"
	-- 2035 = "ctx-rh-insula"
	-- 3000 = "wm-lh-unknown"
	-- 3001 = "wm-lh-bankssts"
	-- 3002 = "wm-lh-caudalanteriorcingulate"
	-- 3003 = "wm-lh-caudalmiddlefrontal"
	-- 3004 = "wm-lh-corpuscallosum"
	-- 3005 = "wm-lh-cuneus"
	-- 3006 = "wm-lh-entorhinal"
	-- 3007 = "wm-lh-fusiform"
	-- 3008 = "wm-lh-inferiorparietal"
	-- 3009 = "wm-lh-inferiortemporal"
	-- 3010 = "wm-lh-isthmuscingulate"
	-- 3011 = "wm-lh-lateraloccipital"
	-- 3012 = "wm-lh-lateralorbitofrontal"
	-- 3013 = "wm-lh-lingual"
	-- 3014 = "wm-lh-medialorbitofrontal"
	-- 3015 = "wm-lh-middletemporal"
	-- 3016 = "wm-lh-parahippocampal"
	-- 3017 = "wm-lh-paracentral"
	-- 3018 = "wm-lh-parsopercularis"
	-- 3019 = "wm-lh-parsorbitalis"
	-- 3020 = "wm-lh-parstriangularis"
	-- 3021 = "wm-lh-pericalcarine"
	-- 3022 = "wm-lh-postcentral"
	-- 3023 = "wm-lh-posteriorcingulate"
	-- 3024 = "wm-lh-precentral"
	-- 3025 = "wm-lh-precuneus"
	-- 3026 = "wm-lh-rostralanteriorcingulate"
	-- 3027 = "wm-lh-rostralmiddlefrontal"
	-- 3028 = "wm-lh-superiorfrontal"
	-- 3029 = "wm-lh-superiorparietal"
	-- 3030 = "wm-lh-superiortemporal"
	-- 3031 = "wm-lh-supramarginal"
	-- 3032 = "wm-lh-frontalpole"
	-- 3033 = "wm-lh-temporalpole"
	-- 3034 = "wm-lh-transversetemporal"
	-- 3035 = "wm-lh-insula"
	-- 4000 = "wm-rh-unknown"
	-- 4001 = "wm-rh-bankssts"
	-- 4002 = "wm-rh-caudalanteriorcingulate"
	-- 4003 = "wm-rh-caudalmiddlefrontal"
	-- 4004 = "wm-rh-corpuscallosum"
	-- 4005 = "wm-rh-cuneus"
	-- 4006 = "wm-rh-entorhinal"
	-- 4007 = "wm-rh-fusiform"
	-- 4008 = "wm-rh-inferiorparietal"
	-- 4009 = "wm-rh-inferiortemporal"
	-- 4010 = "wm-rh-isthmuscingulate"
	-- 4011 = "wm-rh-lateraloccipital"
	-- 4012 = "wm-rh-lateralorbitofrontal"
	-- 4013 = "wm-rh-lingual"
	-- 4014 = "wm-rh-medialorbitofrontal"
	-- 4015 = "wm-rh-middletemporal"
	-- 4016 = "wm-rh-parahippocampal"
	-- 4017 = "wm-rh-paracentral"
	-- 4018 = "wm-rh-parsopercularis"
	-- 4019 = "wm-rh-parsorbitalis"
	-- 4020 = "wm-rh-parstriangularis"
	-- 4021 = "wm-rh-pericalcarine"
	-- 4022 = "wm-rh-postcentral"
	-- 4023 = "wm-rh-posteriorcingulate"
	-- 4024 = "wm-rh-precentral"
	-- 4025 = "wm-rh-precuneus"
	-- 4026 = "wm-rh-rostralanteriorcingulate"
	-- 4027 = "wm-rh-rostralmiddlefrontal"
	-- 4028 = "wm-rh-superiorfrontal"
	-- 4029 = "wm-rh-superiorparietal"
	-- 4030 = "wm-rh-superiortemporal"
	-- 4031 = "wm-rh-supramarginal"
	-- 4032 = "wm-rh-frontalpole"
	-- 4033 = "wm-rh-temporalpole"
	-- 4034 = "wm-rh-transversetemporal"
	-- 4035 = "wm-rh-insula"
	-- 1100 = "ctx-lh-Unknown"
	-- 1101 = "ctx-lh-Corpus_callosum"
	-- 1102 = "ctx-lh-G_and_S_Insula_ONLY_AVERAGE"
	-- 1103 = "ctx-lh-G_cingulate-Isthmus"
	-- 1104 = "ctx-lh-G_cingulate-Main_part"
	-- 1200 = "ctx-lh-G_cingulate-caudal_ACC"
	-- 1201 = "ctx-lh-G_cingulate-rostral_ACC"
	-- 1202 = "ctx-lh-G_cingulate-posterior"
	-- 1205 = "ctx-lh-S_cingulate-caudal_ACC"
	-- 1206 = "ctx-lh-S_cingulate-rostral_ACC"
	-- 1207 = "ctx-lh-S_cingulate-posterior"
	-- 1210 = "ctx-lh-S_pericallosal-caudal"
	-- 1211 = "ctx-lh-S_pericallosal-rostral"
	-- 1212 = "ctx-lh-S_pericallosal-posterior"
	-- 1105 = "ctx-lh-G_cuneus"
	-- 1106 = "ctx-lh-G_frontal_inf-Opercular_part"
	-- 1107 = "ctx-lh-G_frontal_inf-Orbital_part"
	-- 1108 = "ctx-lh-G_frontal_inf-Triangular_part"
	-- 1109 = "ctx-lh-G_frontal_middle"
	-- 1110 = "ctx-lh-G_frontal_superior"
	-- 1111 = "ctx-lh-G_frontomarginal"
	-- 1112 = "ctx-lh-G_insular_long"
	-- 1113 = "ctx-lh-G_insular_short"
	-- 1114 = "ctx-lh-G_and_S_occipital_inferior"
	-- 1115 = "ctx-lh-G_occipital_middle"
	-- 1116 = "ctx-lh-G_occipital_superior"
	-- 1117 = "ctx-lh-G_occipit-temp_lat-Or_fusiform"
	-- 1118 = "ctx-lh-G_occipit-temp_med-Lingual_part"
	-- 1119 = "ctx-lh-G_occipit-temp_med-Parahippocampal_part"
	-- 1120 = "ctx-lh-G_orbital"
	-- 1121 = "ctx-lh-G_paracentral"
	-- 1122 = "ctx-lh-G_parietal_inferior-Angular_part"
	-- 1123 = "ctx-lh-G_parietal_inferior-Supramarginal_part"
	-- 1124 = "ctx-lh-G_parietal_superior"
	-- 1125 = "ctx-lh-G_postcentral"
	-- 1126 = "ctx-lh-G_precentral"
	-- 1127 = "ctx-lh-G_precuneus"
	-- 1128 = "ctx-lh-G_rectus"
	-- 1129 = "ctx-lh-G_subcallosal"
	-- 1130 = "ctx-lh-G_subcentral"
	-- 1131 = "ctx-lh-G_temporal_inferior"
	-- 1132 = "ctx-lh-G_temporal_middle"
	-- 1133 = "ctx-lh-G_temp_sup-G_temp_transv_and_interm_S"
	-- 1134 = "ctx-lh-G_temp_sup-Lateral_aspect"
	-- 1135 = "ctx-lh-G_temp_sup-Planum_polare"
	-- 1136 = "ctx-lh-G_temp_sup-Planum_tempolare"
	-- 1137 = "ctx-lh-G_and_S_transverse_frontopolar"
	-- 1138 = "ctx-lh-Lat_Fissure-ant_sgt-ramus_horizontal"
	-- 1139 = "ctx-lh-Lat_Fissure-ant_sgt-ramus_vertical"
	-- 1140 = "ctx-lh-Lat_Fissure-post_sgt"
	-- 1141 = "ctx-lh-Medial_wall"
	-- 1142 = "ctx-lh-Pole_occipital"
	-- 1143 = "ctx-lh-Pole_temporal"
	-- 1144 = "ctx-lh-S_calcarine"
	-- 1145 = "ctx-lh-S_central"
	-- 1146 = "ctx-lh-S_central_insula"
	-- 1147 = "ctx-lh-S_cingulate-Main_part_and_Intracingulate"
	-- 1148 = "ctx-lh-S_cingulate-Marginalis_part"
	-- 1149 = "ctx-lh-S_circular_insula_anterior"
	-- 1150 = "ctx-lh-S_circular_insula_inferior"
	-- 1151 = "ctx-lh-S_circular_insula_superior"
	-- 1152 = "ctx-lh-S_collateral_transverse_ant"
	-- 1153 = "ctx-lh-S_collateral_transverse_post"
	-- 1154 = "ctx-lh-S_frontal_inferior"
	-- 1155 = "ctx-lh-S_frontal_middle"
	-- 1156 = "ctx-lh-S_frontal_superior"
	-- 1157 = "ctx-lh-S_frontomarginal"
	-- 1158 = "ctx-lh-S_intermedius_primus-Jensen"
	-- 1159 = "ctx-lh-S_intraparietal-and_Parietal_transverse"
	-- 1160 = "ctx-lh-S_occipital_anterior"
	-- 1161 = "ctx-lh-S_occipital_middle_and_Lunatus"
	-- 1162 = "ctx-lh-S_occipital_superior_and_transversalis"
	-- 1163 = "ctx-lh-S_occipito-temporal_lateral"
	-- 1164 = "ctx-lh-S_occipito-temporal_medial_and_S_Lingual"
	-- 1165 = "ctx-lh-S_orbital-H_shapped"
	-- 1166 = "ctx-lh-S_orbital_lateral"
	-- 1167 = "ctx-lh-S_orbital_medial-Or_olfactory"
	-- 1168 = "ctx-lh-S_paracentral"
	-- 1169 = "ctx-lh-S_parieto_occipital"
	-- 1170 = "ctx-lh-S_pericallosal"
	-- 1171 = "ctx-lh-S_postcentral"
	-- 1172 = "ctx-lh-S_precentral-Inferior-part"
	-- 1173 = "ctx-lh-S_precentral-Superior-part"
	-- 1174 = "ctx-lh-S_subcentral_ant"
	-- 1175 = "ctx-lh-S_subcentral_post"
	-- 1176 = "ctx-lh-S_suborbital"
	-- 1177 = "ctx-lh-S_subparietal"
	-- 1178 = "ctx-lh-S_supracingulate"
	-- 1179 = "ctx-lh-S_temporal_inferior"
	-- 1180 = "ctx-lh-S_temporal_superior"
	-- 1181 = "ctx-lh-S_temporal_transverse"
	-- 2100 = "ctx-rh-Unknown"
	-- 2101 = "ctx-rh-Corpus_callosum"
	-- 2102 = "ctx-rh-G_and_S_Insula_ONLY_AVERAGE"
	-- 2103 = "ctx-rh-G_cingulate-Isthmus"
	-- 2104 = "ctx-rh-G_cingulate-Main_part"
	-- 2105 = "ctx-rh-G_cuneus"
	-- 2106 = "ctx-rh-G_frontal_inf-Opercular_part"
	-- 2107 = "ctx-rh-G_frontal_inf-Orbital_part"
	-- 2108 = "ctx-rh-G_frontal_inf-Triangular_part"
	-- 2109 = "ctx-rh-G_frontal_middle"
	-- 2110 = "ctx-rh-G_frontal_superior"
	-- 2111 = "ctx-rh-G_frontomarginal"
	-- 2112 = "ctx-rh-G_insular_long"
	-- 2113 = "ctx-rh-G_insular_short"
	-- 2114 = "ctx-rh-G_and_S_occipital_inferior"
	-- 2115 = "ctx-rh-G_occipital_middle"
	-- 2116 = "ctx-rh-G_occipital_superior"
	-- 2117 = "ctx-rh-G_occipit-temp_lat-Or_fusiform"
	-- 2118 = "ctx-rh-G_occipit-temp_med-Lingual_part"
	-- 2119 = "ctx-rh-G_occipit-temp_med-Parahippocampal_part"
	-- 2120 = "ctx-rh-G_orbital"
	-- 2121 = "ctx-rh-G_paracentral"
	-- 2122 = "ctx-rh-G_parietal_inferior-Angular_part"
	-- 2123 = "ctx-rh-G_parietal_inferior-Supramarginal_part"
	-- 2124 = "ctx-rh-G_parietal_superior"
	-- 2125 = "ctx-rh-G_postcentral"
	-- 2126 = "ctx-rh-G_precentral"
	-- 2127 = "ctx-rh-G_precuneus"
	-- 2128 = "ctx-rh-G_rectus"
	-- 2129 = "ctx-rh-G_subcallosal"
	-- 2130 = "ctx-rh-G_subcentral"
	-- 2131 = "ctx-rh-G_temporal_inferior"
	-- 2132 = "ctx-rh-G_temporal_middle"
	-- 2133 = "ctx-rh-G_temp_sup-G_temp_transv_and_interm_S"
	-- 2134 = "ctx-rh-G_temp_sup-Lateral_aspect"
	-- 2135 = "ctx-rh-G_temp_sup-Planum_polare"
	-- 2136 = "ctx-rh-G_temp_sup-Planum_tempolare"
	-- 2137 = "ctx-rh-G_and_S_transverse_frontopolar"
	-- 2138 = "ctx-rh-Lat_Fissure-ant_sgt-ramus_horizontal"
	-- 2139 = "ctx-rh-Lat_Fissure-ant_sgt-ramus_vertical"
	-- 2140 = "ctx-rh-Lat_Fissure-post_sgt"
	-- 2141 = "ctx-rh-Medial_wall"
	-- 2142 = "ctx-rh-Pole_occipital"
	-- 2143 = "ctx-rh-Pole_temporal"
	-- 2144 = "ctx-rh-S_calcarine"
	-- 2145 = "ctx-rh-S_central"
	-- 2146 = "ctx-rh-S_central_insula"
	-- 2147 = "ctx-rh-S_cingulate-Main_part_and_Intracingulate"
	-- 2148 = "ctx-rh-S_cingulate-Marginalis_part"
	-- 2149 = "ctx-rh-S_circular_insula_anterior"
	-- 2150 = "ctx-rh-S_circular_insula_inferior"
	-- 2151 = "ctx-rh-S_circular_insula_superior"
	-- 2152 = "ctx-rh-S_collateral_transverse_ant"
	-- 2153 = "ctx-rh-S_collateral_transverse_post"
	-- 2154 = "ctx-rh-S_frontal_inferior"
	-- 2155 = "ctx-rh-S_frontal_middle"
	-- 2156 = "ctx-rh-S_frontal_superior"
	-- 2157 = "ctx-rh-S_frontomarginal"
	-- 2158 = "ctx-rh-S_intermedius_primus-Jensen"
	-- 2159 = "ctx-rh-S_intraparietal-and_Parietal_transverse"
	-- 2160 = "ctx-rh-S_occipital_anterior"
	-- 2161 = "ctx-rh-S_occipital_middle_and_Lunatus"
	-- 2162 = "ctx-rh-S_occipital_superior_and_transversalis"
	-- 2163 = "ctx-rh-S_occipito-temporal_lateral"
	-- 2164 = "ctx-rh-S_occipito-temporal_medial_and_S_Lingual"
	-- 2165 = "ctx-rh-S_orbital-H_shapped"
	-- 2166 = "ctx-rh-S_orbital_lateral"
	-- 2167 = "ctx-rh-S_orbital_medial-Or_olfactory"
	-- 2168 = "ctx-rh-S_paracentral"
	-- 2169 = "ctx-rh-S_parieto_occipital"
	-- 2170 = "ctx-rh-S_pericallosal"
	-- 2171 = "ctx-rh-S_postcentral"
	-- 2172 = "ctx-rh-S_precentral-Inferior-part"
	-- 2173 = "ctx-rh-S_precentral-Superior-part"
	-- 2174 = "ctx-rh-S_subcentral_ant"
	-- 2175 = "ctx-rh-S_subcentral_post"
	-- 2176 = "ctx-rh-S_suborbital"
	-- 2177 = "ctx-rh-S_subparietal"
	-- 2178 = "ctx-rh-S_supracingulate"
	-- 2179 = "ctx-rh-S_temporal_inferior"
	-- 2180 = "ctx-rh-S_temporal_superior"
	-- 2181 = "ctx-rh-S_temporal_transverse"
	-- 2200 = "ctx-rh-G_cingulate-caudal_ACC"
	-- 2201 = "ctx-rh-G_cingulate-rostral_ACC"
	-- 2202 = "ctx-rh-G_cingulate-posterior"
	-- 2205 = "ctx-rh-S_cingulate-caudal_ACC"
	-- 2206 = "ctx-rh-S_cingulate-rostral_ACC"
	-- 2207 = "ctx-rh-S_cingulate-posterior"
	-- 2210 = "ctx-rh-S_pericallosal-caudal"
	-- 2211 = "ctx-rh-S_pericallosal-rostral"
	-- 2212 = "ctx-rh-S_pericallosal-posterior"
	-- 3100 = "wm-lh-Unknown"
	-- 3101 = "wm-lh-Corpus_callosum"
	-- 3102 = "wm-lh-G_and_S_Insula_ONLY_AVERAGE"
	-- 3103 = "wm-lh-G_cingulate-Isthmus"
	-- 3104 = "wm-lh-G_cingulate-Main_part"
	-- 3105 = "wm-lh-G_cuneus"
	-- 3106 = "wm-lh-G_frontal_inf-Opercular_part"
	-- 3107 = "wm-lh-G_frontal_inf-Orbital_part"
	-- 3108 = "wm-lh-G_frontal_inf-Triangular_part"
	-- 3109 = "wm-lh-G_frontal_middle"
	-- 3110 = "wm-lh-G_frontal_superior"
	-- 3111 = "wm-lh-G_frontomarginal"
	-- 3112 = "wm-lh-G_insular_long"
	-- 3113 = "wm-lh-G_insular_short"
	-- 3114 = "wm-lh-G_and_S_occipital_inferior"
	-- 3115 = "wm-lh-G_occipital_middle"
	-- 3116 = "wm-lh-G_occipital_superior"
	-- 3117 = "wm-lh-G_occipit-temp_lat-Or_fusiform"
	-- 3118 = "wm-lh-G_occipit-temp_med-Lingual_part"
	-- 3119 = "wm-lh-G_occipit-temp_med-Parahippocampal_part"
	-- 3120 = "wm-lh-G_orbital"
	-- 3121 = "wm-lh-G_paracentral"
	-- 3122 = "wm-lh-G_parietal_inferior-Angular_part"
	-- 3123 = "wm-lh-G_parietal_inferior-Supramarginal_part"
	-- 3124 = "wm-lh-G_parietal_superior"
	-- 3125 = "wm-lh-G_postcentral"
	-- 3126 = "wm-lh-G_precentral"
	-- 3127 = "wm-lh-G_precuneus"
	-- 3128 = "wm-lh-G_rectus"
	-- 3129 = "wm-lh-G_subcallosal"
	-- 3130 = "wm-lh-G_subcentral"
	-- 3131 = "wm-lh-G_temporal_inferior"
	-- 3132 = "wm-lh-G_temporal_middle"
	-- 3133 = "wm-lh-G_temp_sup-G_temp_transv_and_interm_S"
	-- 3134 = "wm-lh-G_temp_sup-Lateral_aspect"
	-- 3135 = "wm-lh-G_temp_sup-Planum_polare"
	-- 3136 = "wm-lh-G_temp_sup-Planum_tempolare"
	-- 3137 = "wm-lh-G_and_S_transverse_frontopolar"
	-- 3138 = "wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal"
	-- 3139 = "wm-lh-Lat_Fissure-ant_sgt-ramus_vertical"
	-- 3140 = "wm-lh-Lat_Fissure-post_sgt"
	-- 3141 = "wm-lh-Medial_wall"
	-- 3142 = "wm-lh-Pole_occipital"
	-- 3143 = "wm-lh-Pole_temporal"
	-- 3144 = "wm-lh-S_calcarine"
	-- 3145 = "wm-lh-S_central"
	-- 3146 = "wm-lh-S_central_insula"
	-- 3147 = "wm-lh-S_cingulate-Main_part_and_Intracingulate"
	-- 3148 = "wm-lh-S_cingulate-Marginalis_part"
	-- 3149 = "wm-lh-S_circular_insula_anterior"
	-- 3150 = "wm-lh-S_circular_insula_inferior"
	-- 3151 = "wm-lh-S_circular_insula_superior"
	-- 3152 = "wm-lh-S_collateral_transverse_ant"
	-- 3153 = "wm-lh-S_collateral_transverse_post"
	-- 3154 = "wm-lh-S_frontal_inferior"
	-- 3155 = "wm-lh-S_frontal_middle"
	-- 3156 = "wm-lh-S_frontal_superior"
	-- 3157 = "wm-lh-S_frontomarginal"
	-- 3158 = "wm-lh-S_intermedius_primus-Jensen"
	-- 3159 = "wm-lh-S_intraparietal-and_Parietal_transverse"
	-- 3160 = "wm-lh-S_occipital_anterior"
	-- 3161 = "wm-lh-S_occipital_middle_and_Lunatus"
	-- 3162 = "wm-lh-S_occipital_superior_and_transversalis"
	-- 3163 = "wm-lh-S_occipito-temporal_lateral"
	-- 3164 = "wm-lh-S_occipito-temporal_medial_and_S_Lingual"
	-- 3165 = "wm-lh-S_orbital-H_shapped"
	-- 3166 = "wm-lh-S_orbital_lateral"
	-- 3167 = "wm-lh-S_orbital_medial-Or_olfactory"
	-- 3168 = "wm-lh-S_paracentral"
	-- 3169 = "wm-lh-S_parieto_occipital"
	-- 3170 = "wm-lh-S_pericallosal"
	-- 3171 = "wm-lh-S_postcentral"
	-- 3172 = "wm-lh-S_precentral-Inferior-part"
	-- 3173 = "wm-lh-S_precentral-Superior-part"
	-- 3174 = "wm-lh-S_subcentral_ant"
	-- 3175 = "wm-lh-S_subcentral_post"
	-- 3176 = "wm-lh-S_suborbital"
	-- 3177 = "wm-lh-S_subparietal"
	-- 3178 = "wm-lh-S_supracingulate"
	-- 3179 = "wm-lh-S_temporal_inferior"
	-- 3180 = "wm-lh-S_temporal_superior"
	-- 3181 = "wm-lh-S_temporal_transverse"
	-- 4100 = "wm-rh-Unknown"
	-- 4101 = "wm-rh-Corpus_callosum"
	-- 4102 = "wm-rh-G_and_S_Insula_ONLY_AVERAGE"
	-- 4103 = "wm-rh-G_cingulate-Isthmus"
	-- 4104 = "wm-rh-G_cingulate-Main_part"
	-- 4105 = "wm-rh-G_cuneus"
	-- 4106 = "wm-rh-G_frontal_inf-Opercular_part"
	-- 4107 = "wm-rh-G_frontal_inf-Orbital_part"
	-- 4108 = "wm-rh-G_frontal_inf-Triangular_part"
	-- 4109 = "wm-rh-G_frontal_middle"
	-- 4110 = "wm-rh-G_frontal_superior"
	-- 4111 = "wm-rh-G_frontomarginal"
	-- 4112 = "wm-rh-G_insular_long"
	-- 4113 = "wm-rh-G_insular_short"
	-- 4114 = "wm-rh-G_and_S_occipital_inferior"
	-- 4115 = "wm-rh-G_occipital_middle"
	-- 4116 = "wm-rh-G_occipital_superior"
	-- 4117 = "wm-rh-G_occipit-temp_lat-Or_fusiform"
	-- 4118 = "wm-rh-G_occipit-temp_med-Lingual_part"
	-- 4119 = "wm-rh-G_occipit-temp_med-Parahippocampal_part"
	-- 4120 = "wm-rh-G_orbital"
	-- 4121 = "wm-rh-G_paracentral"
	-- 4122 = "wm-rh-G_parietal_inferior-Angular_part"
	-- 4123 = "wm-rh-G_parietal_inferior-Supramarginal_part"
	-- 4124 = "wm-rh-G_parietal_superior"
	-- 4125 = "wm-rh-G_postcentral"
	-- 4126 = "wm-rh-G_precentral"
	-- 4127 = "wm-rh-G_precuneus"
	-- 4128 = "wm-rh-G_rectus"
	-- 4129 = "wm-rh-G_subcallosal"
	-- 4130 = "wm-rh-G_subcentral"
	-- 4131 = "wm-rh-G_temporal_inferior"
	-- 4132 = "wm-rh-G_temporal_middle"
	-- 4133 = "wm-rh-G_temp_sup-G_temp_transv_and_interm_S"
	-- 4134 = "wm-rh-G_temp_sup-Lateral_aspect"
	-- 4135 = "wm-rh-G_temp_sup-Planum_polare"
	-- 4136 = "wm-rh-G_temp_sup-Planum_tempolare"
	-- 4137 = "wm-rh-G_and_S_transverse_frontopolar"
	-- 4138 = "wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal"
	-- 4139 = "wm-rh-Lat_Fissure-ant_sgt-ramus_vertical"
	-- 4140 = "wm-rh-Lat_Fissure-post_sgt"
	-- 4141 = "wm-rh-Medial_wall"
	-- 4142 = "wm-rh-Pole_occipital"
	-- 4143 = "wm-rh-Pole_temporal"
	-- 4144 = "wm-rh-S_calcarine"
	-- 4145 = "wm-rh-S_central"
	-- 4146 = "wm-rh-S_central_insula"
	-- 4147 = "wm-rh-S_cingulate-Main_part_and_Intracingulate"
	-- 4148 = "wm-rh-S_cingulate-Marginalis_part"
	-- 4149 = "wm-rh-S_circular_insula_anterior"
	-- 4150 = "wm-rh-S_circular_insula_inferior"
	-- 4151 = "wm-rh-S_circular_insula_superior"
	-- 4152 = "wm-rh-S_collateral_transverse_ant"
	-- 4153 = "wm-rh-S_collateral_transverse_post"
	-- 4154 = "wm-rh-S_frontal_inferior"
	-- 4155 = "wm-rh-S_frontal_middle"
	-- 4156 = "wm-rh-S_frontal_superior"
	-- 4157 = "wm-rh-S_frontomarginal"
	-- 4158 = "wm-rh-S_intermedius_primus-Jensen"
	-- 4159 = "wm-rh-S_intraparietal-and_Parietal_transverse"
	-- 4160 = "wm-rh-S_occipital_anterior"
	-- 4161 = "wm-rh-S_occipital_middle_and_Lunatus"
	-- 4162 = "wm-rh-S_occipital_superior_and_transversalis"
	-- 4163 = "wm-rh-S_occipito-temporal_lateral"
	-- 4164 = "wm-rh-S_occipito-temporal_medial_and_S_Lingual"
	-- 4165 = "wm-rh-S_orbital-H_shapped"
	-- 4166 = "wm-rh-S_orbital_lateral"
	-- 4167 = "wm-rh-S_orbital_medial-Or_olfactory"
	-- 4168 = "wm-rh-S_paracentral"
	-- 4169 = "wm-rh-S_parieto_occipital"
	-- 4170 = "wm-rh-S_pericallosal"
	-- 4171 = "wm-rh-S_postcentral"
	-- 4172 = "wm-rh-S_precentral-Inferior-part"
	-- 4173 = "wm-rh-S_precentral-Superior-part"
	-- 4174 = "wm-rh-S_subcentral_ant"
	-- 4175 = "wm-rh-S_subcentral_post"
	-- 4176 = "wm-rh-S_suborbital"
	-- 4177 = "wm-rh-S_subparietal"
	-- 4178 = "wm-rh-S_supracingulate"
	-- 4179 = "wm-rh-S_temporal_inferior"
	-- 4180 = "wm-rh-S_temporal_superior"
	-- 4181 = "wm-rh-S_temporal_transverse"
	-- 5001 = "Left-UnsegmentedWhiteMatter"
	-- 5002 = "Right-UnsegmentedWhiteMatter"
	-- 5100 = "fmajor"
	-- 5101 = "fminor"
	-- 5102 = "lh.atr"
	-- 5103 = "lh.cab"
	-- 5104 = "lh.ccg"
	-- 5105 = "lh.cst"
	-- 5106 = "lh.ilf"
	-- 5107 = "lh.slfp"
	-- 5108 = "lh.slft"
	-- 5109 = "lh.unc"
	-- 5110 = "rh.atr"
	-- 5111 = "rh.cab"
	-- 5112 = "rh.ccg"
	-- 5113 = "rh.cst"
	-- 5114 = "rh.ilf"
	-- 5115 = "rh.slfp"
	-- 5116 = "rh.slft"
	-- 5117 = "rh.unc"
	-- 5200 = "CC-ForcepsMajor"
	-- 5201 = "CC-ForcepsMinor"
	-- 5202 = "LAntThalRadiation"
	-- 5203 = "LCingulumAngBundle"
	-- 5204 = "LCingulumCingGyrus"
	-- 5205 = "LCorticospinalTract"
	-- 5206 = "LInfLongFas"
	-- 5207 = "LSupLongFasParietal"
	-- 5208 = "LSupLongFasTemporal"
	-- 5209 = "LUncinateFas"
	-- 5210 = "RAntThalRadiation"
	-- 5211 = "RCingulumAngBundle"
	-- 5212 = "RCingulumCingGyrus"
	-- 5213 = "RCorticospinalTract"
	-- 5214 = "RInfLongFas"
	-- 5215 = "RSupLongFasParietal"
	-- 5216 = "RSupLongFasTemporal"
	-- 5217 = "RUncinateFas"
	-- 6000 = "CST-orig"
	-- 6001 = "CST-hammer"
	-- 6002 = "CST-CVS"
	-- 6003 = "CST-flirt"
	-- 6010 = "Left-SLF1"
	-- 6020 = "Right-SLF1"
	-- 6030 = "Left-SLF3"
	-- 6040 = "Right-SLF3"
	-- 6050 = "Left-CST"
	-- 6060 = "Right-CST"
	-- 6070 = "Left-SLF2"
	-- 6080 = "Right-SLF2"
	-- 7001 = "Lateral-nucleus"
	-- 7002 = "Basolateral-nucleus"
	-- 7003 = "Basal-nucleus"
	-- 7004 = "Centromedial-nucleus"
	-- 7005 = "Central-nucleus"
	-- 7006 = "Medial-nucleus"
	-- 7007 = "Cortical-nucleus"
	-- 7008 = "Accessory-Basal-nucleus"
	-- 7009 = "Corticoamygdaloid-transitio"
	-- 7010 = "Anterior-amygdaloid-area-AAA"
	-- 7011 = "Fusion-amygdala-HP-FAH"
	-- 7012 = "Hippocampal-amygdala-transition-HATA"
	-- 7013 = "Endopiriform-nucleus"
	-- 7014 = "Lateral-nucleus-olfactory-tract"
	-- 7015 = "Paralaminar-nucleus"
	-- 7016 = "Intercalated-nucleus"
	-- 7017 = "Prepiriform-cortex"
	-- 7018 = "Periamygdaloid-cortex"
	-- 7019 = "Envelope-Amygdala"
	-- 7020 = "Extranuclear-Amydala"
	-- 7100 = "Brainstem-inferior-colliculus"
	-- 7101 = "Brainstem-cochlear-nucleus"
	-- 8001 = "Thalamus-Anterior"
	-- 8002 = "Thalamus-Ventral-anterior"
	-- 8003 = "Thalamus-Lateral-dorsal"
	-- 8004 = "Thalamus-Lateral-posterior"
	-- 8005 = "Thalamus-Ventral-lateral"
	-- 8006 = "Thalamus-Ventral-posterior-medial"
	-- 8007 = "Thalamus-Ventral-posterior-lateral"
	-- 8008 = "Thalamus-intralaminar"
	-- 8009 = "Thalamus-centromedian"
	-- 8010 = "Thalamus-mediodorsal"
	-- 8011 = "Thalamus-medial"
	-- 8012 = "Thalamus-pulvinar"
	-- 8013 = "Thalamus-lateral-geniculate"
	-- 8014 = "Thalamus-medial-geniculate"
	-- 9000 = "ctx-lh-prefrontal"
	-- 9001 = "ctx-lh-primary-motor"
	-- 9002 = "ctx-lh-premotor"
	-- 9003 = "ctx-lh-temporal"
	-- 9004 = "ctx-lh-posterior-parietal"
	-- 9005 = "ctx-lh-prim-sec-somatosensory"
	-- 9006 = "ctx-lh-occipital"
	-- 9500 = "ctx-rh-prefrontal"
	-- 9501 = "ctx-rh-primary-motor"
	-- 9502 = "ctx-rh-premotor"
	-- 9503 = "ctx-rh-temporal"
	-- 9504 = "ctx-rh-posterior-parietal"
	-- 9505 = "ctx-rh-prim-sec-somatosensory"
	-- 9506 = "ctx-rh-occipital"
	-- 11100 = "ctx_lh_Unknown"
	-- 11101 = "ctx_lh_G_and_S_frontomargin"
	-- 11102 = "ctx_lh_G_and_S_occipital_inf"
	-- 11103 = "ctx_lh_G_and_S_paracentral"
	-- 11104 = "ctx_lh_G_and_S_subcentral"
	-- 11105 = "ctx_lh_G_and_S_transv_frontopol"
	-- 11106 = "ctx_lh_G_and_S_cingul-Ant"
	-- 11107 = "ctx_lh_G_and_S_cingul-Mid-Ant"
	-- 11108 = "ctx_lh_G_and_S_cingul-Mid-Post"
	-- 11109 = "ctx_lh_G_cingul-Post-dorsal"
	-- 11110 = "ctx_lh_G_cingul-Post-ventral"
	-- 11111 = "ctx_lh_G_cuneus"
	-- 11112 = "ctx_lh_G_front_inf-Opercular"
	-- 11113 = "ctx_lh_G_front_inf-Orbital"
	-- 11114 = "ctx_lh_G_front_inf-Triangul"
	-- 11115 = "ctx_lh_G_front_middle"
	-- 11116 = "ctx_lh_G_front_sup"
	-- 11117 = "ctx_lh_G_Ins_lg_and_S_cent_ins"
	-- 11118 = "ctx_lh_G_insular_short"
	-- 11119 = "ctx_lh_G_occipital_middle"
	-- 11120 = "ctx_lh_G_occipital_sup"
	-- 11121 = "ctx_lh_G_oc-temp_lat-fusifor"
	-- 11122 = "ctx_lh_G_oc-temp_med-Lingual"
	-- 11123 = "ctx_lh_G_oc-temp_med-Parahip"
	-- 11124 = "ctx_lh_G_orbital"
	-- 11125 = "ctx_lh_G_pariet_inf-Angular"
	-- 11126 = "ctx_lh_G_pariet_inf-Supramar"
	-- 11127 = "ctx_lh_G_parietal_sup"
	-- 11128 = "ctx_lh_G_postcentral"
	-- 11129 = "ctx_lh_G_precentral"
	-- 11130 = "ctx_lh_G_precuneus"
	-- 11131 = "ctx_lh_G_rectus"
	-- 11132 = "ctx_lh_G_subcallosal"
	-- 11133 = "ctx_lh_G_temp_sup-G_T_transv"
	-- 11134 = "ctx_lh_G_temp_sup-Lateral"
	-- 11135 = "ctx_lh_G_temp_sup-Plan_polar"
	-- 11136 = "ctx_lh_G_temp_sup-Plan_tempo"
	-- 11137 = "ctx_lh_G_temporal_inf"
	-- 11138 = "ctx_lh_G_temporal_middle"
	-- 11139 = "ctx_lh_Lat_Fis-ant-Horizont"
	-- 11140 = "ctx_lh_Lat_Fis-ant-Vertical"
	-- 11141 = "ctx_lh_Lat_Fis-post"
	-- 11142 = "ctx_lh_Medial_wall"
	-- 11143 = "ctx_lh_Pole_occipital"
	-- 11144 = "ctx_lh_Pole_temporal"
	-- 11145 = "ctx_lh_S_calcarine"
	-- 11146 = "ctx_lh_S_central"
	-- 11147 = "ctx_lh_S_cingul-Marginalis"
	-- 11148 = "ctx_lh_S_circular_insula_ant"
	-- 11149 = "ctx_lh_S_circular_insula_inf"
	-- 11150 = "ctx_lh_S_circular_insula_sup"
	-- 11151 = "ctx_lh_S_collat_transv_ant"
	-- 11152 = "ctx_lh_S_collat_transv_post"
	-- 11153 = "ctx_lh_S_front_inf"
	-- 11154 = "ctx_lh_S_front_middle"
	-- 11155 = "ctx_lh_S_front_sup"
	-- 11156 = "ctx_lh_S_interm_prim-Jensen"
	-- 11157 = "ctx_lh_S_intrapariet_and_P_trans"
	-- 11158 = "ctx_lh_S_oc_middle_and_Lunatus"
	-- 11159 = "ctx_lh_S_oc_sup_and_transversal"
	-- 11160 = "ctx_lh_S_occipital_ant"
	-- 11161 = "ctx_lh_S_oc-temp_lat"
	-- 11162 = "ctx_lh_S_oc-temp_med_and_Lingual"
	-- 11163 = "ctx_lh_S_orbital_lateral"
	-- 11164 = "ctx_lh_S_orbital_med-olfact"
	-- 11165 = "ctx_lh_S_orbital-H_Shaped"
	-- 11166 = "ctx_lh_S_parieto_occipital"
	-- 11167 = "ctx_lh_S_pericallosal"
	-- 11168 = "ctx_lh_S_postcentral"
	-- 11169 = "ctx_lh_S_precentral-inf-part"
	-- 11170 = "ctx_lh_S_precentral-sup-part"
	-- 11171 = "ctx_lh_S_suborbital"
	-- 11172 = "ctx_lh_S_subparietal"
	-- 11173 = "ctx_lh_S_temporal_inf"
	-- 11174 = "ctx_lh_S_temporal_sup"
	-- 11175 = "ctx_lh_S_temporal_transverse"
	-- 12100 = "ctx_rh_Unknown"
	-- 12101 = "ctx_rh_G_and_S_frontomargin"
	-- 12102 = "ctx_rh_G_and_S_occipital_inf"
	-- 12103 = "ctx_rh_G_and_S_paracentral"
	-- 12104 = "ctx_rh_G_and_S_subcentral"
	-- 12105 = "ctx_rh_G_and_S_transv_frontopol"
	-- 12106 = "ctx_rh_G_and_S_cingul-Ant"
	-- 12107 = "ctx_rh_G_and_S_cingul-Mid-Ant"
	-- 12108 = "ctx_rh_G_and_S_cingul-Mid-Post"
	-- 12109 = "ctx_rh_G_cingul-Post-dorsal"
	-- 12110 = "ctx_rh_G_cingul-Post-ventral"
	-- 12111 = "ctx_rh_G_cuneus"
	-- 12112 = "ctx_rh_G_front_inf-Opercular"
	-- 12113 = "ctx_rh_G_front_inf-Orbital"
	-- 12114 = "ctx_rh_G_front_inf-Triangul"
	-- 12115 = "ctx_rh_G_front_middle"
	-- 12116 = "ctx_rh_G_front_sup"
	-- 12117 = "ctx_rh_G_Ins_lg_and_S_cent_ins"
	-- 12118 = "ctx_rh_G_insular_short"
	-- 12119 = "ctx_rh_G_occipital_middle"
	-- 12120 = "ctx_rh_G_occipital_sup"
	-- 12121 = "ctx_rh_G_oc-temp_lat-fusifor"
	-- 12122 = "ctx_rh_G_oc-temp_med-Lingual"
	-- 12123 = "ctx_rh_G_oc-temp_med-Parahip"
	-- 12124 = "ctx_rh_G_orbital"
	-- 12125 = "ctx_rh_G_pariet_inf-Angular"
	-- 12126 = "ctx_rh_G_pariet_inf-Supramar"
	-- 12127 = "ctx_rh_G_parietal_sup"
	-- 12128 = "ctx_rh_G_postcentral"
	-- 12129 = "ctx_rh_G_precentral"
	-- 12130 = "ctx_rh_G_precuneus"
	-- 12131 = "ctx_rh_G_rectus"
	-- 12132 = "ctx_rh_G_subcallosal"
	-- 12133 = "ctx_rh_G_temp_sup-G_T_transv"
	-- 12134 = "ctx_rh_G_temp_sup-Lateral"
	-- 12135 = "ctx_rh_G_temp_sup-Plan_polar"
	-- 12136 = "ctx_rh_G_temp_sup-Plan_tempo"
	-- 12137 = "ctx_rh_G_temporal_inf"
	-- 12138 = "ctx_rh_G_temporal_middle"
	-- 12139 = "ctx_rh_Lat_Fis-ant-Horizont"
	-- 12140 = "ctx_rh_Lat_Fis-ant-Vertical"
	-- 12141 = "ctx_rh_Lat_Fis-post"
	-- 12142 = "ctx_rh_Medial_wall"
	-- 12143 = "ctx_rh_Pole_occipital"
	-- 12144 = "ctx_rh_Pole_temporal"
	-- 12145 = "ctx_rh_S_calcarine"
	-- 12146 = "ctx_rh_S_central"
	-- 12147 = "ctx_rh_S_cingul-Marginalis"
	-- 12148 = "ctx_rh_S_circular_insula_ant"
	-- 12149 = "ctx_rh_S_circular_insula_inf"
	-- 12150 = "ctx_rh_S_circular_insula_sup"
	-- 12151 = "ctx_rh_S_collat_transv_ant"
	-- 12152 = "ctx_rh_S_collat_transv_post"
	-- 12153 = "ctx_rh_S_front_inf"
	-- 12154 = "ctx_rh_S_front_middle"
	-- 12155 = "ctx_rh_S_front_sup"
	-- 12156 = "ctx_rh_S_interm_prim-Jensen"
	-- 12157 = "ctx_rh_S_intrapariet_and_P_trans"
	-- 12158 = "ctx_rh_S_oc_middle_and_Lunatus"
	-- 12159 = "ctx_rh_S_oc_sup_and_transversal"
	-- 12160 = "ctx_rh_S_occipital_ant"
	-- 12161 = "ctx_rh_S_oc-temp_lat"
	-- 12162 = "ctx_rh_S_oc-temp_med_and_Lingual"
	-- 12163 = "ctx_rh_S_orbital_lateral"
	-- 12164 = "ctx_rh_S_orbital_med-olfact"
	-- 12165 = "ctx_rh_S_orbital-H_Shaped"
	-- 12166 = "ctx_rh_S_parieto_occipital"
	-- 12167 = "ctx_rh_S_pericallosal"
	-- 12168 = "ctx_rh_S_postcentral"
	-- 12169 = "ctx_rh_S_precentral-inf-part"
	-- 12170 = "ctx_rh_S_precentral-sup-part"
	-- 12171 = "ctx_rh_S_suborbital"
	-- 12172 = "ctx_rh_S_subparietal"
	-- 12173 = "ctx_rh_S_temporal_inf"
	-- 12174 = "ctx_rh_S_temporal_sup"
	-- 12175 = "ctx_rh_S_temporal_transverse"
	-- 13100 = "wm_lh_Unknown"
	-- 13101 = "wm_lh_G_and_S_frontomargin"
	-- 13102 = "wm_lh_G_and_S_occipital_inf"
	-- 13103 = "wm_lh_G_and_S_paracentral"
	-- 13104 = "wm_lh_G_and_S_subcentral"
	-- 13105 = "wm_lh_G_and_S_transv_frontopol"
	-- 13106 = "wm_lh_G_and_S_cingul-Ant"
	-- 13107 = "wm_lh_G_and_S_cingul-Mid-Ant"
	-- 13108 = "wm_lh_G_and_S_cingul-Mid-Post"
	-- 13109 = "wm_lh_G_cingul-Post-dorsal"
	-- 13110 = "wm_lh_G_cingul-Post-ventral"
	-- 13111 = "wm_lh_G_cuneus"
	-- 13112 = "wm_lh_G_front_inf-Opercular"
	-- 13113 = "wm_lh_G_front_inf-Orbital"
	-- 13114 = "wm_lh_G_front_inf-Triangul"
	-- 13115 = "wm_lh_G_front_middle"
	-- 13116 = "wm_lh_G_front_sup"
	-- 13117 = "wm_lh_G_Ins_lg_and_S_cent_ins"
	-- 13118 = "wm_lh_G_insular_short"
	-- 13119 = "wm_lh_G_occipital_middle"
	-- 13120 = "wm_lh_G_occipital_sup"
	-- 13121 = "wm_lh_G_oc-temp_lat-fusifor"
	-- 13122 = "wm_lh_G_oc-temp_med-Lingual"
	-- 13123 = "wm_lh_G_oc-temp_med-Parahip"
	-- 13124 = "wm_lh_G_orbital"
	-- 13125 = "wm_lh_G_pariet_inf-Angular"
	-- 13126 = "wm_lh_G_pariet_inf-Supramar"
	-- 13127 = "wm_lh_G_parietal_sup"
	-- 13128 = "wm_lh_G_postcentral"
	-- 13129 = "wm_lh_G_precentral"
	-- 13130 = "wm_lh_G_precuneus"
	-- 13131 = "wm_lh_G_rectus"
	-- 13132 = "wm_lh_G_subcallosal"
	-- 13133 = "wm_lh_G_temp_sup-G_T_transv"
	-- 13134 = "wm_lh_G_temp_sup-Lateral"
	-- 13135 = "wm_lh_G_temp_sup-Plan_polar"
	-- 13136 = "wm_lh_G_temp_sup-Plan_tempo"
	-- 13137 = "wm_lh_G_temporal_inf"
	-- 13138 = "wm_lh_G_temporal_middle"
	-- 13139 = "wm_lh_Lat_Fis-ant-Horizont"
	-- 13140 = "wm_lh_Lat_Fis-ant-Vertical"
	-- 13141 = "wm_lh_Lat_Fis-post"
	-- 13142 = "wm_lh_Medial_wall"
	-- 13143 = "wm_lh_Pole_occipital"
	-- 13144 = "wm_lh_Pole_temporal"
	-- 13145 = "wm_lh_S_calcarine"
	-- 13146 = "wm_lh_S_central"
	-- 13147 = "wm_lh_S_cingul-Marginalis"
	-- 13148 = "wm_lh_S_circular_insula_ant"
	-- 13149 = "wm_lh_S_circular_insula_inf"
	-- 13150 = "wm_lh_S_circular_insula_sup"
	-- 13151 = "wm_lh_S_collat_transv_ant"
	-- 13152 = "wm_lh_S_collat_transv_post"
	-- 13153 = "wm_lh_S_front_inf"
	-- 13154 = "wm_lh_S_front_middle"
	-- 13155 = "wm_lh_S_front_sup"
	-- 13156 = "wm_lh_S_interm_prim-Jensen"
	-- 13157 = "wm_lh_S_intrapariet_and_P_trans"
	-- 13158 = "wm_lh_S_oc_middle_and_Lunatus"
	-- 13159 = "wm_lh_S_oc_sup_and_transversal"
	-- 13160 = "wm_lh_S_occipital_ant"
	-- 13161 = "wm_lh_S_oc-temp_lat"
	-- 13162 = "wm_lh_S_oc-temp_med_and_Lingual"
	-- 13163 = "wm_lh_S_orbital_lateral"
	-- 13164 = "wm_lh_S_orbital_med-olfact"
	-- 13165 = "wm_lh_S_orbital-H_Shaped"
	-- 13166 = "wm_lh_S_parieto_occipital"
	-- 13167 = "wm_lh_S_pericallosal"
	-- 13168 = "wm_lh_S_postcentral"
	-- 13169 = "wm_lh_S_precentral-inf-part"
	-- 13170 = "wm_lh_S_precentral-sup-part"
	-- 13171 = "wm_lh_S_suborbital"
	-- 13172 = "wm_lh_S_subparietal"
	-- 13173 = "wm_lh_S_temporal_inf"
	-- 13174 = "wm_lh_S_temporal_sup"
	-- 13175 = "wm_lh_S_temporal_transverse"
	-- 14100 = "wm_rh_Unknown"
	-- 14101 = "wm_rh_G_and_S_frontomargin"
	-- 14102 = "wm_rh_G_and_S_occipital_inf"
	-- 14103 = "wm_rh_G_and_S_paracentral"
	-- 14104 = "wm_rh_G_and_S_subcentral"
	-- 14105 = "wm_rh_G_and_S_transv_frontopol"
	-- 14106 = "wm_rh_G_and_S_cingul-Ant"
	-- 14107 = "wm_rh_G_and_S_cingul-Mid-Ant"
	-- 14108 = "wm_rh_G_and_S_cingul-Mid-Post"
	-- 14109 = "wm_rh_G_cingul-Post-dorsal"
	-- 14110 = "wm_rh_G_cingul-Post-ventral"
	-- 14111 = "wm_rh_G_cuneus"
	-- 14112 = "wm_rh_G_front_inf-Opercular"
	-- 14113 = "wm_rh_G_front_inf-Orbital"
	-- 14114 = "wm_rh_G_front_inf-Triangul"
	-- 14115 = "wm_rh_G_front_middle"
	-- 14116 = "wm_rh_G_front_sup"
	-- 14117 = "wm_rh_G_Ins_lg_and_S_cent_ins"
	-- 14118 = "wm_rh_G_insular_short"
	-- 14119 = "wm_rh_G_occipital_middle"
	-- 14120 = "wm_rh_G_occipital_sup"
	-- 14121 = "wm_rh_G_oc-temp_lat-fusifor"
	-- 14122 = "wm_rh_G_oc-temp_med-Lingual"
	-- 14123 = "wm_rh_G_oc-temp_med-Parahip"
	-- 14124 = "wm_rh_G_orbital"
	-- 14125 = "wm_rh_G_pariet_inf-Angular"
	-- 14126 = "wm_rh_G_pariet_inf-Supramar"
	-- 14127 = "wm_rh_G_parietal_sup"
	-- 14128 = "wm_rh_G_postcentral"
	-- 14129 = "wm_rh_G_precentral"
	-- 14130 = "wm_rh_G_precuneus"
	-- 14131 = "wm_rh_G_rectus"
	-- 14132 = "wm_rh_G_subcallosal"
	-- 14133 = "wm_rh_G_temp_sup-G_T_transv"
	-- 14134 = "wm_rh_G_temp_sup-Lateral"
	-- 14135 = "wm_rh_G_temp_sup-Plan_polar"
	-- 14136 = "wm_rh_G_temp_sup-Plan_tempo"
	-- 14137 = "wm_rh_G_temporal_inf"
	-- 14138 = "wm_rh_G_temporal_middle"
	-- 14139 = "wm_rh_Lat_Fis-ant-Horizont"
	-- 14140 = "wm_rh_Lat_Fis-ant-Vertical"
	-- 14141 = "wm_rh_Lat_Fis-post"
	-- 14142 = "wm_rh_Medial_wall"
	-- 14143 = "wm_rh_Pole_occipital"
	-- 14144 = "wm_rh_Pole_temporal"
	-- 14145 = "wm_rh_S_calcarine"
	-- 14146 = "wm_rh_S_central"
	-- 14147 = "wm_rh_S_cingul-Marginalis"
	-- 14148 = "wm_rh_S_circular_insula_ant"
	-- 14149 = "wm_rh_S_circular_insula_inf"
	-- 14150 = "wm_rh_S_circular_insula_sup"
	-- 14151 = "wm_rh_S_collat_transv_ant"
	-- 14152 = "wm_rh_S_collat_transv_post"
	-- 14153 = "wm_rh_S_front_inf"
	-- 14154 = "wm_rh_S_front_middle"
	-- 14155 = "wm_rh_S_front_sup"
	-- 14156 = "wm_rh_S_interm_prim-Jensen"
	-- 14157 = "wm_rh_S_intrapariet_and_P_trans"
	-- 14158 = "wm_rh_S_oc_middle_and_Lunatus"
	-- 14159 = "wm_rh_S_oc_sup_and_transversal"
	-- 14160 = "wm_rh_S_occipital_ant"
	-- 14161 = "wm_rh_S_oc-temp_lat"
	-- 14162 = "wm_rh_S_oc-temp_med_and_Lingual"
	-- 14163 = "wm_rh_S_orbital_lateral"
	-- 14164 = "wm_rh_S_orbital_med-olfact"
	-- 14165 = "wm_rh_S_orbital-H_Shaped"
	-- 14166 = "wm_rh_S_parieto_occipital"
	-- 14167 = "wm_rh_S_pericallosal"
	-- 14168 = "wm_rh_S_postcentral"
	-- 14169 = "wm_rh_S_precentral-inf-part"
	-- 14170 = "wm_rh_S_precentral-sup-part"
	-- 14171 = "wm_rh_S_suborbital"
	-- 14172 = "wm_rh_S_subparietal"
	-- 14173 = "wm_rh_S_temporal_inf"
	-- 14174 = "wm_rh_S_temporal_sup"
	-- 14175 = "wm_rh_S_temporal_transverse"
	-
	-*/
	-
	-/**
	-\page org_mitk_views_connectomicsnetworkoperations The Connectomics Network Operations View
	-
	-\imageMacro{QmitkConnectomicsNetworkOperationsViewIcon_48.png,"Icon of the Connectomics Network Operations View",2.00}
	-
	-This view can be used modify networks and related data.
	-
	-\imageMacro{operationsview.png,"The user interface",4.61}
	-
	-Select a parcellation and press "Convert to RGBA" to create a RGBA image. By doing this conversion it is much easier to discern the different parcels. Furthermore MITK supports 3D visualization of an RGBA image.
	-
	-Select a network and press "Create Connectivity Matrix Image" to create a 2D image of the connectivity matrix. By default the weight of a connection is used as grey value. Using the "Rescale" option will rescale the weights so highest one is 255. Using the "Binary" option will result in a binary connectivity matrix.
	-
	-*/
	-
	-
	-/**
	-\page org_mitk_views_connectomicsstatistics The Connectomics Statistics View
	-
	-\imageMacro{QmitkConnectomicsStatisticsViewIcon_48.png,"Icon of the Connectomics Statistics View",2.00}
	-
	-This view can be used to show statistical analysis of a network.
	-
	-\imageMacro{statisticsview.png,"The user interface",6.58}
	-
	-To calculate network statistics select a network in the datamanager. At this time the following statistics are calculated for the entire network:
	-
	-<ul>
	- <li> The number of vertices in the network
	- <li> The number of edges in the network
	- <li> The number of edges which have the same vertex as beginning and end point
	- <li> The average degree of the nodes in the network
	- <li> The connection density the network (the number of edges divided by the number of possible edges)
	- <li> The unweighted efficiency of the network ( 1 divided by average path length, this is zero for disconnected graphs)
	- <li> The global clustering
	-</ul>
	-
	-Furthermore some statistics are calculated on a per node basis and displayed as histograms:
	-
	-<ul>
	- <li> The degree of each node
	- <li> The (unweighted) betweenness centrality of each node
	- <li> The spread of shortest paths between each pair of nodes (For disconnected graphs the shortest paths with infinite length are omitted for readability)
	-</ul>
	-
	-*/
	-
	-/**
	-\page org_mitk_views_randomparcellationview The Random Parcellation View
	-
	-\imageMacro{QmitkRandomParcellationIcon.png,"Icon of the Random Parcellation View",2.00}
	-
	-\tableofcontents
	-
	-\section org_mitk_views_randomparcellationviewSummary Summary
	-This view is used to create a random parcellation of a segmented image.
	-It was designed to parcellate grey matter to acquire random nodes for network analysis.
	-This document describes how to use this view.
	-
	-\section org_mitk_views_randomparcellationviewOverview Overview
	-
	-When parcellating an image you can either do a parcellation and use the generated parcellation. In which case it will have as many parcellation as seed points were specified. Instead you can choose to merge some of the original parcels untill either none below a threshold size remain, or until a specified minimum number of parcels has been reached.
	-A further option is to "Just Merge Small Parcels". This will result in only neighbouring parcels below a threshold size being merged. Using this option may result in final parcels below the given threshold size if they are not adjacent to another parcel below the threshold size.
	-
	-In all there are four possibilities to get a random parcellation
	-<ul>
	-<li>Without merging
	-<li>Merging with respect to the number of nodes afterwards
	-<li>Merging with respect to the number of voxels of the smallest parcel
	-<li>Merging with respect to the number of voxels of the smallest parcel, where just small parcels are merged
	-</ul>
	-
	-\section org_mitk_views_randomparcellationviewUsage Usage
	-
	-First you have to get a segmentation of the target structure. You can use the Segmentation View to create one.
	-Select it in the Data Manager. Now you can choose which of the possible ways of parcellation you would like.
	-See \ref org_mitk_views_randomparcellationviewOverview for these possibilities.
	-Start the parcellation process using the "Select Random Nodes" button.
	-You will get a new image in the Data Manager. Every voxel of a given parcel will have the same value (0 for background).
	-
	-\section org_mitk_views_randomparcellationviewMethods Methods
	-
	-This Plug-In uses a kind of region growing algorithm. Random seed voxels are set on the segmentation and each is an own region at the beginning. Then voxels are added iteratively to each smallest region, first just the 6-connected ones and later the 26-connected ones and isolated voxels.
	-Specific constraints have to be fulfilled before a voxel is added to a region.
	-The algorithm stops when all voxels are contained in the regions.
	-For merging it is checked which regions are neighbors of the smallest parcel and then a suitable one,
	-according to a cost function, is merged to this parcel. When the merging algorithm stops depends on which stop-mechanism is chosen.
	-
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/documentation/UserManual/QmitkConnectomicsDataViewIcon_48.png b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/documentation/UserManual/QmitkConnectomicsDataViewIcon_48.png
	deleted file mode 100644
	index 94e2d2fe79..0000000000
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/documentation/UserManual/QmitkConnectomicsNetworkOperationsViewIcon_48.png b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/documentation/UserManual/QmitkConnectomicsNetworkOperationsViewIcon_48.png
	deleted file mode 100644
	index 5513fb593b..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/documentation/UserManual/QmitkConnectomicsNetworkOperationsViewIcon_48.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/documentation/UserManual/QmitkConnectomicsStatisticsViewIcon_48.png b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/documentation/UserManual/QmitkConnectomicsStatisticsViewIcon_48.png
	deleted file mode 100644
	index 49cde7dc4a..0000000000
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/documentation/UserManual/QmitkRandomParcellationIcon.png b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/documentation/UserManual/QmitkRandomParcellationIcon.png
	deleted file mode 100644
	index 1fe6bc591c..0000000000
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/documentation/UserManual/connectomics_perspective.png b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/documentation/UserManual/connectomics_perspective.png
	deleted file mode 100644
	index f434f12741..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/documentation/UserManual/connectomics_perspective.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/documentation/UserManual/dataview.png b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/documentation/UserManual/dataview.png
	deleted file mode 100644
	index e6c6890eec..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/documentation/UserManual/dataview.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/documentation/UserManual/operationsview.png b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/documentation/UserManual/operationsview.png
	deleted file mode 100644
	index 15afe9ae1d..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/documentation/UserManual/operationsview.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/documentation/UserManual/statisticsview.png b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/documentation/UserManual/statisticsview.png
	deleted file mode 100644
	index 6c5e97cd18..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/documentation/UserManual/statisticsview.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/documentation/doxygen/modules.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/documentation/doxygen/modules.dox
	deleted file mode 100644
	index 306daa754d..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/documentation/doxygen/modules.dox
	+++ /dev/null
	@@ -1,16 +0,0 @@
	-/**
	- \defgroup org_mitk_gui_qt_diffusionimaging_connectomics org.mitk.gui.qt.diffusionimaging.connectomics
	- \ingroup MITKPlugins
	-
	- \brief This is the diffusionimaging.connectomics plugin.
	-
	-*/
	-
	-/**
	- \defgroup org_mitk_gui_qt_diffusionimaging_connectomics_internal Internal
	- \ingroup org_mitk_gui_qt_diffusionimaging_connectomics
	-
	- \brief This subcategory includes the internal classes of the org.mitk.gui.qt.diffusionimaging.connectomics plugin. Other
	- plugins must not rely on these classes. They contain implementation details and their interface
	- may change at any time. We mean it.
	-*/
	\ No newline at end of file
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/files.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/files.cmake
	deleted file mode 100644
	index 9dd53fc4c1..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/files.cmake
	+++ /dev/null
	@@ -1,65 +0,0 @@
	-set(SRC_CPP_FILES
	- QmitkFreeSurferParcellationHandler.cpp
	- QmitkFreeSurferParcellationWidget.cpp
	-)
	-
	-set(INTERNAL_CPP_FILES
	- QmitkConnectomicsDataView.cpp
	- QmitkConnectomicsNetworkOperationsView.cpp
	- QmitkConnectomicsStatisticsView.cpp
	- QmitkNetworkHistogramCanvas.cpp
	- QmitkRandomParcellationView.cpp
	-
	- Perspectives/QmitkConnectomicsPerspective.cpp
	-
	- mitkPluginActivator.cpp
	-)
	-
	-set(UI_FILES
	- src/internal/QmitkConnectomicsDataViewControls.ui
	- src/internal/QmitkConnectomicsNetworkOperationsViewControls.ui
	- src/internal/QmitkConnectomicsStatisticsViewControls.ui
	- src/internal/QmitkRandomParcellationViewControls.ui
	-
	- src/QmitkFreeSurferParcellationWidgetControls.ui
	-)
	-
	-set(MOC_H_FILES
	- src/internal/mitkPluginActivator.h
	-
	- src/internal/Perspectives/QmitkConnectomicsPerspective.h
	-
	- src/internal/QmitkConnectomicsDataView.h
	- src/internal/QmitkConnectomicsNetworkOperationsView.h
	- src/internal/QmitkConnectomicsStatisticsView.h
	- src/internal/QmitkNetworkHistogramCanvas.h
	- src/internal/QmitkRandomParcellationView.h
	-
	- src/QmitkFreeSurferParcellationHandler.h
	- src/QmitkFreeSurferParcellationWidget.h
	-)
	-
	-set(CACHED_RESOURCE_FILES
	- plugin.xml
	-
	- resources/QmitkConnectomicsDataViewIcon_48.png
	- resources/QmitkConnectomicsNetworkOperationsViewIcon_48.png
	- resources/QmitkConnectomicsStatisticsViewIcon_48.png
	- resources/QmitkRandomParcellationIcon.png
	- resources/parcellation.png
	-)
	-
	-set(QRC_FILES
	- resources/QmitkConnectomics.qrc
	-)
	-
	-
	-set(CPP_FILES )
	-
	-foreach(file ${SRC_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/${file})
	-endforeach(file ${SRC_CPP_FILES})
	-
	-foreach(file ${INTERNAL_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/internal/${file})
	-endforeach(file ${INTERNAL_CPP_FILES})
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/manifest_headers.cmake
	deleted file mode 100644
	index 95d38debb1..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/manifest_headers.cmake
	+++ /dev/null
	@@ -1,5 +0,0 @@
	-set(Plugin-Name "MITK Connectomics")
	-set(Plugin-Version "1.0.0")
	-set(Plugin-Vendor "DKFZ, Medical and Biological Informatics")
	-set(Plugin-ContactAddress "http://www.mitk.org")
	-set(Require-Plugin org.mitk.gui.qt.diffusionimaging org.mitk.gui.qt.common)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/plugin.xml b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/plugin.xml
	deleted file mode 100644
	index 5fb49abd47..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/plugin.xml
	+++ /dev/null
	@@ -1,53 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<?eclipse version="3.0"?>
	-<plugin>
	-
	- <extension point="org.blueberry.ui.views">
	-
	- <view id="org.mitk.views.connectomicsdata"
	- name="Network Data"
	- category="Connectomics"
	- class="QmitkConnectomicsDataView"
	- icon="resources/QmitkConnectomicsDataViewIcon_48.png">
	- <keywordReference id="org.mitk.views.connectomicsdata.Keyword"/>
	- </view>
	-
	- <view id="org.mitk.views.connectomicsstatistics"
	- name="Network Statistics"
	- category="Connectomics"
	- class="QmitkConnectomicsStatisticsView"
	- icon="resources/QmitkConnectomicsStatisticsViewIcon_48.png">
	- <keywordReference id="org.mitk.views.connectomicsstatistics.Keyword"/>
	- </view>
	-
	- <view id="org.mitk.views.randomparcellationview"
	- name="Random Parcellation View"
	- category="Connectomics"
	- class="QmitkRandomParcellationView"
	- icon="resources/QmitkRandomParcellationIcon.png" >
	- <keywordReference id="org.mitk.views.randomparcellationview.Keyword"/>
	- </view>
	-
	- <view id="org.mitk.views.connectomicsnetworkoperations"
	- name="Network Operations"
	- category="Connectomics"
	- class="QmitkConnectomicsNetworkOperationsView"
	- icon="resources/QmitkConnectomicsNetworkOperationsViewIcon_48.png">
	- <keywordReference id="org.mitk.views.connectomicsnetworkoperations.Keyword"/>
	- </view>
	-
	- </extension>
	-
	-
	- <extension point="org.blueberry.ui.perspectives">
	-
	- <perspective id="org.mitk.perspectives.connectomics"
	- name="Connectomics"
	- class="QmitkConnectomicsPerspective"
	- icon="resources/parcellation.png">
	- <keywordReference id="org.mitk.perspectives.connectomics.Keyword"/>
	- </perspective>
	-
	- </extension>
	-
	-</plugin>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/resources/ConnectomicsNetwork.png b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/resources/ConnectomicsNetwork.png
	deleted file mode 100644
	index f434f12741..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/resources/ConnectomicsNetwork.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/resources/QmitkConnectomics.qrc b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/resources/QmitkConnectomics.qrc
	deleted file mode 100644
	index c3a3e8eb13..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/resources/QmitkConnectomics.qrc
	+++ /dev/null
	@@ -1,6 +0,0 @@
	-<RCC>
	- <qresource prefix="/QmitkConnectomics">
	- <file>ConnectomicsNetwork.png</file>
	- <file>QmitkRandomParcellationIcon.png</file>
	- </qresource>
	-</RCC>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/resources/QmitkConnectomicsDataViewIcon_48.png b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/resources/QmitkConnectomicsDataViewIcon_48.png
	deleted file mode 100644
	index 94e2d2fe79..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/resources/QmitkConnectomicsDataViewIcon_48.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/resources/QmitkConnectomicsNetworkOperationsViewIcon_48.png b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/resources/QmitkConnectomicsNetworkOperationsViewIcon_48.png
	deleted file mode 100644
	index 5513fb593b..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/resources/QmitkConnectomicsNetworkOperationsViewIcon_48.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/resources/QmitkConnectomicsStatisticsViewIcon_48.png b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/resources/QmitkConnectomicsStatisticsViewIcon_48.png
	deleted file mode 100644
	index 49cde7dc4a..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/resources/QmitkConnectomicsStatisticsViewIcon_48.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/resources/QmitkConnectomicsStatisticsViewIcon_64.png b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/resources/QmitkConnectomicsStatisticsViewIcon_64.png
	deleted file mode 100644
	index 21fbbf1f42..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/resources/QmitkConnectomicsStatisticsViewIcon_64.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/resources/QmitkRandomParcellationIcon.png b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/resources/QmitkRandomParcellationIcon.png
	deleted file mode 100644
	index 1fe6bc591c..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/resources/QmitkRandomParcellationIcon.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/resources/parcellation.png b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/resources/parcellation.png
	deleted file mode 100644
	index e7ac624e9e..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/resources/parcellation.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/QmitkFreeSurferParcellationHandler.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/QmitkFreeSurferParcellationHandler.cpp
	deleted file mode 100644
	index 804dbc768b..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/QmitkFreeSurferParcellationHandler.cpp
	+++ /dev/null
	@@ -1,138 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkFreeSurferParcellationHandler.h"
	-#include <mitkBaseRenderer.h>
	-#include <mitkDataStorage.h>
	-#include <mitkDataNode.h>
	-#include <mitkImage.h>
	-#include <mitkImagePixelReadAccessor.h>
	-#include <mitkInteractionPositionEvent.h>
	-#include <mitkNodePredicateDataType.h>
	-#include <mitkMousePressEvent.h>
	-#include <mitkMouseWheelEvent.h>
	-#include <usGetModuleContext.h>
	-#include <usModule.h>
	-#include <usModuleRegistry.h>
	-#include <usServiceProperties.h>
	-#include <string>
	-US_USE_NAMESPACE
	-
	-QmitkFreeSurferParcellationHandler::QmitkFreeSurferParcellationHandler() :
	- m_LastPixelvalue( 0 ),
	- m_Translator( mitk::FreeSurferParcellationTranslator::New() )
	-{
	- us::ServiceProperties props;
	- props["name"] = std::string("ParcellationHandler");
	- us::ModuleContext* context = us::ModuleRegistry::GetModule(1)->GetModuleContext();
	- m_ServiceRegistration = context->RegisterService<InteractionEventObserver>( this, props);
	-}
	-QmitkFreeSurferParcellationHandler::~QmitkFreeSurferParcellationHandler()
	-{
	- m_ServiceRegistration.Unregister();
	-}
	-
	-void QmitkFreeSurferParcellationHandler::Notify(InteractionEvent *interactionEvent, bool isHandled)
	-{
	- Q_UNUSED( isHandled )
	- BaseRenderer* sender = interactionEvent->GetSender();
	- InteractionPositionEvent* positionEvent = static_cast<InteractionPositionEvent*>(interactionEvent);
	- TNodePredicateDataType<Image>::Pointer isImageData = TNodePredicateDataType<Image>::New();
	- DataStorage::SetOfObjects::ConstPointer nodes = sender->GetDataStorage()->GetSubset(isImageData).GetPointer();
	- if(nodes.IsNull() \|\| nodes->size() <= 0)
	- return;
	- Point3D worldposition = positionEvent->GetPositionInWorld();
	- for (unsigned int x = 0; x < nodes->size(); x++)
	- {
	- DataNode::Pointer node = static_cast<DataNode::Pointer>( nodes->at(x) );
	- if(node.IsNotNull())
	- {
	- Image::Pointer image = dynamic_cast<Image*>( node->GetData() );
	- if( image.IsNotNull() && image->GetGeometry()->IsInside(worldposition) )
	- {
	- std::string typeStr = image->GetPixelType().GetComponentTypeAsString();
	- int value = 0;
	- try
	- {
	- if( typeStr == "int" )
	- {
	- ImagePixelReadAccessor<int, 3> readAccess( image );
	- value = static_cast<int>( readAccess.GetPixelByWorldCoordinates( worldposition ) );
	- }
	- else if( typeStr == "unsigned_int" )
	- {
	- ImagePixelReadAccessor<unsigned int, 3> readAccess( image );
	- value = static_cast<int>( readAccess.GetPixelByWorldCoordinates( worldposition ) );
	- }
	- else if( typeStr == "unsigned_char" )
	- {
	- ImagePixelReadAccessor<unsigned char, 3> readAccess( image );
	- value = static_cast<int>( readAccess.GetPixelByWorldCoordinates( worldposition ) );
	- }
	- else if( typeStr == "short" )
	- {
	- ImagePixelReadAccessor<short, 3> readAccess( image );
	- value = static_cast<int>( readAccess.GetPixelByWorldCoordinates( worldposition ) );
	- }
	- else if( typeStr == "float" )
	- {
	- ImagePixelReadAccessor<float, 3> readAccess( image );
	- value = static_cast<int>( readAccess.GetPixelByWorldCoordinates( worldposition ) );
	- }
	- else if( typeStr == "double" )
	- {
	- ImagePixelReadAccessor<double, 3> readAccess( image );
	- value = static_cast<int>( readAccess.GetPixelByWorldCoordinates( worldposition ) );
	- }
	- else if( typeStr == "unsigned_short" )
	- {
	- ImagePixelReadAccessor<unsigned short, 3> readAccess( image );
	- value = static_cast<int>( readAccess.GetPixelByWorldCoordinates( worldposition ) );
	- }
	- else
	- {
	- MITK_WARN("QmitkFreeSurferParcellationHandler") << "Pixeltype '" << typeStr << "' is not implemented yet.";
	- return;
	- }
	- emit this->changed( value );
	- QString name( QString::fromStdString( this->m_Translator->GetName( value ) ) );
	- emit this->changed( name );
	- MousePressEvent::Pointer mouseEvent = dynamic_cast<MousePressEvent*>( interactionEvent );
	- MouseWheelEvent::Pointer wheelEvent = dynamic_cast<MouseWheelEvent*>( interactionEvent );
	- if(mouseEvent.IsNotNull())
	- {
	- emit this->clicked( value );
	- emit this->clicked( name );
	- }
	- if( wheelEvent.IsNotNull() )
	- {
	- emit this->scrolled( value );
	- emit this->scrolled( name );
	- }
	- return; // exit loop
	- }
	- catch( const Exception& ex )
	- {
	- MITK_WARN("QmitkFreeSurferParcellationHandler") << "Could not access image for reading pixelvalue due to: " << ex.GetDescription();
	- }
	- catch(...)
	- {
	- MITK_WARN("QmitkFreeSurferParcellationHandler") << "Could not access image for reading pixelvalue.";
	- }
	- }
	- }
	- }
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/QmitkFreeSurferParcellationHandler.h b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/QmitkFreeSurferParcellationHandler.h
	deleted file mode 100644
	index d4a112ec6f..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/QmitkFreeSurferParcellationHandler.h
	+++ /dev/null
	@@ -1,97 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef QmitkFreeSurferParcellationHandler_h
	-#define QmitkFreeSurferParcellationHandler_h
	-
	-// MITK
	-#include <mitkEventStateMachine.h>
	-#include <mitkFreeSurferParcellationTranslator.h>
	-#include <mitkInteractionEventObserver.h>
	-// Qt
	-#include <QObject>
	-
	-/**
	- * @brief This handler returns either the pixelvalue or anatomical label of the current position of the crosshair inside a visible parcellation.
	- * If no parcellation is visible no data is thrown.
	- */
	-class QmitkFreeSurferParcellationHandler : public QObject, public EventStateMachine, public InteractionEventObserver
	-{
	- Q_OBJECT
	- public:
	- mitkClassMacro(QmitkFreeSurferParcellationHandler, DataInteractor)
	- itkNewMacro(QmitkFreeSurferParcellationHandler)
	- QmitkFreeSurferParcellationHandler();
	- ~QmitkFreeSurferParcellationHandler();
	-
	-
	- // Signals
	- Q_SIGNALS:
	- /**
	- * @brief Emitted when pixelValue has changed
	- * @param value of the current selected pixel
	- */
	- void changed(int);
	- /**
	- * @brief Emitted when pixelValue has changed
	- * @param anatomical label
	- */
	- void changed(const QString &);
	- /**
	- * @brief Thrown if and only if the left mousebutton is pressed and pixelValue has changed
	- * @param value of the selected pixel
	- */
	- void clicked(int);
	- /**
	- * @brief Thrown if and only if the left mousebutton is pressed and pixelValue has changed
	- * @param anatomical label
	- */
	- void clicked(const QString &);
	- /**
	- * @brief Thrown if mouse scrolled and pixelvalue changed
	- * @param value of the selected pixel
	- */
	- void scrolled(int);
	- /**
	- * @brief Thrown if mouse scrolled and anatomcial labl changed
	- * @param anatomical label
	- */
	- void scrolled(const QString &);
	-
	-
	- // Methods
	- protected:
	- virtual void Notify(InteractionEvent* interactionEvent,bool isHandled);
	-
	-
	- // Members
	- protected:
	- /**
	- * @brief The current pixelvalue
	- */
	- int m_LastPixelvalue;
	- /**
	- * @brief Translator for coverting pixelvalue into anatomical label
	- */
	- mitk::FreeSurferParcellationTranslator::Pointer m_Translator;
	- /**
	- * Reference to the service registration of the observer,
	- * it is needed to unregister the observer on unload.
	- */
	- us::ServiceRegistration<InteractionEventObserver> m_ServiceRegistration;
	-};
	-
	-#endif //QmitkPixelvalueHandler_h
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/QmitkFreeSurferParcellationWidget.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/QmitkFreeSurferParcellationWidget.cpp
	deleted file mode 100644
	index 18ce0975ab..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/QmitkFreeSurferParcellationWidget.cpp
	+++ /dev/null
	@@ -1,49 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkFreeSurferParcellationWidget.h"
	-
	-QmitkFreeSurferParcellationWidget::QmitkFreeSurferParcellationWidget(QWidget *parent) :
	- QWidget( parent ),
	- m_Handler( new QmitkFreeSurferParcellationHandler() )
	-{
	- this->m_View.setupUi( this );
	- this->connect( this->m_Handler, SIGNAL(clicked(QString)), this, SLOT(OnHandlerClicked(QString)) );
	- this->connect( this->m_Handler, SIGNAL(changed(QString)), this, SLOT(OnHandlerHovered(QString)) );
	-}
	-
	-QmitkFreeSurferParcellationWidget::~QmitkFreeSurferParcellationWidget()
	-{
	- if( m_Handler )
	- {
	- this->disconnect( this->m_Handler, SIGNAL(clicked(QString)), this, SLOT(OnHandlerClicked(QString)) );
	- this->disconnect( this->m_Handler, SIGNAL(changed(QString)), this, SLOT(OnHandlerHovered(QString)) );
	- delete m_Handler;
	- m_Handler = nullptr;
	- }
	-}
	-
	-void QmitkFreeSurferParcellationWidget::OnHandlerClicked(const QString &name)
	-{
	- this->m_View.clickedLabel->setText( name );
	- emit this->Clicked( name );
	-}
	-
	-void QmitkFreeSurferParcellationWidget::OnHandlerHovered(const QString &name)
	-{
	- this->m_View.hoveredLabel->setText( name + " hovered" );
	- emit this->Hovered( name );
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/QmitkFreeSurferParcellationWidget.h b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/QmitkFreeSurferParcellationWidget.h
	deleted file mode 100644
	index 672d341872..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/QmitkFreeSurferParcellationWidget.h
	+++ /dev/null
	@@ -1,66 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef QmitkFreeSurferParcellationWidget_h
	-#define QmitkFreeSurferParcellationWidget_h
	-
	-// Qmitk
	-#include "ui_QmitkFreeSurferParcellationWidgetControls.h"
	-#include <QmitkFreeSurferParcellationHandler.h>
	-// Qt
	-#include <QObject>
	-#include <QString>
	-#include <QWidget>
	-
	-class QmitkFreeSurferParcellationWidget;
	-
	-class QmitkFreeSurferParcellationWidget : public QWidget
	-{
	- Q_OBJECT
	-
	- public:
	- typedef Ui::QmitkFreeSurferParcellationWidgetControls ViewType;
	- typedef QmitkFreeSurferParcellationHandler HandlerType;
	-
	- // Constructors
	- QmitkFreeSurferParcellationWidget( QWidget* parent = 0 );
	- ~QmitkFreeSurferParcellationWidget();
	-
	-
	- // Signals
	- Q_SIGNALS:
	- /**
	- * @brief Emitted when anatomical region is clicked
	- */
	- void Clicked( const QString & );
	- /**
	- * @brief Emitted when anatomical region is hovered
	- */
	- void Hovered( const QString & );
	-
	-
	- // Slots
	- protected slots:
	- void OnHandlerClicked( const QString & name );
	- void OnHandlerHovered( const QString & name );
	-
	- protected:
	- // Members:
	- ViewType m_View;
	- HandlerType* m_Handler;
	-};
	-
	-#endif //QmitkFreeSurferParcellationWidget_h
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/QmitkFreeSurferParcellationWidgetControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/QmitkFreeSurferParcellationWidgetControls.ui
	deleted file mode 100644
	index cb89920243..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/QmitkFreeSurferParcellationWidgetControls.ui
	+++ /dev/null
	@@ -1,103 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<ui version="4.0">
	- <class>QmitkFreeSurferParcellationWidgetControls</class>
	- <widget class="QWidget" name="QmitkFreeSurferParcellationWidgetControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>82</width>
	- <height>52</height>
	- </rect>
	- </property>
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="windowTitle">
	- <string>QmitkTemplate</string>
	- </property>
	- <layout class="QVBoxLayout" name="verticalLayout">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QLabel" name="hoveredLabel">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="text">
	- <string>Unknown hovered</string>
	- </property>
	- <property name="alignment">
	- <set>Qt::AlignLeading\|Qt::AlignLeft\|Qt::AlignTop</set>
	- </property>
	- <property name="wordWrap">
	- <bool>true</bool>
	- </property>
	- <property name="openExternalLinks">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QLabel" name="clickedLabel">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="text">
	- <string>Unknown</string>
	- </property>
	- <property name="alignment">
	- <set>Qt::AlignLeading\|Qt::AlignLeft\|Qt::AlignTop</set>
	- </property>
	- <property name="wordWrap">
	- <bool>true</bool>
	- </property>
	- <property name="openExternalLinks">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <spacer name="verticalSpacer">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- </layout>
	- </widget>
	- <layoutdefault spacing="6" margin="11"/>
	- <resources/>
	- <connections/>
	-</ui>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/Perspectives/QmitkConnectomicsPerspective.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/Perspectives/QmitkConnectomicsPerspective.cpp
	deleted file mode 100644
	index 0f9a3e68c9..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/Perspectives/QmitkConnectomicsPerspective.cpp
	+++ /dev/null
	@@ -1,47 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkConnectomicsPerspective.h"
	-#include "berryIViewLayout.h"
	-
	-void QmitkConnectomicsPerspective::CreateInitialLayout(berry::IPageLayout::Pointer layout)
	-{
	- /////////////////////////////////////////////////////
	- // all di-app perspectives should have the following:
	- /////////////////////////////////////////////////////
	-
	- QString editorArea = layout->GetEditorArea();
	-
	- layout->AddStandaloneViewPlaceholder("org.mitk.views.viewnavigatorview", berry::IPageLayout::LEFT, 0.3f, editorArea, false);
	-
	- layout->AddStandaloneView("org.mitk.views.datamanager", false, berry::IPageLayout::LEFT, 0.3f, editorArea);
	-
	- layout->AddStandaloneView("org.mitk.views.controlvisualizationpropertiesview", false, berry::IPageLayout::BOTTOM, .15f, "org.mitk.views.datamanager");
	-
	- berry::IFolderLayout::Pointer left =
	- layout->CreateFolder("org.mbi.diffusionimaginginternal.leftcontrols", berry::IPageLayout::BOTTOM, 0.15f, "org.mitk.views.controlvisualizationpropertiesview");
	-
	- layout->AddStandaloneViewPlaceholder("org.mitk.views.imagenavigator", berry::IPageLayout::BOTTOM, .7f, "org.mbi.diffusionimaginginternal.leftcontrols", false);
	-
	- /////////////////////////////////////////////
	- // here goes the perspective specific stuff
	- /////////////////////////////////////////////
	-
	- left->AddView("org.mitk.views.connectomicsdata");
	- left->AddView("org.mitk.views.connectomicsstatistics");
	- left->AddView("org.mitk.views.connectomicsnetworkoperations");
	- left->AddView("org.mitk.views.randomparcellationview");
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/Perspectives/QmitkConnectomicsPerspective.h b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/Perspectives/QmitkConnectomicsPerspective.h
	deleted file mode 100644
	index 9060b0185c..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/Perspectives/QmitkConnectomicsPerspective.h
	+++ /dev/null
	@@ -1,36 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef QmitkConnectomicsPerspective_H_
	-#define QmitkConnectomicsPerspective_H_
	-
	-#include <berryIPerspectiveFactory.h>
	-
	-class QmitkConnectomicsPerspective : public QObject, public berry::IPerspectiveFactory
	-{
	- Q_OBJECT
	- Q_INTERFACES(berry::IPerspectiveFactory)
	-
	-public:
	-
	- QmitkConnectomicsPerspective() {}
	- ~QmitkConnectomicsPerspective() {}
	-
	- void CreateInitialLayout(berry::IPageLayout::Pointer layout) override;
	-};
	-
	-#endif /* QmitkConnectomicsPerspective_H_ */
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkConnectomicsDataView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkConnectomicsDataView.cpp
	deleted file mode 100644
	index b6529af14e..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkConnectomicsDataView.cpp
	+++ /dev/null
	@@ -1,522 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-// ####### Blueberry includes #######
	-#include <berryISelectionService.h>
	-#include <berryIWorkbenchWindow.h>
	-
	-// ####### Qmitk includes #######
	-#include "QmitkConnectomicsDataView.h"
	-
	-// ####### Qt includes #######
	-#include <QMessageBox>
	-
	-// ####### ITK includes #######
	-#include <itkRGBAPixel.h>
	-
	-// ####### MITK includes #######
	-
	-#include <mitkConnectomicsConstantsManager.h>
	-#include "mitkConnectomicsSyntheticNetworkGenerator.h"
	-#include "mitkConnectomicsSimulatedAnnealingManager.h"
	-#include "mitkConnectomicsSimulatedAnnealingPermutationModularity.h"
	-#include "mitkConnectomicsSimulatedAnnealingCostFunctionModularity.h"
	-#include <mitkCorrelationCalculator.h>
	-
	-// Includes for image casting between ITK and MITK
	-#include "mitkImageCast.h"
	-#include "mitkITKImageImport.h"
	-#include "mitkImageAccessByItk.h"
	-
	-const std::string QmitkConnectomicsDataView::VIEW_ID = "org.mitk.views.connectomicsdata";
	-
	-QmitkConnectomicsDataView::QmitkConnectomicsDataView()
	-: QmitkAbstractView()
	-, m_Controls( 0 )
	-, m_ConnectomicsNetworkCreator( mitk::ConnectomicsNetworkCreator::New() )
	-, m_demomode( false )
	-, m_currentIndex( 0 )
	-{
	-}
	-
	-QmitkConnectomicsDataView::~QmitkConnectomicsDataView()
	-{
	-}
	-
	-
	-void QmitkConnectomicsDataView::CreateQtPartControl( QWidget *parent )
	-{
	- // build up qt view, unless already done
	- if ( !m_Controls )
	- {
	- // create GUI widgets from the Qt Designer's .ui file
	- m_Controls = new Ui::QmitkConnectomicsDataViewControls;
	- m_Controls->setupUi( parent );
	-
	- QObject::connect( m_Controls->networkifyPushButton, SIGNAL(clicked()), this, SLOT(OnNetworkifyPushButtonClicked()) );
	- QObject::connect( m_Controls->syntheticNetworkCreationPushButton, SIGNAL(clicked()), this, SLOT(OnSyntheticNetworkCreationPushButtonClicked()) );
	- QObject::connect( (QObject*)( m_Controls->syntheticNetworkComboBox ), SIGNAL(currentIndexChanged (int)), this, SLOT(OnSyntheticNetworkComboBoxCurrentIndexChanged(int)) );
	- QObject::connect( m_Controls->createCorrelationMatrixPushButton, SIGNAL(clicked()), this, SLOT(OnCreateCorrelationMatrixPushButtonClicked()) );
	- }
	-
	- // GUI is different for developer and demo mode
	- m_demomode = true;
	- if( m_demomode )
	- {
	- this->m_Controls->networkifyPushButton->show();
	- this->m_Controls->networkifyPushButton->setText( "Create Network" );
	- this->m_Controls->syntheticNetworkOptionsGroupBox->show();
	- //--------------------------- fill comboBox---------------------------
	- this->m_Controls->syntheticNetworkComboBox->insertItem(0,"Regular lattice");
	- this->m_Controls->syntheticNetworkComboBox->insertItem(1,"Heterogenic sphere");
	- this->m_Controls->syntheticNetworkComboBox->insertItem(2,"Random network");
	-
	- this->m_Controls->mappingStrategyComboBox->insertItem(m_ConnectomicsNetworkCreator->EndElementPosition, "Use label of end position of fibers");
	- this->m_Controls->mappingStrategyComboBox->insertItem(m_ConnectomicsNetworkCreator->EndElementPositionAvoidingWhiteMatter, "Extrapolate label");
	- }
	- else
	- {
	- this->m_Controls->networkifyPushButton->show();
	- this->m_Controls->networkifyPushButton->setText( "Networkify" );
	- this->m_Controls->syntheticNetworkOptionsGroupBox->show();
	- //--------------------------- fill comboBox---------------------------
	- this->m_Controls->syntheticNetworkComboBox->insertItem(0,"Regular lattice");
	- this->m_Controls->syntheticNetworkComboBox->insertItem(1,"Heterogenic sphere");
	- this->m_Controls->syntheticNetworkComboBox->insertItem(2,"Random network");
	- this->m_Controls->syntheticNetworkComboBox->insertItem(3,"Scale free network");
	- this->m_Controls->syntheticNetworkComboBox->insertItem(4,"Small world network");
	-
	- this->m_Controls->mappingStrategyComboBox->insertItem(m_ConnectomicsNetworkCreator->EndElementPosition, "Use label of end position of fibers");
	- this->m_Controls->mappingStrategyComboBox->insertItem(m_ConnectomicsNetworkCreator->EndElementPositionAvoidingWhiteMatter, "Extrapolate label");
	- this->m_Controls->mappingStrategyComboBox->insertItem(m_ConnectomicsNetworkCreator->JustEndPointVerticesNoLabel, "Use end position of fibers, no label");
	- }
	-
	- this->WipeDisplay();
	-}
	-
	-
	-void QmitkConnectomicsDataView::SetFocus()
	-{
	- m_Controls->mappingStrategyComboBox->setFocus();
	-}
	-
	-void QmitkConnectomicsDataView::WipeDisplay()
	-{
	- m_Controls->lblWarning->setVisible( true );
	- m_Controls->inputImageOneNameLabel->setText( mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_DASH );
	- m_Controls->inputImageOneNameLabel->setVisible( false );
	- m_Controls->inputImageOneLabel->setVisible( false );
	- m_Controls->inputImageTwoNameLabel->setText( mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_DASH );
	- m_Controls->inputImageTwoNameLabel->setVisible( false );
	- m_Controls->inputImageTwoLabel->setVisible( false );
	-}
	-
	-void QmitkConnectomicsDataView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /part/, const QList<mitk::DataNode::Pointer>& nodes)
	-{
	- this->WipeDisplay();
	-
	- // Valid options are either
	- // 1 image (parcellation)
	- //
	- // 1 image (parcellation)
	- // 1 fiber bundle
	- //
	- // 1 network
	- if( nodes.size() > 2 )
	- {
	- return;
	- }
	-
	- bool alreadyFiberBundleSelected( false ), alreadyImageSelected( false ), currentFormatUnknown( true );
	- // iterate all selected objects, adjust warning visibility
	- for (mitk::DataNode::Pointer node: nodes)
	- {
	- currentFormatUnknown = true;
	-
	- if( node.IsNotNull() && dynamic_cast<mitk::Image*>(node->GetData()) )
	- {
	- currentFormatUnknown = false;
	- if( alreadyImageSelected )
	- {
	- this->WipeDisplay();
	- return;
	- }
	- alreadyImageSelected = true;
	- m_Controls->lblWarning->setVisible( false );
	- m_Controls->inputImageOneNameLabel->setText(node->GetName().c_str());
	- m_Controls->inputImageOneNameLabel->setVisible( true );
	- m_Controls->inputImageOneLabel->setVisible( true );
	- }
	-
	- if( node.IsNotNull() && dynamic_cast<mitk::FiberBundle*>(node->GetData()) )
	- {
	- currentFormatUnknown = false;
	- // a fiber bundle has to be in conjunction with a parcellation
	- if( nodes.size() != 2 \|\| alreadyFiberBundleSelected )
	- {
	- this->WipeDisplay();
	- return;
	- }
	- alreadyFiberBundleSelected = true;
	- m_Controls->lblWarning->setVisible( false );
	- m_Controls->inputImageTwoNameLabel->setText(node->GetName().c_str());
	- m_Controls->inputImageTwoNameLabel->setVisible( true );
	- m_Controls->inputImageTwoLabel->setVisible( true );
	- }
	-
	- { // network section
	- mitk::ConnectomicsNetwork* network = dynamic_cast<mitk::ConnectomicsNetwork*>( node->GetData() );
	- if( node.IsNotNull() && network )
	- {
	- currentFormatUnknown = false;
	- if( nodes.size() != 1 )
	- {
	- // only valid option is a single network
	- this->WipeDisplay();
	- return;
	- }
	- m_Controls->lblWarning->setVisible( false );
	- m_Controls->inputImageOneNameLabel->setText(node->GetName().c_str());
	- m_Controls->inputImageOneNameLabel->setVisible( true );
	- m_Controls->inputImageOneLabel->setVisible( true );
	- }
	- } // end network section
	-
	- if ( currentFormatUnknown )
	- {
	- this->WipeDisplay();
	- return;
	- }
	- } // end for loop
	-}
	-
	-void QmitkConnectomicsDataView::OnSyntheticNetworkComboBoxCurrentIndexChanged(int currentIndex)
	-{
	- m_currentIndex = currentIndex;
	-
	- switch (m_currentIndex) {
	- case 0:
	- this->m_Controls->parameterOneLabel->setText( "Nodes per side" );
	- this->m_Controls->parameterTwoLabel->setText( "Internode distance" );
	- this->m_Controls->parameterOneSpinBox->setEnabled( true );
	- this->m_Controls->parameterOneSpinBox->setValue( 5 );
	- this->m_Controls->parameterTwoDoubleSpinBox->setEnabled( true );
	- this->m_Controls->parameterTwoDoubleSpinBox->setMaximum( 999.999 );
	- this->m_Controls->parameterTwoDoubleSpinBox->setValue( 10.0 );
	- break;
	- case 1:
	- this->m_Controls->parameterOneLabel->setText( "Number of nodes" );
	- this->m_Controls->parameterTwoLabel->setText( "Radius" );
	- this->m_Controls->parameterOneSpinBox->setEnabled( true );
	- this->m_Controls->parameterOneSpinBox->setValue( 1000 );
	- this->m_Controls->parameterTwoDoubleSpinBox->setEnabled( true );
	- this->m_Controls->parameterTwoDoubleSpinBox->setMaximum( 999.999 );
	- this->m_Controls->parameterTwoDoubleSpinBox->setValue( 50.0 );
	- break;
	- case 2:
	- this->m_Controls->parameterOneLabel->setText( "Number of nodes" );
	- this->m_Controls->parameterTwoLabel->setText( "Edge percentage" );
	- this->m_Controls->parameterOneSpinBox->setEnabled( true );
	- this->m_Controls->parameterOneSpinBox->setValue( 100 );
	- this->m_Controls->parameterTwoDoubleSpinBox->setEnabled( true );
	- this->m_Controls->parameterTwoDoubleSpinBox->setMaximum( 1.0 );
	- this->m_Controls->parameterTwoDoubleSpinBox->setValue( 0.5 );
	- break;
	- case 3:
	- //GenerateSyntheticScaleFreeNetwork( network, 1000 );
	- break;
	- case 4:
	- //GenerateSyntheticSmallWorldNetwork( network, 1000 );
	- break;
	- default:
	- this->m_Controls->parameterOneLabel->setText( "Parameter 1" );
	- this->m_Controls->parameterTwoLabel->setText( "Paramater 2" );
	- this->m_Controls->parameterOneSpinBox->setEnabled( false );
	- this->m_Controls->parameterOneSpinBox->setValue( 0 );
	- this->m_Controls->parameterTwoDoubleSpinBox->setEnabled( false );
	- this->m_Controls->parameterTwoDoubleSpinBox->setValue( 0.0 );
	- }
	-}
	-
	-void QmitkConnectomicsDataView::OnSyntheticNetworkCreationPushButtonClicked()
	-{
	- // warn if trying to create a very big network
	- // big network is a network with > 5000 nodes (estimate)
	- // this might fill up the memory to the point it freezes
	- int numberOfNodes( 0 );
	- switch (m_currentIndex) {
	- case 0:
	- numberOfNodes = this->m_Controls->parameterOneSpinBox->value()
	- * this->m_Controls->parameterOneSpinBox->value()
	- * this->m_Controls->parameterOneSpinBox->value();
	- break;
	- case 1:
	- numberOfNodes = this->m_Controls->parameterOneSpinBox->value();
	- break;
	- case 2:
	- numberOfNodes = this->m_Controls->parameterOneSpinBox->value();
	- break;
	- case 3:
	- // not implemented yet
	- break;
	- case 4:
	- // not implemented yet
	- break;
	- default:
	- break;
	- }
	-
	- if( numberOfNodes > 5000 )
	- {
	- QMessageBox msgBox;
	- msgBox.setText("Trying to generate very large network.");
	- msgBox.setIcon( QMessageBox::Warning );
	- msgBox.setInformativeText("You are trying to generate a network with more than 5000 nodes, this is very resource intensive and might lead to program instability. Proceed with network generation?");
	- msgBox.setStandardButtons(QMessageBox::Yes \| QMessageBox::No);
	- msgBox.setDefaultButton(QMessageBox::No);
	- int ret = msgBox.exec();
	-
	- switch (ret) {
	- case QMessageBox::Yes:
	- // continue
	- break;
	- case QMessageBox::No:
	- // stop
	- return;
	- break;
	-
	- default:
	- // should never be reached
	- break;
	- }
	- }
	-
	- // proceed
	- mitk::ConnectomicsSyntheticNetworkGenerator::Pointer generator = mitk::ConnectomicsSyntheticNetworkGenerator::New();
	-
	- mitk::DataNode::Pointer networkNode = mitk::DataNode::New();
	- int parameterOne = this->m_Controls->parameterOneSpinBox->value();
	- double parameterTwo = this->m_Controls->parameterTwoDoubleSpinBox->value();
	- //add network to datastorage
	- networkNode->SetData( generator->CreateSyntheticNetwork( m_currentIndex, parameterOne, parameterTwo ) );
	- networkNode->SetName( mitk::ConnectomicsConstantsManager::CONNECTOMICS_PROPERTY_DEFAULT_CNF_NAME );
	- if( generator->WasGenerationSuccessfull() )
	- {
	- this->GetDataStorage()->Add( networkNode );
	- }
	- else
	- {
	- MITK_WARN << "Problem occured during synthetic network generation.";
	- }
	-
	- mitk::RenderingManager::GetInstance()->InitializeViews(
	- networkNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true );
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	-
	- return;
	-}
	-
	-void QmitkConnectomicsDataView::OnNetworkifyPushButtonClicked()
	-{
	- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
	- if ( nodes.empty() )
	- {
	- QMessageBox::information( nullptr, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_CONNECTOMICS_CREATION, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_SELECTION_WARNING);
	- return;
	- }
	-
	- if (! ( nodes.size() == 2 ) )
	- {
	- QMessageBox::information( nullptr, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_CONNECTOMICS_CREATION, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_SELECTION_WARNING);
	- return;
	- }
	- mitk::DataNode* firstNode = nodes.front();
	- mitk::DataNode* secondNode = nodes.at(1);
	-
	- if (!firstNode)
	- {
	- // Nothing selected. Inform the user and return
	- QMessageBox::information( nullptr, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_CONNECTOMICS_CREATION, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_SELECTION_WARNING);
	- return;
	- }
	-
	- // here we have a valid mitk::DataNode
	-
	- // a node itself is not very useful, we need its data item (the image)
	- mitk::BaseData* firstData = firstNode->GetData();
	- mitk::BaseData* secondData = secondNode->GetData();
	- if (firstData && secondData)
	- {
	- // test if this data item is an image or not (could also be a surface or something totally different)
	- mitk::Image* image = dynamic_cast<mitk::Image*>( firstData );
	- mitk::FiberBundle* fiberBundle = dynamic_cast<mitk::FiberBundle*>( secondData );
	-
	- // check whether order was switched
	- if (! (image && fiberBundle) )
	- {
	- image = dynamic_cast<mitk::Image*>( secondData );
	- fiberBundle = dynamic_cast<mitk::FiberBundle*>( firstData );
	- }
	-
	- if (image && fiberBundle)
	- {
	- mitk::ConnectomicsNetworkCreator::MappingStrategy mappingStrategy =
	- static_cast<mitk::ConnectomicsNetworkCreator::MappingStrategy>(this->m_Controls->mappingStrategyComboBox->currentIndex());
	-
	- m_ConnectomicsNetworkCreator->SetSegmentation( image );
	- m_ConnectomicsNetworkCreator->SetFiberBundle( fiberBundle );
	- m_ConnectomicsNetworkCreator->CalculateCenterOfMass();
	- m_ConnectomicsNetworkCreator->SetEndPointSearchRadius( 15 );
	- m_ConnectomicsNetworkCreator->SetMappingStrategy( mappingStrategy );
	- m_ConnectomicsNetworkCreator->CreateNetworkFromFibersAndSegmentation();
	- mitk::DataNode::Pointer networkNode = mitk::DataNode::New();
	-
	- //add network to datastorage
	- networkNode->SetData( m_ConnectomicsNetworkCreator->GetNetwork() );
	- networkNode->SetName( mitk::ConnectomicsConstantsManager::CONNECTOMICS_PROPERTY_DEFAULT_CNF_NAME );
	- this->GetDataStorage()->Add( networkNode );
	- }
	- }
	-
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-void QmitkConnectomicsDataView::OnCreateCorrelationMatrixPushButtonClicked()
	-{
	-
	- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
	- if ( nodes.empty() )
	- {
	- QMessageBox::information( nullptr, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_CONNECTOMICS, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_FMRI_CORRELATION_SELECTION_WARNING);
	- return;
	- }
	-
	- if( nodes.size() == 1 )
	- {
	- mitk::DataNode* firstNode = nodes.front();
	-
	- if (!firstNode)
	- {
	- // Nothing selected. Inform the user and return
	- QMessageBox::information( nullptr, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_CONNECTOMICS, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_FMRI_CORRELATION_SELECTION_WARNING);
	- return;
	- }
	-
	- // here we have a valid mitk::DataNode
	-
	- // a node itself is not very useful, we need its data item (the image)
	- mitk::BaseData* firstData = firstNode->GetData();
	- if (firstData)
	- {
	- // test if this data item is an image or not (could also be a surface or something totally different)
	- mitk::Image* image = dynamic_cast<mitk::Image*>( firstData );
	- if(image && image->GetDimension() == 4)
	- {
	- AccessFixedDimensionByItk(image, DoWholeCorrelation, 4);
	- }
	- }
	- }
	- else if( nodes.size() == 2 )
	- {
	- mitk::DataNode* firstNode = nodes.front();
	- mitk::DataNode* secondNode = nodes.at(1);
	-
	- if (!firstNode)
	- {
	- // Nothing selected. Inform the user and return
	- QMessageBox::information( nullptr, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_CONNECTOMICS, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_FMRI_CORRELATION_SELECTION_WARNING);
	- return;
	- }
	- if (!secondNode)
	- {
	- // Nothing selected. Inform the user and return
	- QMessageBox::information( nullptr, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_CONNECTOMICS, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_FMRI_CORRELATION_SELECTION_WARNING);
	- return;
	- }
	-
	-
	- // here we have a valid mitk::DataNode
	-
	- // a node itself is not very useful, we need its data item (the image)
	- mitk::BaseData* firstData = firstNode->GetData();
	- mitk::BaseData* secondData = secondNode->GetData();
	- if (firstData && secondData)
	- {
	- // test if this data item is an image or not (could also be a surface or something totally different)
	- mitk::Image* firstImage = dynamic_cast<mitk::Image*>( firstData );
	- mitk::Image* secondImage = dynamic_cast<mitk::Image*>( secondData );
	- if(firstImage && secondImage)
	- {
	- if( firstImage->GetDimension() == 4 && secondImage->GetDimension() == 3 )
	- {
	- AccessFixedDimensionByItk_n(firstImage, DoParcelCorrelation, 4, ( secondImage));
	- }
	- else if( firstImage->GetDimension() == 3 && secondImage->GetDimension() == 4 )
	- {
	- AccessFixedDimensionByItk_n(secondImage, DoParcelCorrelation, 4, ( firstImage));
	- }
	- else
	- {
	- QMessageBox::information( nullptr, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_CONNECTOMICS, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_FMRI_CORRELATION_SELECTION_WARNING);
	- return;
	- }
	- }
	- }
	- }
	-}
	-
	-template< typename TPixel, unsigned int VImageDimension >
	-void QmitkConnectomicsDataView::DoWholeCorrelation( itk::Image<TPixel, VImageDimension>* itkTimeSeriesImage )
	-{
	- typename mitk::CorrelationCalculator<TPixel>::Pointer correlationCalculator = mitk::CorrelationCalculator<TPixel>::New();
	-
	- mitk::Image::Pointer timeSeriesImage = mitk::Image::New();
	- mitk::CastToMitkImage(itkTimeSeriesImage, timeSeriesImage);
	-
	- correlationCalculator->SetTimeSeriesImage( timeSeriesImage );
	- correlationCalculator->SetParcellationImage( nullptr );
	-
	- correlationCalculator->DoWholeCorrelation();
	- const vnl_matrix< double >* vnlmat = correlationCalculator->GetCorrelationMatrix();
	- std::stringstream output;
	- for(unsigned int i(0); i < (*vnlmat).rows(); ++i)
	- {
	- for(unsigned int j(0); j < (*vnlmat).cols(); ++j)
	- {
	- output << (*vnlmat)[i][j] << " ";
	- }
	- output << "\n";
	- }
	- MITK_INFO << "\n" << output.str();
	-}
	-
	-template< typename TPixel, unsigned int VImageDimension >
	-void QmitkConnectomicsDataView::DoParcelCorrelation( itk::Image<TPixel, VImageDimension>* itkTimeSeriesImage, mitk::Image::Pointer parcelImage )
	-{
	- typename mitk::CorrelationCalculator<TPixel>::Pointer correlationCalculator = mitk::CorrelationCalculator<TPixel>::New();
	-
	- mitk::Image::Pointer timeSeriesImage = mitk::Image::New();
	- mitk::CastToMitkImage(itkTimeSeriesImage, timeSeriesImage);
	-
	- correlationCalculator->SetTimeSeriesImage( timeSeriesImage );
	- correlationCalculator->SetParcellationImage( parcelImage );
	-
	- correlationCalculator->DoParcelCorrelation();
	- mitk::DataNode::Pointer networkNode = mitk::DataNode::New();
	- networkNode->SetData( correlationCalculator->GetConnectomicsNetwork() );
	- networkNode->SetName("ParcelCorrelationNetwork");
	- this->GetDataStorage()->Add(networkNode);
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkConnectomicsDataView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkConnectomicsDataView.h
	deleted file mode 100644
	index 55cce873d4..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkConnectomicsDataView.h
	+++ /dev/null
	@@ -1,109 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef QmitkConnectomicsDataView_h
	-#define QmitkConnectomicsDataView_h
	-
	-#include <berryISelectionListener.h>
	-
	-#include <QmitkAbstractView.h>
	-
	-#include "ui_QmitkConnectomicsDataViewControls.h"
	-
	-#include "mitkConnectomicsNetworkCreator.h"
	-#include "mitkConnectomicsNetworkMapper3D.h"
	-
	-// ####### ITK includes #######
	-#include <itkImage.h>
	-
	-/*!
	-\brief QmitkConnectomicsDataView
	-
	-This view provides functionality for the generation of networks. Either from parcellation and fiber bundle or synthetically.
	-*/
	-class QmitkConnectomicsDataView : public QmitkAbstractView
	-{
	- // this is needed for all Qt objects that should have a Qt meta-object
	- // (everything that derives from QObject and wants to have signal/slots)
	- Q_OBJECT
	-
	-public:
	-
	- static const std::string VIEW_ID;
	-
	- QmitkConnectomicsDataView();
	- virtual ~QmitkConnectomicsDataView();
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	-
	- ///
	- /// Sets the focus to an internal widget.
	- ///
	- virtual void SetFocus() override;
	-
	- protected slots:
	-
	- /// \brief Align two images by copying the geometry
	- void OnNetworkifyPushButtonClicked();
	-
	- /// \brief Create synthetic networks
	- void OnSyntheticNetworkCreationPushButtonClicked();
	-
	- /// \brief Adjust parameters depending on synthetic network type
	- void OnSyntheticNetworkComboBoxCurrentIndexChanged(int currentIndex);
	-
	- /// \brief Create #voxel x #voxel correlation matrix of a timeseries image
	- void OnCreateCorrelationMatrixPushButtonClicked();
	-
	-protected:
	-
	- // ####### Functions #######
	- /// \brief called by QmitkAbstractView when DataManager's selection has changed
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- /// \brief Converts an image into a RGBA image
	- template < typename TPixel, unsigned int VImageDimension >
	- void TurnIntoRGBA( itk::Image<TPixel, VImageDimension>* inputImage);
	-
	- /// \brief Wipe display and empty statistics
	- void WipeDisplay();
	-
	- template< typename TPixel, unsigned int VImageDimension >
	- void DoWholeCorrelation( itk::Image<TPixel, VImageDimension>* itkTimeSeriesImage );
	-
	- template< typename TPixel, unsigned int VImageDimension >
	- void DoParcelCorrelation( itk::Image<TPixel, VImageDimension>* itkTimeSeriesImage, mitk::Image::Pointer parcelImage );
	-
	- // ####### Variables #######
	-
	-
	- Ui::QmitkConnectomicsDataViewControls* m_Controls;
	-
	- mitk::ConnectomicsNetworkCreator::Pointer m_ConnectomicsNetworkCreator;
	-
	- mitk::ConnectomicsNetworkMapper3D::Pointer m_NetworkMapper;
	-
	- // Demo/Developer mode toggle
	- bool m_demomode;
	-
	- // The selected synthetic network type
	- int m_currentIndex;
	-};
	-
	-
	-
	-#endif // _QMITKBRAINNETWORKANALYSISVIEW_H_INCLUDED
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkConnectomicsDataViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkConnectomicsDataViewControls.ui
	deleted file mode 100644
	index 30c38e39f9..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkConnectomicsDataViewControls.ui
	+++ /dev/null
	@@ -1,278 +0,0 @@
	-<?xml version="1.0" encoding="utf-8"?>
	-<ui version="4.0">
	- <class>QmitkConnectomicsDataViewControls</class>
	- <widget class="QWidget" name="QmitkConnectomicsDataViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>286</width>
	- <height>639</height>
	- </rect>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="windowTitle">
	- <string>QmitkTemplate</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="verticalSpacing">
	- <number>25</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QGroupBox" name="inputDataGroupBox">
	- <property name="title">
	- <string>Input Data</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_4">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="lblWarning">
	- <property name="styleSheet">
	- <string notr="true">QLabel { color: rgb(255, 0, 0) }</string>
	- </property>
	- <property name="text">
	- <string>Select a parcellation and a tractogram!</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <layout class="QHBoxLayout" name="horizontalLayout_3">
	- <item>
	- <widget class="QLabel" name="inputImageOneLabel">
	- <property name="text">
	- <string>Image 1:</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QLabel" name="inputImageOneNameLabel">
	- <property name="text">
	- <string>-</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </item>
	- <item row="2" column="0">
	- <layout class="QHBoxLayout" name="horizontalLayout_4">
	- <item>
	- <widget class="QLabel" name="inputImageTwoLabel">
	- <property name="text">
	- <string>Image 2:</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QLabel" name="inputImageTwoNameLabel">
	- <property name="text">
	- <string>-</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QGroupBox" name="networkCreationOptionsGroupBox">
	- <property name="title">
	- <string>Network Creation Options</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_2">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QPushButton" name="networkifyPushButton">
	- <property name="toolTip">
	- <string>Create a network from a parcellation and a fiber image</string>
	- </property>
	- <property name="text">
	- <string>Networkify</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QPushButton" name="createCorrelationMatrixPushButton">
	- <property name="text">
	- <string>Create Correlation Matrix</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QComboBox" name="mappingStrategyComboBox"></widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <widget class="QGroupBox" name="syntheticNetworkOptionsGroupBox">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="title">
	- <string>Synthetic Network Options</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_3">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QComboBox" name="syntheticNetworkComboBox"></widget>
	- </item>
	- <item row="3" column="0">
	- <layout class="QHBoxLayout" name="horizontalLayout_2">
	- <item>
	- <widget class="QLabel" name="parameterTwoLabel">
	- <property name="text">
	- <string>Parameter 2</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QDoubleSpinBox" name="parameterTwoDoubleSpinBox">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="decimals">
	- <number>3</number>
	- </property>
	- <property name="maximum">
	- <double>999.899999999999977</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </item>
	- <item row="2" column="0">
	- <layout class="QHBoxLayout" name="horizontalLayout">
	- <item>
	- <widget class="QLabel" name="parameterOneLabel">
	- <property name="text">
	- <string>Parameter 1</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QSpinBox" name="parameterOneSpinBox">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="maximum">
	- <number>9999</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </item>
	- <item row="0" column="0">
	- <widget class="QPushButton" name="syntheticNetworkCreationPushButton">
	- <property name="text">
	- <string>Create Synthetic Networks</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="6" column="0">
	- <widget class="QGroupBox" name="parcellationGroupBox">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="title">
	- <string>Anatomical labeling</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_5">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QmitkFreeSurferParcellationWidget" name="parcellationWidget" native="true"></widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="7" column="0">
	- <spacer name="verticalSpacer_2">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- </layout>
	- </widget>
	- <layoutdefault spacing="6" margin="11"></layoutdefault>
	- <customwidgets>
	- <customwidget>
	- <class>QmitkFreeSurferParcellationWidget</class>
	- <extends>QWidget</extends>
	- <header>QmitkFreeSurferParcellationWidget.h</header>
	- <container>1</container>
	- </customwidget>
	- </customwidgets>
	- <resources></resources>
	- <connections></connections>
	-</ui>
	\ No newline at end of file
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkConnectomicsNetworkOperationsView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkConnectomicsNetworkOperationsView.cpp
	deleted file mode 100644
	index 6501f8a4de..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkConnectomicsNetworkOperationsView.cpp
	+++ /dev/null
	@@ -1,564 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-// ####### Blueberry includes #######
	-#include <berryISelectionService.h>
	-#include <berryIWorkbenchWindow.h>
	-
	-// ####### Qmitk includes #######
	-#include "QmitkConnectomicsNetworkOperationsView.h"
	-
	-// ####### Qt includes #######
	-#include <QMessageBox>
	-
	-// ####### ITK includes #######
	-#include <itkRGBAPixel.h>
	-
	-// ####### MITK includes #######
	-
	-#include <mitkConnectomicsConstantsManager.h>
	-#include "mitkConnectomicsSimulatedAnnealingManager.h"
	-#include "mitkConnectomicsSimulatedAnnealingPermutationModularity.h"
	-#include "mitkConnectomicsSimulatedAnnealingCostFunctionModularity.h"
	-#include <itkConnectomicsNetworkToConnectivityMatrixImageFilter.h>
	-#include <mitkConnectomicsNetworkThresholder.h>
	-#include <mitkFreeSurferParcellationTranslator.h>
	-#include <mitkRenderingModeProperty.h>
	-
	-// Includes for image casting between ITK and MITK
	-#include "mitkImageCast.h"
	-#include "mitkITKImageImport.h"
	-#include "mitkImageAccessByItk.h"
	-
	-const std::string QmitkConnectomicsNetworkOperationsView::VIEW_ID = "org.mitk.views.connectomicsnetworkoperations";
	-
	-QmitkConnectomicsNetworkOperationsView::QmitkConnectomicsNetworkOperationsView()
	-: QmitkAbstractView()
	-, m_Controls( 0 )
	-, m_demomode( false )
	-, m_currentIndex( 0 )
	-{
	-}
	-
	-QmitkConnectomicsNetworkOperationsView::~QmitkConnectomicsNetworkOperationsView()
	-{
	-}
	-
	-
	-void QmitkConnectomicsNetworkOperationsView::CreateQtPartControl( QWidget *parent )
	-{
	- // build up qt view, unless already done
	- if ( !m_Controls )
	- {
	- // create GUI widgets from the Qt Designer's .ui file
	- m_Controls = new Ui::QmitkConnectomicsNetworkOperationsViewControls;
	- m_Controls->setupUi( parent );
	-
	- QObject::connect( m_Controls->convertToRGBAImagePushButton, SIGNAL(clicked()), this, SLOT(OnConvertToRGBAImagePushButtonClicked()) );
	- QObject::connect( m_Controls->assignFreeSurferColorsPushButton, SIGNAL(clicked()), this, SLOT(OnAssignFreeSurferColorsPushButtonClicked()) );
	- QObject::connect( (QObject*)( m_Controls->modularizePushButton ), SIGNAL(clicked()), this, SLOT(OnModularizePushButtonClicked()) );
	- QObject::connect( (QObject*)( m_Controls->prunePushButton ), SIGNAL(clicked()), this, SLOT(OnPrunePushButtonClicked()) );
	- QObject::connect( (QObject*)( m_Controls->createConnectivityMatrixImagePushButton ), SIGNAL(clicked()), this, SLOT(OnCreateConnectivityMatrixImagePushButtonClicked()) );
	- }
	-
	- // GUI is different for developer and demo mode
	- m_demomode = true;
	- if( m_demomode )
	- {
	- this->m_Controls->convertToRGBAImagePushButton->show();
	- this->m_Controls->assignFreeSurferColorsPushButton->show();
	- this->m_Controls->modularizePushButton->hide();
	- this->m_Controls->pruneOptionsGroupBox->show();
	- }
	- else
	- {
	- this->m_Controls->convertToRGBAImagePushButton->show();
	- this->m_Controls->assignFreeSurferColorsPushButton->show();
	- this->m_Controls->modularizePushButton->show();
	- this->m_Controls->pruneOptionsGroupBox->show();
	- }
	-
	- this->WipeDisplay();
	-}
	-
	-
	-void QmitkConnectomicsNetworkOperationsView::SetFocus()
	-{
	- m_Controls->convertToRGBAImagePushButton->setFocus();
	-}
	-
	-void QmitkConnectomicsNetworkOperationsView::WipeDisplay()
	-{
	- m_Controls->lblWarning->setVisible( true );
	- m_Controls->inputImageOneNameLabel->setText( mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_DASH );
	- m_Controls->inputImageOneNameLabel->setVisible( false );
	- m_Controls->inputImageOneLabel->setVisible( false );
	-}
	-
	-void QmitkConnectomicsNetworkOperationsView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /part/, const QList<mitk::DataNode::Pointer>& nodes)
	-{
	- this->WipeDisplay();
	-
	- // Valid options are either
	- if( nodes.size() > 2 )
	- {
	- return;
	- }
	-
	- bool currentFormatUnknown(true), alreadyImageSelected(false);
	-
	- // iterate all selected objects, adjust warning visibility
	- for (mitk::DataNode::Pointer node: nodes)
	- {
	- currentFormatUnknown = true;
	-
	- if( node.IsNotNull() && dynamic_cast<mitk::Image*>(node->GetData()) )
	- {
	- currentFormatUnknown = false;
	- if( alreadyImageSelected )
	- {
	- this->WipeDisplay();
	- return;
	- }
	- alreadyImageSelected = true;
	- m_Controls->lblWarning->setVisible( false );
	- m_Controls->inputImageOneNameLabel->setText(node->GetName().c_str());
	- m_Controls->inputImageOneNameLabel->setVisible( true );
	- m_Controls->inputImageOneLabel->setVisible( true );
	- }
	-
	- if( node.IsNotNull() )
	- { // network section
	- mitk::ConnectomicsNetwork* network = dynamic_cast<mitk::ConnectomicsNetwork*>( node->GetData() );
	- if( network )
	- {
	- currentFormatUnknown = false;
	- if( nodes.size() != 1 )
	- {
	- // only valid option is a single network
	- this->WipeDisplay();
	- return;
	- }
	- m_Controls->lblWarning->setVisible( false );
	- m_Controls->inputImageOneNameLabel->setText(node->GetName().c_str());
	- m_Controls->inputImageOneNameLabel->setVisible( true );
	- m_Controls->inputImageOneLabel->setVisible( true );
	-
	- }
	- } // end network section
	-
	- if ( currentFormatUnknown )
	- {
	- this->WipeDisplay();
	- return;
	- }
	- } // end for loop
	-}
	-
	-void QmitkConnectomicsNetworkOperationsView::OnConvertToRGBAImagePushButtonClicked()
	-{
	- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
	- if (nodes.empty()) return;
	-
	- mitk::DataNode* node = nodes.front();
	-
	- if (!node)
	- {
	- // Nothing selected. Inform the user and return
	- QMessageBox::information( nullptr, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_CONNECTOMICS, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_ONLY_PARCELLATION_SELECTION_WARNING);
	- return;
	- }
	-
	- // here we have a valid mitk::DataNode
	-
	- // a node itself is not very useful, we need its data item (the image)
	- mitk::BaseData* data = node->GetData();
	- if (data)
	- {
	- // test if this data item is an image or not (could also be a surface or something totally different)
	- mitk::Image* image = dynamic_cast<mitk::Image*>( data );
	- if (image)
	- {
	- std::stringstream message;
	- std::string name;
	- message << mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_PERFORMING_IMAGE_PROCESSING_FOR_IMAGE;
	- if (node->GetName(name))
	- {
	- // a property called "name" was found for this DataNode
	- message << "'" << name << "'";
	- }
	- message << ".";
	- MITK_INFO << message.str();
	-
	- // Convert to RGBA
	- AccessByItk( image, TurnIntoRGBA );
	- this->GetDataStorage()->GetNamedNode( mitk::ConnectomicsConstantsManager::CONNECTOMICS_PROPERTY_DEFAULT_RGBA_NAME )->GetData()->SetGeometry( node->GetData()->GetGeometry() );
	-
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- }
	- else
	- {
	- QMessageBox::information( nullptr, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_CONNECTOMICS, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_ONLY_PARCELLATION_SELECTION_WARNING);
	- return;
	- }
	- }
	- else
	- {
	- QMessageBox::information( nullptr, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_CONNECTOMICS, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_ONLY_PARCELLATION_SELECTION_WARNING);
	- return;
	- }
	-}
	-
	-void QmitkConnectomicsNetworkOperationsView::OnAssignFreeSurferColorsPushButtonClicked()
	-{
	- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
	- if (nodes.empty()) return;
	-
	- mitk::DataNode* node = nodes.front();
	-
	- if (!node)
	- {
	- // Nothing selected. Inform the user and return
	- QMessageBox::information( nullptr, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_CONNECTOMICS, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_ONLY_PARCELLATION_SELECTION_WARNING);
	- return;
	- }
	-
	- // here we have a valid mitk::DataNode
	-
	- // a node itself is not very useful, we need its data item (the image)
	- mitk::BaseData* data = node->GetData();
	- if (data)
	- {
	- // test if this data item is an image or not (could also be a surface or something totally different)
	- mitk::Image* image = dynamic_cast<mitk::Image*>( data );
	- if (image)
	- {
	- std::stringstream message;
	- std::string name;
	- message << mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_PERFORMING_IMAGE_PROCESSING_FOR_IMAGE;
	- if (node->GetName(name))
	- {
	- // a property called "name" was found for this DataNode
	- message << "'" << name << "'";
	- }
	- message << ".";
	- MITK_INFO << message.str();
	-
	- // Convert to RGBA
	- AssignFreeSurferColors( node );
	-
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- }
	- else
	- {
	- QMessageBox::information( nullptr, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_CONNECTOMICS, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_ONLY_PARCELLATION_SELECTION_WARNING);
	- return;
	- }
	- }
	- else
	- {
	- QMessageBox::information( nullptr, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_CONNECTOMICS, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_ONLY_PARCELLATION_SELECTION_WARNING);
	- return;
	- }
	-}
	-
	-void QmitkConnectomicsNetworkOperationsView::AssignFreeSurferColors( mitk::DataNode::Pointer node )
	-{
	- mitk::FreeSurferParcellationTranslator::Pointer translator = mitk::FreeSurferParcellationTranslator::New();
	- //translator->AssignLookupTable(node);
	- translator->AssignTransferFunction(node);
	- node->SetProperty("Image Rendering.Mode", mitk::RenderingModeProperty::New(mitk::RenderingModeProperty::COLORTRANSFERFUNCTION_COLOR));
	-}
	-
	-template < typename TPixel, unsigned int VImageDimension >
	-void QmitkConnectomicsNetworkOperationsView::TurnIntoRGBA( itk::Image<TPixel, VImageDimension>* inputImage)
	-{
	- typedef itk::RGBAPixel< unsigned char > RGBAPixelType;
	- typedef itk::Image< TPixel, VImageDimension > TemplateImageType;
	- typedef itk::Image< RGBAPixelType, VImageDimension > RGBAImageType;
	-
	- itk::ImageRegionIterator<TemplateImageType> it_inputImage(inputImage, inputImage->GetLargestPossibleRegion());
	-
	- TPixel minimumValue, maximumValue;
	-
	- it_inputImage.GoToBegin();
	- maximumValue = minimumValue = it_inputImage.Value();
	-
	- for(it_inputImage.GoToBegin(); !it_inputImage.IsAtEnd(); ++it_inputImage)
	- {
	- if ( it_inputImage.Value() < minimumValue )
	- {
	- minimumValue = it_inputImage.Value();
	- }
	- else
	- {
	- if ( it_inputImage.Value() > maximumValue )
	- {
	- maximumValue = it_inputImage.Value();
	- }
	- }
	- }
	-
	- int range = int ( maximumValue - minimumValue ); //needs to be castable to int
	- int offset = int ( minimumValue );
	-
	- if ( range < 0 ) //error
	- {
	- return;
	- }
	-
	- std::vector< unsigned int > histogram;
	- histogram.resize( range + 1, 0 );
	-
	- for(it_inputImage.GoToBegin(); !it_inputImage.IsAtEnd(); ++it_inputImage)
	- {
	- histogram[ int ( it_inputImage.Value() ) - offset ] += 1;
	- }
	-
	- int gapCounter = 0; //this variable will be used to count the empty labels
	-
	- //stores how much has to be subtracted from the image to remove gaps
	- std::vector< TPixel > subtractionStorage;
	- subtractionStorage.resize( range + 1, 0 );
	-
	- for( int index = 0; index <= range; index++ )
	- {
	- if( histogram[ index ] == 0 )
	- {
	- gapCounter++; //if the label is empty, increase gapCounter
	- }
	- else
	- {
	- subtractionStorage[ index ] = TPixel ( gapCounter );
	- }
	- }
	-
	- //remove gaps from label image
	- //for(it_inputImage.GoToBegin(); !it_inputImage.IsAtEnd(); ++it_inputImage)
	- //{
	- // it_inputImage.Value() = it_inputImage.Value() - subtractionStorage[int ( it_inputImage.Value() ) - offset ];
	- //}
	-
	- // create colour vector
	- std::vector< RGBAPixelType > lookupTable;
	-
	- {
	- RGBAPixelType backgroundColour;
	- for( int elementIndex = 0; elementIndex < 4; ++elementIndex )
	- {
	- backgroundColour.SetElement( elementIndex, 0 );
	- }
	-
	- lookupTable.push_back( backgroundColour );
	-
	- for(int colourNumber = 0; colourNumber < range ; ++colourNumber)
	- {
	- RGBAPixelType colour;
	- for( int elementIndex = 0; elementIndex < 3; ++elementIndex )
	- {
	- colour.SetElement( elementIndex, rand() % 256 );
	- }
	- colour.SetAlpha( 255 );
	- lookupTable.push_back( colour );
	- }
	- }
	-
	- // create RGBA image
	- typename RGBAImageType::Pointer rgbaImage = RGBAImageType::New();
	-
	- rgbaImage->SetRegions(inputImage->GetLargestPossibleRegion().GetSize());
	- rgbaImage->SetSpacing(inputImage->GetSpacing());
	- rgbaImage->SetOrigin(inputImage->GetOrigin());
	- rgbaImage->Allocate();
	-
	- //fill with appropriate colours
	- itk::ImageRegionIterator<RGBAImageType> it_rgbaImage(rgbaImage, rgbaImage->GetLargestPossibleRegion());
	-
	- for(it_inputImage.GoToBegin(), it_rgbaImage.GoToBegin(); !it_inputImage.IsAtEnd(); ++it_inputImage, ++it_rgbaImage)
	- {
	- it_rgbaImage.Value() = lookupTable[ int ( it_inputImage.Value() - subtractionStorage[int ( it_inputImage.Value() ) - offset ] ) - offset ];
	- }
	-
	- mitk::Image::Pointer mitkRGBAImage = mitk::ImportItkImage( rgbaImage )->Clone();
	-
	- mitk::DataNode::Pointer rgbaImageNode = mitk::DataNode::New();
	- rgbaImageNode->SetData(mitkRGBAImage);
	- rgbaImageNode->SetProperty(mitk::ConnectomicsConstantsManager::CONNECTOMICS_PROPERTY_NAME, mitk::StringProperty::New(mitk::ConnectomicsConstantsManager::CONNECTOMICS_PROPERTY_DEFAULT_RGBA_NAME));
	- rgbaImageNode->SetBoolProperty( mitk::ConnectomicsConstantsManager::CONNECTOMICS_PROPERTY_VOLUMERENDERING, true);
	- this->GetDataStorage()->Add( rgbaImageNode );
	-}
	-
	-void QmitkConnectomicsNetworkOperationsView::OnModularizePushButtonClicked()
	-{
	- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
	- if ( nodes.empty() )
	- {
	- QMessageBox::information( nullptr, "Modularization calculation", "Please select exactly one network.");
	- return;
	- }
	-
	- for (auto node: nodes)
	- {
	- if( node.IsNotNull() && dynamic_cast<mitk::Image*>(node->GetData()) )
	- {
	- return;
	- }
	-
	- {
	- mitk::ConnectomicsNetwork* network = dynamic_cast<mitk::ConnectomicsNetwork*>( node->GetData() );
	- if( node.IsNotNull() && network )
	- {
	-
	- typedef mitk::ConnectomicsSimulatedAnnealingPermutationModularity::ToModuleMapType MappingType;
	-
	- int depthOfModuleRecursive( 2 );
	- double startTemperature( 2.0 );
	- double stepSize( 4.0 );
	-
	- mitk::ConnectomicsNetwork::Pointer connectomicsNetwork( network );
	- mitk::ConnectomicsSimulatedAnnealingManager::Pointer manager = mitk::ConnectomicsSimulatedAnnealingManager::New();
	- mitk::ConnectomicsSimulatedAnnealingPermutationModularity::Pointer permutation = mitk::ConnectomicsSimulatedAnnealingPermutationModularity::New();
	- mitk::ConnectomicsSimulatedAnnealingCostFunctionModularity::Pointer costFunction = mitk::ConnectomicsSimulatedAnnealingCostFunctionModularity::New();
	-
	- permutation->SetCostFunction( costFunction.GetPointer() );
	- permutation->SetNetwork( connectomicsNetwork );
	- permutation->SetDepth( depthOfModuleRecursive );
	- permutation->SetStepSize( stepSize );
	-
	- manager->SetPermutation( permutation.GetPointer() );
	-
	- manager->RunSimulatedAnnealing( startTemperature, stepSize );
	-
	- MappingType mapping = permutation->GetMapping();
	-
	- MappingType::iterator iter = mapping.begin();
	- MappingType::iterator end = mapping.end();
	-
	- while( iter != end )
	- {
	- MBI_DEBUG << "Vertex " << iter->first << " belongs to module " << iter->second ;
	- MBI_INFO << "Vertex " << iter->first << " belongs to module " << iter->second ;
	- iter++;
	- }
	-
	- MBI_DEBUG << "Overall number of modules is " << permutation->getNumberOfModules( &mapping ) ;
	- MBI_DEBUG << "Cost is " << costFunction->Evaluate( network, &mapping ) ;
	- MBI_INFO << "Overall number of modules is " << permutation->getNumberOfModules( &mapping ) ;
	- MBI_INFO << "Cost is " << costFunction->Evaluate( network, &mapping ) ;
	-
	- return;
	- }
	- }
	- }
	-
	-}
	-
	-void QmitkConnectomicsNetworkOperationsView::OnPrunePushButtonClicked()
	-{
	- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
	- if ( nodes.empty() )
	- {
	- QMessageBox::information( nullptr, "Network pruning", "Please select one or more networks.");
	- return;
	- }
	-
	- for (auto node: nodes)
	- {
	- if( node.IsNotNull() && dynamic_cast<mitk::Image*>(node->GetData()) )
	- {
	- return;
	- }
	-
	- {
	- mitk::ConnectomicsNetwork* network = dynamic_cast<mitk::ConnectomicsNetwork*>( node->GetData() );
	-
	- if( node.IsNotNull() && network )
	- {
	- mitk::ConnectomicsNetworkThresholder::Pointer thresholder = mitk::ConnectomicsNetworkThresholder::New();
	- thresholder->SetNetwork( network );
	- thresholder->SetTargetThreshold( this->m_Controls->targetThresholdSpinBox->value() );
	- thresholder->SetTargetDensity( this->m_Controls->densityThresholdDoubleSpinBox->value() );
	-
	- if( this->m_Controls->thresholdBasedThresholdingCheckBox->isChecked() )
	- {
	- thresholder->SetThresholdingScheme( mitk::ConnectomicsNetworkThresholder::ThresholdBased );
	-
	- mitk::DataNode::Pointer thresholdBasedNode = mitk::DataNode::New();
	- thresholdBasedNode->SetData ( thresholder->GetThresholdedNetwork() );
	- thresholdBasedNode->SetName( "Threshold based" );
	- this->GetDataStorage()->Add(thresholdBasedNode, node );
	- }
	-
	- if( this->m_Controls->largestDensityLowerThanCheckBox->isChecked() )
	- {
	- thresholder->SetThresholdingScheme( mitk::ConnectomicsNetworkThresholder::LargestLowerThanDensity );
	-
	- mitk::DataNode::Pointer thresholdBasedNode = mitk::DataNode::New();
	- thresholdBasedNode->SetData ( thresholder->GetThresholdedNetwork() );
	- thresholdBasedNode->SetName( "Largest density below threshold" );
	- this->GetDataStorage()->Add(thresholdBasedNode, node );
	- }
	-
	- if( this->m_Controls->RandomRemovalThresholdingCheckBox->isChecked() )
	- {
	- thresholder->SetThresholdingScheme( mitk::ConnectomicsNetworkThresholder::RandomRemovalOfWeakest );
	-
	- mitk::DataNode::Pointer thresholdBasedNode = mitk::DataNode::New();
	- thresholdBasedNode->SetData ( thresholder->GetThresholdedNetwork() );
	- thresholdBasedNode->SetName( "Random removal threshold" );
	- this->GetDataStorage()->Add(thresholdBasedNode, node );
	- }
	- }
	- }
	- }
	-}
	-
	-
	-void QmitkConnectomicsNetworkOperationsView::OnCreateConnectivityMatrixImagePushButtonClicked()
	-{
	- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
	- if ( nodes.empty() )
	- {
	- QMessageBox::information( nullptr, "Connectivity Matrix Image creation", "Please select one or more networks.");
	- return;
	- }
	-
	- for (auto node: nodes)
	- {
	- if( node.IsNotNull() && dynamic_cast<mitk::Image*>(node->GetData()) )
	- {
	- return;
	- }
	-
	- {
	- mitk::ConnectomicsNetwork* network = dynamic_cast<mitk::ConnectomicsNetwork*>( node->GetData() );
	- if( node.IsNotNull() && network )
	- {
	- itk::ConnectomicsNetworkToConnectivityMatrixImageFilter::Pointer filter = itk::ConnectomicsNetworkToConnectivityMatrixImageFilter::New();
	- filter->SetInputNetwork( network );
	- filter->SetBinaryConnectivity(m_Controls->binaryCheckBox->isChecked());
	- filter->SetRescaleConnectivity(m_Controls->rescaleCheckBox->isChecked());
	- filter->Update();
	-
	- mitk::Image::Pointer connectivityMatrixImage = mitk::ImportItkImage( filter->GetOutput())->Clone();
	- mitk::DataNode::Pointer connectivityMatrixImageNode = mitk::DataNode::New();
	- connectivityMatrixImageNode->SetData ( connectivityMatrixImage );
	- connectivityMatrixImageNode->SetName( "Connectivity matrix" );
	- this->GetDataStorage()->Add(connectivityMatrixImageNode, node );
	- }
	- }
	- }
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkConnectomicsNetworkOperationsView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkConnectomicsNetworkOperationsView.h
	deleted file mode 100644
	index 08b3655ad2..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkConnectomicsNetworkOperationsView.h
	+++ /dev/null
	@@ -1,107 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef QmitkConnectomicsNetworkOperationsView_h
	-#define QmitkConnectomicsNetworkOperationsView_h
	-
	-#include <berryISelectionListener.h>
	-
	-#include <QmitkAbstractView.h>
	-
	-#include "ui_QmitkConnectomicsNetworkOperationsViewControls.h"
	-
	-#include "mitkConnectomicsNetworkMapper3D.h"
	-
	-// ####### ITK includes #######
	-#include <itkImage.h>
	-
	-/*!
	-\brief QmitkConnectomicsNetworkOperationsView
	-
	-This bundle provides GUI for the brain network analysis algorithms.
	-*/
	-class QmitkConnectomicsNetworkOperationsView : public QmitkAbstractView
	-{
	- // this is needed for all Qt objects that should have a Qt meta-object
	- // (everything that derives from QObject and wants to have signal/slots)
	- Q_OBJECT
	-
	-public:
	-
	- static const std::string VIEW_ID;
	-
	- QmitkConnectomicsNetworkOperationsView();
	- virtual ~QmitkConnectomicsNetworkOperationsView();
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	-
	- ///
	- /// Sets the focus to an internal widget.
	- ///
	- virtual void SetFocus() override;
	-
	- protected slots:
	-
	- /// \brief Called when the user clicks the GUI button
	- void OnConvertToRGBAImagePushButtonClicked();
	-
	- /// \brief Called when the user clicks the GUI button
	- void OnAssignFreeSurferColorsPushButtonClicked();
	-
	- /// \brief Create modularization of network
	- void OnModularizePushButtonClicked();
	-
	- /// \brief Prune network
	- void OnPrunePushButtonClicked();
	-
	- /// \brief Create 2D Connecivity Matrix image from network
	- void OnCreateConnectivityMatrixImagePushButtonClicked();
	-
	-protected:
	-
	- // ####### Functions #######
	- /// \brief called by QmitkAbstractView when DataManager's selection has changed
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- /// \brief Converts an image into a RGBA image
	- template < typename TPixel, unsigned int VImageDimension >
	- void TurnIntoRGBA( itk::Image<TPixel, VImageDimension>* inputImage);
	-
	- /// \brief Assigns an image the Freesurfer LUT
	- void AssignFreeSurferColors( mitk::DataNode::Pointer node );
	-
	- /// \brief Wipe display and empty statistics
	- void WipeDisplay();
	-
	-
	- // ####### Variables #######
	-
	-
	- Ui::QmitkConnectomicsNetworkOperationsViewControls* m_Controls;
	-
	- mitk::ConnectomicsNetworkMapper3D::Pointer m_NetworkMapper;
	-
	- // Demo/Developer mode toggle
	- bool m_demomode;
	-
	- // The selected synthetic network type
	- int m_currentIndex;
	-};
	-
	-
	-
	-#endif // _QMITKBRAINNETWORKANALYSISVIEW_H_INCLUDED
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkConnectomicsNetworkOperationsViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkConnectomicsNetworkOperationsViewControls.ui
	deleted file mode 100644
	index f82c28053d..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkConnectomicsNetworkOperationsViewControls.ui
	+++ /dev/null
	@@ -1,285 +0,0 @@
	-<?xml version="1.0" encoding="utf-8"?>
	-<ui version="4.0">
	- <class>QmitkConnectomicsNetworkOperationsViewControls</class>
	- <widget class="QWidget" name="QmitkConnectomicsNetworkOperationsViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>283</width>
	- <height>639</height>
	- </rect>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="windowTitle">
	- <string>QmitkTemplate</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="verticalSpacing">
	- <number>25</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QGroupBox" name="inputDataGroupBox">
	- <property name="title">
	- <string>Data</string>
	- </property>
	- <layout class="QVBoxLayout" name="verticalLayout_4">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item>
	- <widget class="QLabel" name="lblWarning">
	- <property name="styleSheet">
	- <string notr="true">QLabel { color: rgb(255, 0, 0) }</string>
	- </property>
	- <property name="text">
	- <string>Select a network or a parcellation!</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <layout class="QHBoxLayout" name="horizontalLayout_3">
	- <item>
	- <widget class="QLabel" name="inputImageOneLabel">
	- <property name="text">
	- <string>Image 1:</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QLabel" name="inputImageOneNameLabel">
	- <property name="text">
	- <string>-</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </item>
	- <item>
	- <widget class="QPushButton" name="convertToRGBAImagePushButton">
	- <property name="toolTip">
	- <string>Convert the selected image to RGBA format</string>
	- </property>
	- <property name="text">
	- <string>Turn Into RGBA Image</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QPushButton" name="assignFreeSurferColorsPushButton">
	- <property name="text">
	- <string>Assign FreeSurfer Colors</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QPushButton" name="modularizePushButton">
	- <property name="text">
	- <string>Divide in Modules</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QGroupBox" name="connectivityMatrixImageGroupBox">
	- <property name="title">
	- <string>Connectivity Matrix Image Options</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_2">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QPushButton" name="createConnectivityMatrixImagePushButton">
	- <property name="text">
	- <string>Create Connectivity Matrix Image</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <layout class="QHBoxLayout" name="horizontalLayout_7">
	- <item>
	- <widget class="QCheckBox" name="rescaleCheckBox">
	- <property name="text">
	- <string>Rescale</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </item>
	- <item row="2" column="0">
	- <layout class="QHBoxLayout" name="horizontalLayout_6">
	- <item>
	- <widget class="QCheckBox" name="binaryCheckBox">
	- <property name="text">
	- <string>Binary</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <widget class="QGroupBox" name="pruneOptionsGroupBox">
	- <property name="title">
	- <string>Prune Options</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_3">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QPushButton" name="prunePushButton">
	- <property name="text">
	- <string>Prune Network</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <layout class="QHBoxLayout" name="horizontalLayout_4">
	- <item>
	- <layout class="QVBoxLayout" name="verticalLayout_2">
	- <item>
	- <widget class="QLabel" name="targetDensityLabel">
	- <property name="text">
	- <string>Target Density</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QDoubleSpinBox" name="densityThresholdDoubleSpinBox">
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.010000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </item>
	- <item>
	- <layout class="QVBoxLayout" name="verticalLayout_3">
	- <item>
	- <widget class="QLabel" name="targetThresholdLabel">
	- <property name="text">
	- <string>Target Threshold</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QSpinBox" name="targetThresholdSpinBox"></widget>
	- </item>
	- </layout>
	- </item>
	- </layout>
	- </item>
	- <item row="2" column="0">
	- <layout class="QHBoxLayout" name="horizontalLayout_5">
	- <item>
	- <widget class="QCheckBox" name="thresholdBasedThresholdingCheckBox">
	- <property name="toolTip">
	- <string extracomment="Remove all edges below at and below weight"></string>
	- </property>
	- <property name="text">
	- <string>Threshold weight</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </item>
	- <item row="3" column="0">
	- <layout class="QHBoxLayout" name="horizontalLayout">
	- <item>
	- <widget class="QCheckBox" name="largestDensityLowerThanCheckBox">
	- <property name="toolTip">
	- <string extracomment="Remove all edges of the weakest weight until below target density"></string>
	- </property>
	- <property name="text">
	- <string>Threshold Below Density</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </item>
	- <item row="4" column="0">
	- <layout class="QHBoxLayout" name="horizontalLayout_2">
	- <item>
	- <widget class="QCheckBox" name="RandomRemovalThresholdingCheckBox">
	- <property name="toolTip">
	- <string extracomment="Randomly remove one of the lowest weight edges until the target density is reached"></string>
	- </property>
	- <property name="text">
	- <string>Random Removal Threshold</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="6" column="0">
	- <spacer name="verticalSpacer_2">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- </layout>
	- </widget>
	- <layoutdefault spacing="6" margin="11"></layoutdefault>
	- <resources></resources>
	- <connections></connections>
	-</ui>
	\ No newline at end of file
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkConnectomicsStatisticsView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkConnectomicsStatisticsView.cpp
	deleted file mode 100644
	index 8d6b270242..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkConnectomicsStatisticsView.cpp
	+++ /dev/null
	@@ -1,212 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <berryISelectionService.h>
	-#include <berryIWorkbenchWindow.h>
	-#include "QmitkConnectomicsStatisticsView.h"
	-#include <QMessageBox>
	-#include <QStringList>
	-#include <itkRGBAPixel.h>
	-#include <mbilog.h>
	-#include <mitkConnectomicsConstantsManager.h>
	-#include <mitkConnectomicsStatisticsCalculator.h>
	-#include <mitkConnectomicsRenderingProperties.h>
	-#include "mitkImageCast.h"
	-#include "mitkITKImageImport.h"
	-#include "mitkImageAccessByItk.h"
	-#include <mitkNodePredicateDataType.h>
	-#include <string>
	-
	-const std::string QmitkConnectomicsStatisticsView::VIEW_ID = "org.mitk.views.connectomicsstatistics";
	-
	-QmitkConnectomicsStatisticsView::QmitkConnectomicsStatisticsView()
	- : QmitkAbstractView()
	- , m_Controls( nullptr )
	-{
	-}
	-
	-QmitkConnectomicsStatisticsView::~QmitkConnectomicsStatisticsView()
	-{
	-}
	-
	-void QmitkConnectomicsStatisticsView::CreateQtPartControl( QWidget *parent )
	-{
	- // build up qt view, unless already done
	- if ( !m_Controls )
	- {// create GUI widgets from the Qt Designer's .ui file
	- m_Controls = new Ui::QmitkConnectomicsStatisticsViewControls;
	- m_Controls-> setupUi( parent );
	- connect( m_Controls-> networkBalloonsNodeLabelsComboBox, SIGNAL( currentIndexChanged( int ) ),
	- this, SLOT( OnNetworkBalloonsNodeLabelsComboBoxCurrentIndexChanged( ) ) );
	-
	-
	- m_Controls->m_NetworkBox->SetDataStorage(this->GetDataStorage());
	- mitk::TNodePredicateDataType<mitk::ConnectomicsNetwork>::Pointer isNetwork = mitk::TNodePredicateDataType<mitk::ConnectomicsNetwork>::New();
	- m_Controls->m_NetworkBox->SetPredicate( isNetwork );
	- connect( (QObject*)(m_Controls->m_NetworkBox), SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui()));
	- }
	- this-> WipeDisplay();
	-}
	-
	-void QmitkConnectomicsStatisticsView::SetFocus()
	-{
	- m_Controls->networkStatisticsPlainTextEdit->setFocus();
	-}
	-
	-void QmitkConnectomicsStatisticsView::WipeDisplay()
	-{
	- m_Controls->inputImageOneLabel->setVisible( false );
	- m_Controls->networkStatisticsPlainTextEdit->clear();
	- m_Controls->betweennessNetworkHistogramCanvas->SetHistogram( nullptr );
	- m_Controls->degreeNetworkHistogramCanvas->SetHistogram( nullptr );
	- m_Controls->shortestPathNetworkHistogramCanvas->SetHistogram( nullptr );
	- m_Controls->betweennessNetworkHistogramCanvas->update();
	- m_Controls->degreeNetworkHistogramCanvas->update();
	- m_Controls->shortestPathNetworkHistogramCanvas->update();
	- m_Controls->betweennessNetworkHistogramCanvas->Clear();
	- m_Controls->degreeNetworkHistogramCanvas->Clear();
	- m_Controls->shortestPathNetworkHistogramCanvas->Clear();
	- m_Controls->betweennessNetworkHistogramCanvas->Replot();
	- m_Controls->degreeNetworkHistogramCanvas->Replot();
	- m_Controls->shortestPathNetworkHistogramCanvas->Replot();
	- m_Controls-> networkBalloonsNodeLabelsComboBox-> QComboBox::clear();
	- m_Controls-> networkBalloonsPlainTextEdit-> clear();
	-}
	-
	-void QmitkConnectomicsStatisticsView::OnNetworkBalloonsNodeLabelsComboBoxCurrentIndexChanged( )
	-{
	- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
	-
	- if( nodes.size() != 1 ) { return; }
	-
	- mitk::DataNode::Pointer node = *nodes.begin();
	-
	- if( node.IsNotNull() )
	- {
	- mitk::ConnectomicsNetwork* network =
	- dynamic_cast< mitk::ConnectomicsNetwork* >( node-> GetData() );
	-
	- if( network )
	- {
	- std::string tempCurrentText = m_Controls-> networkBalloonsNodeLabelsComboBox->
	- QComboBox::currentText().toStdString(); // get text of currently selected item.
	-
	- if( tempCurrentText.size() > 3 && tempCurrentText.rfind( ":" ) != tempCurrentText.npos )
	- { // update chosenNode property.
	- tempCurrentText = tempCurrentText.substr( tempCurrentText.rfind( ":" ) + 2 );
	- node-> SetProperty( mitk::connectomicsRenderingNodeChosenNodeName.c_str(),
	- mitk::StringProperty::New( tempCurrentText.c_str() ) );
	- auto renderWindowPart = this->GetRenderWindowPart();
	- if (renderWindowPart)
	- {
	- renderWindowPart->ForceImmediateUpdate(); //RequestUpdate() is too slow.
	- }
	- }
	-
	- std::stringstream balloonTextStream;
	- node-> Update();
	-
	- if( node-> GetProperty( mitk::connectomicsRenderingBalloonTextName.c_str() ) != nullptr &&
	- node-> GetProperty( mitk::connectomicsRenderingBalloonNodeStatsName.c_str() ) != nullptr &&
	- tempCurrentText != "-1" )
	- {
	- balloonTextStream << node-> GetProperty( mitk::connectomicsRenderingBalloonTextName.c_str() )
	- -> GetValueAsString()
	- << node-> GetProperty( mitk::connectomicsRenderingBalloonNodeStatsName.c_str() )
	- -> GetValueAsString() << std::endl;
	- QString balloonQString ( balloonTextStream.str().c_str() );
	- // setPlainText() overwrites, insertPlainText() appends.
	- m_Controls-> networkBalloonsPlainTextEdit-> setPlainText( balloonQString );
	- }
	- if( tempCurrentText == "-1" )
	- {
	- m_Controls-> networkBalloonsPlainTextEdit-> setPlainText( "" );
	- }
	- }
	- }
	- return;
	-}
	-
	-void QmitkConnectomicsStatisticsView::UpdateGui()
	-{
	- this->WipeDisplay();
	-
	- // iterate all selected objects, adjust warning visibility
	- if (m_Controls->m_NetworkBox->GetSelectedNode().IsNotNull())
	- {
	- mitk::ConnectomicsNetwork* network = dynamic_cast<mitk::ConnectomicsNetwork*>( m_Controls->m_NetworkBox->GetSelectedNode()->GetData() );
	-
	- m_Controls->inputImageOneLabel->setVisible( true );
	-
	- std::stringstream statisticsStream;
	-
	- mitk::ConnectomicsStatisticsCalculator::Pointer calculator = mitk::ConnectomicsStatisticsCalculator::New();
	-
	- calculator->SetNetwork( network );
	- calculator->Update();
	-
	- statisticsStream << "# Vertices: " << calculator->GetNumberOfVertices() << "\n";
	- statisticsStream << "# Edges: " << calculator->GetNumberOfEdges() << "\n";
	- statisticsStream << "Average Degree: " << calculator->GetAverageDegree() << "\n";
	- statisticsStream << "Density: " << calculator->GetConnectionDensity() << "\n";
	- statisticsStream << "Small Worldness: " << calculator->GetSmallWorldness() << "\n";
	- statisticsStream << "Average Path Length: " << calculator->GetAveragePathLength() << "\n";
	- statisticsStream << "Efficiency: " << (1 / calculator->GetAveragePathLength() ) << "\n";
	- statisticsStream << "# Connected Components: " << calculator->GetNumberOfConnectedComponents() << "\n";
	- statisticsStream << "Average Component Size: " << calculator->GetAverageComponentSize() << "\n";
	- statisticsStream << "Largest Component Size: " << calculator->GetLargestComponentSize() << "\n";
	- statisticsStream << "Average Clustering Coefficient: " << calculator->GetAverageClusteringCoefficientsC() << "\n";
	- statisticsStream << "Average Vertex Betweenness Centrality: " << calculator->GetAverageVertexBetweennessCentrality() << "\n";
	- statisticsStream << "Average Edge Betweenness Centrality: " << calculator->GetAverageEdgeBetweennessCentrality() << "\n";
	- statisticsStream << "# Isolated Points: " << calculator->GetNumberOfIsolatedPoints() << "\n";
	- statisticsStream << "# End Points: " << calculator->GetNumberOfEndPoints() << "\n";
	- statisticsStream << "Diameter: " << calculator->GetDiameter() << "\n";
	- statisticsStream << "Radius: " << calculator->GetRadius() << "\n";
	- statisticsStream << "Average Eccentricity: " << calculator->GetAverageEccentricity() << "\n";
	- statisticsStream << "# Central Points: " << calculator->GetNumberOfCentralPoints() << "\n";
	-
	- QString statisticsString( statisticsStream.str().c_str() );
	- m_Controls-> networkStatisticsPlainTextEdit-> setPlainText( statisticsString );
	-
	- mitk::ConnectomicsNetwork::Pointer connectomicsNetwork( network );
	- mitk::ConnectomicsHistogramsContainer *histogramContainer = histogramCache[ connectomicsNetwork ];
	- if(histogramContainer)
	- {
	- m_Controls->betweennessNetworkHistogramCanvas->SetHistogram( histogramContainer->GetBetweennessHistogram() );
	- m_Controls->degreeNetworkHistogramCanvas->SetHistogram( histogramContainer->GetDegreeHistogram() );
	- m_Controls->shortestPathNetworkHistogramCanvas->SetHistogram( histogramContainer->GetShortestPathHistogram() );
	- m_Controls->betweennessNetworkHistogramCanvas->DrawProfiles();
	- m_Controls->degreeNetworkHistogramCanvas->DrawProfiles();
	- m_Controls->shortestPathNetworkHistogramCanvas->DrawProfiles();
	- }
	-
	- // For the balloon overlay:
	- if( m_Controls->m_NetworkBox->GetSelectedNode()->GetProperty( mitk::connectomicsRenderingBalloonAllNodeLabelsName.c_str() ) != nullptr )
	- { // QComboBox with node label names and numbers.
	- QString allNodesLabel = m_Controls->m_NetworkBox->GetSelectedNode()->
	- GetProperty( mitk::connectomicsRenderingBalloonAllNodeLabelsName.c_str() )->
	- GetValueAsString().c_str();
	- QStringList allNodesLabelList = allNodesLabel.simplified().split( "," );
	- allNodesLabelList.sort( Qt::CaseInsensitive );
	- m_Controls-> networkBalloonsNodeLabelsComboBox-> QComboBox::addItem( "no node chosen: -1" );
	- m_Controls-> networkBalloonsNodeLabelsComboBox-> QComboBox::addItems( allNodesLabelList );
	- }
	- }
	-}
	-
	-void QmitkConnectomicsStatisticsView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /part/, const QList<mitk::DataNode::Pointer>& )
	-{
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkConnectomicsStatisticsView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkConnectomicsStatisticsView.h
	deleted file mode 100644
	index b1f0aea112..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkConnectomicsStatisticsView.h
	+++ /dev/null
	@@ -1,81 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef QmitkConnectomicsStatisticsView_h
	-#define QmitkConnectomicsStatisticsView_h
	-
	-#include <berryISelectionListener.h>
	-
	-#include <QmitkAbstractView.h>
	-
	-#include "ui_QmitkConnectomicsStatisticsViewControls.h"
	-
	-#include "mitkConnectomicsHistogramCache.h"
	-
	-// ####### ITK includes #######
	-#include <itkImage.h>
	-
	-/*!
	-\brief QmitkConnectomicsStatisticsView
	-
	-This view provides the statistics GUI.
	-*/
	-class QmitkConnectomicsStatisticsView : public QmitkAbstractView
	-{
	- // this is needed for all Qt objects that should have a Qt meta-object
	- // (everything that derives from QObject and wants to have signal/slots)
	- Q_OBJECT
	-
	-public:
	-
	- static const std::string VIEW_ID;
	-
	- QmitkConnectomicsStatisticsView();
	- virtual ~QmitkConnectomicsStatisticsView();
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	-
	- ///
	- /// Sets the focus to an internal widget.
	- ///
	- virtual void SetFocus() override;
	-
	-protected slots:
	-
	- void OnNetworkBalloonsNodeLabelsComboBoxCurrentIndexChanged( );
	- void UpdateGui();
	-
	-protected:
	-
	- // ####### Functions #######
	- /// \brief called by QmitkAbstractView when DataManager's selection has changed
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- /// \brief Wipe display and empty statistics
	- void WipeDisplay();
	-
	-
	- // ####### Variables #######
	- Ui::QmitkConnectomicsStatisticsViewControls* m_Controls;
	-
	- /// Cache for histograms
	- mitk::ConnectomicsHistogramCache histogramCache;
	-};
	-
	-
	-
	-#endif // _QMITKBRAINNETWORKANALYSISVIEW_H_INCLUDED
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkConnectomicsStatisticsViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkConnectomicsStatisticsViewControls.ui
	deleted file mode 100644
	index fccdcfe848..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkConnectomicsStatisticsViewControls.ui
	+++ /dev/null
	@@ -1,296 +0,0 @@
	-<?xml version="1.0" encoding="utf-8"?>
	-<ui version="4.0">
	- <class>QmitkConnectomicsStatisticsViewControls</class>
	- <widget class="QWidget" name="QmitkConnectomicsStatisticsViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>557</width>
	- <height>1218</height>
	- </rect>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="windowTitle">
	- <string>QmitkTemplate</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="verticalSpacing">
	- <number>25</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QGroupBox" name="inputDataGroupBox">
	- <property name="title">
	- <string>Input Data</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_2">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <layout class="QHBoxLayout" name="horizontalLayout_3">
	- <item>
	- <widget class="QLabel" name="inputImageOneLabel">
	- <property name="text">
	- <string>Network:</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QmitkDataStorageComboBox" name="m_NetworkBox"></widget>
	- </item>
	- </layout>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QGroupBox" name="networkStatisticsGroupBox">
	- <property name="title">
	- <string>Network Statistics</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_3">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QPlainTextEdit" name="networkStatisticsPlainTextEdit">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="MinimumExpanding">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="readOnly">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QGroupBox" name="networkBalloonsGroupBox">
	- <property name="title">
	- <string>Informational Balloons.</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_4">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QCheckBox" name="networkBalloonsTextOverlayCheckBox">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="cursor">
	- <cursorShape>PointingHandCursor</cursorShape>
	- </property>
	- <property name="layoutDirection">
	- <enum>Qt::RightToLeft</enum>
	- </property>
	- <property name="text">
	- <string></string>
	- </property>
	- <property name="checked">
	- <bool>true</bool>
	- </property>
	- <property name="tristate">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QComboBox" name="networkBalloonsNodeLabelsComboBox">
	- <property name="editable">
	- <bool>false</bool>
	- </property>
	- <property name="currentIndex">
	- <number>-1</number>
	- </property>
	- <property name="maxVisibleItems">
	- <number>12</number>
	- </property>
	- <property name="insertPolicy">
	- <enum>QComboBox::InsertAlphabetically</enum>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0" colspan="2">
	- <widget class="QPlainTextEdit" name="networkBalloonsPlainTextEdit">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="MinimumExpanding">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="font">
	- <font>
	- <family>MS Shell Dlg 2</family>
	- <pointsize>8</pointsize>
	- </font>
	- </property>
	- <property name="cursor" stdset="0">
	- <cursorShape>IBeamCursor</cursorShape>
	- </property>
	- <property name="acceptDrops">
	- <bool>false</bool>
	- </property>
	- <property name="readOnly">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QGroupBox" name="histogramGroupBox">
	- <property name="title">
	- <string>Histograms</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_5">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QmitkNetworkHistogramCanvas" name="degreeNetworkHistogramCanvas" native="true">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>50</width>
	- <height>150</height>
	- </size>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QmitkNetworkHistogramCanvas" name="betweennessNetworkHistogramCanvas" native="true">
	- <property name="minimumSize">
	- <size>
	- <width>50</width>
	- <height>150</height>
	- </size>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QmitkNetworkHistogramCanvas" name="shortestPathNetworkHistogramCanvas" native="true">
	- <property name="minimumSize">
	- <size>
	- <width>50</width>
	- <height>150</height>
	- </size>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <spacer name="verticalSpacer_2">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- </layout>
	- </widget>
	- <layoutdefault spacing="6" margin="11"></layoutdefault>
	- <customwidgets>
	- <customwidget>
	- <class>QmitkDataStorageComboBox</class>
	- <extends>QComboBox</extends>
	- <header location="global">QmitkDataStorageComboBox.h</header>
	- </customwidget>
	- <customwidget>
	- <class>QmitkNetworkHistogramCanvas</class>
	- <extends>QWidget</extends>
	- <header location="global">internal/QmitkNetworkHistogramCanvas.h</header>
	- <container>1</container>
	- </customwidget>
	- </customwidgets>
	- <resources></resources>
	- <connections>
	- <connection>
	- <sender>networkBalloonsNodeLabelsComboBox</sender>
	- <signal>currentIndexChanged(int)</signal>
	- <receiver>networkBalloonsNodeLabelsComboBox</receiver>
	- <slot>setCurrentIndex(int)</slot>
	- <hints>
	- <hint type="sourcelabel">
	- <x>360</x>
	- <y>409</y>
	- </hint>
	- <hint type="destinationlabel">
	- <x>360</x>
	- <y>409</y>
	- </hint>
	- </hints>
	- </connection>
	- </connections>
	-</ui>
	\ No newline at end of file
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkNetworkHistogramCanvas.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkNetworkHistogramCanvas.cpp
	deleted file mode 100644
	index 814bc009ba..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkNetworkHistogramCanvas.cpp
	+++ /dev/null
	@@ -1,97 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkNetworkHistogramCanvas.h"
	-
	-#include <itkObject.h>
	-
	-#include <QPainter>
	-#include <qwt_text.h>
	-#include <qwt_plot_grid.h>
	-#include <qwt_painter.h>
	-#include <qwt_legend.h>
	-#include <qwt_plot_marker.h>
	-
	-QmitkNetworkHistogramCanvas::QmitkNetworkHistogramCanvas(QWidget * parent, Qt::WindowFlags )
	- : QmitkPlotWidget(parent)
	-{
	- setEnabled(false);
	- setFocusPolicy(Qt::ClickFocus);
	-
	-}
	-
	-QmitkNetworkHistogramCanvas::~QmitkNetworkHistogramCanvas()
	-{
	-}
	-
	-void QmitkNetworkHistogramCanvas::DrawProfiles( )
	-{
	- this->Clear();
	-
	- if( !(m_Histogram) \|\| !( m_Histogram->IsValid() ))
	- {
	- return;
	- }
	-
	- std::vector<double> histogramVector = m_Histogram->GetHistogramVector();
	-
	- // create a data vector which contains the points to be drawn
	- // to create nice bars, the curve takes four points for each bar
	- std::vector< std::pair< double, double > > dataPointsVector;
	-
	- std::pair< double, double > leftBottom, leftTop, rightTop, rightBottom;
	-
	- // how wide the bar is, the gap to the next one will be 1 - barWidth
	- double barWidth( 0.95 );
	- const int range = histogramVector.size();
	-
	- for(int i=0; i < range ; ++i)
	- {
	- leftBottom.first = ((double) i) ;
	- leftBottom.second = 0.0;
	- leftTop.first = ((double) i) ;
	- leftTop.second = histogramVector.at( i );
	- rightTop.first = ((double) i) + barWidth ;
	- rightTop.second = histogramVector.at( i );
	- rightBottom.first = ((double) i) + barWidth ;
	- rightBottom.second = 0.0;
	-
	- dataPointsVector.push_back( leftBottom );
	- dataPointsVector.push_back( leftTop );
	- dataPointsVector.push_back( rightTop );
	- dataPointsVector.push_back( rightBottom );
	- }
	-
	- this->SetPlotTitle( (m_Histogram->GetSubject()).c_str() );
	-
	- QPen pen( Qt::NoPen );
	- QBrush brush( Qt::SolidPattern );
	-
	- brush.setColor( Qt::blue );
	-
	- int curveId = this->InsertCurve( (m_Histogram->GetSubject()).c_str() );
	- this->SetCurveData( curveId, dataPointsVector );
	-
	- this->SetCurvePen( curveId, pen );
	- this->SetCurveBrush( curveId, brush );
	-
	- // Axis 0 is the y axis, axis to the x axis
	- this->m_Plot->setAxisTitle(0, "n");
	- //this->m_Plot->setAxisTitle(2, "");
	-
	- this->Replot();
	-
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkNetworkHistogramCanvas.h b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkNetworkHistogramCanvas.h
	deleted file mode 100644
	index b9e6a3dab0..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkNetworkHistogramCanvas.h
	+++ /dev/null
	@@ -1,73 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef QmitkNetworkHistogramCanvas_H_INCLUDED
	-#define QmitkNetworkHistogramCanvas_H_INCLUDED
	-
	-
	-#include <mitkConnectomicsHistogramBase.h>
	-#include <mitkRenderingManager.h>
	-
	-#include "QmitkPlotWidget.h"
	-
	-#include <QStandardItemModel>
	-#include <qwt_plot.h>
	-#include <QPainter>
	-#include <qwt_plot_picker.h>
	-
	- //##Documentation
	- //## @brief A widget for displaying the data in a ConnectomicsHistogramBase
	-
	-class QmitkNetworkHistogramCanvas : public QmitkPlotWidget
	-{
	-
	- Q_OBJECT
	-
	-public:
	-
	- QmitkNetworkHistogramCanvas( QWidget * parent=nullptr, Qt::WindowFlags f = nullptr );
	- ~QmitkNetworkHistogramCanvas();
	-
	- /** @brief Returns the histogram the canvas is using */
	- mitk::ConnectomicsHistogramBase* GetHistogram()
	- {
	- return m_Histogram;
	- }
	-
	- /** @brief Set the histogram the canvas is to use */
	- void SetHistogram(mitk::ConnectomicsHistogramBase *histogram)
	- {
	- m_Histogram = histogram;
	- }
	-
	- /** @brief Draw the histogram */
	- void DrawProfiles();
	-
	- /** @brief Return the plot */
	- QwtPlot* GetPlot()
	- {
	- return m_Plot;
	- }
	-
	-
	-protected:
	-
	- /** @brief The histogram to be plotted */
	- mitk::ConnectomicsHistogramBase *m_Histogram;
	-
	-};
	-#endif
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkRandomParcellationView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkRandomParcellationView.cpp
	deleted file mode 100644
	index 18bc2269f4..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkRandomParcellationView.cpp
	+++ /dev/null
	@@ -1,358 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-// Qmitk
	-#include "QmitkRandomParcellationView.h"
	-
	-// Blueberry
	-#include <berryISelectionService.h>
	-#include <berryIWorkbenchWindow.h>
	-
	-// Qt
	-#include <QMessageBox>
	-
	-// Includes for image casting between ITK and MITK
	-#include "mitkImageCast.h"
	-#include "mitkImageAccessByItk.h"
	-#include "mitkITKImageImport.h"
	-
	-//To convert integer to string
	-#include <stdlib.h>
	-#include <sstream>
	-
	-//Itk Iterators
	-#include <itkNeighborhoodIterator.h>
	-#include <itkImageRegionIterator.h>
	-
	-// mitk
	-#include <mitkRegionVoxelCounter.h>
	-#include <mitkRandomParcellationGenerator.h>
	-
	-
	-//Child
	-const std::string QmitkRandomParcellationView::PROPERTYNAME = "name";
	-const std::string QmitkRandomParcellationView::PROPERTYOPACITY = "opacity";
	-const std::string QmitkRandomParcellationView::m_NAMEFORRANDOMVOXELIMAGE = "Random Voxel Image";
	-
	-const std::string QmitkRandomParcellationView::VIEW_ID = "org.mitk.views.randomparcellationview";
	-
	-
	-void QmitkRandomParcellationView::SetFocus()
	-{
	- m_Controls.buttonSelectRandomNodes->setFocus();
	-}
	-
	-void QmitkRandomParcellationView::CreateQtPartControl( QWidget *parent )
	-{
	- // create GUI widgets from the Qt Designer's .ui file
	- m_Controls.setupUi( parent );
	- connect( m_Controls.buttonSelectRandomNodes, SIGNAL(clicked()), this, SLOT(SelectRandomNodes()) );
	- connect( m_Controls.checkBoxMerging, SIGNAL(stateChanged(int)),this, SLOT(OnMergingCheckboxChanged(int)));
	- connect( m_Controls.radioButtonNumberParcels, SIGNAL(clicked()), this, SLOT(OnRadioButtonNumberParcelsChanged(int)));
	- connect( m_Controls.radioButtonSmallestParcel, SIGNAL(clicked()), this, SLOT(OnRadioButtonSmallestParcelChanged(int)));
	-}
	-
	-void QmitkRandomParcellationView::OnMergingCheckboxChanged(int )
	-{
	- if (m_Controls.checkBoxMerging->isChecked())
	- {
	- //Make the frame visible
	- m_Controls.frameMerging->setEnabled(true);
	- m_Controls.frameNumberParcels->setEnabled(true);
	- m_Controls.frameSmallestParcel->setEnabled(true);
	- }
	- else
	- {
	- m_Controls.frameMerging->setEnabled(false);
	- }
	-}
	-
	-void QmitkRandomParcellationView::OnRadioButtonNumberParcelsChanged(int )
	-{
	- if (m_Controls.radioButtonNumberParcels->isChecked())
	- {
	- m_Controls.frameNumberParcels->setEnabled(true);
	- m_Controls.radioButtonSmallestParcel->setChecked(false);
	- }
	- else
	- {
	- m_Controls.frameNumberParcels->setEnabled(false);
	- }
	-}
	-
	-void QmitkRandomParcellationView::OnRadioButtonSmallestParcelChanged(int )
	-{
	- if (m_Controls.radioButtonSmallestParcel->isChecked())
	- {
	- m_Controls.frameSmallestParcel->setEnabled(true);
	- m_Controls.radioButtonNumberParcels->setChecked(false);
	- }
	- else
	- {
	- m_Controls.frameSmallestParcel->setEnabled(false);
	- }
	-}
	-
	-void QmitkRandomParcellationView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /part/, const QList<mitk::DataNode::Pointer>& nodes)
	-{
	- // iterate all selected objects, adjust warning visibility
	- for (mitk::DataNode::Pointer node: nodes)
	- {
	- if( node.IsNotNull() && dynamic_cast<mitk::Image*>(node->GetData()) )
	- {
	- m_Controls.labelWarning->setVisible( false );
	- m_Controls.buttonSelectRandomNodes->setEnabled( true );
	- mitk::Image* imageDisplay = dynamic_cast<mitk::Image*>(node->GetData());
	- AccessFixedDimensionByItk(imageDisplay, ShowNumberOfVoxels, 3);
	- return;
	- }
	- }
	-
	- m_Controls.labelWarning->setVisible( true );
	- m_Controls.buttonSelectRandomNodes->setEnabled( false );
	-}
	-
	-template <typename TPixel, unsigned int VImageDimension>
	-void QmitkRandomParcellationView::ShowNumberOfVoxels( itk::Image<TPixel, VImageDimension> * inputImage)
	-{
	-
	- mitk::RegionVoxelCounter<TPixel, VImageDimension> counter;
	- counter.SetRegion(inputImage->GetLargestPossibleRegion());
	- counter.SetImage(inputImage);
	- int numberVoxelsDisplay = counter.VoxelWithValue(1);
	- std::string stringDisplay = "Number of voxels with value 1: ";
	- std::ostringstream convertDisplay;
	- convertDisplay << numberVoxelsDisplay;
	- std::string stringNumberVoxels = convertDisplay.str();
	- stringDisplay += stringNumberVoxels;
	- QString textNumberVoxelsDisplay = QString::fromStdString(stringDisplay);
	- m_Controls.labelNumberVoxels->setText(textNumberVoxelsDisplay);
	-}
	-
	-
	-void QmitkRandomParcellationView::SelectRandomNodes()
	-{
	- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
	- if (nodes.empty()) return;
	-
	- mitk::DataNode* node = nodes.front();
	-
	- if (!node)
	- {
	- // Nothing selected. Inform the user and return
	- QMessageBox::information( nullptr, "No image available", "Please load and select an image before starting image processing.");
	- return;
	- }
	-
	- // here we have a valid mitk::DataNode
	-
	- // a node itself is not very useful, we need its data item (the image)
	- mitk::BaseData* data = node->GetData();
	- if (data)
	- {
	- // test if this data item is an image or not (could also be a surface or something totally different)
	- mitk::Image* image = dynamic_cast<mitk::Image*>( data );
	- if (image)
	- {
	- //get numberNodes (number of nodes) with SpinBox
	- int numberNodes( 0 );
	- numberNodes = m_Controls.spinBoxNumberNodes->value();
	-
	- std::stringstream message;
	- std::string name;
	- message << "Selecting " << numberNodes << " random nodes for ";
	- if (node->GetName(name))
	- {
	- // a property called "name" was found for this DataNode
	- message << "'" << name << "'";
	- }
	- message << ".";
	- MITK_INFO << message.str();
	-
	- //MITK into ITK image, function GetRandomParcels gets executed, Dimension is 3
	- AccessFixedDimensionByItk(image, GetRandomParcels, 3);
	-
	- }
	- }
	-}
	-
	-
	-
	-template <typename TPixel, unsigned int VImageDimension>
	-void QmitkRandomParcellationView::GetRandomParcels( itk::Image<TPixel, VImageDimension> * inputImage)
	-{
	- typedef itk::Image< TPixel, VImageDimension > ImageType;
	- typedef itk::Image< int, VImageDimension > IntegerImageType;
	-
	- //new Image which will contain the parcellation
	- typename IntegerImageType::Pointer voxelImage = IntegerImageType::New();
	-
	- voxelImage->SetRegions(inputImage->GetLargestPossibleRegion().GetSize());
	- voxelImage->SetSpacing(inputImage->GetSpacing());
	- voxelImage->SetOrigin(inputImage->GetOrigin());
	- voxelImage->Allocate();
	-
	- //Voxel iterators
	- itk::ImageRegionIterator<ImageType> it_inputImage(inputImage, inputImage->GetLargestPossibleRegion());
	- itk::ImageRegionIterator<IntegerImageType> it_voxelImage(voxelImage, voxelImage->GetLargestPossibleRegion());
	-
	- //Copy the inputImage -> voxelImage
	- for (it_inputImage.GoToBegin(), it_voxelImage.GoToBegin(); !it_inputImage.IsAtEnd(); ++it_inputImage, ++it_voxelImage)
	- {
	- it_voxelImage.Value() = it_inputImage.Value();
	- }
	-
	- //Neighborhood Iterator
	- typedef itk::NeighborhoodIterator< IntegerImageType > NeighborhoodIteratorType;
	- typename NeighborhoodIteratorType::RadiusType radius;
	- radius.Fill(1);
	-
	- //Counter for voxels with value 1
	- mitk::RegionVoxelCounter<int, 3> counter;
	- counter.SetImage(voxelImage);
	- counter.SetRegion(voxelImage->GetLargestPossibleRegion());
	-
	- int numberVoxels = counter.VoxelWithValue(1);
	-
	- //Get numberNodes with SpinBox
	- int numberNodes(0);
	- numberNodes = m_Controls.spinBoxNumberNodes->value();
	-
	- //WARNINGS
	- if (numberNodes > numberVoxels )
	- {
	- QMessageBox::information( nullptr, "Smaller Number of Nodes", "The number of nodes is greater than the number of voxels. Please choose a smaller number!");
	- return;
	- }
	-
	- if (m_Controls.checkBoxMerging->isChecked() && m_Controls.radioButtonNumberParcels->isChecked())
	- {
	- int numberParcels = m_Controls.spinBoxNumberParcels->value();
	- if (numberNodes<numberParcels )
	- {
	- QMessageBox::information( nullptr, "Smaller Number of Parcels", "The number of parcels is greater than the number of nodes. Please choose a smaller number of parcels!");
	- return;
	- }
	- }
	-
	- if (m_Controls.checkBoxMerging->isChecked() && m_Controls.radioButtonSmallestParcel->isChecked())
	- {
	- int sizeSmallestParcel = m_Controls.spinBoxSmallestParcel->value();
	- if (sizeSmallestParcel > numberVoxels )
	- {
	- QMessageBox::information( nullptr, "Smaller Size", "The size of the smallest parcel is greater than the number of voxels. Please choose a smaller size!");
	- return;
	- }
	- }
	-
	- //Get a RandomParcellationGenerator to generate the parcels
	- mitk::RandomParcellationGenerator<int, 3> generator;
	- generator.SetImage(voxelImage);
	- generator.SetNumberNodes(numberNodes);
	-
	- //Chooses random initial voxels, with which we can start the parcellation growth
	- generator.GetRandomSeedVoxels();
	- //Now we add all the voxels (which share a face with one of the voxels of a region) to a region, particular constraints have to be fulfilled
	- generator.ParcelGrowthOverFaces();
	- //Because of the constraints or the position of some voxels we now add voxels to the regions which just share an edge or vertex with one region
	- generator.FillOverEdgeOrVertex();
	- //Isolated voxels also have to be allocated to the regions
	- generator.AllocateIsolatedVoxels();
	-
	- //Show the sizeOfRegions in the window
	- MITK_DEBUG << "Without merging we get the following size of regions: " << endl;
	- generator.ShowSizeOfRegions();
	-
	- //Check if the Merge-Buttons are chosen
	- int newNumberNodes = 0;
	-
	- if (m_Controls.checkBoxMerging->isChecked())
	- {
	- int givenSizeOfSmallestRegion(0);
	- int desiredNumberOfParcels(0);
	- int givenSizeOfSmallestRegionBeginning = numberVoxels;
	- bool mergingWithNumberParcels(false);
	- bool mergingWithSmallestParcel(false);
	- bool justMergeSmallParcels(false);
	-
	- if (m_Controls.radioButtonSmallestParcel->isChecked() )
	- {
	- mergingWithSmallestParcel = true;
	- givenSizeOfSmallestRegionBeginning = m_Controls.spinBoxSmallestParcel->value();
	- if( m_Controls.checkBoxJustMergeSmallParcels-> isChecked() )
	- {
	- //Spinbox: How many voxels should the smallest parcel have?
	- givenSizeOfSmallestRegion = m_Controls.spinBoxSmallestParcel->value();
	- justMergeSmallParcels = true;
	- }
	- else
	- {
	- givenSizeOfSmallestRegion = numberVoxels;
	- }
	- }
	- else if (m_Controls.radioButtonNumberParcels->isChecked())
	- {
	- givenSizeOfSmallestRegion = numberVoxels;
	- desiredNumberOfParcels = m_Controls.spinBoxNumberParcels->value();
	- mergingWithNumberParcels = true;
	- }
	-
	- //Merge parcels according to a costfunction
	- generator.SetVariablesForMerging(givenSizeOfSmallestRegion, desiredNumberOfParcels, givenSizeOfSmallestRegionBeginning);
	- generator.SetBoolsForMerging(mergingWithNumberParcels, mergingWithSmallestParcel, justMergeSmallParcels);
	- newNumberNodes = generator.MergeParcels();
	-
	- MITK_DEBUG << "After merging we get the following size of regions:" << endl;
	- generator.ShowSizeOfRegions();
	- }
	-
	- //Show NumberOfNodes on the GUI
	- if (m_Controls.checkBoxMerging->isChecked()) //merging was used
	- {
	- ShowNumberOfNodes(newNumberNodes);
	- }
	- else
	- {
	- ShowNumberOfNodes(numberNodes);
	- }
	-
	- //Change the values of the nodes, such that no gaps exist and the values starts with 1
	- generator.SetAppropriateValues();
	-
	- //Get a new data node which contains the random parcellation
	- mitk::Image::Pointer mitkRandomVoxelImage = mitk::GrabItkImageMemory( voxelImage );
	- mitk::DataNode::Pointer newRandomVoxelImageNode = mitk::DataNode::New();
	- newRandomVoxelImageNode->SetData(mitkRandomVoxelImage);
	- newRandomVoxelImageNode->SetProperty(PROPERTYNAME.c_str(),
	- mitk::StringProperty::New(m_NAMEFORRANDOMVOXELIMAGE));
	- newRandomVoxelImageNode->SetProperty(PROPERTYOPACITY.c_str(),
	- mitk::FloatProperty::New(1.0));
	- this->GetDataStorage()->Add( newRandomVoxelImageNode );
	-
	- return;
	-}
	-
	-void QmitkRandomParcellationView::ShowNumberOfNodes(int numberNodes)
	-{
	- std::string string = "Number of nodes: ";
	- std::string stringNumberNodes;
	- std::ostringstream convert;
	- convert << numberNodes;
	- stringNumberNodes = convert.str();
	- string += stringNumberNodes;
	- QString textNumberNodes = QString::fromStdString(string);
	- m_Controls.labelNumberNodes->setText(textNumberNodes);
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkRandomParcellationView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkRandomParcellationView.h
	deleted file mode 100644
	index 7a93554bb3..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkRandomParcellationView.h
	+++ /dev/null
	@@ -1,98 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef RandomParcellationView_h
	-#define RandomParcellationView_h
	-
	-#include <berryISelectionListener.h>
	-
	-#include <QmitkAbstractView.h>
	-
	-#include "ui_QmitkRandomParcellationViewControls.h"
	-
	-#include <vector>
	-
	-#include <itkImage.h>
	-
	-//To use pair
	-#include <utility>
	-
	-
	-/**
	-\brief QmitkRandomParcellationView for GUI Interactions
	-\ingroup ${plugin_target}_internal
	-*/
	-class QmitkRandomParcellationView : public QmitkAbstractView
	-{
	- Q_OBJECT
	-
	-public:
	- static const std::string VIEW_ID;
	- virtual void CreateQtPartControl(QWidget *parent) override;
	-
	- virtual void SetFocus() override;
	-
	- /** \brief Interaction with GUI and mitkRandomParcellationGenerator to get random parcels.*/
	- template <typename TPixel, unsigned int VImageDimension>
	- void GetRandomParcels( itk::Image<TPixel, VImageDimension>* );
	-
	- /** \brief Method to set the default data storage.*/
	- virtual void SetDataStorage(mitk::DataStorage* dataStorage)
	- {
	- m_DataStorage = dataStorage;
	- }
	-
	- protected slots:
	-
	- /** \brief Called when the user clicks the GUI button*/
	- void SelectRandomNodes();
	-
	- /** \brief Called when the user checks the GUI checkbox*/
	- void OnMergingCheckboxChanged(int state);
	-
	- /** \brief Called when the user ckecks the GUI radio button*/
	- void OnRadioButtonNumberParcelsChanged(int state);
	-
	- /** \brief Called when the user ckecks the GUI radio button*/
	- void OnRadioButtonSmallestParcelChanged(int state);
	-
	-protected:
	-
	- mitk::DataStorage* m_DataStorage;
	-
	- //to save an itk image
	- mitk::DataNode::Pointer m_InputImageNode;
	-
	- /** \brief Shows the number of voxels with value one on the GUI*/
	- template <typename TPixel, unsigned int VImageDimension>
	- void ShowNumberOfVoxels( itk::Image<TPixel, VImageDimension> * inputImage);
	-
	- /** \brief Shows the number of nodes on the GUI (may have changed after merging)*/
	- void ShowNumberOfNodes(int numberNodes);
	-
	- /** \brief called by QmitkAbstractView when DataManager's selection has changed*/
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- Ui::QmitkRandomParcellationViewControls m_Controls;
	-
	- static const std::string PROPERTYNAME;
	- static const std::string PROPERTYOPACITY;
	- static const std::string m_NAMEFORRANDOMVOXELIMAGE;
	-
	-};
	-
	-#endif // RandomParcellationView_h
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkRandomParcellationViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkRandomParcellationViewControls.ui
	deleted file mode 100644
	index 0e6a66e144..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/QmitkRandomParcellationViewControls.ui
	+++ /dev/null
	@@ -1,322 +0,0 @@
	-<?xml version="1.0" encoding="utf-8"?>
	-<ui version="4.0">
	- <class>QmitkRandomParcellationViewControls</class>
	- <widget class="QWidget" name="QmitkRandomParcellationViewControls">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>327</width>
	- <height>591</height>
	- </rect>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="windowTitle">
	- <string>QmitkTemplate</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="verticalSpacing">
	- <number>25</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="labelWarning">
	- <property name="styleSheet">
	- <string notr="true">QLabel { color: rgb(255, 0, 0) }</string>
	- </property>
	- <property name="text">
	- <string>Please select an image!</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QGroupBox" name="groupBoxNumberNodes">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="title">
	- <string>Nodes</string>
	- </property>
	- <property name="checkable">
	- <bool>false</bool>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_2">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="text">
	- <string>Choose the number of nodes:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QSpinBox" name="spinBoxNumberNodes">
	- <property name="minimum">
	- <number>2</number>
	- </property>
	- <property name="maximum">
	- <number>5000</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QGroupBox" name="groupBoxMerging">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="title">
	- <string>Merging</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_3">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QCheckBox" name="checkBoxMerging">
	- <property name="text">
	- <string>Merging on</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QFrame" name="frameMerging">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_5">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QRadioButton" name="radioButtonNumberParcels">
	- <property name="text">
	- <string>According to the number of parcels</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QFrame" name="frameNumberParcels">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::StyledPanel</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_6">
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_3">
	- <property name="text">
	- <string>Number of Parcels:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QSpinBox" name="spinBoxNumberParcels">
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>5000</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QRadioButton" name="radioButtonSmallestParcel">
	- <property name="text">
	- <string>According to the size of parcels</string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QFrame" name="frameSmallestParcel">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::StyledPanel</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_7">
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_2">
	- <property name="text">
	- <string>Size of the smallest parcel:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QSpinBox" name="spinBoxSmallestParcel">
	- <property name="minimum">
	- <number>2</number>
	- </property>
	- <property name="maximum">
	- <number>100000</number>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QCheckBox" name="checkBoxJustMergeSmallParcels">
	- <property name="text">
	- <string>Just merge small parcels</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QPushButton" name="buttonSelectRandomNodes">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string>Do image processing</string>
	- </property>
	- <property name="text">
	- <string>Select random nodes</string>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <spacer name="verticalSpacer">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="5" column="0">
	- <widget class="QGroupBox" name="groupBoxCounting">
	- <property name="title">
	- <string>Counting</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_4">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="labelNumberVoxels">
	- <property name="text">
	- <string>Number of voxels with value 1:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="labelNumberNodes">
	- <property name="text">
	- <string>Number of nodes:</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <layoutdefault spacing="6" margin="11"></layoutdefault>
	- <resources></resources>
	- <connections></connections>
	-</ui>
	\ No newline at end of file
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/mitkPluginActivator.cpp
	deleted file mode 100644
	index 28913b3601..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/mitkPluginActivator.cpp
	+++ /dev/null
	@@ -1,47 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkPluginActivator.h"
	-
	-#include "src/internal/QmitkConnectomicsDataView.h"
	-#include "src/internal/QmitkConnectomicsNetworkOperationsView.h"
	-#include "src/internal/QmitkConnectomicsStatisticsView.h"
	-#include "src/internal/QmitkRandomParcellationView.h"
	-#include "src/internal/Perspectives/QmitkConnectomicsPerspective.h"
	-
	-ctkPluginContext* mitk::PluginActivator::m_Context = nullptr;
	-
	-ctkPluginContext* mitk::PluginActivator::GetContext()
	-{
	- return m_Context;
	-}
	-
	-void mitk::PluginActivator::start(ctkPluginContext* context)
	-{
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkConnectomicsPerspective, context)
	-
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkConnectomicsDataView, context)
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkConnectomicsNetworkOperationsView, context)
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkConnectomicsStatisticsView, context)
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkRandomParcellationView, context)
	- m_Context = context;
	-}
	-
	-void mitk::PluginActivator::stop(ctkPluginContext* context)
	-{
	- Q_UNUSED(context)
	- m_Context = nullptr;
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/mitkPluginActivator.h b/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/mitkPluginActivator.h
	deleted file mode 100644
	index 470b0a365e..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.connectomics/src/internal/mitkPluginActivator.h
	+++ /dev/null
	@@ -1,40 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef MITKPLUGINACTIVATOR_H
	-#define MITKPLUGINACTIVATOR_H
	-
	-#include <ctkPluginActivator.h>
	-
	-namespace mitk
	-{
	- class PluginActivator : public QObject, public ctkPluginActivator
	- {
	- Q_OBJECT
	- Q_PLUGIN_METADATA(IID "org.mitk.gui.qt.diffusionimaging.connectomics")
	- Q_INTERFACES(ctkPluginActivator)
	-
	- public:
	- static ctkPluginContext* GetContext();
	-
	- void start(ctkPluginContext* context) override;
	- void stop(ctkPluginContext* context) override;
	-
	- private:
	- static ctkPluginContext* m_Context;
	- };
	-}
	-
	-#endif
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/CMakeLists.txt
	deleted file mode 100644
	index 159cd238a9..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/CMakeLists.txt
	+++ /dev/null
	@@ -1,10 +0,0 @@
	-# The project name must correspond to the directory name of your plug-in
	-# and must not contain periods.
	-project(org_mitk_gui_qt_diffusionimaging_denoising)
	-
	-mitk_create_plugin(
	- SUBPROJECTS MITK-DTI
	- EXPORT_DIRECTIVE DIFFUSIONIMAGING_DENOISING_EXPORT
	- EXPORTED_INCLUDE_SUFFIXES src
	- MODULE_DEPENDS MitkDiffusionCore MitkImageDenoising
	-)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/documentation/UserManual/GaussianFilter.png b/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/documentation/UserManual/GaussianFilter.png
	deleted file mode 100644
	index f30a2364ec..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/documentation/UserManual/GaussianFilter.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/documentation/UserManual/NLM.png b/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/documentation/UserManual/NLM.png
	deleted file mode 100644
	index 34bae8c290..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/documentation/UserManual/NLM.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/documentation/UserManual/QmitkDenoisingViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/documentation/UserManual/QmitkDenoisingViewUserManual.dox
	deleted file mode 100644
	index 3db39ed83d..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/documentation/UserManual/QmitkDenoisingViewUserManual.dox
	+++ /dev/null
	@@ -1,6 +0,0 @@
	-/**
	-\page org_mitk_views_denoisingview DWI Denoising
	-
	-This view provides several methods to denoise diffusion-weighted images. Simply select the image to denoise and press the start button. The default parameters should work relatively well. The NLM method is by far the slowest.
	-
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/documentation/doxygen/modules.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/documentation/doxygen/modules.dox
	deleted file mode 100644
	index e18b74dce1..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/documentation/doxygen/modules.dox
	+++ /dev/null
	@@ -1,16 +0,0 @@
	-/**
	- \defgroup org_mitk_gui_qt_diffusionimaging_denoising org.mitk.gui.qt.diffusionimaging.denoising
	- \ingroup MITKPlugins
	-
	- \brief This is the diffusionimaging.denoising plugin.
	-
	-*/
	-
	-/**
	- \defgroup org_mitk_gui_qt_diffusionimaging_denoising_internal Internal
	- \ingroup org_mitk_gui_qt_diffusionimaging_denoising
	-
	- \brief This subcategory includes the internal classes of the org.mitk.gui.qt.diffusionimaging.denoising plugin. Other
	- plugins must not rely on these classes. They contain implementation details and their interface
	- may change at any time. We mean it.
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/files.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/files.cmake
	deleted file mode 100644
	index e56aa36406..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/files.cmake
	+++ /dev/null
	@@ -1,41 +0,0 @@
	-set(SRC_CPP_FILES
	-
	-
	-)
	-
	-set(INTERNAL_CPP_FILES
	- mitkPluginActivator.cpp
	-
	- QmitkDenoisingView.cpp
	-)
	-
	-set(UI_FILES
	- src/internal/QmitkDenoisingViewControls.ui
	-)
	-
	-set(MOC_H_FILES
	- src/internal/mitkPluginActivator.h
	-
	- src/internal/QmitkDenoisingView.h
	-)
	-
	-set(CACHED_RESOURCE_FILES
	- plugin.xml
	-
	- resources/denoisingicon.png
	-)
	-
	-set(QRC_FILES
	-
	-)
	-
	-
	-set(CPP_FILES )
	-
	-foreach(file ${SRC_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/${file})
	-endforeach(file ${SRC_CPP_FILES})
	-
	-foreach(file ${INTERNAL_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/internal/${file})
	-endforeach(file ${INTERNAL_CPP_FILES})
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/manifest_headers.cmake
	deleted file mode 100644
	index cd38bf46fc..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/manifest_headers.cmake
	+++ /dev/null
	@@ -1,5 +0,0 @@
	-set(Plugin-Name "MITK DWI Denoising")
	-set(Plugin-Version "1.0.0")
	-set(Plugin-Vendor "DKFZ, Medical and Biological Informatics")
	-set(Plugin-ContactAddress "http://www.mitk.org")
	-set(Require-Plugin org.mitk.gui.qt.diffusionimaging org.mitk.gui.qt.common)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/plugin.xml b/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/plugin.xml
	deleted file mode 100644
	index c9f2eddab2..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/plugin.xml
	+++ /dev/null
	@@ -1,24 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<?BlueBerry version="0.1"?>
	-<plugin>
	-
	- <extension point="org.blueberry.ui.views">
	-
	- <view id="org.mitk.views.denoisingview"
	- name="Denoising"
	- category="Preprocessing"
	- class="QmitkDenoisingView"
	- icon="resources/denoisingicon.png">
	- <keywordReference id="org.mitk.views.denoisingview.Keyword"/>
	- </view>
	-
	- </extension>
	-
	-
	- <extension point="org.blueberry.ui.keywords">
	-
	-
	-
	- </extension>
	-
	-</plugin>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/resources/denoisingicon.png b/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/resources/denoisingicon.png
	deleted file mode 100644
	index c2518edc63..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/resources/denoisingicon.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/src/internal/QmitkDenoisingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/src/internal/QmitkDenoisingView.cpp
	deleted file mode 100644
	index fb9f58de2e..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/src/internal/QmitkDenoisingView.cpp
	+++ /dev/null
	@@ -1,232 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-// Blueberry
	-#include <berryISelectionService.h>
	-#include <berryIWorkbenchWindow.h>
	-
	-// Qmitk
	-#include "QmitkDenoisingView.h"
	-#include <mitkImageCast.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <mitkITKImageImport.h>
	-
	-#include <mitkDiffusionPropertyHelper.h>
	-
	-#include <mitkNodePredicateDataType.h>
	-#include <mitkNodePredicateProperty.h>
	-#include <mitkNodePredicateAnd.h>
	-#include <itkTotalVariationDenoisingImageFilter.h>
	-#include <itkNonLocalMeansDenoisingFilter.h>
	-#include <itkDiscreteGaussianImageFilter.h>
	-#include <itkPatchBasedDenoisingImageFilter.h>
	-#include <itkMaskImageFilter.h>
	-#include <itkVectorImageToImageFilter.h>
	-#include <itkComposeImageFilter.h>
	-#include <itkGaussianRandomSpatialNeighborSubsampler.h>
	-#include <itkSpatialNeighborSubsampler.h>
	-#include <QMessageBox>
	-#include <mitkNodePredicateIsDWI.h>
	-
	-const std::string QmitkDenoisingView::VIEW_ID = "org.mitk.views.denoisingview";
	-
	-QmitkDenoisingView::QmitkDenoisingView()
	- : QmitkAbstractView()
	- , m_Controls( 0 )
	- , m_ImageNode(nullptr)
	-{
	-}
	-
	-QmitkDenoisingView::~QmitkDenoisingView()
	-{
	-
	-}
	-
	-void QmitkDenoisingView::CreateQtPartControl( QWidget *parent )
	-{
	- // build up qt view, unless already done
	- if ( !m_Controls )
	- {
	- // create GUI widgets from the Qt Designer's .ui file
	- m_Controls = new Ui::QmitkDenoisingViewControls;
	- m_Controls->setupUi( parent );
	-
	- connect( (QObject*)(m_Controls->m_ApplyButton), SIGNAL(clicked()), this, SLOT(StartDenoising()));
	- connect( (QObject*)(m_Controls->m_SelectFilterComboBox), SIGNAL(activated(int)), this, SLOT(UpdateGui()));
	- connect( (QObject*)(m_Controls->m_InputImageBox), SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui()));
	-
	-
	- m_Controls->m_InputImageBox->SetDataStorage(this->GetDataStorage());
	- mitk::NodePredicateIsDWI::Pointer isImagePredicate = mitk::NodePredicateIsDWI::New();
	- m_Controls->m_InputImageBox->SetPredicate( isImagePredicate );
	-
	- UpdateGui();
	- }
	-}
	-
	-void QmitkDenoisingView::SetFocus()
	-{
	- m_Controls->m_SelectFilterComboBox->setFocus();
	-}
	-
	-void QmitkDenoisingView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /part/, const QList<mitk::DataNode::Pointer>& )
	-{
	-
	-}
	-
	-void QmitkDenoisingView::StartDenoising()
	-{
	- typedef itk::DiscreteGaussianImageFilter < DwiVolumeType, DwiVolumeType > GaussianFilterType;
	- typedef itk::PatchBasedDenoisingImageFilter < DwiVolumeType, DwiVolumeType > NlmFilterType;
	- typedef itk::VectorImageToImageFilter < DiffusionPixelType > ExtractFilterType;
	- typedef itk::ComposeImageFilter < itk::Image<DiffusionPixelType, 3> > ComposeFilterType;
	-
	-
	- m_ImageNode = m_Controls->m_InputImageBox->GetSelectedNode();
	- mitk::Image::Pointer input_image = dynamic_cast<mitk::Image*>(m_ImageNode->GetData());
	-
	- if (!mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(input_image))
	- {
	- QMessageBox::warning(nullptr, "Image not processed", "Input is not a diffusion-weighted image!");
	- return;
	- }
	-
	- DwiImageType::Pointer itkVectorImagePointer = mitk::DiffusionPropertyHelper::GetItkVectorImage(input_image);
	-
	- mitk::Image::Pointer denoised_image = nullptr;
	- mitk::DataNode::Pointer denoised_image_node = mitk::DataNode::New();
	-
	- switch (m_Controls->m_SelectFilterComboBox->currentIndex())
	- {
	- case 0:
	- {
	- ComposeFilterType::Pointer composer = ComposeFilterType::New();
	- for (unsigned int i=0; i<itkVectorImagePointer->GetVectorLength(); ++i)
	- {
	- ExtractFilterType::Pointer extractor = ExtractFilterType::New();
	- extractor->SetInput( itkVectorImagePointer );
	- extractor->SetIndex( i );
	- extractor->Update();
	- DwiVolumeType::Pointer gradient_volume = extractor->GetOutput();
	- itk::TotalVariationDenoisingImageFilter< DwiVolumeType, DwiVolumeType >::Pointer filter = itk::TotalVariationDenoisingImageFilter< DwiVolumeType, DwiVolumeType >::New();
	- filter->SetInput(gradient_volume);
	- filter->SetLambda(m_Controls->m_TvLambdaBox->value());
	- filter->SetNumberIterations(m_Controls->m_TvIterationsBox->value());
	- filter->Update();
	- composer->SetInput(i, filter->GetOutput());
	- }
	- composer->Update();
	- denoised_image = mitk::GrabItkImageMemory(composer->GetOutput());
	- denoised_image_node->SetName( "TotalVariation" );
	- break;
	- }
	- case 1:
	- {
	- ExtractFilterType::Pointer extractor = ExtractFilterType::New();
	- extractor->SetInput( itkVectorImagePointer );
	- ComposeFilterType::Pointer composer = ComposeFilterType::New();
	- for (unsigned int i = 0; i < itkVectorImagePointer->GetVectorLength(); ++i)
	- {
	- extractor->SetIndex(i);
	- extractor->Update();
	- GaussianFilterType::Pointer filter = GaussianFilterType::New();
	- filter->SetVariance(m_Controls->m_GaussVarianceBox->value());
	- filter->SetInput(extractor->GetOutput());
	- filter->Update();
	- composer->SetInput(i, filter->GetOutput());
	- }
	- composer->Update();
	- denoised_image = mitk::GrabItkImageMemory(composer->GetOutput());
	- denoised_image_node->SetName( "Gauss" );
	- break;
	- }
	- case 2:
	- {
	- typedef itk::Statistics::GaussianRandomSpatialNeighborSubsampler< NlmFilterType::PatchSampleType, DwiVolumeType::RegionType > SamplerType;
	- // sampling the image to find similar patches
	- SamplerType::Pointer sampler = SamplerType::New();
	- sampler->SetRadius( m_Controls->m_NlmSearchRadiusBox->value() );
	- sampler->SetVariance( m_Controls->m_NlmSearchRadiusBox->value()*m_Controls->m_NlmSearchRadiusBox->value() );
	- sampler->SetNumberOfResultsRequested( m_Controls->m_NlmNumPatchesBox->value() );
	-
	- MITK_INFO << "Starting NLM denoising";
	- ExtractFilterType::Pointer extractor = ExtractFilterType::New();
	- extractor->SetInput( itkVectorImagePointer );
	- ComposeFilterType::Pointer composer = ComposeFilterType::New();
	- for (unsigned int i = 0; i < itkVectorImagePointer->GetVectorLength(); ++i)
	- {
	- extractor->SetIndex(i);
	- extractor->Update();
	- NlmFilterType::Pointer filter = NlmFilterType::New();
	- filter->SetInput(extractor->GetOutput());
	- filter->SetPatchRadius(m_Controls->m_NlmPatchSizeBox->value());
	- filter->SetNoiseModel(NlmFilterType::RICIAN);
	- filter->UseSmoothDiscPatchWeightsOn();
	- filter->UseFastTensorComputationsOn();
	-
	- filter->SetNumberOfIterations(m_Controls->m_NlmIterationsBox->value());
	- filter->SetSmoothingWeight( 1 );
	- filter->SetKernelBandwidthEstimation(true);
	-
	- filter->SetSampler( sampler );
	- filter->Update();
	- composer->SetInput(i, filter->GetOutput());
	- MITK_INFO << "Gradient " << i << " finished";
	- }
	- composer->Update();
	- denoised_image = mitk::GrabItkImageMemory(composer->GetOutput());
	- denoised_image_node->SetName( "NLM" );
	- break;
	- }
	- }
	-
	- mitk::DiffusionPropertyHelper::CopyProperties(input_image, denoised_image, true);
	- mitk::DiffusionPropertyHelper::InitializeImage( denoised_image );
	-
	- denoised_image_node->SetData( denoised_image );
	- GetDataStorage()->Add(denoised_image_node, m_ImageNode);
	-}
	-
	-void QmitkDenoisingView::UpdateGui()
	-{
	- m_Controls->m_ApplyButton->setEnabled(false);
	- m_Controls->m_TvFrame->setVisible(false);
	- m_Controls->m_NlmFrame->setVisible(false);
	- m_Controls->m_GaussFrame->setVisible(false);
	-
	- switch (m_Controls->m_SelectFilterComboBox->currentIndex())
	- {
	- case 0:
	- {
	- m_Controls->m_TvFrame->setVisible(true);
	- break;
	- }
	- case 1:
	- {
	- m_Controls->m_GaussFrame->setVisible(true);
	- break;
	- }
	- case 2:
	- {
	- m_Controls->m_NlmFrame->setVisible(true);
	- break;
	- }
	- }
	-
	- if (m_Controls->m_InputImageBox->GetSelectedNode().IsNotNull())
	- m_Controls->m_ApplyButton->setEnabled(true);
	-}
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/src/internal/QmitkDenoisingView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/src/internal/QmitkDenoisingView.h
	deleted file mode 100644
	index 066c6f3aae..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/src/internal/QmitkDenoisingView.h
	+++ /dev/null
	@@ -1,78 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _QMITKQmitkDenoisingView_H_INCLUDED
	-#define _QMITKQmitkDenoisingView_H_INCLUDED
	-
	-#include <berryISelectionListener.h>
	-
	-#include <QmitkAbstractView.h>
	-
	-#include "ui_QmitkDenoisingViewControls.h"
	-
	-#include <itkVectorImage.h>
	-#include <itkImage.h>
	-#include <mitkImage.h>
	-#include <QThread>
	-#include <QTimer>
	-
	-
	-/**
	- * \class QmitkDenoisingView
	- * \brief View for denoising diffusion-weighted images.
	- */
	-class QmitkDenoisingView : public QmitkAbstractView
	-{
	- // this is needed for all Qt objects that should have a Qt meta-object
	- // (everything that derives from QObject and wants to have signal/slots)
	- Q_OBJECT
	-
	-public:
	-
	- static const std::string VIEW_ID;
	-
	- QmitkDenoisingView();
	- virtual ~QmitkDenoisingView();
	-
	- /** Typedefs */
	- typedef short DiffusionPixelType;
	- typedef itk::VectorImage<DiffusionPixelType, 3> DwiImageType;
	- typedef itk::Image<DiffusionPixelType, 3> DwiVolumeType;
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	-
	- ///
	- /// Sets the focus to an internal widget.
	- ///
	- virtual void SetFocus() override;
	-
	-private slots:
	-
	- void StartDenoising();
	- void UpdateGui();
	-
	-private:
	-
	- /// \brief called by QmitkAbstractView when DataManager's selection has changed
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- Ui::QmitkDenoisingViewControls* m_Controls;
	- mitk::DataNode::Pointer m_ImageNode;
	-};
	-
	-
	-
	-#endif // _QmitkDenoisingView_H_INCLUDED
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/src/internal/QmitkDenoisingViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/src/internal/QmitkDenoisingViewControls.ui
	deleted file mode 100644
	index f803e29af7..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/src/internal/QmitkDenoisingViewControls.ui
	+++ /dev/null
	@@ -1,354 +0,0 @@
	-<?xml version="1.0" encoding="utf-8"?>
	-<ui version="4.0">
	- <class>QmitkDenoisingViewControls</class>
	- <widget class="QWidget" name="QmitkDenoisingViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>351</width>
	- <height>734</height>
	- </rect>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="windowTitle">
	- <string>QmitkTemplate</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="leftMargin">
	- <number>9</number>
	- </property>
	- <property name="topMargin">
	- <number>9</number>
	- </property>
	- <property name="rightMargin">
	- <number>9</number>
	- </property>
	- <property name="bottomMargin">
	- <number>9</number>
	- </property>
	- <property name="verticalSpacing">
	- <number>25</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QFrame" name="frame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_2">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_DwiLabel">
	- <property name="text">
	- <string>Input Image:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_InputImageBox"></widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QComboBox" name="m_SelectFilterComboBox">
	- <item>
	- <property name="text">
	- <string>Total-variation</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Discrete Gaussian</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Non-local means</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="m_DwiLabel_2">
	- <property name="text">
	- <string>Filter:</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QGroupBox" name="m_TvFrame">
	- <property name="title">
	- <string>Parameters</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_5">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_LabelParameter_4">
	- <property name="text">
	- <string>Lambda:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QDoubleSpinBox" name="m_TvLambdaBox">
	- <property name="decimals">
	- <number>4</number>
	- </property>
	- <property name="minimum">
	- <double>0.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.100000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="m_LabelParameter_5">
	- <property name="text">
	- <string>Iterations:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QSpinBox" name="m_TvIterationsBox">
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>999</number>
	- </property>
	- <property name="value">
	- <number>1</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QGroupBox" name="m_NlmFrame">
	- <property name="title">
	- <string>Parameters</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_6">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_LabelParameter_6">
	- <property name="text">
	- <string>Sampling Radius:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QSpinBox" name="m_NlmNumPatchesBox">
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>999</number>
	- </property>
	- <property name="value">
	- <number>10</number>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="1">
	- <widget class="QSpinBox" name="m_NlmIterationsBox">
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>999</number>
	- </property>
	- <property name="value">
	- <number>4</number>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_NlmSearchRadiusBox">
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>999</number>
	- </property>
	- <property name="value">
	- <number>4</number>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="m_LabelParameter_11">
	- <property name="text">
	- <string>Num. Patches:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QSpinBox" name="m_NlmPatchSizeBox">
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>50</number>
	- </property>
	- <property name="value">
	- <number>1</number>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QLabel" name="m_LabelParameter_9">
	- <property name="text">
	- <string>Iterations:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="m_LabelParameter_7">
	- <property name="text">
	- <string>Patch Size:</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QGroupBox" name="m_GaussFrame">
	- <property name="title">
	- <string>Parameters</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_7">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="1">
	- <widget class="QDoubleSpinBox" name="m_GaussVarianceBox">
	- <property name="decimals">
	- <number>4</number>
	- </property>
	- <property name="minimum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>99999.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>1.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_LabelParameter_10">
	- <property name="text">
	- <string>Variance:</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QCommandLinkButton" name="m_ApplyButton">
	- <property name="text">
	- <string>Start</string>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <spacer name="verticalSpacer">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- </layout>
	- </widget>
	- <layoutdefault spacing="6" margin="11"></layoutdefault>
	- <customwidgets>
	- <customwidget>
	- <class>QmitkDataStorageComboBox</class>
	- <extends>QComboBox</extends>
	- <header location="global">QmitkDataStorageComboBox.h</header>
	- </customwidget>
	- </customwidgets>
	- <resources></resources>
	- <connections></connections>
	-</ui>
	\ No newline at end of file
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/src/internal/mitkPluginActivator.cpp
	deleted file mode 100644
	index 85c332a1cf..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/src/internal/mitkPluginActivator.cpp
	+++ /dev/null
	@@ -1,39 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkPluginActivator.h"
	-
	-#include "src/internal/QmitkDenoisingView.h"
	-
	-
	-ctkPluginContext* mitk::PluginActivator::m_Context = nullptr;
	-
	-ctkPluginContext* mitk::PluginActivator::GetContext()
	-{
	- return m_Context;
	-}
	-
	-void mitk::PluginActivator::start(ctkPluginContext* context)
	-{
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkDenoisingView, context)
	- m_Context = context;
	-}
	-
	-void mitk::PluginActivator::stop(ctkPluginContext* context)
	-{
	- Q_UNUSED(context)
	- m_Context = nullptr;
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/src/internal/mitkPluginActivator.h b/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/src/internal/mitkPluginActivator.h
	deleted file mode 100644
	index 62b1f535d8..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/src/internal/mitkPluginActivator.h
	+++ /dev/null
	@@ -1,40 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef MITKPLUGINACTIVATOR_H
	-#define MITKPLUGINACTIVATOR_H
	-
	-#include <ctkPluginActivator.h>
	-
	-namespace mitk
	-{
	- class PluginActivator : public QObject, public ctkPluginActivator
	- {
	- Q_OBJECT
	- Q_PLUGIN_METADATA(IID "org.mitk.gui.qt.diffusionimaging.denoising")
	- Q_INTERFACES(ctkPluginActivator)
	-
	- public:
	- static ctkPluginContext* GetContext();
	-
	- void start(ctkPluginContext* context) override;
	- void stop(ctkPluginContext* context) override;
	-
	- private:
	- static ctkPluginContext* m_Context;
	- };
	-}
	-
	-#endif
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/CMakeLists.txt
	deleted file mode 100644
	index dcf135c587..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/CMakeLists.txt
	+++ /dev/null
	@@ -1,10 +0,0 @@
	-# The project name must correspond to the directory name of your plug-in
	-# and must not contain periods.
	-project(org_mitk_gui_qt_diffusionimaging_fiberfox)
	-
	-mitk_create_plugin(
	- SUBPROJECTS MITK-DTI
	- EXPORT_DIRECTIVE DIFFUSIONIMAGING_FIBERFOX_EXPORT
	- EXPORTED_INCLUDE_SUFFIXES src
	- MODULE_DEPENDS MitkFiberTracking
	-)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/Fiberfox-Fiducial.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/Fiberfox-Fiducial.png
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/Fiberfox.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/Fiberfox.png
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/FiberfoxExamples.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/FiberfoxExamples.png
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/FiberfoxWholebrain.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/FiberfoxWholebrain.png
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/QmitkFiberGenerationViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/QmitkFiberGenerationViewUserManual.dox
	deleted file mode 100644
	index 77b3929efa..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/QmitkFiberGenerationViewUserManual.dox
	+++ /dev/null
	@@ -1,72 +0,0 @@
	-/**
	-\page org_mitk_views_fibergenerationview Fiber Generator
	-
	-This view provides the user interface for defining artificial white matter fibers.
	-Arbitrary fiber configurations like bent, crossing, kissing, twisting, and fanning bundles can be intuitively defined by positioning only a few 3D waypoints to trigger the automated generation of synthetic fibers.
	-From these fibers a diffusion-weighted signal can be simulated using the Fiberfox View. The view also enables the automatic generation of random fiber configurations (Fig. 3).
	-
	-<b>Available sections:</b>
	- - \ref QmitkFiberGenerationViewUserManualFiberDefinition
	- - \ref QmitkFiberGenerationViewUserManualKnownIssues
	- - \ref QmitkFiberGenerationViewUserManualReferences
	-
	-\section QmitkFiberGenerationViewUserManualFiberDefinition Manual Fiber Definition
	-
	-Fiber strands are defined simply by placing markers in a 3D image volume. The fibers are then interpolated between these fiducials.
	-
	-
	-<b>Example:</b>
	-\li Chose an image volume to place the markers used to define the fiber pathway. If you don't have such an image available switch to the "Signal Generation" tab, define the size and spacing of the desired image and click "Generate Image". If no fiber bundle is selected, this will generate a dummy image that can be used to place the fiducials.
	-\li Start placing fiducials at the desired positions to define the fiber pathway. To do that, click on the button with the circle pictogram, then click at the desired position and plane in the image volume and drag your mouse while keeping the button pressed to generate a circular shape. Adjust the shape using the control points (Fig. 2). The position of control point D introduces a twist of the fibers between two successive fiducials. The actual fiber generation is triggered automatically as soon as you place the second control point.
	-\li In some cases the fibers are entangled in a way that can't be resolved by introducing an additional fiber twist. Fiberfox tries to avoid these situations, which arise from different normal orientations of succeeding fiducials, automatically. In rare cases this is not successful. Use the double-arrow button to flip the fiber positions of the selected fiducial in one dimension. Either the problem is resolved now or you can resolve it manually by adjusting the twist-control point.
	-\li To create non elliptical fiber profile shapes switch to the Fiber Extraction View. This view provides tools to extract subesets of fibers from fiber bundles and enables to cut out arbitrary polygonal fiber shapes from existing bundles.
	-
	-\imageMacro{Fiberfox-Fiducial.png, "Fig. 1: Control points defining the actual shape of the fiducial. A specifies the fiducials position in space\, B and C the two ellipse radii and D the twisting angle between two successive fiducials.",10}
	-
	-<b>Fiber Options:</b>
	-\li <b>Real Time Fibers</b>: If checked, each parameter adjustment (fiducial position, number of fibers, ...) will be directly applied to the selected fiber bundle. If unchecked, the fibers will only be generated if the corresponding button "Generate Fibers" is clicked.
	-\li <b>Fiber Distribution</b>: Specifies if the fiber distribution inside the bundle follows a uniform or normal distribution.
	-\li <b>\# Fibers</b>: Specifies the number of fibers that will be generated for the selected bundle.
	-\li <b>Advanced Options</b>: Show/hide advanced options
	-\li <b>Fiber Sampling</b>: Adjusts the distenace of the fiber sampling points (in mm). A higher sampling rate is needed if high curvatures are modeled.
	-\li <b>Tension, Continuity, Bias</b>: Parameters controlling the shape of the splines interpolation the fiducials. See <a href="http://en.wikipedia.org/wiki/Kochanek%E2%80%93Bartels_spline">Wikipedia</a> for details.
	-
	-
	-<b>Fiducial Options:</b>
	-\li <b>Use Constant Fiducial Radius</b>: If checked, all fiducials are treated as circles with the same radius. The first fiducial of the bundle defines the radius of all other fiducials.
	-\li <b>Align with grid</b>: Click to shift the selected fiducial center points to the next voxel center.
	-
	-<b>Operations:</b>
	-\li <b>Rotation</b>: Define the rotation of the selected fiber bundle around each axis (in degree).
	-\li <b>Translation</b>: Define the translation of the selected fiber bundle along each axis (in mm).
	-\li <b>Scaling</b>: Define a scaling factor for the selected fiber bundle in each dimension.
	-\li <b>Transform Selection</b>: Apply specified rotation, translation and scaling to the selected Bundle/Fiducial
	-\li <b>Copy Bundles</b>: Add copies of the selected fiber bundles to the datamanager.
	-\li <b>Join Bundles</b>: Add new bundle to the datamanager that contains all fibers from the selected bundles.
	-\li <b>Include Fiducials</b>: If checked, the specified transformation is also applied to the fiducials belonging to the selected fiber bundle and the fiducials are also copied.
	-
	-\imageMacro{FiberfoxExamples.png, "Fig. 2: Examples of artificial crossing (a\,b)\, fanning (c\,d)\, highly curved (e\,f)\, kissing (g\,h) and twisting (i\,j) fibers as well as of the corresponding tensor images generated with Fiberfox.",4}
	-
	-\imageMacro{random_phantom.png, "Fig. 3: Example of a random fiber phantom containing all kinds of configurations.",4}
	-
	-\section QmitkFiberGenerationViewUserManualKnownIssues Known Issues
	-
	-\li If a scaling factor is applied to the selcted fiber bundle, the corresponding fiducials are not scaled accordingly.
	-\li In some cases the automatic update of the selected fiber bundle is not triggered even if "Real Time Fibers" is checked, e.g. if a fiducial is deleted. If this happens on can always force an update by pressing the "Generate Fibers" button.
	-
	-If any other issues or feature requests arises during the use of Fiberfox, please don't hesitate to send us an e-mail or directly report the issue in our bugtracker: https://phabricator.mitk.org/maniphest/
	-\section QmitkFiberGenerationViewUserManualReferences References
	-
	-[1] Neher, P.F., Laun, F.B., Stieltjes, B., Maier-Hein, K.H., 2014. Fiberfox: facilitating the creation of realistic white matter software phantoms. Magn Reson Med 72, 1460–1470. doi:10.1002/mrm.25045
	-
	-[2] Neher, P.F., Laun, F.Neher, P.F., Stieltjes, B., Laun, F.B., Meinzer, H.-P., Fritzsche, K.H., 2013. Fiberfox: A novel tool to generate software phantoms of complex fiber geometries, in: Proceedings of International Society of Magnetic Resonance in Medicine.
	-
	-[3] Neher, P.F., Stieltjes, B., Laun, F.B., Meinzer, H.-P., Fritzsche, K.H., 2013. Fiberfox: A novel tool to generate software phantoms of complex fiber geometries, in: Proceedings of International Society of Magnetic Resonance in Medicine.
	-
	-[4] Hering, J., Neher, P.F., Meinzer, H.-P., Maier-Hein, K.H., 2014. Construction of ground-truth data for head motion correction in diffusion MRI, in: Proceedings of International Society of Magnetic Resonance in Medicine.
	-
	-[5] Maier-Hein, Klaus, Neher, Peter, Houde, Jean-Christophe, Caruyer, Emmanuel, Daducci, Alessandro, Dyrby, Tim, … Descoteaux, Maxime. (2015). Tractography Challenge ISMRM 2015 Data [Data set]. Zenodo. http://doi.org/10.5281/zenodo.572345
	-
	-[6] Maier-Hein, Klaus, Neher, Peter, Houde, Jean-Christophe, Caruyer, Emmanuel, Daducci, Alessandro, Dyrby, Tim, … Descoteaux, Maxime. (2017). Tractography Challenge ISMRM 2015 High-resolution Data [Data set]. Zenodo. http://doi.org/10.5281/zenodo.579933
	-
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/QmitkFiberfoxViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/QmitkFiberfoxViewUserManual.dox
	deleted file mode 100644
	index 7a183ecfc8..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/QmitkFiberfoxViewUserManual.dox
	+++ /dev/null
	@@ -1,106 +0,0 @@
	-/**
	-\page org_mitk_views_fiberfoxview Fiberfox DW-MRI Simulation
	-
	-This view provides the user interface for Fiberfox [1,2,3], an interactive simulation tool diffusion-weighted MR images.
	-A diffusion-weighted signal is simulated from arbitrary input fibers using a flexible combination of various diffusion models.
	-It is possible to use manually created artificial fiber bundles (see Fiber Generator View) or fibers obtained in any other way, e.g. using fiber tractography, to simulate the signal (Example: <a href="http://www.tractometer.org/ismrm_2015_challenge/">ISMRM Tractography Challenge</a>).
	-The simulation can be modified using specified acquisition settings such as gradient direction, b-value, image size, image resolution, echo time, and much more.
	-Additionally it enables the simulation of magnetic resonance artifacts including thermal noise, Gibbs ringing, N/2 ghosting, aliasing, susceptibility distortions, eddy currents and motion artifacts.
	-The employed parameters can be saved and loaded as xml file with the ending ".ffp" (Fiberfox parameters).
	-It is furthermore possible to add artifacts to an already existing diffusion-weighted image.
	-
	-<b>Available sections:</b>
	- - \ref QmitkFiberfoxViewUserManualSignalGeneration
	- - \ref QmitkFiberfoxViewUserManualReferences
	-
	-
	-\section QmitkFiberfoxViewUserManualSignalGeneration Signal Generation
	-
	-To generate an artificial signal from the input fibers we follow the concepts recently presented by Panagiotaki et al. in a review and taxonomy of different compartment models:
	-a flexible model combining multiple compartments is used to simulate the anisotropic diffusion inside (intra-axonal compartment) and between axons (inter-axonal compartment), isotropic diffusion outside of the axons (extra-axonal compartment 1)
	-and the restricted diffusion in other cell types (extra-axonal compartment 2) weighted according to their respective volume fraction.
	-
	-A diffusion-weighted image is generated from the fibers by selecting the according fiber bundle in the "Fiber Bundle" combobox and clicking "Generate Image".
	-If some other diffusion-weighted image is selected together with the fiber bundle, Fiberfox directly uses the parameters of the selected image (size, spacing, gradient directions, b-values) for the signal generation process.
	-Additionally a binary image can be selected that defines the tissue area. Voxels outside of this mask will contain no signal, only noise and other effects induced by the acquisiton (ghosts etc.).
	-If a save path is specified, the simualted image will be saved at this location. Eventually generated log files (e.g. recording the head motion) are also saved at this location. If not path is specified,
	-the simualted image will only appear in the data manager and has to be saved manually. Logfiles are then saved in the system specific temp directory.
	-
	-If no fiber bundle but a diffusion-weighted image is selected, the specified artifacts are added to the selected image. In this mode, signal relaxation is disabled since multiple compartments are not available and the input image alrady contains relaxation effects. Also, introducing head motion is not possible since this qould require a contrast change in the weighted volumes.
	-
	-
	-<b>Basic Image Settings:</b>
	-\li <b>Image Dimensions</b>: Specifies actual image size (number of voxels in each dimension).
	-\li <b>Image Spacing</b>: Specifies voxel size in mm. Beware that changing the voxel size also changes the signal strength, e.g. increasing the resolution from <em>2x2x2</em> mm to <em>1x1x1</em> mm decreases the signal obtained for each voxel by a factor 8.
	-\li <b>Gradient Directions</b>: Number of gradients directions distributed equally over the half sphere. 10% baseline images are automatically added.
	-\li <b>b-Value</b>: Diffusion weighting in s/mm². If an existing diffusion-weighted image is used to set the basic parameters, the b-value is defined by the gradient direction magnitudes of this image, which also enables the use of multiple b-values.
	-
	-
	-<b>Advanced Image Settings (activate checkbox "Advanced Options"):</b>
	-\li <b>Acquisition Type</b>: the default acquisition type is a single shot EPI, which acquires a complete k-space slice with one echo. Alternatively, a standard spin echo sequence can be chosen that uses a cartesian k-space sampling scheme and acquires one k-space line with one echo.
	-\li <b>Signal Scale</b>: Additional scaling factor for the signal in each voxel. The default value of 100 results in a maximum signal amplitude of 800 for <em>2x2x2</em> mm voxels. Beware that changing this value without changing the noise variance results in a changed SNR. Adjustment of this value might be needed if the overall signal values are much too high or much too low (depends on a variety of factors like voxel size and relaxation times).
	-\li <b>Number of Channels</b>: Specify the number of coil elements used for the acquisition. The coil elements are circularly arranged around the objects z-axis. Currently the coil distance to the currently imaged object slice in z-direction is not taken into account, so the coil basically seems to move with the currently imaged slice along the z-axis. The signals obtained from the individual coil elements are combined using a sum of squares approach. Beware that the simulation time scales linearly with the number of coils!
	-\li <b>Coil Sensitivity</b>: Using multiple acquisition channels only makes sense if the coil elements have a non-constant sensitivity profile. At the moment linearly as well as exponantially decreasing coil sensitivities are implemented. Using a constant coil sensitivity, the signal received by each coil element is equal regardless of the distance to the coil. In case of a non-constant sensitivity profile the received signal intensities decrease with increasing distance from the coil element. Using a linear profile, about 50% of the signal originating from the slice center is received. In case of an exponential coil sensitivity, only about 32% of the signal originating from the slice center is received.
	-\li <b>Echo Train Length <em>ETL</em></b>: Only relevant for Fast Spin Echo sequence (number of k-space lines acquired with one RF pulse). The echo spacing is set to TE.
	-\li <b>Echo Time <em>TE</em></b>: Time between the 90° excitation pulse and the first spin echo. Increasing this time results in a stronger <em>T2</em>-relaxation effect (<a href="http://en.wikipedia.org/wiki/Relaxation_%28NMR%29">Wikipedia</a>).
	-\li <b>Repetition Time <em>TR</em></b>: Time between two 90° RF pulses. Important for T1 contrast (use short TE and TR for strong T1 weighting).
	-\li <b>Inversion Time <em>TI</em></b>: Time between 180° inversion pulse and 90° RF pulse. If 0, no inversion pulse is simulated.
	-\li <b>Dwell Time</b>: Time to read one line in k-space. Increasing this time results in a stronger <em>T2*</em> effect which causes an attenuation of the higher frequencies in phase direction (here along y-axis) which again results in a blurring effect of sharp edges perpendicular to the phase direction.
	-\li <b><em>T<sub>inhom</sub></em> Relaxation (T2')</b>: Time constant specifying the signal decay due to magnetic field inhomogeneities (also called <em>T2'</em>). Together with the tissue specific relaxation time constant <em>T2</em> this defines the <em>T2</em> decay constant: <em>T2=(T2 T2')/(T2+T2')</em>
	-\li <b>Fiber Radius (in µm)</b>: Used to calculate the volume fractions of the used compartments (fiber, water, etc.). If set to 0 (default) the fiber radius is set automatically so that the voxel containing the most fibers is filled completely. A realistic axon radius ranges from about 5 to 20 microns. Using the automatic estimation the resulting value might very well be much larger or smaller than this range.
	-\li <b>Reverse Phase Encoding Direction</b>: Switch anterior-posterior and posterior-anterior phase encoding.
	-\li <b>Simulate Signal Relaxation</b>: If checked, the relaxation induced signal decay is simulated, other wise the parameters <em>TE</em>, Line Readout Time, <em>T<sub>inhom</sub></em>, and <em>T2</em> are ignored.
	-\li <b>Disable Partial Volume Effects</b>: If checked, the actual volume fractions of the single compartments are ignored. A voxel will either be filled by the intra axonal compartment completely or will contain no fiber at all.
	-\li <b>Output Additional Images</b>: Output a double image for each compartment. The voxel values correspond to the volume fraction of the respective compartment.
	-
	-
	-<b>Compartment Settings:</b>
	-
	-The group-boxes "Intra-axonal Compartment", "Inter-axonal Compartment" and "Extra-axonal Compartments" allow the specification which model to use and the corresponding model parameters. Currently the following models are implemented:
	-\li <b>Stick</b>: The “stick” model describes diffusion in an idealized cylinder with zero radius. Parameter: Diffusivity <em>d</em>
	-\li <b>Zeppelin</b>: Cylindrically symmetric diffusion tensor. Parameters: Parallel diffusivity <em>d<sub>\|\|</sub></em> and perpendicular diffusivity <em>d<sub>⊥</sub></em>
	-\li <b>Tensor</b>: Full diffusion tensor. Parameters: Parallel diffusivity <em>d<sub>\|\|</sub></em> and perpendicular diffusivity constants <em>d<sub>⊥1</sub></em> and <em>d<sub>⊥2</sub></em>
	-\li <b>Ball</b>: Isotropic compartment. Parameter: Diffusivity <em>d</em>
	-\li <b>Astrosticks</b>: Consists of multiple stick models pointing in different directions. The single stick orientations can either be distributed equally over the sphere or are sampled randomly. The model represents signal coming from a type of glial cell called astrocytes, or populations of axons with arbitrary orientation. Parameters: randomization of the stick orientations and diffusivity of the sticks <em>d</em>.
	-\li <b>Dot</b>: Isotropically restricted compartment. No parameter.
	-\li <b>Prototype Signal</b>: EXPERIMENTAL FEATURE!!! The signal is not generated from a parametric model but a prototype signal is sampled from the selected diffusion-weighted image. Parameters: The number of prototype signals that are used for the signal generation (at each fiber position one is picked randomly) and the constraining diffusion parameters for a voxel signal to be included in the list. For a fiber signal one would for example probably select a high <em>FA</em> and for a CSF voxel a low <em>FA</em>.
	-
	-For a detailed description of the individual models, please refer to Panagiotaki <em>et al.</em> "Compartment models of the diffusion MR signal in brain white matter: A taxonomy and comparison".
	-
	-Additionally to the model parameters, each compartment has its own <em>T1</em> and <em>T2</em> signal relaxation constants (in <em>ms</em>). This constants are not relevant if the prototype signal model is used, since in this case signal relaxation is disabled.
	-Furthermore, it is possible to specify a volume fraction map for each compartment:
	-\li The volume fraction maps for compartment 1 and 2 (fiber compartments) are optional. If they are not specified, the corresponding volume fractions are directly determined from the fiber bundle.
	-Additionally, it is assumed that in this case all volume fraction maps of the non-fiber compartments contain values relative to the remaining non-fiber volume, not absolute fractions of the complete voxel volume.
	-This ensures that the automatically determined fiber volumes and the map-defined non-fiber volumes sum up to 1 in each voxel.
	-\li If one non-fiber compartment is used but no corresponding volume fraction map is specified, the corresponding volume is automatically set to the remaining volume (voxel volume - fiber volume).
	-\li If four compartments are used, at least one of the extra axonal compartment volume fraction maps has to be specified. The second one can be automatically determined from the respective other (1-f). If this is the case, the non-fiber volume information is again regarded as relative to the available non-fiber volume.
	-
	-
	-<b>Noise and Artifacts:</b>
	-\li <b>Noise</b>: Add Rician or Chi-Square distributed noise with the specified variance to the signal.
	-\li <b>Spikes</b>: Add signal spikes to the k-space signal resulting in stripe artifacts across the corresponding image slice.
	-\li <b>Aliasing</b>: Aliasing artifacts occur if the FOV in phase direction is smaller than the imaged object. The parameter defines the percentage by which the FOV is shrunk.
	-\li <b>N/2 Ghosts</b>: Specify the offset between successive lines in k-space. This offset causes ghost images in distance N/2 in phase direction due to the alternating EPI readout directions.
	-\li <b>Distortions</b>: Simulate distortions due to magnetic field inhomogeneities. This is achieved by adding an additional phase during the readout process. The input is a frequency map specifying the inhomogeneities. The "Fieldmap Generator" view provides an interface to generate simple artificial frequency maps. To egnerate realistic distortions for an in vivo like dataset we recommend using a frequency map acquired during a real MR scan or one estimated with tools such as FSL TOPUP.
	-\li <b>Motion Artifacts</b>: To simulate motion artifacts, the fiber configuration is moved between the signal simulation of the individual gradient volumes. The motion can be performed randomly, where the parameters are used to define the +/- maximum of the corresponding motion, or linearly, where the parameters define the maximum rotation/translation around/along the corresponding axis at the and of the simulated acquisition.
	-\li <b>Eddy Currents</b>: Eddy current induced magnetic field gradient (in mT/m) at the beginning of the k-space readout. A spatially linear eddy current profile in the direction of the respective diffusion-weighting gradient is used. The eddy current induced gradient decays with a time constant τ=70ms.
	-\li <b>Gibbs Ringing</b>: Ringing artifacts occurring on edges in the image due to the frequency low-pass filtering caused by the limited size of the k-space.
	-
	-\imageMacro{FiberfoxWholebrain.png, "Fig. 1: Realistic simulation of a whole brain dataset with multiple artifacts.",4}
	-
	-
	-\section QmitkFiberfoxViewUserManualReferences References
	-
	-[1] Neher, P.F., Laun, F.B., Stieltjes, B., Maier-Hein, K.H., 2014. Fiberfox: facilitating the creation of realistic white matter software phantoms. Magn Reson Med 72, 1460–1470. doi:10.1002/mrm.25045
	-
	-[2] Neher, P.F., Laun, F.Neher, P.F., Stieltjes, B., Laun, F.B., Meinzer, H.-P., Fritzsche, K.H., 2013. Fiberfox: A novel tool to generate software phantoms of complex fiber geometries, in: Proceedings of International Society of Magnetic Resonance in Medicine.
	-
	-[3] Neher, P.F., Stieltjes, B., Laun, F.B., Meinzer, H.-P., Fritzsche, K.H., 2013. Fiberfox: A novel tool to generate software phantoms of complex fiber geometries, in: Proceedings of International Society of Magnetic Resonance in Medicine.
	-
	-[4] Hering, J., Neher, P.F., Meinzer, H.-P., Maier-Hein, K.H., 2014. Construction of ground-truth data for head motion correction in diffusion MRI, in: Proceedings of International Society of Magnetic Resonance in Medicine.
	-
	-[5] Maier-Hein, Klaus, Neher, Peter, Houde, Jean-Christophe, Caruyer, Emmanuel, Daducci, Alessandro, Dyrby, Tim, … Descoteaux, Maxime. (2015). Tractography Challenge ISMRM 2015 Data [Data set]. Zenodo. http://doi.org/10.5281/zenodo.572345
	-
	-[6] Maier-Hein, Klaus, Neher, Peter, Houde, Jean-Christophe, Caruyer, Emmanuel, Daducci, Alessandro, Dyrby, Tim, … Descoteaux, Maxime. (2017). Tractography Challenge ISMRM 2015 High-resolution Data [Data set]. Zenodo. http://doi.org/10.5281/zenodo.579933
	-
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/QmitkFieldmapGeneratorViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/QmitkFieldmapGeneratorViewUserManual.dox
	deleted file mode 100644
	index 95a735d9a3..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/QmitkFieldmapGeneratorViewUserManual.dox
	+++ /dev/null
	@@ -1,16 +0,0 @@
	-/**
	-\page org_mitk_views_fieldmapgenerator Fieldmap Generator
	-
	-This view allows the creation of artificial frequency maps used by Fiberfox to introduce distortions into diffusion weighted images. The generated images can contain a linear frequency gradient and/or multiple 3D gaussian shaped field inhomogeneities.
	-
	-<b>Example:</b>
	-\li Select a reference image with the combo box. The generated fieldmap will feature the same geometry as the selected image.
	-\li Move the crosshair to the any position in the image and click "Place Field Source".
	-\li A position marker will appear in the render windows and in the datamanager, which indicates the position of a 3D gaussian field distortion that will be introduced upon clicking "Generate Fieldmap".
	-\li The strength and variance of the placed sources can be modified by selecting the corresponding data node in the data manager and adjusting the parameters in the lower part of the view (below "Edit Selected Source").
	-\li To introduce an (additional) linear frequency gradient, specify the gradient below "Add Gradient".
	-\li To finally generate the fieldmap, press "Generate Fieldmap".
	-
	-\imageMacro{fieldmapGenerator.png,"The Fieldmap Generator View. The render window shows a diffusion weighted image of the brain superimposed by a frequency map with two 3D gaussian field inhomogeneities (red).",16.00}
	-
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/fieldmapGenerator.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/fieldmapGenerator.png
	deleted file mode 100644
	index de76c15e65..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/fieldmapGenerator.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/random_phantom.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/random_phantom.png
	deleted file mode 100644
	index cc4f29a0cb..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/UserManual/random_phantom.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/doxygen/modules.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/doxygen/modules.dox
	deleted file mode 100644
	index 8a42de4836..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/documentation/doxygen/modules.dox
	+++ /dev/null
	@@ -1,16 +0,0 @@
	-/**
	- \defgroup org_mitk_gui_qt_diffusionimaging_fiberfox org.mitk.gui.qt.diffusionimaging.fiberfox
	- \ingroup MITKPlugins
	-
	- \brief This is the diffusionimaging.fiberfox plugin.
	-
	-*/
	-
	-/**
	- \defgroup org_mitk_gui_qt_diffusionimaging_fiberfox_internal Internal
	- \ingroup org_mitk_gui_qt_diffusionimaging_fiberfox
	-
	- \brief This subcategory includes the internal classes of the org.mitk.gui.qt.diffusionimaging.fiberfox plugin. Other
	- plugins must not rely on these classes. They contain implementation details and their interface
	- may change at any time. We mean it.
	-*/
	\ No newline at end of file
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/files.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/files.cmake
	deleted file mode 100644
	index 3966936404..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/files.cmake
	+++ /dev/null
	@@ -1,77 +0,0 @@
	-set(SRC_CPP_FILES
	- QmitkTensorModelParametersWidget.cpp
	- QmitkZeppelinModelParametersWidget.cpp
	- QmitkStickModelParametersWidget.cpp
	- QmitkDotModelParametersWidget.cpp
	- QmitkBallModelParametersWidget.cpp
	- QmitkAstrosticksModelParametersWidget.cpp
	- QmitkPrototypeSignalParametersWidget.cpp
	-)
	-
	-set(INTERNAL_CPP_FILES
	- QmitkFiberfoxView.cpp
	- QmitkFieldmapGeneratorView.cpp
	- QmitkFiberGenerationView.cpp
	- mitkPluginActivator.cpp
	-
	- Perspectives/QmitkDIAppSyntheticDataGenerationPerspective.cpp
	-)
	-
	-set(UI_FILES
	- src/internal/QmitkFiberfoxViewControls.ui
	- src/internal/QmitkFieldmapGeneratorViewControls.ui
	- src/internal/QmitkFiberGenerationViewControls.ui
	-
	- src/QmitkTensorModelParametersWidgetControls.ui
	- src/QmitkZeppelinModelParametersWidgetControls.ui
	- src/QmitkStickModelParametersWidgetControls.ui
	- src/QmitkDotModelParametersWidgetControls.ui
	- src/QmitkBallModelParametersWidgetControls.ui
	- src/QmitkAstrosticksModelParametersWidgetControls.ui
	- src/QmitkPrototypeSignalParametersWidgetControls.ui
	-)
	-
	-set(MOC_H_FILES
	- src/internal/mitkPluginActivator.h
	- src/internal/QmitkFiberfoxView.h
	- src/internal/QmitkFieldmapGeneratorView.h
	- src/internal/QmitkFiberGenerationView.h
	-
	- src/QmitkTensorModelParametersWidget.h
	- src/QmitkZeppelinModelParametersWidget.h
	- src/QmitkStickModelParametersWidget.h
	- src/QmitkDotModelParametersWidget.h
	- src/QmitkBallModelParametersWidget.h
	- src/QmitkAstrosticksModelParametersWidget.h
	- src/QmitkPrototypeSignalParametersWidget.h
	-
	- src/internal/Perspectives/QmitkDIAppSyntheticDataGenerationPerspective.h
	-)
	-
	-set(CACHED_RESOURCE_FILES
	- plugin.xml
	-
	- resources/phantom.png
	- resources/syntheticdata.png
	- resources/fieldmap.png
	- resources/models.png
	- resources/download.png
	- resources/right.png
	- resources/stop.png
	- resources/upload.png
	-)
	-
	-set(QRC_FILES
	- resources/QmitkFiberfox.qrc
	-)
	-
	-
	-set(CPP_FILES )
	-
	-foreach(file ${SRC_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/${file})
	-endforeach(file ${SRC_CPP_FILES})
	-
	-foreach(file ${INTERNAL_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/internal/${file})
	-endforeach(file ${INTERNAL_CPP_FILES})
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/manifest_headers.cmake
	deleted file mode 100644
	index 75fc472cfc..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/manifest_headers.cmake
	+++ /dev/null
	@@ -1,5 +0,0 @@
	-set(Plugin-Name "MITK Fiberfox")
	-set(Plugin-Version "1.0.0")
	-set(Plugin-Vendor "DKFZ, Medical and Biological Informatics")
	-set(Plugin-ContactAddress "http://www.mitk.org")
	-set(Require-Plugin org.mitk.gui.qt.diffusionimaging org.mitk.gui.qt.common)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/plugin.xml b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/plugin.xml
	deleted file mode 100644
	index eaeb743a2a..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/plugin.xml
	+++ /dev/null
	@@ -1,76 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<?BlueBerry version="0.1"?>
	-<plugin>
	-
	- <extension point="org.blueberry.ui.views">
	-
	- <view id="org.mitk.views.fiberfoxview"
	- name="Fiberfox"
	- category="Simulated data"
	- class="QmitkFiberfoxView"
	- icon="resources/models.png">
	- <description>Diffusion weighted MRI data simulation tool.</description>
	- <keywordReference id="org.mitk.views.fiberfoxview.Keyword"/>
	- </view>
	-
	- <view id="org.mitk.views.fieldmapgenerator"
	- name="Fieldmap Generator"
	- category="Simulated data"
	- class="QmitkFieldmapGeneratorView"
	- icon="resources/fieldmap.png">
	- <keywordReference id="org.mitk.views.fiberfoxview.Keyword"/>
	- </view>
	-
	- <view id="org.mitk.views.fibergenerationview"
	- name="Fiber Generator"
	- category="Simulated data"
	- class="QmitkFiberGenerationView"
	- icon="resources/phantom.png">
	- <keywordReference id="org.mitk.views.fiberfoxview.Keyword"/>
	- </view>
	-
	- </extension>
	-
	-
	- <extension point="org.blueberry.ui.perspectives">
	-
	- <perspective id="org.mitk.perspectives.syntheticdata"
	- name="Fiberfox MRI Simulations"
	- class="QmitkDIAppSyntheticDataGenerationPerspective"
	- icon="resources/syntheticdata.png">
	- <keywordReference id="org.mitk.perspectives.syntheticdata.Keyword"/>
	- </perspective>
	-
	- </extension>
	-
	-
	- <extension point="org.blueberry.ui.keywords">
	-
	- <keyword label="diffusion" id="org.mitk.views.fiberfoxview.Keyword"/>
	- <keyword label="signal" id="org.mitk.views.fiberfoxview.Keyword"/>
	- <keyword label="simulation" id="org.mitk.views.fiberfoxview.Keyword"/>
	- <keyword label="data" id="org.mitk.views.fiberfoxview.Keyword"/>
	- <keyword label="synthetic" id="org.mitk.views.fiberfoxview.Keyword"/>
	- <keyword label="numeric" id="org.mitk.views.fiberfoxview.Keyword"/>
	- <keyword label="ball" id="org.mitk.views.fiberfoxview.Keyword"/>
	- <keyword label="dot" id="org.mitk.views.fiberfoxview.Keyword"/>
	- <keyword label="astrosticks" id="org.mitk.views.fiberfoxview.Keyword"/>
	- <keyword label="k-space" id="org.mitk.views.fiberfoxview.Keyword"/>
	- <keyword label="acquisition" id="org.mitk.views.fiberfoxview.Keyword"/>
	- <keyword label="artifact" id="org.mitk.views.fiberfoxview.Keyword"/>
	- <keyword label="artefact" id="org.mitk.views.fiberfoxview.Keyword"/>
	- <keyword label="gibbs ringing" id="org.mitk.views.fiberfoxview.Keyword"/>
	- <keyword label="spikes" id="org.mitk.views.fiberfoxview.Keyword"/>
	- <keyword label="distortions" id="org.mitk.views.fiberfoxview.Keyword"/>
	- <keyword label="aliasing" id="org.mitk.views.fiberfoxview.Keyword"/>
	- <keyword label="noise" id="org.mitk.views.fiberfoxview.Keyword"/>
	- <keyword label="fiberfox" id="org.mitk.views.fiberfoxview.Keyword"/>
	- <keyword label="rician" id="org.mitk.views.fiberfoxview.Keyword"/>
	- <keyword label="ghost" id="org.mitk.views.fiberfoxview.Keyword"/>
	- <keyword label="fieldmap" id="org.mitk.views.fiberfoxview.Keyword"/>
	- <keyword label="generator" id="org.mitk.views.fiberfoxview.Keyword"/>
	- <keyword label="fourier" id="org.mitk.views.fiberfoxview.Keyword"/>
	-
	- </extension>
	-
	-</plugin>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/QmitkFiberfox.qrc b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/QmitkFiberfox.qrc
	deleted file mode 100644
	index 6ecec32167..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/QmitkFiberfox.qrc
	+++ /dev/null
	@@ -1,10 +0,0 @@
	-<RCC>
	- <qresource prefix="/QmitkFiberfox">
	- <file>circle.png</file>
	- <file>refresh.xpm</file>
	- <file>download.png</file>
	- <file>right.png</file>
	- <file>stop.png</file>
	- <file>upload.png</file>
	- </qresource>
	-</RCC>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/circle.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/circle.png
	deleted file mode 100644
	index b16472e3b4..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/circle.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/download.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/download.png
	deleted file mode 100644
	index 5949729192..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/download.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/fieldmap.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/fieldmap.png
	deleted file mode 100644
	index 4ce9e63f97..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/fieldmap.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/models.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/models.png
	deleted file mode 100644
	index 3c3a066bf2..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/models.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/phantom.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/phantom.png
	deleted file mode 100644
	index 1fd4e87d50..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/phantom.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/refresh.xpm b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/refresh.xpm
	deleted file mode 100644
	index 878265e17a..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/refresh.xpm
	+++ /dev/null
	@@ -1,322 +0,0 @@
	-/* XPM */
	-static char * view_refresh_xpm[] = {
	-"32 32 287 2",
	-" c None",
	-". c #396AA9",
	-"+ c #3D6CA9",
	-"@ c #3968A8",
	-"# c #3565A5",
	-"$ c #3767A6",
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	-"& c #3A6AA8",
	-"* c #3567A6",
	-"= c #3C6BA8",
	-"- c #4B77B0",
	-"; c #87A6CE",
	-"> c #A5BFDE",
	-", c #B3CAE4",
	-"' c #BAD0E8",
	-") c #B6CEE6",
	-"! c #AFC6E1",
	-"~ c #9CB8D9",
	-"{ c #82A3CB",
	-"] c #537EB5",
	-"^ c #3767A7",
	-"/ c #3869A6",
	-"( c #3364A4",
	-"_ c #3E6CA9",
	-": c #94B1D4",
	-"< c #BCD2E8",
	-"[ c #BBD1E8",
	-"} c #B9D0E7",
	-"\| c #B8CEE6",
	-"1 c #B5CDE5",
	-"2 c #B3CBE5",
	-"3 c #B2CBE5",
	-"4 c #B4CCE5",
	-"5 c #AAC4E1",
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	-"9 c #3F6EAA",
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	-"b c #B8CEE7",
	-"c c #B6CDE6",
	-"d c #B1CAE4",
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	-" j l m n o p q r s t u 4 v w x y z A B C D E F ( ",
	-" G H I J K & L L M N O P Q c g R S T U V W X Y ( ",
	-" = Z ` ...+.@. L #.$.%.&.*.=.-.;.>.,.'.( ",
	-" ).!.K ~.{.]. @ ^./.(._.:.<.<.z [. ",
	-" .N }.\|.1.2. 8 3.4.&.5.6.<.7.# ",
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	-" ( K.G.&.L.M.N.O.^ P. Q.D ",
	-" ( R.G.&.&.S.T.U.V.W. X.Y.Z.`. +.+ ",
	-" ( ++@+#+G.$+%+%+&++=+]..+ -+;+>+,+'+)+ ",
	-" ( A.} !+~+{+*.]+^+/+(+_+:+<+[+}+\|+1+\|+2+3+4+5+6+ ",
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/right.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/right.png
	deleted file mode 100644
	index 3201e76d25..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/right.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/stop.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/stop.png
	deleted file mode 100644
	index 108c60b1a1..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/stop.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/syntheticdata.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/syntheticdata.png
	deleted file mode 100644
	index 1fd4e87d50..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/syntheticdata.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/upload.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/upload.png
	deleted file mode 100644
	index 6abef3f7d7..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/upload.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkAstrosticksModelParametersWidget.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkAstrosticksModelParametersWidget.cpp
	deleted file mode 100644
	index 2a74ed4598..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkAstrosticksModelParametersWidget.cpp
	+++ /dev/null
	@@ -1,42 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-//Qmitk headers
	-#include "QmitkAstrosticksModelParametersWidget.h"
	-#include <itkDiffusionTensor3D.h>
	-
	-const std::string QmitkAstrosticksModelParametersWidget::VIEW_ID = "org.mitk.views.AstrosticksModelParametersWidget";
	-
	-QmitkAstrosticksModelParametersWidget::QmitkAstrosticksModelParametersWidget( QWidget * parent, Qt::WindowFlags )
	- : QWidget(parent)
	-{
	- m_Controls = nullptr;
	- this->CreateQtPartControl(this);
	-}
	-
	-QmitkAstrosticksModelParametersWidget::~QmitkAstrosticksModelParametersWidget()
	-{
	-}
	-
	-void QmitkAstrosticksModelParametersWidget::CreateQtPartControl(QWidget *parent)
	-{
	- if (!m_Controls)
	- {
	- // create GUI widgets
	- m_Controls = new Ui::QmitkAstrosticksModelParametersWidgetControls;
	- m_Controls->setupUi(parent);
	- }
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkAstrosticksModelParametersWidget.h b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkAstrosticksModelParametersWidget.h
	deleted file mode 100644
	index 2ddae96a1f..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkAstrosticksModelParametersWidget.h
	+++ /dev/null
	@@ -1,62 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef _QMITKAstrosticksModelParametersWidget_H_INCLUDED
	-#define _QMITKAstrosticksModelParametersWidget_H_INCLUDED
	-
	-//QT headers
	-#include <QWidget>
	-#include <QString>
	-#include "ui_QmitkAstrosticksModelParametersWidgetControls.h"
	-#include <org_mitk_gui_qt_diffusionimaging_fiberfox_Export.h>
	-
	-/** @brief
	- */
	-class DIFFUSIONIMAGING_FIBERFOX_EXPORT QmitkAstrosticksModelParametersWidget : public QWidget
	-{
	- //this is needed for all Qt objects that should have a MOC object (everything that derives from QObject)
	- Q_OBJECT
	-
	-public:
	-
	- static const std::string VIEW_ID;
	-
	- QmitkAstrosticksModelParametersWidget (QWidget* parent = nullptr, Qt::WindowFlags f = nullptr);
	- virtual ~QmitkAstrosticksModelParametersWidget();
	-
	- virtual void CreateQtPartControl(QWidget *parent);
	-
	- void SetT1(double t1){ m_Controls->m_T1box->setValue(t1); }
	- void SetT2(double t2){ m_Controls->m_T2box->setValue(t2); }
	- void SetD(double d){ m_Controls->m_D1box->setValue(d); }
	- void SetRandomizeSticks(bool r){ m_Controls->m_RandomCheck->setChecked(r); }
	-
	- double GetD(){ return m_Controls->m_D1box->value(); }
	- unsigned int GetT2(){ return m_Controls->m_T2box->value(); }
	- unsigned int GetT1(){ return m_Controls->m_T1box->value(); }
	- bool GetRandomizeSticks(){ return m_Controls->m_RandomCheck->isChecked(); }
	-
	-public slots:
	-
	-protected:
	- // member variables
	- Ui::QmitkAstrosticksModelParametersWidgetControls* m_Controls;
	-
	-private:
	-
	-};
	-
	-#endif // _QMITKAstrosticksModelParametersWidget_H_INCLUDED
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkAstrosticksModelParametersWidgetControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkAstrosticksModelParametersWidgetControls.ui
	deleted file mode 100644
	index 75ee528ada..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkAstrosticksModelParametersWidgetControls.ui
	+++ /dev/null
	@@ -1,147 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<ui version="4.0">
	- <class>QmitkAstrosticksModelParametersWidgetControls</class>
	- <widget class="QWidget" name="QmitkAstrosticksModelParametersWidgetControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>356</width>
	- <height>133</height>
	- </rect>
	- </property>
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="MinimumExpanding" vsizetype="MinimumExpanding">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="windowTitle">
	- <string>Form</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="3" column="0">
	- <widget class="QCheckBox" name="m_RandomCheck">
	- <property name="toolTip">
	- <string>Use random number and orientation of sticks.</string>
	- </property>
	- <property name="text">
	- <string>Randomize Sticks</string>
	- </property>
	- <property name="checked">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QFrame" name="frame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_2">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label">
	- <property name="text">
	- <string><html><head/><body><p><span style=" font-style:italic;">d [mm</span><span style=" font-style:italic; vertical-align:super;">2</span><span style=" font-style:italic;">/s</span><span style=" font-style:italic;">]</span>:</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QDoubleSpinBox" name="m_D1box">
	- <property name="toolTip">
	- <string>Diffusivity along sticks.</string>
	- </property>
	- <property name="decimals">
	- <number>5</number>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.000100000000000</double>
	- </property>
	- <property name="value">
	- <double>0.001000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_5">
	- <property name="text">
	- <string><html><head/><body><p><span style=" font-style:italic;">T2</span> - Relaxation:</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QSpinBox" name="m_T2box">
	- <property name="toolTip">
	- <string>T2 relaxation time of this compartment (in milliseconds).</string>
	- </property>
	- <property name="maximum">
	- <number>999999999</number>
	- </property>
	- <property name="value">
	- <number>96</number>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_6">
	- <property name="text">
	- <string><html><head/><body><p><span style=" font-style:italic;">T1</span> - Relaxation:</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_T1box">
	- <property name="toolTip">
	- <string>T1 relaxation time of this compartment (in milliseconds).</string>
	- </property>
	- <property name="maximum">
	- <number>999999999</number>
	- </property>
	- <property name="value">
	- <number>1459</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <tabstops>
	- <tabstop>m_T2box</tabstop>
	- <tabstop>m_D1box</tabstop>
	- <tabstop>m_RandomCheck</tabstop>
	- </tabstops>
	- <resources/>
	- <connections/>
	-</ui>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkBallModelParametersWidget.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkBallModelParametersWidget.cpp
	deleted file mode 100644
	index 8a470fef75..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkBallModelParametersWidget.cpp
	+++ /dev/null
	@@ -1,42 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-//Qmitk headers
	-#include "QmitkBallModelParametersWidget.h"
	-#include <itkDiffusionTensor3D.h>
	-
	-const std::string QmitkBallModelParametersWidget::VIEW_ID = "org.mitk.views.BallModelParametersWidget";
	-
	-QmitkBallModelParametersWidget::QmitkBallModelParametersWidget( QWidget * parent, Qt::WindowFlags )
	- : QWidget(parent)
	-{
	- m_Controls = nullptr;
	- this->CreateQtPartControl(this);
	-}
	-
	-QmitkBallModelParametersWidget::~QmitkBallModelParametersWidget()
	-{
	-}
	-
	-void QmitkBallModelParametersWidget::CreateQtPartControl(QWidget *parent)
	-{
	- if (!m_Controls)
	- {
	- // create GUI widgets
	- m_Controls = new Ui::QmitkBallModelParametersWidgetControls;
	- m_Controls->setupUi(parent);
	- }
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkBallModelParametersWidget.h b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkBallModelParametersWidget.h
	deleted file mode 100644
	index bab9c9b06d..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkBallModelParametersWidget.h
	+++ /dev/null
	@@ -1,60 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef _QMITKBallModelParametersWidget_H_INCLUDED
	-#define _QMITKBallModelParametersWidget_H_INCLUDED
	-
	-//QT headers
	-#include <QWidget>
	-#include <QString>
	-#include "ui_QmitkBallModelParametersWidgetControls.h"
	-#include <org_mitk_gui_qt_diffusionimaging_fiberfox_Export.h>
	-
	-/** @brief
	- */
	-class DIFFUSIONIMAGING_FIBERFOX_EXPORT QmitkBallModelParametersWidget : public QWidget
	-{
	- //this is needed for all Qt objects that should have a MOC object (everything that derives from QObject)
	- Q_OBJECT
	-
	-public:
	-
	- static const std::string VIEW_ID;
	-
	- QmitkBallModelParametersWidget (QWidget* parent = nullptr, Qt::WindowFlags f = nullptr);
	- virtual ~QmitkBallModelParametersWidget();
	-
	- virtual void CreateQtPartControl(QWidget *parent);
	-
	- void SetT1(double t1){ m_Controls->m_T1box->setValue(t1); }
	- void SetT2(double t2){ m_Controls->m_T2box->setValue(t2); }
	- void SetD(double d){ m_Controls->m_D1box->setValue(d); }
	-
	- double GetD(){ return m_Controls->m_D1box->value(); }
	- unsigned int GetT2(){ return m_Controls->m_T2box->value(); }
	- unsigned int GetT1(){ return m_Controls->m_T1box->value(); }
	-
	-public slots:
	-
	-protected:
	- // member variables
	- Ui::QmitkBallModelParametersWidgetControls* m_Controls;
	-
	-private:
	-
	-};
	-
	-#endif // _QMITKBallModelParametersWidget_H_INCLUDED
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkBallModelParametersWidgetControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkBallModelParametersWidgetControls.ui
	deleted file mode 100644
	index b4d460c400..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkBallModelParametersWidgetControls.ui
	+++ /dev/null
	@@ -1,109 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<ui version="4.0">
	- <class>QmitkBallModelParametersWidgetControls</class>
	- <widget class="QWidget" name="QmitkBallModelParametersWidgetControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>373</width>
	- <height>102</height>
	- </rect>
	- </property>
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="MinimumExpanding" vsizetype="MinimumExpanding">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="windowTitle">
	- <string>Form</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="1" column="1">
	- <widget class="QSpinBox" name="m_T2box">
	- <property name="toolTip">
	- <string>T2 relaxation time of this compartment (in milliseconds).</string>
	- </property>
	- <property name="maximum">
	- <number>999999999</number>
	- </property>
	- <property name="value">
	- <number>96</number>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QDoubleSpinBox" name="m_D1box">
	- <property name="toolTip">
	- <string>Diffusivity along stick.</string>
	- </property>
	- <property name="decimals">
	- <number>5</number>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.000100000000000</double>
	- </property>
	- <property name="value">
	- <double>0.001000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label">
	- <property name="text">
	- <string><html><head/><body><p><span style=" font-style:italic;">d [mm</span><span style=" font-style:italic; vertical-align:super;">2</span><span style=" font-style:italic;">/s]</span>:</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_5">
	- <property name="text">
	- <string><html><head/><body><p><span style=" font-style:italic;">T2</span> - Relaxation:</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_6">
	- <property name="text">
	- <string><html><head/><body><p><span style=" font-style:italic;">T1</span> - Relaxation:</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_T1box">
	- <property name="toolTip">
	- <string>T1 relaxation time of this compartment (in milliseconds).</string>
	- </property>
	- <property name="maximum">
	- <number>999999999</number>
	- </property>
	- <property name="value">
	- <number>1459</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <tabstops>
	- <tabstop>m_T2box</tabstop>
	- <tabstop>m_D1box</tabstop>
	- </tabstops>
	- <resources/>
	- <connections/>
	-</ui>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkDotModelParametersWidget.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkDotModelParametersWidget.cpp
	deleted file mode 100644
	index 70233ab4c1..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkDotModelParametersWidget.cpp
	+++ /dev/null
	@@ -1,42 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-//Qmitk headers
	-#include "QmitkDotModelParametersWidget.h"
	-#include <itkDiffusionTensor3D.h>
	-
	-const std::string QmitkDotModelParametersWidget::VIEW_ID = "org.mitk.views.DotModelParametersWidget";
	-
	-QmitkDotModelParametersWidget::QmitkDotModelParametersWidget( QWidget * parent, Qt::WindowFlags )
	- : QWidget(parent)
	-{
	- m_Controls = nullptr;
	- this->CreateQtPartControl(this);
	-}
	-
	-QmitkDotModelParametersWidget::~QmitkDotModelParametersWidget()
	-{
	-}
	-
	-void QmitkDotModelParametersWidget::CreateQtPartControl(QWidget *parent)
	-{
	- if (!m_Controls)
	- {
	- // create GUI widgets
	- m_Controls = new Ui::QmitkDotModelParametersWidgetControls;
	- m_Controls->setupUi(parent);
	- }
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkDotModelParametersWidget.h b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkDotModelParametersWidget.h
	deleted file mode 100644
	index 1cd55142e3..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkDotModelParametersWidget.h
	+++ /dev/null
	@@ -1,57 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef _QMITKDotModelParametersWidget_H_INCLUDED
	-#define _QMITKDotModelParametersWidget_H_INCLUDED
	-
	-//QT headers
	-#include <QWidget>
	-#include <QString>
	-#include "ui_QmitkDotModelParametersWidgetControls.h"
	-#include <org_mitk_gui_qt_diffusionimaging_fiberfox_Export.h>
	-
	-/** @brief
	- */
	-class DIFFUSIONIMAGING_FIBERFOX_EXPORT QmitkDotModelParametersWidget : public QWidget
	-{
	- //this is needed for all Qt objects that should have a MOC object (everything that derives from QObject)
	- Q_OBJECT
	-
	-public:
	-
	- static const std::string VIEW_ID;
	-
	- QmitkDotModelParametersWidget (QWidget* parent = nullptr, Qt::WindowFlags f = nullptr);
	- virtual ~QmitkDotModelParametersWidget();
	-
	- virtual void CreateQtPartControl(QWidget *parent);
	-
	- void SetT1(double t1){ m_Controls->m_T1box->setValue(t1); }
	- void SetT2(double t2){ m_Controls->m_T2box->setValue(t2); }
	- unsigned int GetT2(){ return m_Controls->m_T2box->value(); }
	- unsigned int GetT1(){ return m_Controls->m_T1box->value(); }
	-
	-public slots:
	-
	-protected:
	- // member variables
	- Ui::QmitkDotModelParametersWidgetControls* m_Controls;
	-
	-private:
	-
	-};
	-
	-#endif // _QMITKDotModelParametersWidget_H_INCLUDED
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkDotModelParametersWidgetControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkDotModelParametersWidgetControls.ui
	deleted file mode 100644
	index f6671c6206..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkDotModelParametersWidgetControls.ui
	+++ /dev/null
	@@ -1,82 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<ui version="4.0">
	- <class>QmitkDotModelParametersWidgetControls</class>
	- <widget class="QWidget" name="QmitkDotModelParametersWidgetControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>349</width>
	- <height>58</height>
	- </rect>
	- </property>
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="MinimumExpanding" vsizetype="MinimumExpanding">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="windowTitle">
	- <string>Form</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_5">
	- <property name="text">
	- <string><html><head/><body><p><span style=" font-style:italic;">T2</span> - Relaxation:</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QSpinBox" name="m_T2box">
	- <property name="toolTip">
	- <string>T2 relaxation time of this compartment (in milliseconds).</string>
	- </property>
	- <property name="maximum">
	- <number>999999999</number>
	- </property>
	- <property name="value">
	- <number>96</number>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_6">
	- <property name="text">
	- <string><html><head/><body><p><span style=" font-style:italic;">T1</span> - Relaxation:</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_T1box">
	- <property name="toolTip">
	- <string>T1 relaxation time of this compartment (in milliseconds).</string>
	- </property>
	- <property name="minimum">
	- <number>-1</number>
	- </property>
	- <property name="maximum">
	- <number>999999999</number>
	- </property>
	- <property name="value">
	- <number>1459</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <resources/>
	- <connections/>
	-</ui>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkPrototypeSignalParametersWidget.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkPrototypeSignalParametersWidget.cpp
	deleted file mode 100644
	index 6222a58682..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkPrototypeSignalParametersWidget.cpp
	+++ /dev/null
	@@ -1,43 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-//Qmitk headers
	-#include "QmitkPrototypeSignalParametersWidget.h"
	-#include <itkDiffusionTensor3D.h>
	-
	-const std::string QmitkPrototypeSignalParametersWidget::VIEW_ID = "org.mitk.views.prototypesignalparameterswidget";
	-
	-QmitkPrototypeSignalParametersWidget::QmitkPrototypeSignalParametersWidget( QWidget * parent, Qt::WindowFlags )
	- : QWidget(parent)
	-{
	- m_Controls = nullptr;
	- this->CreateQtPartControl(this);
	-}
	-
	-QmitkPrototypeSignalParametersWidget::~QmitkPrototypeSignalParametersWidget()
	-{
	-}
	-
	-void QmitkPrototypeSignalParametersWidget::CreateQtPartControl(QWidget *parent)
	-{
	- if (!m_Controls)
	- {
	- // create GUI widgets
	- m_Controls = new Ui::QmitkPrototypeSignalParametersWidgetControls;
	- m_Controls->setupUi(parent);
	-
	- }
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkPrototypeSignalParametersWidget.h b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkPrototypeSignalParametersWidget.h
	deleted file mode 100644
	index 1f390e2f2e..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkPrototypeSignalParametersWidget.h
	+++ /dev/null
	@@ -1,64 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef _QmitkPrototypeSignalParametersWidget_H_INCLUDED
	-#define _QmitkPrototypeSignalParametersWidget_H_INCLUDED
	-
	-//QT headers
	-#include <QWidget>
	-#include <QString>
	-#include "ui_QmitkPrototypeSignalParametersWidgetControls.h"
	-#include <org_mitk_gui_qt_diffusionimaging_fiberfox_Export.h>
	-
	-/** @brief
	- */
	-class DIFFUSIONIMAGING_FIBERFOX_EXPORT QmitkPrototypeSignalParametersWidget : public QWidget
	-{
	- //this is needed for all Qt objects that should have a MOC object (everything that derives from QObject)
	- Q_OBJECT
	-
	-public:
	-
	- static const std::string VIEW_ID;
	-
	- QmitkPrototypeSignalParametersWidget (QWidget* parent = nullptr, Qt::WindowFlags f = nullptr);
	- virtual ~QmitkPrototypeSignalParametersWidget();
	-
	- virtual void CreateQtPartControl(QWidget *parent);
	-
	- void SetMinAdc(double min){ m_Controls->m_MinAdcBox->setValue(min); }
	- void SetMaxAdc(double max){ m_Controls->m_MaxAdcBox->setValue(max); }
	- void SetMinFa(double min){ m_Controls->m_MinFaBox->setValue(min); }
	- void SetMaxFa(double max){ m_Controls->m_MaxFaBox->setValue(max); }
	- void SetNumberOfSamples(int n){ m_Controls->m_NumSamplesBox->setValue(n); }
	-
	- double GetMinAdc(){ return m_Controls->m_MinAdcBox->value(); }
	- double GetMaxAdc(){ return m_Controls->m_MaxAdcBox->value(); }
	- double GetMinFa(){ return m_Controls->m_MinFaBox->value(); }
	- double GetMaxFa(){ return m_Controls->m_MaxFaBox->value(); }
	- double GetNumberOfSamples(){ return m_Controls->m_NumSamplesBox->value(); }
	-
	-public slots:
	-
	-protected:
	- // member variables
	- Ui::QmitkPrototypeSignalParametersWidgetControls* m_Controls;
	-
	-private:
	-
	-};
	-
	-#endif // _QmitkPrototypeSignalParametersWidget_H_INCLUDED
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkPrototypeSignalParametersWidgetControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkPrototypeSignalParametersWidgetControls.ui
	deleted file mode 100644
	index 8bef318689..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkPrototypeSignalParametersWidgetControls.ui
	+++ /dev/null
	@@ -1,163 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<ui version="4.0">
	- <class>QmitkPrototypeSignalParametersWidgetControls</class>
	- <widget class="QWidget" name="QmitkPrototypeSignalParametersWidgetControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>297</width>
	- <height>165</height>
	- </rect>
	- </property>
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="MinimumExpanding" vsizetype="MinimumExpanding">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="windowTitle">
	- <string>Form</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="4" column="0">
	- <widget class="QLabel" name="label_3">
	- <property name="text">
	- <string><html><head/><body><p><span style=" font-style:italic;">Number of Samples</span>:</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label">
	- <property name="text">
	- <string><html><head/><body><p><span style=" font-style:italic;">Min. FA</span>:</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QDoubleSpinBox" name="m_MinFaBox">
	- <property name="toolTip">
	- <string>Diffusivity along second eigenvector.</string>
	- </property>
	- <property name="decimals">
	- <number>5</number>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.010000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.700000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QDoubleSpinBox" name="m_MaxFaBox">
	- <property name="toolTip">
	- <string>Diffusivity along second eigenvector.</string>
	- </property>
	- <property name="decimals">
	- <number>5</number>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.010000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.900000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QDoubleSpinBox" name="m_MinAdcBox">
	- <property name="toolTip">
	- <string>Diffusivity along second eigenvector.</string>
	- </property>
	- <property name="decimals">
	- <number>5</number>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.000100000000000</double>
	- </property>
	- <property name="value">
	- <double>0.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_2">
	- <property name="text">
	- <string><html><head/><body><p><span style=" font-style:italic;">Max. FA</span>:</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label_4">
	- <property name="text">
	- <string><html><head/><body><p><span style=" font-style:italic;">Min. ADC [mm2/s]</span>:</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="1">
	- <widget class="QSpinBox" name="m_NumSamplesBox">
	- <property name="maximum">
	- <number>999999999</number>
	- </property>
	- <property name="value">
	- <number>1000</number>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QLabel" name="label_5">
	- <property name="text">
	- <string><html><head/><body><p><span style=" font-style:italic;">Max. ADC [mm2/s]</span>:</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="1">
	- <widget class="QDoubleSpinBox" name="m_MaxAdcBox">
	- <property name="toolTip">
	- <string>Diffusivity along second eigenvector.</string>
	- </property>
	- <property name="decimals">
	- <number>5</number>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.000100000000000</double>
	- </property>
	- <property name="value">
	- <double>0.001000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <tabstops>
	- <tabstop>m_MaxFaBox</tabstop>
	- </tabstops>
	- <resources/>
	- <connections/>
	-</ui>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkStickModelParametersWidget.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkStickModelParametersWidget.cpp
	deleted file mode 100644
	index 6d05479a34..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkStickModelParametersWidget.cpp
	+++ /dev/null
	@@ -1,42 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-//Qmitk headers
	-#include "QmitkStickModelParametersWidget.h"
	-#include <itkDiffusionTensor3D.h>
	-
	-const std::string QmitkStickModelParametersWidget::VIEW_ID = "org.mitk.views.StickModelParametersWidget";
	-
	-QmitkStickModelParametersWidget::QmitkStickModelParametersWidget( QWidget * parent, Qt::WindowFlags )
	- : QWidget(parent)
	-{
	- m_Controls = nullptr;
	- this->CreateQtPartControl(this);
	-}
	-
	-QmitkStickModelParametersWidget::~QmitkStickModelParametersWidget()
	-{
	-}
	-
	-void QmitkStickModelParametersWidget::CreateQtPartControl(QWidget *parent)
	-{
	- if (!m_Controls)
	- {
	- // create GUI widgets
	- m_Controls = new Ui::QmitkStickModelParametersWidgetControls;
	- m_Controls->setupUi(parent);
	- }
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkStickModelParametersWidget.h b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkStickModelParametersWidget.h
	deleted file mode 100644
	index a70cdbd4c9..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkStickModelParametersWidget.h
	+++ /dev/null
	@@ -1,60 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef _QMITKStickModelParametersWidget_H_INCLUDED
	-#define _QMITKStickModelParametersWidget_H_INCLUDED
	-
	-//QT headers
	-#include <QWidget>
	-#include <QString>
	-#include "ui_QmitkStickModelParametersWidgetControls.h"
	-#include <org_mitk_gui_qt_diffusionimaging_fiberfox_Export.h>
	-
	-/** @brief
	- */
	-class DIFFUSIONIMAGING_FIBERFOX_EXPORT QmitkStickModelParametersWidget : public QWidget
	-{
	- //this is needed for all Qt objects that should have a MOC object (everything that derives from QObject)
	- Q_OBJECT
	-
	-public:
	-
	- static const std::string VIEW_ID;
	-
	- QmitkStickModelParametersWidget (QWidget* parent = nullptr, Qt::WindowFlags f = nullptr);
	- virtual ~QmitkStickModelParametersWidget();
	-
	- virtual void CreateQtPartControl(QWidget *parent);
	-
	- void SetT1(double t1){ m_Controls->m_T1box->setValue(t1); }
	- void SetT2(double t2){ m_Controls->m_T2box->setValue(t2); }
	- void SetD(double d){ m_Controls->m_D1box->setValue(d); }
	-
	- double GetD(){ return m_Controls->m_D1box->value(); }
	- unsigned int GetT2(){ return m_Controls->m_T2box->value(); }
	- unsigned int GetT1(){ return m_Controls->m_T1box->value(); }
	-
	-public slots:
	-
	-protected:
	- // member variables
	- Ui::QmitkStickModelParametersWidgetControls* m_Controls;
	-
	-private:
	-
	-};
	-
	-#endif // _QMITKStickModelParametersWidget_H_INCLUDED
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkStickModelParametersWidgetControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkStickModelParametersWidgetControls.ui
	deleted file mode 100644
	index 7a67fbb067..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkStickModelParametersWidgetControls.ui
	+++ /dev/null
	@@ -1,109 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<ui version="4.0">
	- <class>QmitkStickModelParametersWidgetControls</class>
	- <widget class="QWidget" name="QmitkStickModelParametersWidgetControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>342</width>
	- <height>92</height>
	- </rect>
	- </property>
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="MinimumExpanding" vsizetype="MinimumExpanding">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="windowTitle">
	- <string>Form</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="2" column="1">
	- <widget class="QDoubleSpinBox" name="m_D1box">
	- <property name="toolTip">
	- <string>Diffusivity along stick.</string>
	- </property>
	- <property name="decimals">
	- <number>5</number>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.000100000000000</double>
	- </property>
	- <property name="value">
	- <double>0.001000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QSpinBox" name="m_T2box">
	- <property name="toolTip">
	- <string>T2 relaxation time of this compartment (in milliseconds).</string>
	- </property>
	- <property name="maximum">
	- <number>999999999</number>
	- </property>
	- <property name="value">
	- <number>70</number>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_5">
	- <property name="text">
	- <string><html><head/><body><p><span style=" font-style:italic;">T2</span> - Relaxation:</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label">
	- <property name="text">
	- <string><html><head/><body><p><span style=" font-style:italic;">d [mm</span><span style=" font-style:italic; vertical-align:super;">2</span><span style=" font-style:italic;">/s]</span>:</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_6">
	- <property name="text">
	- <string><html><head/><body><p><span style=" font-style:italic;">T1 </span>- Relaxation:</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_T1box">
	- <property name="toolTip">
	- <string>T1 relaxation time of this compartment (in milliseconds).</string>
	- </property>
	- <property name="maximum">
	- <number>999999999</number>
	- </property>
	- <property name="value">
	- <number>974</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <tabstops>
	- <tabstop>m_T2box</tabstop>
	- <tabstop>m_D1box</tabstop>
	- </tabstops>
	- <resources/>
	- <connections/>
	-</ui>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkTensorModelParametersWidget.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkTensorModelParametersWidget.cpp
	deleted file mode 100644
	index 0fe35289b6..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkTensorModelParametersWidget.cpp
	+++ /dev/null
	@@ -1,63 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-//Qmitk headers
	-#include "QmitkTensorModelParametersWidget.h"
	-#include <itkDiffusionTensor3D.h>
	-
	-const std::string QmitkTensorModelParametersWidget::VIEW_ID = "org.mitk.views.tensormodelparameterswidget";
	-
	-QmitkTensorModelParametersWidget::QmitkTensorModelParametersWidget( QWidget * parent, Qt::WindowFlags )
	- : QWidget(parent)
	-{
	- m_Controls = nullptr;
	- this->CreateQtPartControl(this);
	-}
	-
	-QmitkTensorModelParametersWidget::~QmitkTensorModelParametersWidget()
	-{
	-}
	-
	-void QmitkTensorModelParametersWidget::CreateQtPartControl(QWidget *parent)
	-{
	- if (!m_Controls)
	- {
	- // create GUI widgets
	- m_Controls = new Ui::QmitkTensorModelParametersWidgetControls;
	- m_Controls->setupUi(parent);
	-
	- connect((QObject) m_Controls->m_D1box, SIGNAL(valueChanged(double)), (QObject) this, SLOT(DChanged(double)));
	- connect((QObject) m_Controls->m_D2box, SIGNAL(valueChanged(double)), (QObject) this, SLOT(DChanged(double)));
	- connect((QObject) m_Controls->m_D3box, SIGNAL(valueChanged(double)), (QObject) this, SLOT(DChanged(double)));
	-
	- UpdateUi();
	- }
	-}
	-
	-void QmitkTensorModelParametersWidget::UpdateUi()
	-{
	- itk::DiffusionTensor3D<float> tensor;
	- tensor.Fill(0);
	- tensor.SetElement(0,m_Controls->m_D1box->value());
	- tensor.SetElement(3,m_Controls->m_D2box->value());
	- tensor.SetElement(5,m_Controls->m_D3box->value());
	- m_Controls->m_FaLabel->setText(QString::number(tensor.GetFractionalAnisotropy()));
	-}
	-
	-void QmitkTensorModelParametersWidget::DChanged( double )
	-{
	- UpdateUi();
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkTensorModelParametersWidget.h b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkTensorModelParametersWidget.h
	deleted file mode 100644
	index 28995de88c..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkTensorModelParametersWidget.h
	+++ /dev/null
	@@ -1,67 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef _QMITKTensorModelParametersWidget_H_INCLUDED
	-#define _QMITKTensorModelParametersWidget_H_INCLUDED
	-
	-//QT headers
	-#include <QWidget>
	-#include <QString>
	-#include "ui_QmitkTensorModelParametersWidgetControls.h"
	-#include <org_mitk_gui_qt_diffusionimaging_fiberfox_Export.h>
	-
	-/** @brief
	- */
	-class DIFFUSIONIMAGING_FIBERFOX_EXPORT QmitkTensorModelParametersWidget : public QWidget
	-{
	- //this is needed for all Qt objects that should have a MOC object (everything that derives from QObject)
	- Q_OBJECT
	-
	-public:
	-
	- static const std::string VIEW_ID;
	-
	- QmitkTensorModelParametersWidget (QWidget* parent = nullptr, Qt::WindowFlags f = nullptr);
	- virtual ~QmitkTensorModelParametersWidget();
	-
	- virtual void CreateQtPartControl(QWidget *parent);
	-
	- void SetT1(double t1){ m_Controls->m_T1box->setValue(t1); }
	- void SetT2(double t2){ m_Controls->m_T2box->setValue(t2); }
	- void SetD1(double d1){ m_Controls->m_D1box->setValue(d1); }
	- void SetD2(double d2){ m_Controls->m_D2box->setValue(d2); }
	- void SetD3(double d3){ m_Controls->m_D3box->setValue(d3); }
	-
	- double GetD1(){ return m_Controls->m_D1box->value(); }
	- double GetD2(){ return m_Controls->m_D2box->value(); }
	- double GetD3(){ return m_Controls->m_D3box->value(); }
	- unsigned int GetT2(){ return m_Controls->m_T2box->value(); }
	- unsigned int GetT1(){ return m_Controls->m_T1box->value(); }
	-
	-public slots:
	-
	- void DChanged( double value );
	-
	-protected:
	- // member variables
	- Ui::QmitkTensorModelParametersWidgetControls* m_Controls;
	- void UpdateUi();
	-
	-private:
	-
	-};
	-
	-#endif // _QMITKTensorModelParametersWidget_H_INCLUDED
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkTensorModelParametersWidgetControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkTensorModelParametersWidgetControls.ui
	deleted file mode 100644
	index e5986b0525..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkTensorModelParametersWidgetControls.ui
	+++ /dev/null
	@@ -1,180 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<ui version="4.0">
	- <class>QmitkTensorModelParametersWidgetControls</class>
	- <widget class="QWidget" name="QmitkTensorModelParametersWidgetControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>364</width>
	- <height>190</height>
	- </rect>
	- </property>
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="MinimumExpanding" vsizetype="MinimumExpanding">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="windowTitle">
	- <string>Form</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label">
	- <property name="text">
	- <string><html><head/><body><p><span style=" font-style:italic;">d</span><span style=" vertical-align:sub;">\|\|</span><span style=" font-style:italic;"> [mm</span><span style=" font-style:italic; vertical-align:super;">2</span><span style=" font-style:italic;">/s]</span>:</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="1">
	- <widget class="QDoubleSpinBox" name="m_D3box">
	- <property name="toolTip">
	- <string>Diffusivity along third eigenvector.</string>
	- </property>
	- <property name="decimals">
	- <number>5</number>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.000100000000000</double>
	- </property>
	- <property name="value">
	- <double>0.000250000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QLabel" name="label_3">
	- <property name="text">
	- <string><html><head/><body><p><span style=" font-style:italic;">d</span><span style=" vertical-align:sub;">⟂2</span><span style=" font-style:italic;"> [mm</span><span style=" font-style:italic; vertical-align:super;">2</span><span style=" font-style:italic;">/s]</span>:</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_5">
	- <property name="text">
	- <string><html><head/><body><p><span style=" font-style:italic;">T2</span> - Relaxation:</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="1">
	- <widget class="QLabel" name="m_FaLabel">
	- <property name="toolTip">
	- <string>Fractional anisotropy of resulting tensor.</string>
	- </property>
	- <property name="text">
	- <string><html><head/><body><p>-</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QLabel" name="label_2">
	- <property name="text">
	- <string><html><head/><body><p><span style=" font-style:italic;">d</span><span style=" vertical-align:sub;">⟂1</span><span style=" font-style:italic;"> [mm</span><span style=" font-style:italic; vertical-align:super;">2</span><span style=" font-style:italic;">/s]</span>:</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QDoubleSpinBox" name="m_D1box">
	- <property name="toolTip">
	- <string>Diffusivity along largest eigenvector.</string>
	- </property>
	- <property name="decimals">
	- <number>5</number>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.000100000000000</double>
	- </property>
	- <property name="value">
	- <double>0.001000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <widget class="QLabel" name="label_4">
	- <property name="text">
	- <string><html><head/><body><p><span style=" font-style:italic;">FA</span>:</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="1">
	- <widget class="QDoubleSpinBox" name="m_D2box">
	- <property name="toolTip">
	- <string>Diffusivity along second eigenvector.</string>
	- </property>
	- <property name="decimals">
	- <number>5</number>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.000100000000000</double>
	- </property>
	- <property name="value">
	- <double>0.000250000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QSpinBox" name="m_T2box">
	- <property name="toolTip">
	- <string>T2 relaxation time of this compartment (in milliseconds).</string>
	- </property>
	- <property name="maximum">
	- <number>999999999</number>
	- </property>
	- <property name="value">
	- <number>70</number>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_6">
	- <property name="text">
	- <string><html><head/><body><p><span style=" font-style:italic;">T1</span> - Relaxation:</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_T1box">
	- <property name="toolTip">
	- <string>T1 relaxation time of this compartment (in milliseconds).</string>
	- </property>
	- <property name="maximum">
	- <number>999999999</number>
	- </property>
	- <property name="value">
	- <number>974</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <tabstops>
	- <tabstop>m_T2box</tabstop>
	- <tabstop>m_D1box</tabstop>
	- <tabstop>m_D2box</tabstop>
	- <tabstop>m_D3box</tabstop>
	- </tabstops>
	- <resources/>
	- <connections/>
	-</ui>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkZeppelinModelParametersWidget.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkZeppelinModelParametersWidget.cpp
	deleted file mode 100644
	index 5cf3305f43..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkZeppelinModelParametersWidget.cpp
	+++ /dev/null
	@@ -1,62 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-//Qmitk headers
	-#include "QmitkZeppelinModelParametersWidget.h"
	-#include <itkDiffusionTensor3D.h>
	-
	-const std::string QmitkZeppelinModelParametersWidget::VIEW_ID = "org.mitk.views.ZeppelinModelParameterswidget";
	-
	-QmitkZeppelinModelParametersWidget::QmitkZeppelinModelParametersWidget( QWidget * parent, Qt::WindowFlags )
	- : QWidget(parent)
	-{
	- m_Controls = nullptr;
	- this->CreateQtPartControl(this);
	-}
	-
	-QmitkZeppelinModelParametersWidget::~QmitkZeppelinModelParametersWidget()
	-{
	-}
	-
	-void QmitkZeppelinModelParametersWidget::CreateQtPartControl(QWidget *parent)
	-{
	- if (!m_Controls)
	- {
	- // create GUI widgets
	- m_Controls = new Ui::QmitkZeppelinModelParametersWidgetControls;
	- m_Controls->setupUi(parent);
	-
	- connect((QObject) m_Controls->m_D1box, SIGNAL(valueChanged(double)), (QObject) this, SLOT(DChanged(double)));
	- connect((QObject) m_Controls->m_D2box, SIGNAL(valueChanged(double)), (QObject) this, SLOT(DChanged(double)));
	-
	- UpdateUi();
	- }
	-}
	-
	-void QmitkZeppelinModelParametersWidget::UpdateUi()
	-{
	- itk::DiffusionTensor3D<float> tensor;
	- tensor.Fill(0);
	- tensor.SetElement(0,m_Controls->m_D1box->value());
	- tensor.SetElement(3,m_Controls->m_D2box->value());
	- tensor.SetElement(5,m_Controls->m_D2box->value());
	- m_Controls->m_FaLabel->setText(QString::number(tensor.GetFractionalAnisotropy()));
	-}
	-
	-void QmitkZeppelinModelParametersWidget::DChanged( double )
	-{
	- UpdateUi();
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkZeppelinModelParametersWidget.h b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkZeppelinModelParametersWidget.h
	deleted file mode 100644
	index bf249008f5..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkZeppelinModelParametersWidget.h
	+++ /dev/null
	@@ -1,65 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef _QMITKZeppelinModelParametersWidget_H_INCLUDED
	-#define _QMITKZeppelinModelParametersWidget_H_INCLUDED
	-
	-//QT headers
	-#include <QWidget>
	-#include <QString>
	-#include "ui_QmitkZeppelinModelParametersWidgetControls.h"
	-#include <org_mitk_gui_qt_diffusionimaging_fiberfox_Export.h>
	-
	-/** @brief
	- */
	-class DIFFUSIONIMAGING_FIBERFOX_EXPORT QmitkZeppelinModelParametersWidget : public QWidget
	-{
	- //this is needed for all Qt objects that should have a MOC object (everything that derives from QObject)
	- Q_OBJECT
	-
	-public:
	-
	- static const std::string VIEW_ID;
	-
	- QmitkZeppelinModelParametersWidget (QWidget* parent = nullptr, Qt::WindowFlags f = nullptr);
	- virtual ~QmitkZeppelinModelParametersWidget();
	-
	- virtual void CreateQtPartControl(QWidget *parent);
	-
	- void SetT1(double t1){ m_Controls->m_T1box->setValue(t1); }
	- void SetT2(double t2){ m_Controls->m_T2box->setValue(t2); }
	- void SetD1(double d1){ m_Controls->m_D1box->setValue(d1); }
	- void SetD2(double d2){ m_Controls->m_D2box->setValue(d2); }
	-
	- double GetD1(){ return m_Controls->m_D1box->value(); }
	- double GetD2(){ return m_Controls->m_D2box->value(); }
	- unsigned int GetT2(){ return m_Controls->m_T2box->value(); }
	- unsigned int GetT1(){ return m_Controls->m_T1box->value(); }
	-
	-public slots:
	-
	- void DChanged( double value );
	-
	-protected:
	- // member variables
	- Ui::QmitkZeppelinModelParametersWidgetControls* m_Controls;
	- void UpdateUi();
	-
	-private:
	-
	-};
	-
	-#endif // _QMITKZeppelinModelParametersWidget_H_INCLUDED
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkZeppelinModelParametersWidgetControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkZeppelinModelParametersWidgetControls.ui
	deleted file mode 100644
	index 27cf81447b..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/QmitkZeppelinModelParametersWidgetControls.ui
	+++ /dev/null
	@@ -1,153 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<ui version="4.0">
	- <class>QmitkZeppelinModelParametersWidgetControls</class>
	- <widget class="QWidget" name="QmitkZeppelinModelParametersWidgetControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>355</width>
	- <height>154</height>
	- </rect>
	- </property>
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="MinimumExpanding" vsizetype="MinimumExpanding">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="windowTitle">
	- <string>Form</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label">
	- <property name="text">
	- <string><html><head/><body><p><span style=" font-style:italic;">d</span><span style=" vertical-align:sub;">\|\|</span><span style=" font-style:italic;"> [mm</span><span style=" font-style:italic; vertical-align:super;">2</span><span style=" font-style:italic;">/s]</span>:</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_5">
	- <property name="text">
	- <string><html><head/><body><p><span style=" font-style:italic;">T2</span> - Relaxation:</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QSpinBox" name="m_T2box">
	- <property name="toolTip">
	- <string>T2 relaxation time of this compartment (in milliseconds).</string>
	- </property>
	- <property name="maximum">
	- <number>999999999</number>
	- </property>
	- <property name="value">
	- <number>70</number>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QLabel" name="label_4">
	- <property name="text">
	- <string><html><head/><body><p><span style=" font-style:italic;">FA</span>:</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QLabel" name="label_2">
	- <property name="text">
	- <string><html><head/><body><p><span style=" font-style:italic;">d</span><span style=" vertical-align:sub;">⟂</span><span style=" font-style:italic;"> [mm</span><span style=" font-style:italic; vertical-align:super;">2</span><span style=" font-style:italic;">/s]</span>:</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="1">
	- <widget class="QDoubleSpinBox" name="m_D2box">
	- <property name="toolTip">
	- <string>Diffusivity along second and third eigenvector.</string>
	- </property>
	- <property name="decimals">
	- <number>5</number>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.000100000000000</double>
	- </property>
	- <property name="value">
	- <double>0.000250000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QDoubleSpinBox" name="m_D1box">
	- <property name="toolTip">
	- <string>Diffusivity along largest eigenvector.</string>
	- </property>
	- <property name="decimals">
	- <number>5</number>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.000100000000000</double>
	- </property>
	- <property name="value">
	- <double>0.001000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="1">
	- <widget class="QLabel" name="m_FaLabel">
	- <property name="toolTip">
	- <string>Fractional anisotropy of resulting tensor.</string>
	- </property>
	- <property name="text">
	- <string><html><head/><body><p>-</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_6">
	- <property name="text">
	- <string><html><head/><body><p><span style=" font-style:italic;">T1</span> - Relaxation:</p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_T1box">
	- <property name="toolTip">
	- <string>T1 relaxation time of this compartment (in milliseconds).</string>
	- </property>
	- <property name="maximum">
	- <number>999999999</number>
	- </property>
	- <property name="value">
	- <number>974</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <tabstops>
	- <tabstop>m_T2box</tabstop>
	- <tabstop>m_D1box</tabstop>
	- <tabstop>m_D2box</tabstop>
	- </tabstops>
	- <resources/>
	- <connections/>
	-</ui>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/Perspectives/QmitkDIAppSyntheticDataGenerationPerspective.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/Perspectives/QmitkDIAppSyntheticDataGenerationPerspective.cpp
	deleted file mode 100644
	index cd88f9b3d0..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/Perspectives/QmitkDIAppSyntheticDataGenerationPerspective.cpp
	+++ /dev/null
	@@ -1,50 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkDIAppSyntheticDataGenerationPerspective.h"
	-#include "berryIViewLayout.h"
	-
	-void QmitkDIAppSyntheticDataGenerationPerspective::CreateInitialLayout(berry::IPageLayout::Pointer layout)
	-{
	- /////////////////////////////////////////////////////
	- // all di-app perspectives should have the following:
	- /////////////////////////////////////////////////////
	-
	- QString editorArea = layout->GetEditorArea();
	-
	- layout->AddStandaloneViewPlaceholder("org.mitk.views.viewnavigatorview", berry::IPageLayout::LEFT, 0.3f, editorArea, false);
	-
	- layout->AddStandaloneView("org.mitk.views.datamanager",
	- false, berry::IPageLayout::LEFT, 0.3f, editorArea);
	-
	- layout->AddStandaloneView("org.mitk.views.controlvisualizationpropertiesview",
	- false, berry::IPageLayout::BOTTOM, .15f, "org.mitk.views.datamanager");
	-
	- berry::IFolderLayout::Pointer left =
	- layout->CreateFolder("org.mbi.diffusionimaginginternal.leftcontrols",
	- berry::IPageLayout::BOTTOM, 0.15f, "org.mitk.views.controlvisualizationpropertiesview");
	-
	- layout->AddStandaloneViewPlaceholder("org.mitk.views.imagenavigator",
	- berry::IPageLayout::BOTTOM, .7f, "org.mbi.diffusionimaginginternal.leftcontrols", false);
	-
	- /////////////////////////////////////////////
	- // here goes the perspective specific stuff
	- /////////////////////////////////////////////
	-
	- left->AddView("org.mitk.views.fiberfoxview");
	- left->AddView("org.mitk.views.fibergenerationview");
	- left->AddView("org.mitk.views.fieldmapgenerator");
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/Perspectives/QmitkDIAppSyntheticDataGenerationPerspective.h b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/Perspectives/QmitkDIAppSyntheticDataGenerationPerspective.h
	deleted file mode 100644
	index c057acf282..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/Perspectives/QmitkDIAppSyntheticDataGenerationPerspective.h
	+++ /dev/null
	@@ -1,36 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef QmitkDIAppSyntheticDataGenerationPerspective_H_
	-#define QmitkDIAppSyntheticDataGenerationPerspective_H_
	-
	-#include <berryIPerspectiveFactory.h>
	-
	-class QmitkDIAppSyntheticDataGenerationPerspective : public QObject, public berry::IPerspectiveFactory
	-{
	- Q_OBJECT
	- Q_INTERFACES(berry::IPerspectiveFactory)
	-
	-public:
	-
	- QmitkDIAppSyntheticDataGenerationPerspective() {}
	- ~QmitkDIAppSyntheticDataGenerationPerspective() {}
	-
	- void CreateInitialLayout(berry::IPageLayout::Pointer layout) override;
	-};
	-
	-#endif /* QmitkDIAppSyntheticDataGenerationPerspective_H_ */
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberGenerationView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberGenerationView.cpp
	deleted file mode 100644
	index 8b517283c0..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberGenerationView.cpp
	+++ /dev/null
	@@ -1,1165 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-// Blueberry
	-#include <berryISelectionService.h>
	-#include <berryIWorkbenchWindow.h>
	-
	-// Qmitk
	-#include "QmitkFiberGenerationView.h"
	-
	-// MITK
	-#include <mitkImage.h>
	-#include <mitkImageToItk.h>
	-#include <mitkImageCast.h>
	-#include <mitkProperties.h>
	-#include <mitkPlanarFigureInteractor.h>
	-#include <mitkDataStorage.h>
	-#include <itkFibersFromPlanarFiguresFilter.h>
	-#include <itkTractsToDWIImageFilter.h>
	-#include <mitkTensorImage.h>
	-#include <mitkILinkedRenderWindowPart.h>
	-#include <mitkImageToItk.h>
	-#include <mitkImageCast.h>
	-#include <mitkImageGenerator.h>
	-#include <mitkNodePredicateDataType.h>
	-#include <itkScalableAffineTransform.h>
	-#include <mitkLevelWindowProperty.h>
	-#include <mitkNodePredicateOr.h>
	-#include <mitkNodePredicateAnd.h>
	-#include <mitkNodePredicateNot.h>
	-#include <mitkNodePredicateProperty.h>
	-#include <mitkNodePredicateIsDWI.h>
	-#include <boost/property_tree/ptree.hpp>
	-#define RAPIDXML_NO_EXCEPTIONS
	-#include <boost/property_tree/xml_parser.hpp>
	-#include <boost/foreach.hpp>
	-#include <QFileDialog>
	-#include <QMessageBox>
	-#include "usModuleRegistry.h"
	-#include <mitkChiSquareNoiseModel.h>
	-#include <itksys/SystemTools.hxx>
	-#include <mitkIOUtil.h>
	-#include <QScrollBar>
	-#include <itkInvertIntensityImageFilter.h>
	-#include <QDialogButtonBox>
	-#include <itkAdcImageFilter.h>
	-#include <itkShiftScaleImageFilter.h>
	-#include <mitkITKImageImport.h>
	-#include <itkRandomPhantomFilter.h>
	-
	-#include "mitkNodePredicateDataType.h"
	-#include <mitkNodePredicateProperty.h>
	-#include <mitkNodePredicateAnd.h>
	-#include <mitkNodePredicateNot.h>
	-#include <mitkNodePredicateOr.h>
	-
	-#define _USE_MATH_DEFINES
	-#include <math.h>
	-
	-
	-const std::string QmitkFiberGenerationView::VIEW_ID = "org.mitk.views.fibergenerationview";
	-
	-QmitkFiberGenerationView::QmitkFiberGenerationView()
	- : QmitkAbstractView()
	- , m_Controls( 0 )
	- , m_SelectedImageNode( nullptr )
	-{
	-
	-}
	-
	-// Destructor
	-QmitkFiberGenerationView::~QmitkFiberGenerationView()
	-{
	-}
	-
	-void QmitkFiberGenerationView::CreateQtPartControl( QWidget *parent )
	-{
	- // build up qt view, unless already done
	- if ( !m_Controls )
	- {
	- // create GUI widgets from the Qt Designer's .ui file
	- m_Controls = new Ui::QmitkFiberGenerationViewControls;
	- m_Controls->setupUi( parent );
	-
	- m_ParameterFile = QDir::currentPath()+"/param.ffp";
	-
	- connect(static_cast<QObject>(m_Controls->m_RandomPhantomButton), SIGNAL(clicked()), static_cast<QObject>(this), SLOT(RandomPhantom()));
	- connect(static_cast<QObject>(m_Controls->m_GenerateFibersButton), SIGNAL(clicked()), static_cast<QObject>(this), SLOT(GenerateFibers()));
	- connect(static_cast<QObject>(m_Controls->m_CircleButton), SIGNAL(clicked()), static_cast<QObject>(this), SLOT(OnDrawROI()));
	- connect(static_cast<QObject>(m_Controls->m_FlipButton), SIGNAL(clicked()), static_cast<QObject>(this), SLOT(OnFlipButton()));
	- connect(static_cast<QObject>(m_Controls->m_JoinBundlesButton), SIGNAL(clicked()), static_cast<QObject>(this), SLOT(JoinBundles()));
	- connect(static_cast<QObject>(m_Controls->m_VarianceBox), SIGNAL(valueChanged(double)), static_cast<QObject>(this), SLOT(OnVarianceChanged(double)));
	- connect(static_cast<QObject>(m_Controls->m_DistributionBox), SIGNAL(currentIndexChanged(int)), static_cast<QObject>(this), SLOT(OnDistributionChanged(int)));
	- connect(static_cast<QObject>(m_Controls->m_FiberDensityBox), SIGNAL(valueChanged(int)), static_cast<QObject>(this), SLOT(OnFiberDensityChanged(int)));
	- connect(static_cast<QObject>(m_Controls->m_FiberSamplingBox), SIGNAL(valueChanged(double)), static_cast<QObject>(this), SLOT(OnFiberSamplingChanged(double)));
	- connect(static_cast<QObject>(m_Controls->m_TensionBox), SIGNAL(valueChanged(double)), static_cast<QObject>(this), SLOT(OnTensionChanged(double)));
	- connect(static_cast<QObject>(m_Controls->m_ContinuityBox), SIGNAL(valueChanged(double)), static_cast<QObject>(this), SLOT(OnContinuityChanged(double)));
	- connect(static_cast<QObject>(m_Controls->m_BiasBox), SIGNAL(valueChanged(double)), static_cast<QObject>(this), SLOT(OnBiasChanged(double)));
	-
	- connect(static_cast<QObject>(m_Controls->m_ConstantRadiusBox), SIGNAL(stateChanged(int)), static_cast<QObject>(this), SLOT(OnConstantRadius(int)));
	- connect(static_cast<QObject>(m_Controls->m_CopyBundlesButton), SIGNAL(clicked()), static_cast<QObject>(this), SLOT(CopyBundles()));
	- connect(static_cast<QObject>(m_Controls->m_TransformBundlesButton), SIGNAL(clicked()), static_cast<QObject>(this), SLOT(ApplyTransform()));
	- connect(static_cast<QObject>(m_Controls->m_AlignOnGrid), SIGNAL(clicked()), static_cast<QObject>(this), SLOT(AlignOnGrid()));
	- connect(static_cast<QObject>(m_Controls->m_FidAxis1), SIGNAL(editingFinished()), static_cast<QObject>(this), SLOT(UpdateFiducialPosition()));
	- connect(static_cast<QObject>(m_Controls->m_FidAxis2), SIGNAL(editingFinished()), static_cast<QObject>(this), SLOT(UpdateFiducialPosition()));
	- connect(static_cast<QObject>(m_Controls->m_FidPosX), SIGNAL(editingFinished()), static_cast<QObject>(this), SLOT(UpdateFiducialPosition()));
	- connect(static_cast<QObject>(m_Controls->m_FidPosY), SIGNAL(editingFinished()), static_cast<QObject>(this), SLOT(UpdateFiducialPosition()));
	- connect(static_cast<QObject>(m_Controls->m_FidPosZ), SIGNAL(editingFinished()), static_cast<QObject>(this), SLOT(UpdateFiducialPosition()));
	- connect(static_cast<QObject>(m_Controls->m_FidTwist), SIGNAL(editingFinished()), static_cast<QObject>(this), SLOT(UpdateFiducialPosition()));
	-
	- connect(static_cast<QObject>(m_Controls->m_AdvancedOptionsBox), SIGNAL( stateChanged(int)), static_cast<QObject>(this), SLOT(ShowAdvancedOptions(int)));
	-
	- connect(static_cast<QObject>(m_Controls->m_SaveParametersButton), SIGNAL(clicked()), static_cast<QObject>(this), SLOT(SaveParameters()));
	- connect(static_cast<QObject>(m_Controls->m_LoadParametersButton), SIGNAL(clicked()), static_cast<QObject>(this), SLOT(LoadParameters()));
	- OnDistributionChanged(0);
	- }
	- UpdateGui();
	-}
	-
	-void QmitkFiberGenerationView::RandomPhantom()
	-{
	- itk::RandomPhantomFilter::Pointer filter = itk::RandomPhantomFilter::New();
	- filter->SetNumTracts(m_Controls->m_NumBundlesBox->value());
	- filter->SetMinStreamlineDensity(m_Controls->m_MinDensityBox->value());
	- filter->SetMaxStreamlineDensity(m_Controls->m_MaxDensityBox->value());
	- mitk::Vector3D vol;
	- vol[0] = m_Controls->m_VolumeSizeX->value();
	- vol[1] = m_Controls->m_VolumeSizeY->value();
	- vol[2] = m_Controls->m_VolumeSizeZ->value();
	- filter->SetVolumeSize(vol);
	- filter->SetStepSizeMin(m_Controls->m_StepSizeMinBox->value());
	- filter->SetStepSizeMax(m_Controls->m_StepSizeMaxBox->value());
	- filter->SetCurvynessMin(m_Controls->m_CurvyMinBox->value());
	- filter->SetCurvynessMax(m_Controls->m_CurvyMaxBox->value());
	- filter->SetStartRadiusMin(m_Controls->m_SizeMinBox->value());
	- filter->SetStartRadiusMax(m_Controls->m_SizeMaxBox->value());
	- filter->SetMinTwist(m_Controls->m_MinTwistBox->value());
	- filter->SetMaxTwist(m_Controls->m_MaxTwistBox->value());
	- filter->Update();
	- auto fibs = filter->GetFiberBundles();
	-
	- std::vector< mitk::DataNode::Pointer > fiber_nodes;
	- int c = 1;
	- for (auto fib : fibs)
	- {
	- mitk::DataNode::Pointer node = mitk::DataNode::New();
	- node->SetData( fib );
	- node->SetName("Bundle_" + boost::lexical_cast<std::string>(c));
	- GetDataStorage()->Add(node);
	- fiber_nodes.push_back(node);
	- ++c;
	- }
	-
	-// mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- mitk::RenderingManager::GetInstance()->InitializeViews(GetDataStorage()->ComputeVisibleBoundingGeometry3D());
	-}
	-
	-void QmitkFiberGenerationView::UpdateParametersFromGui()
	-{
	- m_Parameters.ClearFiberParameters();
	- m_Parameters.m_Misc.m_CheckAdvancedFiberOptionsBox = m_Controls->m_AdvancedOptionsBox->isChecked();
	-
	- switch(m_Controls->m_DistributionBox->currentIndex())
	- {
	- case 0:
	- m_Parameters.m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_UNIFORM;
	- break;
	- case 1:
	- m_Parameters.m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_GAUSSIAN;
	- break;
	- default:
	- m_Parameters.m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_UNIFORM;
	- }
	- m_Parameters.m_FiberGen.m_Variance = m_Controls->m_VarianceBox->value();
	- m_Parameters.m_FiberGen.m_Density = m_Controls->m_FiberDensityBox->value();
	- m_Parameters.m_FiberGen.m_Sampling = m_Controls->m_FiberSamplingBox->value();
	- m_Parameters.m_FiberGen.m_Tension = m_Controls->m_TensionBox->value();
	- m_Parameters.m_FiberGen.m_Continuity = m_Controls->m_ContinuityBox->value();
	- m_Parameters.m_FiberGen.m_Bias = m_Controls->m_BiasBox->value();
	- m_Parameters.m_FiberGen.m_Rotation[0] = m_Controls->m_XrotBox->value();
	- m_Parameters.m_FiberGen.m_Rotation[1] = m_Controls->m_YrotBox->value();
	- m_Parameters.m_FiberGen.m_Rotation[2] = m_Controls->m_ZrotBox->value();
	- m_Parameters.m_FiberGen.m_Translation[0] = m_Controls->m_XtransBox->value();
	- m_Parameters.m_FiberGen.m_Translation[1] = m_Controls->m_YtransBox->value();
	- m_Parameters.m_FiberGen.m_Translation[2] = m_Controls->m_ZtransBox->value();
	- m_Parameters.m_FiberGen.m_Scale[0] = m_Controls->m_XscaleBox->value();
	- m_Parameters.m_FiberGen.m_Scale[1] = m_Controls->m_YscaleBox->value();
	- m_Parameters.m_FiberGen.m_Scale[2] = m_Controls->m_ZscaleBox->value();
	-
	- m_Parameters.m_Misc.m_CheckRealTimeFibersBox = m_Controls->m_RealTimeFibers->isChecked();
	- m_Parameters.m_Misc.m_CheckAdvancedFiberOptionsBox = m_Controls->m_AdvancedOptionsBox->isChecked();
	- m_Parameters.m_Misc.m_CheckIncludeFiducialsBox = m_Controls->m_IncludeFiducials->isChecked();
	- m_Parameters.m_Misc.m_CheckConstantRadiusBox = m_Controls->m_ConstantRadiusBox->isChecked();
	-}
	-
	-void QmitkFiberGenerationView::SaveParameters(QString filename)
	-{
	- UpdateParametersFromGui();
	- m_Parameters.SaveParameters(filename.toStdString());
	- m_ParameterFile = filename;
	-}
	-
	-void QmitkFiberGenerationView::SaveParameters()
	-{
	- QString filename = QFileDialog::getSaveFileName(
	- 0,
	- tr("Save Parameters"),
	- m_ParameterFile,
	- tr("Fiberfox Parameters (*.ffp)") );
	-
	- SaveParameters(filename);
	-}
	-
	-void QmitkFiberGenerationView::LoadParameters()
	-{
	- QString filename = QFileDialog::getOpenFileName(0, tr("Load Parameters"), QString(itksys::SystemTools::GetFilenamePath(m_ParameterFile.toStdString()).c_str()), tr("Fiberfox Parameters (*.ffp)") );
	- if(filename.isEmpty() \|\| filename.isNull())
	- return;
	-
	- m_ParameterFile = filename;
	- m_Parameters.LoadParameters(filename.toStdString());
	-
	- if (m_Parameters.m_MissingTags.size()>0)
	- {
	- QString missing("Parameter file might be corrupted. The following parameters could not be read: ");
	- missing += QString(m_Parameters.m_MissingTags.c_str());
	- missing += "\nDefault values have been assigned to the missing parameters.";
	- QMessageBox::information( nullptr, "Warning!", missing);
	- }
	-
	- m_Controls->m_RealTimeFibers->setChecked(m_Parameters.m_Misc.m_CheckRealTimeFibersBox);
	- m_Controls->m_AdvancedOptionsBox->setChecked(m_Parameters.m_Misc.m_CheckAdvancedFiberOptionsBox);
	- m_Controls->m_IncludeFiducials->setChecked(m_Parameters.m_Misc.m_CheckIncludeFiducialsBox);
	- m_Controls->m_ConstantRadiusBox->setChecked(m_Parameters.m_Misc.m_CheckConstantRadiusBox);
	-
	- m_Controls->m_DistributionBox->setCurrentIndex(m_Parameters.m_FiberGen.m_Distribution);
	- m_Controls->m_VarianceBox->setValue(m_Parameters.m_FiberGen.m_Variance);
	- m_Controls->m_FiberDensityBox->setValue(m_Parameters.m_FiberGen.m_Density);
	- m_Controls->m_FiberSamplingBox->setValue(m_Parameters.m_FiberGen.m_Sampling);
	- m_Controls->m_TensionBox->setValue(m_Parameters.m_FiberGen.m_Tension);
	- m_Controls->m_ContinuityBox->setValue(m_Parameters.m_FiberGen.m_Continuity);
	- m_Controls->m_BiasBox->setValue(m_Parameters.m_FiberGen.m_Bias);
	- m_Controls->m_XrotBox->setValue(m_Parameters.m_FiberGen.m_Rotation[0]);
	- m_Controls->m_YrotBox->setValue(m_Parameters.m_FiberGen.m_Rotation[1]);
	- m_Controls->m_ZrotBox->setValue(m_Parameters.m_FiberGen.m_Rotation[2]);
	- m_Controls->m_XtransBox->setValue(m_Parameters.m_FiberGen.m_Translation[0]);
	- m_Controls->m_YtransBox->setValue(m_Parameters.m_FiberGen.m_Translation[1]);
	- m_Controls->m_ZtransBox->setValue(m_Parameters.m_FiberGen.m_Translation[2]);
	- m_Controls->m_XscaleBox->setValue(m_Parameters.m_FiberGen.m_Scale[0]);
	- m_Controls->m_YscaleBox->setValue(m_Parameters.m_FiberGen.m_Scale[1]);
	- m_Controls->m_ZscaleBox->setValue(m_Parameters.m_FiberGen.m_Scale[2]);
	-}
	-
	-void QmitkFiberGenerationView::ShowAdvancedOptions(int state)
	-{
	- if (state)
	- {
	- m_Controls->m_AdvancedFiberOptionsFrame->setVisible(true);
	- m_Controls->m_AdvancedOptionsBox->setChecked(true);
	- }
	- else
	- {
	- m_Controls->m_AdvancedFiberOptionsFrame->setVisible(false);
	- m_Controls->m_AdvancedOptionsBox->setChecked(false);
	- }
	-}
	-
	-void QmitkFiberGenerationView::OnConstantRadius(int value)
	-{
	- if (value>0 && m_Controls->m_RealTimeFibers->isChecked())
	- GenerateFibers();
	-}
	-
	-void QmitkFiberGenerationView::OnDistributionChanged(int value)
	-{
	- if (value==1)
	- m_Controls->m_VarianceBox->setVisible(true);
	- else
	- m_Controls->m_VarianceBox->setVisible(false);
	-
	- if (m_Controls->m_RealTimeFibers->isChecked())
	- GenerateFibers();
	-}
	-
	-void QmitkFiberGenerationView::OnVarianceChanged(double)
	-{
	- if (m_Controls->m_RealTimeFibers->isChecked())
	- GenerateFibers();
	-}
	-
	-void QmitkFiberGenerationView::OnFiberDensityChanged(int)
	-{
	- if (m_Controls->m_RealTimeFibers->isChecked())
	- GenerateFibers();
	-}
	-
	-void QmitkFiberGenerationView::OnFiberSamplingChanged(double)
	-{
	- if (m_Controls->m_RealTimeFibers->isChecked())
	- GenerateFibers();
	-}
	-
	-void QmitkFiberGenerationView::OnTensionChanged(double)
	-{
	- if (m_Controls->m_RealTimeFibers->isChecked())
	- GenerateFibers();
	-}
	-
	-void QmitkFiberGenerationView::OnContinuityChanged(double)
	-{
	- if (m_Controls->m_RealTimeFibers->isChecked())
	- GenerateFibers();
	-}
	-
	-void QmitkFiberGenerationView::OnBiasChanged(double)
	-{
	- if (m_Controls->m_RealTimeFibers->isChecked())
	- GenerateFibers();
	-}
	-
	-void QmitkFiberGenerationView::UpdateFiducialPosition()
	-{
	- if (m_SelectedFiducials.size()!=1)
	- return;
	-
	- mitk::PlanarEllipse* pe = dynamic_cast<mitk::PlanarEllipse*>(m_SelectedFiducials.at(0)->GetData());
	- mitk::BaseGeometry* geom = pe->GetGeometry();
	-
	- // translate
	- mitk::Point3D origin;
	- origin[0] = m_Controls->m_FidPosX->value();
	- origin[1] = m_Controls->m_FidPosY->value();
	- origin[2] = m_Controls->m_FidPosZ->value();
	-
	- // transform control point coordinate into geometry translation
	- auto p0 = pe->GetControlPoint(0);
	- auto p1 = pe->GetControlPoint(1);
	- auto p2 = pe->GetControlPoint(2);
	- auto p3 = pe->GetControlPoint(3);
	-
	- auto v1 = p1 - p0;
	- auto v2 = p2 - p0;
	- auto angle_deg = m_Controls->m_FidTwist->value();
	- auto dot = std::cos(itk::Math::pi*angle_deg/180.0);
	-
	- vnl_matrix_fixed<double, 2, 2> tRot;
	- tRot[0][0] = dot;
	- tRot[1][1] = tRot[0][0];
	- tRot[1][0] = sin(acos(tRot[0][0]));
	- tRot[0][1] = -tRot[1][0];
	- if (angle_deg<0)
	- tRot = tRot.transpose();
	- vnl_vector_fixed<double, 2> vt; vt[0]=1; vt[1]=0;
	- vnl_vector_fixed<double, 2> v3 = tRot*vt;
	-
	- if (v1.GetNorm()<0.0001 \|\| v2.GetNorm()<0.0001)
	- {
	- QMessageBox::information( nullptr, "", "Please select exactly one fiducial.");
	- return;
	- }
	-
	- v1.Normalize();
	- v2.Normalize();
	-
	- p1 = p0 + v1*m_Controls->m_FidAxis1->value();
	- p2 = p0 + v2*m_Controls->m_FidAxis2->value();
	- p3 = p0 + mitk::Vector2D(v3);
	- pe->SetControlPoint(1, p1);
	- pe->SetControlPoint(2, p2);
	- pe->SetControlPoint(3, p3);
	- geom->SetOrigin(origin);
	-
	- pe->Modified();
	-
	- if (m_Controls->m_RealTimeFibers->isChecked())
	- GenerateFibers();
	-
	- UpdateGui();
	-}
	-
	-void QmitkFiberGenerationView::AlignOnGrid()
	-{
	- for (unsigned int i=0; i<m_SelectedFiducials.size(); i++)
	- {
	- mitk::PlanarEllipse::Pointer pe = dynamic_cast<mitk::PlanarEllipse*>(m_SelectedFiducials.at(i)->GetData());
	- mitk::Point3D wc0 = pe->GetWorldControlPoint(0);
	-
	- mitk::DataStorage::SetOfObjects::ConstPointer parentFibs = GetDataStorage()->GetSources(m_SelectedFiducials.at(i));
	- for( mitk::DataStorage::SetOfObjects::const_iterator it = parentFibs->begin(); it != parentFibs->end(); ++it )
	- {
	- mitk::DataNode::Pointer pFibNode = *it;
	- if ( pFibNode.IsNotNull() && dynamic_cast<mitk::FiberBundle*>(pFibNode->GetData()) )
	- {
	- mitk::DataStorage::SetOfObjects::ConstPointer parentImgs = GetDataStorage()->GetSources(pFibNode);
	- for( mitk::DataStorage::SetOfObjects::const_iterator it2 = parentImgs->begin(); it2 != parentImgs->end(); ++it2 )
	- {
	- mitk::DataNode::Pointer pImgNode = *it2;
	- if ( pImgNode.IsNotNull() && dynamic_cast<mitk::Image*>(pImgNode->GetData()) )
	- {
	- mitk::Image::Pointer img = dynamic_cast<mitk::Image*>(pImgNode->GetData());
	- mitk::BaseGeometry::Pointer geom = img->GetGeometry();
	- itk::Index<3> idx;
	- geom->WorldToIndex(wc0, idx);
	-
	- mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2];
	- mitk::Point3D world;
	- geom->IndexToWorld(cIdx,world);
	-
	- mitk::Vector3D trans = world - wc0;
	- pe->GetGeometry()->Translate(trans);
	-
	- break;
	- }
	- }
	- break;
	- }
	- }
	- }
	-
	- for(unsigned int i=0; i<m_SelectedBundles2.size(); i++ )
	- {
	- mitk::DataNode::Pointer fibNode = m_SelectedBundles2.at(i);
	-
	- mitk::DataStorage::SetOfObjects::ConstPointer sources = GetDataStorage()->GetSources(fibNode);
	- for( mitk::DataStorage::SetOfObjects::const_iterator it = sources->begin(); it != sources->end(); ++it )
	- {
	- mitk::DataNode::Pointer imgNode = *it;
	- if ( imgNode.IsNotNull() && dynamic_cast<mitk::Image*>(imgNode->GetData()) )
	- {
	- mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(fibNode);
	- for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 )
	- {
	- mitk::DataNode::Pointer fiducialNode = *it2;
	- if ( fiducialNode.IsNotNull() && dynamic_cast<mitk::PlanarEllipse*>(fiducialNode->GetData()) )
	- {
	- mitk::PlanarEllipse::Pointer pe = dynamic_cast<mitk::PlanarEllipse*>(fiducialNode->GetData());
	- mitk::Point3D wc0 = pe->GetWorldControlPoint(0);
	-
	- mitk::Image::Pointer img = dynamic_cast<mitk::Image*>(imgNode->GetData());
	- mitk::BaseGeometry::Pointer geom = img->GetGeometry();
	- itk::Index<3> idx;
	- geom->WorldToIndex(wc0, idx);
	- mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2];
	- mitk::Point3D world;
	- geom->IndexToWorld(cIdx,world);
	-
	- mitk::Vector3D trans = world - wc0;
	- pe->GetGeometry()->Translate(trans);
	- }
	- }
	-
	- break;
	- }
	- }
	- }
	-
	- for(unsigned int i=0; i<m_SelectedImages.size(); i++ )
	- {
	- mitk::Image::Pointer img = dynamic_cast<mitk::Image*>(m_SelectedImages.at(i)->GetData());
	-
	- mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(m_SelectedImages.at(i));
	- for( mitk::DataStorage::SetOfObjects::const_iterator it = derivations->begin(); it != derivations->end(); ++it )
	- {
	- mitk::DataNode::Pointer fibNode = *it;
	- if ( fibNode.IsNotNull() && dynamic_cast<mitk::FiberBundle*>(fibNode->GetData()) )
	- {
	- mitk::DataStorage::SetOfObjects::ConstPointer derivations2 = GetDataStorage()->GetDerivations(fibNode);
	- for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations2->begin(); it2 != derivations2->end(); ++it2 )
	- {
	- mitk::DataNode::Pointer fiducialNode = *it2;
	- if ( fiducialNode.IsNotNull() && dynamic_cast<mitk::PlanarEllipse*>(fiducialNode->GetData()) )
	- {
	- mitk::PlanarEllipse::Pointer pe = dynamic_cast<mitk::PlanarEllipse*>(fiducialNode->GetData());
	- mitk::Point3D wc0 = pe->GetWorldControlPoint(0);
	-
	- mitk::BaseGeometry::Pointer geom = img->GetGeometry();
	- itk::Index<3> idx;
	- geom->WorldToIndex(wc0, idx);
	- mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2];
	- mitk::Point3D world;
	- geom->IndexToWorld(cIdx,world);
	-
	- mitk::Vector3D trans = world - wc0;
	- pe->GetGeometry()->Translate(trans);
	- }
	- }
	- }
	- }
	- }
	-
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- if (m_Controls->m_RealTimeFibers->isChecked())
	- GenerateFibers();
	-}
	-
	-void QmitkFiberGenerationView::OnFlipButton()
	-{
	- if (m_SelectedFiducial.IsNull())
	- return;
	-
	- std::map<mitk::DataNode*, QmitkPlanarFigureData>::iterator it = m_DataNodeToPlanarFigureData.find(m_SelectedFiducial.GetPointer());
	- if( it != m_DataNodeToPlanarFigureData.end() )
	- {
	- QmitkPlanarFigureData& data = it->second;
	- data.m_Flipped += 1;
	- data.m_Flipped %= 2;
	- }
	-
	- if (m_Controls->m_RealTimeFibers->isChecked())
	- GenerateFibers();
	-}
	-
	-void QmitkFiberGenerationView::OnAddBundle()
	-{
	- if (m_SelectedImageNode.IsNull())
	- return;
	-
	- mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedImageNode);
	-
	- mitk::FiberBundle::Pointer bundle = mitk::FiberBundle::New();
	- mitk::DataNode::Pointer node = mitk::DataNode::New();
	- node->SetData( bundle );
	- QString name = QString("Bundle_%1").arg(children->size());
	- node->SetName(name.toStdString());
	- m_SelectedBundles.push_back(node);
	- UpdateGui();
	-
	- GetDataStorage()->Add(node, m_SelectedImageNode);
	-}
	-
	-void QmitkFiberGenerationView::OnDrawROI()
	-{
	- if (m_SelectedBundles.empty())
	- OnAddBundle();
	- if (m_SelectedBundles.empty())
	- return;
	-
	- mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedBundles.at(0));
	-
	- mitk::PlanarEllipse::Pointer figure = mitk::PlanarEllipse::New();
	-
	- mitk::DataNode::Pointer node = mitk::DataNode::New();
	- node->SetData( figure );
	- node->SetBoolProperty("planarfigure.3drendering", true);
	- node->SetBoolProperty("planarfigure.3drendering.fill", true);
	-
	- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
	- for( int i=0; i<nodes.size(); i++)
	- nodes.at(i)->SetSelected(false);
	-
	- m_SelectedFiducial = node;
	-
	- QString name = QString("Fiducial_%1").arg(children->size());
	- node->SetName(name.toStdString());
	- node->SetSelected(true);
	-
	- this->DisableCrosshairNavigation();
	-
	- mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast<mitk::PlanarFigureInteractor*>(node->GetDataInteractor().GetPointer());
	- if(figureInteractor.IsNull())
	- {
	- figureInteractor = mitk::PlanarFigureInteractor::New();
	- us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "MitkPlanarFigure" );
	- figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule );
	- figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule );
	- figureInteractor->SetDataNode( node );
	- }
	-
	- UpdateGui();
	- GetDataStorage()->Add(node, m_SelectedBundles.at(0));
	-}
	-
	-bool QmitkFiberGenerationView::CompareLayer(mitk::DataNode::Pointer i,mitk::DataNode::Pointer j)
	-{
	- int li = -1;
	- i->GetPropertyValue("layer", li);
	- int lj = -1;
	- j->GetPropertyValue("layer", lj);
	- return li<lj;
	-}
	-
	-void QmitkFiberGenerationView::GenerateFibers()
	-{
	- UpdateGui();
	- if (m_SelectedBundles.empty())
	- {
	- if (m_SelectedFiducial.IsNull())
	- return;
	-
	- mitk::DataStorage::SetOfObjects::ConstPointer parents = GetDataStorage()->GetSources(m_SelectedFiducial);
	- for( mitk::DataStorage::SetOfObjects::const_iterator it = parents->begin(); it != parents->end(); ++it )
	- if(dynamic_cast<mitk::FiberBundle>((it)->GetData()))
	- m_SelectedBundles.push_back(*it);
	-
	- if (m_SelectedBundles.empty())
	- return;
	- }
	-
	- UpdateParametersFromGui();
	-
	- for (unsigned int i=0; i<m_SelectedBundles.size(); i++)
	- {
	- mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedBundles.at(i));
	- std::vector< mitk::DataNode::Pointer > childVector;
	- for( mitk::DataStorage::SetOfObjects::const_iterator it = children->begin(); it != children->end(); ++it )
	- childVector.push_back(*it);
	- std::sort(childVector.begin(), childVector.end(), CompareLayer);
	-
	- std::vector< mitk::PlanarEllipse::Pointer > fib;
	- std::vector< unsigned int > flip;
	- float radius = 1;
	- int count = 0;
	- for( std::vector< mitk::DataNode::Pointer >::const_iterator it = childVector.begin(); it != childVector.end(); ++it )
	- {
	- mitk::DataNode::Pointer node = *it;
	-
	- if ( node.IsNotNull() && dynamic_cast<mitk::PlanarEllipse*>(node->GetData()) )
	- {
	- mitk::PlanarEllipse* ellipse = dynamic_cast<mitk::PlanarEllipse*>(node->GetData());
	- if (m_Controls->m_ConstantRadiusBox->isChecked())
	- {
	- ellipse->SetTreatAsCircle(true);
	- mitk::Point2D c = ellipse->GetControlPoint(0);
	- mitk::Point2D p = ellipse->GetControlPoint(1);
	- mitk::Vector2D v = p-c;
	- if (count==0)
	- {
	- radius = v.GetVnlVector().magnitude();
	- ellipse->SetControlPoint(1, p);
	- ellipse->Modified();
	- }
	- else
	- {
	- v.Normalize();
	- v *= radius;
	- ellipse->SetControlPoint(1, c+v);
	- ellipse->Modified();
	- }
	- }
	- fib.push_back(ellipse);
	-
	- std::map<mitk::DataNode*, QmitkPlanarFigureData>::iterator it = m_DataNodeToPlanarFigureData.find(node.GetPointer());
	- if( it != m_DataNodeToPlanarFigureData.end() )
	- {
	- QmitkPlanarFigureData& data = it->second;
	- flip.push_back(data.m_Flipped);
	- }
	- else
	- flip.push_back(0);
	- }
	- count++;
	- }
	- if (fib.size()>1)
	- {
	- m_Parameters.m_FiberGen.m_Fiducials.push_back(fib);
	- m_Parameters.m_FiberGen.m_FlipList.push_back(flip);
	- }
	- else if (fib.size()>0)
	- m_SelectedBundles.at(i)->SetData( mitk::FiberBundle::New() );
	-
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- }
	-
	- itk::FibersFromPlanarFiguresFilter::Pointer filter = itk::FibersFromPlanarFiguresFilter::New();
	- filter->SetParameters(m_Parameters.m_FiberGen);
	- filter->Update();
	- std::vector< mitk::FiberBundle::Pointer > fiberBundles = filter->GetFiberBundles();
	-
	- for (unsigned int i=0; i<fiberBundles.size(); i++)
	- {
	- m_SelectedBundles.at(i)->SetData( fiberBundles.at(i) );
	- if (fiberBundles.at(i)->GetNumFibers()>50000)
	- m_SelectedBundles.at(i)->SetVisibility(false);
	- }
	-
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-void QmitkFiberGenerationView::ApplyTransform()
	-{
	- std::vector< mitk::DataNode::Pointer > selectedBundles;
	- for(unsigned int i=0; i<m_SelectedImages.size(); i++ )
	- {
	- mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(m_SelectedImages.at(i));
	- for( mitk::DataStorage::SetOfObjects::const_iterator it = derivations->begin(); it != derivations->end(); ++it )
	- {
	- mitk::DataNode::Pointer fibNode = *it;
	- if ( fibNode.IsNotNull() && dynamic_cast<mitk::FiberBundle*>(fibNode->GetData()) )
	- selectedBundles.push_back(fibNode);
	- }
	- }
	- if (selectedBundles.empty())
	- selectedBundles = m_SelectedBundles2;
	-
	- if (!selectedBundles.empty())
	- {
	- for (std::vector<mitk::DataNode::Pointer>::const_iterator it = selectedBundles.begin(); it!=selectedBundles.end(); ++it)
	- {
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle>((it)->GetData());
	- fib->RotateAroundAxis(m_Controls->m_XrotBox->value(), m_Controls->m_YrotBox->value(), m_Controls->m_ZrotBox->value());
	- fib->TranslateFibers(m_Controls->m_XtransBox->value(), m_Controls->m_YtransBox->value(), m_Controls->m_ZtransBox->value());
	- fib->ScaleFibers(m_Controls->m_XscaleBox->value(), m_Controls->m_YscaleBox->value(), m_Controls->m_ZscaleBox->value());
	-
	- // handle child fiducials
	- if (m_Controls->m_IncludeFiducials->isChecked())
	- {
	- mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(*it);
	- for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 )
	- {
	- mitk::DataNode::Pointer fiducialNode = *it2;
	- if ( fiducialNode.IsNotNull() && dynamic_cast<mitk::PlanarEllipse*>(fiducialNode->GetData()) )
	- {
	- mitk::PlanarEllipse* pe = dynamic_cast<mitk::PlanarEllipse*>(fiducialNode->GetData());
	- mitk::BaseGeometry* geom = pe->GetGeometry();
	-
	- // translate
	- mitk::Vector3D world;
	- world[0] = m_Controls->m_XtransBox->value();
	- world[1] = m_Controls->m_YtransBox->value();
	- world[2] = m_Controls->m_ZtransBox->value();
	- geom->Translate(world);
	-
	- // calculate rotation matrix
	- double x = m_Controls->m_XrotBox->value()*itk::Math::pi/180;
	- double y = m_Controls->m_YrotBox->value()*itk::Math::pi/180;
	- double z = m_Controls->m_ZrotBox->value()*itk::Math::pi/180;
	-
	- itk::Matrix< double, 3, 3 > rotX; rotX.SetIdentity();
	- rotX[1][1] = cos(x);
	- rotX[2][2] = rotX[1][1];
	- rotX[1][2] = -sin(x);
	- rotX[2][1] = -rotX[1][2];
	-
	- itk::Matrix< double, 3, 3 > rotY; rotY.SetIdentity();
	- rotY[0][0] = cos(y);
	- rotY[2][2] = rotY[0][0];
	- rotY[0][2] = sin(y);
	- rotY[2][0] = -rotY[0][2];
	-
	- itk::Matrix< double, 3, 3 > rotZ; rotZ.SetIdentity();
	- rotZ[0][0] = cos(z);
	- rotZ[1][1] = rotZ[0][0];
	- rotZ[0][1] = -sin(z);
	- rotZ[1][0] = -rotZ[0][1];
	-
	- itk::Matrix< double, 3, 3 > rot = rotZrotYrotX;
	-
	- // transform control point coordinate into geometry translation
	- geom->SetOrigin(pe->GetWorldControlPoint(0));
	- mitk::Point2D cp; cp.Fill(0.0);
	- pe->SetControlPoint(0, cp);
	-
	- // rotate fiducial
	- geom->GetIndexToWorldTransform()->SetMatrix(rot*geom->GetIndexToWorldTransform()->GetMatrix());
	-
	- // implicit translation
	- mitk::Vector3D trans;
	- trans[0] = geom->GetOrigin()[0]-fib->GetGeometry()->GetCenter()[0];
	- trans[1] = geom->GetOrigin()[1]-fib->GetGeometry()->GetCenter()[1];
	- trans[2] = geom->GetOrigin()[2]-fib->GetGeometry()->GetCenter()[2];
	- mitk::Vector3D newWc = rot*trans;
	- newWc = newWc-trans;
	- geom->Translate(newWc);
	-
	- pe->Modified();
	- }
	- }
	- }
	- }
	- }
	- else
	- {
	- for (unsigned int i=0; i<m_SelectedFiducials.size(); i++)
	- {
	- mitk::PlanarEllipse* pe = dynamic_cast<mitk::PlanarEllipse*>(m_SelectedFiducials.at(i)->GetData());
	- mitk::BaseGeometry* geom = pe->GetGeometry();
	-
	- // translate
	- mitk::Vector3D world;
	- world[0] = m_Controls->m_XtransBox->value();
	- world[1] = m_Controls->m_YtransBox->value();
	- world[2] = m_Controls->m_ZtransBox->value();
	- geom->Translate(world);
	-
	- // calculate rotation matrix
	- double x = m_Controls->m_XrotBox->value()*itk::Math::pi/180;
	- double y = m_Controls->m_YrotBox->value()*itk::Math::pi/180;
	- double z = m_Controls->m_ZrotBox->value()*itk::Math::pi/180;
	- itk::Matrix< double, 3, 3 > rotX; rotX.SetIdentity();
	- rotX[1][1] = cos(x);
	- rotX[2][2] = rotX[1][1];
	- rotX[1][2] = -sin(x);
	- rotX[2][1] = -rotX[1][2];
	- itk::Matrix< double, 3, 3 > rotY; rotY.SetIdentity();
	- rotY[0][0] = cos(y);
	- rotY[2][2] = rotY[0][0];
	- rotY[0][2] = sin(y);
	- rotY[2][0] = -rotY[0][2];
	- itk::Matrix< double, 3, 3 > rotZ; rotZ.SetIdentity();
	- rotZ[0][0] = cos(z);
	- rotZ[1][1] = rotZ[0][0];
	- rotZ[0][1] = -sin(z);
	- rotZ[1][0] = -rotZ[0][1];
	- itk::Matrix< double, 3, 3 > rot = rotZrotYrotX;
	-
	- // transform control point coordinate into geometry translation
	- geom->SetOrigin(pe->GetWorldControlPoint(0));
	- mitk::Point2D cp; cp.Fill(0.0);
	- pe->SetControlPoint(0, cp);
	-
	- // rotate fiducial
	- geom->GetIndexToWorldTransform()->SetMatrix(rot*geom->GetIndexToWorldTransform()->GetMatrix());
	- pe->Modified();
	- }
	- if (m_Controls->m_RealTimeFibers->isChecked())
	- GenerateFibers();
	- }
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-void QmitkFiberGenerationView::CopyBundles()
	-{
	- if ( m_SelectedBundles.size()<1 ){
	- QMessageBox::information( nullptr, "Warning", "Select at least one fiber bundle!");
	- MITK_WARN("QmitkFiberGenerationView") << "Select at least one fiber bundle!";
	- return;
	- }
	-
	- for (std::vector<mitk::DataNode::Pointer>::const_iterator it = m_SelectedBundles.begin(); it!=m_SelectedBundles.end(); ++it)
	- {
	- // find parent image
	- mitk::DataNode::Pointer parentNode;
	- mitk::DataStorage::SetOfObjects::ConstPointer parentImgs = GetDataStorage()->GetSources(*it);
	- for( mitk::DataStorage::SetOfObjects::const_iterator it2 = parentImgs->begin(); it2 != parentImgs->end(); ++it2 )
	- {
	- mitk::DataNode::Pointer pImgNode = *it2;
	- if ( pImgNode.IsNotNull() && dynamic_cast<mitk::Image*>(pImgNode->GetData()) )
	- {
	- parentNode = pImgNode;
	- break;
	- }
	- }
	-
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle>((it)->GetData());
	- mitk::FiberBundle::Pointer newBundle = fib->GetDeepCopy();
	- QString name((*it)->GetName().c_str());
	- name += "_copy";
	-
	- mitk::DataNode::Pointer fbNode = mitk::DataNode::New();
	- fbNode->SetData(newBundle);
	- fbNode->SetName(name.toStdString());
	- fbNode->SetVisibility(true);
	- if (parentNode.IsNotNull())
	- GetDataStorage()->Add(fbNode, parentNode);
	- else
	- GetDataStorage()->Add(fbNode);
	-
	- // copy child fiducials
	- if (m_Controls->m_IncludeFiducials->isChecked())
	- {
	- mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(*it);
	- for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 )
	- {
	- mitk::DataNode::Pointer fiducialNode = *it2;
	- if ( fiducialNode.IsNotNull() && dynamic_cast<mitk::PlanarEllipse*>(fiducialNode->GetData()) )
	- {
	- mitk::PlanarEllipse::Pointer pe = dynamic_cast<mitk::PlanarEllipse*>(fiducialNode->GetData())->Clone();
	- mitk::DataNode::Pointer newNode = mitk::DataNode::New();
	- newNode->SetData(pe);
	- newNode->SetName(fiducialNode->GetName());
	- newNode->SetBoolProperty("planarfigure.3drendering", true);
	- GetDataStorage()->Add(newNode, fbNode);
	-
	- }
	- }
	- }
	- }
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-void QmitkFiberGenerationView::JoinBundles()
	-{
	- if ( m_SelectedBundles.size()<2 ){
	- QMessageBox::information( nullptr, "Warning", "Select at least two fiber bundles!");
	- MITK_WARN("QmitkFiberGenerationView") << "Select at least two fiber bundles!";
	- return;
	- }
	-
	- std::vector< mitk::FiberBundle::Pointer > to_add;
	- std::vector<mitk::DataNode::Pointer>::const_iterator it = m_SelectedBundles.begin();
	- (*it)->SetVisibility(false);
	- mitk::FiberBundle::Pointer newBundle = dynamic_cast<mitk::FiberBundle>((it)->GetData());
	- QString name("");
	- name += QString((*it)->GetName().c_str());
	- ++it;
	- for (; it!=m_SelectedBundles.end(); ++it)
	- {
	- (*it)->SetVisibility(false);
	- to_add.push_back(dynamic_cast<mitk::FiberBundle>((it)->GetData()));
	- }
	-
	- newBundle = newBundle->AddBundles(to_add);
	- mitk::DataNode::Pointer fbNode = mitk::DataNode::New();
	- fbNode->SetData(newBundle);
	- fbNode->SetName("Joined");
	- fbNode->SetVisibility(true);
	- GetDataStorage()->Add(fbNode);
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-void QmitkFiberGenerationView::UpdateGui()
	-{
	- m_Controls->m_FiberGenMessage->setVisible(true);
	- m_Controls->m_TransformBundlesButton->setEnabled(false);
	- m_Controls->m_CopyBundlesButton->setEnabled(false);
	- m_Controls->m_GenerateFibersButton->setEnabled(false);
	- m_Controls->m_FlipButton->setEnabled(false);
	- m_Controls->m_CircleButton->setEnabled(false);
	- m_Controls->m_JoinBundlesButton->setEnabled(false);
	- m_Controls->m_AlignOnGrid->setEnabled(false);
	- m_Controls->m_FiducialAttributeBox->setEnabled(false);
	-
	- // Fiber generation gui
	- if (m_SelectedFiducial.IsNotNull())
	- {
	- m_Controls->m_TransformBundlesButton->setEnabled(true);
	- m_Controls->m_FlipButton->setEnabled(true);
	- m_Controls->m_AlignOnGrid->setEnabled(true);
	- }
	-
	- if (m_SelectedFiducials.size()==1)
	- {
	- m_Controls->m_FiducialAttributeBox->setEnabled(true);
	- mitk::PlanarEllipse* pe = dynamic_cast<mitk::PlanarEllipse*>(m_SelectedFiducials.at(0)->GetData());
	- auto origin = pe->GetGeometry()->GetOrigin();
	- m_Controls->m_FidPosX->setValue(origin[0]);
	- m_Controls->m_FidPosY->setValue(origin[1]);
	- m_Controls->m_FidPosZ->setValue(origin[2]);
	-
	-
	- auto p0 = pe->GetControlPoint(0);
	- auto p1 = pe->GetControlPoint(1);
	- auto p2 = pe->GetControlPoint(2);
	- auto p3 = pe->GetControlPoint(3);
	-
	- auto v1 = p1 - p0;
	- auto v2 = p2 - p0;
	-
	- m_Controls->m_FidAxis1->setValue(v1.GetNorm());
	- m_Controls->m_FidAxis2->setValue(v2.GetNorm());
	-
	- vnl_vector_fixed<double, 2> vt; vt[0]=1; vt[1]=0;
	- auto v3 = p3-p0; v3.Normalize();
	- auto angle = dot_product(vt, v3.GetVnlVector());
	- angle = std::acos(angle)*180.0/itk::Math::pi;
	- if (v3[1]<0)
	- angle *= -1;
	- m_Controls->m_FidTwist->setValue(angle);
	- }
	- else
	- {
	- m_Controls->m_FidPosX->setValue(0);
	- m_Controls->m_FidPosY->setValue(0);
	- m_Controls->m_FidPosZ->setValue(0);
	- m_Controls->m_FidAxis1->setValue(1);
	- m_Controls->m_FidAxis2->setValue(1);
	- m_Controls->m_FidTwist->setValue(0);
	- }
	-
	- if (m_SelectedImageNode.IsNotNull() \|\| !m_SelectedBundles.empty())
	- {
	- m_Controls->m_CircleButton->setEnabled(true);
	- m_Controls->m_FiberGenMessage->setVisible(false);
	- }
	- if (m_SelectedImageNode.IsNotNull() && !m_SelectedBundles.empty())
	- m_Controls->m_AlignOnGrid->setEnabled(true);
	-
	- if (!m_SelectedBundles.empty())
	- {
	- m_Controls->m_TransformBundlesButton->setEnabled(true);
	- m_Controls->m_CopyBundlesButton->setEnabled(true);
	- m_Controls->m_GenerateFibersButton->setEnabled(true);
	-
	- if (m_SelectedBundles.size()>1)
	- m_Controls->m_JoinBundlesButton->setEnabled(true);
	- }
	-}
	-
	-void QmitkFiberGenerationView::OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList<mitk::DataNode::Pointer>& nodes)
	-{
	- m_SelectedBundles2.clear();
	- m_SelectedImages.clear();
	- m_SelectedFiducials.clear();
	- m_SelectedFiducial = nullptr;
	- m_SelectedBundles.clear();
	- m_SelectedImageNode = nullptr;
	-
	- // iterate all selected objects, adjust warning visibility
	- for( int i=0; i<nodes.size(); i++)
	- {
	- mitk::DataNode::Pointer node = nodes.at(i);
	-
	- if( node.IsNotNull() && dynamic_cast<mitk::Image*>(node->GetData()) )
	- {
	- m_SelectedImages.push_back(node);
	- m_SelectedImageNode = node;
	- }
	- else if ( node.IsNotNull() && dynamic_cast<mitk::FiberBundle*>(node->GetData()) )
	- {
	- m_SelectedBundles2.push_back(node);
	- if (m_Controls->m_RealTimeFibers->isChecked())
	- {
	- m_SelectedBundles.push_back(node);
	- mitk::FiberBundle::Pointer newFib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
	- if (newFib->GetNumFibers()!=static_cast<unsigned int>(m_Controls->m_FiberDensityBox->value()))
	- GenerateFibers();
	- }
	- else
	- m_SelectedBundles.push_back(node);
	- }
	- else if ( node.IsNotNull() && dynamic_cast<mitk::PlanarEllipse*>(node->GetData()) )
	- {
	- m_SelectedFiducials.push_back(node);
	- m_SelectedFiducial = node;
	- m_SelectedBundles.clear();
	- mitk::DataStorage::SetOfObjects::ConstPointer parents = GetDataStorage()->GetSources(node);
	- for( mitk::DataStorage::SetOfObjects::const_iterator it = parents->begin(); it != parents->end(); ++it )
	- {
	- mitk::DataNode::Pointer pNode = *it;
	- if ( pNode.IsNotNull() && dynamic_cast<mitk::FiberBundle*>(pNode->GetData()) )
	- m_SelectedBundles.push_back(pNode);
	- }
	- }
	- }
	- UpdateGui();
	-}
	-
	-
	-void QmitkFiberGenerationView::EnableCrosshairNavigation()
	-{
	- if (m_Controls->m_RealTimeFibers->isChecked())
	- GenerateFibers();
	-}
	-
	-void QmitkFiberGenerationView::DisableCrosshairNavigation()
	-{
	-}
	-
	-void QmitkFiberGenerationView::NodeRemoved(const mitk::DataNode* node)
	-{
	- mitk::DataNode* nonConstNode = const_cast<mitk::DataNode*>(node);
	- std::map<mitk::DataNode*, QmitkPlanarFigureData>::iterator it = m_DataNodeToPlanarFigureData.find(nonConstNode);
	-
	- if (dynamic_cast<FiberBundle*>(node->GetData()))
	- {
	- m_SelectedBundles.clear();
	- m_SelectedBundles2.clear();
	- }
	- else if (dynamic_cast<Image*>(node->GetData()))
	- m_SelectedImages.clear();
	-
	- if( it != m_DataNodeToPlanarFigureData.end() )
	- {
	- QmitkPlanarFigureData& data = it->second;
	-
	- // remove observers
	- data.m_Figure->RemoveObserver( data.m_EndPlacementObserverTag );
	- data.m_Figure->RemoveObserver( data.m_SelectObserverTag );
	- data.m_Figure->RemoveObserver( data.m_StartInteractionObserverTag );
	- data.m_Figure->RemoveObserver( data.m_EndInteractionObserverTag );
	-
	- m_DataNodeToPlanarFigureData.erase( it );
	- }
	-}
	-
	-void QmitkFiberGenerationView::NodeAdded( const mitk::DataNode* node )
	-{
	- // add observer for selection in renderwindow
	- mitk::PlanarFigure* figure = dynamic_cast<mitk::PlanarFigure*>(node->GetData());
	- bool isPositionMarker (false);
	- node->GetBoolProperty("isContourMarker", isPositionMarker);
	- if( figure && !isPositionMarker )
	- {
	- MITK_DEBUG << "figure added. will add interactor if needed.";
	- mitk::PlanarFigureInteractor::Pointer figureInteractor
	- = dynamic_cast<mitk::PlanarFigureInteractor*>(node->GetDataInteractor().GetPointer());
	-
	- mitk::DataNode* nonConstNode = const_cast<mitk::DataNode*>( node );
	- if(figureInteractor.IsNull())
	- {
	- figureInteractor = mitk::PlanarFigureInteractor::New();
	- us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "MitkPlanarFigure" );
	- figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule );
	- figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule );
	- figureInteractor->SetDataNode( nonConstNode );
	- }
	-
	- MITK_DEBUG << "will now add observers for planarfigure";
	- QmitkPlanarFigureData data;
	- data.m_Figure = figure;
	-
	- // // add observer for event when figure has been placed
	- typedef itk::SimpleMemberCommand< QmitkFiberGenerationView > SimpleCommandType;
	- // SimpleCommandType::Pointer initializationCommand = SimpleCommandType::New();
	- // initializationCommand->SetCallbackFunction( this, &QmitkFiberGenerationView::PlanarFigureInitialized );
	- // data.m_EndPlacementObserverTag = figure->AddObserver( mitk::EndPlacementPlanarFigureEvent(), initializationCommand );
	-
	- // add observer for event when figure is picked (selected)
	- typedef itk::MemberCommand< QmitkFiberGenerationView > MemberCommandType;
	- MemberCommandType::Pointer selectCommand = MemberCommandType::New();
	- selectCommand->SetCallbackFunction( this, &QmitkFiberGenerationView::PlanarFigureSelected );
	- data.m_SelectObserverTag = figure->AddObserver( mitk::SelectPlanarFigureEvent(), selectCommand );
	-
	- // add observer for event when interaction with figure starts
	- SimpleCommandType::Pointer startInteractionCommand = SimpleCommandType::New();
	- startInteractionCommand->SetCallbackFunction( this, &QmitkFiberGenerationView::DisableCrosshairNavigation);
	- data.m_StartInteractionObserverTag = figure->AddObserver( mitk::StartInteractionPlanarFigureEvent(), startInteractionCommand );
	-
	- // add observer for event when interaction with figure starts
	- SimpleCommandType::Pointer endInteractionCommand = SimpleCommandType::New();
	- endInteractionCommand->SetCallbackFunction( this, &QmitkFiberGenerationView::EnableCrosshairNavigation);
	- data.m_EndInteractionObserverTag = figure->AddObserver( mitk::EndInteractionPlanarFigureEvent(), endInteractionCommand );
	-
	- m_DataNodeToPlanarFigureData[nonConstNode] = data;
	- }
	-}
	-
	-void QmitkFiberGenerationView::PlanarFigureSelected( itk::Object* object, const itk::EventObject& )
	-{
	- mitk::TNodePredicateDataType<mitk::PlanarFigure>::Pointer isPf = mitk::TNodePredicateDataType<mitk::PlanarFigure>::New();
	-
	- mitk::DataStorage::SetOfObjects::ConstPointer allPfs = this->GetDataStorage()->GetSubset( isPf );
	- for ( mitk::DataStorage::SetOfObjects::const_iterator it = allPfs->begin(); it!=allPfs->end(); ++it)
	- {
	- mitk::DataNode* node = *it;
	-
	- if( node->GetData() == object )
	- {
	- node->SetSelected(true);
	- m_SelectedFiducial = node;
	- }
	- else
	- node->SetSelected(false);
	- }
	- UpdateGui();
	- this->RequestRenderWindowUpdate();
	-}
	-
	-void QmitkFiberGenerationView::SetFocus()
	-{
	- m_Controls->m_CircleButton->setFocus();
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberGenerationView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberGenerationView.h
	deleted file mode 100644
	index 5eba22b325..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberGenerationView.h
	+++ /dev/null
	@@ -1,148 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-
	-#include <berryISelectionListener.h>
	-#include <berryIStructuredSelection.h>
	-
	-#include <QmitkAbstractView.h>
	-#include "ui_QmitkFiberGenerationViewControls.h"
	-#include <itkVectorImage.h>
	-#include <itkVectorContainer.h>
	-#include <itkOrientationDistributionFunction.h>
	-
	-#ifndef Q_MOC_RUN
	-#include <mitkFiberBundle.h>
	-#include <mitkPlanarEllipse.h>
	-#include <mitkDiffusionNoiseModel.h>
	-#include <mitkDiffusionSignalModel.h>
	-#include <mitkRicianNoiseModel.h>
	-#include <itkTractsToDWIImageFilter.h>
	-#include <mitkTensorModel.h>
	-#include <mitkBallModel.h>
	-#include <mitkStickModel.h>
	-#include <mitkAstroStickModel.h>
	-#include <mitkDotModel.h>
	-#include <mitkFiberfoxParameters.h>
	-#include <itkStatisticsImageFilter.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-#endif
	-
	-#include <QThread>
	-#include <QObject>
	-#include <QTimer>
	-#include <QTime>
	-
	-
	-class QmitkFiberGenerationView : public QmitkAbstractView
	-{
	-
	- // this is needed for all Qt objects that should have a Qt meta-object
	- // (everything that derives from QObject and wants to have signal/slots)
	- Q_OBJECT
	-
	-public:
	-
	- static const std::string VIEW_ID;
	-
	- QmitkFiberGenerationView();
	- virtual ~QmitkFiberGenerationView();
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	- void SetFocus() override;
	-
	- typedef itk::Image<double, 3> ItkDoubleImgType;
	- typedef itk::Image<float, 3> ItkFloatImgType;
	- typedef itk::Image<unsigned char, 3> ItkUcharImgType;
	-
	-protected slots:
	-
	- void LoadParameters(); ///< load FiberGeneration parameters
	- void SaveParameters(); ///< save FiberGeneration parameters
	-
	- void OnDrawROI(); ///< adds new ROI, handles interactors etc.
	- void OnAddBundle(); ///< adds new fiber bundle to datastorage
	- void OnFlipButton(); ///< negate one coordinate of the fiber waypoints in the selcted planar figure. needed in case of unresolvable twists
	- void GenerateFibers(); ///< generate fibers from the selected ROIs
	-
	- void JoinBundles(); ///< merges selcted fiber bundles into one
	- void CopyBundles(); ///< add copy of the selected bundle to the datamanager
	- void ApplyTransform(); ///< rotate and shift selected bundles
	- void AlignOnGrid(); ///< shift selected fiducials to nearest voxel center
	- void RandomPhantom();
	-
	- void ShowAdvancedOptions(int state);
	-
	- /** update fibers if any parameter changes */
	- void OnFiberDensityChanged(int value);
	- void OnFiberSamplingChanged(double value);
	- void OnTensionChanged(double value);
	- void OnContinuityChanged(double value);
	- void OnBiasChanged(double value);
	- void OnVarianceChanged(double value);
	- void OnDistributionChanged(int value);
	- void OnConstantRadius(int value);
	- void UpdateFiducialPosition();
	-
	-protected:
	-
	- /// \brief called by QmitkAbstractView when DataManager's selection has changed
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- Ui::QmitkFiberGenerationViewControls* m_Controls;
	-
	- void UpdateParametersFromGui();
	- void UpdateGui(); ///< enable/disbale buttons etc. according to current datamanager selection
	- void PlanarFigureSelected( itk::Object* object, const itk::EventObject& );
	- void EnableCrosshairNavigation(); ///< enable crosshair navigation if planar figure interaction ends
	- void DisableCrosshairNavigation(); ///< disable crosshair navigation if planar figure interaction starts
	- void NodeAdded( const mitk::DataNode* node ) override; ///< add observers
	- void NodeRemoved(const mitk::DataNode* node) override; ///< remove observers
	- void SaveParameters(QString filename);
	- static bool CompareLayer(mitk::DataNode::Pointer i,mitk::DataNode::Pointer j);
	-
	- /** structure to keep track of planar figures and observers */
	- struct QmitkPlanarFigureData
	- {
	- QmitkPlanarFigureData()
	- : m_Figure(0)
	- , m_EndPlacementObserverTag(0)
	- , m_SelectObserverTag(0)
	- , m_StartInteractionObserverTag(0)
	- , m_EndInteractionObserverTag(0)
	- , m_Flipped(0)
	- {
	- }
	- mitk::PlanarFigure* m_Figure;
	- unsigned int m_EndPlacementObserverTag;
	- unsigned int m_SelectObserverTag;
	- unsigned int m_StartInteractionObserverTag;
	- unsigned int m_EndInteractionObserverTag;
	- unsigned int m_Flipped;
	- };
	-
	- std::map<mitk::DataNode*, QmitkPlanarFigureData> m_DataNodeToPlanarFigureData; ///< map each planar figure uniquely to a QmitkPlanarFigureData
	- mitk::DataNode::Pointer m_SelectedFiducial; ///< selected planar ellipse
	- mitk::DataNode::Pointer m_SelectedImageNode;
	- std::vector< mitk::DataNode::Pointer > m_SelectedBundles;
	- std::vector< mitk::DataNode::Pointer > m_SelectedBundles2;
	- std::vector< mitk::DataNode::Pointer > m_SelectedFiducials;
	- std::vector< mitk::DataNode::Pointer > m_SelectedImages;
	-
	- QString m_ParameterFile; ///< parameter file name
	- FiberfoxParameters m_Parameters;
	-};
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberGenerationViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberGenerationViewControls.ui
	deleted file mode 100644
	index 29f96f5379..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberGenerationViewControls.ui
	+++ /dev/null
	@@ -1,2012 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<ui version="4.0">
	- <class>QmitkFiberGenerationViewControls</class>
	- <widget class="QWidget" name="QmitkFiberGenerationViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>413</width>
	- <height>1461</height>
	- </rect>
	- </property>
	- <property name="windowTitle">
	- <string>Form</string>
	- </property>
	- <property name="styleSheet">
	- <string notr="true"/>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_2">
	- <item row="6" column="0">
	- <widget class="QCommandLinkButton" name="m_SaveParametersButton">
	- <property name="styleSheet">
	- <string notr="true"/>
	- </property>
	- <property name="text">
	- <string>Save Parameters</string>
	- </property>
	- <property name="icon">
	- <iconset>
	- <normaloff>:/QmitkDiffusionImaging/general_icons/download.ico</normaloff>:/QmitkDiffusionImaging/general_icons/download.ico</iconset>
	- </property>
	- </widget>
	- </item>
	- <item row="7" column="0">
	- <widget class="QCommandLinkButton" name="m_LoadParametersButton">
	- <property name="styleSheet">
	- <string notr="true"/>
	- </property>
	- <property name="text">
	- <string>Load Parameters</string>
	- </property>
	- <property name="icon">
	- <iconset>
	- <normaloff>:/QmitkDiffusionImaging/general_icons/upload.ico</normaloff>:/QmitkDiffusionImaging/general_icons/upload.ico</iconset>
	- </property>
	- </widget>
	- </item>
	- <item row="8" column="0">
	- <spacer name="verticalSpacer">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="0" column="0" rowspan="3">
	- <widget class="QToolBox" name="toolBox">
	- <property name="currentIndex">
	- <number>0</number>
	- </property>
	- <widget class="QWidget" name="page">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>381</width>
	- <height>731</height>
	- </rect>
	- </property>
	- <attribute name="label">
	- <string>Manual Fiber Design</string>
	- </attribute>
	- <layout class="QGridLayout" name="gridLayout">
	- <item row="1" column="0">
	- <widget class="QFrame" name="frame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_3">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QPushButton" name="m_CircleButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="maximumSize">
	- <size>
	- <width>30</width>
	- <height>30</height>
	- </size>
	- </property>
	- <property name="toolTip">
	- <string>Draw elliptical fiducial.</string>
	- </property>
	- <property name="text">
	- <string/>
	- </property>
	- <property name="icon">
	- <iconset resource="../../resources/QmitkFiberfox.qrc">
	- <normaloff>:/QmitkFiberfox/circle.png</normaloff>:/QmitkFiberfox/circle.png</iconset>
	- </property>
	- <property name="iconSize">
	- <size>
	- <width>32</width>
	- <height>32</height>
	- </size>
	- </property>
	- <property name="checkable">
	- <bool>false</bool>
	- </property>
	- <property name="flat">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QPushButton" name="m_FlipButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="maximumSize">
	- <size>
	- <width>30</width>
	- <height>30</height>
	- </size>
	- </property>
	- <property name="toolTip">
	- <string>Flip fiber waypoints of selcted fiducial around one axis.</string>
	- </property>
	- <property name="text">
	- <string/>
	- </property>
	- <property name="icon">
	- <iconset resource="../../resources/QmitkFiberfox.qrc">
	- <normaloff>:/QmitkFiberfox/refresh.xpm</normaloff>:/QmitkFiberfox/refresh.xpm</iconset>
	- </property>
	- <property name="iconSize">
	- <size>
	- <width>32</width>
	- <height>32</height>
	- </size>
	- </property>
	- <property name="checkable">
	- <bool>false</bool>
	- </property>
	- <property name="flat">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="2">
	- <spacer name="horizontalSpacer">
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>40</width>
	- <height>20</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_FiberGenMessage">
	- <property name="styleSheet">
	- <string notr="true">color: rgb(255, 0, 0);</string>
	- </property>
	- <property name="text">
	- <string>Please select an image or an existing fiber bundle to draw the fiber fiducials. If you can't provide a suitable image, generate one using the Fiberfox View.</string>
	- </property>
	- <property name="textFormat">
	- <enum>Qt::AutoText</enum>
	- </property>
	- <property name="alignment">
	- <set>Qt::AlignJustify\|Qt::AlignVCenter</set>
	- </property>
	- <property name="wordWrap">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QGroupBox" name="groupBox_8">
	- <property name="styleSheet">
	- <string notr="true">QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <property name="title">
	- <string>Fiber Options </string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_15">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="2" column="0">
	- <widget class="QFrame" name="frame_5">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_9">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="2" column="0">
	- <widget class="QFrame" name="m_AdvancedFiberOptionsFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_21">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_5">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Tension:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_8">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Fiber Sampling:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QDoubleSpinBox" name="m_TensionBox">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="decimals">
	- <number>3</number>
	- </property>
	- <property name="minimum">
	- <double>-1.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="1">
	- <widget class="QDoubleSpinBox" name="m_BiasBox">
	- <property name="decimals">
	- <number>3</number>
	- </property>
	- <property name="minimum">
	- <double>-1.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_7">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Bias:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_6">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Continuity:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QDoubleSpinBox" name="m_ContinuityBox">
	- <property name="decimals">
	- <number>3</number>
	- </property>
	- <property name="minimum">
	- <double>-1.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QDoubleSpinBox" name="m_FiberSamplingBox">
	- <property name="toolTip">
	- <string>Distance of fiber sampling points (in mm)</string>
	- </property>
	- <property name="decimals">
	- <number>1</number>
	- </property>
	- <property name="minimum">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>1.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QFrame" name="frame_2">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_25">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="verticalSpacing">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_4">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>#Fibers:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_FiberDensityBox">
	- <property name="toolTip">
	- <string>Specify number of fibers to generate for the selected bundle.</string>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>1000000</number>
	- </property>
	- <property name="singleStep">
	- <number>100</number>
	- </property>
	- <property name="value">
	- <number>100</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QCommandLinkButton" name="m_GenerateFibersButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="styleSheet">
	- <string notr="true">QCommandLinkButton:disabled {
	- border: none;
	-}</string>
	- </property>
	- <property name="text">
	- <string>Generate Fibers</string>
	- </property>
	- <property name="icon">
	- <iconset>
	- <normaloff>:/QmitkDiffusionImaging/general_icons/right.ico</normaloff>:/QmitkDiffusionImaging/general_icons/right.ico</iconset>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QFrame" name="frame_3">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_5">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="1">
	- <widget class="QComboBox" name="m_DistributionBox">
	- <property name="toolTip">
	- <string>Select fiber distribution inside of the fiducials.</string>
	- </property>
	- <item>
	- <property name="text">
	- <string>Uniform</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Gaussian</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_9">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Fiber Distribution:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="2">
	- <widget class="QDoubleSpinBox" name="m_VarianceBox">
	- <property name="toolTip">
	- <string>Variance of the gaussian</string>
	- </property>
	- <property name="decimals">
	- <number>3</number>
	- </property>
	- <property name="minimum">
	- <double>0.001000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>10.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.010000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.100000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QFrame" name="frame_8">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_22">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QCheckBox" name="m_RealTimeFibers">
	- <property name="toolTip">
	- <string>Disable to only generate fibers if "Generate Fibers" button is pressed.</string>
	- </property>
	- <property name="text">
	- <string>Real Time Fibers</string>
	- </property>
	- <property name="checked">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QCheckBox" name="m_AdvancedOptionsBox">
	- <property name="toolTip">
	- <string>Disable to only generate fibers if "Generate Fibers" button is pressed.</string>
	- </property>
	- <property name="text">
	- <string>Advanced Options</string>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QGroupBox" name="groupBox_7">
	- <property name="styleSheet">
	- <string notr="true">QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <property name="title">
	- <string>Fiducial Options</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_16">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="2" column="0">
	- <widget class="QGroupBox" name="m_FiducialAttributeBox">
	- <property name="title">
	- <string>Fiducial Attributes</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_4">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="4" column="1">
	- <widget class="QDoubleSpinBox" name="m_FidAxis2">
	- <property name="toolTip">
	- <string>Length of fiducial axis 2</string>
	- </property>
	- <property name="decimals">
	- <number>2</number>
	- </property>
	- <property name="minimum">
	- <double>0.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>9999.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QLabel" name="label_31">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Axis 1:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_26">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Position X:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QDoubleSpinBox" name="m_FidPosX">
	- <property name="toolTip">
	- <string>World Position in mm</string>
	- </property>
	- <property name="decimals">
	- <number>2</number>
	- </property>
	- <property name="minimum">
	- <double>-99999.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>99999.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QDoubleSpinBox" name="m_FidPosZ">
	- <property name="toolTip">
	- <string>World Position in mm</string>
	- </property>
	- <property name="decimals">
	- <number>2</number>
	- </property>
	- <property name="minimum">
	- <double>-360.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>360.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QDoubleSpinBox" name="m_FidPosY">
	- <property name="toolTip">
	- <string>World Position in mm</string>
	- </property>
	- <property name="decimals">
	- <number>2</number>
	- </property>
	- <property name="minimum">
	- <double>-360.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>360.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="1">
	- <widget class="QDoubleSpinBox" name="m_FidAxis1">
	- <property name="toolTip">
	- <string>Length of fiducial axis 1</string>
	- </property>
	- <property name="decimals">
	- <number>2</number>
	- </property>
	- <property name="minimum">
	- <double>0.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>9999.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label_30">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Position Z:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_27">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Position Y:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QLabel" name="label_32">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Axis 2:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <widget class="QLabel" name="label_33">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Twist:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="1">
	- <widget class="QDoubleSpinBox" name="m_FidTwist">
	- <property name="toolTip">
	- <string>Twist in degree</string>
	- </property>
	- <property name="decimals">
	- <number>2</number>
	- </property>
	- <property name="minimum">
	- <double>-180.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>180.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QCheckBox" name="m_ConstantRadiusBox">
	- <property name="toolTip">
	- <string>All fiducials are treated as circles with the same radius as the first fiducial.</string>
	- </property>
	- <property name="text">
	- <string>Use Constant Fiducial Radius</string>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QCommandLinkButton" name="m_AlignOnGrid">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string>Align selected fiducials with voxel grid. Shifts selected fiducials to nearest voxel center.</string>
	- </property>
	- <property name="styleSheet">
	- <string notr="true">QCommandLinkButton:disabled {
	- border: none;
	-}</string>
	- </property>
	- <property name="text">
	- <string>Align With Grid</string>
	- </property>
	- <property name="icon">
	- <iconset>
	- <normaloff>:/QmitkDiffusionImaging/general_icons/right.ico</normaloff>:/QmitkDiffusionImaging/general_icons/right.ico</iconset>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <widget class="QWidget" name="page_2">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>395</width>
	- <height>277</height>
	- </rect>
	- </property>
	- <attribute name="label">
	- <string>Random Phantom</string>
	- </attribute>
	- <layout class="QGridLayout" name="gridLayout_17">
	- <item row="7" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_15">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Volume Size:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_12">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Curvyness:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="1">
	- <widget class="QFrame" name="frame_12">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_14">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_MaxTwistBox">
	- <property name="toolTip">
	- <string>Specify number of fibers to generate for the selected bundle.</string>
	- </property>
	- <property name="minimum">
	- <number>0</number>
	- </property>
	- <property name="maximum">
	- <number>90</number>
	- </property>
	- <property name="singleStep">
	- <number>10</number>
	- </property>
	- <property name="value">
	- <number>30</number>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QSpinBox" name="m_MinTwistBox">
	- <property name="toolTip">
	- <string>Specify number of fibers to generate for the selected bundle.</string>
	- </property>
	- <property name="minimum">
	- <number>0</number>
	- </property>
	- <property name="maximum">
	- <number>90</number>
	- </property>
	- <property name="singleStep">
	- <number>10</number>
	- </property>
	- <property name="value">
	- <number>15</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="6" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_14">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Step Size:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="6" column="1">
	- <widget class="QFrame" name="frame_9">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_8">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QSpinBox" name="m_StepSizeMinBox">
	- <property name="toolTip">
	- <string>Specify number of fibers to generate for the selected bundle.</string>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>100</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>15</number>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_StepSizeMaxBox">
	- <property name="toolTip">
	- <string>Specify number of fibers to generate for the selected bundle.</string>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>100</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>30</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_11">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Streamline Density:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QSpinBox" name="m_NumBundlesBox">
	- <property name="toolTip">
	- <string>Specify number of fibers to generate for the selected bundle.</string>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>1000</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>50</number>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_13">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Start Radii:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="1">
	- <widget class="QFrame" name="frame_6">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_6">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QSpinBox" name="m_CurvyMinBox">
	- <property name="toolTip">
	- <string>Specify number of fibers to generate for the selected bundle.</string>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>90</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>5</number>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_CurvyMaxBox">
	- <property name="toolTip">
	- <string>Specify number of fibers to generate for the selected bundle.</string>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>90</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>45</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="7" column="1">
	- <widget class="QFrame" name="frame_10">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_10">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_VolumeSizeY">
	- <property name="toolTip">
	- <string>Specify number of fibers to generate for the selected bundle.</string>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>1000</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>250</number>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QSpinBox" name="m_VolumeSizeX">
	- <property name="toolTip">
	- <string>Specify number of fibers to generate for the selected bundle.</string>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>1000</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>250</number>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="2">
	- <widget class="QSpinBox" name="m_VolumeSizeZ">
	- <property name="toolTip">
	- <string>Specify number of fibers to generate for the selected bundle.</string>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>1000</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>250</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_16">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Twist:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_10">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>#Bundles:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="1">
	- <widget class="QFrame" name="frame_7">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_7">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QSpinBox" name="m_SizeMinBox">
	- <property name="toolTip">
	- <string>Specify number of fibers to generate for the selected bundle.</string>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>300</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>5</number>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_SizeMaxBox">
	- <property name="toolTip">
	- <string>Specify number of fibers to generate for the selected bundle.</string>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>300</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>25</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QFrame" name="frame_11">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_13">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_MaxDensityBox">
	- <property name="toolTip">
	- <string>Specify number of fibers to generate for the selected bundle.</string>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>10000</number>
	- </property>
	- <property name="singleStep">
	- <number>10</number>
	- </property>
	- <property name="value">
	- <number>200</number>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QSpinBox" name="m_MinDensityBox">
	- <property name="toolTip">
	- <string>Specify number of fibers to generate for the selected bundle.</string>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>10000</number>
	- </property>
	- <property name="singleStep">
	- <number>10</number>
	- </property>
	- <property name="value">
	- <number>50</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="8" column="0">
	- <widget class="QCommandLinkButton" name="m_RandomPhantomButton">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="styleSheet">
	- <string notr="true">QCommandLinkButton:disabled {
	- border: none;
	-}</string>
	- </property>
	- <property name="text">
	- <string>Generate</string>
	- </property>
	- <property name="icon">
	- <iconset>
	- <normaloff>:/QmitkDiffusionImaging/general_icons/right.ico</normaloff>:/QmitkDiffusionImaging/general_icons/right.ico</iconset>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <widget class="QWidget" name="page_3">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>395</width>
	- <height>283</height>
	- </rect>
	- </property>
	- <attribute name="label">
	- <string>Operations</string>
	- </attribute>
	- <layout class="QGridLayout" name="gridLayout_18">
	- <item row="0" column="0">
	- <widget class="QFrame" name="frame_4">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_12">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="1" column="2">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_18">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Y</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QDoubleSpinBox" name="m_XrotBox">
	- <property name="toolTip">
	- <string>Rotation angle (in degree) around x-axis.</string>
	- </property>
	- <property name="decimals">
	- <number>2</number>
	- </property>
	- <property name="minimum">
	- <double>-360.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>360.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_22">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Axis:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="2">
	- <widget class="QDoubleSpinBox" name="m_YrotBox">
	- <property name="toolTip">
	- <string>Rotation angle (in degree) around y-axis.</string>
	- </property>
	- <property name="decimals">
	- <number>2</number>
	- </property>
	- <property name="minimum">
	- <double>-360.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>360.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_21">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Translation:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="3">
	- <widget class="QDoubleSpinBox" name="m_ZtransBox">
	- <property name="toolTip">
	- <string>Translation (in mm) in direction of the z-axis.</string>
	- </property>
	- <property name="decimals">
	- <number>2</number>
	- </property>
	- <property name="minimum">
	- <double>-1000.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>1000.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="2">
	- <widget class="QDoubleSpinBox" name="m_YtransBox">
	- <property name="toolTip">
	- <string>Translation (in mm) in direction of the y-axis.</string>
	- </property>
	- <property name="decimals">
	- <number>2</number>
	- </property>
	- <property name="minimum">
	- <double>-1000.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>1000.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_17">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>X</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_20">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Rotation:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="3">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_19">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Z</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="3">
	- <widget class="QDoubleSpinBox" name="m_ZrotBox">
	- <property name="toolTip">
	- <string>Rotation angle (in degree) around z-axis.</string>
	- </property>
	- <property name="decimals">
	- <number>2</number>
	- </property>
	- <property name="minimum">
	- <double>-360.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>360.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="1">
	- <widget class="QDoubleSpinBox" name="m_XtransBox">
	- <property name="toolTip">
	- <string>Translation (in mm) in direction of the x-axis.</string>
	- </property>
	- <property name="decimals">
	- <number>2</number>
	- </property>
	- <property name="minimum">
	- <double>-1000.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>1000.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_24">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Scaling:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="1">
	- <widget class="QDoubleSpinBox" name="m_XscaleBox">
	- <property name="toolTip">
	- <string>Scaling factor for selected fiber bundle along the x-axis.</string>
	- </property>
	- <property name="minimum">
	- <double>0.010000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>10.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.010000000000000</double>
	- </property>
	- <property name="value">
	- <double>1.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="2">
	- <widget class="QDoubleSpinBox" name="m_YscaleBox">
	- <property name="toolTip">
	- <string>Scaling factor for selected fiber bundle along the y-axis.</string>
	- </property>
	- <property name="minimum">
	- <double>0.010000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>10.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.010000000000000</double>
	- </property>
	- <property name="value">
	- <double>1.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="3">
	- <widget class="QDoubleSpinBox" name="m_ZscaleBox">
	- <property name="toolTip">
	- <string>Scaling factor for selected fiber bundle along the z-axis.</string>
	- </property>
	- <property name="minimum">
	- <double>0.010000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>10.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.010000000000000</double>
	- </property>
	- <property name="value">
	- <double>1.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QCommandLinkButton" name="m_CopyBundlesButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="styleSheet">
	- <string notr="true">QCommandLinkButton:disabled {
	- border: none;
	-}</string>
	- </property>
	- <property name="text">
	- <string>Copy Bundles</string>
	- </property>
	- <property name="icon">
	- <iconset>
	- <normaloff>:/QmitkDiffusionImaging/general_icons/copy2.ico</normaloff>:/QmitkDiffusionImaging/general_icons/copy2.ico</iconset>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QCommandLinkButton" name="m_TransformBundlesButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="styleSheet">
	- <string notr="true">QCommandLinkButton:disabled {
	- border: none;
	-}</string>
	- </property>
	- <property name="text">
	- <string>Transform Selection</string>
	- </property>
	- <property name="icon">
	- <iconset>
	- <normaloff>:/QmitkDiffusionImaging/general_icons/refresh.ico</normaloff>:/QmitkDiffusionImaging/general_icons/refresh.ico</iconset>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QCommandLinkButton" name="m_JoinBundlesButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="styleSheet">
	- <string notr="true">QCommandLinkButton:disabled {
	- border: none;
	-}</string>
	- </property>
	- <property name="text">
	- <string>Join Bundles</string>
	- </property>
	- <property name="icon">
	- <iconset>
	- <normaloff>:/QmitkDiffusionImaging/general_icons/plus.ico</normaloff>:/QmitkDiffusionImaging/general_icons/plus.ico</iconset>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QCheckBox" name="m_IncludeFiducials">
	- <property name="toolTip">
	- <string>If checked, the fiducials belonging to the modified bundle are also modified.</string>
	- </property>
	- <property name="text">
	- <string>Include Fiducials</string>
	- </property>
	- <property name="checked">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <tabstops>
	- <tabstop>m_CircleButton</tabstop>
	- <tabstop>m_FlipButton</tabstop>
	- <tabstop>m_RealTimeFibers</tabstop>
	- <tabstop>m_AdvancedOptionsBox</tabstop>
	- <tabstop>m_DistributionBox</tabstop>
	- <tabstop>m_VarianceBox</tabstop>
	- <tabstop>m_FiberDensityBox</tabstop>
	- <tabstop>m_FiberSamplingBox</tabstop>
	- <tabstop>m_TensionBox</tabstop>
	- <tabstop>m_ContinuityBox</tabstop>
	- <tabstop>m_BiasBox</tabstop>
	- <tabstop>m_GenerateFibersButton</tabstop>
	- <tabstop>m_ConstantRadiusBox</tabstop>
	- <tabstop>m_NumBundlesBox</tabstop>
	- <tabstop>m_MinDensityBox</tabstop>
	- <tabstop>m_MaxDensityBox</tabstop>
	- <tabstop>m_MinTwistBox</tabstop>
	- <tabstop>m_MaxTwistBox</tabstop>
	- <tabstop>m_CurvyMinBox</tabstop>
	- <tabstop>m_CurvyMaxBox</tabstop>
	- <tabstop>m_SizeMinBox</tabstop>
	- <tabstop>m_SizeMaxBox</tabstop>
	- <tabstop>m_StepSizeMinBox</tabstop>
	- <tabstop>m_StepSizeMaxBox</tabstop>
	- <tabstop>m_VolumeSizeX</tabstop>
	- <tabstop>m_VolumeSizeY</tabstop>
	- <tabstop>m_VolumeSizeZ</tabstop>
	- <tabstop>m_RandomPhantomButton</tabstop>
	- <tabstop>m_XrotBox</tabstop>
	- <tabstop>m_YrotBox</tabstop>
	- <tabstop>m_ZrotBox</tabstop>
	- <tabstop>m_XtransBox</tabstop>
	- <tabstop>m_YtransBox</tabstop>
	- <tabstop>m_ZtransBox</tabstop>
	- <tabstop>m_XscaleBox</tabstop>
	- <tabstop>m_YscaleBox</tabstop>
	- <tabstop>m_ZscaleBox</tabstop>
	- <tabstop>m_TransformBundlesButton</tabstop>
	- <tabstop>m_CopyBundlesButton</tabstop>
	- <tabstop>m_JoinBundlesButton</tabstop>
	- <tabstop>m_IncludeFiducials</tabstop>
	- <tabstop>m_SaveParametersButton</tabstop>
	- <tabstop>m_LoadParametersButton</tabstop>
	- <tabstop>m_FidAxis1</tabstop>
	- <tabstop>m_FidPosY</tabstop>
	- <tabstop>m_FidPosZ</tabstop>
	- <tabstop>m_FidAxis2</tabstop>
	- <tabstop>m_FidTwist</tabstop>
	- <tabstop>m_AlignOnGrid</tabstop>
	- <tabstop>m_FidPosX</tabstop>
	- </tabstops>
	- <resources>
	- <include location="../../resources/QmitkFiberfox.qrc"/>
	- </resources>
	- <connections/>
	-</ui>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxView.cpp
	deleted file mode 100644
	index be3ad8ad0a..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxView.cpp
	+++ /dev/null
	@@ -1,2181 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-// Blueberry
	-#include <berryISelectionService.h>
	-#include <berryIWorkbenchWindow.h>
	-
	-// Qmitk
	-#include "QmitkFiberfoxView.h"
	-
	-// MITK
	-#include <mitkImage.h>
	-#include <mitkImageToItk.h>
	-#include <mitkImageCast.h>
	-#include <mitkProperties.h>
	-#include <mitkPlanarFigureInteractor.h>
	-#include <mitkDataStorage.h>
	-#include <itkTractsToDWIImageFilter.h>
	-#include <mitkTensorImage.h>
	-#include <mitkILinkedRenderWindowPart.h>
	-#include <mitkImageToItk.h>
	-#include <mitkImageCast.h>
	-#include <mitkImageGenerator.h>
	-#include <mitkNodePredicateDataType.h>
	-#include <itkScalableAffineTransform.h>
	-#include <mitkLevelWindowProperty.h>
	-#include <mitkNodePredicateOr.h>
	-#include <mitkNodePredicateAnd.h>
	-#include <mitkNodePredicateNot.h>
	-#include <mitkNodePredicateProperty.h>
	-#include <mitkNodePredicateIsDWI.h>
	-#include <boost/property_tree/ptree.hpp>
	-#define RAPIDXML_NO_EXCEPTIONS
	-#include <boost/property_tree/xml_parser.hpp>
	-#include <boost/foreach.hpp>
	-#include <QFileDialog>
	-#include <QMessageBox>
	-#include "usModuleRegistry.h"
	-#include <mitkChiSquareNoiseModel.h>
	-#include <itksys/SystemTools.hxx>
	-#include <mitkIOUtil.h>
	-#include <QScrollBar>
	-#include <itkInvertIntensityImageFilter.h>
	-#include <QDialogButtonBox>
	-#include <itkAdcImageFilter.h>
	-#include <itkShiftScaleImageFilter.h>
	-#include <mitkITKImageImport.h>
	-
	-#include "mitkNodePredicateDataType.h"
	-#include <mitkNodePredicateProperty.h>
	-#include <mitkNodePredicateAnd.h>
	-#include <mitkNodePredicateNot.h>
	-#include <mitkNodePredicateOr.h>
	-
	-QmitkFiberfoxWorker::QmitkFiberfoxWorker(QmitkFiberfoxView* view)
	- : m_View(view)
	-{
	-
	-}
	-
	-void QmitkFiberfoxWorker::run()
	-{
	- try{
	- m_View->m_TractsToDwiFilter->Update();
	- }
	- catch( ... )
	- {
	-
	- }
	- m_View->m_Thread.quit();
	-}
	-
	-const std::string QmitkFiberfoxView::VIEW_ID = "org.mitk.views.fiberfoxview";
	-
	-QmitkFiberfoxView::QmitkFiberfoxView()
	- : QmitkAbstractView()
	- , m_Controls( 0 )
	- , m_SelectedImageNode( nullptr )
	- , m_Worker(this)
	- , m_ThreadIsRunning(false)
	-{
	- m_Worker.moveToThread(&m_Thread);
	- connect(&m_Thread, SIGNAL(started()), this, SLOT(BeforeThread()));
	- connect(&m_Thread, SIGNAL(started()), &m_Worker, SLOT(run()));
	- connect(&m_Thread, SIGNAL(finished()), this, SLOT(AfterThread()));
	- // connect(&m_Thread, SIGNAL(terminated()), this, SLOT(AfterThread()));
	- m_SimulationTimer = new QTimer(this);
	-}
	-
	-void QmitkFiberfoxView::KillThread()
	-{
	- MITK_INFO << "Aborting DWI simulation.";
	- m_TractsToDwiFilter->SetAbortGenerateData(true);
	- m_Controls->m_AbortSimulationButton->setEnabled(false);
	- m_Controls->m_AbortSimulationButton->setText("Aborting simulation ...");
	-}
	-
	-void QmitkFiberfoxView::BeforeThread()
	-{
	- m_SimulationTime = QTime::currentTime();
	- m_SimulationTimer->start(100);
	- m_Controls->m_AbortSimulationButton->setVisible(true);
	- m_Controls->m_GenerateImageButton->setVisible(false);
	- m_Controls->m_SimulationStatusText->setVisible(true);
	- m_ThreadIsRunning = true;
	-}
	-
	-void QmitkFiberfoxView::AfterThread()
	-{
	- UpdateSimulationStatus();
	- m_SimulationTimer->stop();
	- m_Controls->m_AbortSimulationButton->setVisible(false);
	- m_Controls->m_AbortSimulationButton->setEnabled(true);
	- m_Controls->m_AbortSimulationButton->setText("Abort simulation");
	- m_Controls->m_GenerateImageButton->setVisible(true);
	- m_ThreadIsRunning = false;
	-
	- QString statusText;
	- FiberfoxParameters parameters;
	- mitk::Image::Pointer mitkImage = mitk::Image::New();
	-
	- statusText = QString(m_TractsToDwiFilter->GetStatusText().c_str());
	- if (m_TractsToDwiFilter->GetAbortGenerateData())
	- {
	- MITK_INFO << "Simulation aborted.";
	- return;
	- }
	-
	- parameters = m_TractsToDwiFilter->GetParameters();
	-
	- mitkImage = mitk::GrabItkImageMemory( m_TractsToDwiFilter->GetOutput() );
	- if (parameters.m_SignalGen.GetNumWeightedVolumes() > 0)
	- {
	- mitk::DiffusionPropertyHelper::SetGradientContainer(mitkImage, parameters.m_SignalGen.GetItkGradientContainer());
	- mitk::DiffusionPropertyHelper::SetReferenceBValue(mitkImage, parameters.m_SignalGen.GetBvalue());
	- mitk::DiffusionPropertyHelper::InitializeImage( mitkImage );
	- }
	- parameters.m_Misc.m_ResultNode->SetData( mitkImage );
	-
	- GetDataStorage()->Add(parameters.m_Misc.m_ResultNode, parameters.m_Misc.m_ParentNode);
	-
	- if (m_Controls->m_VolumeFractionsBox->isChecked())
	- {
	- if (m_TractsToDwiFilter->GetTickImage().IsNotNull())
	- {
	- mitk::Image::Pointer mitkImage = mitk::Image::New();
	- itk::TractsToDWIImageFilter< short >::Float2DImageType::Pointer itkImage = m_TractsToDwiFilter->GetTickImage();
	- mitkImage = mitk::GrabItkImageMemory( itkImage.GetPointer() );
	- mitk::DataNode::Pointer node = mitk::DataNode::New();
	- node->SetData( mitkImage );
	- node->SetName("Tick Image");
	- GetDataStorage()->Add(node, parameters.m_Misc.m_ResultNode);
	- }
	-
	- if (m_TractsToDwiFilter->GetRfImage().IsNotNull())
	- {
	- mitk::Image::Pointer mitkImage = mitk::Image::New();
	- itk::TractsToDWIImageFilter< short >::Float2DImageType::Pointer itkImage = m_TractsToDwiFilter->GetRfImage();
	- mitkImage = mitk::GrabItkImageMemory( itkImage.GetPointer() );
	- mitk::DataNode::Pointer node = mitk::DataNode::New();
	- node->SetData( mitkImage );
	- node->SetName("RF Image");
	- GetDataStorage()->Add(node, parameters.m_Misc.m_ResultNode);
	- }
	-
	- if (m_TractsToDwiFilter->GetPhaseImage().IsNotNull())
	- {
	- mitk::Image::Pointer phaseImage = mitk::Image::New();
	- itk::TractsToDWIImageFilter< short >::DoubleDwiType::Pointer itkPhase = m_TractsToDwiFilter->GetPhaseImage();
	- phaseImage = mitk::GrabItkImageMemory( itkPhase.GetPointer() );
	- mitk::DataNode::Pointer phaseNode = mitk::DataNode::New();
	- phaseNode->SetData( phaseImage );
	- phaseNode->SetName("Phase Image");
	- GetDataStorage()->Add(phaseNode, parameters.m_Misc.m_ResultNode);
	- }
	-
	- if (m_TractsToDwiFilter->GetKspaceImage().IsNotNull())
	- {
	- mitk::Image::Pointer image = mitk::Image::New();
	- itk::TractsToDWIImageFilter< short >::DoubleDwiType::Pointer itkImage = m_TractsToDwiFilter->GetKspaceImage();
	- image = mitk::GrabItkImageMemory( itkImage.GetPointer() );
	- mitk::DataNode::Pointer node = mitk::DataNode::New();
	- node->SetData( image );
	- node->SetName("k-Space");
	- GetDataStorage()->Add(node, parameters.m_Misc.m_ResultNode);
	- }
	-
	- {
	- mitk::DataNode::Pointer node = mitk::DataNode::New();
	- node->SetData(m_TractsToDwiFilter->GetCoilPointset());
	- node->SetName("Coil Positions");
	- node->SetProperty("pointsize", mitk::FloatProperty::New(parameters.m_SignalGen.m_ImageSpacing[0]/4));
	- node->SetProperty("color", mitk::ColorProperty::New(0, 1, 0));
	- GetDataStorage()->Add(node, parameters.m_Misc.m_ResultNode);
	- }
	-
	- int c = 1;
	- std::vector< itk::TractsToDWIImageFilter< short >::DoubleDwiType::Pointer > output_real = m_TractsToDwiFilter->GetOutputImagesReal();
	- for (auto real : output_real)
	- {
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk(real.GetPointer());
	- image->SetVolume(real->GetBufferPointer());
	-
	- mitk::DataNode::Pointer node = mitk::DataNode::New();
	- node->SetData( image );
	- node->SetName("Coil-"+QString::number(c).toStdString()+"-real");
	- GetDataStorage()->Add(node, parameters.m_Misc.m_ResultNode);
	- ++c;
	- }
	-
	- c = 1;
	- std::vector< itk::TractsToDWIImageFilter< short >::DoubleDwiType::Pointer > output_imag = m_TractsToDwiFilter->GetOutputImagesImag();
	- for (auto imag : output_imag)
	- {
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk(imag.GetPointer());
	- image->SetVolume(imag->GetBufferPointer());
	-
	- mitk::DataNode::Pointer node = mitk::DataNode::New();
	- node->SetData( image );
	- node->SetName("Coil-"+QString::number(c).toStdString()+"-imag");
	- GetDataStorage()->Add(node, parameters.m_Misc.m_ResultNode);
	- ++c;
	- }
	-
	- std::vector< itk::TractsToDWIImageFilter< short >::ItkDoubleImgType::Pointer > volumeFractions = m_TractsToDwiFilter->GetVolumeFractions();
	- for (unsigned int k=0; k<volumeFractions.size(); k++)
	- {
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk(volumeFractions.at(k).GetPointer());
	- image->SetVolume(volumeFractions.at(k)->GetBufferPointer());
	-
	- mitk::DataNode::Pointer node = mitk::DataNode::New();
	- node->SetData( image );
	- node->SetName("CompartmentVolume-"+QString::number(k).toStdString());
	- GetDataStorage()->Add(node, parameters.m_Misc.m_ResultNode);
	- }
	- }
	- m_TractsToDwiFilter = nullptr;
	-
	- if (parameters.m_Misc.m_AfterSimulationMessage.size()>0)
	- QMessageBox::information( nullptr, "Warning", parameters.m_Misc.m_AfterSimulationMessage.c_str());
	-
	- mitk::BaseData::Pointer basedata = parameters.m_Misc.m_ResultNode->GetData();
	- if (basedata.IsNotNull())
	- {
	- mitk::RenderingManager::GetInstance()->InitializeViews(
	- basedata->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true );
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- }
	-
	- if (!parameters.m_Misc.m_OutputPath.empty())
	- {
	- try{
	- QString outputFileName(parameters.m_Misc.m_OutputPath.c_str());
	- outputFileName += parameters.m_Misc.m_ResultNode->GetName().c_str();
	- outputFileName.replace(QString("."), QString("_"));
	- SaveParameters(outputFileName+".ffp");
	- outputFileName += ".dwi";
	- QString status("Saving output image to ");
	- status += outputFileName;
	- m_Controls->m_SimulationStatusText->append(status);
	- mitk::IOUtil::Save(mitkImage, outputFileName.toStdString());
	- m_Controls->m_SimulationStatusText->append("File saved successfully.");
	-
	- }
	- catch (itk::ExceptionObject &e)
	- {
	- QString status("Exception during DWI writing: ");
	- status += e.GetDescription();
	- m_Controls->m_SimulationStatusText->append(status);
	- }
	- catch (...)
	- {
	- m_Controls->m_SimulationStatusText->append("Unknown exception during DWI writing!");
	- }
	- }
	- parameters.m_SignalGen.m_FrequencyMap = nullptr;
	-}
	-
	-void QmitkFiberfoxView::UpdateSimulationStatus()
	-{
	- QString statusText = QString(m_TractsToDwiFilter->GetStatusText().c_str());
	-
	- if (QString::compare(m_SimulationStatusText,statusText)!=0)
	- {
	- m_Controls->m_SimulationStatusText->clear();
	- m_Controls->m_SimulationStatusText->setText(statusText);
	- QScrollBar *vScrollBar = m_Controls->m_SimulationStatusText->verticalScrollBar();
	- vScrollBar->triggerAction(QScrollBar::SliderToMaximum);
	- }
	-}
	-
	-// Destructor
	-QmitkFiberfoxView::~QmitkFiberfoxView()
	-{
	- delete m_SimulationTimer;
	-}
	-
	-void QmitkFiberfoxView::CreateQtPartControl( QWidget *parent )
	-{
	- // build up qt view, unless already done
	- if ( !m_Controls )
	- {
	- // create GUI widgets from the Qt Designer's .ui file
	- m_Controls = new Ui::QmitkFiberfoxViewControls;
	- m_Controls->setupUi( parent );
	-
	- m_Controls->m_StickWidget1->setVisible(true);
	- m_Controls->m_StickWidget2->setVisible(false);
	- m_Controls->m_ZeppelinWidget1->setVisible(false);
	- m_Controls->m_ZeppelinWidget2->setVisible(false);
	- m_Controls->m_TensorWidget1->setVisible(false);
	- m_Controls->m_TensorWidget2->setVisible(false);
	-
	- m_Controls->m_BallWidget1->setVisible(true);
	- m_Controls->m_BallWidget2->setVisible(false);
	- m_Controls->m_BallWidget2->SetT1(4658);
	- m_Controls->m_BallWidget2->SetT2(2200);
	- m_Controls->m_AstrosticksWidget1->setVisible(false);
	- m_Controls->m_AstrosticksWidget2->setVisible(false);
	- m_Controls->m_AstrosticksWidget2->SetT1(4658);
	- m_Controls->m_AstrosticksWidget2->SetT2(2200);
	- m_Controls->m_DotWidget1->setVisible(false);
	- m_Controls->m_DotWidget2->setVisible(false);
	- m_Controls->m_DotWidget2->SetT1(4658);
	- m_Controls->m_DotWidget2->SetT2(2200);
	-
	- m_Controls->m_PrototypeWidget1->setVisible(false);
	- m_Controls->m_PrototypeWidget2->setVisible(false);
	- m_Controls->m_PrototypeWidget3->setVisible(false);
	- m_Controls->m_PrototypeWidget4->setVisible(false);
	-
	- m_Controls->m_PrototypeWidget3->SetMinFa(0.0);
	- m_Controls->m_PrototypeWidget3->SetMaxFa(0.15);
	- m_Controls->m_PrototypeWidget4->SetMinFa(0.0);
	- m_Controls->m_PrototypeWidget4->SetMaxFa(0.15);
	- m_Controls->m_PrototypeWidget3->SetMinAdc(0.0);
	- m_Controls->m_PrototypeWidget3->SetMaxAdc(0.001);
	- m_Controls->m_PrototypeWidget4->SetMinAdc(0.003);
	- m_Controls->m_PrototypeWidget4->SetMaxAdc(0.004);
	-
	- m_Controls->m_Comp2FractionFrame->setVisible(false);
	- m_Controls->m_Comp4FractionFrame->setVisible(false);
	- m_Controls->m_DiffusionPropsMessage->setVisible(false);
	- m_Controls->m_GeometryMessage->setVisible(false);
	- m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false);
	- m_Controls->m_NoiseFrame->setVisible(false);
	- m_Controls->m_ZeroRinging->setVisible(false);
	- m_Controls->m_GhostFrame->setVisible(false);
	- m_Controls->m_DistortionsFrame->setVisible(false);
	- m_Controls->m_EddyFrame->setVisible(false);
	- m_Controls->m_SpikeFrame->setVisible(false);
	- m_Controls->m_AliasingFrame->setVisible(false);
	- m_Controls->m_MotionArtifactFrame->setVisible(false);
	- m_Controls->m_DriftFrame->setVisible(false);
	- m_ParameterFile = QDir::currentPath()+"/param.ffp";
	-
	- m_Controls->m_AbortSimulationButton->setVisible(false);
	- m_Controls->m_SimulationStatusText->setVisible(false);
	-
	- m_Controls->m_FrequencyMapBox->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_Comp1VolumeFraction->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_Comp2VolumeFraction->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_Comp3VolumeFraction->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_Comp4VolumeFraction->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_MaskComboBox->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_TemplateComboBox->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_FiberBundleComboBox->SetDataStorage(this->GetDataStorage());
	-
	- mitk::TNodePredicateDataType<mitk::FiberBundle>::Pointer isFiberBundle = mitk::TNodePredicateDataType<mitk::FiberBundle>::New();
	- mitk::TNodePredicateDataType<mitk::Image>::Pointer isMitkImage = mitk::TNodePredicateDataType<mitk::Image>::New();
	- mitk::NodePredicateIsDWI::Pointer isDwi = mitk::NodePredicateIsDWI::New( );
	- mitk::NodePredicateDataType::Pointer isDti = mitk::NodePredicateDataType::New("TensorImage");
	- mitk::NodePredicateDataType::Pointer isOdf = mitk::NodePredicateDataType::New("Odfmage");
	- mitk::NodePredicateOr::Pointer isDiffusionImage = mitk::NodePredicateOr::New(isDwi, isDti);
	- isDiffusionImage = mitk::NodePredicateOr::New(isDiffusionImage, isOdf);
	- mitk::NodePredicateNot::Pointer noDiffusionImage = mitk::NodePredicateNot::New(isDiffusionImage);
	- mitk::NodePredicateAnd::Pointer isNonDiffMitkImage = mitk::NodePredicateAnd::New(isMitkImage, noDiffusionImage);
	- mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true));
	- mitk::NodePredicateAnd::Pointer isBinaryMitkImage = mitk::NodePredicateAnd::New( isNonDiffMitkImage, isBinaryPredicate );
	-
	- m_Controls->m_FrequencyMapBox->SetPredicate(isNonDiffMitkImage);
	- m_Controls->m_Comp1VolumeFraction->SetPredicate(isNonDiffMitkImage);
	- m_Controls->m_Comp1VolumeFraction->SetZeroEntryText("--");
	- m_Controls->m_Comp2VolumeFraction->SetPredicate(isNonDiffMitkImage);
	- m_Controls->m_Comp2VolumeFraction->SetZeroEntryText("--");
	- m_Controls->m_Comp3VolumeFraction->SetPredicate(isNonDiffMitkImage);
	- m_Controls->m_Comp3VolumeFraction->SetZeroEntryText("--");
	- m_Controls->m_Comp4VolumeFraction->SetPredicate(isNonDiffMitkImage);
	- m_Controls->m_Comp4VolumeFraction->SetZeroEntryText("--");
	- m_Controls->m_MaskComboBox->SetPredicate(isBinaryMitkImage);
	- m_Controls->m_MaskComboBox->SetZeroEntryText("--");
	- m_Controls->m_TemplateComboBox->SetPredicate(isMitkImage);
	- m_Controls->m_TemplateComboBox->SetZeroEntryText("--");
	- m_Controls->m_FiberBundleComboBox->SetPredicate(isFiberBundle);
	- m_Controls->m_FiberBundleComboBox->SetZeroEntryText("--");
	-
	- QFont font;
	- font.setFamily("Courier");
	- font.setStyleHint(QFont::Monospace);
	- font.setFixedPitch(true);
	- font.setPointSize(7);
	- m_Controls->m_SimulationStatusText->setFont(font);
	-
	- connect( m_SimulationTimer, SIGNAL(timeout()), this, SLOT(UpdateSimulationStatus()) );
	- connect((QObject) m_Controls->m_AbortSimulationButton, SIGNAL(clicked()), (QObject) this, SLOT(KillThread()));
	- connect((QObject) m_Controls->m_GenerateImageButton, SIGNAL(clicked()), (QObject) this, SLOT(GenerateImage()));
	- connect((QObject) m_Controls->m_AddNoise, SIGNAL(stateChanged(int)), (QObject) this, SLOT(OnAddNoise(int)));
	- connect((QObject) m_Controls->m_AddGhosts, SIGNAL(stateChanged(int)), (QObject) this, SLOT(OnAddGhosts(int)));
	- connect((QObject) m_Controls->m_AddDistortions, SIGNAL(stateChanged(int)), (QObject) this, SLOT(OnAddDistortions(int)));
	- connect((QObject) m_Controls->m_AddEddy, SIGNAL(stateChanged(int)), (QObject) this, SLOT(OnAddEddy(int)));
	- connect((QObject) m_Controls->m_AddSpikes, SIGNAL(stateChanged(int)), (QObject) this, SLOT(OnAddSpikes(int)));
	- connect((QObject) m_Controls->m_AddAliasing, SIGNAL(stateChanged(int)), (QObject) this, SLOT(OnAddAliasing(int)));
	- connect((QObject) m_Controls->m_AddMotion, SIGNAL(stateChanged(int)), (QObject) this, SLOT(OnAddMotion(int)));
	- connect((QObject) m_Controls->m_AddDrift, SIGNAL(stateChanged(int)), (QObject) this, SLOT(OnAddDrift(int)));
	- connect((QObject) m_Controls->m_AddGibbsRinging, SIGNAL(stateChanged(int)), (QObject) this, SLOT(OnAddRinging(int)));
	-
	- connect((QObject) m_Controls->m_Compartment1Box, SIGNAL(currentIndexChanged(int)), (QObject) this, SLOT(Comp1ModelFrameVisibility(int)));
	- connect((QObject) m_Controls->m_Compartment2Box, SIGNAL(currentIndexChanged(int)), (QObject) this, SLOT(Comp2ModelFrameVisibility(int)));
	- connect((QObject) m_Controls->m_Compartment3Box, SIGNAL(currentIndexChanged(int)), (QObject) this, SLOT(Comp3ModelFrameVisibility(int)));
	- connect((QObject) m_Controls->m_Compartment4Box, SIGNAL(currentIndexChanged(int)), (QObject) this, SLOT(Comp4ModelFrameVisibility(int)));
	-
	- connect((QObject) m_Controls->m_AdvancedOptionsBox_2, SIGNAL( stateChanged(int)), (QObject) this, SLOT(ShowAdvancedOptions(int)));
	- connect((QObject) m_Controls->m_UseBvalsBvecsBox, SIGNAL( stateChanged(int)), (QObject) this, SLOT(OnBvalsBvecsCheck(int)));
	-
	- connect((QObject) m_Controls->m_SaveParametersButton, SIGNAL(clicked()), (QObject) this, SLOT(SaveParameters()));
	- connect((QObject) m_Controls->m_LoadParametersButton, SIGNAL(clicked()), (QObject) this, SLOT(LoadParameters()));
	- connect((QObject) m_Controls->m_OutputPathButton, SIGNAL(clicked()), (QObject) this, SLOT(SetOutputPath()));
	- connect((QObject) m_Controls->m_LoadBvalsButton, SIGNAL(clicked()), (QObject) this, SLOT(SetBvalsEdit()));
	- connect((QObject) m_Controls->m_LoadBvecsButton, SIGNAL(clicked()), (QObject) this, SLOT(SetBvecsEdit()));
	-
	- connect((QObject) m_Controls->m_MaskComboBox, SIGNAL(currentIndexChanged(int)), (QObject) this, SLOT(OnMaskSelected(int)));
	- connect((QObject) m_Controls->m_TemplateComboBox, SIGNAL(currentIndexChanged(int)), (QObject) this, SLOT(OnTemplateSelected(int)));
	- connect((QObject) m_Controls->m_FiberBundleComboBox, SIGNAL(currentIndexChanged(int)), (QObject) this, SLOT(OnFibSelected(int)));
	- connect((QObject) m_Controls->m_LineReadoutTimeBox, SIGNAL( valueChanged(double)), (QObject) this, SLOT(OnTlineChanged()));
	- connect((QObject) m_Controls->m_SizeX, SIGNAL( valueChanged(int)), (QObject) this, SLOT(OnTlineChanged()));
	- }
	- OnTlineChanged();
	- UpdateGui();
	-}
	-
	-void QmitkFiberfoxView::OnTlineChanged()
	-{
	- double num_pix_line = 0;
	- if (m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull()) // use geometry of selected image
	- {
	- mitk::Image::Pointer img = dynamic_cast<mitk::Image*>(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData());
	- num_pix_line = img->GetDimension(0);
	- }
	- else if (m_Controls->m_MaskComboBox->GetSelectedNode().IsNotNull()) // use geometry of mask image
	- {
	- mitk::Image::Pointer img = dynamic_cast<mitk::Image*>(m_Controls->m_MaskComboBox->GetSelectedNode()->GetData());
	- num_pix_line = img->GetDimension(0);
	- }
	- else
	- {
	- num_pix_line = m_Controls->m_SizeX->value();
	- }
	-
	- double value = static_cast<double>(m_Controls->m_LineReadoutTimeBox->value())/1000.0; // line readout time in seconds
	- double dweel_pp = value/num_pix_line; // pixel readout time in seconds
	- double bw = 1/dweel_pp;
	- double bw_pp = bw/num_pix_line;
	- std::string tt = "Bandwidth:\n" + boost::lexical_cast<std::string>(itk::Math::Round<int, double>(bw)) + "Hz\n" + boost::lexical_cast<std::string>(itk::Math::Round<int, double>(bw_pp)) + "Hz/Px";
	- m_Controls->m_LineReadoutTimeBox->setToolTip(tt.c_str());
	-}
	-
	-void QmitkFiberfoxView::OnMaskSelected(int )
	-{
	- UpdateGui();
	-}
	-
	-void QmitkFiberfoxView::OnTemplateSelected(int )
	-{
	- UpdateGui();
	-}
	-
	-void QmitkFiberfoxView::OnFibSelected(int )
	-{
	- UpdateGui();
	-}
	-
	-void QmitkFiberfoxView::OnBvalsBvecsCheck(int )
	-{
	- UpdateGui();
	-}
	-
	-void QmitkFiberfoxView::UpdateParametersFromGui()
	-{
	- m_Parameters.ClearSignalParameters();
	- m_Parameters.m_Misc.m_CheckAdvancedSignalOptionsBox = m_Controls->m_AdvancedOptionsBox_2->isChecked();
	- m_Parameters.m_Misc.m_OutputAdditionalImages = m_Controls->m_VolumeFractionsBox->isChecked();
	-
	- std::string outputPath = m_Controls->m_SavePathEdit->text().toStdString();
	- if (outputPath.compare("-")!=0)
	- {
	- m_Parameters.m_Misc.m_OutputPath = outputPath;
	- m_Parameters.m_Misc.m_OutputPath += "/";
	- }
	- else {
	- m_Parameters.m_Misc.m_OutputPath = "";
	- }
	-
	- if (m_Controls->m_MaskComboBox->GetSelectedNode().IsNotNull())
	- {
	- mitk::Image::Pointer mitkMaskImage = dynamic_cast<mitk::Image*>(m_Controls->m_MaskComboBox->GetSelectedNode()->GetData());
	- mitk::CastToItkImage<ItkUcharImgType>(mitkMaskImage, m_Parameters.m_SignalGen.m_MaskImage);
	- itk::ImageDuplicator<ItkUcharImgType>::Pointer duplicator = itk::ImageDuplicator<ItkUcharImgType>::New();
	- duplicator->SetInputImage(m_Parameters.m_SignalGen.m_MaskImage);
	- duplicator->Update();
	- m_Parameters.m_SignalGen.m_MaskImage = duplicator->GetOutput();
	- }
	-
	- if (m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull() && mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( m_Controls->m_TemplateComboBox->GetSelectedNode())) // use parameters of selected DWI
	- {
	- mitk::Image::Pointer dwi = dynamic_cast<mitk::Image*>(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData());
	-
	- ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New();
	- mitk::CastToItkImage(dwi, itkVectorImagePointer);
	-
	- m_Parameters.m_SignalGen.m_ImageRegion = itkVectorImagePointer->GetLargestPossibleRegion();
	- m_Parameters.m_SignalGen.m_ImageSpacing = itkVectorImagePointer->GetSpacing();
	- m_Parameters.m_SignalGen.m_ImageOrigin = itkVectorImagePointer->GetOrigin();
	- m_Parameters.m_SignalGen.m_ImageDirection = itkVectorImagePointer->GetDirection();
	- m_Parameters.SetBvalue(mitk::DiffusionPropertyHelper::GetReferenceBValue(dwi));
	- m_Parameters.SetGradienDirections(mitk::DiffusionPropertyHelper::GetOriginalGradientContainer(dwi));
	- }
	- else if (m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull()) // use geometry of selected image
	- {
	- mitk::Image::Pointer img = dynamic_cast<mitk::Image*>(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData());
	- itk::Image< float, 3 >::Pointer itkImg = itk::Image< float, 3 >::New();
	- CastToItkImage< itk::Image< float, 3 > >(img, itkImg);
	-
	- m_Parameters.m_SignalGen.m_ImageRegion = itkImg->GetLargestPossibleRegion();
	- m_Parameters.m_SignalGen.m_ImageSpacing = itkImg->GetSpacing();
	- m_Parameters.m_SignalGen.m_ImageOrigin = itkImg->GetOrigin();
	- m_Parameters.m_SignalGen.m_ImageDirection = itkImg->GetDirection();
	-
	- if (m_Controls->m_UseBvalsBvecsBox->isChecked())
	- {
	- double bval;
	- m_Parameters.SetGradienDirections( mitk::gradients::ReadBvalsBvecs(m_Controls->m_LoadBvalsEdit->text().toStdString(), m_Controls->m_LoadBvecsEdit->text().toStdString(), bval) );
	- m_Parameters.SetBvalue(bval);
	- }
	- else
	- {
	- m_Parameters.SetNumWeightedVolumes(m_Controls->m_NumGradientsBox->value());
	- m_Parameters.SetBvalue(m_Controls->m_BvalueBox->value());
	- m_Parameters.GenerateGradientHalfShell();
	- }
	- }
	- else if (m_Parameters.m_SignalGen.m_MaskImage.IsNotNull()) // use geometry of mask image
	- {
	- ItkUcharImgType::Pointer itkImg = m_Parameters.m_SignalGen.m_MaskImage;
	- m_Parameters.m_SignalGen.m_ImageRegion = itkImg->GetLargestPossibleRegion();
	- m_Parameters.m_SignalGen.m_ImageSpacing = itkImg->GetSpacing();
	- m_Parameters.m_SignalGen.m_ImageOrigin = itkImg->GetOrigin();
	- m_Parameters.m_SignalGen.m_ImageDirection = itkImg->GetDirection();
	-
	- if (m_Controls->m_UseBvalsBvecsBox->isChecked())
	- {
	- double bval;
	- m_Parameters.SetGradienDirections( mitk::gradients::ReadBvalsBvecs(m_Controls->m_LoadBvalsEdit->text().toStdString(), m_Controls->m_LoadBvecsEdit->text().toStdString(), bval) );
	- m_Parameters.SetBvalue(bval);
	- }
	- else
	- {
	- m_Parameters.SetNumWeightedVolumes(m_Controls->m_NumGradientsBox->value());
	- m_Parameters.SetBvalue(m_Controls->m_BvalueBox->value());
	- m_Parameters.GenerateGradientHalfShell();
	- }
	- }
	- else // use GUI parameters
	- {
	- m_Parameters.m_SignalGen.m_ImageRegion.SetSize(0, m_Controls->m_SizeX->value());
	- m_Parameters.m_SignalGen.m_ImageRegion.SetSize(1, m_Controls->m_SizeY->value());
	- m_Parameters.m_SignalGen.m_ImageRegion.SetSize(2, m_Controls->m_SizeZ->value());
	- m_Parameters.m_SignalGen.m_ImageSpacing[0] = m_Controls->m_SpacingX->value();
	- m_Parameters.m_SignalGen.m_ImageSpacing[1] = m_Controls->m_SpacingY->value();
	- m_Parameters.m_SignalGen.m_ImageSpacing[2] = m_Controls->m_SpacingZ->value();
	- m_Parameters.m_SignalGen.m_ImageOrigin[0] = m_Parameters.m_SignalGen.m_ImageSpacing[0]/2;
	- m_Parameters.m_SignalGen.m_ImageOrigin[1] = m_Parameters.m_SignalGen.m_ImageSpacing[1]/2;
	- m_Parameters.m_SignalGen.m_ImageOrigin[2] = m_Parameters.m_SignalGen.m_ImageSpacing[2]/2;
	- m_Parameters.m_SignalGen.m_ImageDirection.SetIdentity();
	-
	- if (m_Controls->m_UseBvalsBvecsBox->isChecked())
	- {
	- double bval;
	- m_Parameters.SetGradienDirections( mitk::gradients::ReadBvalsBvecs(m_Controls->m_LoadBvalsEdit->text().toStdString(), m_Controls->m_LoadBvecsEdit->text().toStdString(), bval) );
	- m_Parameters.SetBvalue(bval);
	- }
	- else
	- {
	- m_Parameters.SetNumWeightedVolumes(m_Controls->m_NumGradientsBox->value());
	- m_Parameters.SetBvalue(m_Controls->m_BvalueBox->value());
	- m_Parameters.GenerateGradientHalfShell();
	- }
	- }
	-
	- // signal relaxation
	- m_Parameters.m_SignalGen.m_DoSimulateRelaxation = false;
	- if (m_Controls->m_RelaxationBox->isChecked())
	- {
	- m_Parameters.m_SignalGen.m_DoSimulateRelaxation = true;
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Relaxation", BoolProperty::New(true));
	- m_Parameters.m_Misc.m_ArtifactModelString += "_RELAX";
	- }
	- m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = m_Parameters.m_SignalGen.m_DoSimulateRelaxation;
	-
	- // N/2 ghosts
	- m_Parameters.m_Misc.m_DoAddGhosts = m_Controls->m_AddGhosts->isChecked();
	- m_Parameters.m_SignalGen.m_KspaceLineOffset = m_Controls->m_kOffsetBox->value();
	- if (m_Controls->m_AddGhosts->isChecked())
	- {
	- m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true;
	- m_Parameters.m_Misc.m_ArtifactModelString += "_GHOST";
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Ghost", DoubleProperty::New(m_Parameters.m_SignalGen.m_KspaceLineOffset));
	- }
	-
	- // Aliasing
	- m_Parameters.m_Misc.m_DoAddAliasing = m_Controls->m_AddAliasing->isChecked();
	- m_Parameters.m_SignalGen.m_CroppingFactor = (100-m_Controls->m_WrapBox->value())/100;
	- if (m_Controls->m_AddAliasing->isChecked())
	- {
	- m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true;
	- m_Parameters.m_Misc.m_ArtifactModelString += "_ALIASING";
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Aliasing", DoubleProperty::New(m_Controls->m_WrapBox->value()));
	- }
	-
	- // Spikes
	- m_Parameters.m_Misc.m_DoAddSpikes = m_Controls->m_AddSpikes->isChecked();
	- m_Parameters.m_SignalGen.m_Spikes = m_Controls->m_SpikeNumBox->value();
	- m_Parameters.m_SignalGen.m_SpikeAmplitude = m_Controls->m_SpikeScaleBox->value();
	- if (m_Controls->m_AddSpikes->isChecked())
	- {
	- m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true;
	- m_Parameters.m_Misc.m_ArtifactModelString += "_SPIKES";
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Spikes.Number", IntProperty::New(m_Parameters.m_SignalGen.m_Spikes));
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Spikes.Amplitude", DoubleProperty::New(m_Parameters.m_SignalGen.m_SpikeAmplitude));
	- }
	-
	- // Drift
	- m_Parameters.m_SignalGen.m_DoAddDrift = m_Controls->m_AddDrift->isChecked();
	- m_Parameters.m_SignalGen.m_Drift = static_cast<float>(m_Controls->m_DriftFactor->value())/100;
	- if (m_Controls->m_AddDrift->isChecked())
	- {
	- m_Parameters.m_Misc.m_ArtifactModelString += "_DRIFT";
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Drift", FloatProperty::New(m_Parameters.m_SignalGen.m_Drift));
	- }
	-
	- // gibbs ringing
	- m_Parameters.m_SignalGen.m_DoAddGibbsRinging = m_Controls->m_AddGibbsRinging->isChecked();
	- m_Parameters.m_SignalGen.m_ZeroRinging = m_Controls->m_ZeroRinging->value();
	- if (m_Controls->m_AddGibbsRinging->isChecked())
	- {
	- m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true;
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Ringing", BoolProperty::New(true));
	- m_Parameters.m_Misc.m_ArtifactModelString += "_RINGING";
	- }
	-
	- // add distortions
	- m_Parameters.m_Misc.m_DoAddDistortions = m_Controls->m_AddDistortions->isChecked();
	- if (m_Controls->m_AddDistortions->isChecked() && m_Controls->m_FrequencyMapBox->GetSelectedNode().IsNotNull())
	- {
	- mitk::DataNode::Pointer fMapNode = m_Controls->m_FrequencyMapBox->GetSelectedNode();
	- mitk::Image* img = dynamic_cast<mitk::Image*>(fMapNode->GetData());
	- ItkFloatImgType::Pointer itkImg = ItkFloatImgType::New();
	- CastToItkImage< ItkFloatImgType >(img, itkImg);
	-
	- if (m_Controls->m_TemplateComboBox->GetSelectedNode().IsNull()) // use geometry of frequency map
	- {
	- m_Parameters.m_SignalGen.m_ImageRegion = itkImg->GetLargestPossibleRegion();
	- m_Parameters.m_SignalGen.m_ImageSpacing = itkImg->GetSpacing();
	- m_Parameters.m_SignalGen.m_ImageOrigin = itkImg->GetOrigin();
	- m_Parameters.m_SignalGen.m_ImageDirection = itkImg->GetDirection();
	- }
	-
	- m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true;
	- itk::ImageDuplicator<ItkFloatImgType>::Pointer duplicator = itk::ImageDuplicator<ItkFloatImgType>::New();
	- duplicator->SetInputImage(itkImg);
	- duplicator->Update();
	- m_Parameters.m_SignalGen.m_FrequencyMap = duplicator->GetOutput();
	- m_Parameters.m_Misc.m_ArtifactModelString += "_DISTORTED";
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Distortions", BoolProperty::New(true));
	- }
	-
	- m_Parameters.m_SignalGen.m_EddyStrength = m_Controls->m_EddyGradientStrength->value();
	- m_Parameters.m_Misc.m_DoAddEddyCurrents = m_Controls->m_AddEddy->isChecked();
	- if (m_Controls->m_AddEddy->isChecked())
	- {
	- m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true;
	- m_Parameters.m_Misc.m_ArtifactModelString += "_EDDY";
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Eddy-strength", DoubleProperty::New(m_Parameters.m_SignalGen.m_EddyStrength));
	- }
	-
	- // Motion
	- m_Parameters.m_SignalGen.m_DoAddMotion = false;
	- m_Parameters.m_SignalGen.m_DoRandomizeMotion = m_Controls->m_RandomMotion->isChecked();
	- m_Parameters.m_SignalGen.m_Translation[0] = m_Controls->m_MaxTranslationBoxX->value();
	- m_Parameters.m_SignalGen.m_Translation[1] = m_Controls->m_MaxTranslationBoxY->value();
	- m_Parameters.m_SignalGen.m_Translation[2] = m_Controls->m_MaxTranslationBoxZ->value();
	- m_Parameters.m_SignalGen.m_Rotation[0] = m_Controls->m_MaxRotationBoxX->value();
	- m_Parameters.m_SignalGen.m_Rotation[1] = m_Controls->m_MaxRotationBoxY->value();
	- m_Parameters.m_SignalGen.m_Rotation[2] = m_Controls->m_MaxRotationBoxZ->value();
	- m_Parameters.m_SignalGen.m_MotionVolumes.clear();
	- m_Parameters.m_Misc.m_MotionVolumesBox = m_Controls->m_MotionVolumesBox->text().toStdString();
	-
	- if ( m_Controls->m_AddMotion->isChecked())
	- {
	- m_Parameters.m_SignalGen.m_DoAddMotion = true;
	- m_Parameters.m_Misc.m_ArtifactModelString += "_MOTION";
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Random", BoolProperty::New(m_Parameters.m_SignalGen.m_DoRandomizeMotion));
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-x", DoubleProperty::New(m_Parameters.m_SignalGen.m_Translation[0]));
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-y", DoubleProperty::New(m_Parameters.m_SignalGen.m_Translation[1]));
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-z", DoubleProperty::New(m_Parameters.m_SignalGen.m_Translation[2]));
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-x", DoubleProperty::New(m_Parameters.m_SignalGen.m_Rotation[0]));
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-y", DoubleProperty::New(m_Parameters.m_SignalGen.m_Rotation[1]));
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-z", DoubleProperty::New(m_Parameters.m_SignalGen.m_Rotation[2]));
	-
	- if ( m_Parameters.m_Misc.m_MotionVolumesBox == "random" )
	- {
	- for ( size_t i=0; i < m_Parameters.m_SignalGen.GetNumVolumes(); ++i )
	- {
	- m_Parameters.m_SignalGen.m_MotionVolumes.push_back( bool( rand()%2 ) );
	- }
	- MITK_DEBUG << "QmitkFiberfoxView.cpp: Case m_Misc.m_MotionVolumesBox == \"random\".";
	- }
	-
	- else if ( ! m_Parameters.m_Misc.m_MotionVolumesBox.empty() )
	- {
	- std::stringstream stream( m_Parameters.m_Misc.m_MotionVolumesBox );
	- std::vector<int> numbers;
	- int number = std::numeric_limits<int>::max();
	- while( stream >> number )
	- {
	- if( number < std::numeric_limits<int>::max() )
	- {
	- numbers.push_back( number );
	- }
	- }
	-
	- // If a list of negative numbers is given:
	- if( *(std::min_element( numbers.begin(), numbers.end() )) < 0
	- && *(std::max_element( numbers.begin(), numbers.end() )) <= 0 ) // cave: -0 == +0
	- {
	- for ( size_t i=0; i < m_Parameters.m_SignalGen.GetNumVolumes(); ++i )
	- {
	- m_Parameters.m_SignalGen.m_MotionVolumes.push_back( true );
	- }
	- // set all true except those given.
	- for( auto iter = std::begin( numbers ); iter != std::end( numbers ); ++iter )
	- {
	- if ( -(iter) < (int)m_Parameters.m_SignalGen.GetNumVolumes() && -(iter) >= 0 )
	- {
	- m_Parameters.m_SignalGen.m_MotionVolumes.at( -(*iter) ) = false;
	- }
	- }
	- MITK_DEBUG << "QmitkFiberfoxView.cpp: Case list of negative numbers.";
	- }
	-
	- // If a list of positive numbers is given:
	- else if( *(std::min_element( numbers.begin(), numbers.end() )) >= 0
	- && *(std::max_element( numbers.begin(), numbers.end() )) >= 0 )
	- {
	- for ( size_t i=0; i < m_Parameters.m_SignalGen.GetNumVolumes(); ++i )
	- {
	- m_Parameters.m_SignalGen.m_MotionVolumes.push_back( false );
	- }
	- // set all false except those given.
	- for( auto iter = std::begin( numbers ); iter != std::end( numbers ); ++iter )
	- {
	- if ( iter < (int)m_Parameters.m_SignalGen.GetNumVolumes() && iter >= 0 )
	- {
	- m_Parameters.m_SignalGen.m_MotionVolumes.at( *iter ) = true;
	- }
	- }
	- MITK_DEBUG << "QmitkFiberfoxView.cpp: Case list of positive numbers.";
	- }
	-
	- else
	- {
	- MITK_ERROR << "QmitkFiberfoxView.cpp: Inconsistent list of numbers in m_MotionVolumesBox.";
	- }
	- }
	-
	- else
	- {
	- m_Parameters.m_Misc.m_MotionVolumesBox = ""; // set empty.
	- m_Controls->m_MotionVolumesBox->setText("");
	- for (unsigned int i=0; i<m_Parameters.m_SignalGen.GetNumVolumes(); i++)
	- {
	- m_Parameters.m_SignalGen.m_MotionVolumes.push_back(i);
	- }
	- }
	- }
	-
	- // other imaging parameters
	- m_Parameters.m_SignalGen.m_AcquisitionType = (SignalGenerationParameters::AcquisitionType)m_Controls->m_AcquisitionTypeBox->currentIndex();
	- m_Parameters.m_SignalGen.m_CoilSensitivityProfile = (SignalGenerationParameters::CoilSensitivityProfile)m_Controls->m_CoilSensBox->currentIndex();
	- m_Parameters.m_SignalGen.m_NumberOfCoils = m_Controls->m_NumCoilsBox->value();
	- m_Parameters.m_SignalGen.m_PartialFourier = m_Controls->m_PartialFourier->value();
	- m_Parameters.m_SignalGen.m_ReversePhase = m_Controls->m_ReversePhaseBox->isChecked();
	- m_Parameters.m_SignalGen.m_tLine = m_Controls->m_LineReadoutTimeBox->value();
	- m_Parameters.m_SignalGen.m_tInhom = m_Controls->m_T2starBox->value();
	- m_Parameters.m_SignalGen.m_EchoTrainLength = m_Controls->m_EtlBox->value();
	- m_Parameters.m_SignalGen.m_tEcho = m_Controls->m_TEbox->value();
	- m_Parameters.m_SignalGen.m_tRep = m_Controls->m_TRbox->value();
	- m_Parameters.m_SignalGen.m_tInv = m_Controls->m_TIbox->value();
	- m_Parameters.m_SignalGen.m_DoDisablePartialVolume = m_Controls->m_EnforcePureFiberVoxelsBox->isChecked();
	- m_Parameters.m_SignalGen.m_AxonRadius = m_Controls->m_FiberRadius->value();
	- m_Parameters.m_SignalGen.m_SignalScale = m_Controls->m_SignalScaleBox->value();
	-
	-// double voxelVolume = m_Parameters.m_SignalGen.m_ImageSpacing[0]
	-// * m_Parameters.m_SignalGen.m_ImageSpacing[1]
	-// * m_Parameters.m_SignalGen.m_ImageSpacing[2];
	-// if ( m_Parameters.m_SignalGen.m_SignalScalevoxelVolume > itk::NumericTraits<short>::max()0.75 )
	-// {
	-// m_Parameters.m_SignalGen.m_SignalScale = itk::NumericTraits<short>::max()*0.75/voxelVolume;
	-// m_Controls->m_SignalScaleBox->setValue(m_Parameters.m_SignalGen.m_SignalScale);
	-// QMessageBox::information( nullptr, "Warning",
	-// "Maximum signal exceeding data type limits. Automatically adjusted to "
	-// + QString::number(m_Parameters.m_SignalGen.m_SignalScale)
	-// + " to obtain a maximum signal of 75% of the data type maximum."
	-// " Relaxation and other effects that affect the signal intensities are not accounted for.");
	-// }
	-
	- // Noise
	- m_Parameters.m_Misc.m_DoAddNoise = m_Controls->m_AddNoise->isChecked();
	- m_Parameters.m_SignalGen.m_NoiseVariance = m_Controls->m_NoiseLevel->value();
	- if (m_Controls->m_AddNoise->isChecked())
	- {
	- switch (m_Controls->m_NoiseDistributionBox->currentIndex())
	- {
	- case 0:
	- {
	- if (m_Parameters.m_SignalGen.m_NoiseVariance>0)
	- {
	- m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true;
	- m_Parameters.m_Misc.m_ArtifactModelString += "_COMPLEX-GAUSSIAN-";
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Complex Gaussian"));
	- }
	- break;
	- }
	- case 1:
	- {
	- if (m_Parameters.m_SignalGen.m_NoiseVariance>0)
	- {
	- m_Parameters.m_NoiseModel = std::make_shared< mitk::RicianNoiseModel<ScalarType> >();
	- m_Parameters.m_Misc.m_ArtifactModelString += "_RICIAN-";
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Rician"));
	- m_Parameters.m_NoiseModel->SetNoiseVariance(m_Parameters.m_SignalGen.m_NoiseVariance);
	- }
	- break;
	- }
	- case 2:
	- {
	- if (m_Parameters.m_SignalGen.m_NoiseVariance>0)
	- {
	- m_Parameters.m_NoiseModel = std::make_shared< mitk::ChiSquareNoiseModel<ScalarType> >();
	- m_Parameters.m_Misc.m_ArtifactModelString += "_CHISQUARED-";
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Chi-squared"));
	- m_Parameters.m_NoiseModel->SetNoiseVariance(m_Parameters.m_SignalGen.m_NoiseVariance);
	- }
	- break;
	- }
	- default:
	- {
	- if (m_Parameters.m_SignalGen.m_NoiseVariance>0)
	- {
	- m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true;
	- m_Parameters.m_Misc.m_ArtifactModelString += "_COMPLEX-GAUSSIAN-";
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Complex Gaussian"));
	- }
	- break;
	- }
	- }
	-
	- if (m_Parameters.m_SignalGen.m_NoiseVariance>0)
	- {
	- m_Parameters.m_Misc.m_ArtifactModelString += QString::number(m_Parameters.m_SignalGen.m_NoiseVariance).toStdString();
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Variance", DoubleProperty::New(m_Parameters.m_SignalGen.m_NoiseVariance));
	- }
	- }
	-
	- // signal models
	- {
	- // compartment 1
	- switch (m_Controls->m_Compartment1Box->currentIndex())
	- {
	- case 0:
	- {
	- mitk::StickModel<ScalarType>* model = new mitk::StickModel<ScalarType>();
	- model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections());
	- model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue());
	- model->SetDiffusivity(m_Controls->m_StickWidget1->GetD());
	- model->SetT2(m_Controls->m_StickWidget1->GetT2());
	- model->SetT1(m_Controls->m_StickWidget1->GetT1());
	- model->m_CompartmentId = 1;
	- m_Parameters.m_FiberModelList.push_back(model);
	- m_Parameters.m_Misc.m_SignalModelString += "Stick";
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Stick") );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D", DoubleProperty::New(m_Controls->m_StickWidget1->GetD()) );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(model->GetT2()) );
	- break;
	- }
	- case 1:
	- {
	- mitk::TensorModel<ScalarType>* model = new mitk::TensorModel<ScalarType>();
	- model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections());
	- model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue());
	- model->SetDiffusivity1(m_Controls->m_ZeppelinWidget1->GetD1());
	- model->SetDiffusivity2(m_Controls->m_ZeppelinWidget1->GetD2());
	- model->SetDiffusivity3(m_Controls->m_ZeppelinWidget1->GetD2());
	- model->SetT2(m_Controls->m_ZeppelinWidget1->GetT2());
	- model->SetT1(m_Controls->m_ZeppelinWidget1->GetT1());
	- model->m_CompartmentId = 1;
	- m_Parameters.m_FiberModelList.push_back(model);
	- m_Parameters.m_Misc.m_SignalModelString += "Zeppelin";
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Zeppelin") );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD1()) );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD2()) );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(model->GetT2()) );
	- break;
	- }
	- case 2:
	- {
	- mitk::TensorModel<ScalarType>* model = new mitk::TensorModel<ScalarType>();
	- model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections());
	- model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue());
	- model->SetDiffusivity1(m_Controls->m_TensorWidget1->GetD1());
	- model->SetDiffusivity2(m_Controls->m_TensorWidget1->GetD2());
	- model->SetDiffusivity3(m_Controls->m_TensorWidget1->GetD3());
	- model->SetT2(m_Controls->m_TensorWidget1->GetT2());
	- model->SetT1(m_Controls->m_TensorWidget1->GetT1());
	- model->m_CompartmentId = 1;
	- m_Parameters.m_FiberModelList.push_back(model);
	- m_Parameters.m_Misc.m_SignalModelString += "Tensor";
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Tensor") );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD1()) );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD2()) );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D3", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD3()) );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(model->GetT2()) );
	- break;
	- }
	- case 3:
	- {
	- mitk::RawShModel<ScalarType>* model = new mitk::RawShModel<ScalarType>();
	- m_Parameters.m_SignalGen.m_DoSimulateRelaxation = false;
	- model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections());
	- model->SetMaxNumKernels(m_Controls->m_PrototypeWidget1->GetNumberOfSamples());
	- model->SetFaRange(m_Controls->m_PrototypeWidget1->GetMinFa(), m_Controls->m_PrototypeWidget1->GetMaxFa());
	- model->SetAdcRange(m_Controls->m_PrototypeWidget1->GetMinAdc(), m_Controls->m_PrototypeWidget1->GetMaxAdc());
	- model->m_CompartmentId = 1;
	- m_Parameters.m_FiberModelList.push_back(model);
	- m_Parameters.m_Misc.m_SignalModelString += "Prototype";
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Prototype") );
	- break;
	- }
	- }
	- if (m_Controls->m_Comp1VolumeFraction->GetSelectedNode().IsNotNull())
	- {
	- mitk::DataNode::Pointer volumeNode = m_Controls->m_Comp1VolumeFraction->GetSelectedNode();
	- ItkDoubleImgType::Pointer comp1VolumeImage = ItkDoubleImgType::New();
	- mitk::Image* img = dynamic_cast<mitk::Image*>(volumeNode->GetData());
	- CastToItkImage< ItkDoubleImgType >(img, comp1VolumeImage);
	- m_Parameters.m_FiberModelList.back()->SetVolumeFractionImage(comp1VolumeImage);
	- }
	-
	- // compartment 2
	- switch (m_Controls->m_Compartment2Box->currentIndex())
	- {
	- case 0:
	- break;
	- case 1:
	- {
	- mitk::StickModel<ScalarType>* model = new mitk::StickModel<ScalarType>();
	- model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections());
	- model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue());
	- model->SetDiffusivity(m_Controls->m_StickWidget2->GetD());
	- model->SetT2(m_Controls->m_StickWidget2->GetT2());
	- model->SetT1(m_Controls->m_StickWidget2->GetT1());
	- model->m_CompartmentId = 2;
	- m_Parameters.m_FiberModelList.push_back(model);
	- m_Parameters.m_Misc.m_SignalModelString += "Stick";
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Stick") );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D", DoubleProperty::New(m_Controls->m_StickWidget2->GetD()) );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(model->GetT2()) );
	- break;
	- }
	- case 2:
	- {
	- mitk::TensorModel<ScalarType>* model = new mitk::TensorModel<ScalarType>();
	- model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections());
	- model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue());
	- model->SetDiffusivity1(m_Controls->m_ZeppelinWidget2->GetD1());
	- model->SetDiffusivity2(m_Controls->m_ZeppelinWidget2->GetD2());
	- model->SetDiffusivity3(m_Controls->m_ZeppelinWidget2->GetD2());
	- model->SetT2(m_Controls->m_ZeppelinWidget2->GetT2());
	- model->SetT1(m_Controls->m_ZeppelinWidget2->GetT1());
	- model->m_CompartmentId = 2;
	- m_Parameters.m_FiberModelList.push_back(model);
	- m_Parameters.m_Misc.m_SignalModelString += "Zeppelin";
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Zeppelin") );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD1()) );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD2()) );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(model->GetT2()) );
	- break;
	- }
	- case 3:
	- {
	- mitk::TensorModel<ScalarType>* model = new mitk::TensorModel<ScalarType>();
	- model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections());
	- model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue());
	- model->SetDiffusivity1(m_Controls->m_TensorWidget2->GetD1());
	- model->SetDiffusivity2(m_Controls->m_TensorWidget2->GetD2());
	- model->SetDiffusivity3(m_Controls->m_TensorWidget2->GetD3());
	- model->SetT2(m_Controls->m_TensorWidget2->GetT2());
	- model->SetT1(m_Controls->m_TensorWidget2->GetT1());
	- model->m_CompartmentId = 2;
	- m_Parameters.m_FiberModelList.push_back(model);
	- m_Parameters.m_Misc.m_SignalModelString += "Tensor";
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Tensor") );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD1()) );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD2()) );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D3", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD3()) );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(model->GetT2()) );
	- break;
	- }
	- }
	- if (m_Controls->m_Comp2VolumeFraction->GetSelectedNode().IsNotNull() && m_Parameters.m_FiberModelList.size()==2)
	- {
	- mitk::DataNode::Pointer volumeNode = m_Controls->m_Comp2VolumeFraction->GetSelectedNode();
	- ItkDoubleImgType::Pointer comp1VolumeImage = ItkDoubleImgType::New();
	- mitk::Image* img = dynamic_cast<mitk::Image*>(volumeNode->GetData());
	- CastToItkImage< ItkDoubleImgType >(img, comp1VolumeImage);
	- m_Parameters.m_FiberModelList.back()->SetVolumeFractionImage(comp1VolumeImage);
	- }
	-
	- // compartment 3
	- switch (m_Controls->m_Compartment3Box->currentIndex())
	- {
	- case 0:
	- {
	- mitk::BallModel<ScalarType>* model = new mitk::BallModel<ScalarType>();
	- model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections());
	- model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue());
	- model->SetDiffusivity(m_Controls->m_BallWidget1->GetD());
	- model->SetT2(m_Controls->m_BallWidget1->GetT2());
	- model->SetT1(m_Controls->m_BallWidget1->GetT1());
	- model->m_CompartmentId = 3;
	- m_Parameters.m_NonFiberModelList.push_back(model);
	- m_Parameters.m_Misc.m_SignalModelString += "Ball";
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Ball") );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_BallWidget1->GetD()) );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(model->GetT2()) );
	- break;
	- }
	- case 1:
	- {
	- mitk::AstroStickModel<ScalarType>* model = new mitk::AstroStickModel<ScalarType>();
	- model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections());
	- model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue());
	- model->SetDiffusivity(m_Controls->m_AstrosticksWidget1->GetD());
	- model->SetT2(m_Controls->m_AstrosticksWidget1->GetT2());
	- model->SetT1(m_Controls->m_AstrosticksWidget1->GetT1());
	- model->SetRandomizeSticks(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks());
	- model->m_CompartmentId = 3;
	- m_Parameters.m_NonFiberModelList.push_back(model);
	- m_Parameters.m_Misc.m_SignalModelString += "Astrosticks";
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Astrosticks") );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget1->GetD()) );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(model->GetT2()) );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()) );
	- break;
	- }
	- case 2:
	- {
	- mitk::DotModel<ScalarType>* model = new mitk::DotModel<ScalarType>();
	- model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections());
	- model->SetT2(m_Controls->m_DotWidget1->GetT2());
	- model->SetT1(m_Controls->m_DotWidget1->GetT1());
	- model->m_CompartmentId = 3;
	- m_Parameters.m_NonFiberModelList.push_back(model);
	- m_Parameters.m_Misc.m_SignalModelString += "Dot";
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Dot") );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(model->GetT2()) );
	- break;
	- }
	- case 3:
	- {
	- mitk::RawShModel<ScalarType>* model = new mitk::RawShModel<ScalarType>();
	- m_Parameters.m_SignalGen.m_DoSimulateRelaxation = false;
	- model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections());
	- model->SetMaxNumKernels(m_Controls->m_PrototypeWidget3->GetNumberOfSamples());
	- model->SetFaRange(m_Controls->m_PrototypeWidget3->GetMinFa(), m_Controls->m_PrototypeWidget3->GetMaxFa());
	- model->SetAdcRange(m_Controls->m_PrototypeWidget3->GetMinAdc(), m_Controls->m_PrototypeWidget3->GetMaxAdc());
	- model->m_CompartmentId = 3;
	- m_Parameters.m_NonFiberModelList.push_back(model);
	- m_Parameters.m_Misc.m_SignalModelString += "Prototype";
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Prototype") );
	- break;
	- }
	- }
	- if (m_Controls->m_Comp3VolumeFraction->GetSelectedNode().IsNotNull())
	- {
	- mitk::DataNode::Pointer volumeNode = m_Controls->m_Comp3VolumeFraction->GetSelectedNode();
	- ItkDoubleImgType::Pointer comp1VolumeImage = ItkDoubleImgType::New();
	- mitk::Image* img = dynamic_cast<mitk::Image*>(volumeNode->GetData());
	- CastToItkImage< ItkDoubleImgType >(img, comp1VolumeImage);
	- m_Parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp1VolumeImage);
	- }
	-
	- switch (m_Controls->m_Compartment4Box->currentIndex())
	- {
	- case 0:
	- break;
	- case 1:
	- {
	- mitk::BallModel<ScalarType>* model = new mitk::BallModel<ScalarType>();
	- model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections());
	- model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue());
	- model->SetDiffusivity(m_Controls->m_BallWidget2->GetD());
	- model->SetT2(m_Controls->m_BallWidget2->GetT2());
	- model->SetT1(m_Controls->m_BallWidget2->GetT1());
	- model->m_CompartmentId = 4;
	- m_Parameters.m_NonFiberModelList.push_back(model);
	- m_Parameters.m_Misc.m_SignalModelString += "Ball";
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Ball") );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_BallWidget2->GetD()) );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(model->GetT2()) );
	- break;
	- }
	- case 2:
	- {
	- mitk::AstroStickModel<ScalarType>* model = new mitk::AstroStickModel<ScalarType>();
	- model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections());
	- model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue());
	- model->SetDiffusivity(m_Controls->m_AstrosticksWidget2->GetD());
	- model->SetT2(m_Controls->m_AstrosticksWidget2->GetT2());
	- model->SetT1(m_Controls->m_AstrosticksWidget2->GetT1());
	- model->SetRandomizeSticks(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks());
	- model->m_CompartmentId = 4;
	- m_Parameters.m_NonFiberModelList.push_back(model);
	- m_Parameters.m_Misc.m_SignalModelString += "Astrosticks";
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Astrosticks") );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget2->GetD()) );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(model->GetT2()) );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()) );
	- break;
	- }
	- case 3:
	- {
	- mitk::DotModel<ScalarType>* model = new mitk::DotModel<ScalarType>();
	- model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections());
	- model->SetT2(m_Controls->m_DotWidget2->GetT2());
	- model->SetT1(m_Controls->m_DotWidget2->GetT1());
	- model->m_CompartmentId = 4;
	- m_Parameters.m_NonFiberModelList.push_back(model);
	- m_Parameters.m_Misc.m_SignalModelString += "Dot";
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Dot") );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(model->GetT2()) );
	- break;
	- }
	- case 4:
	- {
	- mitk::RawShModel<ScalarType>* model = new mitk::RawShModel<ScalarType>();
	- m_Parameters.m_SignalGen.m_DoSimulateRelaxation = false;
	- model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections());
	- model->SetMaxNumKernels(m_Controls->m_PrototypeWidget4->GetNumberOfSamples());
	- model->SetFaRange(m_Controls->m_PrototypeWidget4->GetMinFa(), m_Controls->m_PrototypeWidget4->GetMaxFa());
	- model->SetAdcRange(m_Controls->m_PrototypeWidget4->GetMinAdc(), m_Controls->m_PrototypeWidget4->GetMaxAdc());
	- model->m_CompartmentId = 4;
	- m_Parameters.m_NonFiberModelList.push_back(model);
	- m_Parameters.m_Misc.m_SignalModelString += "Prototype";
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") );
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Prototype") );
	- break;
	- }
	- }
	- if (m_Controls->m_Comp4VolumeFraction->GetSelectedNode().IsNotNull() && m_Parameters.m_NonFiberModelList.size()==2)
	- {
	- mitk::DataNode::Pointer volumeNode = m_Controls->m_Comp4VolumeFraction->GetSelectedNode();
	- ItkDoubleImgType::Pointer compVolumeImage = ItkDoubleImgType::New();
	- mitk::Image* img = dynamic_cast<mitk::Image*>(volumeNode->GetData());
	- CastToItkImage< ItkDoubleImgType >(img, compVolumeImage);
	- m_Parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(compVolumeImage);
	- }
	- }
	-
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.SignalScale", IntProperty::New(m_Parameters.m_SignalGen.m_SignalScale));
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.FiberRadius", IntProperty::New(m_Parameters.m_SignalGen.m_AxonRadius));
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Tinhom", DoubleProperty::New(m_Parameters.m_SignalGen.m_tInhom));
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.echoTrainLength", IntProperty::New(m_Parameters.m_SignalGen.m_EchoTrainLength));
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Tline", DoubleProperty::New(m_Parameters.m_SignalGen.m_tLine));
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.TE", DoubleProperty::New(m_Parameters.m_SignalGen.m_tEcho));
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.b-value", DoubleProperty::New(m_Parameters.m_SignalGen.GetBvalue()));
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.NoPartialVolume", BoolProperty::New(m_Parameters.m_SignalGen.m_DoDisablePartialVolume));
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Relaxation", BoolProperty::New(m_Parameters.m_SignalGen.m_DoSimulateRelaxation));
	- m_Parameters.m_Misc.m_ResultNode->AddProperty("binary", BoolProperty::New(false));
	-}
	-
	-void QmitkFiberfoxView::SaveParameters(QString filename)
	-{
	- UpdateParametersFromGui();
	- std::vector< int > bVals = m_Parameters.m_SignalGen.GetBvalues();
	- std::cout << "b-values: ";
	- for (auto v : bVals)
	- std::cout << v << " ";
	- std::cout << std::endl;
	- bool ok = true;
	- bool first = true;
	- bool dosampling = false;
	- mitk::Image::Pointer diffImg = nullptr;
	- itk::Image< itk::DiffusionTensor3D< double >, 3 >::Pointer tensorImage = nullptr;
	- const int shOrder = 2;
	- typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,shOrder,ODF_SAMPLING_SIZE> QballFilterType;
	- QballFilterType::CoefficientImageType::Pointer itkFeatureImage = nullptr;
	- ItkDoubleImgType::Pointer adcImage = nullptr;
	-
	- for (unsigned int i=0; i<m_Parameters.m_FiberModelList.size()+m_Parameters.m_NonFiberModelList.size(); i++)
	- {
	- mitk::RawShModel<>* model = nullptr;
	- if (i<m_Parameters.m_FiberModelList.size())
	- {
	- model = dynamic_cast< mitk::RawShModel<>* >(m_Parameters.m_FiberModelList.at(i));
	- }
	- else
	- {
	- model = dynamic_cast< mitk::RawShModel<>* >(m_Parameters.m_NonFiberModelList.at(i-m_Parameters.m_FiberModelList.size()));
	- }
	-
	- if ( model!=nullptr && model->GetNumberOfKernels() <= 0 )
	- {
	- if (first==true)
	- {
	- if ( QMessageBox::question(nullptr, "Prototype signal sampling",
	- "Do you want to sample prototype signals from the selected diffusion-weighted imag and save them?",
	- QMessageBox::Yes, QMessageBox::No) == QMessageBox::Yes )
	- dosampling = true;
	-
	- first = false;
	- if ( dosampling && (m_Controls->m_TemplateComboBox->GetSelectedNode().IsNull()
	- \|\| !mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(
	- dynamic_cast<mitk::Image*>(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()) ) ) )
	- {
	- QMessageBox::information(nullptr, "Parameter file not saved", "No diffusion-weighted image selected to sample signal from.");
	- return;
	- }
	- else if (dosampling)
	- {
	- diffImg = dynamic_cast<mitk::Image*>(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData());
	-
	- typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, double > TensorReconstructionImageFilterType;
	- TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New();
	- ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New();
	- mitk::CastToItkImage(diffImg, itkVectorImagePointer);
	- filter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg));
	- filter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg),
	- itkVectorImagePointer );
	-
	- filter->Update();
	- tensorImage = filter->GetOutput();
	-
	- QballFilterType::Pointer qballfilter = QballFilterType::New();
	-
	- qballfilter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg));
	- qballfilter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg),
	- itkVectorImagePointer );
	- qballfilter->SetLambda(0.006);
	- qballfilter->SetNormalizationMethod(QballFilterType::QBAR_RAW_SIGNAL);
	- qballfilter->Update();
	- itkFeatureImage = qballfilter->GetCoefficientImage();
	-
	- itk::AdcImageFilter< short, double >::Pointer adcFilter = itk::AdcImageFilter< short, double >::New();
	- adcFilter->SetInput( itkVectorImagePointer );
	- adcFilter->SetGradientDirections(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg));
	- adcFilter->SetB_value(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg));
	- adcFilter->Update();
	- adcImage = adcFilter->GetOutput();
	- }
	- }
	-
	-
	- typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, double > TensorReconstructionImageFilterType;
	- TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New();
	- ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New();
	- mitk::CastToItkImage(diffImg, itkVectorImagePointer);
	- filter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg));
	- filter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg), itkVectorImagePointer );
	-
	- filter->Update();
	- tensorImage = filter->GetOutput();
	-
	- QballFilterType::Pointer qballfilter = QballFilterType::New();
	- qballfilter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg));
	- qballfilter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg),
	- itkVectorImagePointer );
	- qballfilter->SetLambda(0.006);
	- qballfilter->SetNormalizationMethod(QballFilterType::QBAR_RAW_SIGNAL);
	- qballfilter->Update();
	- itkFeatureImage = qballfilter->GetCoefficientImage();
	-
	- itk::AdcImageFilter< short, double >::Pointer adcFilter = itk::AdcImageFilter< short, double >::New();
	- adcFilter->SetInput( itkVectorImagePointer );
	- adcFilter->SetGradientDirections(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg));
	- adcFilter->SetB_value(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg));
	- adcFilter->Update();
	- adcImage = adcFilter->GetOutput();
	-
	- if (dosampling && diffImg.IsNotNull())
	- {
	- ok = model->SampleKernels(diffImg, m_Parameters.m_SignalGen.m_MaskImage, tensorImage, itkFeatureImage, adcImage);
	- if (!ok)
	- {
	- QMessageBox::information( nullptr, "Parameter file not saved", "No valid prototype signals could be sampled.");
	- return;
	- }
	- }
	- }
	- }
	-
	- m_Parameters.SaveParameters(filename.toStdString());
	- m_ParameterFile = filename;
	-}
	-
	-void QmitkFiberfoxView::SaveParameters()
	-{
	- QString filename = QFileDialog::getSaveFileName(
	- 0,
	- tr("Save Parameters"),
	- m_ParameterFile,
	- tr("Fiberfox Parameters (*.ffp)") );
	-
	- SaveParameters(filename);
	-}
	-
	-void QmitkFiberfoxView::LoadParameters()
	-{
	- QString filename = QFileDialog::getOpenFileName(0, tr("Load Parameters"), QString(itksys::SystemTools::GetFilenamePath(m_ParameterFile.toStdString()).c_str()), tr("Fiberfox Parameters (*.ffp)") );
	- if(filename.isEmpty() \|\| filename.isNull())
	- return;
	-
	- m_ParameterFile = filename;
	- m_Parameters.LoadParameters(filename.toStdString());
	-
	- if (m_Parameters.m_MissingTags.size()>0)
	- {
	- QString missing("Parameter file might be corrupted. The following parameters could not be read: ");
	- missing += QString(m_Parameters.m_MissingTags.c_str());
	- missing += "\nDefault values have been assigned to the missing parameters.";
	- QMessageBox::information( nullptr, "Warning!", missing);
	- }
	-
	- // image generation parameters
	- m_Controls->m_SizeX->setValue(m_Parameters.m_SignalGen.m_ImageRegion.GetSize(0));
	- m_Controls->m_SizeY->setValue(m_Parameters.m_SignalGen.m_ImageRegion.GetSize(1));
	- m_Controls->m_SizeZ->setValue(m_Parameters.m_SignalGen.m_ImageRegion.GetSize(2));
	- m_Controls->m_SpacingX->setValue(m_Parameters.m_SignalGen.m_ImageSpacing[0]);
	- m_Controls->m_SpacingY->setValue(m_Parameters.m_SignalGen.m_ImageSpacing[1]);
	- m_Controls->m_SpacingZ->setValue(m_Parameters.m_SignalGen.m_ImageSpacing[2]);
	- m_Controls->m_NumGradientsBox->setValue(m_Parameters.m_SignalGen.GetNumWeightedVolumes());
	- m_Controls->m_BvalueBox->setValue(m_Parameters.m_SignalGen.GetBvalue());
	- m_Controls->m_SignalScaleBox->setValue(m_Parameters.m_SignalGen.m_SignalScale);
	- m_Controls->m_TEbox->setValue(m_Parameters.m_SignalGen.m_tEcho);
	- m_Controls->m_LineReadoutTimeBox->setValue(m_Parameters.m_SignalGen.m_tLine);
	- m_Controls->m_T2starBox->setValue(m_Parameters.m_SignalGen.m_tInhom);
	- m_Controls->m_EtlBox->setValue(m_Parameters.m_SignalGen.m_EchoTrainLength);
	- m_Controls->m_FiberRadius->setValue(m_Parameters.m_SignalGen.m_AxonRadius);
	- m_Controls->m_RelaxationBox->setChecked(m_Parameters.m_SignalGen.m_DoSimulateRelaxation);
	- m_Controls->m_EnforcePureFiberVoxelsBox->setChecked(m_Parameters.m_SignalGen.m_DoDisablePartialVolume);
	- m_Controls->m_ReversePhaseBox->setChecked(m_Parameters.m_SignalGen.m_ReversePhase);
	- m_Controls->m_PartialFourier->setValue(m_Parameters.m_SignalGen.m_PartialFourier);
	- m_Controls->m_TRbox->setValue(m_Parameters.m_SignalGen.m_tRep);
	- m_Controls->m_TIbox->setValue(m_Parameters.m_SignalGen.m_tInv);
	- m_Controls->m_NumCoilsBox->setValue(m_Parameters.m_SignalGen.m_NumberOfCoils);
	- m_Controls->m_CoilSensBox->setCurrentIndex(m_Parameters.m_SignalGen.m_CoilSensitivityProfile);
	- m_Controls->m_AcquisitionTypeBox->setCurrentIndex(m_Parameters.m_SignalGen.m_AcquisitionType);
	-
	- if (!m_Parameters.m_Misc.m_BvalsFile.empty())
	- {
	- m_Controls->m_UseBvalsBvecsBox->setChecked(true);
	- m_Controls->m_LoadBvalsEdit->setText(QString(m_Parameters.m_Misc.m_BvalsFile.c_str()));
	- }
	- else
	- m_Controls->m_LoadBvalsEdit->setText("-");
	-
	- if (!m_Parameters.m_Misc.m_BvecsFile.empty())
	- {
	- m_Controls->m_UseBvalsBvecsBox->setChecked(true);
	- m_Controls->m_LoadBvecsEdit->setText(QString(m_Parameters.m_Misc.m_BvecsFile.c_str()));
	- }
	- else
	- m_Controls->m_LoadBvecsEdit->setText("-");
	-
	- if (m_Parameters.m_NoiseModel!=nullptr)
	- {
	- m_Controls->m_AddNoise->setChecked(m_Parameters.m_Misc.m_DoAddNoise);
	- if (dynamic_cast<mitk::RicianNoiseModel<double>*>(m_Parameters.m_NoiseModel.get()))
	- {
	- m_Controls->m_NoiseDistributionBox->setCurrentIndex(0);
	- }
	- else if (dynamic_cast<mitk::ChiSquareNoiseModel<double>*>(m_Parameters.m_NoiseModel.get()))
	- {
	- m_Controls->m_NoiseDistributionBox->setCurrentIndex(1);
	- }
	- m_Controls->m_NoiseLevel->setValue(m_Parameters.m_NoiseModel->GetNoiseVariance());
	- }
	- else
	- {
	- m_Controls->m_AddNoise->setChecked(m_Parameters.m_Misc.m_DoAddNoise);
	- m_Controls->m_NoiseLevel->setValue(m_Parameters.m_SignalGen.m_NoiseVariance);
	- }
	-
	- m_Controls->m_VolumeFractionsBox->setChecked(m_Parameters.m_Misc.m_OutputAdditionalImages);
	- m_Controls->m_AdvancedOptionsBox_2->setChecked(m_Parameters.m_Misc.m_CheckAdvancedSignalOptionsBox);
	- m_Controls->m_AddGhosts->setChecked(m_Parameters.m_Misc.m_DoAddGhosts);
	- m_Controls->m_AddAliasing->setChecked(m_Parameters.m_Misc.m_DoAddAliasing);
	- m_Controls->m_AddDistortions->setChecked(m_Parameters.m_Misc.m_DoAddDistortions);
	- m_Controls->m_AddSpikes->setChecked(m_Parameters.m_Misc.m_DoAddSpikes);
	- m_Controls->m_AddEddy->setChecked(m_Parameters.m_Misc.m_DoAddEddyCurrents);
	- m_Controls->m_AddDrift->setChecked(m_Parameters.m_SignalGen.m_DoAddDrift);
	-
	- m_Controls->m_kOffsetBox->setValue(m_Parameters.m_SignalGen.m_KspaceLineOffset);
	- m_Controls->m_WrapBox->setValue(100*(1-m_Parameters.m_SignalGen.m_CroppingFactor));
	- m_Controls->m_DriftFactor->setValue(100*m_Parameters.m_SignalGen.m_Drift);
	- m_Controls->m_SpikeNumBox->setValue(m_Parameters.m_SignalGen.m_Spikes);
	- m_Controls->m_SpikeScaleBox->setValue(m_Parameters.m_SignalGen.m_SpikeAmplitude);
	- m_Controls->m_EddyGradientStrength->setValue(m_Parameters.m_SignalGen.m_EddyStrength);
	- m_Controls->m_AddGibbsRinging->setChecked(m_Parameters.m_SignalGen.m_DoAddGibbsRinging);
	- m_Controls->m_ZeroRinging->setValue(m_Parameters.m_SignalGen.m_ZeroRinging);
	- m_Controls->m_AddMotion->setChecked(m_Parameters.m_SignalGen.m_DoAddMotion);
	- m_Controls->m_RandomMotion->setChecked(m_Parameters.m_SignalGen.m_DoRandomizeMotion);
	- m_Controls->m_MotionVolumesBox->setText(QString(m_Parameters.m_Misc.m_MotionVolumesBox.c_str()));
	-
	- m_Controls->m_MaxTranslationBoxX->setValue(m_Parameters.m_SignalGen.m_Translation[0]);
	- m_Controls->m_MaxTranslationBoxY->setValue(m_Parameters.m_SignalGen.m_Translation[1]);
	- m_Controls->m_MaxTranslationBoxZ->setValue(m_Parameters.m_SignalGen.m_Translation[2]);
	- m_Controls->m_MaxRotationBoxX->setValue(m_Parameters.m_SignalGen.m_Rotation[0]);
	- m_Controls->m_MaxRotationBoxY->setValue(m_Parameters.m_SignalGen.m_Rotation[1]);
	- m_Controls->m_MaxRotationBoxZ->setValue(m_Parameters.m_SignalGen.m_Rotation[2]);
	-
	- m_Controls->m_Compartment1Box->setCurrentIndex(0);
	- m_Controls->m_Compartment2Box->setCurrentIndex(0);
	- m_Controls->m_Compartment3Box->setCurrentIndex(0);
	- m_Controls->m_Compartment4Box->setCurrentIndex(0);
	-
	- for (unsigned int i=0; i<m_Parameters.m_FiberModelList.size()+m_Parameters.m_NonFiberModelList.size(); i++)
	- {
	- mitk::DiffusionSignalModel<ScalarType>* signalModel = nullptr;
	- if (i<m_Parameters.m_FiberModelList.size())
	- signalModel = m_Parameters.m_FiberModelList.at(i);
	- else
	- signalModel = m_Parameters.m_NonFiberModelList.at(i-m_Parameters.m_FiberModelList.size());
	-
	- mitk::DataNode::Pointer compVolNode;
	- if ( signalModel->GetVolumeFractionImage().IsNotNull() )
	- {
	- compVolNode = mitk::DataNode::New();
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk(signalModel->GetVolumeFractionImage().GetPointer());
	- image->SetVolume(signalModel->GetVolumeFractionImage()->GetBufferPointer());
	-
	- compVolNode->SetData( image );
	- compVolNode->SetName("Compartment volume "+QString::number(signalModel->m_CompartmentId).toStdString());
	- GetDataStorage()->Add(compVolNode);
	- }
	-
	- switch (signalModel->m_CompartmentId)
	- {
	- case 1:
	- {
	- if (compVolNode.IsNotNull())
	- m_Controls->m_Comp1VolumeFraction->SetSelectedNode(compVolNode);
	- if (dynamic_cast<mitk::StickModel<>*>(signalModel))
	- {
	- mitk::StickModel<>* model = dynamic_cast<mitk::StickModel<>*>(signalModel);
	- m_Controls->m_StickWidget1->SetT2(model->GetT2());
	- m_Controls->m_StickWidget1->SetT1(model->GetT1());
	- m_Controls->m_StickWidget1->SetD(model->GetDiffusivity());
	- m_Controls->m_Compartment1Box->setCurrentIndex(0);
	- break;
	- }
	- else if (dynamic_cast<mitk::TensorModel<>*>(signalModel))
	- {
	- mitk::TensorModel<>* model = dynamic_cast<mitk::TensorModel<>*>(signalModel);
	- m_Controls->m_TensorWidget1->SetT2(model->GetT2());
	- m_Controls->m_TensorWidget1->SetT1(model->GetT1());
	- m_Controls->m_TensorWidget1->SetD1(model->GetDiffusivity1());
	- m_Controls->m_TensorWidget1->SetD2(model->GetDiffusivity2());
	- m_Controls->m_TensorWidget1->SetD3(model->GetDiffusivity3());
	- m_Controls->m_Compartment1Box->setCurrentIndex(2);
	- break;
	- }
	- else if (dynamic_cast<mitk::RawShModel<>*>(signalModel))
	- {
	- mitk::RawShModel<>* model = dynamic_cast<mitk::RawShModel<>*>(signalModel);
	- m_Controls->m_PrototypeWidget1->SetNumberOfSamples(model->GetMaxNumKernels());
	- m_Controls->m_PrototypeWidget1->SetMinFa(model->GetFaRange().first);
	- m_Controls->m_PrototypeWidget1->SetMaxFa(model->GetFaRange().second);
	- m_Controls->m_PrototypeWidget1->SetMinAdc(model->GetAdcRange().first);
	- m_Controls->m_PrototypeWidget1->SetMaxAdc(model->GetAdcRange().second);
	- m_Controls->m_Compartment1Box->setCurrentIndex(3);
	- break;
	- }
	- break;
	- }
	- case 2:
	- {
	- if (compVolNode.IsNotNull())
	- m_Controls->m_Comp2VolumeFraction->SetSelectedNode(compVolNode);
	- if (dynamic_cast<mitk::StickModel<>*>(signalModel))
	- {
	- mitk::StickModel<>* model = dynamic_cast<mitk::StickModel<>*>(signalModel);
	- m_Controls->m_StickWidget2->SetT2(model->GetT2());
	- m_Controls->m_StickWidget2->SetT1(model->GetT1());
	- m_Controls->m_StickWidget2->SetD(model->GetDiffusivity());
	- m_Controls->m_Compartment2Box->setCurrentIndex(1);
	- break;
	- }
	- else if (dynamic_cast<mitk::TensorModel<>*>(signalModel))
	- {
	- mitk::TensorModel<>* model = dynamic_cast<mitk::TensorModel<>*>(signalModel);
	- m_Controls->m_TensorWidget2->SetT2(model->GetT2());
	- m_Controls->m_TensorWidget2->SetT1(model->GetT1());
	- m_Controls->m_TensorWidget2->SetD1(model->GetDiffusivity1());
	- m_Controls->m_TensorWidget2->SetD2(model->GetDiffusivity2());
	- m_Controls->m_TensorWidget2->SetD3(model->GetDiffusivity3());
	- m_Controls->m_Compartment2Box->setCurrentIndex(3);
	- break;
	- }
	- break;
	- }
	- case 3:
	- {
	- if (compVolNode.IsNotNull())
	- m_Controls->m_Comp3VolumeFraction->SetSelectedNode(compVolNode);
	- if (dynamic_cast<mitk::BallModel<>*>(signalModel))
	- {
	- mitk::BallModel<>* model = dynamic_cast<mitk::BallModel<>*>(signalModel);
	- m_Controls->m_BallWidget1->SetT2(model->GetT2());
	- m_Controls->m_BallWidget1->SetT1(model->GetT1());
	- m_Controls->m_BallWidget1->SetD(model->GetDiffusivity());
	- m_Controls->m_Compartment3Box->setCurrentIndex(0);
	- break;
	- }
	- else if (dynamic_cast<mitk::AstroStickModel<>*>(signalModel))
	- {
	- mitk::AstroStickModel<>* model = dynamic_cast<mitk::AstroStickModel<>*>(signalModel);
	- m_Controls->m_AstrosticksWidget1->SetT2(model->GetT2());
	- m_Controls->m_AstrosticksWidget1->SetT1(model->GetT1());
	- m_Controls->m_AstrosticksWidget1->SetD(model->GetDiffusivity());
	- m_Controls->m_AstrosticksWidget1->SetRandomizeSticks(model->GetRandomizeSticks());
	- m_Controls->m_Compartment3Box->setCurrentIndex(1);
	- break;
	- }
	- else if (dynamic_cast<mitk::DotModel<>*>(signalModel))
	- {
	- mitk::DotModel<>* model = dynamic_cast<mitk::DotModel<>*>(signalModel);
	- m_Controls->m_DotWidget1->SetT2(model->GetT2());
	- m_Controls->m_DotWidget1->SetT1(model->GetT1());
	- m_Controls->m_Compartment3Box->setCurrentIndex(2);
	- break;
	- }
	- else if (dynamic_cast<mitk::RawShModel<>*>(signalModel))
	- {
	- mitk::RawShModel<>* model = dynamic_cast<mitk::RawShModel<>*>(signalModel);
	- m_Controls->m_PrototypeWidget3->SetNumberOfSamples(model->GetMaxNumKernels());
	- m_Controls->m_PrototypeWidget3->SetMinFa(model->GetFaRange().first);
	- m_Controls->m_PrototypeWidget3->SetMaxFa(model->GetFaRange().second);
	- m_Controls->m_PrototypeWidget3->SetMinAdc(model->GetAdcRange().first);
	- m_Controls->m_PrototypeWidget3->SetMaxAdc(model->GetAdcRange().second);
	- m_Controls->m_Compartment3Box->setCurrentIndex(3);
	- break;
	- }
	- break;
	- }
	- case 4:
	- {
	- if (compVolNode.IsNotNull())
	- m_Controls->m_Comp4VolumeFraction->SetSelectedNode(compVolNode);
	- if (dynamic_cast<mitk::BallModel<>*>(signalModel))
	- {
	- mitk::BallModel<>* model = dynamic_cast<mitk::BallModel<>*>(signalModel);
	- m_Controls->m_BallWidget2->SetT2(model->GetT2());
	- m_Controls->m_BallWidget2->SetT1(model->GetT1());
	- m_Controls->m_BallWidget2->SetD(model->GetDiffusivity());
	- m_Controls->m_Compartment4Box->setCurrentIndex(1);
	- break;
	- }
	- else if (dynamic_cast<mitk::AstroStickModel<>*>(signalModel))
	- {
	- mitk::AstroStickModel<>* model = dynamic_cast<mitk::AstroStickModel<>*>(signalModel);
	- m_Controls->m_AstrosticksWidget2->SetT2(model->GetT2());
	- m_Controls->m_AstrosticksWidget2->SetT1(model->GetT1());
	- m_Controls->m_AstrosticksWidget2->SetD(model->GetDiffusivity());
	- m_Controls->m_AstrosticksWidget2->SetRandomizeSticks(model->GetRandomizeSticks());
	- m_Controls->m_Compartment4Box->setCurrentIndex(2);
	- break;
	- }
	- else if (dynamic_cast<mitk::DotModel<>*>(signalModel))
	- {
	- mitk::DotModel<>* model = dynamic_cast<mitk::DotModel<>*>(signalModel);
	- m_Controls->m_DotWidget2->SetT2(model->GetT2());
	- m_Controls->m_DotWidget2->SetT1(model->GetT1());
	- m_Controls->m_Compartment4Box->setCurrentIndex(3);
	- break;
	- }
	- else if (dynamic_cast<mitk::RawShModel<>*>(signalModel))
	- {
	- mitk::RawShModel<>* model = dynamic_cast<mitk::RawShModel<>*>(signalModel);
	- m_Controls->m_PrototypeWidget4->SetNumberOfSamples(model->GetMaxNumKernels());
	- m_Controls->m_PrototypeWidget4->SetMinFa(model->GetFaRange().first);
	- m_Controls->m_PrototypeWidget4->SetMaxFa(model->GetFaRange().second);
	- m_Controls->m_PrototypeWidget4->SetMinAdc(model->GetAdcRange().first);
	- m_Controls->m_PrototypeWidget4->SetMaxAdc(model->GetAdcRange().second);
	- m_Controls->m_Compartment4Box->setCurrentIndex(4);
	- break;
	- }
	- break;
	- }
	- }
	- }
	-
	- if ( m_Parameters.m_SignalGen.m_MaskImage )
	- {
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk(m_Parameters.m_SignalGen.m_MaskImage.GetPointer());
	- image->SetVolume(m_Parameters.m_SignalGen.m_MaskImage->GetBufferPointer());
	-
	- mitk::DataNode::Pointer node = mitk::DataNode::New();
	- node->SetData( image );
	- node->SetName("Tissue mask");
	- GetDataStorage()->Add(node);
	- m_Controls->m_MaskComboBox->SetSelectedNode(node);
	- }
	-
	- if ( m_Parameters.m_SignalGen.m_FrequencyMap )
	- {
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk(m_Parameters.m_SignalGen.m_FrequencyMap.GetPointer());
	- image->SetVolume(m_Parameters.m_SignalGen.m_FrequencyMap->GetBufferPointer());
	-
	- mitk::DataNode::Pointer node = mitk::DataNode::New();
	- node->SetData( image );
	- node->SetName("Frequency map");
	- GetDataStorage()->Add(node);
	- m_Controls->m_FrequencyMapBox->SetSelectedNode(node);
	- }
	-}
	-
	-void QmitkFiberfoxView::ShowAdvancedOptions(int state)
	-{
	- if (state)
	- {
	- m_Controls->m_AdvancedSignalOptionsFrame->setVisible(true);
	- m_Controls->m_AdvancedOptionsBox_2->setChecked(true);
	- }
	- else
	- {
	- m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false);
	- m_Controls->m_AdvancedOptionsBox_2->setChecked(false);
	- }
	-}
	-
	-void QmitkFiberfoxView::Comp1ModelFrameVisibility(int index)
	-{
	- m_Controls->m_StickWidget1->setVisible(false);
	- m_Controls->m_ZeppelinWidget1->setVisible(false);
	- m_Controls->m_TensorWidget1->setVisible(false);
	- m_Controls->m_PrototypeWidget1->setVisible(false);
	-
	- switch (index)
	- {
	- case 0:
	- m_Controls->m_StickWidget1->setVisible(true);
	- break;
	- case 1:
	- m_Controls->m_ZeppelinWidget1->setVisible(true);
	- break;
	- case 2:
	- m_Controls->m_TensorWidget1->setVisible(true);
	- break;
	- case 3:
	- m_Controls->m_PrototypeWidget1->setVisible(true);
	- break;
	- }
	-}
	-
	-void QmitkFiberfoxView::Comp2ModelFrameVisibility(int index)
	-{
	- m_Controls->m_StickWidget2->setVisible(false);
	- m_Controls->m_ZeppelinWidget2->setVisible(false);
	- m_Controls->m_TensorWidget2->setVisible(false);
	- m_Controls->m_Comp2FractionFrame->setVisible(false);
	-
	- switch (index)
	- {
	- case 0:
	- break;
	- case 1:
	- m_Controls->m_StickWidget2->setVisible(true);
	- m_Controls->m_Comp2FractionFrame->setVisible(true);
	- break;
	- case 2:
	- m_Controls->m_ZeppelinWidget2->setVisible(true);
	- m_Controls->m_Comp2FractionFrame->setVisible(true);
	- break;
	- case 3:
	- m_Controls->m_TensorWidget2->setVisible(true);
	- m_Controls->m_Comp2FractionFrame->setVisible(true);
	- break;
	- }
	-}
	-
	-void QmitkFiberfoxView::Comp3ModelFrameVisibility(int index)
	-{
	- m_Controls->m_BallWidget1->setVisible(false);
	- m_Controls->m_AstrosticksWidget1->setVisible(false);
	- m_Controls->m_DotWidget1->setVisible(false);
	- m_Controls->m_PrototypeWidget3->setVisible(false);
	-
	- switch (index)
	- {
	- case 0:
	- m_Controls->m_BallWidget1->setVisible(true);
	- break;
	- case 1:
	- m_Controls->m_AstrosticksWidget1->setVisible(true);
	- break;
	- case 2:
	- m_Controls->m_DotWidget1->setVisible(true);
	- break;
	- case 3:
	- m_Controls->m_PrototypeWidget3->setVisible(true);
	- break;
	- }
	-}
	-
	-void QmitkFiberfoxView::Comp4ModelFrameVisibility(int index)
	-{
	- m_Controls->m_BallWidget2->setVisible(false);
	- m_Controls->m_AstrosticksWidget2->setVisible(false);
	- m_Controls->m_DotWidget2->setVisible(false);
	- m_Controls->m_PrototypeWidget4->setVisible(false);
	- m_Controls->m_Comp4FractionFrame->setVisible(false);
	-
	- switch (index)
	- {
	- case 0:
	- break;
	- case 1:
	- m_Controls->m_BallWidget2->setVisible(true);
	- m_Controls->m_Comp4FractionFrame->setVisible(true);
	- break;
	- case 2:
	- m_Controls->m_AstrosticksWidget2->setVisible(true);
	- m_Controls->m_Comp4FractionFrame->setVisible(true);
	- break;
	- case 3:
	- m_Controls->m_DotWidget2->setVisible(true);
	- m_Controls->m_Comp4FractionFrame->setVisible(true);
	- break;
	- case 4:
	- m_Controls->m_PrototypeWidget4->setVisible(true);
	- m_Controls->m_Comp4FractionFrame->setVisible(true);
	- break;
	- }
	-}
	-
	-void QmitkFiberfoxView::OnAddMotion(int value)
	-{
	- if (value>0)
	- m_Controls->m_MotionArtifactFrame->setVisible(true);
	- else
	- m_Controls->m_MotionArtifactFrame->setVisible(false);
	-}
	-
	-void QmitkFiberfoxView::OnAddDrift(int value)
	-{
	- if (value>0)
	- m_Controls->m_DriftFrame->setVisible(true);
	- else
	- m_Controls->m_DriftFrame->setVisible(false);
	-}
	-
	-void QmitkFiberfoxView::OnAddAliasing(int value)
	-{
	- if (value>0)
	- m_Controls->m_AliasingFrame->setVisible(true);
	- else
	- m_Controls->m_AliasingFrame->setVisible(false);
	-}
	-
	-void QmitkFiberfoxView::OnAddSpikes(int value)
	-{
	- if (value>0)
	- m_Controls->m_SpikeFrame->setVisible(true);
	- else
	- m_Controls->m_SpikeFrame->setVisible(false);
	-}
	-
	-void QmitkFiberfoxView::OnAddEddy(int value)
	-{
	- if (value>0)
	- m_Controls->m_EddyFrame->setVisible(true);
	- else
	- m_Controls->m_EddyFrame->setVisible(false);
	-}
	-
	-void QmitkFiberfoxView::OnAddDistortions(int value)
	-{
	- if (value>0)
	- m_Controls->m_DistortionsFrame->setVisible(true);
	- else
	- m_Controls->m_DistortionsFrame->setVisible(false);
	-}
	-
	-void QmitkFiberfoxView::OnAddGhosts(int value)
	-{
	- if (value>0)
	- m_Controls->m_GhostFrame->setVisible(true);
	- else
	- m_Controls->m_GhostFrame->setVisible(false);
	-}
	-
	-void QmitkFiberfoxView::OnAddNoise(int value)
	-{
	- if (value>0)
	- m_Controls->m_NoiseFrame->setVisible(true);
	- else
	- m_Controls->m_NoiseFrame->setVisible(false);
	-}
	-
	-void QmitkFiberfoxView::OnAddRinging(int value)
	-{
	- if (value>0)
	- m_Controls->m_ZeroRinging->setVisible(true);
	- else
	- m_Controls->m_ZeroRinging->setVisible(false);
	-}
	-
	-QmitkFiberfoxView::GradientListType QmitkFiberfoxView::GenerateHalfShell(int NPoints)
	-{
	- NPoints *= 2;
	- GradientListType pointshell;
	-
	- int numB0 = NPoints/20;
	- if (numB0==0)
	- numB0=1;
	- GradientType g;
	- g.Fill(0.0);
	- for (int i=0; i<numB0; i++)
	- pointshell.push_back(g);
	-
	- if (NPoints==0)
	- return pointshell;
	-
	- vnl_vector<double> theta; theta.set_size(NPoints);
	- vnl_vector<double> phi; phi.set_size(NPoints);
	- double C = sqrt(4*itk::Math::pi);
	- phi(0) = 0.0;
	- phi(NPoints-1) = 0.0;
	- for(int i=0; i<NPoints; i++)
	- {
	- theta(i) = acos(-1.0+2.0*i/(NPoints-1.0)) - itk::Math::pi / 2.0;
	- if( i>0 && i<NPoints-1)
	- {
	- phi(i) = (phi(i-1) + C /
	- sqrt(NPoints(1-(-1.0+2.0i/(NPoints-1.0))(-1.0+2.0i/(NPoints-1.0)))));
	- // % (2*DIST_POINTSHELL_PI);
	- }
	- }
	-
	- for(int i=0; i<NPoints; i++)
	- {
	- g[2] = sin(theta(i));
	- if (g[2]<0)
	- continue;
	- g[0] = cos(theta(i)) * cos(phi(i));
	- g[1] = cos(theta(i)) * sin(phi(i));
	- pointshell.push_back(g);
	- }
	-
	- return pointshell;
	-}
	-
	-template<int ndirs>
	-std::vector<itk::Vector<double,3> > QmitkFiberfoxView::MakeGradientList()
	-{
	- std::vector<itk::Vector<double,3> > retval;
	- vnl_matrix_fixed<double, 3, ndirs>* U =
	- itk::PointShell<ndirs, vnl_matrix_fixed<double, 3, ndirs> >::DistributePointShell();
	-
	-
	- // Add 0 vector for B0
	- int numB0 = ndirs/10;
	- if (numB0==0)
	- numB0=1;
	- itk::Vector<double,3> v;
	- v.Fill(0.0);
	- for (int i=0; i<numB0; i++)
	- {
	- retval.push_back(v);
	- }
	-
	- for(int i=0; i<ndirs;i++)
	- {
	- itk::Vector<double,3> v;
	- v[0] = U->get(0,i); v[1] = U->get(1,i); v[2] = U->get(2,i);
	- retval.push_back(v);
	- }
	-
	- return retval;
	-}
	-
	-void QmitkFiberfoxView::GenerateImage()
	-{
	- if (m_Controls->m_FiberBundleComboBox->GetSelectedNode().IsNull() && !mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( m_Controls->m_TemplateComboBox->GetSelectedNode()))
	- {
	- mitk::Image::Pointer image = mitk::ImageGenerator::GenerateGradientImage<unsigned int>(
	- m_Controls->m_SizeX->value(),
	- m_Controls->m_SizeY->value(),
	- m_Controls->m_SizeZ->value(),
	- m_Controls->m_SpacingX->value(),
	- m_Controls->m_SpacingY->value(),
	- m_Controls->m_SpacingZ->value());
	- mitk::Point3D origin;
	- origin[0] = m_Controls->m_SpacingX->value()/2;
	- origin[1] = m_Controls->m_SpacingY->value()/2;
	- origin[2] = m_Controls->m_SpacingZ->value()/2;
	- image->SetOrigin(origin);
	-
	- mitk::DataNode::Pointer node = mitk::DataNode::New();
	- node->SetData( image );
	- node->SetName("Dummy");
	- GetDataStorage()->Add(node);
	- m_SelectedImageNode = node;
	-
	- mitk::BaseData::Pointer basedata = node->GetData();
	- if (basedata.IsNotNull())
	- {
	- mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true );
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- }
	- UpdateGui();
	- QMessageBox::information(nullptr, "Template image generated", "You have selected no fiber bundle or diffusion-weighted image, which can be used to simulate a new diffusion-weighted image. A template image with the specified geometry has been generated that can be used to draw artificial fibers (see view 'Fiber Generator').");
	- }
	- else if (m_Controls->m_FiberBundleComboBox->GetSelectedNode().IsNotNull())
	- SimulateImageFromFibers(m_Controls->m_FiberBundleComboBox->GetSelectedNode());
	- else if ( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( m_Controls->m_TemplateComboBox->GetSelectedNode()) )
	- SimulateForExistingDwi(m_Controls->m_TemplateComboBox->GetSelectedNode());
	- else
	- QMessageBox::information(nullptr, "No image generated", "You have selected no fiber bundle or diffusion-weighted image, which can be used to simulate a new diffusion-weighted image.");
	-}
	-
	-void QmitkFiberfoxView::SetFocus()
	-{
	-}
	-
	-void QmitkFiberfoxView::SimulateForExistingDwi(mitk::DataNode* imageNode)
	-{
	- bool isDiffusionImage( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast<mitk::Image *>(imageNode->GetData())) );
	- if ( !isDiffusionImage )
	- {
	- return;
	- }
	-
	- UpdateParametersFromGui();
	-
	- mitk::Image::Pointer diffImg = dynamic_cast<mitk::Image*>(imageNode->GetData());
	- ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New();
	- mitk::CastToItkImage(diffImg, itkVectorImagePointer);
	-
	- m_TractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New();
	- m_Parameters.m_Misc.m_ParentNode = imageNode;
	- m_Parameters.m_SignalGen.m_SignalScale = 1;
	-
	- m_Parameters.m_Misc.m_ResultNode->SetName("b"+QString::number(m_Parameters.m_SignalGen.GetBvalue()).toStdString()
	- +"_"+m_Parameters.m_Misc.m_SignalModelString
	- +m_Parameters.m_Misc.m_ArtifactModelString);
	-
	- m_Parameters.ApplyDirectionMatrix();
	- m_TractsToDwiFilter->SetParameters(m_Parameters);
	- m_TractsToDwiFilter->SetInputImage(itkVectorImagePointer);
	- m_Thread.start(QThread::LowestPriority);
	-}
	-
	-void QmitkFiberfoxView::SimulateImageFromFibers(mitk::DataNode* fiberNode)
	-{
	- mitk::FiberBundle::Pointer fiberBundle = dynamic_cast<mitk::FiberBundle*>(fiberNode->GetData());
	- if (fiberBundle->GetNumFibers()<=0) { return; }
	-
	- UpdateParametersFromGui();
	-
	- m_TractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New();
	- m_Parameters.m_Misc.m_ParentNode = fiberNode;
	-
	- m_Parameters.m_Misc.m_ResultNode->SetName("b"+QString::number(m_Parameters.m_SignalGen.GetBvalue()).toStdString()
	- +"_"+m_Parameters.m_Misc.m_SignalModelString
	- +m_Parameters.m_Misc.m_ArtifactModelString);
	-
	- if ( m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull()
	- && mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast<mitk::Image*>
	- (m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()) ) )
	- {
	- bool first = true;
	- bool ok = true;
	- mitk::Image::Pointer diffImg = dynamic_cast<mitk::Image*>(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData());
	- itk::Image< itk::DiffusionTensor3D< double >, 3 >::Pointer tensorImage = nullptr;
	- const int shOrder = 2;
	- typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,shOrder,ODF_SAMPLING_SIZE> QballFilterType;
	- QballFilterType::CoefficientImageType::Pointer itkFeatureImage = nullptr;
	- ItkDoubleImgType::Pointer adcImage = nullptr;
	-
	- for (unsigned int i=0; i<m_Parameters.m_FiberModelList.size()+m_Parameters.m_NonFiberModelList.size(); i++)
	- {
	- mitk::RawShModel<>* model = nullptr;
	- if (i<m_Parameters.m_FiberModelList.size())
	- model = dynamic_cast< mitk::RawShModel<>* >(m_Parameters.m_FiberModelList.at(i));
	- else
	- model = dynamic_cast< mitk::RawShModel<>* >(m_Parameters.m_NonFiberModelList.at(i-m_Parameters.m_FiberModelList.size()));
	-
	- if (model!=0 && model->GetNumberOfKernels()<=0)
	- {
	- if (first==true)
	- {
	- ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New();
	- mitk::CastToItkImage(diffImg, itkVectorImagePointer);
	-
	- typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, double > TensorReconstructionImageFilterType;
	- TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New();
	- filter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg));
	- filter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg),
	- itkVectorImagePointer );
	- filter->Update();
	- tensorImage = filter->GetOutput();
	-
	- QballFilterType::Pointer qballfilter = QballFilterType::New();
	- qballfilter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg),
	- itkVectorImagePointer );
	- qballfilter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg));
	- qballfilter->SetLambda(0.006);
	- qballfilter->SetNormalizationMethod(QballFilterType::QBAR_RAW_SIGNAL);
	- qballfilter->Update();
	- itkFeatureImage = qballfilter->GetCoefficientImage();
	-
	- itk::AdcImageFilter< short, double >::Pointer adcFilter = itk::AdcImageFilter< short, double >::New();
	- adcFilter->SetInput( itkVectorImagePointer );
	- adcFilter->SetGradientDirections(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg));
	- adcFilter->SetB_value(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg));
	- adcFilter->Update();
	- adcImage = adcFilter->GetOutput();
	- }
	- ok = model->SampleKernels(diffImg, m_Parameters.m_SignalGen.m_MaskImage, tensorImage, itkFeatureImage, adcImage);
	- if (!ok)
	- break;
	- }
	- }
	-
	- if (!ok)
	- {
	- QMessageBox::information( nullptr, "Simulation cancelled", "No valid prototype signals could be sampled.");
	- return;
	- }
	- }
	- else if ( m_Controls->m_Compartment1Box->currentIndex()==3
	- \|\| m_Controls->m_Compartment3Box->currentIndex()==3
	- \|\| m_Controls->m_Compartment4Box->currentIndex()==4 )
	- {
	- QMessageBox::information( nullptr, "Simulation cancelled",
	- "Prototype signal but no diffusion-weighted image selected to sample signal from.");
	- return;
	- }
	-
	- m_Parameters.ApplyDirectionMatrix();
	- m_TractsToDwiFilter->SetParameters(m_Parameters);
	- m_TractsToDwiFilter->SetFiberBundle(fiberBundle);
	- m_Thread.start(QThread::LowestPriority);
	-}
	-
	-void QmitkFiberfoxView::SetBvalsEdit()
	-{
	- // SELECT FOLDER DIALOG
	- std::string filename;
	- filename = QFileDialog::getOpenFileName(nullptr, "Select bvals file", QString(filename.c_str())).toStdString();
	-
	- if (filename.empty())
	- m_Controls->m_LoadBvalsEdit->setText("-");
	- else
	- m_Controls->m_LoadBvalsEdit->setText(QString(filename.c_str()));
	-}
	-
	-void QmitkFiberfoxView::SetBvecsEdit()
	-{
	- // SELECT FOLDER DIALOG
	- std::string filename;
	- filename = QFileDialog::getOpenFileName(nullptr, "Select bvecs file", QString(filename.c_str())).toStdString();
	-
	- if (filename.empty())
	- m_Controls->m_LoadBvecsEdit->setText("-");
	- else
	- m_Controls->m_LoadBvecsEdit->setText(QString(filename.c_str()));
	-}
	-
	-void QmitkFiberfoxView::SetOutputPath()
	-{
	- // SELECT FOLDER DIALOG
	- std::string outputPath;
	- outputPath = QFileDialog::getExistingDirectory(nullptr, "Save images to...", QString(outputPath.c_str())).toStdString();
	-
	- if (outputPath.empty())
	- m_Controls->m_SavePathEdit->setText("-");
	- else
	- {
	- outputPath += "/";
	- m_Controls->m_SavePathEdit->setText(QString(outputPath.c_str()));
	- }
	-}
	-
	-void QmitkFiberfoxView::UpdateGui()
	-{
	- OnTlineChanged();
	- m_Controls->m_GeometryFrame->setEnabled(true);
	- m_Controls->m_GeometryMessage->setVisible(false);
	- m_Controls->m_DiffusionPropsMessage->setVisible(false);
	-
	- m_Controls->m_LoadGradientsFrame->setVisible(false);
	- m_Controls->m_GenerateGradientsFrame->setVisible(false);
	- if (m_Controls->m_UseBvalsBvecsBox->isChecked())
	- m_Controls->m_LoadGradientsFrame->setVisible(true);
	- else
	- m_Controls->m_GenerateGradientsFrame->setVisible(true);
	-
	- // Signal generation gui
	- if (m_Controls->m_MaskComboBox->GetSelectedNode().IsNotNull() \|\| m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull())
	- {
	- m_Controls->m_GeometryMessage->setVisible(true);
	- m_Controls->m_GeometryFrame->setEnabled(false);
	- }
	-
	- if ( m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull()
	- && mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(
	- dynamic_cast<mitk::Image*>(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()) ) )
	- {
	- m_Controls->m_DiffusionPropsMessage->setVisible(true);
	- m_Controls->m_GeometryMessage->setVisible(true);
	- m_Controls->m_GeometryFrame->setEnabled(false);
	-
	- m_Controls->m_LoadGradientsFrame->setVisible(false);
	- m_Controls->m_GenerateGradientsFrame->setVisible(false);
	- }
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxView.h
	deleted file mode 100644
	index 21345843cd..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxView.h
	+++ /dev/null
	@@ -1,173 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-
	-#include <berryISelectionListener.h>
	-#include <berryIStructuredSelection.h>
	-
	-#include <QmitkAbstractView.h>
	-#include "ui_QmitkFiberfoxViewControls.h"
	-#include <itkVectorImage.h>
	-#include <itkVectorContainer.h>
	-#include <itkOrientationDistributionFunction.h>
	-
	-#ifndef Q_MOC_RUN
	-#include <mitkFiberBundle.h>
	-#include <mitkPlanarEllipse.h>
	-#include <mitkDiffusionNoiseModel.h>
	-#include <mitkDiffusionSignalModel.h>
	-#include <mitkRicianNoiseModel.h>
	-#include <itkTractsToDWIImageFilter.h>
	-#include <mitkTensorModel.h>
	-#include <mitkBallModel.h>
	-#include <mitkStickModel.h>
	-#include <mitkAstroStickModel.h>
	-#include <mitkDotModel.h>
	-#include <mitkFiberfoxParameters.h>
	-#include <itkStatisticsImageFilter.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-#endif
	-
	-#include <QThread>
	-#include <QObject>
	-#include <QTimer>
	-#include <QTime>
	-
	-/*!
	-\brief View for fiber based diffusion software phantoms (Fiberfox). See "Fiberfox: Facilitating the creation of realistic white matter software phantoms" (DOI: 10.1002/mrm.25045) for details.
	-*/
	-
	-// Forward Qt class declarations
	-
	-class QmitkFiberfoxView;
	-
	-class QmitkFiberfoxWorker : public QObject
	-{
	- Q_OBJECT
	-
	-public:
	-
	- QmitkFiberfoxWorker(QmitkFiberfoxView* view);
	-
	-public slots:
	-
	- void run();
	-
	-private:
	-
	- QmitkFiberfoxView* m_View;
	-};
	-
	-class QmitkFiberfoxView : public QmitkAbstractView
	-{
	-
	- // this is needed for all Qt objects that should have a Qt meta-object
	- // (everything that derives from QObject and wants to have signal/slots)
	- Q_OBJECT
	-
	-public:
	-
	- static const std::string VIEW_ID;
	-
	- QmitkFiberfoxView();
	- virtual ~QmitkFiberfoxView();
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	- void SetFocus() override;
	-
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionType GradientDirectionType;
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionsContainerType GradientDirectionContainerType;
	- typedef itk::Vector<double,3> GradientType;
	- typedef std::vector<GradientType> GradientListType;
	- typedef itk::VectorImage< short, 3 > ItkDwiType;
	- typedef itk::Image<double, 3> ItkDoubleImgType;
	- typedef itk::Image<float, 3> ItkFloatImgType;
	- typedef itk::Image<unsigned char, 3> ItkUcharImgType;
	-
	- template<int ndirs> std::vector<itk::Vector<double,3> > MakeGradientList();
	-
	-protected slots:
	-
	- void SetOutputPath(); ///< path where image is automatically saved to after the simulation is finished
	- void LoadParameters(); ///< load fiberfox parameters
	- void SaveParameters(); ///< save fiberfox parameters
	- void SetBvalsEdit();
	- void SetBvecsEdit();
	-
	- void BeforeThread();
	- void AfterThread();
	- void KillThread(); ///< abort simulation
	- void UpdateSimulationStatus(); ///< print simulation progress and satus messages
	-
	- void GenerateImage(); ///< start image simulation
	- void Comp1ModelFrameVisibility(int index); ///< only show parameters of selected signal model for compartment 1
	- void Comp2ModelFrameVisibility(int index); ///< only show parameters of selected signal model for compartment 2
	- void Comp3ModelFrameVisibility(int index); ///< only show parameters of selected signal model for compartment 3
	- void Comp4ModelFrameVisibility(int index); ///< only show parameters of selected signal model for compartment 4
	- void ShowAdvancedOptions(int state);
	-
	- /** update GUI elements */
	- void OnAddNoise(int value);
	- void OnAddGhosts(int value);
	- void OnAddDistortions(int value);
	- void OnAddEddy(int value);
	- void OnAddSpikes(int value);
	- void OnAddAliasing(int value);
	- void OnAddMotion(int value);
	- void OnAddDrift(int value);
	- void OnAddRinging(int value);
	- void OnMaskSelected(int value);
	- void OnFibSelected(int value);
	- void OnTemplateSelected(int value);
	- void OnBvalsBvecsCheck(int value);
	- void OnTlineChanged();
	-
	-protected:
	-
	- GradientListType GenerateHalfShell(int NPoints); ///< generate vectors distributed over the halfsphere
	-
	- Ui::QmitkFiberfoxViewControls* m_Controls;
	-
	- void SimulateForExistingDwi(mitk::DataNode* imageNode); ///< add artifacts to existing diffusion weighted image
	- void SimulateImageFromFibers(mitk::DataNode* fiberNode); ///< simulate new diffusion weighted image
	- void UpdateParametersFromGui(); ///< update fiberfox paramater object
	- void UpdateGui(); ///< enable/disbale buttons etc. according to current datamanager selection
	- void PlanarFigureSelected( itk::Object* object, const itk::EventObject& );
	- void EnableCrosshairNavigation(); ///< enable crosshair navigation if planar figure interaction ends
	- void DisableCrosshairNavigation(); ///< disable crosshair navigation if planar figure interaction starts
	-
	- void SaveParameters(QString filename);
	-
	-
	- mitk::DataNode::Pointer m_SelectedImageNode;
	-
	- QString m_ParameterFile; ///< parameter file name
	-
	- // GUI thread
	- QmitkFiberfoxWorker m_Worker; ///< runs filter
	- QThread m_Thread; ///< worker thread
	- bool m_ThreadIsRunning;
	- QTimer* m_SimulationTimer;
	- QTime m_SimulationTime;
	- QString m_SimulationStatusText;
	-
	- /** Image filters that do all the simulations. */
	- itk::TractsToDWIImageFilter< short >::Pointer m_TractsToDwiFilter;
	-
	- friend class QmitkFiberfoxWorker;
	- FiberfoxParameters m_Parameters;
	-};
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxViewControls.ui
	deleted file mode 100644
	index fe7ddca672..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxViewControls.ui
	+++ /dev/null
	@@ -1,2891 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<ui version="4.0">
	- <class>QmitkFiberfoxViewControls</class>
	- <widget class="QWidget" name="QmitkFiberfoxViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>490</width>
	- <height>2775</height>
	- </rect>
	- </property>
	- <property name="windowTitle">
	- <string>Form</string>
	- </property>
	- <property name="styleSheet">
	- <string notr="true"/>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_2">
	- <item row="3" column="0">
	- <widget class="QGroupBox" name="m_IntraAxonalGroupBox">
	- <property name="styleSheet">
	- <string notr="true">QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <property name="title">
	- <string>Intra-axonal Compartment</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_13">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="3" column="0">
	- <widget class="QmitkTensorModelParametersWidget" name="m_TensorWidget1" native="true"/>
	- </item>
	- <item row="1" column="0">
	- <widget class="QmitkStickModelParametersWidget" name="m_StickWidget1" native="true"/>
	- </item>
	- <item row="4" column="0">
	- <widget class="QmitkPrototypeSignalParametersWidget" name="m_PrototypeWidget1" native="true"/>
	- </item>
	- <item row="0" column="0">
	- <widget class="QComboBox" name="m_Compartment1Box">
	- <property name="toolTip">
	- <string>Select signal model for intra-axonal compartment.</string>
	- </property>
	- <item>
	- <property name="text">
	- <string>Stick Model</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Zeppelin Model</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Tensor Model</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Prototype Signal</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QmitkZeppelinModelParametersWidget" name="m_ZeppelinWidget1" native="true"/>
	- </item>
	- <item row="5" column="0">
	- <widget class="QFrame" name="m_Comp1FractionFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_26">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_NoiseLabel_6">
	- <property name="text">
	- <string>Volume Fraction:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBoxWithSelectNone" name="m_Comp1VolumeFraction">
	- <property name="toolTip">
	- <string>Optional! If no volume fraction map for this compartment is set, the corresponding volume fractions are calculated from the input fibers.</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QGroupBox" name="groupBox_5">
	- <property name="styleSheet">
	- <string notr="true">QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <property name="title">
	- <string>Inter-axonal Compartment</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_17">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QComboBox" name="m_Compartment2Box">
	- <property name="toolTip">
	- <string>Select signal model for intra-axonal compartment.</string>
	- </property>
	- <item>
	- <property name="text">
	- <string>--</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Stick Model</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Zeppelin Model</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Tensor Model</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QmitkZeppelinModelParametersWidget" name="m_ZeppelinWidget2" native="true"/>
	- </item>
	- <item row="2" column="0">
	- <widget class="QmitkStickModelParametersWidget" name="m_StickWidget2" native="true"/>
	- </item>
	- <item row="3" column="0">
	- <widget class="QmitkTensorModelParametersWidget" name="m_TensorWidget2" native="true"/>
	- </item>
	- <item row="4" column="0">
	- <widget class="QmitkPrototypeSignalParametersWidget" name="m_PrototypeWidget2" native="true"/>
	- </item>
	- <item row="5" column="0">
	- <widget class="QFrame" name="m_Comp2FractionFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_27">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_NoiseLabel_7">
	- <property name="text">
	- <string>Volume Fraction:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBoxWithSelectNone" name="m_Comp2VolumeFraction">
	- <property name="toolTip">
	- <string>Optional! If no volume fraction map for this compartment is set, the corresponding volume fractions are calculated from the input fibers.</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QGroupBox" name="groupBox">
	- <property name="styleSheet">
	- <string notr="true">QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <property name="title">
	- <string>Image Settings</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="2" column="0">
	- <widget class="QLabel" name="m_GeometryMessage">
	- <property name="styleSheet">
	- <string notr="true">color: rgb(255, 0, 0);</string>
	- </property>
	- <property name="text">
	- <string>Using geometry of selected image!</string>
	- </property>
	- </widget>
	- </item>
	- <item row="9" column="0">
	- <widget class="QFrame" name="m_AdvancedSignalOptionsFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_23">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="horizontalSpacing">
	- <number>6</number>
	- </property>
	- <item row="8" column="1">
	- <widget class="QSpinBox" name="m_TIbox">
	- <property name="toolTip">
	- <string>Inversion time (in ms) for inversion recovery sequences. If 0, no inversion pulse is simulated.</string>
	- </property>
	- <property name="minimum">
	- <number>0</number>
	- </property>
	- <property name="maximum">
	- <number>999999999</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>0</number>
	- </property>
	- </widget>
	- </item>
	- <item row="11" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_12">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string><html><head/><body><p><span style=" font-style:italic;">T</span><span style=" font-style:italic; vertical-align:sub;">inhom</span> Relaxation: </p></body></html></string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="11" column="1">
	- <widget class="QSpinBox" name="m_T2starBox">
	- <property name="toolTip">
	- <string>Relaxation time due to magnetic field inhomogeneities (T2', in milliseconds).</string>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>10000</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>50</number>
	- </property>
	- </widget>
	- </item>
	- <item row="7" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_14">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string><html><head/><body><p>Repetition Time <span style=" font-style:italic;">TR</span>: </p></body></html></string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="1">
	- <widget class="QSpinBox" name="m_TEbox">
	- <property name="toolTip">
	- <string>TE in milliseconds</string>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>999999999</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>100</number>
	- </property>
	- </widget>
	- </item>
	- <item row="10" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_32">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Partial Fourier:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="10" column="1">
	- <widget class="QDoubleSpinBox" name="m_PartialFourier">
	- <property name="toolTip">
	- <string>Partial fourier factor (0.5-1)</string>
	- </property>
	- <property name="decimals">
	- <number>3</number>
	- </property>
	- <property name="minimum">
	- <double>0.500000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>1.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="14" column="0">
	- <widget class="QCheckBox" name="m_ReversePhaseBox">
	- <property name="toolTip">
	- <string>Output one image per compartment containing the corresponding volume fractions per voxel.</string>
	- </property>
	- <property name="text">
	- <string>Reverse Phase Encoding Direction</string>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="9" column="1">
	- <widget class="QDoubleSpinBox" name="m_LineReadoutTimeBox">
	- <property name="toolTip">
	- <string>Dwell time (time to read one line in k-space) in ms.</string>
	- </property>
	- <property name="decimals">
	- <number>4</number>
	- </property>
	- <property name="maximum">
	- <double>100.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>1.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QSpinBox" name="m_NumCoilsBox">
	- <property name="toolTip">
	- <string>Number of coil elements used for the acquisiton.</string>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>128</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>1</number>
	- </property>
	- </widget>
	- </item>
	- <item row="13" column="1">
	- <widget class="QDoubleSpinBox" name="m_FiberRadius">
	- <property name="toolTip">
	- <string>Fiber radius used to calculate volume fractions (in µm). Set to 0 for automatic radius estimation.</string>
	- </property>
	- <property name="maximum">
	- <double>9999.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="9" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_15">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Dwell Time:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="16" column="0">
	- <widget class="QCheckBox" name="m_EnforcePureFiberVoxelsBox">
	- <property name="toolTip">
	- <string>Disable partial volume. Treat voxel content as fiber-only if at least one fiber is present.</string>
	- </property>
	- <property name="text">
	- <string>Disable Partial Volume Effects</string>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_TensorsToDWINumDirsLabel_6">
	- <property name="text">
	- <string>Acquisition Type:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="13" column="0">
	- <widget class="QLabel" name="m_TensorsToDWINumDirsLabel_4">
	- <property name="text">
	- <string>Fiber Radius:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="m_TensorsToDWINumDirsLabel_5">
	- <property name="text">
	- <string>Signal Scale:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_13">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string><html><head/><body><p>Number of Channels:</p></body></html></string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="7" column="1">
	- <widget class="QSpinBox" name="m_TRbox">
	- <property name="toolTip">
	- <string>TR in milliseconds</string>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>999999999</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>4000</number>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QComboBox" name="m_AcquisitionTypeBox">
	- <item>
	- <property name="text">
	- <string>Single Shot EPI</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Conventional Spin Echo</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Fast Spin Echo</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QSpinBox" name="m_SignalScaleBox">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>100000</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>100</number>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="1">
	- <widget class="QComboBox" name="m_CoilSensBox">
	- <item>
	- <property name="text">
	- <string>Constant</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Linear</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Exponential</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- <item row="15" column="0">
	- <widget class="QCheckBox" name="m_RelaxationBox">
	- <property name="toolTip">
	- <string><html><head/><body><p><span style=" font-style:italic;">TE</span>, <span style=" font-style:italic;">T</span><span style=" font-style:italic; vertical-align:sub;">inhom</span> and <span style=" font-style:italic;">T2</span> will have no effect if unchecked.</p></body></html></string>
	- </property>
	- <property name="text">
	- <string>Simulate Signal Relaxation</string>
	- </property>
	- <property name="checked">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_33">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string><html><head/><body><p>Echo Time <span style=" font-style:italic;">TE</span>: </p></body></html></string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_34">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string><html><head/><body><p>Coil Sensitivity:</p></body></html></string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="8" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_17">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string><html><head/><body><p>Inversion Time <span style=" font-style:italic;">TI</span>: </p></body></html></string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="17" column="0">
	- <widget class="QCheckBox" name="m_VolumeFractionsBox">
	- <property name="toolTip">
	- <string>Output phase image and volume fraction maps.</string>
	- </property>
	- <property name="text">
	- <string>Output Additional Images</string>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_35">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string><html><head/><body><p>Echo Train Length: </p></body></html></string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="1">
	- <widget class="QSpinBox" name="m_EtlBox">
	- <property name="toolTip">
	- <string>Only relevant for Fast Spin Echo sequence (number of k-space lines acquired with one RF pulse)</string>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>999999999</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>8</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="7" column="0">
	- <widget class="QFrame" name="m_GenerateGradientsFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_24">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>6</number>
	- </property>
	- <item row="2" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string><html><head/><body><p>b-Value<span style=" font-style:italic;"> [s/mm</span><span style=" font-style:italic; vertical-align:super;">2</span><span style=" font-style:italic;">]</span>:</p></body></html></string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QSpinBox" name="m_BvalueBox">
	- <property name="toolTip">
	- <string>b-value in s/mm²</string>
	- </property>
	- <property name="minimum">
	- <number>0</number>
	- </property>
	- <property name="maximum">
	- <number>10000</number>
	- </property>
	- <property name="singleStep">
	- <number>100</number>
	- </property>
	- <property name="value">
	- <number>1000</number>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="m_TensorsToDWINumDirsLabel">
	- <property name="text">
	- <string>Gradient Directions:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QSpinBox" name="m_NumGradientsBox">
	- <property name="toolTip">
	- <string>Number of gradient directions distributed over the half sphere.</string>
	- </property>
	- <property name="minimum">
	- <number>0</number>
	- </property>
	- <property name="maximum">
	- <number>10000</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>30</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="8" column="0">
	- <widget class="QCheckBox" name="m_AdvancedOptionsBox_2">
	- <property name="text">
	- <string>Advanced Options</string>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QLabel" name="m_DiffusionPropsMessage">
	- <property name="styleSheet">
	- <string notr="true">color: rgb(255, 0, 0);</string>
	- </property>
	- <property name="text">
	- <string>Using gradients of selected DWI!</string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QFrame" name="m_GeometryFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_7">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="2" column="2">
	- <widget class="QDoubleSpinBox" name="m_SpacingY">
	- <property name="decimals">
	- <number>3</number>
	- </property>
	- <property name="minimum">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>50.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>2.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label_2">
	- <property name="text">
	- <string>Image Spacing:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="3">
	- <widget class="QDoubleSpinBox" name="m_SpacingZ">
	- <property name="decimals">
	- <number>3</number>
	- </property>
	- <property name="minimum">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>50.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>2.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QDoubleSpinBox" name="m_SpacingX">
	- <property name="decimals">
	- <number>3</number>
	- </property>
	- <property name="minimum">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>50.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>2.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label">
	- <property name="text">
	- <string>Image Dimensions:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_SizeX">
	- <property name="toolTip">
	- <string>Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions.</string>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>1000</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>20</number>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="2">
	- <widget class="QSpinBox" name="m_SizeY">
	- <property name="toolTip">
	- <string>Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions.</string>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>1000</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>20</number>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="3">
	- <widget class="QSpinBox" name="m_SizeZ">
	- <property name="toolTip">
	- <string>Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions.</string>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>1000</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>3</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <widget class="QCheckBox" name="m_UseBvalsBvecsBox">
	- <property name="text">
	- <string>Use bvals/bvecs files</string>
	- </property>
	- </widget>
	- </item>
	- <item row="6" column="0">
	- <widget class="QFrame" name="m_LoadGradientsFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_3">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="2">
	- <widget class="QToolButton" name="m_LoadBvalsButton">
	- <property name="text">
	- <string>...</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="2">
	- <widget class="QToolButton" name="m_LoadBvecsButton">
	- <property name="text">
	- <string>...</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QLineEdit" name="m_LoadBvalsEdit">
	- <property name="text">
	- <string>-</string>
	- </property>
	- <property name="readOnly">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label_12">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Bvecs:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_11">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Bvals:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QLineEdit" name="m_LoadBvecsEdit">
	- <property name="text">
	- <string>-</string>
	- </property>
	- <property name="readOnly">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <widget class="QGroupBox" name="groupBox_6">
	- <property name="styleSheet">
	- <string notr="true">QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <property name="title">
	- <string>Extra-axonal Compartments</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_14">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="18" column="0">
	- <widget class="QFrame" name="m_Comp4FractionFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_30">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_NoiseLabel_9">
	- <property name="text">
	- <string>Volume Fraction:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBoxWithSelectNone" name="m_Comp4VolumeFraction">
	- <property name="toolTip">
	- <string/>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="6" column="0">
	- <widget class="QComboBox" name="m_Compartment3Box">
	- <property name="toolTip">
	- <string>Select signal model for extra-axonal compartment.</string>
	- </property>
	- <item>
	- <property name="text">
	- <string>Ball Model</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Astrosticks Model</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Dot Model</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Prototype Signal</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- <item row="8" column="0">
	- <widget class="QmitkAstrosticksModelParametersWidget" name="m_AstrosticksWidget1" native="true"/>
	- </item>
	- <item row="10" column="0">
	- <widget class="QmitkPrototypeSignalParametersWidget" name="m_PrototypeWidget3" native="true"/>
	- </item>
	- <item row="16" column="0">
	- <widget class="QmitkDotModelParametersWidget" name="m_DotWidget2" native="true"/>
	- </item>
	- <item row="9" column="0">
	- <widget class="QmitkDotModelParametersWidget" name="m_DotWidget1" native="true"/>
	- </item>
	- <item row="12" column="0">
	- <widget class="Line" name="line_2">
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- </widget>
	- </item>
	- <item row="11" column="0">
	- <widget class="QFrame" name="m_Comp3FractionFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_29">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_NoiseLabel_8">
	- <property name="text">
	- <string>Volume Fraction:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBoxWithSelectNone" name="m_Comp3VolumeFraction">
	- <property name="toolTip">
	- <string>Optional! If no volume fraction map for this compartment is set, the corresponding volume fractions are calculated from the input fibers.</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="14" column="0">
	- <widget class="QmitkBallModelParametersWidget" name="m_BallWidget2" native="true"/>
	- </item>
	- <item row="7" column="0">
	- <widget class="QmitkBallModelParametersWidget" name="m_BallWidget1" native="true"/>
	- </item>
	- <item row="15" column="0">
	- <widget class="QmitkAstrosticksModelParametersWidget" name="m_AstrosticksWidget2" native="true"/>
	- </item>
	- <item row="13" column="0">
	- <widget class="QComboBox" name="m_Compartment4Box">
	- <property name="toolTip">
	- <string>Select signal model for extra-axonal compartment.</string>
	- </property>
	- <item>
	- <property name="text">
	- <string>--</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Ball Model</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Astrosticks Model</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Dot Model</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Prototype Signal</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- <item row="17" column="0">
	- <widget class="QmitkPrototypeSignalParametersWidget" name="m_PrototypeWidget4" native="true"/>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="6" column="0">
	- <widget class="QGroupBox" name="groupBox_3">
	- <property name="styleSheet">
	- <string notr="true">QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <property name="title">
	- <string>Noise and other Artifacts</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_6">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="8" column="0">
	- <widget class="Line" name="line_7">
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- </widget>
	- </item>
	- <item row="19" column="0">
	- <widget class="QFrame" name="m_MotionArtifactFrame">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_18">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="horizontalSpacing">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QCheckBox" name="m_RandomMotion">
	- <property name="toolTip">
	- <string>Toggle between random movement and linear movement.</string>
	- </property>
	- <property name="text">
	- <string>Randomize motion</string>
	- </property>
	- <property name="checked">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QGroupBox" name="m_RotationArtifactFrame">
	- <property name="styleSheet">
	- <string notr="true">QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <property name="title">
	- <string>Rotation</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_19">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>9</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_36">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Degree:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_29">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>x</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_28">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Axis:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QDoubleSpinBox" name="m_MaxRotationBoxX">
	- <property name="toolTip">
	- <string>Maximum rotation around x-axis.</string>
	- </property>
	- <property name="decimals">
	- <number>1</number>
	- </property>
	- <property name="minimum">
	- <double>-360.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>360.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="3">
	- <widget class="QDoubleSpinBox" name="m_MaxRotationBoxZ">
	- <property name="toolTip">
	- <string>Maximum rotation around z-axis.</string>
	- </property>
	- <property name="decimals">
	- <number>1</number>
	- </property>
	- <property name="minimum">
	- <double>-360.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>360.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="value">
	- <double>15.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="2">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_30">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>y</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="3">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_31">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>z</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="2">
	- <widget class="QDoubleSpinBox" name="m_MaxRotationBoxY">
	- <property name="toolTip">
	- <string>Maximum rotation around y-axis.</string>
	- </property>
	- <property name="decimals">
	- <number>1</number>
	- </property>
	- <property name="minimum">
	- <double>-360.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>360.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QGroupBox" name="m_TranslationArtifactFrame">
	- <property name="styleSheet">
	- <string notr="true">QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <property name="title">
	- <string>Translation</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_28">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_48">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Distance:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_51">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>x</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="2">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_52">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>y</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_47">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Axis:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="3">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_53">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>z</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QDoubleSpinBox" name="m_MaxTranslationBoxX">
	- <property name="toolTip">
	- <string>Maximum translation along x-axis.</string>
	- </property>
	- <property name="decimals">
	- <number>1</number>
	- </property>
	- <property name="minimum">
	- <double>-1000.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>1000.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="2">
	- <widget class="QDoubleSpinBox" name="m_MaxTranslationBoxY">
	- <property name="toolTip">
	- <string>Maximum translation along y-axis.</string>
	- </property>
	- <property name="decimals">
	- <number>1</number>
	- </property>
	- <property name="minimum">
	- <double>-1000.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>1000.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="3">
	- <widget class="QDoubleSpinBox" name="m_MaxTranslationBoxZ">
	- <property name="toolTip">
	- <string>Maximum translation along z-axis.</string>
	- </property>
	- <property name="decimals">
	- <number>1</number>
	- </property>
	- <property name="minimum">
	- <double>-1000.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>1000.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QFrame" name="frame_7">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_31">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_3">
	- <property name="text">
	- <string>Motion volumes:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QLineEdit" name="m_MotionVolumesBox">
	- <property name="toolTip">
	- <string>Type in the volume indices that should be affected by motion (e.g. "0 3 7" whithout quotation marks). Leave blank for motion in all volumes. Type in "random" to randomly select volumes for motion. A list of negative numbers (e.g. -1 -2 -3) excludes volumes (e.g. 1 2 3) selects all remaining volumes.</string>
	- </property>
	- <property name="text">
	- <string>random</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QFrame" name="m_SpikeFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QFormLayout" name="formLayout_9">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_NoiseLabel_2">
	- <property name="text">
	- <string>Num. Spikes:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_SpikeNumBox">
	- <property name="toolTip">
	- <string>The number of randomly occurring signal spikes.</string>
	- </property>
	- <property name="value">
	- <number>1</number>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QDoubleSpinBox" name="m_SpikeScaleBox">
	- <property name="toolTip">
	- <string>Spike amplitude relative to the largest signal amplitude of the corresponding k-space slice.</string>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.100000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="m_NoiseLabel_4">
	- <property name="text">
	- <string>Scale:</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="10" column="0">
	- <widget class="QFrame" name="m_AliasingFrame">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QFormLayout" name="formLayout_10">
	- <property name="horizontalSpacing">
	- <number>6</number>
	- </property>
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_27">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Shrink FOV (%):</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QDoubleSpinBox" name="m_WrapBox">
	- <property name="toolTip">
	- <string>Shrink FOV by this percentage.</string>
	- </property>
	- <property name="decimals">
	- <number>1</number>
	- </property>
	- <property name="minimum">
	- <double>0.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>90.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>40.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <widget class="Line" name="line_8">
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- </widget>
	- </item>
	- <item row="16" column="0">
	- <widget class="QFrame" name="m_DriftFrame">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QFormLayout" name="formLayout_11">
	- <property name="horizontalSpacing">
	- <number>6</number>
	- </property>
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_35">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Signal Reduction (%):</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QDoubleSpinBox" name="m_DriftFactor">
	- <property name="toolTip">
	- <string>Global signal in last simulated volume is specified percentage lower than in the first volume.</string>
	- </property>
	- <property name="decimals">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <double>100.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="value">
	- <double>6.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="13" column="0">
	- <widget class="QFrame" name="m_DistortionsFrame">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QFormLayout" name="formLayout_7">
	- <property name="horizontalSpacing">
	- <number>6</number>
	- </property>
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_25">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Frequency Map:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_FrequencyMapBox">
	- <property name="toolTip">
	- <string>Select image specifying the frequency inhomogeneities (in Hz).</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="23" column="0">
	- <widget class="QFrame" name="m_EddyFrame">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QFormLayout" name="formLayout_8">
	- <property name="fieldGrowthPolicy">
	- <enum>QFormLayout::AllNonFixedFieldsGrow</enum>
	- </property>
	- <property name="horizontalSpacing">
	- <number>6</number>
	- </property>
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_26">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Gradient:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QDoubleSpinBox" name="m_EddyGradientStrength">
	- <property name="toolTip">
	- <string>Eddy current induced magnetic field gradient (in mT/m).</string>
	- </property>
	- <property name="decimals">
	- <number>5</number>
	- </property>
	- <property name="maximum">
	- <double>1000.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.001000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.002000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="11" column="0">
	- <widget class="Line" name="line_6">
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- </widget>
	- </item>
	- <item row="22" column="0">
	- <widget class="QCheckBox" name="m_AddEddy">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Add Eddy Current Effects</string>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="12" column="0">
	- <widget class="QCheckBox" name="m_AddDistortions">
	- <property name="text">
	- <string>Add Distortions</string>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QCheckBox" name="m_AddSpikes">
	- <property name="text">
	- <string>Add Spikes</string>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="15" column="0">
	- <widget class="QCheckBox" name="m_AddDrift">
	- <property name="text">
	- <string>Add Signal Drift</string>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QFrame" name="m_NoiseFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QFormLayout" name="formLayout_5">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QLabel" name="m_NoiseLabel">
	- <property name="text">
	- <string>Variance:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QDoubleSpinBox" name="m_NoiseLevel">
	- <property name="toolTip">
	- <string>Variance of selected noise distribution.</string>
	- </property>
	- <property name="decimals">
	- <number>10</number>
	- </property>
	- <property name="minimum">
	- <double>0.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>999999999.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.001000000000000</double>
	- </property>
	- <property name="value">
	- <double>50.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_NoiseLabel_5">
	- <property name="text">
	- <string>Distribution:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QComboBox" name="m_NoiseDistributionBox">
	- <property name="toolTip">
	- <string>Noise distribution</string>
	- </property>
	- <item>
	- <property name="text">
	- <string>Complex Gaussian</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Rician</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="14" column="0">
	- <widget class="Line" name="line_5">
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- </widget>
	- </item>
	- <item row="17" column="0">
	- <widget class="Line" name="line_10">
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- </widget>
	- </item>
	- <item row="7" column="0">
	- <widget class="QFrame" name="m_GhostFrame">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QFormLayout" name="formLayout_6">
	- <property name="horizontalSpacing">
	- <number>6</number>
	- </property>
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_23">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>K-Space Line Offset:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QDoubleSpinBox" name="m_kOffsetBox">
	- <property name="toolTip">
	- <string>A larger offset increases the inensity of the ghost image.</string>
	- </property>
	- <property name="decimals">
	- <number>3</number>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.010000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.250000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="18" column="0">
	- <widget class="QCheckBox" name="m_AddMotion">
	- <property name="text">
	- <string>Add Motion Artifacts</string>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="6" column="0">
	- <widget class="QCheckBox" name="m_AddGhosts">
	- <property name="text">
	- <string>Add N/2 Ghosts</string>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="21" column="0">
	- <widget class="Line" name="line_4">
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- </widget>
	- </item>
	- <item row="25" column="0">
	- <widget class="QCheckBox" name="m_AddGibbsRinging">
	- <property name="toolTip">
	- <string>Add ringing artifacts occuring at strong edges in the image.</string>
	- </property>
	- <property name="text">
	- <string>Add Gibbs Ringing</string>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="Line" name="line_9">
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QCheckBox" name="m_AddNoise">
	- <property name="text">
	- <string>Add Noise</string>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="24" column="0">
	- <widget class="Line" name="line">
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- </widget>
	- </item>
	- <item row="9" column="0">
	- <widget class="QCheckBox" name="m_AddAliasing">
	- <property name="text">
	- <string>Add Aliasing</string>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="26" column="0">
	- <widget class="QSpinBox" name="m_ZeroRinging">
	- <property name="toolTip">
	- <string>If > 0, ringing is simulated by by setting the defined percentage of higher frequencies to 0 in k-space. Otherwise, the input to the k-space simulation is generated with twice the resolution and cropped during k-space simulation (much slower).</string>
	- </property>
	- <property name="maximum">
	- <number>100</number>
	- </property>
	- <property name="value">
	- <number>10</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="7" column="0">
	- <spacer name="verticalSpacer">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="1" column="0">
	- <widget class="QFrame" name="frame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_4">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="1">
	- <widget class="QCommandLinkButton" name="m_SaveParametersButton">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="toolTip">
	- <string><html><head/><body><p>Start DWI generation from selected fiber bundle.</p><p>If no fiber bundle but an existing diffusion weighted image is selected, the enabled artifacts are added to this image.</p><p>If neither a fiber bundle nor a diffusion weighted image is selected, a grayscale image containing a simple gradient is generated.</p></body></html></string>
	- </property>
	- <property name="styleSheet">
	- <string notr="true"/>
	- </property>
	- <property name="text">
	- <string>Save Parameters</string>
	- </property>
	- <property name="icon">
	- <iconset resource="../../resources/QmitkFiberfox.qrc">
	- <normaloff>:/QmitkFiberfox/download.png</normaloff>:/QmitkFiberfox/download.png</iconset>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QCommandLinkButton" name="m_LoadParametersButton">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="toolTip">
	- <string><html><head/><body><p>Start DWI generation from selected fiber bundle.</p><p>If no fiber bundle but an existing diffusion weighted image is selected, the enabled artifacts are added to this image.</p><p>If neither a fiber bundle nor a diffusion weighted image is selected, a grayscale image containing a simple gradient is generated.</p></body></html></string>
	- </property>
	- <property name="styleSheet">
	- <string notr="true"/>
	- </property>
	- <property name="text">
	- <string>Load Parameters</string>
	- </property>
	- <property name="icon">
	- <iconset resource="../../resources/QmitkFiberfox.qrc">
	- <normaloff>:/QmitkFiberfox/upload.png</normaloff>:/QmitkFiberfox/upload.png</iconset>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QFrame" name="frame_9">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_32">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QCommandLinkButton" name="m_GenerateImageButton">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="toolTip">
	- <string><html><head/><body><p>Start DWI generation from selected fiber bundle.</p><p>If no fiber bundle but an existing diffusion weighted image is selected, the enabled artifacts are added to this image.</p><p>If neither a fiber bundle nor a diffusion weighted image is selected, a grayscale image containing a simple gradient is generated.</p></body></html></string>
	- </property>
	- <property name="styleSheet">
	- <string notr="true"/>
	- </property>
	- <property name="text">
	- <string>Start Simulation</string>
	- </property>
	- <property name="icon">
	- <iconset resource="../../resources/QmitkFiberfox.qrc">
	- <normaloff>:/QmitkFiberfox/right.png</normaloff>:/QmitkFiberfox/right.png</iconset>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QGroupBox" name="groupBox_2">
	- <property name="styleSheet">
	- <string notr="true">QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <property name="title">
	- <string>Input Data</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_10">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="4" column="2">
	- <widget class="QFrame" name="frame_6">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_20">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLineEdit" name="m_SavePathEdit">
	- <property name="text">
	- <string>-</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QToolButton" name="m_OutputPathButton">
	- <property name="text">
	- <string>...</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="2" column="2">
	- <widget class="QmitkDataStorageComboBoxWithSelectNone" name="m_MaskComboBox">
	- <property name="toolTip">
	- <string><html><head/><body><p>Select a binary image to define the area of signal generation. Outside of the mask image only noise will be actively generated.</p></body></html></string>
	- </property>
	- <property name="sizeAdjustPolicy">
	- <enum>QComboBox::AdjustToMinimumContentsLength</enum>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0" rowspan="2" colspan="2">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_16">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Fiber Bundle:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QLabel" name="label_10">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Save path:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_3">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Tissue Mask:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="2">
	- <widget class="QmitkDataStorageComboBoxWithSelectNone" name="m_FiberBundleComboBox">
	- <property name="toolTip">
	- <string><html><head/><body><p>Select a fiber bundle to generate the white matter signal from. You can either use the fiber definition tab to manually define an input fiber bundle or you can also use any existing bundle, e.g. yielded by a tractography algorithm.</p></body></html></string>
	- </property>
	- <property name="sizeAdjustPolicy">
	- <enum>QComboBox::AdjustToMinimumContentsLength</enum>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel_11">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Template Image:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="2">
	- <widget class="QmitkDataStorageComboBoxWithSelectNone" name="m_TemplateComboBox">
	- <property name="toolTip">
	- <string><html><head/><body><p>The parameters for the simulation (e.g. spacing, size, diffuison-weighted gradients, b-value) are adopted from this image.</p></body></html></string>
	- </property>
	- <property name="sizeAdjustPolicy">
	- <enum>QComboBox::AdjustToMinimumContentsLength</enum>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QCommandLinkButton" name="m_AbortSimulationButton">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="toolTip">
	- <string>Stop current simulation.</string>
	- </property>
	- <property name="styleSheet">
	- <string notr="true"/>
	- </property>
	- <property name="text">
	- <string>Abort Simulation</string>
	- </property>
	- <property name="icon">
	- <iconset resource="../../resources/QmitkFiberfox.qrc">
	- <normaloff>:/QmitkFiberfox/stop.png</normaloff>:/QmitkFiberfox/stop.png</iconset>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QTextEdit" name="m_SimulationStatusText">
	- <property name="font">
	- <font>
	- <family>Courier</family>
	- <pointsize>7</pointsize>
	- </font>
	- </property>
	- <property name="readOnly">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <customwidgets>
	- <customwidget>
	- <class>QmitkDataStorageComboBox</class>
	- <extends>QComboBox</extends>
	- <header location="global">QmitkDataStorageComboBox.h</header>
	- </customwidget>
	- <customwidget>
	- <class>QmitkDataStorageComboBoxWithSelectNone</class>
	- <extends>QComboBox</extends>
	- <header>QmitkDataStorageComboBoxWithSelectNone.h</header>
	- </customwidget>
	- <customwidget>
	- <class>QmitkTensorModelParametersWidget</class>
	- <extends>QWidget</extends>
	- <header location="global">QmitkTensorModelParametersWidget.h</header>
	- <container>1</container>
	- </customwidget>
	- <customwidget>
	- <class>QmitkStickModelParametersWidget</class>
	- <extends>QWidget</extends>
	- <header location="global">QmitkStickModelParametersWidget.h</header>
	- <container>1</container>
	- </customwidget>
	- <customwidget>
	- <class>QmitkZeppelinModelParametersWidget</class>
	- <extends>QWidget</extends>
	- <header location="global">QmitkZeppelinModelParametersWidget.h</header>
	- <container>1</container>
	- </customwidget>
	- <customwidget>
	- <class>QmitkBallModelParametersWidget</class>
	- <extends>QWidget</extends>
	- <header location="global">QmitkBallModelParametersWidget.h</header>
	- <container>1</container>
	- </customwidget>
	- <customwidget>
	- <class>QmitkAstrosticksModelParametersWidget</class>
	- <extends>QWidget</extends>
	- <header location="global">QmitkAstrosticksModelParametersWidget.h</header>
	- <container>1</container>
	- </customwidget>
	- <customwidget>
	- <class>QmitkDotModelParametersWidget</class>
	- <extends>QWidget</extends>
	- <header>QmitkDotModelParametersWidget.h</header>
	- <container>1</container>
	- </customwidget>
	- <customwidget>
	- <class>QmitkPrototypeSignalParametersWidget</class>
	- <extends>QWidget</extends>
	- <header>QmitkPrototypeSignalParametersWidget.h</header>
	- <container>1</container>
	- </customwidget>
	- </customwidgets>
	- <tabstops>
	- <tabstop>m_FiberBundleComboBox</tabstop>
	- <tabstop>m_MaskComboBox</tabstop>
	- <tabstop>m_TemplateComboBox</tabstop>
	- <tabstop>m_SavePathEdit</tabstop>
	- <tabstop>m_OutputPathButton</tabstop>
	- <tabstop>m_GenerateImageButton</tabstop>
	- <tabstop>m_AbortSimulationButton</tabstop>
	- <tabstop>m_SimulationStatusText</tabstop>
	- <tabstop>m_LoadParametersButton</tabstop>
	- <tabstop>m_SaveParametersButton</tabstop>
	- <tabstop>m_SizeX</tabstop>
	- <tabstop>m_SizeY</tabstop>
	- <tabstop>m_SizeZ</tabstop>
	- <tabstop>m_SpacingX</tabstop>
	- <tabstop>m_SpacingY</tabstop>
	- <tabstop>m_SpacingZ</tabstop>
	- <tabstop>m_UseBvalsBvecsBox</tabstop>
	- <tabstop>m_LoadBvalsEdit</tabstop>
	- <tabstop>m_LoadBvalsButton</tabstop>
	- <tabstop>m_LoadBvecsEdit</tabstop>
	- <tabstop>m_LoadBvecsButton</tabstop>
	- <tabstop>m_NumGradientsBox</tabstop>
	- <tabstop>m_BvalueBox</tabstop>
	- <tabstop>m_AdvancedOptionsBox_2</tabstop>
	- <tabstop>m_AcquisitionTypeBox</tabstop>
	- <tabstop>m_SignalScaleBox</tabstop>
	- <tabstop>m_NumCoilsBox</tabstop>
	- <tabstop>m_CoilSensBox</tabstop>
	- <tabstop>m_TEbox</tabstop>
	- <tabstop>m_TRbox</tabstop>
	- <tabstop>m_TIbox</tabstop>
	- <tabstop>m_LineReadoutTimeBox</tabstop>
	- <tabstop>m_PartialFourier</tabstop>
	- <tabstop>m_T2starBox</tabstop>
	- <tabstop>m_FiberRadius</tabstop>
	- <tabstop>m_ReversePhaseBox</tabstop>
	- <tabstop>m_RelaxationBox</tabstop>
	- <tabstop>m_EnforcePureFiberVoxelsBox</tabstop>
	- <tabstop>m_VolumeFractionsBox</tabstop>
	- <tabstop>m_Compartment1Box</tabstop>
	- <tabstop>m_Comp1VolumeFraction</tabstop>
	- <tabstop>m_Compartment2Box</tabstop>
	- <tabstop>m_Comp2VolumeFraction</tabstop>
	- <tabstop>m_Compartment3Box</tabstop>
	- <tabstop>m_Comp3VolumeFraction</tabstop>
	- <tabstop>m_Compartment4Box</tabstop>
	- <tabstop>m_Comp4VolumeFraction</tabstop>
	- <tabstop>m_AddNoise</tabstop>
	- <tabstop>m_NoiseDistributionBox</tabstop>
	- <tabstop>m_NoiseLevel</tabstop>
	- <tabstop>m_AddSpikes</tabstop>
	- <tabstop>m_SpikeNumBox</tabstop>
	- <tabstop>m_SpikeScaleBox</tabstop>
	- <tabstop>m_AddGhosts</tabstop>
	- <tabstop>m_kOffsetBox</tabstop>
	- <tabstop>m_AddAliasing</tabstop>
	- <tabstop>m_WrapBox</tabstop>
	- <tabstop>m_AddDistortions</tabstop>
	- <tabstop>m_FrequencyMapBox</tabstop>
	- <tabstop>m_AddDrift</tabstop>
	- <tabstop>m_DriftFactor</tabstop>
	- <tabstop>m_AddMotion</tabstop>
	- <tabstop>m_RandomMotion</tabstop>
	- <tabstop>m_MotionVolumesBox</tabstop>
	- <tabstop>m_MaxRotationBoxX</tabstop>
	- <tabstop>m_MaxRotationBoxY</tabstop>
	- <tabstop>m_MaxRotationBoxZ</tabstop>
	- <tabstop>m_MaxTranslationBoxX</tabstop>
	- <tabstop>m_MaxTranslationBoxY</tabstop>
	- <tabstop>m_MaxTranslationBoxZ</tabstop>
	- <tabstop>m_AddEddy</tabstop>
	- <tabstop>m_EddyGradientStrength</tabstop>
	- <tabstop>m_AddGibbsRinging</tabstop>
	- <tabstop>m_ZeroRinging</tabstop>
	- </tabstops>
	- <resources>
	- <include location="../../resources/QmitkFiberfox.qrc"/>
	- </resources>
	- <connections/>
	-</ui>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFieldmapGeneratorView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFieldmapGeneratorView.cpp
	deleted file mode 100644
	index 5a50e4ff51..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFieldmapGeneratorView.cpp
	+++ /dev/null
	@@ -1,274 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-// Blueberry
	-#include <berryISelectionService.h>
	-#include <berryIWorkbenchWindow.h>
	-
	-// MITK
	-#include "QmitkFieldmapGeneratorView.h"
	-#include <QmitkDataStorageComboBox.h>
	-#include <mitkNodePredicateDataType.h>
	-#include <itkFieldmapGeneratorFilter.h>
	-#include <mitkImage.h>
	-#include <mitkSliceNavigationController.h>
	-#include <QmitkRenderWindow.h>
	-
	-const std::string QmitkFieldmapGeneratorView::VIEW_ID = "org.mitk.views.fieldmapgenerator";
	-
	-QmitkFieldmapGeneratorView::QmitkFieldmapGeneratorView()
	- : QmitkAbstractView()
	- , m_Controls( 0 )
	-{
	-
	-}
	-
	-QmitkFieldmapGeneratorView::~QmitkFieldmapGeneratorView()
	-{
	-
	-}
	-
	-void QmitkFieldmapGeneratorView::CreateQtPartControl( QWidget *parent )
	-{
	- // build up qt view, unless already done
	- if ( !m_Controls )
	- {
	- // create GUI widgets from the Qt Designer's .ui file
	- m_Controls = new Ui::QmitkFieldmapGeneratorViewControls;
	- m_Controls->setupUi( parent );
	-
	- m_Controls->m_SelectedImageBox->SetDataStorage(this->GetDataStorage());
	- mitk::TNodePredicateDataType<mitk::Image>::Pointer isMitkImage = mitk::TNodePredicateDataType<mitk::Image>::New();
	- m_Controls->m_SelectedImageBox->SetPredicate(isMitkImage);
	-
	- m_SliceChangeListener.RenderWindowPartActivated(this->GetRenderWindowPart());
	- connect(&m_SliceChangeListener, SIGNAL(SliceChanged()), this, SLOT(OnSliceChanged()));
	-
	- connect((QObject) m_Controls->m_GenerateFieldmap, SIGNAL(clicked()), (QObject) this, SLOT(GenerateFieldmap()));
	- connect((QObject) m_Controls->m_PlaceFieldSource, SIGNAL(clicked()), (QObject) this, SLOT(PlaceFieldSource()));
	- connect((QObject) m_Controls->m_SourceVarianceBox, SIGNAL(valueChanged(double)), (QObject) this, SLOT(OnVarianceChanged(double)));
	- connect((QObject) m_Controls->m_SourceHeightBox, SIGNAL(valueChanged(double)), (QObject) this, SLOT(OnHeightChanged(double)));
	-
	- }
	-}
	-
	-void QmitkFieldmapGeneratorView::SetFocus()
	-{
	- m_Controls->m_SelectedImageBox->setFocus();
	-}
	-
	-void QmitkFieldmapGeneratorView::OnVarianceChanged(double value)
	-{
	- if (m_SelectedSource.IsNotNull())
	- {
	- m_SelectedSource->SetProperty("pointsize", mitk::FloatProperty::New(value));
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- }
	-}
	-
	-void QmitkFieldmapGeneratorView::OnHeightChanged(double value)
	-{
	- if (m_SelectedSource.IsNotNull())
	- {
	- m_SelectedSource->SetProperty("color", mitk::ColorProperty::New(0, 0, value/100.0));
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- }
	-}
	-
	-void QmitkFieldmapGeneratorView::PlaceFieldSource()
	-{
	- if (m_Controls->m_SelectedImageBox->GetSelectedNode().IsNull() \|\| !this->GetRenderWindowPart())
	- {
	- m_Controls->m_WorldPosLabel->setText("-");
	- m_Controls->m_IndexLabel->setText("-");
	- return;
	- }
	-
	- mitk::Point3D index;
	- mitk::Image::Pointer img = dynamic_cast<mitk::Image*>(m_Controls->m_SelectedImageBox->GetSelectedNode()->GetData());
	- mitk::BaseGeometry* geom = img->GetGeometry();
	-
	- if ( geom->IsInside(m_WorldPoint) )
	- {
	- img->GetGeometry()->WorldToIndex(m_WorldPoint, index);
	- mitk::PointSet::Pointer pointSet = mitk::PointSet::New();
	- pointSet->InsertPoint(0, m_WorldPoint);
	-
	-
	- mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_Controls->m_SelectedImageBox->GetSelectedNode());
	-
	- mitk::DataNode::Pointer node = mitk::DataNode::New();
	- node->SetData(pointSet);
	- QString name = QString("FieldSource_%1").arg(children->size());
	- node->SetName(name.toStdString());
	- node->SetVisibility(true);
	-
	- float minSpacing;
	- if(geom->GetSpacing()[0]<geom->GetSpacing()[1] && geom->GetSpacing()[0]<geom->GetSpacing()[2])
	- minSpacing = geom->GetSpacing()[0];
	- else if (geom->GetSpacing()[1] < geom->GetSpacing()[2])
	- minSpacing = geom->GetSpacing()[1];
	- else
	- minSpacing = geom->GetSpacing()[2];
	-
	- node->SetProperty("pointsize", mitk::FloatProperty::New(minSpacing*5));
	- node->SetProperty("color", mitk::ColorProperty::New(0, 0, 1));
	-
	- GetDataStorage()->Add(node, m_Controls->m_SelectedImageBox->GetSelectedNode());
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- }
	-}
	-
	-void QmitkFieldmapGeneratorView::GenerateFieldmap()
	-{
	- if (m_Controls->m_SelectedImageBox->GetSelectedNode().IsNull())
	- return;
	-
	- mitk::Image::Pointer img = dynamic_cast<mitk::Image*>(m_Controls->m_SelectedImageBox->GetSelectedNode()->GetData());
	- mitk::BaseGeometry* geom = img->GetGeometry();
	-
	- typedef itk::Image< double, 3 > FieldMapType;
	- itk::Vector<double> spacing; ///< output image spacing
	- mitk::Point3D origin; ///< output image origin
	- itk::FieldmapGeneratorFilter< FieldMapType >::MatrixType directionMatrix; ///< output image rotation
	- itk::FieldmapGeneratorFilter< FieldMapType >::OutputImageRegionType imageRegion; ///< output image size
	-
	- spacing = geom->GetSpacing();
	- origin = geom->GetOrigin();
	- imageRegion.SetSize(0, img->GetDimension(0));
	- imageRegion.SetSize(1, img->GetDimension(1));
	- imageRegion.SetSize(2, img->GetDimension(2));
	- for (int r=0; r<3; r++)
	- for (int c=0; c<3; c++)
	- directionMatrix[r][c]=geom->GetMatrixColumn(c)[r]/spacing[c];
	-
	- std::vector< double > variances;
	- std::vector< double > heights;
	- std::vector< mitk::Point3D > worldPositions;
	-
	- mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_Controls->m_SelectedImageBox->GetSelectedNode());
	- for( mitk::DataStorage::SetOfObjects::const_iterator it = children->begin(); it != children->end(); ++it )
	- if(dynamic_cast<mitk::PointSet>((it)->GetData()))
	- {
	- float var = 0; (*it)->GetPropertyValue("pointsize", var); variances.push_back(var);
	- float color[3]; (it)->GetColor(color); heights.push_back(color[2]100);
	- mitk::PointSet* ps = dynamic_cast<mitk::PointSet>((it)->GetData());
	- mitk::Point3D point;
	- ps->GetPointIfExists(0, &point);
	- worldPositions.push_back(point);
	- }
	-
	- vnl_vector_fixed< double, 3 > gradient, offset;
	- gradient[0] = m_Controls->m_xGradientBox->value();
	- gradient[1] = m_Controls->m_yGradientBox->value();
	- gradient[2] = m_Controls->m_zGradientBox->value();
	- offset[0] = m_Controls->m_xOffsetBox->value();
	- offset[1] = m_Controls->m_yOffsetBox->value();
	- offset[2] = m_Controls->m_zOffsetBox->value();
	-
	- itk::FieldmapGeneratorFilter< FieldMapType >::Pointer filter = itk::FieldmapGeneratorFilter< FieldMapType >::New();
	- filter->SetHeights(heights);
	- filter->SetVariances(variances);
	- filter->SetWorldPositions(worldPositions);
	- filter->SetSpacing(spacing);
	- filter->SetOrigin(origin);
	- filter->SetDirectionMatrix(directionMatrix);
	- filter->SetImageRegion(imageRegion);
	- filter->SetGradient(gradient);
	- filter->SetOffset(offset);
	- filter->Update();
	-
	- mitk::DataNode::Pointer resultNode = mitk::DataNode::New();
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk(filter->GetOutput(0));
	- image->SetVolume(filter->GetOutput(0)->GetBufferPointer());
	- resultNode->SetData( image );
	- resultNode->SetName(m_Controls->m_SelectedImageBox->GetSelectedNode()->GetName()+"_Fieldmap");
	- GetDataStorage()->Add(resultNode);
	-}
	-
	-void QmitkFieldmapGeneratorView::Visible()
	-{
	-
	-}
	-
	-void QmitkFieldmapGeneratorView::Hidden()
	-{
	-
	-}
	-
	-void QmitkFieldmapGeneratorView::Activated()
	-{
	- m_SliceChangeListener.RenderWindowPartActivated(this->GetRenderWindowPart());
	- connect(&m_SliceChangeListener, SIGNAL(SliceChanged()), this, SLOT(OnSliceChanged()));
	-}
	-
	-void QmitkFieldmapGeneratorView::Deactivated()
	-{
	-}
	-
	-void QmitkFieldmapGeneratorView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /part/, const QList<mitk::DataNode::Pointer>& nodes)
	-{
	- if (m_Controls->m_SelectedImageBox->GetSelectedNode().IsNotNull())
	- m_Controls->m_SelectedImageBox->GetSelectedNode()->RemoveObserver( m_PropertyObserverTag );
	-
	- m_Controls->m_InputData->setTitle("Please Select Reference Image");
	- m_SelectedSource = nullptr;
	-
	- // iterate selection
	- for (mitk::DataNode::Pointer node: nodes)
	- {
	- if ( node.IsNotNull() && (dynamic_cast<mitk::PointSet*>(node->GetData())) )
	- {
	- m_Controls->m_SourceNameLabel->setText(node->GetName().c_str());
	- m_SelectedSource = node;
	- float variance = 0; node->GetPropertyValue("pointsize", variance);
	- m_Controls->m_SourceVarianceBox->setValue(variance);
	-
	- float color[3]; node->GetColor(color);
	- m_Controls->m_SourceHeightBox->setValue(color[2]*100);
	- }
	- }
	-
	- if (m_Controls->m_SelectedImageBox->GetSelectedNode().IsNotNull())
	- {
	- m_Controls->m_InputData->setTitle("Reference Image");
	- }
	-}
	-
	-void QmitkFieldmapGeneratorView::OnSliceChanged()
	-{
	- if (m_Controls->m_SelectedImageBox->GetSelectedNode().IsNull() \|\| !this->GetRenderWindowPart())
	- {
	- m_Controls->m_WorldPosLabel->setText("-");
	- m_Controls->m_IndexLabel->setText("-");
	- return;
	- }
	-
	- m_WorldPoint = this->GetRenderWindowPart()->GetSelectedPosition();
	- QString posSting = QString::number(m_WorldPoint[0]); posSting += ", "; posSting += QString::number(m_WorldPoint[1]); posSting += ", "; posSting += QString::number(m_WorldPoint[2]);
	- m_Controls->m_WorldPosLabel->setText(posSting.toStdString().c_str());
	-
	- mitk::Point3D index;
	- mitk::Image::Pointer img = dynamic_cast<mitk::Image*>(m_Controls->m_SelectedImageBox->GetSelectedNode()->GetData());
	-
	- if ( m_Controls->m_SelectedImageBox->GetSelectedNode()->GetData()->GetGeometry()->IsInside(m_WorldPoint) )
	- {
	- img->GetGeometry()->WorldToIndex(m_WorldPoint, index);
	- posSting = QString::number(index[0]); posSting += ", "; posSting += QString::number(index[1]); posSting += ", "; posSting += QString::number(index[2]);
	- m_Controls->m_IndexLabel->setText(posSting.toStdString().c_str());
	- }
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFieldmapGeneratorView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFieldmapGeneratorView.h
	deleted file mode 100644
	index ca09d0b32c..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFieldmapGeneratorView.h
	+++ /dev/null
	@@ -1,86 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _QMITKQmitkFieldmapGeneratorView_H_INCLUDED
	-#define _QMITKQmitkFieldmapGeneratorView_H_INCLUDED
	-
	-#include <berryISelectionListener.h>
	-#include <QmitkAbstractView.h>
	-#include <mitkIRenderWindowPartListener.h>
	-#include "ui_QmitkFieldmapGeneratorViewControls.h"
	-#include <mitkPointSet.h>
	-#include <itkImage.h>
	-#include "mitkILifecycleAwarePart.h"
	-#include <QmitkSliceNavigationListener.h>
	-
	-/*!
	- \brief Generate float image with artificial frequency maps used by Fiberfox. Simulates additional frequencies at (possibly multiple) positions based on 3D gaussians with the specified variance and amplitude and/or as a linear gradient in the image.
	-* See "Fiberfox: Facilitating the creation of realistic white matter software phantoms" (DOI: 10.1002/mrm.25045) for details.
	-*/
	-
	-class QmitkFieldmapGeneratorView : public QmitkAbstractView, public mitk::ILifecycleAwarePart
	-{
	- // this is needed for all Qt objects that should have a Qt meta-object
	- // (everything that derives from QObject and wants to have signal/slots)
	- Q_OBJECT
	-
	-public:
	-
	- static const std::string VIEW_ID;
	-
	- QmitkFieldmapGeneratorView();
	- virtual ~QmitkFieldmapGeneratorView();
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	-
	- virtual void SetFocus() override;
	-
	- virtual void Activated() override;
	- virtual void Deactivated() override;
	- virtual void Visible() override;
	- virtual void Hidden() override;
	-
	-
	-protected slots:
	-
	- void GenerateFieldmap();
	- void PlaceFieldSource();
	- void OnVarianceChanged(double value);
	- void OnHeightChanged(double value);
	- void OnSliceChanged();
	-
	-protected:
	-
	- /// \brief called by QmitkAbstractView when DataManager's selection has changed
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- Ui::QmitkFieldmapGeneratorViewControls* m_Controls;
	-
	- /** observer flags */
	- int m_SliceObserverTag1;
	- int m_SliceObserverTag2;
	- int m_SliceObserverTag3;
	- int m_PropertyObserverTag;
	-
	- mitk::Point3D m_WorldPoint;
	- mitk::DataNode::Pointer m_SelectedSource;
	- QmitkSliceNavigationListener m_SliceChangeListener;
	-};
	-
	-
	-
	-#endif // _QmitkFieldmapGeneratorView_H_INCLUDED
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFieldmapGeneratorViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFieldmapGeneratorViewControls.ui
	deleted file mode 100644
	index 4f15c732be..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFieldmapGeneratorViewControls.ui
	+++ /dev/null
	@@ -1,386 +0,0 @@
	-<?xml version="1.0" encoding="utf-8"?>
	-<ui version="4.0">
	- <class>QmitkFieldmapGeneratorViewControls</class>
	- <widget class="QWidget" name="QmitkFieldmapGeneratorViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>358</width>
	- <height>536</height>
	- </rect>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="windowTitle">
	- <string>QmitkTemplate</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_5">
	- <property name="leftMargin">
	- <number>9</number>
	- </property>
	- <property name="topMargin">
	- <number>9</number>
	- </property>
	- <property name="rightMargin">
	- <number>9</number>
	- </property>
	- <property name="bottomMargin">
	- <number>9</number>
	- </property>
	- <property name="verticalSpacing">
	- <number>25</number>
	- </property>
	- <item row="3" column="0">
	- <widget class="QFrame" name="frame_2">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_6">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="2" column="0">
	- <widget class="QCommandLinkButton" name="m_PlaceFieldSource">
	- <property name="text">
	- <string>Place Field Source</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QFrame" name="frame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_2">
	- <property name="text">
	- <string>World Coordinates:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QLabel" name="m_WorldPosLabel">
	- <property name="text">
	- <string>-</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_3">
	- <property name="text">
	- <string>Index:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QLabel" name="m_IndexLabel">
	- <property name="text">
	- <string>-</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QCommandLinkButton" name="m_GenerateFieldmap">
	- <property name="text">
	- <string>Generate Fieldmap</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QGroupBox" name="m_InputData">
	- <property name="title">
	- <string>Please Select Reference Image</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_3">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QmitkDataStorageComboBox" name="m_SelectedImageBox"></widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QGroupBox" name="groupBox_2">
	- <property name="title">
	- <string>Add Gradient</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_4">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="1">
	- <widget class="QLabel" name="label_10">
	- <property name="text">
	- <string>Gradient</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_7">
	- <property name="text">
	- <string>x:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QLabel" name="label_9">
	- <property name="text">
	- <string>z:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="1">
	- <widget class="QDoubleSpinBox" name="m_zGradientBox">
	- <property name="decimals">
	- <number>4</number>
	- </property>
	- <property name="minimum">
	- <double>-1000.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>1000.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QDoubleSpinBox" name="m_xGradientBox">
	- <property name="decimals">
	- <number>4</number>
	- </property>
	- <property name="minimum">
	- <double>-1000.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>1000.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label_8">
	- <property name="text">
	- <string>y:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QDoubleSpinBox" name="m_yGradientBox">
	- <property name="decimals">
	- <number>4</number>
	- </property>
	- <property name="minimum">
	- <double>-1000.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>1000.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="2">
	- <widget class="QLabel" name="label_11">
	- <property name="text">
	- <string>Offset</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="2">
	- <widget class="QDoubleSpinBox" name="m_xOffsetBox">
	- <property name="decimals">
	- <number>4</number>
	- </property>
	- <property name="minimum">
	- <double>-1000.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>1000.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="2">
	- <widget class="QDoubleSpinBox" name="m_yOffsetBox">
	- <property name="decimals">
	- <number>4</number>
	- </property>
	- <property name="minimum">
	- <double>-1000.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>1000.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="2">
	- <widget class="QDoubleSpinBox" name="m_zOffsetBox">
	- <property name="decimals">
	- <number>4</number>
	- </property>
	- <property name="minimum">
	- <double>-1000.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>1000.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="6" column="0">
	- <spacer name="spacer1">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeType">
	- <enum>QSizePolicy::Expanding</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>220</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="5" column="0">
	- <widget class="QGroupBox" name="groupBox">
	- <property name="title">
	- <string>Edit Selected Source</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_2">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_6">
	- <property name="text">
	- <string>Name:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label_5">
	- <property name="text">
	- <string>Height:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_4">
	- <property name="text">
	- <string>Variance:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QLabel" name="m_SourceNameLabel">
	- <property name="text">
	- <string>-</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QDoubleSpinBox" name="m_SourceVarianceBox">
	- <property name="maximum">
	- <double>999999.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QDoubleSpinBox" name="m_SourceHeightBox">
	- <property name="maximum">
	- <double>999999.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <layoutdefault spacing="6" margin="11"></layoutdefault>
	- <customwidgets>
	- <customwidget>
	- <class>QmitkDataStorageComboBox</class>
	- <extends>QComboBox</extends>
	- <header location="global">QmitkDataStorageComboBox.h</header>
	- </customwidget>
	- </customwidgets>
	- <resources></resources>
	- <connections></connections>
	-</ui>
	\ No newline at end of file
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/mitkPluginActivator.cpp
	deleted file mode 100644
	index a63feeaef4..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/mitkPluginActivator.cpp
	+++ /dev/null
	@@ -1,46 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkPluginActivator.h"
	-
	-#include "src/internal/Perspectives/QmitkDIAppSyntheticDataGenerationPerspective.h"
	-
	-#include "src/internal/QmitkFiberfoxView.h"
	-#include "src/internal/QmitkFiberGenerationView.h"
	-#include "src/internal/QmitkFieldmapGeneratorView.h"
	-
	-ctkPluginContext* mitk::PluginActivator::m_Context = nullptr;
	-
	-ctkPluginContext* mitk::PluginActivator::GetContext()
	-{
	- return m_Context;
	-}
	-
	-void mitk::PluginActivator::start(ctkPluginContext* context)
	-{
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkDIAppSyntheticDataGenerationPerspective, context)
	-
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberfoxView, context)
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkFieldmapGeneratorView, context)
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberGenerationView, context)
	- m_Context = context;
	-}
	-
	-void mitk::PluginActivator::stop(ctkPluginContext* context)
	-{
	- Q_UNUSED(context)
	- m_Context = nullptr;
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/mitkPluginActivator.h b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/mitkPluginActivator.h
	deleted file mode 100644
	index c49af4f79f..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/mitkPluginActivator.h
	+++ /dev/null
	@@ -1,40 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef MITKPLUGINACTIVATOR_H
	-#define MITKPLUGINACTIVATOR_H
	-
	-#include <ctkPluginActivator.h>
	-
	-namespace mitk
	-{
	- class PluginActivator : public QObject, public ctkPluginActivator
	- {
	- Q_OBJECT
	- Q_PLUGIN_METADATA(IID "org.mitk.gui.qt.diffusionimaging.fiberfox")
	- Q_INTERFACES(ctkPluginActivator)
	-
	- public:
	- static ctkPluginContext* GetContext();
	-
	- void start(ctkPluginContext* context) override;
	- void stop(ctkPluginContext* context) override;
	-
	- private:
	- static ctkPluginContext* m_Context;
	- };
	-}
	-
	-#endif
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/CMakeLists.txt
	deleted file mode 100644
	index 35b0da5e17..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/CMakeLists.txt
	+++ /dev/null
	@@ -1,10 +0,0 @@
	-# The project name must correspond to the directory name of your plug-in
	-# and must not contain periods.
	-project(org_mitk_gui_qt_diffusionimaging_fiberprocessing)
	-
	-mitk_create_plugin(
	- SUBPROJECTS MITK-DTI
	- EXPORT_DIRECTIVE DIFFUSIONIMAGING_FIBERPROCESSING_EXPORT
	- EXPORTED_INCLUDE_SUFFIXES src
	- MODULE_DEPENDS MitkFiberTracking MitkChart MitkMultilabel
	-)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/documentation/UserManual/DirectionExtractionFib.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/documentation/UserManual/DirectionExtractionFib.png
	deleted file mode 100644
	index 2495435ef0..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/documentation/UserManual/DirectionExtractionFib.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/documentation/UserManual/DirectionExtractionPeaks.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/documentation/UserManual/DirectionExtractionPeaks.png
	deleted file mode 100644
	index c60f49754b..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/documentation/UserManual/DirectionExtractionPeaks.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/documentation/UserManual/QmitkFiberClusteringViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/documentation/UserManual/QmitkFiberClusteringViewUserManual.dox
	deleted file mode 100644
	index f6a0db93bb..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/documentation/UserManual/QmitkFiberClusteringViewUserManual.dox
	+++ /dev/null
	@@ -1,38 +0,0 @@
	-/**
	-\page org_mitk_views_fiberclustering Fiber Clustering
	-
	-Cluster fibers using an extended version of the QuickBundles method (see [1,2]). Corrseponding command line tool is MitkFiberClustering.
	-
	-\section SecInput Input Data
	-
	-- Tractogram: Input streamlines to be clustered.
	-- Input Centroids: Optionally input a set of streamlines around which the streamlines of the input tractograms are clustered. No new clusters are created in this case. Each input streamline is assigned to the neares centroid.
	-
	-\section SecParams Parameters
	-
	-- Cluster Size: Metric distance threshold for a streamline to be assigned to a cluster (cluster size).
	-- Fiber Points: Resample the input streamlines to the given number of points. For scalar map and anatomical metrics this value should be much larger than for streamline shape-based metrics.
	-- Min. Fibers per Cluster: Clusters with a smaller number of streamlines are discarded.
	-- Max. Clusters: Only the N largest clusters are retained.
	-- Merge Duplicate Clusters: Merge clusters based on the distance of their respective centroids using the given metric threshold. No merging is performed for a metric threshold of 0.
	-- Output Centroids: Output the final cluster centroids.
	-
	-\section SecMetrics Metrics
	-
	-All metrics can be combined using the average weighted metric value.
	-
	-- Euclidean: Equivalent to the the MDF of [1]. Command line tool metric string EU_MEAN.
	-- Euclidean STDEV: Standard deviation of the point-wise euclidean distance. Fibers that run parallel have a low distance with this metric, regardless of their absolute distance. Command line tool metric string EU_STD.
	-- Euclidean Maximum: Use maximum value of the point-weise euclidean distance. Command line tool metric string EU_MAX.
	-- Streamline Length: Absolute streamline length difference. Command line tool metric string LENGTH.
	-- Anatomical: Metric based on white matter parcellation histograms along the tracts (see [3]). Command line tool metric string MAP.
	-- Scalar Map: Use the average point-wise scalar map value differences (e.g. FA) of two streamlines as distance metric. Command line tool metric string ANAT.
	-
	-[1] Garyfallidis, Eleftherios, Matthew Brett, Marta Morgado Correia, Guy B. Williams, and Ian Nimmo-Smith. “QuickBundles, a Method for Tractography Simplification.” Frontiers in Neuroscience 6 (2012).
	-
	-[2] Garyfallidis, Eleftherios, Marc-Alexandre Côté, François Rheault, and Maxime Descoteaux. “QuickBundlesX: Sequential Clustering of Millions of Streamlines in Multiple Levels of Detail at Record Execution Time.” ISMRM2016 (Singapore), 2016.
	-
	-[3] Siless, Viviana, Ken Chang, Bruce Fischl, and Anastasia Yendiki. “AnatomiCuts: Hierarchical Clustering of Tractography Streamlines Based on Anatomical Similarity.” NeuroImage 166 (February 1, 2018): 32–45. https://doi.org/10.1016/j.neuroimage.2017.10.058.
	-
	-
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/documentation/UserManual/QmitkFiberFitViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/documentation/UserManual/QmitkFiberFitViewUserManual.dox
	deleted file mode 100644
	index 7c7d344aca..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/documentation/UserManual/QmitkFiberFitViewUserManual.dox
	+++ /dev/null
	@@ -1,30 +0,0 @@
	-/**
	-\page org_mitk_views_fiberfit Fiber Fit
	-
	-Linearly fits a scalar weight for each streamline in order to optimally explain the input image. Corrseponding command line tool is MitkFitFibersToImage.
	-
	-\section SecFiberFitParams Input Data and Parameters
	-
	-- Image: The image data used to fit the fiber weights. Possible input types:
	- - Peak images. The input peak magnitudes are approximated using the voxel-wise fixel magnitudes obtained from the input tractogram.
	- - Raw diffusion-weighted images. The dMRI signal is approximated using a tensor model with fixed diffusion parameters. Tensor orientations are determined by the input tractogram.
	- - Sclar valued images (e.g. FA, axon density maps, ...).
	-- Tractogram: The method fits a weight for each streamline in the input tractogram. In the command line tool, a list of separate bundles can be used as input.
	-- Regularization:
	- - Voxel-wise Variance: Constrain the fiber weights to be similar in one voxe (similar to [1]). Command line tool string "VoxelVariance".
	- - Variance: Constrain the fiber weights to be globally similar (mean squared deaviation of weights from mean weight). Command line tool string "Variance".
	- - Mean-squared magnitude: Enforce small weights using the mean-squared magnitude of the streamlines as regularization factor. Command line tool string "MSM".
	- - Lasso: L1 regularization of the streamline weights. Enforces a sparse weight vector. Command line tool string "Lasso".
	- - Group Lasso: Useful if individual bundles are used as input (command-line tool only). This regularization tries to explain the signal with as few bundles as possible penalizing the bundle-wise root mean squared magnitude of the weighs (see [2]). Command line tool string "GroupLasso".
	- - Group Variance: Constrain the fiber weights to be similar for each bundle individually (command-line tool only). Command line tool string "GrouplVariance".
	- - No regularization. Command line tool string "NONE".
	-- Suppress Outliers: Perform second optimization run with an upper weight bound based on the first weight estimation (99% quantile).
	-- Output Residuals: Add residual images to the data manager.
	-
	-[1] Smith, Robert E., Jacques-Donald Tournier, Fernando Calamante, and Alan Connelly. “SIFT2: Enabling Dense Quantitative Assessment of Brain White Matter Connectivity Using Streamlines Tractography.” NeuroImage 119, no. Supplement C (October 1, 2015): 338–51. https://doi.org/10.1016/j.neuroimage.2015.06.092.
	-
	-[2] Yuan, Ming, and Yi Lin. “Model Selection and Estimation in Regression with Grouped Variables.” Journal of the Royal Statistical Society: Series B (Statistical Methodology) 68, no. 1 (February 1, 2006): 49–67. https://doi.org/10.1111/j.1467-9868.2005.00532.x.
	-
	-[3] Pestilli, Franco, Jason D. Yeatman, Ariel Rokem, Kendrick N. Kay, and Brian A. Wandell. “Evaluation and Statistical Inference for Human Connectomes.” Nature Methods 11, no. 10 (October 2014): 1058–63. https://doi.org/10.1038/nmeth.3098.
	-
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/documentation/UserManual/QmitkFiberProcessingViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/documentation/UserManual/QmitkFiberProcessingViewUserManual.dox
	deleted file mode 100644
	index 46f70c978c..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/documentation/UserManual/QmitkFiberProcessingViewUserManual.dox
	+++ /dev/null
	@@ -1,9 +0,0 @@
	-/**
	-\page org_mitk_views_fiberprocessing Fiber Processing
	-
	-This view provides tools to extract subbundles from a given fiber bundle, to remove unwanted fibers (e.g. via length, curvature, directional and fiber weight constraints) and to modify the properties of a fiber bundles such as coloring or fiber sampling.
	-
	-<b>Fiber Extraction:</b>
	-Place ROIs in the 2D render widgets (cricles or polygons) and extract fibers from the bundle that pass through these ROIs by selecting the according ROI and fiber bundle in the datamanger and starting the extraction. The ROIs can be combined via logical operations. All fibers that pass through the thus generated composite ROI are extracted. The extraction can also be performed using 3D ROIs represented as binary mask images. In this extraction method, the logical operations are not implemented at the moment.
	-
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/documentation/UserManual/QmitkFiberQuantificationViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/documentation/UserManual/QmitkFiberQuantificationViewUserManual.dox
	deleted file mode 100644
	index af33fc3fbf..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/documentation/UserManual/QmitkFiberQuantificationViewUserManual.dox
	+++ /dev/null
	@@ -1,32 +0,0 @@
	-/**
	-\page org_mitk_views_fiberquantification Fiber Quantification
	-
	-This view provides tools to derive additional information (such as tract density images and principal fiber direction maps) from tractograms.
	-
	-\section SecFiberQuantInput Input Data
	-
	-- Tractogram: The input streamlines.
	-- Reference Image: The output images will have the same geometry as this reference image (optional). If a reference image with DICOM tags is used, the resulting tract envelope can be saved as DICOM Segmentation Object.
	-
	-\section SecFDI Fiber-derived Images
	-
	-- Tract density image: The voxel values correspond to the sum of all fiber segment lengths in the respective voxel.
	-- Normalized TDI: 0-1 normalized version of the TDI.
	-- Binary envelope: Generate a binary segmentation from the input tractogram.
	-- Fiber bundle image: Generate a 2D rgba image representation of the fiber bundle.
	-- Fiber endings image: Generate a 2D image showing the locations of fiber endpoints.
	-- Fiber endings pointset: Generate a poinset containing the locations of fiber endpoints (not recommended for large tractograms).
	-
	-\section SecPD Principal Fiber Directions
	-
	-Calculate the voxel-wise principal fiber directions (fixels) from a tractogram.
	-- Max. Peaks: Maximum number of output directions per voxel.
	-- Angular Threshold: Cluster directions that are close together using the specified threshold (in degree).
	-- Size Threshold: Discard principal directions with a magnitude smaller than the specified threshold. This value is the vector magnitude raltive to the largest vector in the voxel.
	-- Normalization: Normalize the principal fiber directions by the global maximum, the voxel-wise maximum or each direction individually.
	-- Output #Directions per Voxel: Generate an image that contains the number of principal directions per voxel as values.
	-
	-\imageMacro{DirectionExtractionFib.png, "Input fiber bundle",10}
	-\imageMacro{DirectionExtractionPeaks.png, "Output principal fiber directions",10}
	-
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/documentation/doxygen/modules.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/documentation/doxygen/modules.dox
	deleted file mode 100644
	index bd2816019b..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/documentation/doxygen/modules.dox
	+++ /dev/null
	@@ -1,16 +0,0 @@
	-/**
	- \defgroup org_mitk_gui_qt_diffusionimaging_fiberprocessing org.mitk.gui.qt.diffusionimaging.fiberprocessing
	- \ingroup MITKPlugins
	-
	- \brief This is the diffusionimaging.fiberprocessing plugin.
	-
	-*/
	-
	-/**
	- \defgroup org_mitk_gui_qt_diffusionimaging_fiberprocessing_internal Internal
	- \ingroup org_mitk_gui_qt_diffusionimaging_fiberprocessing
	-
	- \brief This subcategory includes the internal classes of the org.mitk.gui.qt.diffusionimaging.fiberprocessing plugin. Other
	- plugins must not rely on these classes. They contain implementation details and their interface
	- may change at any time. We mean it.
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/files.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/files.cmake
	deleted file mode 100644
	index 0f586c99c6..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/files.cmake
	+++ /dev/null
	@@ -1,63 +0,0 @@
	-set(SRC_CPP_FILES
	-
	-
	-)
	-
	-set(INTERNAL_CPP_FILES
	- mitkPluginActivator.cpp
	-
	- QmitkFiberQuantificationView.cpp
	- QmitkFiberProcessingView.cpp
	- QmitkFiberClusteringView.cpp
	- QmitkFiberFitView.cpp
	- QmitkTractometryView.cpp
	-
	- Perspectives/QmitkFiberProcessingPerspective.cpp
	-)
	-
	-set(UI_FILES
	- src/internal/QmitkFiberQuantificationViewControls.ui
	- src/internal/QmitkFiberProcessingViewControls.ui
	- src/internal/QmitkFiberClusteringViewControls.ui
	- src/internal/QmitkFiberFitViewControls.ui
	- src/internal/QmitkTractometryViewControls.ui
	-)
	-
	-set(MOC_H_FILES
	- src/internal/mitkPluginActivator.h
	-
	- src/internal/QmitkFiberQuantificationView.h
	- src/internal/QmitkFiberProcessingView.h
	- src/internal/QmitkFiberClusteringView.h
	- src/internal/QmitkFiberFitView.h
	- src/internal/QmitkTractometryView.h
	-
	- src/internal/Perspectives/QmitkFiberProcessingPerspective.h
	-)
	-
	-set(CACHED_RESOURCE_FILES
	- plugin.xml
	-
	- resources/FiberBundleOperations.png
	- resources/FiberQuantification.png
	- resources/FiberClustering.png
	- resources/FiberFit.png
	- resources/Tractometry.png
	- resources/circle.png
	- resources/polygon.png
	-)
	-
	-set(QRC_FILES
	- resources/QmitkFiberprocessing.qrc
	-)
	-
	-
	-set(CPP_FILES )
	-
	-foreach(file ${SRC_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/${file})
	-endforeach(file ${SRC_CPP_FILES})
	-
	-foreach(file ${INTERNAL_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/internal/${file})
	-endforeach(file ${INTERNAL_CPP_FILES})
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/manifest_headers.cmake
	deleted file mode 100644
	index 2f6a8b321e..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/manifest_headers.cmake
	+++ /dev/null
	@@ -1,5 +0,0 @@
	-set(Plugin-Name "MITK Fiber Processing")
	-set(Plugin-Version "1.0.0")
	-set(Plugin-Vendor "DKFZ, Medical and Biological Informatics")
	-set(Plugin-ContactAddress "http://www.mitk.org")
	-set(Require-Plugin org.mitk.gui.qt.diffusionimaging org.mitk.gui.qt.common)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/plugin.xml b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/plugin.xml
	deleted file mode 100644
	index 41500049dd..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/plugin.xml
	+++ /dev/null
	@@ -1,163 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<?BlueBerry version="0.1"?>
	-<plugin>
	-
	- <extension point="org.blueberry.ui.views">
	-
	- <view id="org.mitk.views.fiberquantification"
	- name="Fiber Quantification"
	- category="Fiber processing"
	- class="QmitkFiberQuantificationView"
	- icon="resources/FiberQuantification.png">
	- <keywordReference id="org.mitk.views.fiberquantification.Keyword"/>
	- </view>
	-
	- <view id="org.mitk.views.fiberprocessing"
	- name="Fiber Processing"
	- category="Fiber processing"
	- class="QmitkFiberProcessingView"
	- icon="resources/FiberBundleOperations.png">
	- <keywordReference id="org.mitk.views.fiberprocessing.Keyword"/>
	- </view>
	-
	- <view id="org.mitk.views.fiberclustering"
	- name="Fiber Clustering"
	- category="Fiber processing"
	- class="QmitkFiberClusteringView"
	- icon="resources/FiberClustering.png">
	- <keywordReference id="org.mitk.views.fiberclustering.Keyword"/>
	- </view>
	-
	- <view id="org.mitk.views.fiberfit"
	- name="Fiber Fit"
	- category="Fiber processing"
	- class="QmitkFiberFitView"
	- icon="resources/FiberFit.png">
	- <keywordReference id="org.mitk.views.fiberfit.Keyword"/>
	- </view>
	-
	- <view id="org.mitk.views.tractometry"
	- name="Tractometry"
	- category="Fiber processing"
	- class="QmitkTractometryView"
	- icon="resources/Tractometry.png">
	- <keywordReference id="org.mitk.views.tractometry.Keyword"/>
	- </view>
	-
	- </extension>
	-
	-
	- <extension point="org.blueberry.ui.perspectives">
	-
	- <perspective id="org.mitk.perspectives.fiberprocessings"
	- name="Fiber Processing"
	- class="QmitkFiberProcessingPerspective"
	- icon="resources/FiberBundleOperations.png">
	- <description>This perspective contains all views necessary to post process fibers.</description>
	- <keywordReference id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- </perspective>
	-
	- </extension>
	-
	- <extension point="org.blueberry.ui.keywords">
	-
	- <keyword label="cluster" id="org.mitk.views.fiberclustering.Keyword"/>
	- <keyword label="fiber" id="org.mitk.views.fiberclustering.Keyword"/>
	- <keyword label="quickbundles" id="org.mitk.views.fiberclustering.Keyword"/>
	- <keyword label="clustering" id="org.mitk.views.fiberclustering.Keyword"/>
	-
	- <keyword label="fit" id="org.mitk.views.fiberfit.Keyword"/>
	- <keyword label="sift" id="org.mitk.views.fiberfit.Keyword"/>
	- <keyword label="life" id="org.mitk.views.fiberfit.Keyword"/>
	- <keyword label="fiber" id="org.mitk.views.fiberfit.Keyword"/>
	-
	- <keyword label="processing" id="org.mitk.views.fiberprocessing.Keyword"/>
	- <keyword label="extract" id="org.mitk.views.fiberprocessing.Keyword"/>
	- <keyword label="remove" id="org.mitk.views.fiberprocessing.Keyword"/>
	- <keyword label="fiber" id="org.mitk.views.fiberprocessing.Keyword"/>
	- <keyword label="bundle" id="org.mitk.views.fiberprocessing.Keyword"/>
	- <keyword label="color" id="org.mitk.views.fiberprocessing.Keyword"/>
	- <keyword label="mirror" id="org.mitk.views.fiberprocessing.Keyword"/>
	- <keyword label="threshold" id="org.mitk.views.fiberprocessing.Keyword"/>
	- <keyword label="prune" id="org.mitk.views.fiberprocessing.Keyword"/>
	- <keyword label="select" id="org.mitk.views.fiberprocessing.Keyword"/>
	- <keyword label="segment" id="org.mitk.views.fiberprocessing.Keyword"/>
	- <keyword label="dissect" id="org.mitk.views.fiberprocessing.Keyword"/>
	- <keyword label="modify" id="org.mitk.views.fiberprocessing.Keyword"/>
	- <keyword label="join" id="org.mitk.views.fiberprocessing.Keyword"/>
	- <keyword label="merge" id="org.mitk.views.fiberprocessing.Keyword"/>
	- <keyword label="add" id="org.mitk.views.fiberprocessing.Keyword"/>
	- <keyword label="subtract" id="org.mitk.views.fiberprocessing.Keyword"/>
	- <keyword label="difference" id="org.mitk.views.fiberprocessing.Keyword"/>
	-
	- <keyword label="fiber" id="org.mitk.views.fiberquantification.Keyword"/>
	- <keyword label="quantification" id="org.mitk.views.fiberquantification.Keyword"/>
	- <keyword label="statistics" id="org.mitk.views.fiberquantification.Keyword"/>
	- <keyword label="length" id="org.mitk.views.fiberquantification.Keyword"/>
	- <keyword label="number" id="org.mitk.views.fiberquantification.Keyword"/>
	- <keyword label="principal" id="org.mitk.views.fiberquantification.Keyword"/>
	- <keyword label="direction" id="org.mitk.views.fiberquantification.Keyword"/>
	- <keyword label="peak" id="org.mitk.views.fiberquantification.Keyword"/>
	- <keyword label="main" id="org.mitk.views.fiberquantification.Keyword"/>
	- <keyword label="tract" id="org.mitk.views.fiberquantification.Keyword"/>
	- <keyword label="density" id="org.mitk.views.fiberquantification.Keyword"/>
	- <keyword label="image" id="org.mitk.views.fiberquantification.Keyword"/>
	- <keyword label="TDI" id="org.mitk.views.fiberquantification.Keyword"/>
	- <keyword label="envelope" id="org.mitk.views.fiberquantification.Keyword"/>
	- <keyword label="hull" id="org.mitk.views.fiberquantification.Keyword"/>
	- <keyword label="endpoints" id="org.mitk.views.fiberquantification.Keyword"/>
	- <keyword label="end" id="org.mitk.views.fiberquantification.Keyword"/>
	- <keyword label="endings" id="org.mitk.views.fiberquantification.Keyword"/>
	-
	-
	- <keyword label="cluster" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="fiber" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="quickbundles" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="clustering" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	-
	- <keyword label="fit" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="sift" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="life" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="fiber" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	-
	- <keyword label="processing" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="extract" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="remove" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="fiber" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="bundle" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="color" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="mirror" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="threshold" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="prune" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="select" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="segment" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="dissect" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="modify" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="join" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="merge" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="add" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="subtract" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="difference" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	-
	- <keyword label="fiber" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="quantification" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="statistics" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="length" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="number" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="principal" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="direction" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="peak" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="main" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="tract" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="density" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="image" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="TDI" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="envelope" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="hull" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="endpoints" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="end" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	- <keyword label="endings" id="org.mitk.perspectives.fiberprocessings.Keyword"/>
	-
	- </extension>
	-
	-</plugin>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/FiberBundle.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/FiberBundle.png
	deleted file mode 100644
	index 7b16f42421..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/FiberBundle.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/FiberBundleOperations.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/FiberBundleOperations.png
	deleted file mode 100644
	index 9c02e31cf7..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/FiberBundleOperations.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/FiberClustering.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/FiberClustering.png
	deleted file mode 100644
	index 5989a0be85..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/FiberClustering.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/FiberFit.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/FiberFit.png
	deleted file mode 100644
	index f978b84774..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/FiberFit.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/FiberQuantification.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/FiberQuantification.png
	deleted file mode 100644
	index 63ae3a5007..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/FiberQuantification.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/QmitkFiberprocessing.qrc b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/QmitkFiberprocessing.qrc
	deleted file mode 100644
	index 991f2d10e7..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/QmitkFiberprocessing.qrc
	+++ /dev/null
	@@ -1,7 +0,0 @@
	-<RCC>
	- <qresource prefix="/QmitkFiberprocessing">
	- <file>FiberBundle.png</file>
	- <file>circle.png</file>
	- <file>polygon.png</file>
	- </qresource>
	-</RCC>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/Tractometry.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/Tractometry.png
	deleted file mode 100644
	index 85c6c25cfc..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/Tractometry.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/circle.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/circle.png
	deleted file mode 100644
	index b16472e3b4..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/circle.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/polygon.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/polygon.png
	deleted file mode 100644
	index 4eae1bbba4..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/polygon.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/Perspectives/QmitkFiberProcessingPerspective.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/Perspectives/QmitkFiberProcessingPerspective.cpp
	deleted file mode 100644
	index d8529d2770..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/Perspectives/QmitkFiberProcessingPerspective.cpp
	+++ /dev/null
	@@ -1,51 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkFiberProcessingPerspective.h"
	-#include "berryIViewLayout.h"
	-
	-void QmitkFiberProcessingPerspective::CreateInitialLayout(berry::IPageLayout::Pointer layout)
	-{
	- /////////////////////////////////////////////////////
	- // all di-app perspectives should have the following:
	- /////////////////////////////////////////////////////
	-
	- QString editorArea = layout->GetEditorArea();
	-
	- layout->AddStandaloneViewPlaceholder("org.mitk.views.viewnavigatorview", berry::IPageLayout::LEFT, 0.3f, editorArea, false);
	-
	- layout->AddStandaloneView("org.mitk.views.datamanager",
	- false, berry::IPageLayout::LEFT, 0.3f, editorArea);
	-
	- layout->AddStandaloneView("org.mitk.views.controlvisualizationpropertiesview",
	- false, berry::IPageLayout::BOTTOM, .15f, "org.mitk.views.datamanager");
	-
	- berry::IFolderLayout::Pointer left =
	- layout->CreateFolder("org.mbi.diffusionimaginginternal.leftcontrols",
	- berry::IPageLayout::BOTTOM, 0.15f, "org.mitk.views.controlvisualizationpropertiesview");
	-
	- layout->AddStandaloneViewPlaceholder("org.mitk.views.imagenavigator",
	- berry::IPageLayout::BOTTOM, .7f, "org.mbi.diffusionimaginginternal.leftcontrols", false);
	-
	- /////////////////////////////////////////////
	- // here goes the perspective specific stuff
	- /////////////////////////////////////////////
	-
	- left->AddView("org.mitk.views.fiberprocessing");
	- left->AddView("org.mitk.views.fiberquantification");
	- left->AddView("org.mitk.views.fiberclustering");
	- left->AddView("org.mitk.views.fiberfit");
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/Perspectives/QmitkFiberProcessingPerspective.h b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/Perspectives/QmitkFiberProcessingPerspective.h
	deleted file mode 100644
	index faa6d4d3a1..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/Perspectives/QmitkFiberProcessingPerspective.h
	+++ /dev/null
	@@ -1,36 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef QmitkFiberProcessingPerspective_H_
	-#define QmitkFiberProcessingPerspective_H_
	-
	-#include <berryIPerspectiveFactory.h>
	-
	-class QmitkFiberProcessingPerspective : public QObject, public berry::IPerspectiveFactory
	-{
	- Q_OBJECT
	- Q_INTERFACES(berry::IPerspectiveFactory)
	-
	-public:
	-
	- QmitkFiberProcessingPerspective() {}
	- ~QmitkFiberProcessingPerspective() {}
	-
	- void CreateInitialLayout(berry::IPageLayout::Pointer layout) override;
	-};
	-
	-#endif /* QmitkFiberProcessingPerspective_H_ */
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberClusteringView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberClusteringView.cpp
	deleted file mode 100644
	index b2afe53671..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberClusteringView.cpp
	+++ /dev/null
	@@ -1,232 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-// Blueberry
	-#include <berryISelectionService.h>
	-#include <berryIWorkbenchWindow.h>
	-
	-#include "QmitkFiberClusteringView.h"
	-
	-#include <mitkNodePredicateDataType.h>
	-#include <mitkNodePredicateDimension.h>
	-#include <mitkNodePredicateAnd.h>
	-#include <mitkImageCast.h>
	-#include <mitkImageAccessByItk.h>
	-#include <itkTractClusteringFilter.h>
	-#include <mitkFiberBundle.h>
	-#include <mitkClusteringMetricEuclideanMean.h>
	-#include <mitkClusteringMetricEuclideanMax.h>
	-#include <mitkClusteringMetricEuclideanStd.h>
	-#include <mitkClusteringMetricAnatomic.h>
	-#include <mitkClusteringMetricScalarMap.h>
	-#include <mitkClusteringMetricInnerAngles.h>
	-#include <mitkClusteringMetricLength.h>
	-#include <QMessageBox>
	-
	-const std::string QmitkFiberClusteringView::VIEW_ID = "org.mitk.views.fiberclustering";
	-using namespace mitk;
	-
	-QmitkFiberClusteringView::QmitkFiberClusteringView()
	- : QmitkAbstractView()
	- , m_Controls( nullptr )
	-{
	-
	-}
	-
	-// Destructor
	-QmitkFiberClusteringView::~QmitkFiberClusteringView()
	-{
	-
	-}
	-
	-void QmitkFiberClusteringView::CreateQtPartControl( QWidget *parent )
	-{
	- // build up qt view, unless already done
	- if ( !m_Controls )
	- {
	- // create GUI widgets from the Qt Designer's .ui file
	- m_Controls = new Ui::QmitkFiberClusteringViewControls;
	- m_Controls->setupUi( parent );
	-
	- connect( m_Controls->m_StartButton, SIGNAL(clicked()), this, SLOT(StartClustering()) );
	- connect( m_Controls->m_TractBox, SIGNAL(currentIndexChanged(int)), this, SLOT(FiberSelectionChanged()) );
	-
	- mitk::TNodePredicateDataType<mitk::FiberBundle>::Pointer isFib = mitk::TNodePredicateDataType<mitk::FiberBundle>::New();
	- m_Controls->m_TractBox->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_TractBox->SetPredicate(isFib);
	-
	- m_Controls->m_InCentroidsBox->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_InCentroidsBox->SetPredicate(isFib);
	- m_Controls->m_InCentroidsBox->SetZeroEntryText("--");
	-
	-
	- mitk::TNodePredicateDataType<mitk::Image>::Pointer imageP = mitk::TNodePredicateDataType<mitk::Image>::New();
	- mitk::NodePredicateDimension::Pointer dimP = mitk::NodePredicateDimension::New(3);
	-
	- m_Controls->m_MapBox->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_MapBox->SetPredicate(mitk::NodePredicateAnd::New(imageP, dimP));
	-
	- m_Controls->m_ParcellationBox->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_ParcellationBox->SetPredicate(mitk::NodePredicateAnd::New(imageP, dimP));
	-
	- m_Controls->m_MetricBox6->setVisible(false);
	- m_Controls->m_MetricWeight6->setVisible(false);
	-
	- FiberSelectionChanged();
	- }
	-
	-}
	-
	-void QmitkFiberClusteringView::SetFocus()
	-{
	- FiberSelectionChanged();
	-}
	-
	-void QmitkFiberClusteringView::FiberSelectionChanged()
	-{
	- if (m_Controls->m_TractBox->GetSelectedNode().IsNull())
	- m_Controls->m_StartButton->setEnabled(false);
	- else
	- m_Controls->m_StartButton->setEnabled(true);
	-}
	-
	-void QmitkFiberClusteringView::StartClustering()
	-{
	- if (m_Controls->m_TractBox->GetSelectedNode().IsNull())
	- return;
	-
	- mitk::DataNode::Pointer node = m_Controls->m_TractBox->GetSelectedNode();
	- float clusterSize = m_Controls->m_ClusterSizeBox->value();
	-
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
	-
	- float max_d = 0;
	- int i=1;
	- std::vector< float > distances;
	- while (max_d < fib->GetGeometry()->GetDiagonalLength()/2)
	- {
	- distances.push_back(clusterSize*i);
	- max_d = clusterSize*i;
	- ++i;
	- }
	-
	- itk::TractClusteringFilter::Pointer clusterer = itk::TractClusteringFilter::New();
	- clusterer->SetDistances(distances);
	- clusterer->SetTractogram(fib);
	- if (m_Controls->m_InCentroidsBox->GetSelectedNode().IsNotNull())
	- {
	- mitk::FiberBundle::Pointer in_centroids = dynamic_cast<mitk::FiberBundle*>(m_Controls->m_InCentroidsBox->GetSelectedNode()->GetData());
	- clusterer->SetInCentroids(in_centroids);
	- }
	-
	- std::vector< mitk::ClusteringMetric* > metrics;
	- if (m_Controls->m_MetricBox1->isChecked())
	- {
	- mitk::ClusteringMetricEuclideanMean* metric = new mitk::ClusteringMetricEuclideanMean();
	- metric->SetScale(m_Controls->m_MetricWeight1->value());
	- metrics.push_back(metric);
	- }
	- if (m_Controls->m_MetricBox2->isChecked())
	- {
	- mitk::ClusteringMetricEuclideanStd* metric = new mitk::ClusteringMetricEuclideanStd();
	- metric->SetScale(m_Controls->m_MetricWeight2->value());
	- metrics.push_back(metric);
	- }
	- if (m_Controls->m_MetricBox3->isChecked())
	- {
	- mitk::ClusteringMetricEuclideanMax* metric = new mitk::ClusteringMetricEuclideanMax();
	- metric->SetScale(m_Controls->m_MetricWeight3->value());
	- metrics.push_back(metric);
	- }
	- if (m_Controls->m_MetricBox6->isChecked())
	- {
	- mitk::ClusteringMetricInnerAngles* metric = new mitk::ClusteringMetricInnerAngles();
	- metric->SetScale(m_Controls->m_MetricWeight6->value());
	- metrics.push_back(metric);
	- }
	- if (m_Controls->m_MetricBox7->isChecked())
	- {
	- mitk::ClusteringMetricLength* metric = new mitk::ClusteringMetricLength();
	- metric->SetScale(m_Controls->m_MetricWeight7->value());
	- metrics.push_back(metric);
	- }
	-
	- if (m_Controls->m_ParcellationBox->GetSelectedNode().IsNotNull() && m_Controls->m_MetricBox4->isChecked())
	- {
	- mitk::Image::Pointer mitk_map = dynamic_cast<mitk::Image*>(m_Controls->m_ParcellationBox->GetSelectedNode()->GetData());
	-
	- ShortImageType::Pointer itk_map = ShortImageType::New();
	- mitk::CastToItkImage(mitk_map, itk_map);
	- mitk::ClusteringMetricAnatomic* metric = new mitk::ClusteringMetricAnatomic();
	- metric->SetParcellations({itk_map});
	- metric->SetScale(m_Controls->m_MetricWeight4->value());
	- metrics.push_back(metric);
	- }
	- if (m_Controls->m_MapBox->GetSelectedNode().IsNotNull() && m_Controls->m_MetricBox5->isChecked())
	- {
	- mitk::Image::Pointer mitk_map = dynamic_cast<mitk::Image*>(m_Controls->m_MapBox->GetSelectedNode()->GetData());
	-
	- FloatImageType::Pointer itk_map = FloatImageType::New();
	- mitk::CastToItkImage(mitk_map, itk_map);
	- mitk::ClusteringMetricScalarMap* metric = new mitk::ClusteringMetricScalarMap();
	- metric->SetImages({itk_map});
	- metric->SetScale(m_Controls->m_MetricWeight5->value());
	- metrics.push_back(metric);
	- }
	-
	- if (metrics.empty())
	- {
	- QMessageBox::warning(nullptr, "Warning", "No metric selected!");
	- return;
	- }
	-
	- clusterer->SetMetrics(metrics);
	- clusterer->SetMergeDuplicateThreshold(m_Controls->m_MergeDuplicatesBox->value());
	- clusterer->SetNumPoints(m_Controls->m_FiberPointsBox->value());
	- clusterer->SetMaxClusters(m_Controls->m_MaxClustersBox->value());
	- clusterer->SetMinClusterSize(m_Controls->m_MinFibersBox->value());
	- clusterer->Update();
	- std::vector<mitk::FiberBundle::Pointer> tracts = clusterer->GetOutTractograms();
	- std::vector<mitk::FiberBundle::Pointer> centroids = clusterer->GetOutCentroids();
	-
	- unsigned int c = 0;
	- for (auto f : tracts)
	- {
	- mitk::DataNode::Pointer new_node = mitk::DataNode::New();
	- new_node->SetData(f);
	- new_node->SetName("Cluster_" + boost::lexical_cast<std::string>(c));
	- if (m_Controls->m_InCentroidsBox->GetSelectedNode().IsNotNull())
	- this->GetDataStorage()->Add(new_node, m_Controls->m_InCentroidsBox->GetSelectedNode());
	- else
	- this->GetDataStorage()->Add(new_node, node);
	- node->SetVisibility(false);
	-
	- if (m_Controls->m_CentroidsBox->isChecked())
	- {
	- mitk::DataNode::Pointer new_node2 = mitk::DataNode::New();
	- new_node2->SetData(centroids.at(c));
	- new_node2->SetName("Centroid_" + boost::lexical_cast<std::string>(c));
	- this->GetDataStorage()->Add(new_node2, new_node);
	- }
	- ++c;
	- }
	-}
	-
	-void QmitkFiberClusteringView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /part/, const QList<mitk::DataNode::Pointer>& )
	-{
	-
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberClusteringView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberClusteringView.h
	deleted file mode 100644
	index 585ff5f55e..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberClusteringView.h
	+++ /dev/null
	@@ -1,68 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef QmitkFiberClusteringView_h
	-#define QmitkFiberClusteringView_h
	-
	-#include <QmitkAbstractView.h>
	-#include "ui_QmitkFiberClusteringViewControls.h"
	-#include <itkImage.h>
	-
	-/*!
	-\brief Cluster fibers by shape and image properties
	-
	-*/
	-class QmitkFiberClusteringView : public QmitkAbstractView
	-{
	- // this is needed for all Qt objects that should have a Qt meta-object
	- // (everything that derives from QObject and wants to have signal/slots)
	- Q_OBJECT
	-
	-public:
	-
	- static const std::string VIEW_ID;
	-
	- QmitkFiberClusteringView();
	- virtual ~QmitkFiberClusteringView();
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	-
	- typedef itk::Image< float, 3 > FloatImageType;
	- typedef itk::Image< short, 3 > ShortImageType;
	-
	- ///
	- /// Sets the focus to an internal widget.
	- ///
	- virtual void SetFocus() override;
	-
	-protected slots:
	-
	- void StartClustering();
	- void FiberSelectionChanged();
	-
	-protected:
	-
	- /// \brief called by QmitkAbstractView when DataManager's selection has changed
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- Ui::QmitkFiberClusteringViewControls* m_Controls;
	-
	-};
	-
	-
	-
	-#endif // _QMITKFIBERTRACKINGVIEW_H_INCLUDED
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberClusteringViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberClusteringViewControls.ui
	deleted file mode 100644
	index b9edec8bfc..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberClusteringViewControls.ui
	+++ /dev/null
	@@ -1,524 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<ui version="4.0">
	- <class>QmitkFiberClusteringViewControls</class>
	- <widget class="QWidget" name="QmitkFiberClusteringViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>474</width>
	- <height>695</height>
	- </rect>
	- </property>
	- <property name="windowTitle">
	- <string>Form</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_10">
	- <property name="verticalSpacing">
	- <number>25</number>
	- </property>
	- <item row="4" column="0">
	- <spacer name="verticalSpacer">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="2" column="0">
	- <widget class="QGroupBox" name="groupBox">
	- <property name="title">
	- <string>Metrics</string>
	- </property>
	- <layout class="QFormLayout" name="formLayout">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QDoubleSpinBox" name="m_MetricWeight1">
	- <property name="toolTip">
	- <string>Weighting factor for metric values.</string>
	- </property>
	- <property name="decimals">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <double>999.000000000000000</double>
	- </property>
	- <property name="value">
	- <double>1.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QCheckBox" name="m_MetricBox1">
	- <property name="text">
	- <string>Euclidean</string>
	- </property>
	- <property name="checked">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QDoubleSpinBox" name="m_MetricWeight2">
	- <property name="toolTip">
	- <string>Weighting factor for metric values.</string>
	- </property>
	- <property name="decimals">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <double>999.000000000000000</double>
	- </property>
	- <property name="value">
	- <double>1.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QCheckBox" name="m_MetricBox2">
	- <property name="text">
	- <string>Euclidean STDEV</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QDoubleSpinBox" name="m_MetricWeight3">
	- <property name="toolTip">
	- <string>Weighting factor for metric values.</string>
	- </property>
	- <property name="decimals">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <double>999.000000000000000</double>
	- </property>
	- <property name="value">
	- <double>1.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QCheckBox" name="m_MetricBox3">
	- <property name="text">
	- <string>Euclidean Maximum</string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QDoubleSpinBox" name="m_MetricWeight7">
	- <property name="toolTip">
	- <string>Weighting factor for metric values.</string>
	- </property>
	- <property name="decimals">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <double>999.000000000000000</double>
	- </property>
	- <property name="value">
	- <double>1.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QDoubleSpinBox" name="m_MetricWeight6">
	- <property name="toolTip">
	- <string>Weighting factor for metric values.</string>
	- </property>
	- <property name="decimals">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <double>999.000000000000000</double>
	- </property>
	- <property name="value">
	- <double>1.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="1">
	- <widget class="QCheckBox" name="m_MetricBox6">
	- <property name="text">
	- <string>Inner Angles</string>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <widget class="QDoubleSpinBox" name="m_MetricWeight4">
	- <property name="toolTip">
	- <string>Weighting factor for metric values.</string>
	- </property>
	- <property name="decimals">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <double>999.000000000000000</double>
	- </property>
	- <property name="value">
	- <double>1.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="1">
	- <widget class="QFrame" name="frame_2">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_3">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>6</number>
	- </property>
	- <item row="0" column="1">
	- <widget class="QCheckBox" name="m_MetricBox4">
	- <property name="toolTip">
	- <string>Distance is based on the selected parcellation.</string>
	- </property>
	- <property name="text">
	- <string>Anatomical</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="2">
	- <widget class="QmitkDataStorageComboBox" name="m_ParcellationBox">
	- <property name="toolTip">
	- <string>Distance is based on the selected parcellation.</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="6" column="0">
	- <widget class="QDoubleSpinBox" name="m_MetricWeight5">
	- <property name="toolTip">
	- <string>Weighting factor for metric values.</string>
	- </property>
	- <property name="decimals">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <double>999.000000000000000</double>
	- </property>
	- <property name="value">
	- <double>30.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="6" column="1">
	- <widget class="QFrame" name="frame_3">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QCheckBox" name="m_MetricBox5">
	- <property name="toolTip">
	- <string>Distance is based on the scalar map values along the tract.</string>
	- </property>
	- <property name="text">
	- <string>Scalar Map</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_MapBox">
	- <property name="toolTip">
	- <string>Distance is based on the scalar map values along the tract.</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="3" column="1">
	- <widget class="QCheckBox" name="m_MetricBox7">
	- <property name="text">
	- <string>Streamline Length</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QGroupBox" name="groupBox_2">
	- <property name="title">
	- <string>Input Data</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_4">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_12">
	- <property name="text">
	- <string>Input Centroids:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QmitkDataStorageComboBoxWithSelectNone" name="m_InCentroidsBox">
	- <property name="toolTip">
	- <string>If set, the input tractogram is clustered around the input centroids and no new clusters are created.</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QCommandLinkButton" name="m_StartButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="maximumSize">
	- <size>
	- <width>200</width>
	- <height>16777215</height>
	- </size>
	- </property>
	- <property name="font">
	- <font>
	- <pointsize>11</pointsize>
	- </font>
	- </property>
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Start</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_3">
	- <property name="text">
	- <string>Tractogram:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_TractBox"/>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QGroupBox" name="groupBox_3">
	- <property name="title">
	- <string>Parameters</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_5">
	- <item row="2" column="1">
	- <widget class="QSpinBox" name="m_MinFibersBox">
	- <property name="toolTip">
	- <string>Only output clusters with ate least the specified number of fibers.</string>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>9999999</number>
	- </property>
	- <property name="value">
	- <number>50</number>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="1">
	- <widget class="QSpinBox" name="m_MaxClustersBox">
	- <property name="toolTip">
	- <string>Only output the N largest clusters. Zero means no limit.</string>
	- </property>
	- <property name="maximum">
	- <number>99999999</number>
	- </property>
	- <property name="value">
	- <number>10</number>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label_4">
	- <property name="text">
	- <string>Min. Fibers per Cluster:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QLabel" name="label_2">
	- <property name="text">
	- <string>Max. Clusters:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_6">
	- <property name="text">
	- <string>Fiber Points:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="1">
	- <widget class="QDoubleSpinBox" name="m_MergeDuplicatesBox">
	- <property name="toolTip">
	- <string>Merge duplicate clusters withthe specified distance threshold. If threshold is < 0, the threshold is set to half of the specified cluster size.</string>
	- </property>
	- <property name="minimum">
	- <double>-1.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>99999.000000000000000</double>
	- </property>
	- <property name="value">
	- <double>-1.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_5">
	- <property name="text">
	- <string>Cluster Size:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_ClusterSizeBox">
	- <property name="toolTip">
	- <string>Cluster size in mm.</string>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>9999999</number>
	- </property>
	- <property name="value">
	- <number>20</number>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QSpinBox" name="m_FiberPointsBox">
	- <property name="toolTip">
	- <string>Fibers are resampled to the desired number of points for clustering. Smaller is faster but less accurate.</string>
	- </property>
	- <property name="minimum">
	- <number>2</number>
	- </property>
	- <property name="maximum">
	- <number>9999999</number>
	- </property>
	- <property name="value">
	- <number>12</number>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QLabel" name="label_10">
	- <property name="text">
	- <string>Merge Duplicate Clusters:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <widget class="QLabel" name="label_11">
	- <property name="text">
	- <string>Output Centroids:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="1">
	- <widget class="QCheckBox" name="m_CentroidsBox">
	- <property name="text">
	- <string/>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <customwidgets>
	- <customwidget>
	- <class>QmitkDataStorageComboBox</class>
	- <extends>QComboBox</extends>
	- <header location="global">QmitkDataStorageComboBox.h</header>
	- </customwidget>
	- <customwidget>
	- <class>QmitkDataStorageComboBoxWithSelectNone</class>
	- <extends>QComboBox</extends>
	- <header>QmitkDataStorageComboBoxWithSelectNone.h</header>
	- </customwidget>
	- </customwidgets>
	- <resources/>
	- <connections/>
	-</ui>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberFitView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberFitView.cpp
	deleted file mode 100644
	index 2374247305..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberFitView.cpp
	+++ /dev/null
	@@ -1,265 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#include <berryISelectionService.h>
	-#include <berryIWorkbenchWindow.h>
	-
	-#include "QmitkFiberFitView.h"
	-
	-#include <mitkNodePredicateDataType.h>
	-#include <mitkImageCast.h>
	-#include <mitkImageAccessByItk.h>
	-#include <mitkImage.h>
	-#include <mitkPeakImage.h>
	-#include <mitkFiberBundle.h>
	-#include <itkFitFibersToImageFilter.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <mitkTensorModel.h>
	-#include <mitkITKImageImport.h>
	-#include <mitkNodePredicateDimension.h>
	-#include <mitkNodePredicateAnd.h>
	-#include <mitkNodePredicateOr.h>
	-
	-const std::string QmitkFiberFitView::VIEW_ID = "org.mitk.views.fiberfit";
	-using namespace mitk;
	-
	-QmitkFiberFitView::QmitkFiberFitView()
	- : QmitkAbstractView()
	- , m_Controls( nullptr )
	-{
	-
	-}
	-
	-// Destructor
	-QmitkFiberFitView::~QmitkFiberFitView()
	-{
	-
	-}
	-
	-void QmitkFiberFitView::CreateQtPartControl( QWidget *parent )
	-{
	- // build up qt view, unless already done
	- if ( !m_Controls )
	- {
	- // create GUI widgets from the Qt Designer's .ui file
	- m_Controls = new Ui::QmitkFiberFitViewControls;
	- m_Controls->setupUi( parent );
	-
	- connect( m_Controls->m_StartButton, SIGNAL(clicked()), this, SLOT(StartFit()) );
	-
	- connect( m_Controls->m_ImageBox, SIGNAL(currentIndexChanged(int)), this, SLOT(DataSelectionChanged()) );
	- connect( m_Controls->m_TractBox, SIGNAL(currentIndexChanged(int)), this, SLOT(DataSelectionChanged()) );
	-
	- mitk::TNodePredicateDataType<mitk::FiberBundle>::Pointer isFib = mitk::TNodePredicateDataType<mitk::FiberBundle>::New();
	- mitk::TNodePredicateDataType<mitk::Image>::Pointer isImage = mitk::TNodePredicateDataType<mitk::Image>::New();
	- mitk::NodePredicateDimension::Pointer is3D = mitk::NodePredicateDimension::New(3);
	-
	- m_Controls->m_TractBox->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_TractBox->SetPredicate(isFib);
	-
	- m_Controls->m_ImageBox->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_ImageBox->SetPredicate( mitk::NodePredicateOr::New( mitk::NodePredicateAnd::New(isImage, is3D), mitk::TNodePredicateDataType<mitk::PeakImage>::New()) );
	-
	- DataSelectionChanged();
	- }
	-}
	-
	-void QmitkFiberFitView::DataSelectionChanged()
	-{
	- if (m_Controls->m_TractBox->GetSelectedNode().IsNull() \|\| m_Controls->m_ImageBox->GetSelectedNode().IsNull())
	- m_Controls->m_StartButton->setEnabled(false);
	- else
	- m_Controls->m_StartButton->setEnabled(true);
	-}
	-
	-void QmitkFiberFitView::SetFocus()
	-{
	- DataSelectionChanged();
	-}
	-
	-void QmitkFiberFitView::StartFit()
	-{
	- if (m_Controls->m_TractBox->GetSelectedNode().IsNull() \|\| m_Controls->m_ImageBox->GetSelectedNode().IsNull())
	- return;
	-
	- mitk::FiberBundle::Pointer input_tracts = dynamic_cast<mitk::FiberBundle*>(m_Controls->m_TractBox->GetSelectedNode()->GetData())->GetDeepCopy();
	-
	- mitk::DataNode::Pointer node = m_Controls->m_ImageBox->GetSelectedNode();
	- itk::FitFibersToImageFilter::Pointer fitter = itk::FitFibersToImageFilter::New();
	-
	- mitk::Image::Pointer mitk_image = dynamic_cast<mitk::Image*>(node->GetData());
	- mitk::PeakImage::Pointer mitk_peak_image = dynamic_cast<mitk::PeakImage*>(node->GetData());
	- if (mitk_peak_image.IsNotNull())
	- {
	- typedef mitk::ImageToItk< mitk::PeakImage::ItkPeakImageType > CasterType;
	- CasterType::Pointer caster = CasterType::New();
	- caster->SetInput(mitk_peak_image);
	- caster->Update();
	- mitk::PeakImage::ItkPeakImageType::Pointer peak_image = caster->GetOutput();
	- fitter->SetPeakImage(peak_image);
	- }
	- else
	- {
	- if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(mitk_image))
	- {
	- fitter->SetDiffImage(mitk::DiffusionPropertyHelper::GetItkVectorImage(mitk_image));
	- mitk::TensorModel<>* model = new mitk::TensorModel<>();
	- model->SetBvalue(1000);
	- model->SetDiffusivity1(0.0010);
	- model->SetDiffusivity2(0.00015);
	- model->SetDiffusivity3(0.00015);
	- model->SetGradientList(mitk::DiffusionPropertyHelper::GetGradientContainer(mitk_image));
	- fitter->SetSignalModel(model);
	- }
	- else
	- {
	- itk::FitFibersToImageFilter::DoubleImgType::Pointer scalar_image = itk::FitFibersToImageFilter::DoubleImgType::New();
	- mitk::CastToItkImage(mitk_image, scalar_image);
	- fitter->SetScalarImage(scalar_image);
	- }
	- }
	-
	- if (m_Controls->m_ReguTypeBox->currentIndex()==0)
	- fitter->SetRegularization(VnlCostFunction::REGU::VOXEL_VARIANCE);
	- else if (m_Controls->m_ReguTypeBox->currentIndex()==1)
	- fitter->SetRegularization(VnlCostFunction::REGU::VARIANCE);
	- else if (m_Controls->m_ReguTypeBox->currentIndex()==2)
	- fitter->SetRegularization(VnlCostFunction::REGU::MSM);
	- else if (m_Controls->m_ReguTypeBox->currentIndex()==3)
	- fitter->SetRegularization(VnlCostFunction::REGU::LASSO);
	- else if (m_Controls->m_ReguTypeBox->currentIndex()==4)
	- fitter->SetRegularization(VnlCostFunction::REGU::NONE);
	-
	- fitter->SetTractograms({input_tracts});
	- fitter->SetFitIndividualFibers(true);
	- fitter->SetMaxIterations(20);
	- fitter->SetVerbose(true);
	- fitter->SetGradientTolerance(1e-5);
	- fitter->SetLambda(m_Controls->m_ReguBox->value());
	- fitter->SetFilterOutliers(m_Controls->m_OutliersBox->isChecked());
	- fitter->Update();
	-
	- mitk::FiberBundle::Pointer output_tracts = fitter->GetTractograms().at(0);
	- output_tracts->ColorFibersByFiberWeights(false, true);
	- mitk::DataNode::Pointer new_node = mitk::DataNode::New();
	- new_node->SetData(output_tracts);
	- new_node->SetName("Fitted");
	- this->GetDataStorage()->Add(new_node, node);
	- m_Controls->m_TractBox->GetSelectedNode()->SetVisibility(false);
	-
	- if (m_Controls->m_ResidualsBox->isChecked() && mitk_peak_image.IsNotNull())
	- {
	- {
	- mitk::PeakImage::ItkPeakImageType::Pointer itk_image = fitter->GetFittedImage();
	-
	- mitk::Image::Pointer mitk_image = dynamic_cast<Image*>(PeakImage::New().GetPointer());
	- mitk::CastToMitkImage(itk_image, mitk_image);
	- mitk_image->SetVolume(itk_image->GetBufferPointer());
	-
	- mitk::DataNode::Pointer new_node = mitk::DataNode::New();
	- new_node->SetData(mitk_image);
	- new_node->SetName("Fitted");
	- this->GetDataStorage()->Add(new_node, node);
	- }
	-
	- {
	- mitk::PeakImage::ItkPeakImageType::Pointer itk_image = fitter->GetResidualImage();
	-
	- mitk::Image::Pointer mitk_image = dynamic_cast<Image*>(PeakImage::New().GetPointer());
	- mitk::CastToMitkImage(itk_image, mitk_image);
	- mitk_image->SetVolume(itk_image->GetBufferPointer());
	-
	- mitk::DataNode::Pointer new_node = mitk::DataNode::New();
	- new_node->SetData(mitk_image);
	- new_node->SetName("Residual");
	- this->GetDataStorage()->Add(new_node, node);
	- }
	-
	- {
	- mitk::PeakImage::ItkPeakImageType::Pointer itk_image = fitter->GetUnderexplainedImage();
	-
	- mitk::Image::Pointer mitk_image = dynamic_cast<Image*>(PeakImage::New().GetPointer());
	- mitk::CastToMitkImage(itk_image, mitk_image);
	- mitk_image->SetVolume(itk_image->GetBufferPointer());
	-
	- mitk::DataNode::Pointer new_node = mitk::DataNode::New();
	- new_node->SetData(mitk_image);
	- new_node->SetName("Underexplained");
	- this->GetDataStorage()->Add(new_node, node);
	- }
	-
	- {
	- mitk::PeakImage::ItkPeakImageType::Pointer itk_image = fitter->GetOverexplainedImage();
	-
	- mitk::Image::Pointer mitk_image = dynamic_cast<Image*>(PeakImage::New().GetPointer());
	- mitk::CastToMitkImage(itk_image, mitk_image);
	- mitk_image->SetVolume(itk_image->GetBufferPointer());
	-
	- mitk::DataNode::Pointer new_node = mitk::DataNode::New();
	- new_node->SetData(mitk_image);
	- new_node->SetName("Overexplained");
	- this->GetDataStorage()->Add(new_node, node);
	- }
	- }
	- else if (m_Controls->m_ResidualsBox->isChecked() && mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(mitk_image))
	- {
	- {
	- mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetFittedImageDiff().GetPointer() );
	- mitk::DiffusionPropertyHelper::CopyProperties(mitk_image, outImage, true);
	- mitk::DiffusionPropertyHelper::InitializeImage( outImage );
	-
	- mitk::DataNode::Pointer new_node = mitk::DataNode::New();
	- new_node->SetData(outImage);
	- new_node->SetName("Fitted");
	- this->GetDataStorage()->Add(new_node, node);
	- }
	-
	- {
	- mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetResidualImageDiff().GetPointer() );
	- mitk::DiffusionPropertyHelper::CopyProperties(mitk_image, outImage, true);
	- mitk::DiffusionPropertyHelper::InitializeImage( outImage );
	-
	- mitk::DataNode::Pointer new_node = mitk::DataNode::New();
	- new_node->SetData(outImage);
	- new_node->SetName("Residual");
	- this->GetDataStorage()->Add(new_node, node);
	- }
	- }
	- else if (m_Controls->m_ResidualsBox->isChecked())
	- {
	- {
	- mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetFittedImageScalar().GetPointer() );
	- mitk::DataNode::Pointer new_node = mitk::DataNode::New();
	- new_node->SetData(outImage);
	- new_node->SetName("Fitted");
	- this->GetDataStorage()->Add(new_node, node);
	- }
	-
	- {
	- mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetResidualImageScalar().GetPointer() );
	- mitk::DataNode::Pointer new_node = mitk::DataNode::New();
	- new_node->SetData(outImage);
	- new_node->SetName("Residual");
	- this->GetDataStorage()->Add(new_node, node);
	- }
	- }
	-}
	-
	-void QmitkFiberFitView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /part/, const QList<mitk::DataNode::Pointer>& )
	-{
	-
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberFitView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberFitView.h
	deleted file mode 100644
	index e43184379c..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberFitView.h
	+++ /dev/null
	@@ -1,65 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef QmitkFiberFitView_h
	-#define QmitkFiberFitView_h
	-
	-#include <QmitkAbstractView.h>
	-#include "ui_QmitkFiberFitViewControls.h"
	-#include <itkImage.h>
	-
	-/*!
	-\brief Weight fibers by linearly fitting them to the image data.
	-
	-*/
	-class QmitkFiberFitView : public QmitkAbstractView
	-{
	- // this is needed for all Qt objects that should have a Qt meta-object
	- // (everything that derives from QObject and wants to have signal/slots)
	- Q_OBJECT
	-
	-public:
	-
	- static const std::string VIEW_ID;
	-
	- QmitkFiberFitView();
	- virtual ~QmitkFiberFitView();
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	-
	- ///
	- /// Sets the focus to an internal widget.
	- ///
	- virtual void SetFocus() override;
	-
	-protected slots:
	-
	- void StartFit();
	- void DataSelectionChanged();
	-
	-protected:
	-
	- /// \brief called by QmitkAbstractView when DataManager's selection has changed
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- Ui::QmitkFiberFitViewControls* m_Controls;
	-
	-};
	-
	-
	-
	-#endif // _QMITKFIBERTRACKINGVIEW_H_INCLUDED
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberFitViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberFitViewControls.ui
	deleted file mode 100644
	index 53549e238c..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberFitViewControls.ui
	+++ /dev/null
	@@ -1,227 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<ui version="4.0">
	- <class>QmitkFiberFitViewControls</class>
	- <widget class="QWidget" name="QmitkFiberFitViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>484</width>
	- <height>574</height>
	- </rect>
	- </property>
	- <property name="windowTitle">
	- <string>Form</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_10">
	- <item row="0" column="0">
	- <widget class="QFrame" name="frame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_2">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>6</number>
	- </property>
	- <item row="4" column="1">
	- <widget class="QCheckBox" name="m_OutliersBox">
	- <property name="text">
	- <string/>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <widget class="QLabel" name="label_6">
	- <property name="text">
	- <string>Output Residuals:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_TractBox"/>
	- </item>
	- <item row="3" column="1">
	- <widget class="QDoubleSpinBox" name="m_ReguBox">
	- <property name="toolTip">
	- <string>Weight for regularization.</string>
	- </property>
	- <property name="decimals">
	- <number>4</number>
	- </property>
	- <property name="maximum">
	- <double>999999.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>1.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_4">
	- <property name="text">
	- <string>Tractogram:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="6" column="0">
	- <widget class="QCommandLinkButton" name="m_StartButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="maximumSize">
	- <size>
	- <width>200</width>
	- <height>16777215</height>
	- </size>
	- </property>
	- <property name="font">
	- <font>
	- <pointsize>11</pointsize>
	- </font>
	- </property>
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Start</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_ImageBox">
	- <property name="toolTip">
	- <string/>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QLabel" name="label_2">
	- <property name="text">
	- <string>λ:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_3">
	- <property name="text">
	- <string>Image:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="1">
	- <widget class="QCheckBox" name="m_ResidualsBox">
	- <property name="text">
	- <string/>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QLabel" name="label_5">
	- <property name="text">
	- <string>Suppress Outliers:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label_7">
	- <property name="text">
	- <string>Regularization:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QComboBox" name="m_ReguTypeBox">
	- <item>
	- <property name="text">
	- <string>Voxel-wise Variance</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Variance</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Mean Squared Magnitude</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Lasso</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>None</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <spacer name="verticalSpacer">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- </layout>
	- </widget>
	- <customwidgets>
	- <customwidget>
	- <class>QmitkDataStorageComboBox</class>
	- <extends>QComboBox</extends>
	- <header location="global">QmitkDataStorageComboBox.h</header>
	- </customwidget>
	- </customwidgets>
	- <resources/>
	- <connections/>
	-</ui>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingView.cpp
	deleted file mode 100644
	index 7ad7ab5c0c..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingView.cpp
	+++ /dev/null
	@@ -1,1731 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-// Blueberry
	-#include <berryISelectionService.h>
	-#include <berryIWorkbenchPart.h>
	-#include <berryIWorkbenchWindow.h>
	-
	-// Qmitk
	-#include "QmitkFiberProcessingView.h"
	-
	-#include <QMessageBox>
	-
	-#include <mitkNodePredicateProperty.h>
	-#include <mitkImageCast.h>
	-#include <mitkPointSet.h>
	-#include <mitkPlanarCircle.h>
	-#include <mitkPlanarPolygon.h>
	-#include <mitkPlanarRectangle.h>
	-#include <mitkPlanarFigureInteractor.h>
	-#include <mitkImageAccessByItk.h>
	-#include <mitkDataNodeObject.h>
	-#include <mitkTensorImage.h>
	-#include "usModuleRegistry.h"
	-#include <itkFiberCurvatureFilter.h>
	-
	-#include "mitkNodePredicateDataType.h"
	-#include <mitkNodePredicateProperty.h>
	-#include <mitkNodePredicateAnd.h>
	-#include <mitkNodePredicateNot.h>
	-#include <mitkNodePredicateOr.h>
	-
	-#include <itkResampleImageFilter.h>
	-#include <itkGaussianInterpolateImageFunction.h>
	-#include <itkImageRegionIteratorWithIndex.h>
	-#include <itkTractsToFiberEndingsImageFilter.h>
	-#include <itkTractDensityImageFilter.h>
	-#include <itkImageRegion.h>
	-#include <itkTractsToRgbaImageFilter.h>
	-#include <itkFiberExtractionFilter.h>
	-
	-#include <boost/algorithm/string.hpp>
	-#include <boost/lexical_cast.hpp>
	-
	-const std::string QmitkFiberProcessingView::VIEW_ID = "org.mitk.views.fiberprocessing";
	-const std::string id_DataManager = "org.mitk.views.datamanager";
	-using namespace mitk;
	-
	-QmitkFiberProcessingView::QmitkFiberProcessingView()
	- : QmitkAbstractView()
	- , m_Controls( 0 )
	- , m_CircleCounter(0)
	- , m_PolygonCounter(0)
	- , m_UpsamplingFactor(1)
	-{
	-
	-}
	-
	-// Destructor
	-QmitkFiberProcessingView::~QmitkFiberProcessingView()
	-{
	- RemoveObservers();
	-}
	-
	-void QmitkFiberProcessingView::CreateQtPartControl( QWidget *parent )
	-{
	- // build up qt view, unless already done
	- if ( !m_Controls )
	- {
	- // create GUI widgets from the Qt Designer's .ui file
	- m_Controls = new Ui::QmitkFiberProcessingViewControls;
	- m_Controls->setupUi( parent );
	-
	- connect( m_Controls->m_CircleButton, SIGNAL( clicked() ), this, SLOT( OnDrawCircle() ) );
	- connect( m_Controls->m_PolygonButton, SIGNAL( clicked() ), this, SLOT( OnDrawPolygon() ) );
	- connect(m_Controls->PFCompoANDButton, SIGNAL(clicked()), this, SLOT(GenerateAndComposite()) );
	- connect(m_Controls->PFCompoORButton, SIGNAL(clicked()), this, SLOT(GenerateOrComposite()) );
	- connect(m_Controls->PFCompoNOTButton, SIGNAL(clicked()), this, SLOT(GenerateNotComposite()) );
	- connect(m_Controls->m_GenerateRoiImage, SIGNAL(clicked()), this, SLOT(GenerateRoiImage()) );
	-
	- connect(m_Controls->m_JoinBundles, SIGNAL(clicked()), this, SLOT(JoinBundles()) );
	- connect(m_Controls->m_SubstractBundles, SIGNAL(clicked()), this, SLOT(SubstractBundles()) );
	- connect(m_Controls->m_CopyBundle, SIGNAL(clicked()), this, SLOT(CopyBundles()) );
	-
	- connect(m_Controls->m_ExtractFibersButton, SIGNAL(clicked()), this, SLOT(Extract()));
	- connect(m_Controls->m_RemoveButton, SIGNAL(clicked()), this, SLOT(Remove()));
	- connect(m_Controls->m_ModifyButton, SIGNAL(clicked()), this, SLOT(Modify()));
	-
	- connect(m_Controls->m_ExtractionMethodBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui()));
	- connect(m_Controls->m_RemovalMethodBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui()));
	- connect(m_Controls->m_ModificationMethodBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui()));
	- connect(m_Controls->m_ExtractionBoxMask, SIGNAL(currentIndexChanged(int)), this, SLOT(OnMaskExtractionChanged()));
	-
	- m_Controls->m_ColorMapBox->SetDataStorage(this->GetDataStorage());
	- mitk::TNodePredicateDataType<mitk::Image>::Pointer isMitkImage = mitk::TNodePredicateDataType<mitk::Image>::New();
	- mitk::NodePredicateDataType::Pointer isDwi = mitk::NodePredicateDataType::New("DiffusionImage");
	- mitk::NodePredicateDataType::Pointer isDti = mitk::NodePredicateDataType::New("TensorImage");
	- mitk::NodePredicateDataType::Pointer isOdf = mitk::NodePredicateDataType::New("OdfImage");
	- mitk::NodePredicateOr::Pointer isDiffusionImage = mitk::NodePredicateOr::New(isDwi, isDti);
	- isDiffusionImage = mitk::NodePredicateOr::New(isDiffusionImage, isOdf);
	- mitk::NodePredicateNot::Pointer noDiffusionImage = mitk::NodePredicateNot::New(isDiffusionImage);
	- mitk::NodePredicateAnd::Pointer finalPredicate = mitk::NodePredicateAnd::New(isMitkImage, noDiffusionImage);
	- m_Controls->m_ColorMapBox->SetPredicate(finalPredicate);
	- }
	-
	- UpdateGui();
	- OnMaskExtractionChanged();
	-}
	-
	-void QmitkFiberProcessingView::OnMaskExtractionChanged()
	-{
	- m_Controls->m_FiberExtractionFractionLabel->setVisible(false);
	- m_Controls->m_FiberExtractionFractionBox->setVisible(false);
	-
	- m_Controls->m_FiberExtractionThresholdLabel->setVisible(false);
	- m_Controls->m_FiberExtractionThresholdBox->setVisible(false);
	-
	- m_Controls->m_InterpolateRoiBox->setVisible(false);
	- m_Controls->m_BothEnds->setVisible(false);
	-
	- m_Controls->m_LabelsBox->setVisible(false);
	- m_Controls->m_LabelsLabel->setVisible(false);
	-
	- if (m_Controls->m_ExtractionBoxMask->currentIndex() == 2 \|\| m_Controls->m_ExtractionBoxMask->currentIndex() == 3)
	- {
	- m_Controls->m_FiberExtractionFractionLabel->setVisible(true);
	- m_Controls->m_FiberExtractionFractionBox->setVisible(true);
	-
	- m_Controls->m_FiberExtractionThresholdLabel->setVisible(true);
	- m_Controls->m_FiberExtractionThresholdBox->setVisible(true);
	-
	- m_Controls->m_InterpolateRoiBox->setVisible(true);
	- }
	- else if (m_Controls->m_ExtractionBoxMask->currentIndex() == 0 \|\| m_Controls->m_ExtractionBoxMask->currentIndex() == 1)
	- {
	- if (m_Controls->m_ExtractionBoxMask->currentIndex() != 3)
	- m_Controls->m_BothEnds->setVisible(true);
	- m_Controls->m_InterpolateRoiBox->setVisible(true);
	-
	- m_Controls->m_FiberExtractionThresholdLabel->setVisible(true);
	- m_Controls->m_FiberExtractionThresholdBox->setVisible(true);
	- }
	- else if (m_Controls->m_ExtractionBoxMask->currentIndex() == 4)
	- {
	- m_Controls->m_BothEnds->setVisible(true);
	-
	- m_Controls->m_LabelsBox->setVisible(true);
	- m_Controls->m_LabelsLabel->setVisible(true);
	- }
	-}
	-
	-void QmitkFiberProcessingView::SetFocus()
	-{
	- m_Controls->toolBoxx->setFocus();
	-}
	-
	-void QmitkFiberProcessingView::Modify()
	-{
	- switch (m_Controls->m_ModificationMethodBox->currentIndex())
	- {
	- case 0:
	- {
	- ResampleSelectedBundlesSpline();
	- break;
	- }
	- case 1:
	- {
	- ResampleSelectedBundlesLinear();
	- break;
	- }
	- case 2:
	- {
	- CompressSelectedBundles();
	- break;
	- }
	- case 3:
	- {
	- DoImageColorCoding();
	- break;
	- }
	- case 4:
	- {
	- MirrorFibers();
	- break;
	- }
	- case 5:
	- {
	- WeightFibers();
	- break;
	- }
	- case 6:
	- {
	- DoCurvatureColorCoding();
	- break;
	- }
	- case 7:
	- {
	- DoWeightColorCoding();
	- break;
	- }
	- case 8:
	- {
	- DoLengthColorCoding();
	- break;
	- }
	- }
	-}
	-
	-void QmitkFiberProcessingView::WeightFibers()
	-{
	- float weight = this->m_Controls->m_BundleWeightBox->value();
	- for (auto node : m_SelectedFB)
	- {
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
	- fib->SetFiberWeights(weight);
	- }
	-
	-}
	-
	-void QmitkFiberProcessingView::Remove()
	-{
	- switch (m_Controls->m_RemovalMethodBox->currentIndex())
	- {
	- case 0:
	- {
	- RemoveDir();
	- break;
	- }
	- case 1:
	- {
	- PruneBundle();
	- break;
	- }
	- case 2:
	- {
	- ApplyCurvatureThreshold();
	- break;
	- }
	- case 3:
	- {
	- RemoveWithMask(false);
	- break;
	- }
	- case 4:
	- {
	- RemoveWithMask(true);
	- break;
	- }
	- case 5:
	- {
	- ApplyWeightThreshold();
	- break;
	- }
	- case 6:
	- {
	- ApplyDensityThreshold();
	- break;
	- }
	- }
	-}
	-
	-void QmitkFiberProcessingView::Extract()
	-{
	- switch (m_Controls->m_ExtractionMethodBox->currentIndex())
	- {
	- case 0:
	- {
	- ExtractWithPlanarFigure();
	- break;
	- }
	- case 1:
	- {
	- switch (m_Controls->m_ExtractionBoxMask->currentIndex())
	- {
	- {
	- case 0:
	- ExtractWithMask(true, false, false);
	- break;
	- }
	- {
	- case 1:
	- ExtractWithMask(true, true, false);
	- break;
	- }
	- {
	- case 2:
	- ExtractWithMask(false, false, false);
	- break;
	- }
	- {
	- case 3:
	- ExtractWithMask(false, true, false);
	- break;
	- }
	- {
	- case 4:
	- ExtractWithMask(true, false, true);
	- break;
	- }
	- }
	- break;
	- }
	- }
	-}
	-
	-void QmitkFiberProcessingView::PruneBundle()
	-{
	- int minLength = this->m_Controls->m_PruneFibersMinBox->value();
	- int maxLength = this->m_Controls->m_PruneFibersMaxBox->value();
	- for (auto node : m_SelectedFB)
	- {
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
	- if (!fib->RemoveShortFibers(minLength))
	- QMessageBox::information(nullptr, "No output generated:", "The resulting fiber bundle contains no fibers.");
	- else if (!fib->RemoveLongFibers(maxLength))
	- QMessageBox::information(nullptr, "No output generated:", "The resulting fiber bundle contains no fibers.");
	- }
	- RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-void QmitkFiberProcessingView::ApplyWeightThreshold()
	-{
	- float thr = this->m_Controls->m_WeightThresholdBox->value();
	- std::vector< DataNode::Pointer > nodes = m_SelectedFB;
	- for (auto node : nodes)
	- {
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
	-
	- mitk::FiberBundle::Pointer newFib = fib->FilterByWeights(thr);
	- if (newFib->GetNumFibers()>0)
	- {
	- newFib->ColorFibersByFiberWeights(false, true);
	- node->SetData(newFib);
	- }
	- else
	- QMessageBox::information(nullptr, "No output generated:", "The resulting fiber bundle contains no fibers.");
	- }
	- RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-void QmitkFiberProcessingView::ApplyDensityThreshold()
	-{
	- float thr = this->m_Controls->m_DensityThresholdBox->value();
	- float ol = this->m_Controls->m_DensityOverlapBox->value();
	- std::vector< DataNode::Pointer > nodes = m_SelectedFB;
	- for (auto node : nodes)
	- {
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
	-
	- itk::TractDensityImageFilter< ItkFloatImageType >::Pointer generator = itk::TractDensityImageFilter< ItkFloatImageType >::New();
	- generator->SetFiberBundle(fib);
	- generator->SetBinaryOutput(false);
	- generator->SetOutputAbsoluteValues(false);
	- generator->Update();
	-
	- itk::FiberExtractionFilter<float>::Pointer extractor = itk::FiberExtractionFilter<float>::New();
	- extractor->SetRoiImages({generator->GetOutput()});
	- extractor->SetInputFiberBundle(fib);
	- extractor->SetOverlapFraction(ol);
	- extractor->SetInterpolate(true);
	- extractor->SetThreshold(thr);
	- extractor->SetNoNegatives(true);
	- extractor->Update();
	-
	- if (extractor->GetPositives().empty())
	- {
	- QMessageBox::information(nullptr, "No output generated:", "The resulting fiber bundle contains no fibers.");
	- continue;
	- }
	-
	- mitk::FiberBundle::Pointer newFib = extractor->GetPositives().at(0);
	- if (newFib->GetNumFibers()>0)
	- node->SetData(newFib);
	- else
	- QMessageBox::information(nullptr, "No output generated:", "The resulting fiber bundle contains no fibers.");
	- }
	- RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-void QmitkFiberProcessingView::ApplyCurvatureThreshold()
	-{
	- int angle = this->m_Controls->m_CurvSpinBox->value();
	- int dist = this->m_Controls->m_CurvDistanceSpinBox->value();
	- std::vector< DataNode::Pointer > nodes = m_SelectedFB;
	- for (auto node : nodes)
	- {
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
	-
	- itk::FiberCurvatureFilter::Pointer filter = itk::FiberCurvatureFilter::New();
	- filter->SetInputFiberBundle(fib);
	- filter->SetAngularDeviation(angle);
	- filter->SetDistance(dist);
	- filter->SetRemoveFibers(m_Controls->m_RemoveCurvedFibersBox->isChecked());
	- filter->Update();
	- mitk::FiberBundle::Pointer newFib = filter->GetOutputFiberBundle();
	- if (newFib->GetNumFibers()>0)
	- {
	- newFib->ColorFibersByOrientation();
	- node->SetData(newFib);
	- }
	- else
	- QMessageBox::information(nullptr, "No output generated:", "The resulting fiber bundle contains no fibers.");
	- }
	- RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-void QmitkFiberProcessingView::RemoveDir()
	-{
	- for (auto node : m_SelectedFB)
	- {
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
	- vnl_vector_fixed<double,3> dir;
	- dir[0] = m_Controls->m_ExtractDirX->value();
	- dir[1] = m_Controls->m_ExtractDirY->value();
	- dir[2] = m_Controls->m_ExtractDirZ->value();
	- fib->RemoveDir(dir,cos((float)m_Controls->m_ExtractAngle->value()*itk::Math::pi/180));
	- }
	- RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-void QmitkFiberProcessingView::RemoveWithMask(bool removeInside)
	-{
	- if (m_RoiImageNode.IsNull())
	- return;
	-
	- mitk::Image::Pointer mitkMask = dynamic_cast<mitk::Image*>(m_RoiImageNode->GetData());
	- for (auto node : m_SelectedFB)
	- {
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
	-
	- ItkUCharImageType::Pointer mask = ItkUCharImageType::New();
	- mitk::CastToItkImage(mitkMask, mask);
	- mitk::FiberBundle::Pointer newFib = fib->RemoveFibersOutside(mask, removeInside);
	- if (newFib->GetNumFibers()<=0)
	- {
	- QMessageBox::information(nullptr, "No output generated:", "The resulting fiber bundle contains no fibers.");
	- continue;
	- }
	- node->SetData(newFib);
	- }
	- RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-void QmitkFiberProcessingView::ExtractWithMask(bool onlyEnds, bool invert, bool labelmap)
	-{
	- if (m_RoiImageNode.IsNull())
	- return;
	-
	- mitk::Image::Pointer mitkMask = dynamic_cast<mitk::Image*>(m_RoiImageNode->GetData());
	- for (auto node : m_SelectedFB)
	- {
	- std::string roi_name = m_RoiImageNode->GetName();
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
	- ItkFloatImageType::Pointer mask = ItkFloatImageType::New();
	- mitk::CastToItkImage(mitkMask, mask);
	-
	- itk::FiberExtractionFilter<float>::Pointer extractor = itk::FiberExtractionFilter<float>::New();
	- extractor->SetInputFiberBundle(fib);
	- extractor->SetRoiImages({mask});
	- extractor->SetRoiImageNames({roi_name});
	- extractor->SetThreshold(m_Controls->m_FiberExtractionThresholdBox->value());
	- extractor->SetOverlapFraction(m_Controls->m_FiberExtractionFractionBox->value());
	- extractor->SetBothEnds(m_Controls->m_BothEnds->isChecked());
	- extractor->SetInterpolate(m_Controls->m_InterpolateRoiBox->isChecked());
	- extractor->SetMinFibersPerTract(m_Controls->m_MinExtractedFibersBox->value());
	- extractor->SetSplitByRoi(true);
	- if (invert)
	- extractor->SetNoPositives(true);
	- else
	- extractor->SetNoNegatives(true);
	-
	- if (labelmap)
	- {
	- std::string labels_string = m_Controls->m_LabelsBox->text().toStdString();
	- if (labels_string!="ALL")
	- {
	- std::vector<std::string> strs;
	- boost::split(strs,labels_string,boost::is_any_of(" ,;\t"));
	-
	- std::vector< unsigned short > labels_vector;
	- for (auto v : strs)
	- {
	- try{
	- unsigned short l = boost::lexical_cast<unsigned short>(v);
	- labels_vector.push_back(l);
	- }
	- catch(...)
	- {
	-
	- }
	- }
	- extractor->SetLabels(labels_vector);
	- }
	-
	- extractor->SetInterpolate(false);
	- extractor->SetInputType(itk::FiberExtractionFilter<float>::INPUT::LABEL_MAP);
	- extractor->SetSplitLabels(true);
	- onlyEnds = true;
	- }
	-
	- if (onlyEnds)
	- extractor->SetMode(itk::FiberExtractionFilter<float>::MODE::ENDPOINTS);
	- extractor->Update();
	-
	- std::vector< mitk::FiberBundle::Pointer > newFibs;
	- if (invert)
	- newFibs = extractor->GetNegatives();
	- else
	- newFibs = extractor->GetPositives();
	-
	- if (newFibs.empty())
	- {
	- QMessageBox::information(nullptr, "No output generated:", "No fibers could be extracted.");
	- continue;
	- }
	-
	- auto labels = extractor->GetPositiveLabels();
	- for (unsigned int i=0; i<newFibs.size(); ++i)
	- {
	- DataNode::Pointer newNode = DataNode::New();
	- auto fib = newFibs.at(i);
	-
	- newNode->SetData(fib);
	- std::string name = roi_name;
	- if (i<labels.size())
	- name = labels.at(i);
	-
	- if (invert)
	- {
	- if (onlyEnds)
	- name = "not-ending-in-" + name;
	- else
	- name = "not-passing-" + name;
	- }
	- else if (!labelmap)
	- {
	- if (onlyEnds)
	- name = "ending-in-" + name;
	- else
	- name = "passing-" + name;
	- }
	-
	- newNode->SetName(name);
	- GetDataStorage()->Add(newNode, node);
	- }
	- node->SetVisibility(false);
	- }
	-}
	-
	-void QmitkFiberProcessingView::GenerateRoiImage()
	-{
	- if (m_SelectedPF.empty())
	- return;
	-
	- mitk::BaseGeometry::Pointer geometry;
	- if (!m_SelectedFB.empty())
	- {
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(m_SelectedFB.front()->GetData());
	- geometry = fib->GetGeometry();
	- }
	- else if (m_SelectedImage)
	- geometry = m_SelectedImage->GetGeometry();
	- else
	- return;
	-
	- itk::Vector<double,3> spacing = geometry->GetSpacing();
	- spacing /= m_UpsamplingFactor;
	-
	- mitk::Point3D newOrigin = geometry->GetOrigin();
	- mitk::Geometry3D::BoundsArrayType bounds = geometry->GetBounds();
	- newOrigin[0] += bounds.GetElement(0);
	- newOrigin[1] += bounds.GetElement(2);
	- newOrigin[2] += bounds.GetElement(4);
	-
	- itk::Matrix<double, 3, 3> direction;
	- itk::ImageRegion<3> imageRegion;
	- for (int i=0; i<3; i++)
	- for (int j=0; j<3; j++)
	- direction[j][i] = geometry->GetMatrixColumn(i)[j]/spacing[j];
	- imageRegion.SetSize(0, geometry->GetExtent(0)*m_UpsamplingFactor);
	- imageRegion.SetSize(1, geometry->GetExtent(1)*m_UpsamplingFactor);
	- imageRegion.SetSize(2, geometry->GetExtent(2)*m_UpsamplingFactor);
	-
	- m_PlanarFigureImage = ItkUCharImageType::New();
	- m_PlanarFigureImage->SetSpacing( spacing ); // Set the image spacing
	- m_PlanarFigureImage->SetOrigin( newOrigin ); // Set the image origin
	- m_PlanarFigureImage->SetDirection( direction ); // Set the image direction
	- m_PlanarFigureImage->SetRegions( imageRegion );
	- m_PlanarFigureImage->Allocate();
	- m_PlanarFigureImage->FillBuffer( 0 );
	-
	- Image::Pointer tmpImage = Image::New();
	- tmpImage->InitializeByItk(m_PlanarFigureImage.GetPointer());
	- tmpImage->SetVolume(m_PlanarFigureImage->GetBufferPointer());
	-
	- std::string name = m_SelectedPF.at(0)->GetName();
	- WritePfToImage(m_SelectedPF.at(0), tmpImage);
	- for (unsigned int i=1; i<m_SelectedPF.size(); i++)
	- {
	- name += "+";
	- name += m_SelectedPF.at(i)->GetName();
	- WritePfToImage(m_SelectedPF.at(i), tmpImage);
	- }
	-
	- DataNode::Pointer node = DataNode::New();
	- tmpImage = Image::New();
	- tmpImage->InitializeByItk(m_PlanarFigureImage.GetPointer());
	- tmpImage->SetVolume(m_PlanarFigureImage->GetBufferPointer());
	- node->SetData(tmpImage);
	- node->SetName(name);
	- this->GetDataStorage()->Add(node);
	-}
	-
	-void QmitkFiberProcessingView::WritePfToImage(mitk::DataNode::Pointer node, mitk::Image* image)
	-{
	- if (dynamic_cast<mitk::PlanarFigure*>(node->GetData()))
	- {
	- m_PlanarFigure = dynamic_cast<mitk::PlanarFigure*>(node->GetData());
	- AccessFixedDimensionByItk_2(
	- image,
	- InternalReorientImagePlane, 3,
	- m_PlanarFigure->GetGeometry(), -1);
	-
	- AccessFixedDimensionByItk_2(
	- m_InternalImage,
	- InternalCalculateMaskFromPlanarFigure,
	- 3, 2, node->GetName() );
	- }
	- else if (dynamic_cast<mitk::PlanarFigureComposite*>(node->GetData()))
	- {
	- DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(node);
	- for (unsigned int i=0; i<children->Size(); i++)
	- {
	- WritePfToImage(children->at(i), image);
	- }
	- }
	-}
	-
	-template < typename TPixel, unsigned int VImageDimension >
	-void QmitkFiberProcessingView::InternalReorientImagePlane( const itk::Image< TPixel, VImageDimension > image, mitk::BaseGeometry planegeo3D, int additionalIndex )
	-{
	- typedef itk::Image< TPixel, VImageDimension > ImageType;
	- typedef itk::Image< float, VImageDimension > FloatImageType;
	-
	- typedef itk::ResampleImageFilter<ImageType, FloatImageType, double> ResamplerType;
	- typename ResamplerType::Pointer resampler = ResamplerType::New();
	-
	- mitk::PlaneGeometry* planegeo = dynamic_cast<mitk::PlaneGeometry*>(planegeo3D);
	-
	- float upsamp = m_UpsamplingFactor;
	- float gausssigma = 0.5;
	-
	- // Spacing
	- typename ResamplerType::SpacingType spacing = planegeo->GetSpacing();
	- spacing[0] = image->GetSpacing()[0] / upsamp;
	- spacing[1] = image->GetSpacing()[1] / upsamp;
	- spacing[2] = image->GetSpacing()[2];
	- resampler->SetOutputSpacing( spacing );
	-
	- // Size
	- typename ResamplerType::SizeType size;
	- size[0] = planegeo->GetExtentInMM(0) / spacing[0];
	- size[1] = planegeo->GetExtentInMM(1) / spacing[1];
	- size[2] = 1;
	- resampler->SetSize( size );
	-
	- // Origin
	- typename mitk::Point3D orig = planegeo->GetOrigin();
	- typename mitk::Point3D corrorig;
	- planegeo3D->WorldToIndex(orig,corrorig);
	- corrorig[0] += 0.5/upsamp;
	- corrorig[1] += 0.5/upsamp;
	- corrorig[2] += 0;
	- planegeo3D->IndexToWorld(corrorig,corrorig);
	- resampler->SetOutputOrigin(corrorig );
	-
	- // Direction
	- typename ResamplerType::DirectionType direction;
	- typename mitk::AffineTransform3D::MatrixType matrix = planegeo->GetIndexToWorldTransform()->GetMatrix();
	- for(unsigned int c=0; c<matrix.ColumnDimensions; c++)
	- {
	- double sum = 0;
	- for(unsigned int r=0; r<matrix.RowDimensions; r++)
	- sum += matrix(r,c)*matrix(r,c);
	- for(unsigned int r=0; r<matrix.RowDimensions; r++)
	- direction(r,c) = matrix(r,c)/sqrt(sum);
	- }
	- resampler->SetOutputDirection( direction );
	-
	- // Gaussian interpolation
	- if(gausssigma != 0)
	- {
	- double sigma[3];
	- for( unsigned int d = 0; d < 3; d++ )
	- sigma[d] = gausssigma * image->GetSpacing()[d];
	- double alpha = 2.0;
	- typedef itk::GaussianInterpolateImageFunction<ImageType, double> GaussianInterpolatorType;
	- typename GaussianInterpolatorType::Pointer interpolator = GaussianInterpolatorType::New();
	- interpolator->SetInputImage( image );
	- interpolator->SetParameters( sigma, alpha );
	- resampler->SetInterpolator( interpolator );
	- }
	- else
	- {
	- typedef typename itk::LinearInterpolateImageFunction<ImageType, double> InterpolatorType;
	- typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
	- interpolator->SetInputImage( image );
	- resampler->SetInterpolator( interpolator );
	- }
	-
	- resampler->SetInput( image );
	- resampler->SetDefaultPixelValue(0);
	- resampler->Update();
	-
	- if(additionalIndex < 0)
	- {
	- this->m_InternalImage = mitk::Image::New();
	- this->m_InternalImage->InitializeByItk( resampler->GetOutput() );
	- this->m_InternalImage->SetVolume( resampler->GetOutput()->GetBufferPointer() );
	- }
	-}
	-
	-template < typename TPixel, unsigned int VImageDimension >
	-void QmitkFiberProcessingView::InternalCalculateMaskFromPlanarFigure( itk::Image< TPixel, VImageDimension > *image, unsigned int axis, std::string )
	-{
	- typedef itk::Image< TPixel, VImageDimension > ImageType;
	-
	- // Generate mask image as new image with same header as input image and
	- // initialize with "1".
	- ItkUCharImageType::Pointer newMaskImage = ItkUCharImageType::New();
	- newMaskImage->SetSpacing( image->GetSpacing() ); // Set the image spacing
	- newMaskImage->SetOrigin( image->GetOrigin() ); // Set the image origin
	- newMaskImage->SetDirection( image->GetDirection() ); // Set the image direction
	- newMaskImage->SetRegions( image->GetLargestPossibleRegion() );
	- newMaskImage->Allocate();
	- newMaskImage->FillBuffer( 1 );
	-
	- // Generate VTK polygon from (closed) PlanarFigure polyline
	- // (The polyline points are shifted by -0.5 in z-direction to make sure
	- // that the extrusion filter, which afterwards elevates all points by +0.5
	- // in z-direction, creates a 3D object which is cut by the the plane z=0)
	- const PlaneGeometry *planarFigurePlaneGeometry = m_PlanarFigure->GetPlaneGeometry();
	- const PlanarFigure::PolyLineType planarFigurePolyline = m_PlanarFigure->GetPolyLine( 0 );
	- const BaseGeometry *imageGeometry3D = m_InternalImage->GetGeometry( 0 );
	-
	- vtkPolyData *polyline = vtkPolyData::New();
	- polyline->Allocate( 1, 1 );
	-
	- // Determine x- and y-dimensions depending on principal axis
	- int i0, i1;
	- switch ( axis )
	- {
	- case 0:
	- i0 = 1;
	- i1 = 2;
	- break;
	- case 1:
	- i0 = 0;
	- i1 = 2;
	- break;
	- case 2:
	- default:
	- i0 = 0;
	- i1 = 1;
	- break;
	- }
	-
	- // Create VTK polydata object of polyline contour
	- vtkPoints *points = vtkPoints::New();
	- PlanarFigure::PolyLineType::const_iterator it;
	- unsigned int numberOfPoints = 0;
	-
	- for ( it = planarFigurePolyline.begin(); it != planarFigurePolyline.end(); ++it )
	- {
	- Point3D point3D;
	-
	- // Convert 2D point back to the local index coordinates of the selected image
	- Point2D point2D = *it;
	- planarFigurePlaneGeometry->WorldToIndex(point2D, point2D);
	- point2D[0] -= 0.5/m_UpsamplingFactor;
	- point2D[1] -= 0.5/m_UpsamplingFactor;
	- planarFigurePlaneGeometry->IndexToWorld(point2D, point2D);
	- planarFigurePlaneGeometry->Map( point2D, point3D );
	-
	- // Polygons (partially) outside of the image bounds can not be processed further due to a bug in vtkPolyDataToImageStencil
	- if ( !imageGeometry3D->IsInside( point3D ) )
	- {
	- float bounds[2] = {0,0};
	- bounds[0] =
	- this->m_InternalImage->GetLargestPossibleRegion().GetSize().GetElement(i0);
	- bounds[1] =
	- this->m_InternalImage->GetLargestPossibleRegion().GetSize().GetElement(i1);
	-
	- imageGeometry3D->WorldToIndex( point3D, point3D );
	-
	- if (point3D[i0]<0)
	- point3D[i0] = 0.0;
	- else if (point3D[i0]>bounds[0])
	- point3D[i0] = bounds[0]-0.001;
	-
	- if (point3D[i1]<0)
	- point3D[i1] = 0.0;
	- else if (point3D[i1]>bounds[1])
	- point3D[i1] = bounds[1]-0.001;
	-
	- points->InsertNextPoint( point3D[i0], point3D[i1], -0.5 );
	- numberOfPoints++;
	- }
	- else
	- {
	- imageGeometry3D->WorldToIndex( point3D, point3D );
	- // Add point to polyline array
	- points->InsertNextPoint( point3D[i0], point3D[i1], -0.5 );
	- numberOfPoints++;
	- }
	- }
	- polyline->SetPoints( points );
	- points->Delete();
	-
	- vtkIdType *ptIds = new vtkIdType[numberOfPoints];
	- for ( vtkIdType i = 0; i < numberOfPoints; ++i )
	- ptIds[i] = i;
	- polyline->InsertNextCell( VTK_POLY_LINE, numberOfPoints, ptIds );
	-
	- // Extrude the generated contour polygon
	- vtkLinearExtrusionFilter *extrudeFilter = vtkLinearExtrusionFilter::New();
	- extrudeFilter->SetInputData( polyline );
	- extrudeFilter->SetScaleFactor( 1 );
	- extrudeFilter->SetExtrusionTypeToNormalExtrusion();
	- extrudeFilter->SetVector( 0.0, 0.0, 1.0 );
	-
	- // Make a stencil from the extruded polygon
	- vtkPolyDataToImageStencil *polyDataToImageStencil = vtkPolyDataToImageStencil::New();
	- polyDataToImageStencil->SetInputConnection( extrudeFilter->GetOutputPort() );
	-
	- // Export from ITK to VTK (to use a VTK filter)
	- typedef itk::VTKImageImport< ItkUCharImageType > ImageImportType;
	- typedef itk::VTKImageExport< ItkUCharImageType > ImageExportType;
	-
	- typename ImageExportType::Pointer itkExporter = ImageExportType::New();
	- itkExporter->SetInput( newMaskImage );
	-
	- vtkImageImport *vtkImporter = vtkImageImport::New();
	- this->ConnectPipelines( itkExporter, vtkImporter );
	- vtkImporter->Update();
	-
	- // Apply the generated image stencil to the input image
	- vtkImageStencil *imageStencilFilter = vtkImageStencil::New();
	- imageStencilFilter->SetInputConnection( vtkImporter->GetOutputPort() );
	- imageStencilFilter->SetStencilConnection(polyDataToImageStencil->GetOutputPort() );
	- imageStencilFilter->ReverseStencilOff();
	- imageStencilFilter->SetBackgroundValue( 0 );
	- imageStencilFilter->Update();
	-
	- // Export from VTK back to ITK
	- vtkImageExport *vtkExporter = vtkImageExport::New();
	- vtkExporter->SetInputConnection( imageStencilFilter->GetOutputPort() );
	- vtkExporter->Update();
	-
	- typename ImageImportType::Pointer itkImporter = ImageImportType::New();
	- this->ConnectPipelines( vtkExporter, itkImporter );
	- itkImporter->Update();
	-
	- // calculate cropping bounding box
	- m_InternalImageMask3D = itkImporter->GetOutput();
	- m_InternalImageMask3D->SetDirection(image->GetDirection());
	-
	- itk::ImageRegionConstIterator<ItkUCharImageType>
	- itmask(m_InternalImageMask3D, m_InternalImageMask3D->GetLargestPossibleRegion());
	- itk::ImageRegionIterator<ImageType>
	- itimage(image, image->GetLargestPossibleRegion());
	-
	- itmask.GoToBegin();
	- itimage.GoToBegin();
	-
	- typename ImageType::SizeType lowersize = {{itk::NumericTraits<unsigned long>::max(),itk::NumericTraits<unsigned long>::max(),itk::NumericTraits<unsigned long>::max()}};
	- typename ImageType::SizeType uppersize = {{0,0,0}};
	- while( !itmask.IsAtEnd() )
	- {
	- if(itmask.Get() == 0)
	- itimage.Set(0);
	- else
	- {
	- typename ImageType::IndexType index = itimage.GetIndex();
	- typename ImageType::SizeType signedindex;
	- signedindex[0] = index[0];
	- signedindex[1] = index[1];
	- signedindex[2] = index[2];
	-
	- lowersize[0] = signedindex[0] < lowersize[0] ? signedindex[0] : lowersize[0];
	- lowersize[1] = signedindex[1] < lowersize[1] ? signedindex[1] : lowersize[1];
	- lowersize[2] = signedindex[2] < lowersize[2] ? signedindex[2] : lowersize[2];
	-
	- uppersize[0] = signedindex[0] > uppersize[0] ? signedindex[0] : uppersize[0];
	- uppersize[1] = signedindex[1] > uppersize[1] ? signedindex[1] : uppersize[1];
	- uppersize[2] = signedindex[2] > uppersize[2] ? signedindex[2] : uppersize[2];
	- }
	-
	- ++itmask;
	- ++itimage;
	- }
	-
	- typename ImageType::IndexType index;
	- index[0] = lowersize[0];
	- index[1] = lowersize[1];
	- index[2] = lowersize[2];
	-
	- typename ImageType::SizeType size;
	- size[0] = uppersize[0] - lowersize[0] + 1;
	- size[1] = uppersize[1] - lowersize[1] + 1;
	- size[2] = uppersize[2] - lowersize[2] + 1;
	-
	- itk::ImageRegion<3> cropRegion = itk::ImageRegion<3>(index, size);
	-
	- // crop internal mask
	- typedef itk::RegionOfInterestImageFilter< ItkUCharImageType, ItkUCharImageType > ROIMaskFilterType;
	- typename ROIMaskFilterType::Pointer roi2 = ROIMaskFilterType::New();
	- roi2->SetRegionOfInterest(cropRegion);
	- roi2->SetInput(m_InternalImageMask3D);
	- roi2->Update();
	- m_InternalImageMask3D = roi2->GetOutput();
	-
	- Image::Pointer tmpImage = Image::New();
	- tmpImage->InitializeByItk(m_InternalImageMask3D.GetPointer());
	- tmpImage->SetVolume(m_InternalImageMask3D->GetBufferPointer());
	-
	- Image::Pointer tmpImage2 = Image::New();
	- tmpImage2->InitializeByItk(m_PlanarFigureImage.GetPointer());
	- const BaseGeometry *pfImageGeometry3D = tmpImage2->GetGeometry( 0 );
	-
	- const BaseGeometry *intImageGeometry3D = tmpImage->GetGeometry( 0 );
	-
	- typedef itk::ImageRegionIteratorWithIndex<ItkUCharImageType> IteratorType;
	- IteratorType imageIterator (m_InternalImageMask3D, m_InternalImageMask3D->GetRequestedRegion());
	- imageIterator.GoToBegin();
	- while ( !imageIterator.IsAtEnd() )
	- {
	- unsigned char val = imageIterator.Value();
	- if (val>0)
	- {
	- itk::Index<3> index = imageIterator.GetIndex();
	- Point3D point;
	- point[0] = index[0];
	- point[1] = index[1];
	- point[2] = index[2];
	-
	- intImageGeometry3D->IndexToWorld(point, point);
	- pfImageGeometry3D->WorldToIndex(point, point);
	-
	- point[i0] += 0.5;
	- point[i1] += 0.5;
	-
	- index[0] = point[0];
	- index[1] = point[1];
	- index[2] = point[2];
	-
	- if (pfImageGeometry3D->IsIndexInside(index))
	- m_PlanarFigureImage->SetPixel(index, 1);
	- }
	- ++imageIterator;
	- }
	-
	- // Clean up VTK objects
	- polyline->Delete();
	- extrudeFilter->Delete();
	- polyDataToImageStencil->Delete();
	- vtkImporter->Delete();
	- imageStencilFilter->Delete();
	- //vtkExporter->Delete(); // TODO: crashes when outcommented; memory leak??
	- delete[] ptIds;
	-}
	-
	-void QmitkFiberProcessingView::UpdateGui()
	-{
	- m_Controls->m_FibLabel->setText("<font color='red'>mandatory</font>");
	- m_Controls->m_PfLabel->setText("<font color='grey'>needed for extraction</font>");
	- m_Controls->m_InputData->setTitle("Please Select Input Data");
	-
	- m_Controls->m_RemoveButton->setEnabled(false);
	-
	- m_Controls->m_PlanarFigureButtonsFrame->setEnabled(false);
	- m_Controls->PFCompoANDButton->setEnabled(false);
	- m_Controls->PFCompoORButton->setEnabled(false);
	- m_Controls->PFCompoNOTButton->setEnabled(false);
	-
	- m_Controls->m_GenerateRoiImage->setEnabled(false);
	- m_Controls->m_ExtractFibersButton->setEnabled(false);
	- m_Controls->m_ModifyButton->setEnabled(false);
	-
	- m_Controls->m_CopyBundle->setEnabled(false);
	- m_Controls->m_JoinBundles->setEnabled(false);
	- m_Controls->m_SubstractBundles->setEnabled(false);
	-
	- // disable alle frames
	- m_Controls->m_BundleWeightFrame->setVisible(false);
	- m_Controls->m_ExtactionFramePF->setVisible(false);
	- m_Controls->m_RemoveDirectionFrame->setVisible(false);
	- m_Controls->m_RemoveLengthFrame->setVisible(false);
	- m_Controls->m_RemoveCurvatureFrame->setVisible(false);
	- m_Controls->m_RemoveByWeightFrame->setVisible(false);
	- m_Controls->m_RemoveByDensityFrame->setVisible(false);
	- m_Controls->m_SmoothFibersFrame->setVisible(false);
	- m_Controls->m_CompressFibersFrame->setVisible(false);
	- m_Controls->m_ColorFibersFrame->setVisible(false);
	- m_Controls->m_MirrorFibersFrame->setVisible(false);
	- m_Controls->m_MaskExtractionFrame->setVisible(false);
	- m_Controls->m_ColorMapBox->setVisible(false);
	-
	- bool pfSelected = !m_SelectedPF.empty();
	- bool fibSelected = !m_SelectedFB.empty();
	- bool multipleFibsSelected = (m_SelectedFB.size()>1);
	- bool maskSelected = m_RoiImageNode.IsNotNull();
	- bool imageSelected = m_SelectedImage.IsNotNull();
	-
	- // toggle visibility of elements according to selected method
	- switch ( m_Controls->m_ExtractionMethodBox->currentIndex() )
	- {
	- case 0:
	- m_Controls->m_ExtactionFramePF->setVisible(true);
	- break;
	- case 1:
	- m_Controls->m_MaskExtractionFrame->setVisible(true);
	- break;
	- }
	-
	- switch ( m_Controls->m_RemovalMethodBox->currentIndex() )
	- {
	- case 0:
	- m_Controls->m_RemoveDirectionFrame->setVisible(true);
	- if ( fibSelected )
	- m_Controls->m_RemoveButton->setEnabled(true);
	- break;
	- case 1:
	- m_Controls->m_RemoveLengthFrame->setVisible(true);
	- if ( fibSelected )
	- m_Controls->m_RemoveButton->setEnabled(true);
	- break;
	- case 2:
	- m_Controls->m_RemoveCurvatureFrame->setVisible(true);
	- if ( fibSelected )
	- m_Controls->m_RemoveButton->setEnabled(true);
	- break;
	- case 3:
	- break;
	- case 4:
	- break;
	- case 5:
	- m_Controls->m_RemoveByWeightFrame->setVisible(true);
	- if ( fibSelected )
	- m_Controls->m_RemoveButton->setEnabled(true);
	- break;
	- case 6:
	- m_Controls->m_RemoveByDensityFrame->setVisible(true);
	- if ( fibSelected )
	- m_Controls->m_RemoveButton->setEnabled(true);
	- break;
	- }
	-
	- switch ( m_Controls->m_ModificationMethodBox->currentIndex() )
	- {
	- case 0:
	- m_Controls->m_SmoothFibersFrame->setVisible(true);
	- break;
	- case 1:
	- m_Controls->m_SmoothFibersFrame->setVisible(true);
	- break;
	- case 2:
	- m_Controls->m_CompressFibersFrame->setVisible(true);
	- break;
	- case 3:
	- m_Controls->m_ColorFibersFrame->setVisible(true);
	- m_Controls->m_ColorMapBox->setVisible(true);
	- break;
	- case 4:
	- m_Controls->m_MirrorFibersFrame->setVisible(true);
	- if (m_SelectedSurfaces.size()>0)
	- m_Controls->m_ModifyButton->setEnabled(true);
	- break;
	- case 5:
	- m_Controls->m_BundleWeightFrame->setVisible(true);
	- break;
	- case 6:
	- m_Controls->m_ColorFibersFrame->setVisible(true);
	- break;
	- case 7:
	- m_Controls->m_ColorFibersFrame->setVisible(true);
	- break;
	- case 8:
	- m_Controls->m_ColorFibersFrame->setVisible(true);
	- break;
	- }
	-
	- // are fiber bundles selected?
	- if ( fibSelected )
	- {
	- m_Controls->m_CopyBundle->setEnabled(true);
	- m_Controls->m_ModifyButton->setEnabled(true);
	- m_Controls->m_PlanarFigureButtonsFrame->setEnabled(true);
	- m_Controls->m_FibLabel->setText(QString(m_SelectedFB.at(0)->GetName().c_str()));
	-
	- // one bundle and one planar figure needed to extract fibers
	- if (pfSelected && m_Controls->m_ExtractionMethodBox->currentIndex()==0)
	- {
	- m_Controls->m_InputData->setTitle("Input Data");
	- m_Controls->m_PfLabel->setText(QString(m_SelectedPF.at(0)->GetName().c_str()));
	- m_Controls->m_ExtractFibersButton->setEnabled(true);
	- }
	-
	- // more than two bundles needed to join/subtract
	- if (multipleFibsSelected)
	- {
	- m_Controls->m_FibLabel->setText("multiple bundles selected");
	-
	- m_Controls->m_JoinBundles->setEnabled(true);
	- m_Controls->m_SubstractBundles->setEnabled(true);
	- }
	-
	- if (maskSelected && m_Controls->m_ExtractionMethodBox->currentIndex()==1)
	- {
	- m_Controls->m_InputData->setTitle("Input Data");
	- m_Controls->m_PfLabel->setText(QString(m_RoiImageNode->GetName().c_str()));
	- m_Controls->m_ExtractFibersButton->setEnabled(true);
	- }
	-
	- if (maskSelected && (m_Controls->m_RemovalMethodBox->currentIndex()==3 \|\| m_Controls->m_RemovalMethodBox->currentIndex()==4) )
	- {
	- m_Controls->m_InputData->setTitle("Input Data");
	- m_Controls->m_PfLabel->setText(QString(m_RoiImageNode->GetName().c_str()));
	- m_Controls->m_RemoveButton->setEnabled(true);
	- }
	- }
	-
	- // are planar figures selected?
	- if (pfSelected)
	- {
	- if ( fibSelected \|\| m_SelectedImage.IsNotNull())
	- m_Controls->m_GenerateRoiImage->setEnabled(true);
	-
	- if (m_SelectedPF.size() > 1)
	- {
	- m_Controls->PFCompoANDButton->setEnabled(true);
	- m_Controls->PFCompoORButton->setEnabled(true);
	- }
	- else
	- m_Controls->PFCompoNOTButton->setEnabled(true);
	- }
	-
	- // is image selected
	- if (imageSelected \|\| maskSelected)
	- {
	- m_Controls->m_PlanarFigureButtonsFrame->setEnabled(true);
	- }
	-}
	-
	-void QmitkFiberProcessingView::NodeRemoved(const mitk::DataNode* node )
	-{
	- for (auto fnode: m_SelectedFB)
	- if (node == fnode)
	- {
	- m_SelectedFB.clear();
	- break;
	- }
	-
	- berry::IWorkbenchPart::Pointer nullPart;
	- QList<mitk::DataNode::Pointer> nodes;
	- OnSelectionChanged(nullPart, nodes);
	-}
	-
	-void QmitkFiberProcessingView::NodeAdded(const mitk::DataNode* )
	-{
	- if (!m_Controls->m_InteractiveBox->isChecked())
	- {
	- berry::IWorkbenchPart::Pointer nullPart;
	- QList<mitk::DataNode::Pointer> nodes;
	- OnSelectionChanged(nullPart, nodes);
	- }
	-}
	-
	-void QmitkFiberProcessingView::OnEndInteraction()
	-{
	- if (m_Controls->m_InteractiveBox->isChecked())
	- ExtractWithPlanarFigure(true);
	-}
	-
	-void QmitkFiberProcessingView::AddObservers()
	-{
	- typedef itk::SimpleMemberCommand< QmitkFiberProcessingView > SimpleCommandType;
	- for (auto node : m_SelectedPF)
	- {
	- mitk::PlanarFigure* figure = dynamic_cast<mitk::PlanarFigure*>(node->GetData());
	- if (figure!=nullptr)
	- {
	- figure->RemoveAllObservers();
	-
	- // add observer for event when interaction with figure starts
	- SimpleCommandType::Pointer endInteractionCommand = SimpleCommandType::New();
	- endInteractionCommand->SetCallbackFunction( this, &QmitkFiberProcessingView::OnEndInteraction);
	- m_EndInteractionObserverTag = figure->AddObserver( mitk::EndInteractionPlanarFigureEvent(), endInteractionCommand );
	- }
	- }
	-}
	-
	-void QmitkFiberProcessingView::RemoveObservers()
	-{
	- for (auto node : m_SelectedPF)
	- {
	- mitk::PlanarFigure* figure = dynamic_cast<mitk::PlanarFigure*>(node->GetData());
	- if (figure!=nullptr)
	- figure->RemoveAllObservers();
	- }
	-}
	-
	-void QmitkFiberProcessingView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /part/, const QList<mitk::DataNode::Pointer>& nodes)
	-{
	- RemoveObservers();
	-
	- //reset existing Vectors containing FiberBundles and PlanarFigures from a previous selection
	- std::vector<mitk::DataNode::Pointer> lastSelectedFB = m_SelectedFB;
	- m_SelectedFB.clear();
	- m_SelectedPF.clear();
	- m_SelectedSurfaces.clear();
	- m_SelectedImage = nullptr;
	- m_RoiImageNode = nullptr;
	-
	- for (auto node: nodes)
	- {
	- if ( dynamic_cast<mitk::FiberBundle*>(node->GetData()) )
	- m_SelectedFB.push_back(node);
	- else if (dynamic_cast<mitk::PlanarPolygon>(node->GetData()) \|\| dynamic_cast<mitk::PlanarFigureComposite>(node->GetData()) \|\| dynamic_cast<mitk::PlanarCircle*>(node->GetData()))
	- m_SelectedPF.push_back(node);
	- else if (dynamic_cast<mitk::Image*>(node->GetData()))
	- {
	- m_SelectedImage = dynamic_cast<mitk::Image*>(node->GetData());
	- if (m_SelectedImage->GetDimension()==3)
	- m_RoiImageNode = node;
	- }
	- else if (dynamic_cast<mitk::Surface*>(node->GetData()))
	- m_SelectedSurfaces.push_back(dynamic_cast<mitk::Surface*>(node->GetData()));
	- }
	-
	- // if we perform interactive fiber extraction, we want to avoid auto-selection of the extracted bundle
	- if (m_SelectedFB.empty() && m_Controls->m_InteractiveBox->isChecked())
	- m_SelectedFB = lastSelectedFB;
	-
	- // if no fibers or surfaces are selected, select topmost
	- if (m_SelectedFB.empty() && m_SelectedSurfaces.empty())
	- {
	- int maxLayer = 0;
	- itk::VectorContainer<unsigned int, mitk::DataNode::Pointer>::ConstPointer nodes = this->GetDataStorage()->GetAll();
	- for (unsigned int i=0; i<nodes->Size(); i++)
	- if (dynamic_cast<mitk::FiberBundle*>(nodes->at(i)->GetData()))
	- {
	- mitk::DataStorage::SetOfObjects::ConstPointer sources = GetDataStorage()->GetSources(nodes->at(i));
	- if (sources->Size()>0)
	- continue;
	-
	- int layer = 0;
	- nodes->at(i)->GetPropertyValue("layer", layer);
	- if (layer>=maxLayer)
	- {
	- maxLayer = layer;
	- m_SelectedFB.clear();
	- m_SelectedFB.push_back(nodes->at(i));
	- }
	- }
	- }
	-
	- // if no plar figure is selected, select topmost
	- if (m_SelectedPF.empty())
	- {
	- int maxLayer = 0;
	- itk::VectorContainer<unsigned int, mitk::DataNode::Pointer>::ConstPointer nodes = this->GetDataStorage()->GetAll();
	- for (unsigned int i=0; i<nodes->Size(); i++)
	- if (dynamic_cast<mitk::PlanarPolygon>(nodes->at(i)->GetData()) \|\| dynamic_cast<mitk::PlanarFigureComposite>(nodes->at(i)->GetData()) \|\| dynamic_cast<mitk::PlanarCircle*>(nodes->at(i)->GetData()))
	- {
	- mitk::DataStorage::SetOfObjects::ConstPointer sources = GetDataStorage()->GetSources(nodes->at(i));
	- if (sources->Size()>0)
	- continue;
	-
	- int layer = 0;
	- nodes->at(i)->GetPropertyValue("layer", layer);
	- if (layer>=maxLayer)
	- {
	- maxLayer = layer;
	- m_SelectedPF.clear();
	- m_SelectedPF.push_back(nodes->at(i));
	- }
	- }
	- }
	-
	- AddObservers();
	- UpdateGui();
	-}
	-
	-void QmitkFiberProcessingView::OnDrawPolygon()
	-{
	- mitk::PlanarPolygon::Pointer figure = mitk::PlanarPolygon::New();
	- figure->ClosedOn();
	- this->AddFigureToDataStorage(figure, QString("Polygon%1").arg(++m_PolygonCounter));
	-}
	-
	-void QmitkFiberProcessingView::OnDrawCircle()
	-{
	- mitk::PlanarCircle::Pointer figure = mitk::PlanarCircle::New();
	- this->AddFigureToDataStorage(figure, QString("Circle%1").arg(++m_CircleCounter));
	-}
	-
	-void QmitkFiberProcessingView::AddFigureToDataStorage(mitk::PlanarFigure* figure, const QString& name, const char , mitk::BaseProperty )
	-{
	- // initialize figure's geometry with empty geometry
	- mitk::PlaneGeometry::Pointer emptygeometry = mitk::PlaneGeometry::New();
	- figure->SetPlaneGeometry( emptygeometry );
	-
	- //set desired data to DataNode where Planarfigure is stored
	- mitk::DataNode::Pointer newNode = mitk::DataNode::New();
	- newNode->SetName(name.toStdString());
	- newNode->SetData(figure);
	- newNode->SetBoolProperty("planarfigure.3drendering", true);
	- newNode->SetBoolProperty("planarfigure.3drendering.fill", true);
	-
	- mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast<mitk::PlanarFigureInteractor*>(newNode->GetDataInteractor().GetPointer());
	- if(figureInteractor.IsNull())
	- {
	- figureInteractor = mitk::PlanarFigureInteractor::New();
	- us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "MitkPlanarFigure" );
	- figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule );
	- figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule );
	- figureInteractor->SetDataNode(newNode);
	- }
	-
	- // figure drawn on the topmost layer / image
	- GetDataStorage()->Add(newNode );
	-
	- RemoveObservers();
	- for(unsigned int i = 0; i < m_SelectedPF.size(); i++)
	- m_SelectedPF[i]->SetSelected(false);
	-
	- newNode->SetSelected(true);
	- m_SelectedPF.clear();
	- m_SelectedPF.push_back(newNode);
	- AddObservers();
	- UpdateGui();
	-}
	-
	-void QmitkFiberProcessingView::ExtractWithPlanarFigure(bool interactive)
	-{
	- if ( m_SelectedFB.empty() \|\| m_SelectedPF.empty() ){
	- QMessageBox::information( nullptr, "Warning", "No fibe bundle selected!");
	- return;
	- }
	-
	- try
	- {
	- std::vector<mitk::DataNode::Pointer> fiberBundles = m_SelectedFB;
	- mitk::DataNode::Pointer planarFigure = m_SelectedPF.at(0);
	- for (unsigned int i=0; i<fiberBundles.size(); i++)
	- {
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(fiberBundles.at(i)->GetData());
	- mitk::FiberBundle::Pointer extFB = fib->ExtractFiberSubset(planarFigure, GetDataStorage());
	-
	- if (interactive && m_Controls->m_InteractiveBox->isChecked())
	- {
	- if (m_InteractiveNode.IsNull())
	- {
	- m_InteractiveNode = mitk::DataNode::New();
	- QString name("Interactive");
	- m_InteractiveNode->SetName(name.toStdString());
	- GetDataStorage()->Add(m_InteractiveNode);
	- }
	- float op = 5.0/sqrt(fib->GetNumFibers());
	- float currentOp = 0;
	- fiberBundles.at(i)->GetFloatProperty("opacity", currentOp);
	-
	- if (currentOp!=op)
	- {
	- fib->SetFiberColors(255, 255, 255);
	- fiberBundles.at(i)->SetFloatProperty("opacity", op);
	- fiberBundles.at(i)->SetBoolProperty("Fiber2DfadeEFX", false);
	- }
	- m_InteractiveNode->SetData(extFB);
	- }
	- else
	- {
	- if (extFB->GetNumFibers()<=0)
	- {
	- QMessageBox::information(nullptr, "No output generated:", "The resulting fiber bundle contains no fibers.");
	- continue;
	- }
	-
	- mitk::DataNode::Pointer node;
	- node = mitk::DataNode::New();
	- node->SetData(extFB);
	- QString name(fiberBundles.at(i)->GetName().c_str());
	- name += "*";
	- node->SetName(name.toStdString());
	- fiberBundles.at(i)->SetVisibility(false);
	- GetDataStorage()->Add(node);
	- }
	- }
	- }
	- catch(const std::out_of_range& )
	- {
	- QMessageBox::warning( nullptr, "Fiber extraction failed", "Did you only create the planar figure, using the circle or polygon button, but forgot to actually place it in the image afterwards? \nAfter creating a planar figure, simply left-click at the desired position in the image or on the tractogram to place it.");
	- }
	-}
	-
	-void QmitkFiberProcessingView::GenerateAndComposite()
	-{
	- mitk::PlanarFigureComposite::Pointer PFCAnd = mitk::PlanarFigureComposite::New();
	- PFCAnd->setOperationType(mitk::PlanarFigureComposite::AND);
	-
	- mitk::DataNode::Pointer newPFCNode;
	- newPFCNode = mitk::DataNode::New();
	- newPFCNode->SetName("AND");
	- newPFCNode->SetData(PFCAnd);
	-
	- AddCompositeToDatastorage(newPFCNode, m_SelectedPF);
	- RemoveObservers();
	- m_SelectedPF.clear();
	- m_SelectedPF.push_back(newPFCNode);
	- AddObservers();
	- UpdateGui();
	-}
	-
	-void QmitkFiberProcessingView::GenerateOrComposite()
	-{
	- mitk::PlanarFigureComposite::Pointer PFCOr = mitk::PlanarFigureComposite::New();
	- PFCOr->setOperationType(mitk::PlanarFigureComposite::OR);
	-
	- mitk::DataNode::Pointer newPFCNode;
	- newPFCNode = mitk::DataNode::New();
	- newPFCNode->SetName("OR");
	- newPFCNode->SetData(PFCOr);
	-
	- RemoveObservers();
	- AddCompositeToDatastorage(newPFCNode, m_SelectedPF);
	- m_SelectedPF.clear();
	- m_SelectedPF.push_back(newPFCNode);
	- UpdateGui();
	-}
	-
	-void QmitkFiberProcessingView::GenerateNotComposite()
	-{
	- mitk::PlanarFigureComposite::Pointer PFCNot = mitk::PlanarFigureComposite::New();
	- PFCNot->setOperationType(mitk::PlanarFigureComposite::NOT);
	-
	- mitk::DataNode::Pointer newPFCNode;
	- newPFCNode = mitk::DataNode::New();
	- newPFCNode->SetName("NOT");
	- newPFCNode->SetData(PFCNot);
	-
	- RemoveObservers();
	- AddCompositeToDatastorage(newPFCNode, m_SelectedPF);
	- m_SelectedPF.clear();
	- m_SelectedPF.push_back(newPFCNode);
	- AddObservers();
	- UpdateGui();
	-}
	-
	-void QmitkFiberProcessingView::AddCompositeToDatastorage(mitk::DataNode::Pointer pfc, std::vector<mitk::DataNode::Pointer> children, mitk::DataNode::Pointer parentNode )
	-{
	- pfc->SetSelected(true);
	- if (parentNode.IsNotNull())
	- GetDataStorage()->Add(pfc, parentNode);
	- else
	- GetDataStorage()->Add(pfc);
	-
	- for (auto child : children)
	- {
	- if (dynamic_cast<PlanarFigure*>(child->GetData()))
	- {
	- mitk::DataNode::Pointer newChild;
	- newChild = mitk::DataNode::New();
	- newChild->SetData(dynamic_cast<PlanarFigure*>(child->GetData()));
	- newChild->SetName( child->GetName() );
	- newChild->SetBoolProperty("planarfigure.3drendering", true);
	- newChild->SetBoolProperty("planarfigure.3drendering.fill", true);
	-
	- GetDataStorage()->Add(newChild, pfc);
	- GetDataStorage()->Remove(child);
	- }
	- else if (dynamic_cast<PlanarFigureComposite*>(child->GetData()))
	- {
	- mitk::DataNode::Pointer newChild;
	- newChild = mitk::DataNode::New();
	- newChild->SetData(dynamic_cast<PlanarFigureComposite*>(child->GetData()));
	- newChild->SetName( child->GetName() );
	-
	- std::vector< mitk::DataNode::Pointer > grandChildVector;
	- mitk::DataStorage::SetOfObjects::ConstPointer grandchildren = GetDataStorage()->GetDerivations(child);
	- for( mitk::DataStorage::SetOfObjects::const_iterator it = grandchildren->begin(); it != grandchildren->end(); ++it )
	- grandChildVector.push_back(*it);
	-
	- AddCompositeToDatastorage(newChild, grandChildVector, pfc);
	- GetDataStorage()->Remove(child);
	- }
	- }
	- UpdateGui();
	-}
	-
	-void QmitkFiberProcessingView::CopyBundles()
	-{
	- if ( m_SelectedFB.empty() ){
	- QMessageBox::information( nullptr, "Warning", "Select at least one fiber bundle!");
	- MITK_WARN("QmitkFiberProcessingView") << "Select at least one fiber bundle!";
	- return;
	- }
	-
	- for (auto node : m_SelectedFB)
	- {
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
	- mitk::FiberBundle::Pointer newFib = fib->GetDeepCopy();
	-
	- node->SetVisibility(false);
	- QString name("");
	- name += QString(m_SelectedFB.at(0)->GetName().c_str());
	- name += "_copy";
	-
	- mitk::DataNode::Pointer fbNode = mitk::DataNode::New();
	- fbNode->SetData(newFib);
	- fbNode->SetName(name.toStdString());
	- fbNode->SetVisibility(true);
	- GetDataStorage()->Add(fbNode);
	- }
	- UpdateGui();
	-}
	-
	-void QmitkFiberProcessingView::JoinBundles()
	-{
	- if ( m_SelectedFB.size()<2 ){
	- QMessageBox::information( nullptr, "Warning", "Select at least two fiber bundles!");
	- MITK_WARN("QmitkFiberProcessingView") << "Select at least two fiber bundles!";
	- return;
	- }
	-
	- m_SelectedFB.at(0)->SetVisibility(false);
	- mitk::FiberBundle::Pointer newBundle = dynamic_cast<mitk::FiberBundle*>(m_SelectedFB.at(0)->GetData());
	-
	- std::vector< mitk::FiberBundle::Pointer > tractograms;
	- for (unsigned int i=1; i<m_SelectedFB.size(); i++)
	- {
	- m_SelectedFB.at(i)->SetVisibility(false);
	- tractograms.push_back(dynamic_cast<mitk::FiberBundle*>(m_SelectedFB.at(i)->GetData()));
	- }
	- newBundle = newBundle->AddBundles(tractograms);
	-
	- mitk::DataNode::Pointer fbNode = mitk::DataNode::New();
	- fbNode->SetData(newBundle);
	- fbNode->SetName("Joined_Tractograms");
	- fbNode->SetVisibility(true);
	- GetDataStorage()->Add(fbNode);
	- UpdateGui();
	-}
	-
	-void QmitkFiberProcessingView::SubstractBundles()
	-{
	- if ( m_SelectedFB.size()<2 ){
	- QMessageBox::information( nullptr, "Warning", "Select at least two fiber bundles!");
	- MITK_WARN("QmitkFiberProcessingView") << "Select at least two fiber bundles!";
	- return;
	- }
	-
	- mitk::FiberBundle::Pointer newBundle = dynamic_cast<mitk::FiberBundle*>(m_SelectedFB.at(0)->GetData());
	- m_SelectedFB.at(0)->SetVisibility(false);
	- QString name("");
	- name += QString(m_SelectedFB.at(0)->GetName().c_str());
	- for (unsigned int i=1; i<m_SelectedFB.size(); i++)
	- {
	- newBundle = newBundle->SubtractBundle(dynamic_cast<mitk::FiberBundle*>(m_SelectedFB.at(i)->GetData()));
	- if (newBundle.IsNull())
	- break;
	- name += "-"+QString(m_SelectedFB.at(i)->GetName().c_str());
	- m_SelectedFB.at(i)->SetVisibility(false);
	- }
	- if (newBundle.IsNull())
	- {
	- QMessageBox::information(nullptr, "No output generated:", "The resulting fiber bundle contains no fibers. Did you select the fiber bundles in the correct order? X-Y is not equal to Y-X!");
	- return;
	- }
	-
	- mitk::DataNode::Pointer fbNode = mitk::DataNode::New();
	- fbNode->SetData(newBundle);
	- fbNode->SetName(name.toStdString());
	- fbNode->SetVisibility(true);
	- GetDataStorage()->Add(fbNode);
	- UpdateGui();
	-}
	-
	-void QmitkFiberProcessingView::ResampleSelectedBundlesSpline()
	-{
	- double factor = this->m_Controls->m_SmoothFibersBox->value();
	- for (auto node : m_SelectedFB)
	- {
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
	- fib->ResampleSpline(factor);
	- }
	- RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-void QmitkFiberProcessingView::ResampleSelectedBundlesLinear()
	-{
	- double factor = this->m_Controls->m_SmoothFibersBox->value();
	- for (auto node : m_SelectedFB)
	- {
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
	- fib->ResampleLinear(factor);
	- }
	- RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-void QmitkFiberProcessingView::CompressSelectedBundles()
	-{
	- double factor = this->m_Controls->m_ErrorThresholdBox->value();
	- for (auto node : m_SelectedFB)
	- {
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
	- fib->Compress(factor);
	- fib->ColorFibersByOrientation();
	- }
	- RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-void QmitkFiberProcessingView::DoImageColorCoding()
	-{
	- if (m_Controls->m_ColorMapBox->GetSelectedNode().IsNull())
	- {
	- QMessageBox::information(nullptr, "Bundle coloring aborted:", "No image providing the scalar values for coloring the selected bundle available.");
	- return;
	- }
	-
	- for (auto node : m_SelectedFB)
	- {
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
	- fib->ColorFibersByScalarMap(dynamic_cast<mitk::Image*>(m_Controls->m_ColorMapBox->GetSelectedNode()->GetData()), m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_NormalizeColorValues->isChecked());
	- }
	-
	- if (auto renderWindowPart = this->GetRenderWindowPart())
	- {
	- renderWindowPart->RequestUpdate();
	- }
	-}
	-
	-
	-void QmitkFiberProcessingView::DoCurvatureColorCoding()
	-{
	- for (auto node : m_SelectedFB)
	- {
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
	- fib->ColorFibersByCurvature(m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_NormalizeColorValues->isChecked());
	- }
	-
	- if (auto renderWindowPart = this->GetRenderWindowPart())
	- {
	- renderWindowPart->RequestUpdate();
	- }
	-}
	-
	-void QmitkFiberProcessingView::DoLengthColorCoding()
	-{
	- for (auto node : m_SelectedFB)
	- {
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
	- fib->ColorFibersByLength(m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_NormalizeColorValues->isChecked());
	- }
	-
	- if (auto renderWindowPart = this->GetRenderWindowPart())
	- {
	- renderWindowPart->RequestUpdate();
	- }
	-}
	-
	-void QmitkFiberProcessingView::DoWeightColorCoding()
	-{
	- for (auto node : m_SelectedFB)
	- {
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
	- fib->ColorFibersByFiberWeights(m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_NormalizeColorValues->isChecked());
	- }
	-
	- if (auto renderWindowPart = this->GetRenderWindowPart())
	- {
	- renderWindowPart->RequestUpdate();
	- }
	-}
	-
	-void QmitkFiberProcessingView::MirrorFibers()
	-{
	- unsigned int axis = this->m_Controls->m_MirrorFibersBox->currentIndex();
	- for (auto node : m_SelectedFB)
	- {
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
	- if (m_SelectedImage.IsNotNull())
	- fib->SetReferenceGeometry(m_SelectedImage->GetGeometry());
	- fib->MirrorFibers(axis);
	- }
	-
	-
	- for (auto surf : m_SelectedSurfaces)
	- {
	- vtkSmartPointer<vtkPolyData> poly = surf->GetVtkPolyData();
	- vtkSmartPointer<vtkPoints> vtkNewPoints = vtkSmartPointer<vtkPoints>::New();
	-
	- for (int i=0; i<poly->GetNumberOfPoints(); i++)
	- {
	- double* point = poly->GetPoint(i);
	- point[axis] *= -1;
	- vtkNewPoints->InsertNextPoint(point);
	- }
	- poly->SetPoints(vtkNewPoints);
	- surf->CalculateBoundingBox();
	- }
	-
	- if (auto renderWindowPart = this->GetRenderWindowPart())
	- {
	- renderWindowPart->RequestUpdate();
	- }
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingView.h
	deleted file mode 100644
	index 50e7649deb..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingView.h
	+++ /dev/null
	@@ -1,203 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef QmitkFiberProcessingView_h
	-#define QmitkFiberProcessingView_h
	-
	-#include <QmitkAbstractView.h>
	-#include "ui_QmitkFiberProcessingViewControls.h"
	-
	-#include <mitkPlanarFigureComposite.h>
	-#include <mitkFiberBundle.h>
	-#include <mitkSurface.h>
	-
	-#include <itkCastImageFilter.h>
	-#include <itkVTKImageImport.h>
	-#include <itkVTKImageExport.h>
	-#include <itkRegionOfInterestImageFilter.h>
	-
	-#include <vtkLinearExtrusionFilter.h>
	-#include <vtkPolyDataToImageStencil.h>
	-#include <vtkSelectEnclosedPoints.h>
	-#include <vtkImageImport.h>
	-#include <vtkImageExport.h>
	-#include <vtkImageStencil.h>
	-#include <vtkSmartPointer.h>
	-#include <vtkSelection.h>
	-#include <vtkSelectionNode.h>
	-#include <vtkExtractSelectedThresholds.h>
	-#include <vtkFloatArray.h>
	-
	-/*!
	-\brief View to process fiber bundles. Supplies methods to extract fibers from the bundle, fiber resampling, mirroring, join and subtract bundles and much more.
	-*/
	-class QmitkFiberProcessingView : public QmitkAbstractView
	-{
	- // this is needed for all Qt objects that should have a Qt meta-object
	- // (everything that derives from QObject and wants to have signal/slots)
	- Q_OBJECT
	-
	-public:
	-
	- typedef itk::Image< unsigned char, 3 > ItkUCharImageType;
	- typedef itk::Image< float, 3 > ItkFloatImageType;
	-
	- static const std::string VIEW_ID;
	-
	- QmitkFiberProcessingView();
	- virtual ~QmitkFiberProcessingView();
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	-
	- ///
	- /// Sets the focus to an internal widget.
	- ///
	- virtual void SetFocus() override;
	-
	-protected slots:
	-
	- void OnDrawCircle(); ///< add circle interactors etc.
	- void OnDrawPolygon(); ///< add circle interactors etc.
	- void GenerateAndComposite();
	- void GenerateOrComposite();
	- void GenerateNotComposite();
	-
	- void CopyBundles(); ///< add copies of selected bundles to data storage
	- void JoinBundles(); ///< merge selected fiber bundles
	- void SubstractBundles(); ///< subtract bundle A from bundle B. Not commutative! Defined by order of selection.
	- void GenerateRoiImage(); ///< generate binary image of selected planar figures.
	-
	- void Remove();
	- void Extract();
	- void Modify();
	- void UpdateGui(); ///< update button activity etc. dpending on current datamanager selection
	- void OnMaskExtractionChanged();
	-
	- virtual void AddFigureToDataStorage(mitk::PlanarFigure* figure, const QString& name, const char propertyKey = nullptr, mitk::BaseProperty property = nullptr );
	-
	-protected:
	-
	- void MirrorFibers(); ///< mirror bundle on the specified plane
	- void ResampleSelectedBundlesSpline(); ///<
	- void ResampleSelectedBundlesLinear(); ///<
	- void DoImageColorCoding(); ///< color fibers by selected scalar image
	- void DoWeightColorCoding(); ///< color fibers by their respective weights
	- void DoLengthColorCoding(); ///< color fibers by length
	- void DoCurvatureColorCoding(); ///< color fibers by curvature
	- void CompressSelectedBundles(); ///< remove points below certain error threshold
	- void WeightFibers();
	- void ApplyWeightThreshold();
	- void ApplyDensityThreshold();
	-
	- void RemoveWithMask(bool removeInside);
	- void RemoveDir();
	- void ApplyCurvatureThreshold(); ///< remove/split fibers with a too high curvature threshold
	- void PruneBundle(); ///< remove too short/too long fibers
	-
	- void ExtractWithMask(bool onlyEnds, bool invert, bool labelmap);
	- void ExtractWithPlanarFigure(bool interactive=false);
	-
	- void OnEndInteraction();
	-
	- /// \brief called by QmitkAbstractView when DataManager's selection has changed
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- Ui::QmitkFiberProcessingViewControls* m_Controls;
	-
	- /** Connection from VTK to ITK */
	- template <typename VTK_Exporter, typename ITK_Importer>
	- void ConnectPipelines(VTK_Exporter* exporter, ITK_Importer importer)
	- {
	- importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback());
	-
	- importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback());
	- importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback());
	- importer->SetSpacingCallback(exporter->GetSpacingCallback());
	- importer->SetOriginCallback(exporter->GetOriginCallback());
	- importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback());
	-
	- importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback());
	-
	- importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback());
	- importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback());
	- importer->SetDataExtentCallback(exporter->GetDataExtentCallback());
	- importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback());
	- importer->SetCallbackUserData(exporter->GetCallbackUserData());
	- }
	-
	- template <typename ITK_Exporter, typename VTK_Importer>
	- void ConnectPipelines(ITK_Exporter exporter, VTK_Importer* importer)
	- {
	- importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback());
	-
	- importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback());
	- importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback());
	- importer->SetSpacingCallback(exporter->GetSpacingCallback());
	- importer->SetOriginCallback(exporter->GetOriginCallback());
	- importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback());
	-
	- importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback());
	-
	- importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback());
	- importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback());
	- importer->SetDataExtentCallback(exporter->GetDataExtentCallback());
	- importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback());
	- importer->SetCallbackUserData(exporter->GetCallbackUserData());
	- }
	-
	- template < typename TPixel, unsigned int VImageDimension >
	- void InternalCalculateMaskFromPlanarFigure(
	- itk::Image< TPixel, VImageDimension > *image, unsigned int axis, std::string nodeName );
	-
	- template < typename TPixel, unsigned int VImageDimension >
	- void InternalReorientImagePlane(
	- const itk::Image< TPixel, VImageDimension > image, mitk::BaseGeometry planegeo3D, int additionalIndex );
	-
	- int m_CircleCounter; ///< used for data node naming
	- int m_PolygonCounter; ///< used for data node naming
	- std::vector<mitk::DataNode::Pointer> m_SelectedFB; ///< selected fiber bundle nodes
	- std::vector<mitk::DataNode::Pointer> m_SelectedPF; ///< selected planar figure nodes
	- std::vector<mitk::Surface::Pointer> m_SelectedSurfaces;
	- mitk::Image::Pointer m_SelectedImage;
	- mitk::Image::Pointer m_InternalImage;
	- mitk::PlanarFigure::Pointer m_PlanarFigure;
	- ItkUCharImageType::Pointer m_InternalImageMask3D;
	- ItkUCharImageType::Pointer m_PlanarFigureImage;
	- float m_UpsamplingFactor; ///< upsampling factor for all image generations
	- mitk::DataNode::Pointer m_RoiImageNode;
	-
	- unsigned int m_StartInteractionObserverTag;
	- unsigned int m_EndInteractionObserverTag;
	- mitk::DataNode::Pointer m_InteractiveNode;
	-
	- void AddCompositeToDatastorage(mitk::DataNode::Pointer pfc, std::vector<mitk::DataNode::Pointer> children, mitk::DataNode::Pointer parentNode=nullptr);
	- void debugPFComposition(mitk::PlanarFigureComposite::Pointer , int );
	- void WritePfToImage(mitk::DataNode::Pointer node, mitk::Image* image);
	- mitk::DataNode::Pointer GenerateTractDensityImage(mitk::FiberBundle::Pointer fib, bool binary, bool absolute);
	- mitk::DataNode::Pointer GenerateColorHeatmap(mitk::FiberBundle::Pointer fib);
	- mitk::DataNode::Pointer GenerateFiberEndingsImage(mitk::FiberBundle::Pointer fib);
	- mitk::DataNode::Pointer GenerateFiberEndingsPointSet(mitk::FiberBundle::Pointer fib);
	-
	- void NodeAdded( const mitk::DataNode* node ) override;
	- void NodeRemoved(const mitk::DataNode* node) override;
	- void RemoveObservers();
	- void AddObservers();
	-};
	-
	-
	-
	-#endif // _QMITKFIBERTRACKINGVIEW_H_INCLUDED
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingViewControls.ui
	deleted file mode 100644
	index 8708175130..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingViewControls.ui
	+++ /dev/null
	@@ -1,1731 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<ui version="4.0">
	- <class>QmitkFiberProcessingViewControls</class>
	- <widget class="QWidget" name="QmitkFiberProcessingViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>385</width>
	- <height>711</height>
	- </rect>
	- </property>
	- <property name="windowTitle">
	- <string>Form</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_3">
	- <property name="leftMargin">
	- <number>9</number>
	- </property>
	- <property name="topMargin">
	- <number>9</number>
	- </property>
	- <property name="rightMargin">
	- <number>9</number>
	- </property>
	- <property name="bottomMargin">
	- <number>9</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QToolBox" name="toolBoxx">
	- <property name="font">
	- <font>
	- <weight>75</weight>
	- <bold>true</bold>
	- </font>
	- </property>
	- <property name="currentIndex">
	- <number>0</number>
	- </property>
	- <property name="tabSpacing">
	- <number>5</number>
	- </property>
	- <widget class="QWidget" name="page">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>353</width>
	- <height>503</height>
	- </rect>
	- </property>
	- <attribute name="label">
	- <string>Fiber Extraction</string>
	- </attribute>
	- <attribute name="toolTip">
	- <string>Extract a fiber subset from the selected fiber bundle using manually placed planar figures as waypoints or binary regions of interest.</string>
	- </attribute>
	- <layout class="QGridLayout" name="gridLayout_14">
	- <item row="7" column="0">
	- <spacer name="verticalSpacer_5">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="4" column="0">
	- <widget class="QFrame" name="m_MaskExtractionFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_19">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="2" column="0">
	- <widget class="QLabel" name="m_FiberExtractionFractionLabel">
	- <property name="text">
	- <string>Min. overlap:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QLabel" name="m_FiberExtractionThresholdLabel">
	- <property name="text">
	- <string>Threshold:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QLabel" name="label_20">
	- <property name="text">
	- <string>Min. num. fibers:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="2">
	- <widget class="QDoubleSpinBox" name="m_FiberExtractionThresholdBox">
	- <property name="toolTip">
	- <string>Threshold on ROI image for positions to be considered as positive.</string>
	- </property>
	- <property name="decimals">
	- <number>3</number>
	- </property>
	- <property name="maximum">
	- <double>9999.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.500000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="2">
	- <widget class="QComboBox" name="m_ExtractionBoxMask">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <item>
	- <property name="text">
	- <string>Ending in ROI</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Not ending in ROI</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Passing ROI</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Not passing ROI</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Labelmap</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- <item row="7" column="0">
	- <widget class="QCheckBox" name="m_BothEnds">
	- <property name="text">
	- <string>Both ends</string>
	- </property>
	- <property name="checked">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="6" column="0">
	- <widget class="QCheckBox" name="m_InterpolateRoiBox">
	- <property name="text">
	- <string>Interpolate ROI </string>
	- </property>
	- <property name="checked">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="2">
	- <widget class="QSpinBox" name="m_MinExtractedFibersBox">
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>999999999</number>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_16">
	- <property name="text">
	- <string>Extract fibers:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="2">
	- <widget class="QDoubleSpinBox" name="m_FiberExtractionFractionBox">
	- <property name="toolTip">
	- <string>Minimum overlap of streamlines and ROI in terms of streamline length. Zero means that one streamline point inside the ROI is enough to be considered as "overlapping".</string>
	- </property>
	- <property name="decimals">
	- <number>3</number>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <widget class="QLabel" name="m_LabelsLabel">
	- <property name="text">
	- <string>Labels:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="2">
	- <widget class="QLineEdit" name="m_LabelsBox">
	- <property name="toolTip">
	- <string>Label values seperated by whitespace.</string>
	- </property>
	- <property name="text">
	- <string>ALL</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="6" column="0">
	- <widget class="QCommandLinkButton" name="m_ExtractFibersButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="maximumSize">
	- <size>
	- <width>200</width>
	- <height>16777215</height>
	- </size>
	- </property>
	- <property name="font">
	- <font>
	- <pointsize>11</pointsize>
	- </font>
	- </property>
	- <property name="toolTip">
	- <string>Extract fibers passing through selected ROI or composite ROI. Select ROI and fiber bundle to execute.</string>
	- </property>
	- <property name="text">
	- <string>Extract</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QComboBox" name="m_ExtractionMethodBox">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <item>
	- <property name="text">
	- <string>Extract using planar figures</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Extract using ROI image</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QFrame" name="m_ExtactionFramePF">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_8">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>6</number>
	- </property>
	- <item row="3" column="0">
	- <widget class="QCheckBox" name="m_InteractiveBox">
	- <property name="text">
	- <string>Interactive Extraction</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QFrame" name="m_PlanarFigureButtonsFrame">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>200</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="maximumSize">
	- <size>
	- <width>16777215</width>
	- <height>60</height>
	- </size>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QPushButton" name="m_CircleButton">
	- <property name="maximumSize">
	- <size>
	- <width>30</width>
	- <height>30</height>
	- </size>
	- </property>
	- <property name="toolTip">
	- <string>Draw circular ROI. Select reference fiber bundle to execute.</string>
	- </property>
	- <property name="text">
	- <string/>
	- </property>
	- <property name="icon">
	- <iconset resource="../../../../../debug/MITK-build/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/org_mitk_gui_qt_diffusionimaging_fiberprocessing_cached.qrc">
	- <normaloff>:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/circle.png</normaloff>:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/circle.png</iconset>
	- </property>
	- <property name="iconSize">
	- <size>
	- <width>32</width>
	- <height>32</height>
	- </size>
	- </property>
	- <property name="checkable">
	- <bool>false</bool>
	- </property>
	- <property name="flat">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="2">
	- <spacer name="horizontalSpacer">
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>40</width>
	- <height>20</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="0" column="1">
	- <widget class="QPushButton" name="m_PolygonButton">
	- <property name="maximumSize">
	- <size>
	- <width>30</width>
	- <height>30</height>
	- </size>
	- </property>
	- <property name="toolTip">
	- <string>Draw polygonal ROI. Select reference fiber bundle to execute.</string>
	- </property>
	- <property name="text">
	- <string/>
	- </property>
	- <property name="icon">
	- <iconset resource="../../../../../debug/MITK-build/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/org_mitk_gui_qt_diffusionimaging_fiberprocessing_cached.qrc">
	- <normaloff>:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/polygon.png</normaloff>:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/polygon.png</iconset>
	- </property>
	- <property name="iconSize">
	- <size>
	- <width>32</width>
	- <height>32</height>
	- </size>
	- </property>
	- <property name="checkable">
	- <bool>true</bool>
	- </property>
	- <property name="flat">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QFrame" name="m_PlanarFigureButtonsFrame_2">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>200</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="maximumSize">
	- <size>
	- <width>16777215</width>
	- <height>60</height>
	- </size>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_5">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="2">
	- <widget class="QCommandLinkButton" name="PFCompoNOTButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="maximumSize">
	- <size>
	- <width>60</width>
	- <height>16777215</height>
	- </size>
	- </property>
	- <property name="toolTip">
	- <string>Create NOT composition from selected ROI.</string>
	- </property>
	- <property name="text">
	- <string>NOT</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QCommandLinkButton" name="PFCompoORButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="maximumSize">
	- <size>
	- <width>60</width>
	- <height>16777215</height>
	- </size>
	- </property>
	- <property name="toolTip">
	- <string>Create OR composition with selected ROIs.</string>
	- </property>
	- <property name="text">
	- <string>OR</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="3">
	- <spacer name="horizontalSpacer_3">
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>40</width>
	- <height>20</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="0" column="0">
	- <widget class="QCommandLinkButton" name="PFCompoANDButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="maximumSize">
	- <size>
	- <width>60</width>
	- <height>16777215</height>
	- </size>
	- </property>
	- <property name="toolTip">
	- <string>Create AND composition with selected ROIs.</string>
	- </property>
	- <property name="text">
	- <string>AND</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QCommandLinkButton" name="m_GenerateRoiImage">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="maximumSize">
	- <size>
	- <width>16777215</width>
	- <height>16777215</height>
	- </size>
	- </property>
	- <property name="font">
	- <font>
	- <pointsize>11</pointsize>
	- </font>
	- </property>
	- <property name="toolTip">
	- <string>Generate a binary image containing all selected ROIs. Select at least one ROI (planar figure) and a reference fiber bundle or image.</string>
	- </property>
	- <property name="text">
	- <string>Generate ROI Image</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <widget class="QWidget" name="page_3">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>353</width>
	- <height>456</height>
	- </rect>
	- </property>
	- <attribute name="label">
	- <string>Fiber Removal</string>
	- </attribute>
	- <attribute name="toolTip">
	- <string>Remove fibers that satisfy certain criteria from the selected bundle.</string>
	- </attribute>
	- <layout class="QGridLayout" name="gridLayout_4">
	- <item row="1" column="0">
	- <widget class="QFrame" name="m_RemoveDirectionFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_2">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="horizontalSpacing">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label">
	- <property name="text">
	- <string>X:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_3">
	- <property name="text">
	- <string>Y:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QDoubleSpinBox" name="m_ExtractDirX"/>
	- </item>
	- <item row="1" column="1">
	- <widget class="QDoubleSpinBox" name="m_ExtractDirY"/>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label_4">
	- <property name="text">
	- <string>Z:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QDoubleSpinBox" name="m_ExtractDirZ"/>
	- </item>
	- <item row="3" column="0">
	- <widget class="QLabel" name="label_5">
	- <property name="text">
	- <string>Angle:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="1">
	- <widget class="QDoubleSpinBox" name="m_ExtractAngle">
	- <property name="toolTip">
	- <string>Angular deviation threshold in degree</string>
	- </property>
	- <property name="decimals">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <double>90.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="value">
	- <double>25.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QFrame" name="m_RemoveByWeightFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_20">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>0</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_18">
	- <property name="text">
	- <string>Weight threshold:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QDoubleSpinBox" name="m_WeightThresholdBox">
	- <property name="toolTip">
	- <string>Only fibers with weight larger than this threshold are kept.</string>
	- </property>
	- <property name="decimals">
	- <number>5</number>
	- </property>
	- <property name="maximum">
	- <double>99999.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="6" column="0">
	- <widget class="QCommandLinkButton" name="m_RemoveButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="maximumSize">
	- <size>
	- <width>200</width>
	- <height>16777215</height>
	- </size>
	- </property>
	- <property name="font">
	- <font>
	- <pointsize>11</pointsize>
	- </font>
	- </property>
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Remove</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QComboBox" name="m_RemovalMethodBox">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <item>
	- <property name="text">
	- <string>Remove fibers in direction</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Remove fibers by length</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Remove fibers by curvature</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Remove fiber parts outside mask</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Remove fiber parts inside mask</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Remove fibers by weight</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Remove fibers by tract density</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QFrame" name="m_RemoveCurvatureFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_11">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="2" column="2">
	- <widget class="QCheckBox" name="m_RemoveCurvedFibersBox">
	- <property name="toolTip">
	- <string>If unchecked, the fiber exceeding the threshold will be split in two instead of removed.</string>
	- </property>
	- <property name="text">
	- <string>Remove Fiber</string>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="2">
	- <widget class="QFrame" name="frame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_12">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="verticalSpacing">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_8">
	- <property name="text">
	- <string>Max. Angular Deviation:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="2">
	- <spacer name="horizontalSpacer_5">
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>40</width>
	- <height>20</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="0" column="1">
	- <widget class="QDoubleSpinBox" name="m_CurvSpinBox">
	- <property name="toolTip">
	- <string>Maximum angular deviation in degree</string>
	- </property>
	- <property name="maximum">
	- <double>180.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>30.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_14">
	- <property name="text">
	- <string>Distance:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QDoubleSpinBox" name="m_CurvDistanceSpinBox">
	- <property name="toolTip">
	- <string>Distance in mm</string>
	- </property>
	- <property name="decimals">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <double>999.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="value">
	- <double>10.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="7" column="0">
	- <spacer name="verticalSpacer_4">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="2" column="0">
	- <widget class="QFrame" name="m_RemoveLengthFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_6">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="2">
	- <spacer name="horizontalSpacer_4">
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>40</width>
	- <height>20</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_PruneFibersMinBox">
	- <property name="toolTip">
	- <string>Minimum fiber length in mm</string>
	- </property>
	- <property name="minimum">
	- <number>0</number>
	- </property>
	- <property name="maximum">
	- <number>999999999</number>
	- </property>
	- <property name="value">
	- <number>20</number>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_9">
	- <property name="text">
	- <string>Max. Length:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_7">
	- <property name="text">
	- <string>Min. Length:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QSpinBox" name="m_PruneFibersMaxBox">
	- <property name="toolTip">
	- <string>Maximum fiber length in mm</string>
	- </property>
	- <property name="minimum">
	- <number>0</number>
	- </property>
	- <property name="maximum">
	- <number>999999999</number>
	- </property>
	- <property name="value">
	- <number>300</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <widget class="QFrame" name="m_RemoveByDensityFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_21">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="horizontalSpacing">
	- <number>0</number>
	- </property>
	- <property name="verticalSpacing">
	- <number>6</number>
	- </property>
	- <item row="1" column="1">
	- <widget class="QDoubleSpinBox" name="m_DensityThresholdBox">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="decimals">
	- <number>5</number>
	- </property>
	- <property name="minimum">
	- <double>0.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>10.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.010000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_19">
	- <property name="text">
	- <string>Density threshold:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label_21">
	- <property name="text">
	- <string>Min. overlap:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QDoubleSpinBox" name="m_DensityOverlapBox">
	- <property name="toolTip">
	- <string>Tracts have to spend at least this fraction of their length inside the specified density region.</string>
	- </property>
	- <property name="decimals">
	- <number>3</number>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.500000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <widget class="QWidget" name="page_4">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>367</width>
	- <height>408</height>
	- </rect>
	- </property>
	- <attribute name="label">
	- <string>Bundle Modification</string>
	- </attribute>
	- <attribute name="toolTip">
	- <string>Modify the selected bundle with operations such as fiber resampling, FA coloring, etc.</string>
	- </attribute>
	- <layout class="QGridLayout" name="gridLayout_10">
	- <item row="2" column="0">
	- <widget class="QFrame" name="m_CompressFibersFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_15">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="horizontalSpacing">
	- <number>0</number>
	- </property>
	- <property name="verticalSpacing">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_10">
	- <property name="text">
	- <string>Error threshold in mm:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QDoubleSpinBox" name="m_ErrorThresholdBox">
	- <property name="maximum">
	- <double>999999999.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.100000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QFrame" name="m_MirrorFibersFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_17">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="horizontalSpacing">
	- <number>0</number>
	- </property>
	- <property name="verticalSpacing">
	- <number>6</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QComboBox" name="m_MirrorFibersBox">
	- <item>
	- <property name="text">
	- <string>Sagittal</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Coronal</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Axial</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_13">
	- <property name="text">
	- <string>Select direction:</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QFrame" name="m_ColorFibersFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_16">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="horizontalSpacing">
	- <number>0</number>
	- </property>
	- <property name="verticalSpacing">
	- <number>6</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QCheckBox" name="m_FiberOpacityBox">
	- <property name="toolTip">
	- <string>If checked, the image values are not only used to color the fibers but are also used as opaxity values.</string>
	- </property>
	- <property name="text">
	- <string>Values as opacity</string>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QmitkDataStorageComboBox" name="m_ColorMapBox"/>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_12">
	- <property name="text">
	- <string>Scalar map:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QCheckBox" name="m_NormalizeColorValues">
	- <property name="toolTip">
	- <string>The values used to color the fibers are min-max normalized. If not checked, the values should be between 0 and 1.</string>
	- </property>
	- <property name="text">
	- <string>Normalize values</string>
	- </property>
	- <property name="checked">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QComboBox" name="m_ModificationMethodBox">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <item>
	- <property name="text">
	- <string>Resample fibers (spline)</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Resample fibers (linear)</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Compress fibers</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Color fibers by scalar map (e.g. FA)</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Mirror fibers</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Weight bundle</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Color fibers by curvature</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Color fibers by fiber weights</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Color fibers by length</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QFrame" name="m_SmoothFibersFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_7">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="horizontalSpacing">
	- <number>0</number>
	- </property>
	- <property name="verticalSpacing">
	- <number>6</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QDoubleSpinBox" name="m_SmoothFibersBox">
	- <property name="minimum">
	- <double>0.010000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>999999999.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>1.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_11">
	- <property name="text">
	- <string>Point distance in mm:</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="7" column="0">
	- <spacer name="verticalSpacer_3">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="6" column="0">
	- <widget class="QCommandLinkButton" name="m_ModifyButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="maximumSize">
	- <size>
	- <width>200</width>
	- <height>16777215</height>
	- </size>
	- </property>
	- <property name="font">
	- <font>
	- <pointsize>11</pointsize>
	- </font>
	- </property>
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Execute</string>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <widget class="QFrame" name="m_BundleWeightFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_18">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_15">
	- <property name="text">
	- <string>Weight:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QDoubleSpinBox" name="m_BundleWeightBox">
	- <property name="decimals">
	- <number>7</number>
	- </property>
	- <property name="maximum">
	- <double>999999999.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>1.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <widget class="QWidget" name="page_2">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>367</width>
	- <height>182</height>
	- </rect>
	- </property>
	- <attribute name="label">
	- <string>Bundle Operations</string>
	- </attribute>
	- <attribute name="toolTip">
	- <string>Join, subtract or copy bundles.</string>
	- </attribute>
	- <layout class="QGridLayout" name="gridLayout_13">
	- <item row="0" column="0">
	- <widget class="QCommandLinkButton" name="m_SubstractBundles">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="maximumSize">
	- <size>
	- <width>200</width>
	- <height>16777215</height>
	- </size>
	- </property>
	- <property name="font">
	- <font>
	- <pointsize>11</pointsize>
	- </font>
	- </property>
	- <property name="toolTip">
	- <string>Returns all fibers contained in bundle X that are not contained in bundle Y (not commutative!). Select at least two fiber bundles to execute.</string>
	- </property>
	- <property name="text">
	- <string>Substract</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <spacer name="verticalSpacer_2">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="0" column="2">
	- <widget class="QCommandLinkButton" name="m_JoinBundles">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="maximumSize">
	- <size>
	- <width>200</width>
	- <height>16777215</height>
	- </size>
	- </property>
	- <property name="font">
	- <font>
	- <pointsize>11</pointsize>
	- </font>
	- </property>
	- <property name="toolTip">
	- <string>Merge selected fiber bundles. Select at least two fiber bundles to execute.</string>
	- </property>
	- <property name="text">
	- <string>Join</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QCommandLinkButton" name="m_CopyBundle">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="maximumSize">
	- <size>
	- <width>200</width>
	- <height>16777215</height>
	- </size>
	- </property>
	- <property name="font">
	- <font>
	- <pointsize>11</pointsize>
	- </font>
	- </property>
	- <property name="toolTip">
	- <string>Merge selected fiber bundles. Select at least two fiber bundles to execute.</string>
	- </property>
	- <property name="text">
	- <string>Copy</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QGroupBox" name="m_InputData">
	- <property name="title">
	- <string>Please Select Input Data</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_9">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="1">
	- <widget class="QLabel" name="m_FibLabel">
	- <property name="text">
	- <string><html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html></string>
	- </property>
	- <property name="wordWrap">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QLabel" name="m_PfLabel">
	- <property name="text">
	- <string><html><head/><body><p><span style=" color:#969696;">needed for extraction</span></p></body></html></string>
	- </property>
	- <property name="wordWrap">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_2">
	- <property name="toolTip">
	- <string>Input DTI</string>
	- </property>
	- <property name="text">
	- <string>Fiber Bundle:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_6">
	- <property name="toolTip">
	- <string>Binary seed ROI. If not specified, the whole image area is seeded.</string>
	- </property>
	- <property name="text">
	- <string>ROI:</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <spacer name="verticalSpacer">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- </layout>
	- </widget>
	- <customwidgets>
	- <customwidget>
	- <class>QmitkDataStorageComboBox</class>
	- <extends>QComboBox</extends>
	- <header location="global">QmitkDataStorageComboBox.h</header>
	- </customwidget>
	- </customwidgets>
	- <resources>
	- <include location="../../../../../debug/MITK-build/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/org_mitk_gui_qt_diffusionimaging_fiberprocessing_cached.qrc"/>
	- </resources>
	- <connections/>
	-</ui>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberQuantificationView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberQuantificationView.cpp
	deleted file mode 100644
	index cf1d2653b4..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberQuantificationView.cpp
	+++ /dev/null
	@@ -1,461 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-// Blueberry
	-#include <berryISelectionService.h>
	-#include <berryIWorkbenchWindow.h>
	-
	-// Qmitk
	-#include "QmitkFiberQuantificationView.h"
	-
	-// Qt
	-#include <QMessageBox>
	-
	-// MITK
	-#include <mitkNodePredicateDataType.h>
	-#include <mitkNodePredicateDimension.h>
	-#include <mitkNodePredicateAnd.h>
	-#include <mitkImageCast.h>
	-#include <mitkPeakImage.h>
	-#include <mitkLabelSetImage.h>
	-#include <mitkDICOMSegmentationConstants.h>
	-#include <mitkDICOMSegmentationPropertyHelper.cpp>
	-#include <mitkDICOMQIPropertyHelper.h>
	-
	-// ITK
	-#include <itkTractDensityImageFilter.h>
	-#include <itkTractsToRgbaImageFilter.h>
	-#include <itkTractsToVectorImageFilter.h>
	-#include <itkTractsToFiberEndingsImageFilter.h>
	-
	-#include <mitkLexicalCast.h>
	-
	-const std::string QmitkFiberQuantificationView::VIEW_ID = "org.mitk.views.fiberquantification";
	-using namespace mitk;
	-
	-QmitkFiberQuantificationView::QmitkFiberQuantificationView()
	- : QmitkAbstractView()
	- , m_Controls( 0 )
	- , m_UpsamplingFactor(5)
	- , m_Visible(false)
	-{
	-
	-}
	-
	-// Destructor
	-QmitkFiberQuantificationView::~QmitkFiberQuantificationView()
	-{
	-
	-}
	-
	-void QmitkFiberQuantificationView::CreateQtPartControl( QWidget *parent )
	-{
	- // build up qt view, unless already done
	- if ( !m_Controls )
	- {
	- // create GUI widgets from the Qt Designer's .ui file
	- m_Controls = new Ui::QmitkFiberQuantificationViewControls;
	- m_Controls->setupUi( parent );
	-
	- connect( m_Controls->m_ProcessFiberBundleButton, SIGNAL(clicked()), this, SLOT(ProcessSelectedBundles()) );
	- connect( m_Controls->m_ExtractFiberPeaks, SIGNAL(clicked()), this, SLOT(CalculateFiberDirections()) );
	-
	- m_Controls->m_TractBox->SetDataStorage(this->GetDataStorage());
	- mitk::TNodePredicateDataType<mitk::FiberBundle>::Pointer isFib = mitk::TNodePredicateDataType<mitk::FiberBundle>::New();
	- m_Controls->m_TractBox->SetPredicate( isFib );
	-
	- m_Controls->m_ImageBox->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_ImageBox->SetZeroEntryText("--");
	- mitk::TNodePredicateDataType<mitk::Image>::Pointer isImagePredicate = mitk::TNodePredicateDataType<mitk::Image>::New();
	- mitk::NodePredicateDimension::Pointer is3D = mitk::NodePredicateDimension::New(3);
	- m_Controls->m_ImageBox->SetPredicate( mitk::NodePredicateAnd::New(isImagePredicate, is3D) );
	-
	- connect( (QObject*)(m_Controls->m_TractBox), SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui()));
	- connect( (QObject*)(m_Controls->m_ImageBox), SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui()));
	- }
	-}
	-
	-void QmitkFiberQuantificationView::Activated()
	-{
	-
	-}
	-
	-void QmitkFiberQuantificationView::Deactivated()
	-{
	-
	-}
	-
	-void QmitkFiberQuantificationView::Visible()
	-{
	- m_Visible = true;
	-}
	-
	-void QmitkFiberQuantificationView::Hidden()
	-{
	- m_Visible = false;
	-}
	-
	-void QmitkFiberQuantificationView::SetFocus()
	-{
	- m_Controls->m_ProcessFiberBundleButton->setFocus();
	-}
	-
	-void QmitkFiberQuantificationView::CalculateFiberDirections()
	-{
	- typedef itk::Image<unsigned char, 3> ItkUcharImgType;
	-
	- // load fiber bundle
	- mitk::FiberBundle::Pointer inputTractogram = dynamic_cast<mitk::FiberBundle*>(m_SelectedFB.back()->GetData());
	-
	- itk::TractsToVectorImageFilter<float>::Pointer fOdfFilter = itk::TractsToVectorImageFilter<float>::New();
	- if (m_SelectedImage.IsNotNull())
	- {
	- ItkUcharImgType::Pointer itkMaskImage = ItkUcharImgType::New();
	- mitk::CastToItkImage<ItkUcharImgType>(m_SelectedImage, itkMaskImage);
	- fOdfFilter->SetMaskImage(itkMaskImage);
	- }
	-
	- // extract directions from fiber bundle
	- fOdfFilter->SetFiberBundle(inputTractogram);
	- fOdfFilter->SetAngularThreshold(cos(m_Controls->m_AngularThreshold->value()*itk::Math::pi/180));
	- switch (m_Controls->m_FiberDirNormBox->currentIndex())
	- {
	- case 0:
	- fOdfFilter->SetNormalizationMethod(itk::TractsToVectorImageFilter<float>::NormalizationMethods::GLOBAL_MAX);
	- break;
	- case 1:
	- fOdfFilter->SetNormalizationMethod(itk::TractsToVectorImageFilter<float>::NormalizationMethods::SINGLE_VEC_NORM);
	- break;
	- case 2:
	- fOdfFilter->SetNormalizationMethod(itk::TractsToVectorImageFilter<float>::NormalizationMethods::MAX_VEC_NORM);
	- break;
	- }
	- fOdfFilter->SetSizeThreshold(m_Controls->m_PeakThreshold->value());
	- fOdfFilter->SetMaxNumDirections(m_Controls->m_MaxNumDirections->value());
	- fOdfFilter->Update();
	-
	- QString name = m_SelectedFB.back()->GetName().c_str();
	-
	- if (m_Controls->m_NumDirectionsBox->isChecked())
	- {
	- mitk::Image::Pointer mitkImage = mitk::Image::New();
	- mitkImage->InitializeByItk( fOdfFilter->GetNumDirectionsImage().GetPointer() );
	- mitkImage->SetVolume( fOdfFilter->GetNumDirectionsImage()->GetBufferPointer() );
	-
	- mitk::DataNode::Pointer node = mitk::DataNode::New();
	- node->SetData(mitkImage);
	- node->SetName((name+"_NUM_DIRECTIONS").toStdString().c_str());
	- GetDataStorage()->Add(node, m_SelectedFB.back());
	- }
	-
	- Image::Pointer mitkImage = dynamic_cast<Image*>(PeakImage::New().GetPointer());
	- mitk::CastToMitkImage(fOdfFilter->GetDirectionImage(), mitkImage);
	- mitkImage->SetVolume(fOdfFilter->GetDirectionImage()->GetBufferPointer());
	-
	- mitk::DataNode::Pointer node = mitk::DataNode::New();
	- node->SetData(mitkImage);
	- node->SetName( (name+"_DIRECTIONS").toStdString().c_str());
	- GetDataStorage()->Add(node, m_SelectedFB.back());
	-}
	-
	-void QmitkFiberQuantificationView::UpdateGui()
	-{
	- m_SelectedFB.clear();
	- if (m_Controls->m_TractBox->GetSelectedNode().IsNotNull())
	- m_SelectedFB.push_back(m_Controls->m_TractBox->GetSelectedNode());
	-
	- m_SelectedImage = nullptr;
	- if (m_Controls->m_ImageBox->GetSelectedNode().IsNotNull())
	- m_SelectedImage = dynamic_cast<mitk::Image*>(m_Controls->m_ImageBox->GetSelectedNode()->GetData());
	-
	- m_Controls->m_ProcessFiberBundleButton->setEnabled(!m_SelectedFB.empty());
	- m_Controls->m_ExtractFiberPeaks->setEnabled(!m_SelectedFB.empty());
	-}
	-
	-void QmitkFiberQuantificationView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /part/, const QList<mitk::DataNode::Pointer>& )
	-{
	- UpdateGui();
	-}
	-
	-void QmitkFiberQuantificationView::ProcessSelectedBundles()
	-{
	- if ( m_SelectedFB.empty() ){
	- QMessageBox::information( nullptr, "Warning", "No fibe bundle selected!");
	- MITK_WARN("QmitkFiberQuantificationView") << "no fibe bundle selected";
	- return;
	- }
	-
	- int generationMethod = m_Controls->m_GenerationBox->currentIndex();
	-
	- for( unsigned int i=0; i<m_SelectedFB.size(); i++ )
	- {
	- mitk::DataNode::Pointer node = m_SelectedFB[i];
	- if (node.IsNotNull() && dynamic_cast<mitk::FiberBundle*>(node->GetData()))
	- {
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
	- QString name(node->GetName().c_str());
	- DataNode::Pointer newNode = nullptr;
	- switch(generationMethod){
	- case 0:
	- newNode = GenerateTractDensityImage(fib, false, true, node->GetName());
	- name += "_TDI";
	- break;
	- case 1:
	- newNode = GenerateTractDensityImage(fib, false, false, node->GetName());
	- name += "_TDI";
	- break;
	- case 2:
	- newNode = GenerateTractDensityImage(fib, true, false, node->GetName());
	- name += "_envelope";
	- break;
	- case 3:
	- newNode = GenerateColorHeatmap(fib);
	- break;
	- case 4:
	- newNode = GenerateFiberEndingsImage(fib);
	- name += "_fiber_endings";
	- break;
	- case 5:
	- newNode = GenerateFiberEndingsPointSet(fib);
	- name += "_fiber_endings";
	- break;
	- }
	- if (newNode.IsNotNull())
	- {
	- newNode->SetName(name.toStdString());
	- GetDataStorage()->Add(newNode);
	- }
	- }
	- }
	-}
	-
	-// generate pointset displaying the fiber endings
	-mitk::DataNode::Pointer QmitkFiberQuantificationView::GenerateFiberEndingsPointSet(mitk::FiberBundle::Pointer fib)
	-{
	- mitk::PointSet::Pointer pointSet = mitk::PointSet::New();
	- vtkSmartPointer<vtkPolyData> fiberPolyData = fib->GetFiberPolyData();
	-
	- int count = 0;
	- int numFibers = fib->GetNumFibers();
	- for( int i=0; i<numFibers; i++ )
	- {
	- vtkCell* cell = fiberPolyData->GetCell(i);
	- int numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- if (numPoints>0)
	- {
	- double* point = points->GetPoint(0);
	- itk::Point<float,3> itkPoint = mitk::imv::GetItkPoint(point);
	- pointSet->InsertPoint(count, itkPoint);
	- count++;
	- }
	- if (numPoints>2)
	- {
	- double* point = points->GetPoint(numPoints-1);
	- itk::Point<float,3> itkPoint = mitk::imv::GetItkPoint(point);
	- pointSet->InsertPoint(count, itkPoint);
	- count++;
	- }
	- }
	-
	- mitk::DataNode::Pointer node = mitk::DataNode::New();
	- node->SetData( pointSet );
	- return node;
	-}
	-
	-// generate image displaying the fiber endings
	-mitk::DataNode::Pointer QmitkFiberQuantificationView::GenerateFiberEndingsImage(mitk::FiberBundle::Pointer fib)
	-{
	- typedef unsigned int OutPixType;
	- typedef itk::Image<OutPixType,3> OutImageType;
	-
	- typedef itk::TractsToFiberEndingsImageFilter< OutImageType > ImageGeneratorType;
	- ImageGeneratorType::Pointer generator = ImageGeneratorType::New();
	- generator->SetFiberBundle(fib);
	- generator->SetUpsamplingFactor(m_Controls->m_UpsamplingSpinBox->value());
	- if (m_SelectedImage.IsNotNull())
	- {
	- OutImageType::Pointer itkImage = OutImageType::New();
	- CastToItkImage(m_SelectedImage, itkImage);
	- generator->SetInputImage(itkImage);
	- generator->SetUseImageGeometry(true);
	- }
	- generator->Update();
	-
	- // get output image
	- OutImageType::Pointer outImg = generator->GetOutput();
	- mitk::Image::Pointer img = mitk::Image::New();
	- img->InitializeByItk(outImg.GetPointer());
	- img->SetVolume(outImg->GetBufferPointer());
	-
	- // init data node
	- mitk::DataNode::Pointer node = mitk::DataNode::New();
	- node->SetData(img);
	- return node;
	-}
	-
	-// generate rgba heatmap from fiber bundle
	-mitk::DataNode::Pointer QmitkFiberQuantificationView::GenerateColorHeatmap(mitk::FiberBundle::Pointer fib)
	-{
	- typedef itk::RGBAPixel<unsigned char> OutPixType;
	- typedef itk::Image<OutPixType, 3> OutImageType;
	- typedef itk::TractsToRgbaImageFilter< OutImageType > ImageGeneratorType;
	- ImageGeneratorType::Pointer generator = ImageGeneratorType::New();
	- generator->SetFiberBundle(fib);
	- generator->SetUpsamplingFactor(m_Controls->m_UpsamplingSpinBox->value());
	- if (m_SelectedImage.IsNotNull())
	- {
	- itk::Image<unsigned char, 3>::Pointer itkImage = itk::Image<unsigned char, 3>::New();
	- CastToItkImage(m_SelectedImage, itkImage);
	- generator->SetInputImage(itkImage);
	- generator->SetUseImageGeometry(true);
	- }
	- generator->Update();
	-
	- // get output image
	- typedef itk::Image<OutPixType,3> OutType;
	- OutType::Pointer outImg = generator->GetOutput();
	- mitk::Image::Pointer img = mitk::Image::New();
	- img->InitializeByItk(outImg.GetPointer());
	- img->SetVolume(outImg->GetBufferPointer());
	-
	- // init data node
	- mitk::DataNode::Pointer node = mitk::DataNode::New();
	- node->SetData(img);
	- return node;
	-}
	-
	-// generate tract density image from fiber bundle
	-mitk::DataNode::Pointer QmitkFiberQuantificationView::GenerateTractDensityImage(mitk::FiberBundle::Pointer fib, bool binary, bool absolute, std::string name)
	-{
	- mitk::DataNode::Pointer node = mitk::DataNode::New();
	- if (binary)
	- {
	- typedef unsigned char OutPixType;
	- typedef itk::Image<OutPixType, 3> OutImageType;
	-
	- itk::TractDensityImageFilter< OutImageType >::Pointer generator = itk::TractDensityImageFilter< OutImageType >::New();
	- generator->SetFiberBundle(fib);
	- generator->SetBinaryOutput(binary);
	- generator->SetOutputAbsoluteValues(absolute);
	- generator->SetUpsamplingFactor(m_Controls->m_UpsamplingSpinBox->value());
	- if (m_SelectedImage.IsNotNull())
	- {
	- OutImageType::Pointer itkImage = OutImageType::New();
	- CastToItkImage(m_SelectedImage, itkImage);
	- generator->SetInputImage(itkImage);
	- generator->SetUseImageGeometry(true);
	-
	- }
	- generator->Update();
	-
	- // get output image
	- typedef itk::Image<OutPixType,3> OutType;
	- OutType::Pointer outImg = generator->GetOutput();
	- mitk::Image::Pointer img = mitk::Image::New();
	- img->InitializeByItk(outImg.GetPointer());
	- img->SetVolume(outImg->GetBufferPointer());
	-
	-
	- if (m_SelectedImage.IsNotNull())
	- {
	- mitk::LabelSetImage::Pointer multilabelImage = mitk::LabelSetImage::New();
	- multilabelImage->InitializeByLabeledImage(img);
	- multilabelImage->GetActiveLabelSet()->SetActiveLabel(1);
	- mitk::Label::Pointer label = multilabelImage->GetActiveLabel();
	- label->SetName("Tractogram");
	-
	- // Add Segmented Property Category Code Sequence tags (0062, 0003): Sequence defining the general category of this
	- // segment.
	- // (0008,0100) Code Value
	- label->SetProperty(
	- DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_VALUE_PATH()).c_str(),
	- TemporoSpatialStringProperty::New("T-D000A"));
	-
	- // (0008,0102) Coding Scheme Designator
	- label->SetProperty(
	- DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_SCHEME_PATH()).c_str(),
	- TemporoSpatialStringProperty::New("SRT"));
	-
	- // (0008,0104) Code Meaning
	- label->SetProperty(
	- DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_MEANING_PATH()).c_str(),
	- TemporoSpatialStringProperty::New("Anatomical Structure"));
	- //------------------------------------------------------------
	- // Add Segmented Property Type Code Sequence (0062, 000F): Sequence defining the specific property type of this
	- // segment.
	- // (0008,0100) Code Value
	- label->SetProperty(
	- DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_VALUE_PATH()).c_str(),
	- TemporoSpatialStringProperty::New("DUMMY"));
	-
	- // (0008,0102) Coding Scheme Designator
	- label->SetProperty(
	- DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_SCHEME_PATH()).c_str(),
	- TemporoSpatialStringProperty::New("SRT"));
	-
	- // (0008,0104) Code Meaning
	- label->SetProperty(
	- DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_MEANING_PATH()).c_str(),
	- TemporoSpatialStringProperty::New(name));
	-
	- //Error: is undeclared// mitk::DICOMQIPropertyHandler::DeriveDICOMSourceProperties(m_SelectedImage, multilabelImage);
	-
	- // init data node
	- node->SetData(multilabelImage);
	- }
	- else
	- {
	- // init data node
	- node->SetData(img);
	- }
	-
	- }
	- else
	- {
	- typedef float OutPixType;
	- typedef itk::Image<OutPixType, 3> OutImageType;
	-
	- itk::TractDensityImageFilter< OutImageType >::Pointer generator = itk::TractDensityImageFilter< OutImageType >::New();
	- generator->SetFiberBundle(fib);
	- generator->SetBinaryOutput(binary);
	- generator->SetOutputAbsoluteValues(absolute);
	- generator->SetUpsamplingFactor(m_Controls->m_UpsamplingSpinBox->value());
	- if (m_SelectedImage.IsNotNull())
	- {
	- OutImageType::Pointer itkImage = OutImageType::New();
	- CastToItkImage(m_SelectedImage, itkImage);
	- generator->SetInputImage(itkImage);
	- generator->SetUseImageGeometry(true);
	-
	- }
	- //generator->SetDoFiberResampling(false);
	- generator->Update();
	-
	- // get output image
	- typedef itk::Image<OutPixType,3> OutType;
	- OutType::Pointer outImg = generator->GetOutput();
	- mitk::Image::Pointer img = mitk::Image::New();
	- img->InitializeByItk(outImg.GetPointer());
	- img->SetVolume(outImg->GetBufferPointer());
	-
	- // init data node
	- node->SetData(img);
	- }
	- return node;
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberQuantificationView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberQuantificationView.h
	deleted file mode 100644
	index cfdd9a446a..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberQuantificationView.h
	+++ /dev/null
	@@ -1,86 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef QmitkFiberQuantificationView_h
	-#define QmitkFiberQuantificationView_h
	-
	-#include <QmitkAbstractView.h>
	-#include "ui_QmitkFiberQuantificationViewControls.h"
	-
	-#include <mitkFiberBundle.h>
	-#include <mitkPointSet.h>
	-#include <itkCastImageFilter.h>
	-#include <mitkILifecycleAwarePart.h>
	-
	-/*!
	-\brief Generation of images from fiber bundles (TDI, envelopes, endpoint distribution) and extraction of principal fiber directions from tractograms.
	-
	-*/
	-class QmitkFiberQuantificationView : public QmitkAbstractView, public mitk::ILifecycleAwarePart
	-{
	- // this is needed for all Qt objects that should have a Qt meta-object
	- // (everything that derives from QObject and wants to have signal/slots)
	- Q_OBJECT
	-
	-public:
	-
	- typedef itk::Image< unsigned char, 3 > itkUCharImageType;
	-
	- static const std::string VIEW_ID;
	-
	- QmitkFiberQuantificationView();
	- virtual ~QmitkFiberQuantificationView();
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	-
	- ///
	- /// Sets the focus to an internal widget.
	- ///
	- virtual void SetFocus() override;
	-
	- virtual void Activated() override;
	- virtual void Deactivated() override;
	- virtual void Visible() override;
	- virtual void Hidden() override;
	-
	-protected slots:
	-
	- void ProcessSelectedBundles(); ///< start selected operation on fiber bundle (e.g. tract density image generation)
	- void CalculateFiberDirections(); ///< Calculate main fiber directions from tractogram
	- void UpdateGui(); ///< update button activity etc. dpending on current datamanager selection
	-
	-protected:
	-
	- /// \brief called by QmitkAbstractView when DataManager's selection has changed
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- Ui::QmitkFiberQuantificationViewControls* m_Controls;
	-
	- std::vector<mitk::DataNode::Pointer> m_SelectedFB; ///< selected fiber bundle nodes
	- mitk::Image::Pointer m_SelectedImage;
	- float m_UpsamplingFactor; ///< upsampling factor for all image generations
	-
	- mitk::DataNode::Pointer GenerateTractDensityImage(mitk::FiberBundle::Pointer fib, bool binary, bool absolute, std::string name);
	- mitk::DataNode::Pointer GenerateColorHeatmap(mitk::FiberBundle::Pointer fib);
	- mitk::DataNode::Pointer GenerateFiberEndingsImage(mitk::FiberBundle::Pointer fib);
	- mitk::DataNode::Pointer GenerateFiberEndingsPointSet(mitk::FiberBundle::Pointer fib);
	- bool m_Visible;
	-};
	-
	-
	-
	-#endif // _QMITKFIBERTRACKINGVIEW_H_INCLUDED
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberQuantificationViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberQuantificationViewControls.ui
	deleted file mode 100644
	index a2cd04430c..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberQuantificationViewControls.ui
	+++ /dev/null
	@@ -1,420 +0,0 @@
	-<?xml version="1.0" encoding="utf-8"?>
	-<ui version="4.0">
	- <class>QmitkFiberQuantificationViewControls</class>
	- <widget class="QWidget" name="QmitkFiberQuantificationViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>365</width>
	- <height>581</height>
	- </rect>
	- </property>
	- <property name="windowTitle">
	- <string>Form</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_10">
	- <property name="verticalSpacing">
	- <number>25</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QGroupBox" name="groupBox_2">
	- <property name="title">
	- <string>Fiber-derived images</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_3">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QCommandLinkButton" name="m_ProcessFiberBundleButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="maximumSize">
	- <size>
	- <width>200</width>
	- <height>16777215</height>
	- </size>
	- </property>
	- <property name="font">
	- <font>
	- <pointsize>11</pointsize>
	- </font>
	- </property>
	- <property name="toolTip">
	- <string>Perform selected operation on all selected fiber bundles.</string>
	- </property>
	- <property name="text">
	- <string>Generate Image</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QDoubleSpinBox" name="m_UpsamplingSpinBox">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="toolTip">
	- <string>Upsampling factor</string>
	- </property>
	- <property name="decimals">
	- <number>1</number>
	- </property>
	- <property name="minimum">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>10.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>1.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QComboBox" name="m_GenerationBox">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <item>
	- <property name="text">
	- <string>Tract Density Image (TDI)</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Normalized TDI</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Binary Envelope</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Fiber Bundle Image</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Fiber Endings Image</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Fiber Endings Pointset</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QGroupBox" name="groupBox_4">
	- <property name="title">
	- <string>Principal Fiber Directions</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_6">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QFrame" name="frame_2">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_5">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="1" column="1">
	- <widget class="QDoubleSpinBox" name="m_AngularThreshold">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="toolTip">
	- <string>Fiber directions with an angle smaller than the defined threshold are clustered.</string>
	- </property>
	- <property name="decimals">
	- <number>2</number>
	- </property>
	- <property name="minimum">
	- <double>0.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>90.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="value">
	- <double>30.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QDoubleSpinBox" name="m_PeakThreshold">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="toolTip">
	- <string><html><head/><body><p>Directions shorter than the defined threshold are discarded.</p></body></html></string>
	- </property>
	- <property name="decimals">
	- <number>3</number>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.300000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label">
	- <property name="text">
	- <string>Angular Threshold:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_2">
	- <property name="text">
	- <string>Max. Peaks:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label_3">
	- <property name="text">
	- <string>Size Threshold:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_MaxNumDirections">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="toolTip">
	- <string>Maximum number of fiber directions per voxel.</string>
	- </property>
	- <property name="maximum">
	- <number>100</number>
	- </property>
	- <property name="value">
	- <number>3</number>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QLabel" name="label_4">
	- <property name="text">
	- <string>Normalization:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="1">
	- <widget class="QComboBox" name="m_FiberDirNormBox">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="currentIndex">
	- <number>0</number>
	- </property>
	- <item>
	- <property name="text">
	- <string>Global maximum</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Single vector</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Voxel-wise maximum</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QCheckBox" name="m_NumDirectionsBox">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="toolTip">
	- <string>Image containing the number of distinct fiber clusters per voxel.</string>
	- </property>
	- <property name="text">
	- <string>Output #Directions per Voxel</string>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QCommandLinkButton" name="m_ExtractFiberPeaks">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="text">
	- <string>Generate Directions</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QGroupBox" name="groupBox">
	- <property name="title">
	- <string>Input Data</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_TractBox"></widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QmitkDataStorageComboBoxWithSelectNone" name="m_ImageBox"></widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_5">
	- <property name="text">
	- <string>Tractogram:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_6">
	- <property name="text">
	- <string>Reference Image:</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <spacer name="verticalSpacer">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- </layout>
	- </widget>
	- <customwidgets>
	- <customwidget>
	- <class>QmitkDataStorageComboBox</class>
	- <extends>QComboBox</extends>
	- <header location="global">QmitkDataStorageComboBox.h</header>
	- </customwidget>
	- <customwidget>
	- <class>QmitkDataStorageComboBoxWithSelectNone</class>
	- <extends>QComboBox</extends>
	- <header>QmitkDataStorageComboBoxWithSelectNone.h</header>
	- </customwidget>
	- </customwidgets>
	- <resources></resources>
	- <connections></connections>
	-</ui>
	\ No newline at end of file
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryView.cpp
	deleted file mode 100644
	index 857007275e..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryView.cpp
	+++ /dev/null
	@@ -1,352 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#include <berryISelectionService.h>
	-#include <berryIWorkbenchWindow.h>
	-
	-#include "QmitkTractometryView.h"
	-
	-#include <mitkNodePredicateDataType.h>
	-#include <mitkNodePredicateDimension.h>
	-#include <mitkNodePredicateAnd.h>
	-#include <mitkImageCast.h>
	-#include <mitkImageAccessByItk.h>
	-#include <mitkImage.h>
	-#include <mitkFiberBundle.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <mitkITKImageImport.h>
	-#include <mitkPixelTypeMultiplex.h>
	-#include <mitkImagePixelReadAccessor.h>
	-#include <berryIPreferences.h>
	-#include <berryWorkbenchPlugin.h>
	-#include <berryQtPreferences.h>
	-#include <vtkLookupTable.h>
	-#include <QClipboard>
	-#include <mitkLexicalCast.h>
	-#include <QmitkChartWidget.h>
	-
	-
	-const std::string QmitkTractometryView::VIEW_ID = "org.mitk.views.tractometry";
	-using namespace mitk;
	-
	-QmitkTractometryView::QmitkTractometryView()
	- : QmitkAbstractView()
	- , m_Controls( nullptr )
	- , m_Visible(false)
	-{
	-
	-}
	-
	-// Destructor
	-QmitkTractometryView::~QmitkTractometryView()
	-{
	-
	-}
	-
	-void QmitkTractometryView::CreateQtPartControl( QWidget *parent )
	-{
	- // build up qt view, unless already done
	- if ( !m_Controls )
	- {
	- // create GUI widgets from the Qt Designer's .ui file
	- m_Controls = new Ui::QmitkTractometryViewControls;
	- m_Controls->setupUi( parent );
	-
	- connect( m_Controls->m_SamplingPointsBox, SIGNAL(valueChanged(int)), this, SLOT(UpdateGui()) );
	- connect( m_Controls->m_StDevBox, SIGNAL(stateChanged(int)), this, SLOT(UpdateGui()) );
	-
	- mitk::TNodePredicateDataType<mitk::Image>::Pointer imageP = mitk::TNodePredicateDataType<mitk::Image>::New();
	- mitk::NodePredicateDimension::Pointer dimP = mitk::NodePredicateDimension::New(3);
	-
	- m_Controls->m_ImageBox->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_ImageBox->SetPredicate(mitk::NodePredicateAnd::New(imageP, dimP));
	-
	- m_Controls->m_ChartWidget->SetTheme(GetColorTheme());
	- m_Controls->m_ChartWidget->SetXAxisLabel("Tract position");
	- m_Controls->m_ChartWidget->SetYAxisLabel("Image Value");
	-
	- }
	-}
	-
	-::QmitkChartWidget::ColorTheme QmitkTractometryView::GetColorTheme()
	-{
	- berry::IPreferencesService* prefService = berry::WorkbenchPlugin::GetDefault()->GetPreferencesService();
	- berry::IPreferences::Pointer m_StylePref = prefService->GetSystemPreferences()->Node(berry::QtPreferences::QT_STYLES_NODE);
	-
	- QString styleName = m_StylePref->Get(berry::QtPreferences::QT_STYLE_NAME, "");
	-
	- if (styleName == ":/org.blueberry.ui.qt/darkstyle.qss")
	- {
	- return QmitkChartWidget::ColorTheme::darkstyle;
	- }
	- else
	- {
	- return QmitkChartWidget::ColorTheme::lightstyle;
	- }
	-}
	-
	-void QmitkTractometryView::SetFocus()
	-{
	-}
	-
	-void QmitkTractometryView::UpdateGui()
	-{
	- berry::IWorkbenchPart::Pointer nullPart;
	- OnSelectionChanged(nullPart, QList<mitk::DataNode::Pointer>(m_CurrentSelection));
	-}
	-
	-bool QmitkTractometryView::Flip(vtkSmartPointer< vtkPolyData > polydata1, int i, vtkSmartPointer< vtkPolyData > ref_poly)
	-{
	- double d_direct = 0;
	- double d_flipped = 0;
	-
	- vtkCell* cell1 = polydata1->GetCell(0);
	- if (ref_poly!=nullptr)
	- cell1 = ref_poly->GetCell(0);
	- auto numPoints1 = cell1->GetNumberOfPoints();
	- vtkPoints* points1 = cell1->GetPoints();
	-
	- std::vector<itk::Point<double, 3>> ref_points;
	- for (int j=0; j<numPoints1; ++j)
	- {
	- double* p1 = points1->GetPoint(j);
	- itk::Point<double, 3> itk_p;
	- itk_p[0] = p1[0];
	- itk_p[1] = p1[1];
	- itk_p[2] = p1[2];
	- ref_points.push_back(itk_p);
	- }
	-
	- vtkCell* cell2 = polydata1->GetCell(i);
	- vtkPoints* points2 = cell2->GetPoints();
	-
	- for (int j=0; j<numPoints1; ++j)
	- {
	- auto p1 = ref_points.at(j);
	-
	- double* p2 = points2->GetPoint(j);
	- d_direct = (p1[0]-p2[0])(p1[0]-p2[0]) + (p1[1]-p2[1])(p1[1]-p2[1]) + (p1[2]-p2[2])*(p1[2]-p2[2]);
	-
	- double* p3 = points2->GetPoint(numPoints1-j-1);
	- d_flipped = (p1[0]-p3[0])(p1[0]-p3[0]) + (p1[1]-p3[1])(p1[1]-p3[1]) + (p1[2]-p3[2])*(p1[2]-p3[2]);
	- }
	-
	- if (d_direct>d_flipped)
	- return true;
	- return false;
	-}
	-
	-template <typename TPixel>
	-void QmitkTractometryView::ImageValuesAlongTract(const mitk::PixelType, mitk::Image::Pointer image, mitk::FiberBundle::Pointer fib, std::vector<std::vector<double> > &data, std::string& clipboard_string)
	-{
	- unsigned int num_points = m_Controls->m_SamplingPointsBox->value();
	- mitk::ImagePixelReadAccessor<TPixel,3> readimage(image, image->GetVolumeData(0));
	- mitk::FiberBundle::Pointer working_fib = fib->GetDeepCopy();
	- working_fib->ResampleToNumPoints(num_points);
	- vtkSmartPointer< vtkPolyData > polydata = working_fib->GetFiberPolyData();
	-
	- std::vector<std::vector<double> > all_values;
	- std::vector< double > mean_values;
	- for (unsigned int i=0; i<num_points; ++i)
	- mean_values.push_back(0);
	-
	- double min = 100000.0;
	- double max = 0;
	- double mean = 0;
	- for (unsigned int i=0; i<working_fib->GetNumFibers(); ++i)
	- {
	- vtkCell* cell = polydata->GetCell(i);
	- auto numPoints = cell->GetNumberOfPoints();
	- vtkPoints* points = cell->GetPoints();
	-
	- std::vector< double > fib_vals;
	-
	- bool flip = false;
	- if (i>0)
	- flip = Flip(polydata, i);
	- else if (m_ReferencePolyData!=nullptr)
	- flip = Flip(polydata, 0, m_ReferencePolyData);
	-
	- for (int j=0; j<numPoints; j++)
	- {
	- double* p;
	- if (flip)
	- p = points->GetPoint(numPoints - j - 1);
	- else
	- p = points->GetPoint(j);
	-
	- Point3D px;
	- px[0] = p[0];
	- px[1] = p[1];
	- px[2] = p[2];
	- double pixelValue = static_cast<double>(readimage.GetPixelByWorldCoordinates(px));
	- fib_vals.push_back(pixelValue);
	- mean += pixelValue;
	- if (pixelValue<min)
	- min = pixelValue;
	- else if (pixelValue>max)
	- max = pixelValue;
	-
	- mean_values.at(j) += pixelValue;
	- }
	-
	- all_values.push_back(fib_vals);
	- }
	-
	- if (m_ReferencePolyData==nullptr)
	- m_ReferencePolyData = polydata;
	-
	- std::vector< double > std_values1;
	- std::vector< double > std_values2;
	- for (unsigned int i=0; i<num_points; ++i)
	- {
	- mean_values.at(i) /= working_fib->GetNumFibers();
	- double stdev = 0;
	-
	- for (unsigned int j=0; j<all_values.size(); ++j)
	- {
	- double diff = mean_values.at(i) - all_values.at(j).at(i);
	- diff *= diff;
	- stdev += diff;
	- }
	- stdev /= all_values.size();
	- stdev = std::sqrt(stdev);
	- std_values1.push_back(mean_values.at(i) + stdev);
	- std_values2.push_back(mean_values.at(i) - stdev);
	-
	- clipboard_string += boost::lexical_cast<std::string>(mean_values.at(i));
	- clipboard_string += " ";
	- clipboard_string += boost::lexical_cast<std::string>(stdev);
	- clipboard_string += "\n";
	- }
	- clipboard_string += "\n";
	-
	- data.push_back(mean_values);
	- data.push_back(std_values1);
	- data.push_back(std_values2);
	-
	- MITK_INFO << "Min: " << min;
	- MITK_INFO << "Max: " << max;
	- MITK_INFO << "Mean: " << mean/working_fib->GetNumberOfPoints();
	-}
	-
	-void QmitkTractometryView::Activated()
	-{
	-
	-}
	-
	-void QmitkTractometryView::Deactivated()
	-{
	-
	-}
	-
	-void QmitkTractometryView::Visible()
	-{
	- m_Visible = true;
	- QList<mitk::DataNode::Pointer> selection = GetDataManagerSelection();
	- berry::IWorkbenchPart::Pointer nullPart;
	- OnSelectionChanged(nullPart, selection);
	-}
	-
	-void QmitkTractometryView::Hidden()
	-{
	- m_Visible = false;
	-}
	-
	-std::string QmitkTractometryView::RGBToHexString(double *rgb)
	-{
	- std::ostringstream os;
	- for (int i = 0; i < 3; ++i)
	- {
	- os << std::setw(2) << std::setfill('0') << std::hex
	- << static_cast<int>(rgb[i] * 255);
	- }
	- return os.str();
	-}
	-
	-void QmitkTractometryView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /part/, const QList<mitk::DataNode::Pointer>& nodes)
	-{
	- if (!m_Visible)
	- return;
	-
	- m_CurrentSelection.clear();
	- if(m_Controls->m_ImageBox->GetSelectedNode().IsNull())
	- return;
	-
	- std::string clipboardString = "";
	- m_ReferencePolyData = nullptr;
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(m_Controls->m_ImageBox->GetSelectedNode()->GetData());
	-
	- vtkSmartPointer<vtkLookupTable> lookupTable = vtkSmartPointer<vtkLookupTable>::New();
	- lookupTable->SetTableRange(0.0, 1.0);
	- lookupTable->Build();
	-
	- int num_tracts = 0;
	- for (auto node: nodes)
	- if ( dynamic_cast<mitk::FiberBundle*>(node->GetData()) )
	- num_tracts++;
	-
	- int c = 1;
	- this->m_Controls->m_ChartWidget->Clear();
	- for (auto node: nodes)
	- {
	- if ( dynamic_cast<mitk::FiberBundle*>(node->GetData()) )
	- {
	- clipboardString += node->GetName() + "\n";
	- clipboardString += "mean stdev\n";
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
	- m_CurrentSelection.push_back(node);
	-
	- std::vector< std::vector< double > > data;
	- mitkPixelTypeMultiplex4( ImageValuesAlongTract, image->GetPixelType(), image, fib, data, clipboardString );
	-
	- m_Controls->m_ChartWidget->AddData1D(data.at(0), node->GetName() + " Mean", QmitkChartWidget::ChartType::line);
	- if (m_Controls->m_StDevBox->isChecked())
	- {
	- this->m_Controls->m_ChartWidget->AddData1D(data.at(1), node->GetName() + " +STDEV", QmitkChartWidget::ChartType::line);
	- this->m_Controls->m_ChartWidget->AddData1D(data.at(2), node->GetName() + " -STDEV", QmitkChartWidget::ChartType::line);
	- }
	-
	- double color[3];
	- if (num_tracts>1)
	- {
	- float scalar_color = ( (float)c/num_tracts - 1.0/num_tracts )/(1.0-1.0/num_tracts);
	- lookupTable->GetColor(1.0 - scalar_color, color);
	- }
	- else
	- lookupTable->GetColor(0, color);
	-
	- this->m_Controls->m_ChartWidget->SetColor(node->GetName() + " Mean", RGBToHexString(color));
	-
	- if (m_Controls->m_StDevBox->isChecked())
	- {
	- color[0] *= 0.5;
	- color[1] *= 0.5;
	- color[2] *= 0.5;
	- this->m_Controls->m_ChartWidget->SetColor(node->GetName() + " +STDEV", RGBToHexString(color));
	- this->m_Controls->m_ChartWidget->SetColor(node->GetName() + " -STDEV", RGBToHexString(color));
	- }
	-
	- this->m_Controls->m_ChartWidget->Show(true);
	- this->m_Controls->m_ChartWidget->SetShowDataPoints(false);
	- ++c;
	- }
	- }
	-
	- QApplication::clipboard()->setText(clipboardString.c_str(), QClipboard::Clipboard);
	-
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryView.h
	deleted file mode 100644
	index 3176bddae5..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryView.h
	+++ /dev/null
	@@ -1,81 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef QmitkTractometryView_h
	-#define QmitkTractometryView_h
	-
	-#include <QmitkAbstractView.h>
	-#include "ui_QmitkTractometryViewControls.h"
	-#include <itkImage.h>
	-#include <mitkImage.h>
	-#include <mitkPixelType.h>
	-#include <mitkFiberBundle.h>
	-#include <mitkILifecycleAwarePart.h>
	-#include <QmitkChartWidget.h>
	-
	-/*!
	-\brief Weight fibers by linearly fitting them to the image data.
	-
	-*/
	-class QmitkTractometryView : public QmitkAbstractView, public mitk::ILifecycleAwarePart
	-{
	- // this is needed for all Qt objects that should have a Qt meta-object
	- // (everything that derives from QObject and wants to have signal/slots)
	- Q_OBJECT
	-
	-public:
	-
	- static const std::string VIEW_ID;
	-
	- QmitkTractometryView();
	- virtual ~QmitkTractometryView();
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	-
	- template <typename TPixel>
	- void ImageValuesAlongTract(const mitk::PixelType, mitk::Image::Pointer image, mitk::FiberBundle::Pointer fib, std::vector< std::vector< double > >& data, std::string& clipboard_string);
	-
	- virtual void SetFocus() override;
	-
	- virtual void Activated() override;
	- virtual void Deactivated() override;
	- virtual void Visible() override;
	- virtual void Hidden() override;
	-
	-protected slots:
	-
	- void UpdateGui();
	-
	-protected:
	-
	- /// \brief called by QmitkAbstractView when DataManager's selection has changed
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	- QmitkChartWidget::ColorTheme GetColorTheme();
	-
	- Ui::QmitkTractometryViewControls* m_Controls;
	-
	- bool Flip(vtkSmartPointer< vtkPolyData > polydata1, int i, vtkSmartPointer<vtkPolyData> ref_poly=nullptr);
	- std::string RGBToHexString(double *rgb);
	-
	- vtkSmartPointer< vtkPolyData > m_ReferencePolyData;
	- QList<mitk::DataNode::Pointer> m_CurrentSelection;
	- bool m_Visible;
	-};
	-
	-
	-
	-#endif // _QMITKFIBERTRACKINGVIEW_H_INCLUDED
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryViewControls.ui
	deleted file mode 100644
	index ed26c9061b..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryViewControls.ui
	+++ /dev/null
	@@ -1,136 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<ui version="4.0">
	- <class>QmitkTractometryViewControls</class>
	- <widget class="QWidget" name="QmitkTractometryViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>484</width>
	- <height>574</height>
	- </rect>
	- </property>
	- <property name="windowTitle">
	- <string>Form</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_10">
	- <item row="0" column="0">
	- <widget class="QFrame" name="frame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_2">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>6</number>
	- </property>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_ImageBox">
	- <property name="toolTip">
	- <string/>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_3">
	- <property name="text">
	- <string>Input Image:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QSpinBox" name="m_SamplingPointsBox">
	- <property name="minimum">
	- <number>3</number>
	- </property>
	- <property name="maximum">
	- <number>99999</number>
	- </property>
	- <property name="value">
	- <number>20</number>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_4">
	- <property name="text">
	- <string>Sampling Points:</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <spacer name="verticalSpacer">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="2" column="0">
	- <widget class="QmitkChartWidget" name="m_ChartWidget" native="true">
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>600</height>
	- </size>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QCheckBox" name="m_StDevBox">
	- <property name="text">
	- <string>Show STDEV</string>
	- </property>
	- <property name="checked">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <customwidgets>
	- <customwidget>
	- <class>QmitkDataStorageComboBox</class>
	- <extends>QComboBox</extends>
	- <header location="global">QmitkDataStorageComboBox.h</header>
	- </customwidget>
	- <customwidget>
	- <class>QmitkChartWidget</class>
	- <extends>QWidget</extends>
	- <header location="global">QmitkChartWidget.h</header>
	- </customwidget>
	- </customwidgets>
	- <resources/>
	- <connections/>
	-</ui>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/mitkPluginActivator.cpp
	deleted file mode 100644
	index 7ae0cfc39d..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/mitkPluginActivator.cpp
	+++ /dev/null
	@@ -1,51 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkPluginActivator.h"
	-
	-#include "src/internal/Perspectives/QmitkFiberProcessingPerspective.h"
	-
	-#include "src/internal/QmitkFiberProcessingView.h"
	-#include "src/internal/QmitkFiberQuantificationView.h"
	-#include "src/internal/QmitkFiberClusteringView.h"
	-#include "src/internal/QmitkFiberFitView.h"
	-#include "src/internal/QmitkTractometryView.h"
	-
	-
	-ctkPluginContext* mitk::PluginActivator::m_Context = nullptr;
	-
	-ctkPluginContext* mitk::PluginActivator::GetContext()
	-{
	- return m_Context;
	-}
	-
	-void mitk::PluginActivator::start(ctkPluginContext* context)
	-{
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberProcessingPerspective, context)
	-
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberQuantificationView, context)
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberProcessingView, context)
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberClusteringView, context)
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkFiberFitView, context)
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkTractometryView, context)
	- m_Context = context;
	-}
	-
	-void mitk::PluginActivator::stop(ctkPluginContext* context)
	-{
	- Q_UNUSED(context)
	- m_Context = nullptr;
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/mitkPluginActivator.h b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/mitkPluginActivator.h
	deleted file mode 100644
	index 28db6bd576..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/mitkPluginActivator.h
	+++ /dev/null
	@@ -1,40 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef MITKPLUGINACTIVATOR_H
	-#define MITKPLUGINACTIVATOR_H
	-
	-#include <ctkPluginActivator.h>
	-
	-namespace mitk
	-{
	- class PluginActivator : public QObject, public ctkPluginActivator
	- {
	- Q_OBJECT
	- Q_PLUGIN_METADATA(IID "org.mitk.gui.qt.diffusionimaging.fiberprocessing")
	- Q_INTERFACES(ctkPluginActivator)
	-
	- public:
	- static ctkPluginContext* GetContext();
	-
	- void start(ctkPluginContext* context) override;
	- void stop(ctkPluginContext* context) override;
	-
	- private:
	- static ctkPluginContext* m_Context;
	- };
	-}
	-
	-#endif
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/CMakeLists.txt
	deleted file mode 100644
	index 654e260138..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/CMakeLists.txt
	+++ /dev/null
	@@ -1,10 +0,0 @@
	-# The project name must correspond to the directory name of your plug-in
	-# and must not contain periods.
	-project(org_mitk_gui_qt_diffusionimaging_ivim)
	-
	-mitk_create_plugin(
	- SUBPROJECTS MITK-DTI
	- EXPORT_DIRECTIVE DIFFUSIONIMAGING_IVIM_EXPORT
	- EXPORTED_INCLUDE_SUFFIXES src
	- MODULE_DEPENDS MitkQtWidgetsExt MitkQuantification
	-)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/documentation/UserManual/QmitkUserIVIMViewManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/documentation/UserManual/QmitkUserIVIMViewManual.dox
	deleted file mode 100644
	index 6549fe1d78..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/documentation/UserManual/QmitkUserIVIMViewManual.dox
	+++ /dev/null
	@@ -1,41 +0,0 @@
	-/**
	-\page org_mitk_views_ivim Intra-voxel incoherent motion estimation (IVIM)
	-
	-The required input for the "Intra-voxel incoherent motion estimation" (IVIM) is a diffusion weighted image (.dwi or .hdwi) that was acquired with several different b-values.
	-
	-\imageMacro{ivimview.png,"The IVIM View",13.91}
	-
	-Once an input image is selected in the datamanager, the IVIM view allows for interactive exploration of the dataset (click around in the image and watch the estimated parameters in the figure of the view) as well as generation of f-, D-, and D*-maps (activate the checkmarks and press "Generate Output Images").
	-
	-The "neglect b<" threshold allows you to ignore b-values smaller then a threshold for the initial fit of f and D. D* is then estimated using all measurements.
	-
	-The exact values of the current fit are always given in the legend underneath the figure.
	-
	-\section QmitkIVIMViewROIAnalysis Region of interest analysis
	-
	-Create region of interest: To create a new segmentatin, open the "quantification" perspective, select the tab "Segmentation", and create a segmentation of the structure of interest. Alternatively, of course, you may also load a binary image from file or generate your segmentation in any other possible way.
	-
	-IVIM in region of interset: Go back to the "IVIM" perspective and select both, the diffusion image and the segmentation (holding the CTRL key). A red message should appear "Averaging N voxels".
	-
	-\section QmitkIVIMViewExport Export
	-
	-All model parameters and corresponding curves can be exported to clipboard using the buttons underneath the figure.
	-
	-\section QmitkIVIMViewAdvanced Advanced Settings
	-
	-Advanced users, that know what they are doing, can change the method for the model-fit under "Advanced Settings" on the very bottom of the view. 3-param fit, linear fit of f/D, and fix D* are among the options.
	-
	-\section QmitkIVIMViewReferences Suggested Readings
	-
	-Toward an optimal distribution of b values for intravoxel incoherent motion imaging.
	-Lemke A, Stieltjes B, Schad LR, Laun FB.
	-Magn Reson Imaging. 2011 Jul;29(6):766-76. Epub 2011 May 5.
	-PMID: 21549538
	-
	-Differentiation of pancreas carcinoma from healthy pancreatic tissue using multiple b-values: comparison of apparent diffusion coefficient and intravoxel incoherent motion derived parameters.
	-Lemke A, Laun FB, Klauss M, Re TJ, Simon D, Delorme S, Schad LR, Stieltjes B.
	-Invest Radiol. 2009 Dec;44(12):769-75.
	-PMID: 19838121
	-
	-
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/documentation/UserManual/ivimview.png b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/documentation/UserManual/ivimview.png
	deleted file mode 100644
	index 10d3ba01b1..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/documentation/UserManual/ivimview.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/documentation/doxygen/modules.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/documentation/doxygen/modules.dox
	deleted file mode 100644
	index 94d0333ffd..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/documentation/doxygen/modules.dox
	+++ /dev/null
	@@ -1,16 +0,0 @@
	-/**
	- \defgroup org_mitk_gui_qt_diffusionimaging_ivim org.mitk.gui.qt.diffusionimaging.ivim
	- \ingroup MITKPlugins
	-
	- \brief This is the diffusionimaging.ivim plugin.
	-
	-*/
	-
	-/**
	- \defgroup org_mitk_gui_qt_diffusionimaging_ivim_internal Internal
	- \ingroup org_mitk_gui_qt_diffusionimaging_ivim
	-
	- \brief This subcategory includes the internal classes of the org.mitk.gui.qt.diffusionimaging.ivim plugin. Other
	- plugins must not rely on these classes. They contain implementation details and their interface
	- may change at any time. We mean it.
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/files.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/files.cmake
	deleted file mode 100644
	index 4d36129c3e..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/files.cmake
	+++ /dev/null
	@@ -1,46 +0,0 @@
	-set(SRC_CPP_FILES
	- QmitkIVIMWidget.cpp
	- QmitkKurtosisWidget.cpp
	-)
	-
	-set(INTERNAL_CPP_FILES
	- mitkPluginActivator.cpp
	-
	- QmitkIVIMView.cpp
	-
	- Perspectives/QmitkDIAppIVIMPerspective.cpp
	-)
	-
	-set(UI_FILES
	- src/internal/QmitkIVIMViewControls.ui
	-)
	-
	-set(MOC_H_FILES
	- src/internal/mitkPluginActivator.h
	-
	- src/internal/QmitkIVIMView.h
	-
	- src/internal/Perspectives/QmitkDIAppIVIMPerspective.h
	-)
	-
	-set(CACHED_RESOURCE_FILES
	- plugin.xml
	-
	- resources/IVIM_48.png
	- resources/ivim.png
	-)
	-
	-set(QRC_FILES
	-
	-)
	-
	-
	-set(CPP_FILES )
	-
	-foreach(file ${SRC_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/${file})
	-endforeach(file ${SRC_CPP_FILES})
	-
	-foreach(file ${INTERNAL_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/internal/${file})
	-endforeach(file ${INTERNAL_CPP_FILES})
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/manifest_headers.cmake
	deleted file mode 100644
	index 3385c26aaf..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/manifest_headers.cmake
	+++ /dev/null
	@@ -1,5 +0,0 @@
	-set(Plugin-Name "MITK IVIM")
	-set(Plugin-Version "1.0.0")
	-set(Plugin-Vendor "DKFZ, Medical and Biological Informatics")
	-set(Plugin-ContactAddress "http://www.mitk.org")
	-set(Require-Plugin org.mitk.gui.qt.diffusionimaging org.mitk.gui.qt.common)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/plugin.xml b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/plugin.xml
	deleted file mode 100644
	index 668eebc1cc..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/plugin.xml
	+++ /dev/null
	@@ -1,29 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<?BlueBerry version="0.1"?>
	-<plugin>
	-
	- <extension point="org.blueberry.ui.views">
	-
	- <view id="org.mitk.views.ivim"
	- name="IVIM"
	- category="Quantification"
	- class="QmitkIVIMView"
	- icon="resources/IVIM_48.png">
	- <keywordReference id="org.mitk.views.ivim.Keyword"/>
	- </view>
	-
	- </extension>
	-
	-
	- <extension point="org.blueberry.ui.perspectives">
	-
	- <perspective id="org.mitk.perspectives.ivim"
	- name="Intra-Voxel Incoherent Motion (IVIM)"
	- class="QmitkDIAppIVIMPerspective"
	- icon="resources/ivim.png">
	- <keywordReference id="org.mitk.perspectives.ivim.Keyword"/>
	- </perspective>
	-
	- </extension>
	-
	-</plugin>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/resources/IVIM_48.png b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/resources/IVIM_48.png
	deleted file mode 100644
	index 9fe2494651..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/resources/IVIM_48.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/resources/ivim.png b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/resources/ivim.png
	deleted file mode 100644
	index 9fe2494651..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/resources/ivim.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/QmitkIVIMWidget.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/QmitkIVIMWidget.cpp
	deleted file mode 100644
	index 52f211290a..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/QmitkIVIMWidget.cpp
	+++ /dev/null
	@@ -1,148 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkIVIMWidget.h"
	-
	-#include "mitkHistogramGenerator.h"
	-
	-
	-#include <qwt_scale_engine.h>
	-#include <qwt_legend.h>
	-
	-
	-QmitkIVIMWidget::QmitkIVIMWidget( QWidget * parent )
	- : QmitkPlotWidget(parent)
	-{
	- // this->SetAxisTitle( QwtPlot::xBottom, "Grayvalue" );
	- // this->SetAxisTitle( QwtPlot::yLeft, "Probability" );
	- // this->Replot();
	- QFrame* canvas = qobject_cast<QFrame*>(m_Plot->canvas());
	- if (canvas)
	- {
	- canvas->setLineWidth(0);
	- canvas->setContentsMargins(0,0,0,0);
	- }
	-
	- auto logScale = new QwtLogScaleEngine();
	- m_Plot->setAxisScaleEngine(0, logScale);
	-
	- m_Plot->setAxisScale( 0, 0.15, 1.0 );
	-}
	-
	-
	-
	-QmitkIVIMWidget::~QmitkIVIMWidget()
	-{
	-}
	-
	-
	-void QmitkIVIMWidget::DrawGauss()
	-{
	-
	-}
	-
	-
	-void QmitkIVIMWidget::ClearItemModel()
	-{
	-
	-}
	-
	-std::vector<double> QmitkIVIMWidget::vec(const vnl_vector<double>& vector)
	-{
	- std::vector<double> retval(vector.size());
	- for(unsigned int i=0; i<vector.size(); i++)
	- {
	- retval.at(i) = vector[i];
	- }
	- return retval;
	-}
	-
	-void QmitkIVIMWidget::SetParameters( IVIMFilterType::IVIMSnapshot snap )
	-{
	- this->Clear();
	- if (snap.bvalues.empty())
	- return;
	-
	- QString s("f=%1, D=%2, D*=%3");
	- s = s.arg(snap.currentF,4);
	- s = s.arg(snap.currentD,4);
	- s = s.arg(snap.currentDStar,4);
	- int curveId = this->InsertCurve( s.toLatin1(), QColor(Qt::black) );
	- this->SetCurvePen( curveId, QPen( Qt::NoPen ) );
	-
	- QPen pen;
	- pen.setColor( QColor(Qt::red) );
	- pen.setWidth(2);
	- double maxb = snap.bvalues.max_value();
	- vnl_vector<double> xvals(2);
	- vnl_vector<double> yvals(2);
	- xvals[0] = 0;
	- xvals[1] = maxb;
	- yvals[0] = 1-snap.currentFunceiled;
	- yvals[1] = yvals[0]exp(-maxb snap.currentD);
	- curveId = this->InsertCurve( "contribution of D to the signal", pen.color() );
	- this->SetCurveData( curveId, vec(xvals), vec(yvals) );
	- this->SetCurvePen( curveId, pen );
	- this->SetCurveAntialiasingOn( curveId );
	-
	- if(snap.currentDStar != 0)
	- {
	- pen.setColor(Qt::black);
	- int nsampling = 50;
	- xvals.set_size(nsampling);
	- yvals.set_size(nsampling);
	- double f = 1-snap.currentFunceiled;
	- for(int i=0; i<nsampling; i++)
	- {
	- xvals[i] = (((1.0)i)/(1.0nsampling))*maxb;
	- yvals[i] = fexp(- xvals[i] snap.currentD) + (1-f)exp(- xvals[i] (snap.currentD+snap.currentDStar));
	- }
	- curveId = this->InsertCurve( "resulting fit of the model" );
	- this->SetCurveData( curveId, vec(xvals), vec(yvals) );
	- this->SetCurvePen( curveId, pen );
	- this->SetCurveAntialiasingOn( curveId );
	- }
	-
	- // plot points after all curves to force prettier legend formatting
	- // lines
	- // points
	- curveId = this->InsertCurve( "ignored measurement points" );
	- this->SetCurveData( curveId, vec(snap.bvalues), vec(snap.allmeas) );
	- this->SetCurvePen( curveId, QPen(Qt::NoPen) );
	- QwtSymbol* whiteSymbol = new QwtSymbol(QwtSymbol::Diamond, QColor(Qt::white), QColor(Qt::black), QSize(8,8));
	- this->SetCurveSymbol(curveId, whiteSymbol);
	-
	- curveId = this->InsertCurve( "points first fit" );
	- this->SetCurveData( curveId, vec(snap.bvals1), vec(snap.meas1) );
	- this->SetCurvePen( curveId, QPen( Qt::NoPen ) );
	- QwtSymbol* redSymbol = new QwtSymbol(QwtSymbol::Diamond, QColor(Qt::red), QColor(Qt::red), QSize(8,8));
	- this->SetCurveSymbol(curveId, redSymbol);
	-
	- if(snap.currentDStar != 0)
	- {
	- curveId = this->InsertCurve( "additional points second fit" );
	- this->SetCurveData( curveId, vec(snap.bvals2), vec(snap.meas2) );
	- this->SetCurvePen( curveId, QPen( Qt::NoPen ) );
	- QwtSymbol* blackSymbol = new QwtSymbol(QwtSymbol::Diamond, QColor(Qt::black), QColor(Qt::black), QSize(8,8));
	- this->SetCurveSymbol(curveId, blackSymbol);
	- }
	-
	- auto legend = new QwtLegend();
	- m_Plot->insertLegend(legend, QwtPlot::BottomLegend);
	-
	- this->Replot();
	-
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/QmitkIVIMWidget.h b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/QmitkIVIMWidget.h
	deleted file mode 100644
	index f3da316d1c..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/QmitkIVIMWidget.h
	+++ /dev/null
	@@ -1,58 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef QmitkIVIMWidget_H_
	-#define QmitkIVIMWidget_H_
	-
	-#include "QmitkPlotWidget.h"
	-
	-#include "mitkImage.h"
	-
	-#include "itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.h"
	-
	-
	-/**
	- * \brief Widget for displaying image histograms based on the vtkQtChart
	- * framework
	- */
	-class QmitkIVIMWidget : public QmitkPlotWidget
	-{
	-
	-public:
	-
	- typedef itk::DiffusionIntravoxelIncoherentMotionReconstructionImageFilter<short, float> IVIMFilterType;
	-
	- typedef mitk::Image::HistogramType HistogramType;
	- typedef mitk::Image::HistogramType::ConstIterator HistogramConstIteratorType;
	-
	- void SetParameters( IVIMFilterType::IVIMSnapshot snap );
	-
	- QmitkIVIMWidget( QWidget * /parent = 0 /);
	- virtual ~QmitkIVIMWidget();
	-
	- void DrawGauss();
	-
	- void ClearItemModel();
	-
	- std::vector< std::vector<double>* > m_Vals;
	-
	-private:
	-
	- std::vector<double> vec(const vnl_vector<double>& vector);
	-
	-};
	-
	-#endif /* QmitkIVIMWidget_H_ */
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/QmitkKurtosisWidget.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/QmitkKurtosisWidget.cpp
	deleted file mode 100644
	index 8c963068a8..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/QmitkKurtosisWidget.cpp
	+++ /dev/null
	@@ -1,161 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkKurtosisWidget.h"
	-
	-#include <qwt_scale_engine.h>
	-#include <qwt_legend.h>
	-
	-QmitkKurtosisWidget::QmitkKurtosisWidget(QWidget *parent)
	- : QmitkPlotWidget(parent)
	-{
	- QFrame* canvas = qobject_cast< QFrame* >( m_Plot->canvas() );
	- if( canvas )
	- {
	- canvas->setLineWidth(0);
	- canvas->setContentsMargins(0, 0, 0, 0);
	- }
	-
	-}
	-
	-QmitkKurtosisWidget::~QmitkKurtosisWidget()
	-{
	-
	-}
	-
	-
	-void QmitkKurtosisWidget::SetData(KurtosisFilterType::KurtosisSnapshot snap)
	-{
	- this->Clear();
	-
	- if( snap.bvalues.empty() )
	- return;
	-
	- double max_y_val = 1.4 * fmax( snap.measurements[0], snap.m_BzeroFit );
	-
	- auto logScale = new QwtLogScaleEngine();
	- m_Plot->setAxisScaleEngine(0, logScale );
	- m_Plot->setAxisScale(0, 0.1, max_y_val );
	-
	- QString s("D=%1, K=%2");
	- s = s.arg( snap.m_D, 4); s = s.arg( snap.m_K, 4);
	-
	- // insert formatted value string to legend (curve without pen)
	- int curveId = this->InsertCurve( s.toLatin1(), QColor( Qt::black ) );
	- this->SetCurvePen( curveId, QPen( Qt::NoPen ) );
	-
	- QPen pen;
	- pen.setColor( QColor( Qt::red ));
	- pen.setWidth(2);
	- pen.setStyle( Qt::PenStyle::DashLine );
	-
	- // get the x-axis maximum
	- const double max_bvalue = snap.bvalues.max_value();
	-
	- //
	- // Data-points
	- //
	- auto measured_values = toStdVec( snap.measurements );
	- double y_bzero = measured_values[0];
	-
	- if( snap.m_fittedBZero )
	- {
	- /*auto c_measurements_curve = this->InsertCurve( "Corrected measured values with fitted b=0" );
	- this->SetCurveData( c_measurements_curve, toStdVec( snap.fit_bvalues ), toStdVec( snap.fit_measurements / snap.m_BzeroFit ) );
	- this->SetCurvePen( c_measurements_curve, QPen(Qt::NoPen) );
	- QwtSymbol* whiteDiamond = new QwtSymbol(QwtSymbol::Diamond, QColor(Qt::white), QColor(Qt::black), QSize(8,8));
	- this->SetCurveSymbol( c_measurements_curve, whiteDiamond );*/
	-
	- std::vector<double> single_bzero;
	- single_bzero.push_back(0);
	-
	- std::vector<double> fitted_bzero;
	- fitted_bzero.push_back( snap.m_BzeroFit );
	-
	- auto c_measurements_bzero = this->InsertCurve( "Fitted b=0" );
	- this->SetCurveData( c_measurements_bzero, single_bzero, fitted_bzero );
	- this->SetCurvePen( c_measurements_bzero, QPen(Qt::NoPen) );
	- QwtSymbol* blackDiamond = new QwtSymbol(QwtSymbol::Diamond, QColor(Qt::black), QColor(Qt::black), QSize(8,8));
	- this->SetCurveSymbol( c_measurements_bzero, blackDiamond );
	-
	- y_bzero = snap.m_BzeroFit;
	-
	- MITK_DEBUG("Kurtosis.Widget.Bzero") << "[Fitted] " << snap.m_BzeroFit << ": [Measured] " << snap.measurements[0];
	- }
	-
	-
	- auto measurements_curve = this->InsertCurve( "Measured values" );
	- this->SetCurveData( measurements_curve, toStdVec( snap.bvalues ), measured_values );
	- this->SetCurvePen( measurements_curve, QPen(Qt::NoPen) );
	- QwtSymbol* redDiamond = new QwtSymbol(QwtSymbol::Diamond, QColor(Qt::red), QColor(Qt::red), QSize(8,8));
	- this->SetCurveSymbol( measurements_curve, redDiamond );
	-
	- //
	- // Kurtosis - full modelled signal
	- //
	- pen.setColor( QColor( Qt::black ));
	- pen.setStyle( Qt::SolidLine );
	- const unsigned int num_samples = 50;
	-
	- vnl_vector<double> x_K_model(num_samples);
	- vnl_vector<double> y_K_model(num_samples);
	-
	- vnl_vector<double> y_D_model(num_samples);
	-
	- const double x_tics_offset = max_bvalue / static_cast<double>( num_samples );
	-
	- for( unsigned int i=0; i<num_samples; ++i)
	- {
	- x_K_model[i] = i * x_tics_offset;
	-
	- double bval = x_K_model[i];
	- y_K_model[i] = y_bzero * exp( -bval * snap.m_D + bvalbval snap.m_D * snap.m_D * snap.m_K / 6.0 );
	- y_D_model[i] = y_bzero * exp( -bval * snap.m_D );
	- }
	-
	- auto kurtosis_curve = this->InsertCurve( "Resulting fit of the model" );
	- this->SetCurveData( kurtosis_curve, toStdVec( x_K_model ), toStdVec( y_K_model ) );
	- this->SetCurvePen( kurtosis_curve, pen );
	- this->SetCurveAntialiasingOn( kurtosis_curve );
	-
	- auto d_curve = this->InsertCurve( "D-part of the fitted model" );
	- this->SetCurveData( d_curve, toStdVec( x_K_model ), toStdVec( y_D_model ) );
	-
	- pen.setColor( QColor( Qt::red));
	- pen.setStyle( Qt::PenStyle::DashLine );
	- this->SetCurvePen( d_curve, pen );
	- this->SetCurveAntialiasingOn( d_curve );
	-
	- //
	- // add Legend
	- //
	- auto legend = new QwtLegend();
	- legend->setMaxColumns(3);
	- m_Plot->insertLegend( legend, QwtPlot::BottomLegend );
	-
	- this->Replot();
	-}
	-
	-std::vector<double> QmitkKurtosisWidget::toStdVec(const vnl_vector<double>& vector)
	-{
	- std::vector<double> retval(vector.size());
	- for(unsigned int i=0; i<vector.size(); i++)
	- {
	- retval.at(i) = vector[i];
	- }
	- return retval;
	-}
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/QmitkKurtosisWidget.h b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/QmitkKurtosisWidget.h
	deleted file mode 100644
	index 8da35fa1c6..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/QmitkKurtosisWidget.h
	+++ /dev/null
	@@ -1,45 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef QMITKKURTOSISWIDGET_H
	-#define QMITKKURTOSISWIDGET_H
	-
	-#include "QmitkPlotWidget.h"
	-
	-#include "itkDiffusionKurtosisReconstructionImageFilter.h"
	-
	-
	-class QmitkKurtosisWidget : public QmitkPlotWidget
	-{
	-public:
	-
	- typedef itk::DiffusionKurtosisReconstructionImageFilter<short, float> KurtosisFilterType;
	-
	- QmitkKurtosisWidget( QWidget* /* parent */);
	- virtual ~QmitkKurtosisWidget();
	-
	- void SetData( KurtosisFilterType::KurtosisSnapshot snap );
	-
	- std::vector< std::vector<double>* > m_Vals;
	-
	-private:
	-
	- std::vector<double> toStdVec(const vnl_vector<double>& vector);
	-
	-};
	-
	-#endif // QMITKKURTOSISWIDGET_H
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/Perspectives/QmitkDIAppIVIMPerspective.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/Perspectives/QmitkDIAppIVIMPerspective.cpp
	deleted file mode 100644
	index a5c930c5e2..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/Perspectives/QmitkDIAppIVIMPerspective.cpp
	+++ /dev/null
	@@ -1,46 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkDIAppIVIMPerspective.h"
	-#include "berryIViewLayout.h"
	-
	-void QmitkDIAppIVIMPerspective::CreateInitialLayout(berry::IPageLayout::Pointer layout)
	-{
	- /////////////////////////////////////////////////////
	- // all di-app perspectives should have the following:
	- /////////////////////////////////////////////////////
	-
	- QString editorArea = layout->GetEditorArea();
	-
	- layout->AddStandaloneViewPlaceholder("org.mitk.views.viewnavigatorview", berry::IPageLayout::LEFT, 0.3f, editorArea, false);
	-
	- layout->AddStandaloneView("org.mitk.views.datamanager", false, berry::IPageLayout::LEFT, 0.3f, editorArea);
	-
	- layout->AddStandaloneView("org.mitk.views.controlvisualizationpropertiesview", false, berry::IPageLayout::BOTTOM, .15f, "org.mitk.views.datamanager");
	-
	- berry::IFolderLayout::Pointer left =
	- layout->CreateFolder("org.mbi.diffusionimaginginternal.leftcontrols", berry::IPageLayout::BOTTOM, 0.15f, "org.mitk.views.controlvisualizationpropertiesview");
	-
	- layout->AddStandaloneViewPlaceholder("org.mitk.views.imagenavigator", berry::IPageLayout::BOTTOM, .7f, "org.mbi.diffusionimaginginternal.leftcontrols", false);
	-
	- /////////////////////////////////////////////
	- // here goes the perspective specific stuff
	- /////////////////////////////////////////////
	-
	- left->AddView("org.mitk.views.ivim");
	- left->AddView("org.mitk.views.segmentation");
	- left->AddView("org.mitk.views.imagestatistics");
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/Perspectives/QmitkDIAppIVIMPerspective.h b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/Perspectives/QmitkDIAppIVIMPerspective.h
	deleted file mode 100644
	index 79997d2e37..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/Perspectives/QmitkDIAppIVIMPerspective.h
	+++ /dev/null
	@@ -1,36 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef QmitkDIAppIVIMPerspective_H_
	-#define QmitkDIAppIVIMPerspective_H_
	-
	-#include <berryIPerspectiveFactory.h>
	-
	-class QmitkDIAppIVIMPerspective : public QObject, public berry::IPerspectiveFactory
	-{
	- Q_OBJECT
	- Q_INTERFACES(berry::IPerspectiveFactory)
	-
	-public:
	-
	- QmitkDIAppIVIMPerspective() {}
	- ~QmitkDIAppIVIMPerspective() {}
	-
	- void CreateInitialLayout(berry::IPageLayout::Pointer layout) override;
	-};
	-
	-#endif /* QmitkDIAppIVIMPerspective_H_ */
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/QmitkIVIMView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/QmitkIVIMView.cpp
	deleted file mode 100644
	index 6b84a4c707..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/QmitkIVIMView.cpp
	+++ /dev/null
	@@ -1,928 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-// Blueberry
	-#include <berryISelectionService.h>
	-#include <berryIWorkbenchWindow.h>
	-
	-// Qmitk
	-#include "QmitkIVIMView.h"
	-
	-// qt
	-#include "qmessagebox.h"
	-#include "qclipboard.h"
	-
	-// mitk
	-#include "mitkImage.h"
	-#include "mitkImageCast.h"
	-
	-#include "mitkLookupTable.h"
	-#include "mitkLookupTableProperty.h"
	-#include <mitkSliceNavigationController.h>
	-#include <QmitkRenderWindow.h>
	-
	-// itk
	-#include "itkScalarImageToHistogramGenerator.h"
	-#include "itkRegionOfInterestImageFilter.h"
	-#include "itkImageRegionConstIteratorWithIndex.h"
	-
	-// itk/mitk
	-#include "itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.h"
	-#include "itkRegularizedIVIMReconstructionFilter.h"
	-#include "mitkImageCast.h"
	-#include <mitkImageStatisticsHolder.h>
	-#include <mitkNodePredicateIsDWI.h>
	-#include <mitkNodePredicateDimension.h>
	-#include <mitkNodePredicateProperty.h>
	-#include <mitkNodePredicateAnd.h>
	-#include <mitkNodePredicateDataType.h>
	-
	-const std::string QmitkIVIMView::VIEW_ID = "org.mitk.views.ivim";
	-
	-QmitkIVIMView::QmitkIVIMView()
	- : QmitkAbstractView()
	- , m_Controls( 0 )
	- , m_Active(false)
	- , m_Visible(false)
	- , m_HoldUpdate(false)
	-{
	-}
	-
	-QmitkIVIMView::~QmitkIVIMView()
	-{
	-}
	-
	-void QmitkIVIMView::CreateQtPartControl( QWidget *parent )
	-{
	- // hold update untill all elements are set
	- this->m_HoldUpdate = true;
	-
	- // build up qt view, unless already done
	- if ( !m_Controls )
	- {
	- // create GUI widgets from the Qt Designer's .ui file
	- m_Controls = new Ui::QmitkIVIMViewControls;
	- m_Controls->setupUi( parent );
	-
	- connect( m_Controls->m_ButtonStart, SIGNAL(clicked()), this, SLOT(FittIVIMStart()) );
	- connect( m_Controls->m_ButtonAutoThres, SIGNAL(clicked()), this, SLOT(AutoThreshold()) );
	-
	- connect( m_Controls->m_MethodCombo, SIGNAL(currentIndexChanged(int)), this, SLOT(MethodCombo(int)) );
	-
	- connect( m_Controls->m_DStarSlider, SIGNAL(valueChanged(int)), this, SLOT(DStarSlider(int)) );
	- connect( m_Controls->m_BThreshSlider, SIGNAL(valueChanged(int)), this, SLOT(BThreshSlider(int)) );
	- connect( m_Controls->m_S0ThreshSlider, SIGNAL(valueChanged(int)), this, SLOT(S0ThreshSlider(int)) );
	- connect( m_Controls->m_NumItSlider, SIGNAL(valueChanged(int)), this, SLOT(NumItsSlider(int)) );
	- connect( m_Controls->m_LambdaSlider, SIGNAL(valueChanged(int)), this, SLOT(LambdaSlider(int)) );
	-
	- connect( m_Controls->m_CheckDStar, SIGNAL(clicked()), this, SLOT(Checkbox()) );
	- connect( m_Controls->m_CheckD, SIGNAL(clicked()), this, SLOT(Checkbox()) );
	- connect( m_Controls->m_Checkf, SIGNAL(clicked()), this, SLOT(Checkbox()) );
	-
	- connect( m_Controls->m_ChooseMethod, SIGNAL(clicked()), this, SLOT(ChooseMethod()) );
	- connect( m_Controls->m_CurveClipboard, SIGNAL(clicked()), this, SLOT(ClipboardCurveButtonClicked()) );
	- connect( m_Controls->m_ValuesClipboard, SIGNAL(clicked()), this, SLOT(ClipboardStatisticsButtonClicked()) );
	-
	- // connect all kurtosis actions to a recompute
	- connect( m_Controls->m_KurtosisRangeWidget, SIGNAL( rangeChanged(double, double)), this, SLOT(OnKurtosisParamsChanged() ) );
	- //connect( m_Controls->m_MaximalBValueWidget, SIGNAL( valueChanged(double)), this, SLOT( OnKurtosisParamsChanged() ) );
	- connect( m_Controls->m_OmitBZeroCB, SIGNAL( stateChanged(int) ), this, SLOT( OnKurtosisParamsChanged() ) );
	- connect( m_Controls->m_KurtosisFitScale, SIGNAL( currentIndexChanged(int)), this, SLOT( OnKurtosisParamsChanged() ) );
	- connect( m_Controls->m_UseKurtosisBoundsCB, SIGNAL(clicked() ), this, SLOT( OnKurtosisParamsChanged() ) );
	-
	- m_SliceChangeListener.RenderWindowPartActivated(this->GetRenderWindowPart());
	- connect(&m_SliceChangeListener, SIGNAL(SliceChanged()), this, SLOT(OnSliceChanged()));
	-
	-
	- m_Controls->m_DwiBox->SetDataStorage(this->GetDataStorage());
	- mitk::NodePredicateIsDWI::Pointer isDwi = mitk::NodePredicateIsDWI::New();
	- m_Controls->m_DwiBox->SetPredicate( isDwi );
	- connect( (QObject*)(m_Controls->m_DwiBox), SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui()));
	-
	- m_Controls->m_MaskBox->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_MaskBox->SetZeroEntryText("--");
	- mitk::TNodePredicateDataType<mitk::Image>::Pointer isImagePredicate = mitk::TNodePredicateDataType<mitk::Image>::New();
	- mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true));
	- mitk::NodePredicateDimension::Pointer is3D = mitk::NodePredicateDimension::New(3);
	- m_Controls->m_MaskBox->SetPredicate( mitk::NodePredicateAnd::New(isBinaryPredicate, mitk::NodePredicateAnd::New(isImagePredicate, is3D)) );
	- connect( (QObject*)(m_Controls->m_MaskBox), SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui()));
	-
	- connect( (QObject*)(m_Controls->m_ModelTabSelectionWidget), SIGNAL(currentChanged(int)), this, SLOT(UpdateGui()));
	-
	- }
	-
	- QString dstar = QString::number(m_Controls->m_DStarSlider->value()/1000.0);
	- m_Controls->m_DStarLabel->setText(dstar);
	-
	- QString bthresh = QString::number(m_Controls->m_BThreshSlider->value()*5.0);
	- m_Controls->m_BThreshLabel->setText(bthresh);
	-
	- QString s0thresh = QString::number(m_Controls->m_S0ThreshSlider->value()*0.5);
	- m_Controls->m_S0ThreshLabel->setText(s0thresh);
	-
	- QString numits = QString::number(m_Controls->m_NumItSlider->value());
	- m_Controls->m_NumItsLabel->setText(numits);
	-
	- QString lambda = QString::number(m_Controls->m_LambdaSlider->value()*.00001);
	- m_Controls->m_LambdaLabel->setText(lambda);
	-
	- m_Controls->m_MethodCombo->setVisible(m_Controls->m_ChooseMethod->isChecked());
	- m_Controls->m_Warning->setVisible(false);
	-
	- MethodCombo(m_Controls->m_MethodCombo->currentIndex());
	-
	- m_Controls->m_KurtosisRangeWidget->setSingleStep(0.1);
	- m_Controls->m_KurtosisRangeWidget->setRange( 0.0, 10.0 );
	- m_Controls->m_KurtosisRangeWidget->setMaximumValue( 5.0 );
	-
	- // LogScale not working yet, have to fix that first
	- // m_Controls->m_KurtosisFitScale->setEnabled(false);
	-
	-
	- //m_Controls->m_MaximalBValueWidget->setVisible( false );
	-
	- // release update block after the UI-elements were all set
	- this->m_HoldUpdate = false;
	-
	-}
	-
	-void QmitkIVIMView::SetFocus()
	-{
	- m_Controls->m_ButtonAutoThres->setFocus();
	-}
	-
	-void QmitkIVIMView::Checkbox()
	-{
	- OnSliceChanged();
	-}
	-
	-void QmitkIVIMView::MethodCombo(int val)
	-{
	- switch(val)
	- {
	- case 0:
	- m_Controls->m_DstarFrame->setVisible(false);
	- m_Controls->m_NeglSiFrame->setVisible(true);
	- m_Controls->m_NeglBframe->setVisible(false);
	- m_Controls->m_IterationsFrame->setVisible(false);
	- m_Controls->m_LambdaFrame->setVisible(false);
	- break;
	- case 1:
	- m_Controls->m_DstarFrame->setVisible(true);
	- m_Controls->m_NeglSiFrame->setVisible(true);
	- m_Controls->m_NeglBframe->setVisible(false);
	- m_Controls->m_IterationsFrame->setVisible(false);
	- m_Controls->m_LambdaFrame->setVisible(false);
	- break;
	- case 2:
	- m_Controls->m_DstarFrame->setVisible(false);
	- m_Controls->m_NeglSiFrame->setVisible(true);
	- m_Controls->m_NeglBframe->setVisible(true);
	- m_Controls->m_IterationsFrame->setVisible(false);
	- m_Controls->m_LambdaFrame->setVisible(false);
	- break;
	- case 3:
	- m_Controls->m_DstarFrame->setVisible(false);
	- m_Controls->m_NeglSiFrame->setVisible(true);
	- m_Controls->m_NeglBframe->setVisible(true);
	- m_Controls->m_IterationsFrame->setVisible(false);
	- m_Controls->m_LambdaFrame->setVisible(false);
	- break;
	- case 4:
	- m_Controls->m_DstarFrame->setVisible(false);
	- m_Controls->m_NeglSiFrame->setVisible(false);
	- m_Controls->m_NeglBframe->setVisible(false);
	- m_Controls->m_IterationsFrame->setVisible(false);
	- m_Controls->m_LambdaFrame->setVisible(false);
	- break;
	- }
	-
	- OnSliceChanged();
	-}
	-
	-void QmitkIVIMView::DStarSlider (int val)
	-{
	- QString sval = QString::number(val/1000.0);
	- m_Controls->m_DStarLabel->setText(sval);
	-
	- OnSliceChanged();
	-}
	-
	-void QmitkIVIMView::BThreshSlider (int val)
	-{
	- QString sval = QString::number(val*5.0);
	- m_Controls->m_BThreshLabel->setText(sval);
	-
	- OnSliceChanged();
	-}
	-
	-void QmitkIVIMView::S0ThreshSlider (int val)
	-{
	- QString sval = QString::number(val*0.5);
	- m_Controls->m_S0ThreshLabel->setText(sval);
	-
	- OnSliceChanged();
	-}
	-
	-void QmitkIVIMView::NumItsSlider (int val)
	-{
	- QString sval = QString::number(val);
	- m_Controls->m_NumItsLabel->setText(sval);
	-
	- OnSliceChanged();
	-}
	-
	-void QmitkIVIMView::LambdaSlider (int val)
	-{
	- QString sval = QString::number(val*.00001);
	- m_Controls->m_LambdaLabel->setText(sval);
	-
	- OnSliceChanged();
	-}
	-
	-void QmitkIVIMView::UpdateGui()
	-{
	- if (m_Controls->m_DwiBox->GetSelectedNode().IsNotNull())
	- {
	- m_Controls->m_VisualizeResultsWidget->setVisible(true);
	- m_Controls->m_KurtosisVisualizationWidget->setVisible(true);
	-
	- m_HoldUpdate = false;
	- }
	- else
	- {
	- m_Controls->m_VisualizeResultsWidget->setVisible(false);
	- m_Controls->m_KurtosisVisualizationWidget->setVisible(false);
	- }
	-
	- m_Controls->m_ButtonStart->setEnabled( m_Controls->m_DwiBox->GetSelectedNode().IsNotNull() );
	- m_Controls->m_ButtonAutoThres->setEnabled( m_Controls->m_DwiBox->GetSelectedNode().IsNotNull() );
	-
	- m_Controls->m_ControlsFrame->setEnabled( m_Controls->m_DwiBox->GetSelectedNode().IsNotNull() );
	- m_Controls->m_BottomControlsFrame->setEnabled( m_Controls->m_DwiBox->GetSelectedNode().IsNotNull() );
	-
	- OnSliceChanged();
	-}
	-
	-void QmitkIVIMView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /part/, const QList<mitk::DataNode::Pointer>& )
	-{
	- UpdateGui();
	-}
	-
	-void QmitkIVIMView::AutoThreshold()
	-{
	- if (m_Controls->m_DwiBox->GetSelectedNode().IsNull())
	- {
	- // Nothing selected. Inform the user and return
	- QMessageBox::information( nullptr, "Template", "Please load and select a diffusion image before starting image processing.");
	- return;
	- }
	-
	- mitk::Image* dimg = dynamic_cast<mitk::Image*>(m_Controls->m_DwiBox->GetSelectedNode()->GetData());
	-
	- if (!dimg)
	- {
	- // Nothing selected. Inform the user and return
	- QMessageBox::information( nullptr, "Template", "No valid diffusion image was found.");
	- return;
	- }
	-
	- // find bzero index
	- int index = -1;
	- auto directions = mitk::DiffusionPropertyHelper::GetGradientContainer(dimg);
	- for(DirContainerType::ConstIterator it = directions->Begin();
	- it != directions->End(); ++it)
	- {
	- index++;
	- GradientDirectionType g = it.Value();
	- if(g[0] == 0 && g[1] == 0 && g[2] == 0 )
	- break;
	- }
	-
	- VecImgType::Pointer vecimg = VecImgType::New();
	- mitk::CastToItkImage(dimg, vecimg);
	-
	- int vecLength = vecimg->GetVectorLength();
	- index = index > vecLength-1 ? vecLength-1 : index;
	-
	- MITK_INFO << "Performing Histogram Analysis on Channel" << index;
	-
	- typedef itk::Image<short,3> ImgType;
	- ImgType::Pointer img = ImgType::New();
	- mitk::CastToItkImage(dimg, img);
	-
	- itk::ImageRegionIterator<ImgType> itw (img, img->GetLargestPossibleRegion() );
	- itw.GoToBegin();
	-
	- itk::ImageRegionConstIterator<VecImgType> itr (vecimg, vecimg->GetLargestPossibleRegion() );
	- itr.GoToBegin();
	-
	- while(!itr.IsAtEnd())
	- {
	- itw.Set(itr.Get().GetElement(index));
	- ++itr;
	- ++itw;
	- }
	-
	- typedef itk::Statistics::ScalarImageToHistogramGenerator< ImgType >
	- HistogramGeneratorType;
	- typedef HistogramGeneratorType::HistogramType HistogramType;
	-
	- HistogramGeneratorType::Pointer histogramGenerator = HistogramGeneratorType::New();
	- histogramGenerator->SetInput( img );
	- histogramGenerator->SetMarginalScale( 10 ); // Defines y-margin width of histogram
	- histogramGenerator->SetNumberOfBins( 100 ); // CT range [-1024, +2048] --> bin size 4 values
	- histogramGenerator->SetHistogramMin( dimg->GetStatistics()->GetScalarValueMin() );
	- histogramGenerator->SetHistogramMax( dimg->GetStatistics()->GetScalarValueMax() * .5 );
	- histogramGenerator->Compute();
	-
	- HistogramType::ConstIterator iter = histogramGenerator->GetOutput()->Begin();
	- float maxFreq = 0;
	- float maxValue = 0;
	- while ( iter != histogramGenerator->GetOutput()->End() )
	- {
	- if(iter.GetFrequency() > maxFreq)
	- {
	- maxFreq = iter.GetFrequency();
	- maxValue = iter.GetMeasurementVector()[0];
	- }
	- ++iter;
	- }
	-
	- maxValue *= 2;
	-
	- int sliderPos = maxValue * 2;
	- m_Controls->m_S0ThreshSlider->setValue(sliderPos);
	- S0ThreshSlider(sliderPos);
	-}
	-
	-void QmitkIVIMView::FittIVIMStart()
	-{
	- if (m_Controls->m_DwiBox->GetSelectedNode().IsNull())
	- {
	- QMessageBox::information( nullptr, "Template", "No valid diffusion-weighted image selected.");
	- return;
	- }
	- mitk::Image* img = dynamic_cast<mitk::Image*>(m_Controls->m_DwiBox->GetSelectedNode()->GetData());
	-
	-
	- VecImgType::Pointer vecimg = VecImgType::New();
	- mitk::CastToItkImage(img, vecimg);
	-
	- OutImgType::IndexType dummy;
	-
	- if( m_Controls->m_ModelTabSelectionWidget->currentIndex() )
	- {
	- // KURTOSIS
	- KurtosisFilterType::Pointer filter = KurtosisFilterType::New();
	- filter->SetInput(vecimg);
	- filter->SetReferenceBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(img));
	- filter->SetGradientDirections(mitk::DiffusionPropertyHelper::GetGradientContainer(img));
	- filter->SetSmoothingSigma( this->m_Controls->m_SigmaSpinBox->value() );
	-
	- if( this->m_Controls->m_UseKurtosisBoundsCB->isChecked() )
	- filter->SetBoundariesForKurtosis( this->m_Controls->m_KurtosisRangeWidget->minimumValue(), this->m_Controls->m_KurtosisRangeWidget->maximumValue() );
	-
	- filter->SetFittingScale( static_cast<itk::FitScale>(this->m_Controls->m_KurtosisFitScale->currentIndex() ) );
	-
	- if( m_Controls->m_MaskBox->GetSelectedNode().IsNotNull() )
	- {
	- mitk::Image::Pointer maskImg = dynamic_cast<mitk::Image*>(m_Controls->m_MaskBox->GetSelectedNode()->GetData());
	- typedef itk::Image<short, 3> MaskImgType;
	-
	- MaskImgType::Pointer maskItk;
	- CastToItkImage( maskImg, maskItk );
	-
	- filter->SetImageMask( maskItk );
	- }
	-
	- filter->Update();
	-
	- mitk::LookupTable::Pointer kurt_map_lut = mitk::LookupTable::New();
	- kurt_map_lut->SetType( mitk::LookupTable::JET_TRANSPARENT );
	- mitk::LookupTableProperty::Pointer kurt_lut_prop =
	- mitk::LookupTableProperty::New();
	- kurt_lut_prop->SetLookupTable( kurt_map_lut );
	-
	- mitk::Image::Pointer dimage = mitk::Image::New();
	- dimage->InitializeByItk( filter->GetOutput(0) );
	- dimage->SetVolume( filter->GetOutput(0)->GetBufferPointer());
	-
	- mitk::Image::Pointer kimage = mitk::Image::New();
	- kimage->InitializeByItk( filter->GetOutput(1) );
	- kimage->SetVolume( filter->GetOutput(1)->GetBufferPointer());
	-
	- QString new_dname = "Kurtosis_DMap";
	- new_dname.append("_Method-"+m_Controls->m_KurtosisFitScale->currentText());
	- QString new_kname = "Kurtosis_KMap";
	- new_kname.append("_Method-"+m_Controls->m_KurtosisFitScale->currentText());
	-
	- if( this->m_Controls->m_CheckKurtD->isChecked() )
	- {
	- mitk::DataNode::Pointer dnode = mitk::DataNode::New();
	- dnode->SetData( dimage );
	- dnode->SetName(new_dname.toLatin1());
	- dnode->SetProperty("LookupTable", kurt_lut_prop );
	- GetDataStorage()->Add(dnode, m_Controls->m_DwiBox->GetSelectedNode());
	- }
	-
	- if( this->m_Controls->m_CheckKurtK->isChecked() )
	- {
	- mitk::DataNode::Pointer knode = mitk::DataNode::New();
	- knode->SetData( kimage );
	- knode->SetName(new_kname.toLatin1());
	- knode->SetProperty("LookupTable", kurt_lut_prop );
	- GetDataStorage()->Add(knode, m_Controls->m_DwiBox->GetSelectedNode());
	- }
	-
	- }
	- else
	- {
	- FittIVIM(vecimg, mitk::DiffusionPropertyHelper::GetGradientContainer(img), mitk::DiffusionPropertyHelper::GetReferenceBValue(img), true, dummy);
	-
	- OutputToDatastorage(m_Controls->m_DwiBox->GetSelectedNode());
	- }
	-}
	-
	-void QmitkIVIMView::OnKurtosisParamsChanged()
	-{
	- OnSliceChanged();
	-}
	-
	-void QmitkIVIMView::OnSliceChanged()
	-{
	- if(m_HoldUpdate \|\| !m_Visible)
	- return;
	-
	- m_Controls->m_Warning->setVisible(false);
	- if(!m_Controls \|\| m_Controls->m_DwiBox->GetSelectedNode().IsNull())
	- return;
	-
	- m_Controls->m_VisualizeResultsWidget->setVisible(false);
	- m_Controls->m_KurtosisVisualizationWidget->setVisible(false);
	-
	- mitk::Image::Pointer diffusionImg = dynamic_cast<mitk::Image*>(m_Controls->m_DwiBox->GetSelectedNode()->GetData());
	- mitk::Image::Pointer maskImg = nullptr;
	- if (m_Controls->m_MaskBox->GetSelectedNode().IsNotNull())
	- maskImg = dynamic_cast<mitk::Image*>(m_Controls->m_MaskBox->GetSelectedNode()->GetData());
	-
	- if (!this->GetRenderWindowPart()) return;
	-
	- VecImgType::Pointer vecimg = VecImgType::New();
	- mitk::CastToItkImage(diffusionImg, vecimg);
	-
	- VecImgType::Pointer roiImage = VecImgType::New();
	-
	- bool success = false;
	- if(maskImg.IsNull())
	- {
	- int roisize = 0;
	- if(m_Controls->m_MethodCombo->currentIndex() == 4)
	- roisize = 5;
	-
	- mitk::Point3D pos = this->GetRenderWindowPart()->GetSelectedPosition();
	-
	- VecImgType::IndexType crosspos;
	- diffusionImg->GetGeometry()->WorldToIndex(pos, crosspos);
	- if (!vecimg->GetLargestPossibleRegion().IsInside(crosspos))
	- {
	- m_Controls->m_Warning->setText(QString("Crosshair position not inside of selected diffusion weighted image. Reinit needed!"));
	- m_Controls->m_Warning->setVisible(true);
	- return;
	- }
	- else
	- m_Controls->m_Warning->setVisible(false);
	-
	- VecImgType::IndexType index;
	- index[0] = crosspos[0] - roisize; index[0] = index[0] < 0 ? 0 : index[0];
	- index[1] = crosspos[1] - roisize; index[1] = index[1] < 0 ? 0 : index[1];
	- index[2] = crosspos[2] - roisize; index[2] = index[2] < 0 ? 0 : index[2];
	-
	- VecImgType::SizeType size;
	- size[0] = roisize*2+1;
	- size[1] = roisize*2+1;
	- size[2] = roisize*2+1;
	-
	- VecImgType::SizeType maxSize = vecimg->GetLargestPossibleRegion().GetSize();
	- size[0] = index[0]+size[0] > maxSize[0] ? maxSize[0]-index[0] : size[0];
	- size[1] = index[1]+size[1] > maxSize[1] ? maxSize[1]-index[1] : size[1];
	- size[2] = index[2]+size[2] > maxSize[2] ? maxSize[2]-index[2] : size[2];
	-
	- VecImgType::RegionType region;
	- region.SetSize( size );
	- region.SetIndex( index );
	- vecimg->SetRequestedRegion( region );
	-
	- VecImgType::IndexType newstart;
	- newstart.Fill(0);
	-
	- VecImgType::RegionType newregion;
	- newregion.SetSize( size );
	- newregion.SetIndex( newstart );
	-
	- roiImage->CopyInformation( vecimg );
	- roiImage->SetRegions( newregion );
	- roiImage->SetOrigin( pos );
	- roiImage->Allocate();
	- roiImage->SetPixel(newstart, vecimg->GetPixel(index));
	-
	- if( m_Controls->m_ModelTabSelectionWidget->currentIndex() )
	- {
	- success = FitKurtosis(roiImage,
	- mitk::DiffusionPropertyHelper::GetGradientContainer(diffusionImg),
	- mitk::DiffusionPropertyHelper::GetReferenceBValue(diffusionImg),
	- newstart);
	- }
	- else
	- {
	- success = FittIVIM(roiImage,
	- mitk::DiffusionPropertyHelper::GetGradientContainer(diffusionImg),
	- mitk::DiffusionPropertyHelper::GetReferenceBValue(diffusionImg),
	- false,
	- crosspos);
	- }
	- }
	- else
	- {
	- typedef itk::Image<float,3> MaskImgType;
	-
	- MaskImgType::Pointer maskItk;
	- CastToItkImage( maskImg, maskItk );
	-
	- mitk::Point3D pos;
	- pos[0] = 0;
	- pos[1] = 0;
	- pos[2] = 0;
	-
	- VecImgType::IndexType index;
	- index[0] = 0;
	- index[1] = 0;
	- index[2] = 0;
	-
	- VecImgType::SizeType size;
	- size[0] = 1;
	- size[1] = 1;
	- size[2] = 1;
	-
	- VecImgType::RegionType region;
	- region.SetSize( size );
	- region.SetIndex( index );
	- vecimg->SetRequestedRegion( region );
	-
	- // iterators over output and input
	- itk::ImageRegionConstIteratorWithIndex<VecImgType>
	- vecit(vecimg, vecimg->GetLargestPossibleRegion());
	-
	- itk::VariableLengthVector<double> avg(vecimg->GetVectorLength());
	- avg.Fill(0);
	-
	- float numPixels = 0;
	- while ( ! vecit.IsAtEnd() )
	- {
	- VecImgType::PointType point;
	- vecimg->TransformIndexToPhysicalPoint(vecit.GetIndex(), point);
	-
	- MaskImgType::IndexType index;
	- maskItk->TransformPhysicalPointToIndex(point, index);
	-
	- if(maskItk->GetPixel(index) != 0)
	- {
	- avg += vecit.Get();
	- numPixels += 1.0;
	- }
	-
	- // update iterators
	- ++vecit;
	-
	- }
	-
	- avg /= numPixels;
	-
	- m_Controls->m_Warning->setText(QString("Averaging ")+QString::number((int)numPixels)+QString(" voxels!"));
	- m_Controls->m_Warning->setVisible(true);
	-
	- roiImage->CopyInformation( vecimg );
	- roiImage->SetRegions( region );
	- roiImage->SetOrigin( pos );
	- roiImage->Allocate();
	- roiImage->SetPixel(index, avg);
	-
	- if( m_Controls->m_ModelTabSelectionWidget->currentIndex() )
	- {
	- success = FitKurtosis(roiImage,
	- mitk::DiffusionPropertyHelper::GetGradientContainer(diffusionImg),
	- mitk::DiffusionPropertyHelper::GetReferenceBValue(diffusionImg),
	- index);
	- }
	- else
	- {
	- success = FittIVIM(roiImage,
	- mitk::DiffusionPropertyHelper::GetGradientContainer(diffusionImg),
	- mitk::DiffusionPropertyHelper::GetReferenceBValue(diffusionImg),
	- false,
	- index);
	- }
	-
	- // do not update until selection changed, the values will remain the same as long as the mask is selected!
	- m_HoldUpdate = true;
	-
	- }
	-
	- vecimg->SetRegions( vecimg->GetLargestPossibleRegion() );
	-
	- if (success)
	- {
	- // 0 - IVIM, 1 - Kurtosis
	- if( m_Controls->m_ModelTabSelectionWidget->currentIndex() )
	- {
	- m_Controls->m_KurtosisVisualizationWidget->setVisible(true);
	- m_Controls->m_KurtosisVisualizationWidget->SetData(m_KurtosisSnap);
	- }
	- else
	- {
	- m_Controls->m_VisualizeResultsWidget->setVisible(true);
	- m_Controls->m_VisualizeResultsWidget->SetParameters(m_Snap);
	- }
	- }
	-}
	-
	-bool QmitkIVIMView::FitKurtosis( itk::VectorImage<short, 3> vecimg, DirContainerType dirs, float bval, OutImgType::IndexType &crosspos )
	-{
	- KurtosisFilterType::Pointer filter = KurtosisFilterType::New();
	-
	- itk::KurtosisFitConfiguration fit_config;
	- fit_config.omit_bzero = this->m_Controls->m_OmitBZeroCB->isChecked();
	- if( this->m_Controls->m_UseKurtosisBoundsCB->isChecked() )
	- {
	- fit_config.use_K_limits = true;
	- vnl_vector_fixed<double, 2> k_limits;
	- k_limits[0] = this->m_Controls->m_KurtosisRangeWidget->minimumValue();
	- k_limits[1] = this->m_Controls->m_KurtosisRangeWidget->maximumValue();
	-
	- fit_config.K_limits = k_limits;
	-
	- }
	- fit_config.fit_scale = static_cast<itk::FitScale>(this->m_Controls->m_KurtosisFitScale->currentIndex() );
	-
	- m_KurtosisSnap = filter->GetSnapshot( vecimg->GetPixel( crosspos ), dirs, bval, fit_config );
	-
	- return true;
	-}
	-
	-
	-bool QmitkIVIMView::FittIVIM(itk::VectorImage<short,3>* vecimg, DirContainerType* dirs, float bval, bool multivoxel, OutImgType::IndexType &crosspos)
	-{
	- IVIMFilterType::Pointer filter = IVIMFilterType::New();
	- filter->SetInput(vecimg);
	- filter->SetGradientDirections(dirs);
	- filter->SetBValue(bval);
	-
	- switch(m_Controls->m_MethodCombo->currentIndex())
	- {
	-
	- case 0:
	- filter->SetMethod(IVIMFilterType::IVIM_FIT_ALL);
	- filter->SetS0Thres(m_Controls->m_S0ThreshLabel->text().toDouble());
	- break;
	-
	- case 1:
	- filter->SetMethod(IVIMFilterType::IVIM_DSTAR_FIX);
	- filter->SetDStar(m_Controls->m_DStarLabel->text().toDouble());
	- filter->SetS0Thres(m_Controls->m_S0ThreshLabel->text().toDouble());
	- break;
	-
	- case 2:
	- filter->SetMethod(IVIMFilterType::IVIM_D_THEN_DSTAR);
	- filter->SetBThres(m_Controls->m_BThreshLabel->text().toDouble());
	- filter->SetS0Thres(m_Controls->m_S0ThreshLabel->text().toDouble());
	- filter->SetFitDStar(m_Controls->m_CheckDStar->isChecked());
	- break;
	-
	- case 3:
	- filter->SetMethod(IVIMFilterType::IVIM_LINEAR_D_THEN_F);
	- filter->SetBThres(m_Controls->m_BThreshLabel->text().toDouble());
	- filter->SetS0Thres(m_Controls->m_S0ThreshLabel->text().toDouble());
	- filter->SetFitDStar(m_Controls->m_CheckDStar->isChecked());
	- break;
	-
	- case 4:
	- filter->SetMethod(IVIMFilterType::IVIM_REGULARIZED);
	- filter->SetBThres(m_Controls->m_BThreshLabel->text().toDouble());
	- filter->SetS0Thres(m_Controls->m_S0ThreshLabel->text().toDouble());
	- filter->SetNumberIterations(m_Controls->m_NumItsLabel->text().toInt());
	- filter->SetLambda(m_Controls->m_LambdaLabel->text().toDouble());
	- filter->SetFitDStar(m_Controls->m_CheckDStar->isChecked());
	- break;
	- }
	-
	- if(!multivoxel)
	- {
	- filter->SetFitDStar(true);
	- }
	-
	- filter->SetNumberOfThreads(1);
	- filter->SetVerbose(false);
	- filter->SetCrossPosition(crosspos);
	-
	- try{
	- filter->Update();
	- m_Snap = filter->GetSnapshot();
	- m_DStarMap = filter->GetOutput(2);
	- m_DMap = filter->GetOutput(1);
	- m_fMap = filter->GetOutput();
	- }
	- catch (itk::ExceptionObject &ex)
	- {
	- MITK_INFO << ex ;
	- m_Controls->m_Warning->setText(QString("IVIM fit not possible: ")+ex.GetDescription());
	- m_Controls->m_Warning->setVisible(true);
	- return false;
	- }
	- return true;
	-}
	-
	-void QmitkIVIMView::OutputToDatastorage(mitk::DataNode::Pointer node)
	-{
	- if(m_Controls->m_CheckDStar->isChecked())
	- {
	- mitk::Image::Pointer dstarimage = mitk::Image::New();
	- dstarimage->InitializeByItk(m_DStarMap.GetPointer());
	- dstarimage->SetVolume(m_DStarMap->GetBufferPointer());
	- QString newname2 = ""; newname2 = newname2.append("IVIM_DStarMap_Method-%1").arg(m_Controls->m_MethodCombo->currentText());
	- mitk::DataNode::Pointer node2=mitk::DataNode::New();
	- node2->SetData( dstarimage );
	- node2->SetName(newname2.toLatin1());
	- GetDataStorage()->Add(node2, node);
	- }
	-
	- if(m_Controls->m_CheckD->isChecked())
	- {
	- mitk::Image::Pointer dimage = mitk::Image::New();
	- dimage->InitializeByItk(m_DMap.GetPointer());
	- dimage->SetVolume(m_DMap->GetBufferPointer());
	- QString newname1 = ""; newname1 = newname1.append("IVIM_DMap_Method-%1").arg(m_Controls->m_MethodCombo->currentText());
	- mitk::DataNode::Pointer node1=mitk::DataNode::New();
	- node1->SetData( dimage );
	- node1->SetName(newname1.toLatin1());
	- GetDataStorage()->Add(node1, node);
	- }
	-
	- if(m_Controls->m_Checkf->isChecked())
	- {
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk(m_fMap.GetPointer());
	- image->SetVolume(m_fMap->GetBufferPointer());
	- QString newname0 = ""; newname0 = newname0.append("IVIM_fMap_Method-%1").arg(m_Controls->m_MethodCombo->currentText());
	- mitk::DataNode::Pointer node3=mitk::DataNode::New();
	- node3->SetData( image );
	- node3->SetName(newname0.toLatin1());
	- GetDataStorage()->Add(node3, node);
	- }
	-
	- this->GetRenderWindowPart()->RequestUpdate();
	-}
	-
	-void QmitkIVIMView::ChooseMethod()
	-{
	- m_Controls->m_MethodCombo->setVisible(m_Controls->m_ChooseMethod->isChecked());
	-}
	-
	-void QmitkIVIMView::ClipboardCurveButtonClicked()
	-{
	- // Kurtosis
	- if ( m_Controls->m_ModelTabSelectionWidget->currentIndex() )
	- {
	- std::stringstream ss;
	- QString clipboard("Measurement Points\n");
	-
	- ss << m_KurtosisSnap.bvalues << "\n" << m_KurtosisSnap.measurements << "\n\n";
	- ss << "Fitted Values ( D K [b_0] ) \n" << m_KurtosisSnap.m_D << " " << m_KurtosisSnap.m_K;
	- if( m_KurtosisSnap.m_fittedBZero )
	- ss << " " << m_KurtosisSnap.m_BzeroFit;
	-
	- ss << "\n\n";
	- clipboard.append( QString( ss.str().c_str() ));
	-
	- ss.str( std::string() );
	- ss.clear();
	-
	- QApplication::clipboard()->setText(
	- clipboard, QClipboard::Clipboard );
	- }
	- else
	- {
	-
	- QString clipboard("Measurement Points\n");
	- for ( unsigned int i=0; i<m_Snap.bvalues.size(); i++)
	- {
	- clipboard = clipboard.append( "%L1 \t" )
	- .arg( m_Snap.bvalues[i], 0, 'f', 2 );
	- }
	- clipboard = clipboard.append( "\n" );
	-
	- for ( unsigned int i=0; i<m_Snap.allmeas.size(); i++)
	- {
	- clipboard = clipboard.append( "%L1 \t" )
	- .arg( m_Snap.allmeas[i], 0, 'f', 2 );
	- }
	- clipboard = clipboard.append( "\n" );
	-
	-
	- clipboard = clipboard.append( "1st Linear Fit of D and f \n" );
	- double maxb = m_Snap.bvalues.max_value();
	- clipboard = clipboard.append( "%L1 \t %L2 \n %L3 \t %L4 \n" )
	- .arg( (float) 0, 0, 'f', 2 )
	- .arg( maxb, 0, 'f', 2 )
	- .arg(1-m_Snap.currentFunceiled, 0, 'f', 2 )
	- .arg((1-m_Snap.currentFunceiled)exp(-maxb m_Snap.currentD), 0, 'f', 2 );
	-
	-
	- int nsampling = 50;
	- double f = 1-m_Snap.currentFunceiled;
	- clipboard = clipboard.append("Final Model\n");
	- for(int i=0; i<nsampling; i++)
	- {
	- double x = (((1.0)i)/(1.0nsampling))*maxb;
	- clipboard = clipboard.append( "%L1 \t" )
	- .arg( x, 0, 'f', 2 );
	- }
	- clipboard = clipboard.append( "\n" );
	-
	- for(int i=0; i<nsampling; i++)
	- {
	- double x = (((1.0)i)/(1.0nsampling))*maxb;
	- double y = fexp(- x m_Snap.currentD) + (1-f)exp(- x (m_Snap.currentD+m_Snap.currentDStar));
	- clipboard = clipboard.append( "%L1 \t" )
	- .arg( y, 0, 'f', 2 );
	- }
	- clipboard = clipboard.append( "\n" );
	-
	- QApplication::clipboard()->setText(
	- clipboard, QClipboard::Clipboard );
	- }
	-}
	-
	-
	-void QmitkIVIMView::ClipboardStatisticsButtonClicked()
	-{
	- // Kurtosis
	- if ( m_Controls->m_ModelTabSelectionWidget->currentIndex() )
	- {
	-
	- QString clipboard( "D \t K \n" );
	- clipboard = clipboard.append( "%L1 \t %L2" )
	- .arg( m_KurtosisSnap.m_D, 0, 'f', 10 )
	- .arg( m_KurtosisSnap.m_K, 0, 'f', 10 ) ;
	-
	- QApplication::clipboard()->setText(
	- clipboard, QClipboard::Clipboard );
	- }
	- else
	- {
	- QString clipboard( "f \t D \t D* \n" );
	- clipboard = clipboard.append( "%L1 \t %L2 \t %L3" )
	- .arg( m_Snap.currentF, 0, 'f', 10 )
	- .arg( m_Snap.currentD, 0, 'f', 10 )
	- .arg( m_Snap.currentDStar, 0, 'f', 10 ) ;
	-
	- QApplication::clipboard()->setText(
	- clipboard, QClipboard::Clipboard );
	- }
	-}
	-
	-void QmitkIVIMView::Activated()
	-{
	- m_Active = true;
	-}
	-
	-void QmitkIVIMView::Deactivated()
	-{
	- m_Active = false;
	-}
	-
	-void QmitkIVIMView::Visible()
	-{
	- m_Visible = true;
	-
	- QList<mitk::DataNode::Pointer> selection = GetDataManagerSelection();
	- berry::IWorkbenchPart::Pointer nullPart;
	- OnSelectionChanged(nullPart, selection);
	-}
	-
	-void QmitkIVIMView::Hidden()
	-{
	- m_Visible = false;
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/QmitkIVIMView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/QmitkIVIMView.h
	deleted file mode 100644
	index 3e6420bf21..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/QmitkIVIMView.h
	+++ /dev/null
	@@ -1,127 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _QMITKIVIMVIEW_H_INCLUDED
	-#define _QMITKIVIMVIEW_H_INCLUDED
	-
	-#include <berryISelectionListener.h>
	-
	-#include <QmitkAbstractView.h>
	-#include <mitkILifecycleAwarePart.h>
	-#include <mitkIRenderWindowPartListener.h>
	-
	-#include "ui_QmitkIVIMViewControls.h"
	-
	-#include "itkVectorImage.h"
	-#include "itkImage.h"
	-
	-#include <mitkDiffusionPropertyHelper.h>
	-#include "itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.h"
	-#include "itkDiffusionKurtosisReconstructionImageFilter.h"
	-#include <QmitkSliceNavigationListener.h>
	-
	-/*!
	- \brief QmitkIVIMView
	-
	- \warning This application module is not yet documented. Use "svn blame/praise/annotate" and ask the author to provide basic documentation.
	-*/
	-
	-class QmitkIVIMView : public QmitkAbstractView, public mitk::ILifecycleAwarePart
	-{
	- // this is needed for all Qt objects that should have a Qt meta-object
	- // (everything that derives from QObject and wants to have signal/slots)
	- Q_OBJECT
	-
	-public:
	-
	- static const std::string VIEW_ID;
	-
	- QmitkIVIMView();
	- virtual ~QmitkIVIMView();
	-
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionType GradientDirectionType;
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionsContainerType DirContainerType;
	- typedef itk::DiffusionIntravoxelIncoherentMotionReconstructionImageFilter<short, float> IVIMFilterType;
	- typedef itk::DiffusionKurtosisReconstructionImageFilter<short, float> KurtosisFilterType;
	- typedef itk::VectorImage<short,3> VecImgType;
	- typedef itk::Image<float,3> OutImgType;
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	-
	- ///
	- /// Sets the focus to an internal widget.
	- ///
	- virtual void SetFocus() override;
	-
	- void OutputToDatastorage(mitk::DataNode::Pointer node);
	- bool FittIVIM(itk::VectorImage<short,3>* vecimg, DirContainerType* dirs, float bval, bool multivoxel, OutImgType::IndexType &crosspos);
	-
	- void Activated() override;
	- void Deactivated() override;
	- void Visible() override;
	- void Hidden() override;
	-
	-protected slots:
	-
	- void OnSliceChanged();
	-
	- /// \brief Called when the user clicks the GUI button
	- void FittIVIMStart();
	- void AutoThreshold();
	-
	- void MethodCombo(int val);
	- void Checkbox();
	-
	- void DStarSlider(int val);
	- void BThreshSlider(int val);
	- void S0ThreshSlider(int val);
	- void NumItsSlider(int val);
	- void LambdaSlider(int val);
	- void ChooseMethod();
	- void ClipboardStatisticsButtonClicked();
	- void ClipboardCurveButtonClicked();
	-
	- void OnKurtosisParamsChanged();
	- void UpdateGui();
	-
	-protected:
	-
	- /// \brief called by QmitkAbstractView when DataManager's selection has changed
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- bool FitKurtosis( itk::VectorImage<short, 3> vecimg, DirContainerType dirs, float bval, OutImgType::IndexType &crosspos);
	-
	- Ui::QmitkIVIMViewControls* m_Controls;
	-
	- OutImgType::Pointer m_DStarMap;
	- OutImgType::Pointer m_DMap;
	- OutImgType::Pointer m_fMap;
	-
	- IVIMFilterType::IVIMSnapshot m_Snap;
	- KurtosisFilterType::KurtosisSnapshot m_KurtosisSnap;
	-
	- bool m_Active;
	- bool m_Visible;
	-
	- bool m_HoldUpdate;
	- QmitkSliceNavigationListener m_SliceChangeListener;
	-
	-};
	-
	-
	-
	-#endif // _QMITKIVIMVIEW_H_INCLUDED
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/QmitkIVIMViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/QmitkIVIMViewControls.ui
	deleted file mode 100644
	index 3d114861ae..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/QmitkIVIMViewControls.ui
	+++ /dev/null
	@@ -1,1187 +0,0 @@
	-<?xml version="1.0" encoding="utf-8"?>
	-<ui version="4.0">
	- <class>QmitkIVIMViewControls</class>
	- <widget class="QWidget" name="QmitkIVIMViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>423</width>
	- <height>1563</height>
	- </rect>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="windowTitle">
	- <string>QmitkTemplate</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_11">
	- <property name="leftMargin">
	- <number>9</number>
	- </property>
	- <property name="topMargin">
	- <number>9</number>
	- </property>
	- <property name="rightMargin">
	- <number>9</number>
	- </property>
	- <property name="bottomMargin">
	- <number>9</number>
	- </property>
	- <property name="verticalSpacing">
	- <number>9</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QGroupBox" name="groupBox">
	- <property name="title">
	- <string>Intra Voxel Incoherent Motion Estimation</string>
	- </property>
	- <layout class="QVBoxLayout" name="verticalLayout">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>9</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- </layout>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QGroupBox" name="m_InputData">
	- <property name="title">
	- <string>Input Data</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_8">
	- <property name="toolTip">
	- <string>Optional ROI image</string>
	- </property>
	- <property name="text">
	- <string>ROI:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_7">
	- <property name="toolTip">
	- <string>DWI to analyze</string>
	- </property>
	- <property name="text">
	- <string>Raw DWI:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_DwiBox"></widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QmitkDataStorageComboBoxWithSelectNone" name="m_MaskBox"></widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QFrame" name="m_ControlsFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_13">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_Warning">
	- <property name="styleSheet">
	- <string notr="true"></string>
	- </property>
	- <property name="text">
	- <string>warning display</string>
	- </property>
	- <property name="textFormat">
	- <enum>Qt::RichText</enum>
	- </property>
	- <property name="wordWrap">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- <widget class="QFrame" name="dstar">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>16</width>
	- <height>16</height>
	- </rect>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QHBoxLayout" name="horizontalLayout">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- </layout>
	- </widget>
	- <widget class="QFrame" name="thres">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>16</width>
	- <height>16</height>
	- </rect>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QHBoxLayout" name="horizontalLayout_2">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- </layout>
	- </widget>
	- <widget class="QFrame" name="thres_2">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>16</width>
	- <height>16</height>
	- </rect>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QHBoxLayout" name="horizontalLayout_3">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- </layout>
	- </widget>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QFrame" name="m_FigureWidgetFrame">
	- <property name="frameShape">
	- <enum>QFrame::StyledPanel</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_14">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QTabWidget" name="m_ModelTabSelectionWidget">
	- <property name="currentIndex">
	- <number>0</number>
	- </property>
	- <widget class="QWidget" name="m_IVIMTab">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <attribute name="title">
	- <string>IVIM</string>
	- </attribute>
	- <layout class="QVBoxLayout" name="verticalLayout_9">
	- <item>
	- <widget class="QGroupBox" name="groupBox_3">
	- <property name="title">
	- <string>Parameters</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_2">
	- <property name="spacing">
	- <number>9</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QFrame" name="m_DstarFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_7">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_2">
	- <property name="maximumSize">
	- <size>
	- <width>80</width>
	- <height>16777215</height>
	- </size>
	- </property>
	- <property name="text">
	- <string>D*</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QScrollBar" name="m_DStarSlider">
	- <property name="maximum">
	- <number>100</number>
	- </property>
	- <property name="value">
	- <number>60</number>
	- </property>
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="2">
	- <widget class="QLabel" name="m_DStarLabel">
	- <property name="maximumSize">
	- <size>
	- <width>51</width>
	- <height>16777215</height>
	- </size>
	- </property>
	- <property name="text">
	- <string>200</string>
	- </property>
	- <property name="alignment">
	- <set>Qt::AlignRight\|Qt::AlignTrailing\|Qt::AlignVCenter</set>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QFrame" name="m_NeglBframe">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_8">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_3">
	- <property name="maximumSize">
	- <size>
	- <width>80</width>
	- <height>16777215</height>
	- </size>
	- </property>
	- <property name="text">
	- <string>neglect b<</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QScrollBar" name="m_BThreshSlider">
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="maximum">
	- <number>250</number>
	- </property>
	- <property name="value">
	- <number>34</number>
	- </property>
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="2">
	- <widget class="QLabel" name="m_BThreshLabel">
	- <property name="maximumSize">
	- <size>
	- <width>51</width>
	- <height>16777215</height>
	- </size>
	- </property>
	- <property name="text">
	- <string>46.5</string>
	- </property>
	- <property name="alignment">
	- <set>Qt::AlignRight\|Qt::AlignTrailing\|Qt::AlignVCenter</set>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QFrame" name="m_IterationsFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_6">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_5">
	- <property name="maximumSize">
	- <size>
	- <width>80</width>
	- <height>16777215</height>
	- </size>
	- </property>
	- <property name="text">
	- <string>#iterations</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QScrollBar" name="m_NumItSlider">
	- <property name="maximum">
	- <number>100</number>
	- </property>
	- <property name="value">
	- <number>10</number>
	- </property>
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="2">
	- <widget class="QLabel" name="m_NumItsLabel">
	- <property name="maximumSize">
	- <size>
	- <width>30</width>
	- <height>16777215</height>
	- </size>
	- </property>
	- <property name="text">
	- <string>TextLabel</string>
	- </property>
	- <property name="alignment">
	- <set>Qt::AlignRight\|Qt::AlignTrailing\|Qt::AlignVCenter</set>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QFrame" name="m_LambdaFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_10">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_6">
	- <property name="maximumSize">
	- <size>
	- <width>80</width>
	- <height>16777215</height>
	- </size>
	- </property>
	- <property name="text">
	- <string>lambda</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QScrollBar" name="m_LambdaSlider">
	- <property name="maximum">
	- <number>1000</number>
	- </property>
	- <property name="value">
	- <number>10</number>
	- </property>
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="2">
	- <widget class="QFrame" name="frame_5">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Minimum" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_4">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_LambdaLabel">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Minimum" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="maximumSize">
	- <size>
	- <width>30</width>
	- <height>16777215</height>
	- </size>
	- </property>
	- <property name="text">
	- <string>TextLabel</string>
	- </property>
	- <property name="alignment">
	- <set>Qt::AlignRight\|Qt::AlignTrailing\|Qt::AlignVCenter</set>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QToolButton" name="m_ButtonAutoThres_3">
	- <property name="maximumSize">
	- <size>
	- <width>15</width>
	- <height>16777215</height>
	- </size>
	- </property>
	- <property name="toolTip">
	- <string>Calculate threshold from histogram</string>
	- </property>
	- <property name="text">
	- <string>*</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QFrame" name="m_NeglSiFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Plain</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_9">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_4">
	- <property name="maximumSize">
	- <size>
	- <width>80</width>
	- <height>16777215</height>
	- </size>
	- </property>
	- <property name="text">
	- <string>neglect Si<</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QScrollBar" name="m_S0ThreshSlider">
	- <property name="maximum">
	- <number>100</number>
	- </property>
	- <property name="value">
	- <number>0</number>
	- </property>
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="2">
	- <widget class="QFrame" name="frame_2">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Minimum" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_3">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_S0ThreshLabel">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Minimum" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="maximumSize">
	- <size>
	- <width>30</width>
	- <height>16777215</height>
	- </size>
	- </property>
	- <property name="text">
	- <string>TextLabel</string>
	- </property>
	- <property name="alignment">
	- <set>Qt::AlignRight\|Qt::AlignTrailing\|Qt::AlignVCenter</set>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QToolButton" name="m_ButtonAutoThres">
	- <property name="maximumSize">
	- <size>
	- <width>15</width>
	- <height>16777215</height>
	- </size>
	- </property>
	- <property name="toolTip">
	- <string>Calculate threshold from histogram</string>
	- </property>
	- <property name="text">
	- <string>*</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <widget class="QFrame" name="frame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QHBoxLayout" name="horizontalLayout_4">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QLabel" name="label">
	- <property name="minimumSize">
	- <size>
	- <width>80</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="text">
	- <string>Output Images</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QCheckBox" name="m_Checkf">
	- <property name="text">
	- <string>f</string>
	- </property>
	- <property name="checked">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QCheckBox" name="m_CheckD">
	- <property name="text">
	- <string>D</string>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QCheckBox" name="m_CheckDStar">
	- <property name="text">
	- <string>D*</string>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <widget class="QmitkIVIMWidget" name="m_VisualizeResultsWidget" native="true">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>400</height>
	- </size>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <layout class="QVBoxLayout" name="verticalLayout_3">
	- <item>
	- <widget class="QCheckBox" name="m_ChooseMethod">
	- <property name="text">
	- <string>Choose Method</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QComboBox" name="m_MethodCombo">
	- <property name="currentIndex">
	- <number>2</number>
	- </property>
	- <item>
	- <property name="text">
	- <string>3 Param. Fit</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Fit D & f with fixed D* value</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Fit D & f (high b), then fit D*</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Linearly fit D & f (high b), then fit D*</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Regularized</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- </layout>
	- </item>
	- </layout>
	- </widget>
	- <widget class="QWidget" name="m_KurtosisTab">
	- <attribute name="title">
	- <string>Kurtosis</string>
	- </attribute>
	- <layout class="QVBoxLayout" name="verticalLayout_10">
	- <item>
	- <widget class="QFrame" name="frame_6">
	- <property name="frameShape">
	- <enum>QFrame::StyledPanel</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <property name="lineWidth">
	- <number>2</number>
	- </property>
	- <layout class="QHBoxLayout" name="horizontalLayout_6">
	- <property name="leftMargin">
	- <number>2</number>
	- </property>
	- <property name="topMargin">
	- <number>2</number>
	- </property>
	- <property name="rightMargin">
	- <number>2</number>
	- </property>
	- <property name="bottomMargin">
	- <number>2</number>
	- </property>
	- <item>
	- <layout class="QGridLayout" name="gridLayout_5">
	- <item row="8" column="0">
	- <widget class="QLabel" name="label_10">
	- <property name="text">
	- <string>Smoothing sigma</string>
	- </property>
	- </widget>
	- </item>
	- <item row="10" column="0">
	- <widget class="QLabel" name="label_12">
	- <property name="text">
	- <string>Select Fit Type</string>
	- </property>
	- </widget>
	- </item>
	- <item row="6" column="2">
	- <widget class="QCheckBox" name="m_OmitBZeroCB">
	- <property name="text">
	- <string>Omit b=0 Measurement</string>
	- </property>
	- </widget>
	- </item>
	- <item row="7" column="0">
	- <widget class="QLabel" name="label_9">
	- <property name="minimumSize">
	- <size>
	- <width>80</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="text">
	- <string>Output Images</string>
	- </property>
	- </widget>
	- </item>
	- <item row="9" column="0">
	- <widget class="QLabel" name="label_11">
	- <property name="toolTip">
	- <string>Force the fitting of K to remain within the given boundaries</string>
	- </property>
	- <property name="text">
	- <string>Boundaries for K</string>
	- </property>
	- </widget>
	- </item>
	- <item row="10" column="2">
	- <widget class="QComboBox" name="m_KurtosisFitScale">
	- <property name="toolTip">
	- <string>Select if the data is fitted directly (straight) or the logarithmic equation is used</string>
	- </property>
	- <item>
	- <property name="text">
	- <string>Straight Fit</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Logarithmic Fit</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- <item row="7" column="2">
	- <layout class="QHBoxLayout" name="horizontalLayout_5">
	- <property name="spacing">
	- <number>2</number>
	- </property>
	- <property name="sizeConstraint">
	- <enum>QLayout::SetMaximumSize</enum>
	- </property>
	- <item>
	- <widget class="QCheckBox" name="m_CheckKurtD">
	- <property name="text">
	- <string>D</string>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QCheckBox" name="m_CheckKurtK">
	- <property name="text">
	- <string>K</string>
	- </property>
	- <property name="checked">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </item>
	- <item row="9" column="2">
	- <widget class="ctkRangeWidget" name="m_KurtosisRangeWidget" native="true"></widget>
	- </item>
	- <item row="8" column="2">
	- <widget class="QDoubleSpinBox" name="m_SigmaSpinBox">
	- <property name="toolTip">
	- <string>Signa for gaussian smoothing applied prior to map computation</string>
	- </property>
	- <property name="minimum">
	- <double>0.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>5.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="9" column="1">
	- <widget class="QCheckBox" name="m_UseKurtosisBoundsCB">
	- <property name="text">
	- <string>On</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <widget class="QmitkKurtosisWidget" name="m_KurtosisVisualizationWidget" native="true">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>400</height>
	- </size>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QCommandLinkButton" name="m_ButtonStart">
	- <property name="text">
	- <string>Generate Output Images</string>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <widget class="QFrame" name="frame_3">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_12">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QFrame" name="m_BottomControlsFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QVBoxLayout" name="verticalLayout_6">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QFrame" name="frame_4">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QHBoxLayout" name="horizontalLayout_7">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QPushButton" name="m_CurveClipboard">
	- <property name="text">
	- <string>Datapoints to Clipboard</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <widget class="QPushButton" name="m_ValuesClipboard">
	- <property name="text">
	- <string>Parameters to Clipboard</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <layoutdefault spacing="6" margin="11"></layoutdefault>
	- <customwidgets>
	- <customwidget>
	- <class>QmitkDataStorageComboBox</class>
	- <extends>QComboBox</extends>
	- <header location="global">QmitkDataStorageComboBox.h</header>
	- </customwidget>
	- <customwidget>
	- <class>QmitkDataStorageComboBoxWithSelectNone</class>
	- <extends>QComboBox</extends>
	- <header>QmitkDataStorageComboBoxWithSelectNone.h</header>
	- </customwidget>
	- <customwidget>
	- <class>QmitkIVIMWidget</class>
	- <extends>QWidget</extends>
	- <header>QmitkIVIMWidget.h</header>
	- <container>1</container>
	- </customwidget>
	- <customwidget>
	- <class>QmitkKurtosisWidget</class>
	- <extends>QWidget</extends>
	- <header>QmitkKurtosisWidget.h</header>
	- <container>1</container>
	- </customwidget>
	- <customwidget>
	- <class>ctkRangeWidget</class>
	- <extends>QWidget</extends>
	- <header>ctkRangeWidget.h</header>
	- <container>1</container>
	- </customwidget>
	- </customwidgets>
	- <resources></resources>
	- <connections></connections>
	-</ui>
	\ No newline at end of file
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/mitkPluginActivator.cpp
	deleted file mode 100644
	index bfd1fcaabc..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/mitkPluginActivator.cpp
	+++ /dev/null
	@@ -1,43 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkPluginActivator.h"
	-
	-#include "src/internal/Perspectives/QmitkDIAppIVIMPerspective.h"
	-
	-#include "src/internal/QmitkIVIMView.h"
	-
	-ctkPluginContext* mitk::PluginActivator::m_Context = nullptr;
	-
	-ctkPluginContext* mitk::PluginActivator::GetContext()
	-{
	-
	- return m_Context;
	-}
	-
	-void mitk::PluginActivator::start(ctkPluginContext* context)
	-{
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkDIAppIVIMPerspective, context)
	-
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkIVIMView, context)
	- m_Context = context;
	-}
	-
	-void mitk::PluginActivator::stop(ctkPluginContext* context)
	-{
	- Q_UNUSED(context)
	- m_Context = nullptr;
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/mitkPluginActivator.h b/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/mitkPluginActivator.h
	deleted file mode 100644
	index a83335661e..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.ivim/src/internal/mitkPluginActivator.h
	+++ /dev/null
	@@ -1,40 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef MITKPLUGINACTIVATOR_H
	-#define MITKPLUGINACTIVATOR_H
	-
	-#include <ctkPluginActivator.h>
	-
	-namespace mitk
	-{
	- class PluginActivator : public QObject, public ctkPluginActivator
	- {
	- Q_OBJECT
	- Q_PLUGIN_METADATA(IID "org.mitk.gui.qt.diffusionimaging.ivim")
	- Q_INTERFACES(ctkPluginActivator)
	-
	- public:
	- static ctkPluginContext* GetContext();
	-
	- void start(ctkPluginContext* context) override;
	- void stop(ctkPluginContext* context) override;
	-
	- private:
	- static ctkPluginContext* m_Context;
	- };
	-}
	-
	-#endif
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/CMakeLists.txt
	deleted file mode 100644
	index a5d753484d..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/CMakeLists.txt
	+++ /dev/null
	@@ -1,10 +0,0 @@
	-# The project name must correspond to the directory name of your plug-in
	-# and must not contain periods.
	-project(org_mitk_gui_qt_diffusionimaging_odfpeaks)
	-
	-mitk_create_plugin(
	- SUBPROJECTS MITK-DTI
	- EXPORT_DIRECTIVE DIFFUSIONIMAGING_ODFPEAKS_EXPORT
	- EXPORTED_INCLUDE_SUFFIXES src
	- MODULE_DEPENDS MitkFiberTracking
	-)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/documentation/UserManual/QmitkOdfMaximaExtractionViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/documentation/UserManual/QmitkOdfMaximaExtractionViewUserManual.dox
	deleted file mode 100644
	index 6c724bad14..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/documentation/UserManual/QmitkOdfMaximaExtractionViewUserManual.dox
	+++ /dev/null
	@@ -1,9 +0,0 @@
	-/**
	-\page org_mitk_views_odfmaximaextraction ODF Peak Extraction
	-
	-This view provides the user interface to extract the principal diffusion direction of tensors and the peaks of spherical harmonic ODFs using gradient descent optimization.
	-
	-The output peaks can for example be used for streamline tractography.
	-
	-
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/documentation/UserManual/crossingmaxima.png b/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/documentation/UserManual/crossingmaxima.png
	deleted file mode 100644
	index d837353a80..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/documentation/UserManual/crossingmaxima.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/documentation/doxygen/modules.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/documentation/doxygen/modules.dox
	deleted file mode 100644
	index ee8b11ba22..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/documentation/doxygen/modules.dox
	+++ /dev/null
	@@ -1,16 +0,0 @@
	-/**
	- \defgroup org_mitk_gui_qt_diffusionimaging_odfpeaks org.mitk.gui.qt.diffusionimaging.odfpeaks
	- \ingroup MITKPlugins
	-
	- \brief This is the diffusionimaging.odfpeaks plugin.
	-
	-*/
	-
	-/**
	- \defgroup org_mitk_gui_qt_diffusionimaging_odfpeaks_internal Internal
	- \ingroup org_mitk_gui_qt_diffusionimaging_odfpeaks
	-
	- \brief This subcategory includes the internal classes of the org.mitk.gui.qt.diffusionimaging.odfpeaks plugin. Other
	- plugins must not rely on these classes. They contain implementation details and their interface
	- may change at any time. We mean it.
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/files.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/files.cmake
	deleted file mode 100644
	index 593e107eb6..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/files.cmake
	+++ /dev/null
	@@ -1,42 +0,0 @@
	-set(SRC_CPP_FILES
	-
	-
	-)
	-
	-set(INTERNAL_CPP_FILES
	- mitkPluginActivator.cpp
	-
	- QmitkOdfMaximaExtractionView.cpp
	-)
	-
	-set(UI_FILES
	- src/internal/QmitkOdfMaximaExtractionViewControls.ui
	-)
	-
	-set(MOC_H_FILES
	- src/internal/mitkPluginActivator.h
	-
	- src/internal/QmitkOdfMaximaExtractionView.h
	-
	-)
	-
	-set(CACHED_RESOURCE_FILES
	- plugin.xml
	-
	- resources/odf_peaks.png
	-)
	-
	-set(QRC_FILES
	-
	-)
	-
	-
	-set(CPP_FILES )
	-
	-foreach(file ${SRC_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/${file})
	-endforeach(file ${SRC_CPP_FILES})
	-
	-foreach(file ${INTERNAL_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/internal/${file})
	-endforeach(file ${INTERNAL_CPP_FILES})
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/manifest_headers.cmake
	deleted file mode 100644
	index 01c8d1dc61..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/manifest_headers.cmake
	+++ /dev/null
	@@ -1,5 +0,0 @@
	-set(Plugin-Name "MITK ODF Peaks")
	-set(Plugin-Version "1.0.0")
	-set(Plugin-Vendor "DKFZ, Medical and Biological Informatics")
	-set(Plugin-ContactAddress "http://www.mitk.org")
	-set(Require-Plugin org.mitk.gui.qt.diffusionimaging org.mitk.gui.qt.common)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/plugin.xml b/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/plugin.xml
	deleted file mode 100644
	index 533ed16939..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/plugin.xml
	+++ /dev/null
	@@ -1,32 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<?BlueBerry version="0.1"?>
	-<plugin>
	-
	- <extension point="org.blueberry.ui.views">
	-
	- <view id="org.mitk.views.odfmaximaextraction"
	- name="Peak Extraction"
	- category="Signal modeling"
	- class="QmitkOdfMaximaExtractionView"
	- icon="resources/odf_peaks.png">
	- <keywordReference id="org.mitk.views.odfmaximaextraction.Keyword"/>
	- </view>
	-
	- </extension>
	-
	- <extension point="org.blueberry.ui.keywords">
	-
	- <keyword label="ODF" id="org.mitk.views.odfmaximaextraction.Keyword"/>
	- <keyword label="SH" id="org.mitk.views.odfmaximaextraction.Keyword"/>
	- <keyword label="spherical harmonic" id="org.mitk.views.odfmaximaextraction.Keyword"/>
	- <keyword label="maximum" id="org.mitk.views.odfmaximaextraction.Keyword"/>
	- <keyword label="peak" id="org.mitk.views.odfmaximaextraction.Keyword"/>
	- <keyword label="main" id="org.mitk.views.odfmaximaextraction.Keyword"/>
	- <keyword label="FOD" id="org.mitk.views.odfmaximaextraction.Keyword"/>
	- <keyword label="direction" id="org.mitk.views.odfmaximaextraction.Keyword"/>
	- <keyword label="fODF" id="org.mitk.views.odfmaximaextraction.Keyword"/>
	- <keyword label="dODF" id="org.mitk.views.odfmaximaextraction.Keyword"/>
	-
	- </extension>
	-
	-</plugin>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/resources/odf_peaks.png b/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/resources/odf_peaks.png
	deleted file mode 100644
	index 5c2c59e76d..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/resources/odf_peaks.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/src/internal/QmitkOdfMaximaExtractionView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/src/internal/QmitkOdfMaximaExtractionView.cpp
	deleted file mode 100644
	index 6c91624318..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/src/internal/QmitkOdfMaximaExtractionView.cpp
	+++ /dev/null
	@@ -1,382 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-//misc
	-#include <QFileDialog>
	-
	-// Blueberry
	-#include <berryISelectionService.h>
	-#include <berryIWorkbenchWindow.h>
	-
	-// Qmitk
	-#include "QmitkOdfMaximaExtractionView.h"
	-
	-#include <mitkImageCast.h>
	-#include <mitkFiberBundle.h>
	-#include <mitkImage.h>
	-#include <mitkImageToItk.h>
	-#include <mitkTensorImage.h>
	-#include <itkVectorImage.h>
	-#include <itkOdfMaximaExtractionFilter.h>
	-#include <itkOdfMaximaExtractionFilter.h>
	-#include <itkShCoefficientImageImporter.h>
	-#include <itkDiffusionTensorPrincipalDirectionImageFilter.h>
	-#include <mitkNodePredicateAnd.h>
	-#include <mitkNodePredicateDimension.h>
	-#include <mitkNodePredicateOr.h>
	-#include <mitkNodePredicateNot.h>
	-#include <mitkNodePredicateDataType.h>
	-#include <mitkNodePredicateProperty.h>
	-#include <mitkNodePredicateIsDWI.h>
	-#include <mitkPeakImage.h>
	-#include <mitkShImage.h>
	-
	-// Qt
	-#include <QMessageBox>
	-
	-const std::string QmitkOdfMaximaExtractionView::VIEW_ID = "org.mitk.views.odfmaximaextractionview";
	-using namespace mitk;
	-
	-QmitkOdfMaximaExtractionView::QmitkOdfMaximaExtractionView()
	- : m_Controls(nullptr)
	-{
	-
	-}
	-
	-// Destructor
	-QmitkOdfMaximaExtractionView::~QmitkOdfMaximaExtractionView()
	-{
	-
	-}
	-
	-
	-void QmitkOdfMaximaExtractionView::CreateQtPartControl(QWidget *parent)
	-{
	- // build up qt view, unless already done
	- if (!m_Controls)
	- {
	- // create GUI widgets from the Qt Designer's .ui file
	- m_Controls = new Ui::QmitkOdfMaximaExtractionViewControls;
	- m_Controls->setupUi(parent);
	-
	- connect((QObject)m_Controls->m_StartPeakExtractionButton, SIGNAL(clicked()), (QObject) this, SLOT(StartPeakExtraction()));
	- connect((QObject)m_Controls->m_ImportShCoeffs, SIGNAL(clicked()), (QObject) this, SLOT(ConvertShCoeffs()));
	-
	- m_Controls->m_MaskBox->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_ImageBox->SetDataStorage(this->GetDataStorage());
	-
	- mitk::TNodePredicateDataType<mitk::ShImage>::Pointer isShImage = mitk::TNodePredicateDataType<mitk::ShImage>::New();
	- mitk::TNodePredicateDataType<mitk::TensorImage>::Pointer isTensorImage = mitk::TNodePredicateDataType<mitk::TensorImage>::New();
	-
	- mitk::NodePredicateNot::Pointer isDwi = mitk::NodePredicateNot::New(mitk::NodePredicateIsDWI::New());
	- mitk::NodePredicateNot::Pointer isOdf = mitk::NodePredicateNot::New(mitk::NodePredicateDataType::New("OdfImage"));
	- mitk::NodePredicateAnd::Pointer unwanted = mitk::NodePredicateAnd::New(isOdf, isDwi);
	- mitk::NodePredicateDimension::Pointer dim3 = mitk::NodePredicateDimension::New(3);
	- mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true));
	-
	- m_Controls->m_MaskBox->SetPredicate(mitk::NodePredicateAnd::New(mitk::NodePredicateAnd::New(unwanted, dim3), isBinaryPredicate));
	- m_Controls->m_ImageBox->SetPredicate(mitk::NodePredicateOr::New(isTensorImage, isShImage));
	- m_Controls->m_MaskBox->SetZeroEntryText("--");
	-
	- connect( (QObject)(m_Controls->m_ImageBox), SIGNAL(OnSelectionChanged(const mitk::DataNode)), this, SLOT(OnImageSelectionChanged()) );
	-
	- m_Controls->m_StartPeakExtractionButton->setVisible(false);
	- m_Controls->m_ImportShCoeffs->setVisible(false);
	- }
	-}
	-
	-void QmitkOdfMaximaExtractionView::SetFocus()
	-{
	-}
	-
	-void QmitkOdfMaximaExtractionView::StartPeakExtraction()
	-{
	- if (dynamic_cast<TensorImage*>(m_Controls->m_ImageBox->GetSelectedNode()->GetData()) != nullptr)
	- {
	- StartTensorPeakExtraction(dynamic_cast<TensorImage*>(m_Controls->m_ImageBox->GetSelectedNode()->GetData()));
	- }
	- else
	- {
	- StartMaximaExtraction(dynamic_cast<Image*>(m_Controls->m_ImageBox->GetSelectedNode()->GetData()));
	- }
	-}
	-
	-template<int shOrder>
	-void QmitkOdfMaximaExtractionView::TemplatedConvertShCoeffs(mitk::Image* mitkImg)
	-{
	- typedef itk::ShCoefficientImageImporter< float, shOrder > FilterType;
	- typedef mitk::ImageToItk< itk::Image< float, 4 > > CasterType;
	- CasterType::Pointer caster = CasterType::New();
	- caster->SetInput(mitkImg);
	- caster->Update();
	-
	- typename FilterType::Pointer filter = FilterType::New();
	- filter->SetInputImage(caster->GetOutput());
	- filter->GenerateData();
	- typename FilterType::CoefficientImageType::Pointer itkCi = filter->GetCoefficientImage();
	-
	- {
	- mitk::Image::Pointer img = dynamic_cast<mitk::Image*>(mitk::ShImage::New().GetPointer());
	- img->InitializeByItk(itkCi.GetPointer());
	- img->SetVolume(itkCi->GetBufferPointer());
	- DataNode::Pointer node = DataNode::New();
	- node->SetData(img);
	-
	- QString name(m_Controls->m_ImageBox->GetSelectedNode()->GetName().c_str());
	- name += "_ShImage_Imported";
	- node->SetName(name.toStdString().c_str());
	-
	- GetDataStorage()->Add(node, m_Controls->m_ImageBox->GetSelectedNode());
	- }
	-}
	-
	-void QmitkOdfMaximaExtractionView::ConvertShCoeffs()
	-{
	- if (m_Controls->m_ImageBox->GetSelectedNode().IsNull())
	- return;
	-
	- Image::Pointer mitkImg = dynamic_cast<Image*>(m_Controls->m_ImageBox->GetSelectedNode()->GetData());
	- if (mitkImg->GetDimension() != 4 && mitkImg->GetLargestPossibleRegion().GetSize()[3]<6)
	- {
	- MITK_INFO << "wrong image type (need 4 dimensions)";
	- return;
	- }
	-
	- int nrCoeffs = mitkImg->GetLargestPossibleRegion().GetSize()[3];
	- switch (nrCoeffs)
	- {
	- case 6:
	- TemplatedConvertShCoeffs<2>(mitkImg);
	- break;
	- case 15:
	- TemplatedConvertShCoeffs<4>(mitkImg);
	- break;
	- case 28:
	- TemplatedConvertShCoeffs<6>(mitkImg);
	- break;
	- case 45:
	- TemplatedConvertShCoeffs<8>(mitkImg);
	- break;
	- case 66:
	- TemplatedConvertShCoeffs<10>(mitkImg);
	- break;
	- case 91:
	- TemplatedConvertShCoeffs<12>(mitkImg);
	- break;
	- default :
	- QMessageBox::warning(nullptr, "Error", "Only spherical harmonics orders 2-12 are supported.", QMessageBox::Ok);
	- }
	-}
	-
	-void QmitkOdfMaximaExtractionView::StartTensorPeakExtraction(mitk::TensorImage* img)
	-{
	- typedef itk::DiffusionTensorPrincipalDirectionImageFilter< float > MaximaExtractionFilterType;
	- MaximaExtractionFilterType::Pointer filter = MaximaExtractionFilterType::New();
	- filter->SetUsePolarCoordinates(false);
	-
	- mitk::BaseGeometry::Pointer geometry;
	- try{
	- ItkTensorImage::Pointer itkImage = ItkTensorImage::New();
	- CastToItkImage(img, itkImage);
	- filter->SetInput(itkImage);
	- geometry = img->GetGeometry();
	- }
	- catch (itk::ExceptionObject &e)
	- {
	- MITK_INFO << "wrong image type: " << e.what();
	- QMessageBox::warning(nullptr, "Wrong pixel type", "Could not perform Tensor Principal Direction Extraction due to Image has wrong pixel type.", QMessageBox::Ok);
	- return;
	- }
	-
	- if (m_Controls->m_MaskBox->GetSelectedNode().IsNotNull())
	- {
	- ItkUcharImgType::Pointer itkMaskImage = ItkUcharImgType::New();
	- Image::Pointer mitkMaskImg = dynamic_cast<Image*>(m_Controls->m_MaskBox->GetSelectedNode()->GetData());
	- CastToItkImage(mitkMaskImg, itkMaskImage);
	- filter->SetMaskImage(itkMaskImage);
	- }
	-
	- if (m_Controls->m_NormalizationBox->currentIndex() == 0)
	- filter->SetNormalizeVectors(false);
	- filter->SetFaThreshold(m_Controls->m_AbsoluteThresholdBox->value());
	-
	- filter->Update();
	-
	- MaximaExtractionFilterType::PeakImageType::Pointer itkImg = filter->GetPeakImage();
	- mitk::Image::Pointer mitkPeakImage = dynamic_cast<Image*>(PeakImage::New().GetPointer());
	- CastToMitkImage(itkImg, mitkPeakImage);
	-
	- DataNode::Pointer node = DataNode::New();
	- node->SetData(mitkPeakImage);
	- QString name(m_Controls->m_ImageBox->GetSelectedNode()->GetName().c_str());
	- name += "_PrincipalDirection";
	- node->SetName(name.toStdString().c_str());
	- GetDataStorage()->Add(node, m_Controls->m_ImageBox->GetSelectedNode());
	-
	- if (m_Controls->m_OutputNumDirectionsBox->isChecked())
	- {
	- ItkUcharImgType::Pointer numDirImage = filter->GetOutput();
	- mitk::Image::Pointer image2 = mitk::Image::New();
	- image2->InitializeByItk(numDirImage.GetPointer());
	- image2->SetVolume(numDirImage->GetBufferPointer());
	- DataNode::Pointer node2 = DataNode::New();
	- node2->SetData(image2);
	- QString name(m_Controls->m_ImageBox->GetSelectedNode()->GetName().c_str());
	- name += "_NumDirections";
	- node2->SetName(name.toStdString().c_str());
	- GetDataStorage()->Add(node2, m_Controls->m_ImageBox->GetSelectedNode());
	- }
	-}
	-
	-template<int shOrder>
	-void QmitkOdfMaximaExtractionView::StartMaximaExtraction(Image *image)
	-{
	- typedef itk::OdfMaximaExtractionFilter< float, shOrder, ODF_SAMPLING_SIZE > MaximaExtractionFilterType;
	- typename MaximaExtractionFilterType::Pointer filter = MaximaExtractionFilterType::New();
	-
	- switch (m_Controls->m_ToolkitBox->currentIndex())
	- {
	- case 0:
	- filter->SetToolkit(MaximaExtractionFilterType::MRTRIX);
	- break;
	- case 1:
	- filter->SetToolkit(MaximaExtractionFilterType::FSL);
	- break;
	- default:
	- filter->SetToolkit(MaximaExtractionFilterType::MRTRIX);
	- }
	-
	- mitk::BaseGeometry::Pointer geometry;
	- try{
	- typedef ImageToItk< typename MaximaExtractionFilterType::CoefficientImageType > CasterType;
	- typename CasterType::Pointer caster = CasterType::New();
	- caster->SetInput(image);
	- caster->Update();
	- filter->SetInput(caster->GetOutput());
	- geometry = image->GetGeometry();
	- }
	- catch (itk::ExceptionObject &e)
	- {
	- MITK_INFO << "wrong image type: " << e.what();
	- QMessageBox::warning(nullptr, "Wrong pixel type", "Could not perform Finite Differences Extraction due to Image has wrong pixel type.", QMessageBox::Ok);
	- return;
	- }
	-
	- filter->SetAngularThreshold(cos((float)m_Controls->m_AngularThreshold->value()*itk::Math::pi / 180));
	- filter->SetMaxNumPeaks(m_Controls->m_MaxNumPeaksBox->value());
	- filter->SetRelativePeakThreshold(m_Controls->m_PeakThresholdBox->value());
	- filter->SetAbsolutePeakThreshold(m_Controls->m_AbsoluteThresholdBox->value());
	- filter->SetScaleByGfa(m_Controls->m_ScaleByGfaBox->isChecked());
	-
	- if (m_Controls->m_MaskBox->GetSelectedNode().IsNotNull())
	- {
	- ItkUcharImgType::Pointer itkMaskImage = ItkUcharImgType::New();
	- Image::Pointer mitkMaskImg = dynamic_cast<Image*>(m_Controls->m_MaskBox->GetSelectedNode()->GetData());
	- CastToItkImage(mitkMaskImg, itkMaskImage);
	- filter->SetMaskImage(itkMaskImage);
	- }
	-
	- switch (m_Controls->m_NormalizationBox->currentIndex())
	- {
	- case 0:
	- filter->SetNormalizationMethod(MaximaExtractionFilterType::NO_NORM);
	- break;
	- case 1:
	- filter->SetNormalizationMethod(MaximaExtractionFilterType::MAX_VEC_NORM);
	- break;
	- case 2:
	- filter->SetNormalizationMethod(MaximaExtractionFilterType::SINGLE_VEC_NORM);
	- break;
	- }
	-
	- filter->Update();
	-
	- typename MaximaExtractionFilterType::PeakImageType::Pointer itkImg = filter->GetPeakImage();
	- mitk::Image::Pointer img = dynamic_cast<Image*>(PeakImage::New().GetPointer());
	- CastToMitkImage(itkImg, img);
	-
	- DataNode::Pointer node = DataNode::New();
	- node->SetData(img);
	- QString name(m_Controls->m_ImageBox->GetSelectedNode()->GetName().c_str());
	- name += "_PEAKS";
	- node->SetName(name.toStdString().c_str());
	- GetDataStorage()->Add(node, m_Controls->m_ImageBox->GetSelectedNode());
	-
	- if (m_Controls->m_OutputNumDirectionsBox->isChecked())
	- {
	- ItkUcharImgType::Pointer numDirImage = filter->GetNumDirectionsImage();
	- mitk::Image::Pointer image2 = mitk::Image::New();
	- CastToMitkImage(numDirImage, image2);
	-
	- DataNode::Pointer node2 = DataNode::New();
	- node2->SetData(image2);
	- QString name(m_Controls->m_ImageBox->GetSelectedNode()->GetName().c_str());
	- name += "_NUM_DIRECTIONS";
	- node2->SetName(name.toStdString().c_str());
	- GetDataStorage()->Add(node2, m_Controls->m_ImageBox->GetSelectedNode());
	- }
	-}
	-
	-void QmitkOdfMaximaExtractionView::StartMaximaExtraction(Image* img)
	-{
	- mitk::PixelType pixT = img->GetPixelType();
	-
	- switch (pixT.GetNumberOfComponents())
	- {
	- case 6:
	- StartMaximaExtraction<2>(img);
	- break;
	- case 15:
	- StartMaximaExtraction<4>(img);
	- break;
	- case 28:
	- StartMaximaExtraction<6>(img);
	- break;
	- case 45:
	- StartMaximaExtraction<8>(img);
	- break;
	- case 66:
	- StartMaximaExtraction<10>(img);
	- break;
	- case 91:
	- StartMaximaExtraction<12>(img);
	- break;
	- default :
	- QMessageBox::warning(nullptr, "Error", "Only spherical harmonics orders 2-12 are supported.", QMessageBox::Ok);
	- }
	-}
	-
	-void QmitkOdfMaximaExtractionView::OnSelectionChanged(berry::IWorkbenchPart::Pointer , const QList<mitk::DataNode::Pointer>& nodes)
	-{
	- (void) nodes;
	- this->OnImageSelectionChanged();
	-}
	-
	-void QmitkOdfMaximaExtractionView::OnImageSelectionChanged()
	-{
	- m_Controls->m_StartPeakExtractionButton->setVisible(false);
	- m_Controls->m_ImportShCoeffs->setVisible(false);
	-
	- mitk::DataNode::Pointer node = m_Controls->m_ImageBox->GetSelectedNode();
	- if (node.IsNull())
	- return;
	-
	- Image::Pointer img = dynamic_cast<Image*>(node->GetData());
	- if (img->GetDimension()==4)
	- m_Controls->m_ImportShCoeffs->setVisible(true);
	- else
	- m_Controls->m_StartPeakExtractionButton->setVisible(true);
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/src/internal/QmitkOdfMaximaExtractionView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/src/internal/QmitkOdfMaximaExtractionView.h
	deleted file mode 100644
	index 4af483b372..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/src/internal/QmitkOdfMaximaExtractionView.h
	+++ /dev/null
	@@ -1,87 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-
	-#include <berryISelectionListener.h>
	-#include <berryIStructuredSelection.h>
	-
	-#include <QmitkAbstractView.h>
	-#include "ui_QmitkOdfMaximaExtractionViewControls.h"
	-#include <itkVectorImage.h>
	-#include <itkVectorContainer.h>
	-#include <itkOrientationDistributionFunction.h>
	-#include <QmitkDataStorageComboBoxWithSelectNone.h>
	-#include <mitkTensorImage.h>
	-
	-/*!
	-\brief View providing several methods to extract peaks from the spherical harmonic representation of ODFs or from tensors
	-*/
	-
	-// Forward Qt class declarations
	-
	-
	-class QmitkOdfMaximaExtractionView : public QmitkAbstractView
	-{
	-
	- // this is needed for all Qt objects that should have a Qt meta-object
	- // (everything that derives from QObject and wants to have signal/slots)
	- Q_OBJECT
	-
	-public:
	-
	- static const std::string VIEW_ID;
	-
	- QmitkOdfMaximaExtractionView();
	- virtual ~QmitkOdfMaximaExtractionView();
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	-
	- ///
	- /// Sets the focus to an internal widget.
	- ///
	- virtual void SetFocus() override;
	-
	- typedef itk::Image<unsigned char, 3> ItkUcharImgType;
	- typedef itk::Image< itk::DiffusionTensor3D< float >, 3 > ItkTensorImage;
	- typedef itk::Image< itk::Vector< float, 3>, 3 > ItkDirectionImage3DType; ///< contains a 3D vector in each voxel
	-
	- protected slots:
	-
	- void ConvertShCoeffs(); ///< convert spherical harmonic coefficients to the according mitk datatype
	- void StartPeakExtraction();
	- void OnImageSelectionChanged();
	-
	-protected:
	-
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- void StartMaximaExtraction(mitk::Image* img); ///< ODF maxima extraction using finite differences on the densely sampled sphere
	- void StartTensorPeakExtraction(mitk::TensorImage* img); ///< extract principal eigenvectors from tensor image
	-
	- /// \brief called by QmitkAbstractView when DataManager's selection has changed
	-
	- Ui::QmitkOdfMaximaExtractionViewControls* m_Controls;
	-
	- template<int shOrder> void TemplatedConvertShCoeffs(mitk::Image* mitkImg);
	- template<int shOrder> void StartMaximaExtraction(mitk::Image* image); ///< ODF maxima extraction using finite differences on the densely sampled sphere
	-
	-private:
	-
	- };
	-
	-
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/src/internal/QmitkOdfMaximaExtractionViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/src/internal/QmitkOdfMaximaExtractionViewControls.ui
	deleted file mode 100644
	index 5c17c07146..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/src/internal/QmitkOdfMaximaExtractionViewControls.ui
	+++ /dev/null
	@@ -1,473 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<ui version="4.0">
	- <class>QmitkOdfMaximaExtractionViewControls</class>
	- <widget class="QWidget" name="QmitkOdfMaximaExtractionViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>397</width>
	- <height>848</height>
	- </rect>
	- </property>
	- <property name="windowTitle">
	- <string>Form</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_2">
	- <property name="verticalSpacing">
	- <number>25</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QFrame" name="frame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_7">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="2" column="0">
	- <widget class="QCommandLinkButton" name="m_ImportShCoeffs">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="toolTip">
	- <string>Generate ODF image and MITK compatible SH coefficient from other toolkits.</string>
	- </property>
	- <property name="text">
	- <string>Start SH Coefficient Import</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QCommandLinkButton" name="m_StartPeakExtractionButton">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="toolTip">
	- <string>Extract ODF peaks using finite differences on the densely sampled ODF surface.</string>
	- </property>
	- <property name="text">
	- <string>Start Peak Extraction</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QGroupBox" name="m_InputData">
	- <property name="title">
	- <string>Please Select Input Data</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_5">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_4">
	- <property name="toolTip">
	- <string>Select a tensor image or a SH coefficient image (generate using Q-Ball reconstruction view).</string>
	- </property>
	- <property name="text">
	- <string>ShCoeff/DTI:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_3">
	- <property name="text">
	- <string>Mask Image:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_ImageBox"/>
	- </item>
	- <item row="1" column="1">
	- <widget class="QmitkDataStorageComboBoxWithSelectNone" name="m_MaskBox"/>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="6" column="0">
	- <widget class="QGroupBox" name="groupBox_2">
	- <property name="title">
	- <string>Additional Output</string>
	- </property>
	- <layout class="QFormLayout" name="formLayout_2">
	- <property name="fieldGrowthPolicy">
	- <enum>QFormLayout::AllNonFixedFieldsGrow</enum>
	- </property>
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QCheckBox" name="m_OutputNumDirectionsBox">
	- <property name="toolTip">
	- <string>Output unsigned char image containing the number of directions per voxel.</string>
	- </property>
	- <property name="text">
	- <string>#Peaks per Voxel</string>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="7" column="0">
	- <widget class="QGroupBox" name="groupBox">
	- <property name="title">
	- <string>Parameters</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QFrame" name="frame_2">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_4">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="horizontalSpacing">
	- <number>6</number>
	- </property>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label_8">
	- <property name="text">
	- <string>Vector Normalization:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QComboBox" name="m_NormalizationBox">
	- <property name="toolTip">
	- <string><html><head/><body><p>The vector fields are always coorected for image spacing and using the lagest eigenvalue in case of the tensor peak extraction. This is done for visualizytion purposes. The output direction images are not affected.</p></body></html></string>
	- </property>
	- <property name="currentIndex">
	- <number>1</number>
	- </property>
	- <item>
	- <property name="text">
	- <string>No Normalization</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>MAX Normalize</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Single Vec Normalization</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QFrame" name="m_CoeffImageFrame">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_3">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="horizontalSpacing">
	- <number>6</number>
	- </property>
	- <item row="3" column="1">
	- <widget class="QDoubleSpinBox" name="m_PeakThresholdBox">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="toolTip">
	- <string>Peak threshold relative to the largest peak per voxel.</string>
	- </property>
	- <property name="decimals">
	- <number>3</number>
	- </property>
	- <property name="minimum">
	- <double>0.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.400000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label_5">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="text">
	- <string>Max. Peaks:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="1">
	- <widget class="QDoubleSpinBox" name="m_AbsoluteThresholdBox">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="toolTip">
	- <string>Absolute threshold on the peak magnitudes.</string>
	- </property>
	- <property name="decimals">
	- <number>3</number>
	- </property>
	- <property name="minimum">
	- <double>0.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.010000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.030000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QSpinBox" name="m_MaxNumPeaksBox">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="toolTip">
	- <string>Maximum number of peaks to extract.</string>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>1000</number>
	- </property>
	- <property name="value">
	- <number>3</number>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <widget class="QLabel" name="label_11">
	- <property name="text">
	- <string>Angular Threshold:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="1">
	- <widget class="QSpinBox" name="m_AngularThreshold">
	- <property name="toolTip">
	- <string>Discard peaks that er closer to a larger peak.</string>
	- </property>
	- <property name="minimum">
	- <number>0</number>
	- </property>
	- <property name="maximum">
	- <number>90</number>
	- </property>
	- <property name="value">
	- <number>15</number>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QLabel" name="label_7">
	- <property name="text">
	- <string>Absolute Threshold:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QLabel" name="label_6">
	- <property name="text">
	- <string>Relative Threshold:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="6" column="0">
	- <widget class="QLabel" name="label_12">
	- <property name="text">
	- <string>Scale by GFA:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="6" column="1">
	- <widget class="QCheckBox" name="m_ScaleByGfaBox">
	- <property name="toolTip">
	- <string>Scale ODF values and successively the peaks by the GFA in the respective voxels.</string>
	- </property>
	- <property name="text">
	- <string/>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="17" column="0">
	- <spacer name="verticalSpacer">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>259</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="8" column="0">
	- <widget class="QGroupBox" name="groupBox_3">
	- <property name="title">
	- <string>Spherical Harmonic Convention</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_6">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QComboBox" name="m_ToolkitBox">
	- <property name="toolTip">
	- <string>Define SH coefficient convention (depends on toolkit)</string>
	- </property>
	- <property name="currentIndex">
	- <number>0</number>
	- </property>
	- <item>
	- <property name="text">
	- <string>MITK/MRtrix</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>FSL</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <customwidgets>
	- <customwidget>
	- <class>QmitkDataStorageComboBox</class>
	- <extends>QComboBox</extends>
	- <header location="global">QmitkDataStorageComboBox.h</header>
	- </customwidget>
	- <customwidget>
	- <class>QmitkDataStorageComboBoxWithSelectNone</class>
	- <extends>QComboBox</extends>
	- <header>QmitkDataStorageComboBoxWithSelectNone.h</header>
	- </customwidget>
	- </customwidgets>
	- <resources/>
	- <connections/>
	-</ui>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/src/internal/mitkPluginActivator.cpp
	deleted file mode 100644
	index 66bc5d6201..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/src/internal/mitkPluginActivator.cpp
	+++ /dev/null
	@@ -1,38 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkPluginActivator.h"
	-
	-#include "src/internal/QmitkOdfMaximaExtractionView.h"
	-
	-ctkPluginContext* mitk::PluginActivator::m_Context = nullptr;
	-
	-ctkPluginContext* mitk::PluginActivator::GetContext()
	-{
	- return m_Context;
	-}
	-
	-void mitk::PluginActivator::start(ctkPluginContext* context)
	-{
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkOdfMaximaExtractionView, context)
	- m_Context = context;
	-}
	-
	-void mitk::PluginActivator::stop(ctkPluginContext* context)
	-{
	- Q_UNUSED(context)
	- m_Context = nullptr;
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/src/internal/mitkPluginActivator.h b/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/src/internal/mitkPluginActivator.h
	deleted file mode 100644
	index dff80a7a0b..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.odfpeaks/src/internal/mitkPluginActivator.h
	+++ /dev/null
	@@ -1,40 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef MITKPLUGINACTIVATOR_H
	-#define MITKPLUGINACTIVATOR_H
	-
	-#include <ctkPluginActivator.h>
	-
	-namespace mitk
	-{
	- class PluginActivator : public QObject, public ctkPluginActivator
	- {
	- Q_OBJECT
	- Q_PLUGIN_METADATA(IID "org.mitk.gui.qt.diffusionimaging.odfpeaks")
	- Q_INTERFACES(ctkPluginActivator)
	-
	- public:
	- static ctkPluginContext* GetContext();
	-
	- void start(ctkPluginContext* context) override;
	- void stop(ctkPluginContext* context) override;
	-
	- private:
	- static ctkPluginContext* m_Context;
	- };
	-}
	-
	-#endif
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/CMakeLists.txt
	deleted file mode 100644
	index d944180266..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/CMakeLists.txt
	+++ /dev/null
	@@ -1,10 +0,0 @@
	-# The project name must correspond to the directory name of your plug-in
	-# and must not contain periods.
	-project(org_mitk_gui_qt_diffusionimaging_partialvolume)
	-
	-mitk_create_plugin(
	- SUBPROJECTS MITK-DTI
	- EXPORT_DIRECTIVE DIFFUSIONIMAGING_PARTIALVOLUME_EXPORT
	- EXPORTED_INCLUDE_SUFFIXES src
	- MODULE_DEPENDS MitkQtWidgetsExt MitkDiffusionCore MitkFiberTracking
	-)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/documentation/UserManual/QmitkPartialVolumeAnalysisViewManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/documentation/UserManual/QmitkPartialVolumeAnalysisViewManual.dox
	deleted file mode 100644
	index cf1a997015..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/documentation/UserManual/QmitkPartialVolumeAnalysisViewManual.dox
	+++ /dev/null
	@@ -1,25 +0,0 @@
	-/**
	-\page org_mitk_views_partialvolumeanalysisview Partial Volume Analysis
	-
	-The "Partial Volume Analysis" view can be found in the "Quantification" perspective. It allows for robust quantification of diffusion or other scalar measures in the presents of two classes (e.g. fiber vs. non-fiber) and partial volume between them. The algorithm estimates a probabilistic segmentation of the three classes and returns a weighted average of the measure of interest within the each class.
	-
	-\imageMacro{pvanalysisview.png,"The Partial Volume Analysis View",16.00}
	-
	-\section QmitkPVAAnalysisUserManualExport Export
	-
	-All measures are automatically written to the clipboard once the estimation is updated. For scalar images, the mean and the variance of the gaussian selected in the radio-box above is copied out. If 'All' is selected, then all means and variances are carried out as a tab-separated list. For tensor images, the values for all scalar measures (FA, MD, RD and AD) are carried out to the clipboard.
	-
	-The histogram export is provided by the button underneath the histogram. The values can be pasted to excel or any text editor.
	-
	-\section QmitkPVAAnalysisUserManualAdvancedSettings Advanced Settings
	-
	-Are not recommended for use yet.
	-
	-\section QmitkPVAAnalysisUserManualSuggestedReadings Suggested Readings
	-
	-Diffusion tensor imaging in primary brain tumors: reproducible quantitative analysis of corpus callosum infiltration and contralateral involvement using a probabilistic mixture model.
	-Stieltjes B, Schlüter M, Didinger B, Weber MA, Hahn HK, Parzer P, Rexilius J, Konrad-Verse O, Peitgen HO, Essig M.
	-Neuroimage. 2006 Jun;31(2):531-42. Epub 2006 Feb 14.
	-PMID: 16478665
	-
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/documentation/UserManual/pvanalysisview.png b/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/documentation/UserManual/pvanalysisview.png
	deleted file mode 100644
	index 2348d2bc80..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/documentation/UserManual/pvanalysisview.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/documentation/doxygen/modules.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/documentation/doxygen/modules.dox
	deleted file mode 100644
	index fccda8eb4b..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/documentation/doxygen/modules.dox
	+++ /dev/null
	@@ -1,16 +0,0 @@
	-/**
	- \defgroup org_mitk_gui_qt_diffusionimaging_partialvolume org.mitk.gui.qt.diffusionimaging.partialvolume
	- \ingroup MITKPlugins
	-
	- \brief This is the diffusionimaging.partialvolume plugin.
	-
	-*/
	-
	-/**
	- \defgroup org_mitk_gui_qt_diffusionimaging_partialvolume_internal Internal
	- \ingroup org_mitk_gui_qt_diffusionimaging_partialvolume
	-
	- \brief This subcategory includes the internal classes of the org.mitk.gui.qt.diffusionimaging.partialvolume plugin. Other
	- plugins must not rely on these classes. They contain implementation details and their interface
	- may change at any time. We mean it.
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/files.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/files.cmake
	deleted file mode 100644
	index 6ca97feded..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/files.cmake
	+++ /dev/null
	@@ -1,42 +0,0 @@
	-set(SRC_CPP_FILES
	- QmitkPartialVolumeAnalysisWidget.cpp
	-)
	-
	-set(INTERNAL_CPP_FILES
	- mitkPluginActivator.cpp
	-
	- QmitkPartialVolumeAnalysisView.cpp
	-)
	-
	-set(UI_FILES
	- src/internal/QmitkPartialVolumeAnalysisViewControls.ui
	-)
	-
	-set(MOC_H_FILES
	- src/internal/mitkPluginActivator.h
	-
	- src/internal/QmitkPartialVolumeAnalysisView.h
	-
	- src/QmitkPartialVolumeAnalysisWidget.h
	-)
	-
	-set(CACHED_RESOURCE_FILES
	- plugin.xml
	-
	- resources/PartialVolumeAnalysis_24.png
	-)
	-
	-set(QRC_FILES
	-
	-)
	-
	-
	-set(CPP_FILES )
	-
	-foreach(file ${SRC_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/${file})
	-endforeach(file ${SRC_CPP_FILES})
	-
	-foreach(file ${INTERNAL_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/internal/${file})
	-endforeach(file ${INTERNAL_CPP_FILES})
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/manifest_headers.cmake
	deleted file mode 100644
	index a7e7171515..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/manifest_headers.cmake
	+++ /dev/null
	@@ -1,5 +0,0 @@
	-set(Plugin-Name "MITK Partial Volume Analysis")
	-set(Plugin-Version "1.0.0")
	-set(Plugin-Vendor "DKFZ, Medical and Biological Informatics")
	-set(Plugin-ContactAddress "http://www.mitk.org")
	-set(Require-Plugin org.mitk.gui.qt.diffusionimaging org.mitk.gui.qt.common)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/plugin.xml b/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/plugin.xml
	deleted file mode 100644
	index c3504da478..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/plugin.xml
	+++ /dev/null
	@@ -1,24 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<?BlueBerry version="0.1"?>
	-<plugin>
	-
	- <extension point="org.blueberry.ui.views">
	-
	- <view id="org.mitk.views.partialvolumeanalysisview"
	- name="PV Analysis"
	- category="Quantification"
	- class="QmitkPartialVolumeAnalysisView"
	- icon="resources/PartialVolumeAnalysis_24.png">
	- <keywordReference id="org.mitk.views.partialvolumeanalysisview.Keyword"/>
	- </view>
	-
	- </extension>
	-
	-
	- <extension point="org.blueberry.ui.keywords">
	-
	-
	-
	- </extension>
	-
	-</plugin>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/resources/PartialVolumeAnalysis_24.png b/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/resources/PartialVolumeAnalysis_24.png
	deleted file mode 100644
	index 6eec03c8ed..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/resources/PartialVolumeAnalysis_24.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/resources/PartialVolumeAnalysis_48.png b/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/resources/PartialVolumeAnalysis_48.png
	deleted file mode 100644
	index 8387f1486d..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/resources/PartialVolumeAnalysis_48.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/resources/PartialVolumeAnalysis_48.xcf b/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/resources/PartialVolumeAnalysis_48.xcf
	deleted file mode 100644
	index 24328a1355..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/resources/PartialVolumeAnalysis_48.xcf and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/resources/PartialVolumeAnalysis_64.png b/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/resources/PartialVolumeAnalysis_64.png
	deleted file mode 100644
	index 322dae0037..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/resources/PartialVolumeAnalysis_64.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/src/QmitkPartialVolumeAnalysisWidget.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/src/QmitkPartialVolumeAnalysisWidget.cpp
	deleted file mode 100644
	index 95e340b4a4..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/src/QmitkPartialVolumeAnalysisWidget.cpp
	+++ /dev/null
	@@ -1,144 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkPartialVolumeAnalysisWidget.h"
	-
	-#include <QPen>
	-#include <QFrame>
	-
	-QmitkPartialVolumeAnalysisWidget::QmitkPartialVolumeAnalysisWidget( QWidget * parent )
	- : QmitkPlotWidget(parent)
	-{
	-// this->SetAxisTitle( QwtPlot::xBottom, "Grayvalue" );
	- // this->SetAxisTitle( QwtPlot::yLeft, "Probability" );
	-// this->Replot();
	- QFrame* canvas = qobject_cast<QFrame*>(m_Plot->canvas());
	- if (canvas)
	- {
	- canvas->setLineWidth(0);
	- canvas->setContentsMargins(0,0,0,0);
	- }
	-}
	-
	-
	-
	-QmitkPartialVolumeAnalysisWidget::~QmitkPartialVolumeAnalysisWidget()
	-{
	-}
	-
	-
	-void QmitkPartialVolumeAnalysisWidget::DrawGauss()
	-{
	-
	-}
	-
	-
	-void QmitkPartialVolumeAnalysisWidget::ClearItemModel()
	-{
	-
	-}
	-
	-void QmitkPartialVolumeAnalysisWidget::SetParameters( ParamsType params, ResultsType results, HistType *hist )
	-{
	- this->Clear();
	-
	- if(params != nullptr && results != nullptr)
	- {
	- for(unsigned int i=0; i<m_Vals.size(); i++)
	- {
	- delete m_Vals[i];
	- }
	-
	- m_Vals.clear();
	- m_Vals.push_back(hist->GetXVals());
	- m_Vals.push_back(hist->GetHVals());
	-
	-
	- std::vector<double> *xVals = hist->GetXVals();
	- std::vector<double> *fiberVals = new std::vector<double>(results->GetFiberVals());
	- std::vector<double> *nonFiberVals = new std::vector<double>(results->GetNonFiberVals());
	- std::vector<double> *mixedVals = new std::vector<double>(results->GetMixedVals());
	- std::vector<double> *combiVals = new std::vector<double>(results->GetCombiVals());
	-
	-
	- double fiberFA = 0.0;
	- double weights = 0.0;
	-
	- for(unsigned int i=0; i<xVals->size(); ++i)
	- {
	-
	- fiberFA += xVals->at(i) * fiberVals->at(i);
	- weights += fiberVals->at(i);
	- }
	-
	- fiberFA = fiberFA / weights;
	-
	- QPen pen( Qt::SolidLine );
	- pen.setWidth(1);
	-
	- QwtText plot_title("Compartment Histograms " );
	- plot_title.setFont( QFont("Helvetica", 10, QFont::Bold) );
	- this->SetPlotTitle( plot_title );
	-
	- pen.setColor(Qt::black);
	- int curveId = this->InsertCurve( "Histogram" );
	- this->SetCurveData( curveId, (m_Vals[0]), (m_Vals[1]) );
	- this->SetCurvePen( curveId, pen );
	- this->SetCurveAntialiasingOn( curveId );
	- // this->SetCurveTitle( curveId, "Image Histogram" );
	-
	- pen.setColor(Qt::blue);
	- pen.setWidth(2);
	- curveId = this->InsertCurve( "Combined" );
	- this->SetCurveData( curveId, (hist->GetXVals()), (combiVals) );
	- this->SetCurvePen( curveId, pen );
	- m_Vals.push_back(combiVals);
	- this->SetCurveAntialiasingOn( curveId );
	-
	-
	- curveId = this->InsertCurve( "Tissue class" );
	- this->SetCurveData(curveId, (hist->GetXVals()), (fiberVals));
	- this->SetCurvePen( curveId, QPen( Qt::NoPen ) );
	- this->SetCurveBrush(curveId, QBrush(QColor::fromRgbF(1,0,0,.5), Qt::SolidPattern));
	- m_Vals.push_back(fiberVals);
	-
	-
	- curveId = this->InsertCurve( "Non-tissue class" );
	- this->SetCurveData( curveId, (hist->GetXVals()), (nonFiberVals) );
	- this->SetCurvePen( curveId, QPen( Qt::NoPen ) );
	- this->SetCurveBrush(curveId, QBrush(QColor::fromRgbF(0,1,0,.5), Qt::SolidPattern));
	- m_Vals.push_back(nonFiberVals);
	-
	-
	- curveId = this->InsertCurve( "Mixed (PV) class" );
	- this->SetCurveData( curveId, (hist->GetXVals()), (mixedVals) );
	- this->SetCurvePen( curveId, QPen( Qt::NoPen ) );
	- this->SetCurveBrush(curveId, QBrush(QColor::fromRgbF(.7,.7,.7,.5), Qt::SolidPattern));
	- m_Vals.push_back(mixedVals);
	-
	- auto legend = new QwtLegend();
	- m_Plot->insertLegend( legend, QwtPlot::TopLegend );
	-
	- this->Replot();
	-
	-
	-
	- }
	-
	- this->Replot();
	-
	-}
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/src/QmitkPartialVolumeAnalysisWidget.h b/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/src/QmitkPartialVolumeAnalysisWidget.h
	deleted file mode 100644
	index 6853b7b742..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/src/QmitkPartialVolumeAnalysisWidget.h
	+++ /dev/null
	@@ -1,57 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef QmitkPartialVolumeAnalysisWidget_H_
	-#define QmitkPartialVolumeAnalysisWidget_H_
	-
	-#include "QmitkPlotWidget.h"
	-#include <org_mitk_gui_qt_diffusionimaging_partialvolume_Export.h>
	-
	-#include "mitkImage.h"
	-#include "mitkPartialVolumeAnalysisClusteringCalculator.h"
	-
	-
	-/**
	- * \brief Widget for displaying image histograms based on the vtkQtChart
	- * framework
	- */
	-class DIFFUSIONIMAGING_PARTIALVOLUME_EXPORT QmitkPartialVolumeAnalysisWidget : public QmitkPlotWidget
	-{
	- Q_OBJECT
	-
	-public:
	- typedef mitk::Image::HistogramType HistogramType;
	- typedef mitk::Image::HistogramType::ConstIterator HistogramConstIteratorType;
	-
	- typedef mitk::PartialVolumeAnalysisClusteringCalculator ClusteringType;
	- typedef ClusteringType::ParamsType ParamsType;
	- typedef ClusteringType::ClusterResultType ResultsType;
	- typedef ClusteringType::HistType HistType;
	-
	- /** \brief Set histogram to be displayed directly. */
	- void SetParameters( ParamsType params, ResultsType results, HistType *hist );
	-
	- QmitkPartialVolumeAnalysisWidget( QWidget * /parent = 0 /);
	- virtual ~QmitkPartialVolumeAnalysisWidget();
	-
	- void DrawGauss();
	-
	- void ClearItemModel();
	-
	- std::vector< std::vector<double>* > m_Vals;
	-};
	-
	-#endif /* QmitkPartialVolumeAnalysisWidget_H_ */
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/src/internal/QmitkPartialVolumeAnalysisView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/src/internal/QmitkPartialVolumeAnalysisView.cpp
	deleted file mode 100644
	index c6a01f14c1..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/src/internal/QmitkPartialVolumeAnalysisView.cpp
	+++ /dev/null
	@@ -1,2139 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkPartialVolumeAnalysisView.h"
	-
	-#include <limits>
	-
	-#include <qlabel.h>
	-#include <qspinbox.h>
	-#include <qpushbutton.h>
	-#include <qcheckbox.h>
	-#include <qgroupbox.h>
	-#include <qradiobutton.h>
	-#include <qlineedit.h>
	-#include <qclipboard.h>
	-#include <qfiledialog.h>
	-
	-#include <berryIEditorPart.h>
	-#include <berryIWorkbenchPage.h>
	-#include <berryPlatform.h>
	-
	-
	-#include "QmitkSliderNavigatorWidget.h"
	-#include <QMessageBox>
	-
	-#include "mitkNodePredicateDataType.h"
	-#include "mitkNodePredicateOr.h"
	-#include "mitkImageTimeSelector.h"
	-#include "mitkProperties.h"
	-#include "mitkProgressBar.h"
	-#include "mitkImageCast.h"
	-#include "mitkImageToItk.h"
	-#include "mitkITKImageImport.h"
	-#include "mitkDataNodeObject.h"
	-#include "mitkNodePredicateData.h"
	-#include "mitkPlanarFigureInteractor.h"
	-#include "mitkTensorImage.h"
	-#include "mitkPlanarCircle.h"
	-#include "mitkPlanarRectangle.h"
	-#include "mitkPlanarPolygon.h"
	-#include "mitkPartialVolumeAnalysisClusteringCalculator.h"
	-#include "usModuleRegistry.h"
	-
	-#include <itkVectorImage.h>
	-#include "itkTensorDerivedMeasurementsFilter.h"
	-#include "itkDiffusionTensor3D.h"
	-#include "itkCartesianToPolarVectorImageFilter.h"
	-#include "itkPolarToCartesianVectorImageFilter.h"
	-#include "itkBinaryThresholdImageFilter.h"
	-#include "itkMaskImageFilter.h"
	-#include "itkCastImageFilter.h"
	-#include "itkImageMomentsCalculator.h"
	-#include <itkResampleImageFilter.h>
	-#include <itkGaussianInterpolateImageFunction.h>
	-#include <itkNearestNeighborInterpolateImageFunction.h>
	-#include <itkImageDuplicator.h>
	-
	-#include <vnl/vnl_vector.h>
	-
	-const std::string QmitkPartialVolumeAnalysisView::VIEW_ID =
	- "org.mitk.views.partialvolumeanalysisview";
	-
	-class QmitkRequestStatisticsUpdateEvent : public QEvent
	-{
	-public:
	- enum Type
	- {
	- StatisticsUpdateRequest = QEvent::MaxUser - 1025
	- };
	-
	- QmitkRequestStatisticsUpdateEvent()
	- : QEvent( (QEvent::Type) StatisticsUpdateRequest ) {};
	-};
	-
	-
	-
	-typedef itk::Image<short, 3> ImageType;
	-typedef itk::Image<float, 3> FloatImageType;
	-typedef itk::Image<itk::Vector<float,3>, 3> VectorImageType;
	-
	-inline bool my_isnan(float x)
	-{
	- volatile float d = x;
	-
	- if(d!=d)
	- return true;
	-
	- if(d==d)
	- return false;
	- return d != d;
	-
	-}
	-
	-QmitkPartialVolumeAnalysisView::QmitkPartialVolumeAnalysisView(QObject * /parent/, const char * /name/)
	- : QmitkAbstractView(),
	- m_Controls(nullptr),
	- m_TimeStepperAdapter(nullptr),
	- m_MeasurementInfoRenderer(nullptr),
	- m_MeasurementInfoAnnotation(nullptr),
	- m_IsTensorImage(false),
	- m_SelectedRenderWindow(nullptr),
	- m_LastRenderWindow(nullptr),
	- m_ImageObserverTag(-1),
	- m_ImageMaskObserverTag(-1),
	- m_PlanarFigureObserverTag(-1),
	- m_CurrentStatisticsValid(false),
	- m_StatisticsUpdatePending(false),
	- m_GaussianSigmaChangedSliding(false),
	- m_NumberBinsSliding(false),
	- m_UpsamplingChangedSliding(false),
	- m_EllipseCounter(0),
	- m_RectangleCounter(0),
	- m_PolygonCounter(0),
	- m_CurrentFigureNodeInitialized(false),
	- m_QuantifyClass(2),
	- m_IconTexOFF(new QIcon(":/QmitkPartialVolumeAnalysisView/texIntOFFIcon.png")),
	- m_IconTexON(new QIcon(":/QmitkPartialVolumeAnalysisView/texIntONIcon.png")),
	- m_TexIsOn(true),
	- m_Visible(false)
	-{
	-
	-}
	-
	-
	-QmitkPartialVolumeAnalysisView::~QmitkPartialVolumeAnalysisView()
	-{
	- if ( m_SelectedImage.IsNotNull() )
	- m_SelectedImage->RemoveObserver( m_ImageObserverTag );
	- if ( m_SelectedImageMask.IsNotNull() )
	- m_SelectedImageMask->RemoveObserver( m_ImageMaskObserverTag );
	- if ( m_SelectedPlanarFigure.IsNotNull() )
	- {
	- m_SelectedPlanarFigure->RemoveObserver( m_PlanarFigureObserverTag );
	- m_SelectedPlanarFigure->RemoveObserver( m_InitializedObserverTag );
	- }
	-
	- this->GetDataStorage()->AddNodeEvent -= mitk::MessageDelegate1<QmitkPartialVolumeAnalysisView
	- , const mitk::DataNode*>( this, &QmitkPartialVolumeAnalysisView::NodeAddedInDataStorage );
	-
	- m_SelectedPlanarFigureNodes->NodeChanged.RemoveListener( mitk::MessageDelegate1<QmitkPartialVolumeAnalysisView
	- , const mitk::DataNode*>( this, &QmitkPartialVolumeAnalysisView::NodeChanged ) );
	-
	- m_SelectedPlanarFigureNodes->NodeRemoved.RemoveListener( mitk::MessageDelegate1<QmitkPartialVolumeAnalysisView
	- , const mitk::DataNode*>( this, &QmitkPartialVolumeAnalysisView::NodeRemoved ) );
	-
	- m_SelectedPlanarFigureNodes->PropertyChanged.RemoveListener( mitk::MessageDelegate2<QmitkPartialVolumeAnalysisView
	- , const mitk::DataNode, const mitk::BaseProperty>( this, &QmitkPartialVolumeAnalysisView::PropertyChanged ) );
	-
	- m_SelectedImageNodes->NodeChanged.RemoveListener( mitk::MessageDelegate1<QmitkPartialVolumeAnalysisView
	- , const mitk::DataNode*>( this, &QmitkPartialVolumeAnalysisView::NodeChanged ) );
	-
	- m_SelectedImageNodes->NodeRemoved.RemoveListener( mitk::MessageDelegate1<QmitkPartialVolumeAnalysisView
	- , const mitk::DataNode*>( this, &QmitkPartialVolumeAnalysisView::NodeRemoved ) );
	-
	- m_SelectedImageNodes->PropertyChanged.RemoveListener( mitk::MessageDelegate2<QmitkPartialVolumeAnalysisView
	- , const mitk::DataNode, const mitk::BaseProperty>( this, &QmitkPartialVolumeAnalysisView::PropertyChanged ) );
	-}
	-
	-
	-void QmitkPartialVolumeAnalysisView::CreateQtPartControl(QWidget *parent)
	-{
	- if (m_Controls == nullptr)
	- {
	- m_Controls = new Ui::QmitkPartialVolumeAnalysisViewControls;
	- m_Controls->setupUi(parent);
	- this->CreateConnections();
	- }
	-
	- SetHistogramVisibility();
	-
	- m_Controls->m_TextureIntON->setIcon(*m_IconTexON);
	-
	- m_Controls->m_SimilarAnglesFrame->setVisible(false);
	- m_Controls->m_SimilarAnglesLabel->setVisible(false);
	-
	- vtkTextProperty *textProp = vtkTextProperty::New();
	- textProp->SetColor(1.0, 1.0, 1.0);
	-
	- m_MeasurementInfoAnnotation = vtkCornerAnnotation::New();
	- m_MeasurementInfoAnnotation->SetMaximumFontSize(12);
	- m_MeasurementInfoAnnotation->SetTextProperty(textProp);
	-
	- m_MeasurementInfoRenderer = vtkRenderer::New();
	- m_MeasurementInfoRenderer->AddActor(m_MeasurementInfoAnnotation);
	-
	- m_SelectedPlanarFigureNodes = mitk::DataStorageSelection::New(this->GetDataStorage(), false);
	-
	- m_SelectedPlanarFigureNodes->NodeChanged.AddListener( mitk::MessageDelegate1<QmitkPartialVolumeAnalysisView
	- , const mitk::DataNode*>( this, &QmitkPartialVolumeAnalysisView::NodeChanged ) );
	-
	- m_SelectedPlanarFigureNodes->NodeRemoved.AddListener( mitk::MessageDelegate1<QmitkPartialVolumeAnalysisView
	- , const mitk::DataNode*>( this, &QmitkPartialVolumeAnalysisView::NodeRemoved ) );
	-
	- m_SelectedPlanarFigureNodes->PropertyChanged.AddListener( mitk::MessageDelegate2<QmitkPartialVolumeAnalysisView
	- , const mitk::DataNode, const mitk::BaseProperty>( this, &QmitkPartialVolumeAnalysisView::PropertyChanged ) );
	-
	- m_SelectedImageNodes = mitk::DataStorageSelection::New(this->GetDataStorage(), false);
	-
	- m_SelectedImageNodes->PropertyChanged.AddListener( mitk::MessageDelegate2<QmitkPartialVolumeAnalysisView
	- , const mitk::DataNode, const mitk::BaseProperty>( this, &QmitkPartialVolumeAnalysisView::PropertyChanged ) );
	-
	- m_SelectedImageNodes->NodeChanged.AddListener( mitk::MessageDelegate1<QmitkPartialVolumeAnalysisView
	- , const mitk::DataNode*>( this, &QmitkPartialVolumeAnalysisView::NodeChanged ) );
	-
	- m_SelectedImageNodes->NodeRemoved.AddListener( mitk::MessageDelegate1<QmitkPartialVolumeAnalysisView
	- , const mitk::DataNode*>( this, &QmitkPartialVolumeAnalysisView::NodeRemoved ) );
	-
	- this->GetDataStorage()->AddNodeEvent.AddListener( mitk::MessageDelegate1<QmitkPartialVolumeAnalysisView
	- , const mitk::DataNode*>( this, &QmitkPartialVolumeAnalysisView::NodeAddedInDataStorage ) );
	-
	- Select(nullptr,true,true);
	-
	- SetAdvancedVisibility();
	-}
	-
	-void QmitkPartialVolumeAnalysisView::SetFocus()
	-{
	- m_Controls->m_CircleButton->setFocus();
	-}
	-
	-void QmitkPartialVolumeAnalysisView::SetHistogramVisibility()
	-{
	- m_Controls->m_HistogramWidget->setVisible(m_Controls->m_DisplayHistogramCheckbox->isChecked());
	-}
	-
	-void QmitkPartialVolumeAnalysisView::SetAdvancedVisibility()
	-{
	- m_Controls->frame_7->setVisible(m_Controls->m_AdvancedCheckbox->isChecked());
	-}
	-
	-void QmitkPartialVolumeAnalysisView::CreateConnections()
	-{
	- if ( m_Controls )
	- {
	-
	- connect( m_Controls->m_DisplayHistogramCheckbox, SIGNAL( clicked() )
	- , this, SLOT( SetHistogramVisibility() ) );
	-
	- connect( m_Controls->m_AdvancedCheckbox, SIGNAL( clicked() )
	- , this, SLOT( SetAdvancedVisibility() ) );
	-
	-
	- connect( m_Controls->m_NumberBinsSlider, SIGNAL( sliderReleased () ),
	- this, SLOT( NumberBinsReleasedSlider( ) ) );
	- connect( m_Controls->m_UpsamplingSlider, SIGNAL( sliderReleased( ) ),
	- this, SLOT( UpsamplingReleasedSlider( ) ) );
	- connect( m_Controls->m_GaussianSigmaSlider, SIGNAL( sliderReleased( ) ),
	- this, SLOT( GaussianSigmaReleasedSlider( ) ) );
	- connect( m_Controls->m_SimilarAnglesSlider, SIGNAL( sliderReleased( ) ),
	- this, SLOT( SimilarAnglesReleasedSlider( ) ) );
	-
	- connect( m_Controls->m_NumberBinsSlider, SIGNAL( valueChanged (int) ),
	- this, SLOT( NumberBinsChangedSlider( int ) ) );
	- connect( m_Controls->m_UpsamplingSlider, SIGNAL( valueChanged( int ) ),
	- this, SLOT( UpsamplingChangedSlider( int ) ) );
	- connect( m_Controls->m_GaussianSigmaSlider, SIGNAL( valueChanged( int ) ),
	- this, SLOT( GaussianSigmaChangedSlider( int ) ) );
	- connect( m_Controls->m_SimilarAnglesSlider, SIGNAL( valueChanged( int ) ),
	- this, SLOT( SimilarAnglesChangedSlider(int) ) );
	-
	- connect( m_Controls->m_OpacitySlider, SIGNAL( valueChanged( int ) ),
	- this, SLOT( OpacityChangedSlider(int) ) );
	-
	- connect( (QObject)(m_Controls->m_ButtonCopyHistogramToClipboard), SIGNAL(clicked()),(QObject) this, SLOT(ToClipBoard()));
	-
	- connect( m_Controls->m_CircleButton, SIGNAL( clicked() )
	- , this, SLOT( ActionDrawEllipseTriggered() ) );
	-
	- connect( m_Controls->m_RectangleButton, SIGNAL( clicked() )
	- , this, SLOT( ActionDrawRectangleTriggered() ) );
	-
	- connect( m_Controls->m_PolygonButton, SIGNAL( clicked() )
	- , this, SLOT( ActionDrawPolygonTriggered() ) );
	-
	- connect( m_Controls->m_GreenRadio, SIGNAL( clicked(bool) )
	- , this, SLOT( GreenRadio(bool) ) );
	-
	- connect( m_Controls->m_PartialVolumeRadio, SIGNAL( clicked(bool) )
	- , this, SLOT( PartialVolumeRadio(bool) ) );
	-
	- connect( m_Controls->m_BlueRadio, SIGNAL( clicked(bool) )
	- , this, SLOT( BlueRadio(bool) ) );
	-
	- connect( m_Controls->m_AllRadio, SIGNAL( clicked(bool) )
	- , this, SLOT( AllRadio(bool) ) );
	-
	- connect( m_Controls->m_EstimateCircle, SIGNAL( clicked() )
	- , this, SLOT( EstimateCircle() ) );
	-
	- connect( (QObject*)(m_Controls->m_TextureIntON), SIGNAL(clicked()), this, SLOT(TextIntON()) );
	-
	- connect( m_Controls->m_ExportClusteringResultsButton, SIGNAL(clicked()), this, SLOT(ExportClusteringResults()));
	- }
	-}
	-
	-void QmitkPartialVolumeAnalysisView::ExportClusteringResults()
	-{
	- if (m_ClusteringResult.IsNull() \|\| m_SelectedImage.IsNull())
	- return;
	-
	- mitk::BaseGeometry* geometry = m_SelectedImage->GetGeometry();
	-
	- itk::Image< short, 3>::Pointer referenceImage = itk::Image< short, 3>::New();
	-
	- itk::Vector<double,3> newSpacing = geometry->GetSpacing();
	- mitk::Point3D newOrigin = geometry->GetOrigin();
	- mitk::Geometry3D::BoundsArrayType bounds = geometry->GetBounds();
	- newOrigin[0] += bounds.GetElement(0);
	- newOrigin[1] += bounds.GetElement(2);
	- newOrigin[2] += bounds.GetElement(4);
	- itk::Matrix<double, 3, 3> newDirection;
	- itk::ImageRegion<3> imageRegion;
	- for (int i=0; i<3; i++)
	- for (int j=0; j<3; j++)
	- newDirection[j][i] = geometry->GetMatrixColumn(i)[j]/newSpacing[j];
	- imageRegion.SetSize(0, geometry->GetExtent(0));
	- imageRegion.SetSize(1, geometry->GetExtent(1));
	- imageRegion.SetSize(2, geometry->GetExtent(2));
	-
	- // apply new image parameters
	- referenceImage->SetSpacing( newSpacing );
	- referenceImage->SetOrigin( newOrigin );
	- referenceImage->SetDirection( newDirection );
	- referenceImage->SetRegions( imageRegion );
	- referenceImage->Allocate();
	-
	- typedef itk::Image< float, 3 > OutType;
	- mitk::Image::Pointer mitkInImage = dynamic_cast<mitk::Image*>(m_ClusteringResult->GetData());
	-
	- typedef itk::Image< itk::RGBAPixel<unsigned char>, 3 > ItkRgbaImageType;
	- typedef mitk::ImageToItk< ItkRgbaImageType > CasterType;
	-
	- CasterType::Pointer caster = CasterType::New();
	- caster->SetInput(mitkInImage);
	- caster->Update();
	- ItkRgbaImageType::Pointer itkInImage = caster->GetOutput();
	-
	- typedef itk::ExtractChannelFromRgbaImageFilter< itk::Image< short, 3>, OutType > ExtractionFilterType;
	- ExtractionFilterType::Pointer filter = ExtractionFilterType::New();
	- filter->SetInput(itkInImage);
	- filter->SetChannel(ExtractionFilterType::ALPHA);
	- filter->SetReferenceImage(referenceImage);
	- filter->Update();
	- OutType::Pointer outImg = filter->GetOutput();
	-
	- mitk::Image::Pointer img = mitk::Image::New(); img->InitializeByItk(outImg.GetPointer());
	- img->SetVolume(outImg->GetBufferPointer());
	-
	- // init data node
	- mitk::DataNode::Pointer node = mitk::DataNode::New();
	- node->SetData(img);
	- node->SetName("Clustering Result");
	- GetDataStorage()->Add(node);
	-}
	-
	-void QmitkPartialVolumeAnalysisView::EstimateCircle()
	-{
	- typedef itk::Image<unsigned char, 3> SegImageType;
	- SegImageType::Pointer mask_itk = SegImageType::New();
	-
	- typedef mitk::ImageToItk<SegImageType> CastType;
	- CastType::Pointer caster = CastType::New();
	- caster->SetInput(m_SelectedImageMask);
	- caster->Update();
	-
	- typedef itk::ImageMomentsCalculator< SegImageType > MomentsType;
	- MomentsType::Pointer momentsCalc = MomentsType::New();
	- momentsCalc->SetImage(caster->GetOutput());
	- momentsCalc->Compute();
	- MomentsType::VectorType cog = momentsCalc->GetCenterOfGravity();
	- MomentsType::MatrixType axes = momentsCalc->GetPrincipalAxes();
	-
	- // moments-coord conversion
	- // third coordinate min oder max?
	-
	- // max-min = extent
	-
	- MomentsType::AffineTransformPointer trafo = momentsCalc->GetPhysicalAxesToPrincipalAxesTransform();
	-
	- itk::ImageRegionIterator<SegImageType>
	- itimage(caster->GetOutput(), caster->GetOutput()->GetLargestPossibleRegion());
	- itimage.GoToBegin();
	-
	- double max = -9999999999.0;
	- double min = 9999999999.0;
	-
	- while( !itimage.IsAtEnd() )
	- {
	- if(itimage.Get())
	- {
	- ImageType::IndexType index = itimage.GetIndex();
	-
	- itk::Point<float,3> point;
	- caster->GetOutput()->TransformIndexToPhysicalPoint(index,point);
	-
	- itk::Point<float,3> newPoint;
	- newPoint = trafo->TransformPoint(point);
	-
	- if(newPoint[2]<min)
	- min = newPoint[2];
	-
	- if(newPoint[2]>max)
	- max = newPoint[2];
	- }
	- ++itimage;
	- }
	-
	- double extent = max - min;
	- MITK_DEBUG << "EXTENT = " << extent;
	-
	- mitk::Point3D origin;
	- mitk::Vector3D right, bottom, normal;
	-
	- double factor = 1000.0;
	- mitk::FillVector3D(origin, cog[0]-factoraxes[1][0]-factoraxes[2][0],
	- cog[1]-factoraxes[1][1]-factoraxes[2][1],
	- cog[2]-factoraxes[1][2]-factoraxes[2][2]);
	- // mitk::FillVector3D(normal, axis[0][0],axis[0][1],axis[0][2]);
	- mitk::FillVector3D(bottom, 2factoraxes[1][0], 2factoraxes[1][1], 2factoraxes[1][2]);
	- mitk::FillVector3D(right, 2factoraxes[2][0], 2factoraxes[2][1], 2factoraxes[2][2]);
	-
	- mitk::PlaneGeometry::Pointer planegeometry = mitk::PlaneGeometry::New();
	- planegeometry->InitializeStandardPlane(right.GetVnlVector(), bottom.GetVnlVector());
	- planegeometry->SetOrigin(origin);
	-
	- double len1 = sqrt(axes[1][0]axes[1][0] + axes[1][1]axes[1][1] + axes[1][2]*axes[1][2]);
	- double len2 = sqrt(axes[2][0]axes[2][0] + axes[2][1]axes[2][1] + axes[2][2]*axes[2][2]);
	-
	- mitk::Point2D point1;
	- point1[0] = factor*len1;
	- point1[1] = factor*len2;
	-
	- mitk::Point2D point2;
	- point2[0] = factorlen1+extent.5;
	- point2[1] = factor*len2;
	-
	- mitk::PlanarCircle::Pointer circle = mitk::PlanarCircle::New();
	- circle->SetPlaneGeometry(planegeometry);
	- circle->PlaceFigure( point1 );
	- circle->SetControlPoint(0,point1);
	- circle->SetControlPoint(1,point2);
	- //circle->SetCurrentControlPoint( point2 );
	-
	- mitk::PlanarFigure::PolyLineType polyline = circle->GetPolyLine( 0 );
	- MITK_DEBUG << "SIZE of planar figure polyline: " << polyline.size();
	-
	- AddFigureToDataStorage(circle, "Circle");
	-
	-}
	-
	-bool QmitkPartialVolumeAnalysisView::AssertDrawingIsPossible(bool checked)
	-{
	- if (m_SelectedImageNodes->GetNode().IsNull())
	- {
	- checked = false;
	- this->HandleException("Please select an image!", dynamic_cast<QWidget *>(this->parent()), true);
	- return false;
	- }
	-
	- //this->GetRenderWindowPart(OPEN)->EnableSlicingPlanes(false);
	-
	- return checked;
	-}
	-
	-void QmitkPartialVolumeAnalysisView::ActionDrawEllipseTriggered()
	-{
	- bool checked = m_Controls->m_CircleButton->isChecked();
	- if(!this->AssertDrawingIsPossible(checked))
	- return;
	-
	- mitk::PlanarCircle::Pointer figure = mitk::PlanarCircle::New();
	- // using PV_ prefix for planar figures from this view
	- // to distinguish them from that ones created throught the measurement view
	- this->AddFigureToDataStorage(figure, QString("PV_Circle%1").arg(++m_EllipseCounter));
	-
	- MITK_DEBUG << "PlanarCircle created ...";
	-}
	-
	-void QmitkPartialVolumeAnalysisView::ActionDrawRectangleTriggered()
	-{
	- bool checked = m_Controls->m_RectangleButton->isChecked();
	- if(!this->AssertDrawingIsPossible(checked))
	- return;
	-
	- mitk::PlanarRectangle::Pointer figure = mitk::PlanarRectangle::New();
	- // using PV_ prefix for planar figures from this view
	- // to distinguish them from that ones created throught the measurement view
	- this->AddFigureToDataStorage(figure, QString("PV_Rectangle%1").arg(++m_RectangleCounter));
	-
	- MITK_DEBUG << "PlanarRectangle created ...";
	-}
	-
	-void QmitkPartialVolumeAnalysisView::ActionDrawPolygonTriggered()
	-{
	- bool checked = m_Controls->m_PolygonButton->isChecked();
	- if(!this->AssertDrawingIsPossible(checked))
	- return;
	-
	- mitk::PlanarPolygon::Pointer figure = mitk::PlanarPolygon::New();
	- figure->ClosedOn();
	- // using PV_ prefix for planar figures from this view
	- // to distinguish them from that ones created throught the measurement view
	- this->AddFigureToDataStorage(figure, QString("PV_Polygon%1").arg(++m_PolygonCounter));
	-
	- MITK_DEBUG << "PlanarPolygon created ...";
	-}
	-
	-void QmitkPartialVolumeAnalysisView::AddFigureToDataStorage(mitk::PlanarFigure* figure, const QString& name,
	- const char propertyKey, mitk::BaseProperty property )
	-{
	-
	- mitk::DataNode::Pointer newNode = mitk::DataNode::New();
	- newNode->SetName(name.toStdString());
	- newNode->SetData(figure);
	-
	- // Add custom property, if available
	- if ( (propertyKey != nullptr) && (property != nullptr) )
	- {
	- newNode->AddProperty( propertyKey, property );
	- }
	-
	- // figure drawn on the topmost layer / image
	- this->GetDataStorage()->Add(newNode, m_SelectedImageNodes->GetNode() );
	-
	- QList<mitk::DataNode::Pointer> selectedNodes = this->GetDataManagerSelection();
	- for(int i = 0; i < selectedNodes.size(); ++i)
	- {
	- selectedNodes[i]->SetSelected(false);
	- }
	-
	- std::vector<mitk::DataNode *> selectedPFNodes = m_SelectedPlanarFigureNodes->GetNodes();
	- for(std::size_t i = 0; i < selectedPFNodes.size(); ++i)
	- {
	- selectedPFNodes[i]->SetSelected(false);
	- }
	- newNode->SetSelected(true);
	-
	- Select(newNode);
	-}
	-
	-void QmitkPartialVolumeAnalysisView::PlanarFigureInitialized()
	-{
	- if(m_SelectedPlanarFigureNodes->GetNode().IsNull())
	- return;
	-
	- m_CurrentFigureNodeInitialized = true;
	-
	- this->Select(m_SelectedPlanarFigureNodes->GetNode());
	-
	- m_Controls->m_CircleButton->setChecked(false);
	- m_Controls->m_RectangleButton->setChecked(false);
	- m_Controls->m_PolygonButton->setChecked(false);
	-
	- //this->GetRenderWindowPart(OPEN)->EnableSlicingPlanes(true);
	- this->RequestStatisticsUpdate();
	-
	-}
	-
	-void QmitkPartialVolumeAnalysisView::PlanarFigureFocus(mitk::DataNode* node)
	-{
	- mitk::PlanarFigure* _PlanarFigure = 0;
	- _PlanarFigure = dynamic_cast<mitk::PlanarFigure*> (node->GetData());
	-
	- if (_PlanarFigure)
	- {
	-
	- FindRenderWindow(node);
	-
	- const mitk::PlaneGeometry* _PlaneGeometry = _PlanarFigure->GetPlaneGeometry();
	-
	- // make node visible
	- if (m_SelectedRenderWindow)
	- {
	- mitk::Point3D centerP = _PlaneGeometry->GetOrigin();
	- m_SelectedRenderWindow->GetSliceNavigationController()->ReorientSlices(
	- centerP, _PlaneGeometry->GetNormal());
	- m_SelectedRenderWindow->GetSliceNavigationController()->SelectSliceByPoint(
	- centerP);
	- }
	- }
	-}
	-
	-void QmitkPartialVolumeAnalysisView::FindRenderWindow(mitk::DataNode* node)
	-{
	- if (node && dynamic_cast<mitk::PlanarFigure*> (node->GetData()))
	- {
	- m_SelectedRenderWindow = 0;
	- bool PlanarFigureInitializedWindow = false;
	-
	- foreach(QmitkRenderWindow * window, this->GetRenderWindowPart()->GetQmitkRenderWindows().values())
	- {
	- if (!m_SelectedRenderWindow && node->GetBoolProperty("PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, window->GetRenderer()))
	- {
	- m_SelectedRenderWindow = window;
	- }
	- }
	- }
	-}
	-
	-
	-void QmitkPartialVolumeAnalysisView::OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList<mitk::DataNode::Pointer> &nodes)
	-{
	- m_Controls->m_InputData->setTitle("Please Select Input Data");
	-
	- if (!m_Visible)
	- return;
	-
	- if ( nodes.empty() )
	- {
	- if (m_ClusteringResult.IsNotNull())
	- {
	- this->GetDataStorage()->Remove(m_ClusteringResult);
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- }
	-
	- Select(nullptr, true, true);
	- }
	-
	- for (int i=0; i<nodes.size(); i++)
	- Select(nodes.at(i));
	-}
	-
	-void QmitkPartialVolumeAnalysisView::Select( mitk::DataNode::Pointer node, bool clearMaskOnFirstArgnullptr, bool clearImageOnFirstArgnullptr )
	-{
	- // Clear any unreferenced images
	- this->RemoveOrphanImages();
	-
	- bool somethingChanged = false;
	- if(node.IsNull())
	- {
	- somethingChanged = true;
	-
	- if(clearMaskOnFirstArgnullptr)
	- {
	- if ( (m_SelectedImageMask.IsNotNull()) && (m_ImageMaskObserverTag >= 0) )
	- {
	- m_SelectedImageMask->RemoveObserver( m_ImageMaskObserverTag );
	- m_ImageMaskObserverTag = -1;
	- }
	-
	- if ( (m_SelectedPlanarFigure.IsNotNull()) && (m_PlanarFigureObserverTag >= 0) )
	- {
	- m_SelectedPlanarFigure->RemoveObserver( m_PlanarFigureObserverTag );
	- m_PlanarFigureObserverTag = -1;
	- }
	-
	- if ( (m_SelectedPlanarFigure.IsNotNull()) && (m_InitializedObserverTag >= 0) )
	- {
	- m_SelectedPlanarFigure->RemoveObserver( m_InitializedObserverTag );
	- m_InitializedObserverTag = -1;
	- }
	-
	- m_SelectedPlanarFigure = nullptr;
	- m_SelectedPlanarFigureNodes->RemoveAllNodes();
	- m_CurrentFigureNodeInitialized = false;
	- m_SelectedRenderWindow = 0;
	-
	- m_SelectedMaskNode = nullptr;
	- m_SelectedImageMask = nullptr;
	-
	- }
	-
	- if(clearImageOnFirstArgnullptr)
	- {
	- if ( (m_SelectedImage.IsNotNull()) && (m_ImageObserverTag >= 0) )
	- {
	- m_SelectedImage->RemoveObserver( m_ImageObserverTag );
	- m_ImageObserverTag = -1;
	- }
	-
	- m_SelectedImageNodes->RemoveAllNodes();
	- m_SelectedImage = nullptr;
	-
	- m_IsTensorImage = false;
	- m_FAImage = nullptr;
	- m_RDImage = nullptr;
	- m_ADImage = nullptr;
	- m_MDImage = nullptr;
	- m_CAImage = nullptr;
	- m_DirectionComp1Image = nullptr;
	- m_DirectionComp2Image = nullptr;
	- m_AngularErrorImage = nullptr;
	-
	- m_Controls->m_SimilarAnglesFrame->setVisible(false);
	- m_Controls->m_SimilarAnglesLabel->setVisible(false);
	- }
	- }
	- else
	- {
	- typedef itk::SimpleMemberCommand< QmitkPartialVolumeAnalysisView > ITKCommandType;
	- ITKCommandType::Pointer changeListener;
	- changeListener = ITKCommandType::New();
	- changeListener->SetCallbackFunction( this, &QmitkPartialVolumeAnalysisView::RequestStatisticsUpdate );
	-
	- // Get selected element
	- mitk::TensorImage selectedTensorImage = dynamic_cast< mitk::TensorImage >( node->GetData() );
	- mitk::Image selectedImage = dynamic_cast< mitk::Image >( node->GetData() );
	- mitk::PlanarFigure selectedPlanar = dynamic_cast< mitk::PlanarFigure >( node->GetData() );
	-
	- bool isMask = false;
	- bool isImage = false;
	- bool isPlanar = false;
	- bool isTensorImage = false;
	-
	- if (selectedTensorImage != nullptr)
	- {
	- isTensorImage = true;
	- }
	- else if(selectedImage != nullptr)
	- {
	- node->GetPropertyValue("binary", isMask);
	- isImage = !isMask;
	- }
	- else if ( (selectedPlanar != nullptr) )
	- {
	- isPlanar = true;
	- }
	-
	- // image
	- if(isImage && selectedImage->GetDimension()==3)
	- {
	- if(selectedImage != m_SelectedImage.GetPointer())
	- {
	- somethingChanged = true;
	-
	- if ( (m_SelectedImage.IsNotNull()) && (m_ImageObserverTag >= 0) )
	- {
	- m_SelectedImage->RemoveObserver( m_ImageObserverTag );
	- m_ImageObserverTag = -1;
	- }
	-
	- *m_SelectedImageNodes = node;
	- m_SelectedImage = selectedImage;
	- m_IsTensorImage = false;
	- m_FAImage = nullptr;
	- m_RDImage = nullptr;
	- m_ADImage = nullptr;
	- m_MDImage = nullptr;
	- m_CAImage = nullptr;
	- m_DirectionComp1Image = nullptr;
	- m_DirectionComp2Image = nullptr;
	- m_AngularErrorImage = nullptr;
	-
	- // Add change listeners to selected objects
	- m_ImageObserverTag = m_SelectedImage->AddObserver(
	- itk::ModifiedEvent(), changeListener );
	-
	- m_Controls->m_SimilarAnglesFrame->setVisible(false);
	- m_Controls->m_SimilarAnglesLabel->setVisible(false);
	-
	- m_Controls->m_SelectedImageLabel->setText( m_SelectedImageNodes->GetNode()->GetName().c_str() );
	- }
	- }
	-
	- //planar
	- if(isPlanar)
	- {
	- if(selectedPlanar != m_SelectedPlanarFigure.GetPointer())
	- {
	- MITK_DEBUG << "Planar selection changed";
	- somethingChanged = true;
	-
	- // Possibly previous change listeners
	- if ( (m_SelectedPlanarFigure.IsNotNull()) && (m_PlanarFigureObserverTag >= 0) )
	- {
	- m_SelectedPlanarFigure->RemoveObserver( m_PlanarFigureObserverTag );
	- m_PlanarFigureObserverTag = -1;
	- }
	-
	- if ( (m_SelectedPlanarFigure.IsNotNull()) && (m_InitializedObserverTag >= 0) )
	- {
	- m_SelectedPlanarFigure->RemoveObserver( m_InitializedObserverTag );
	- m_InitializedObserverTag = -1;
	- }
	-
	- m_SelectedPlanarFigure = selectedPlanar;
	- *m_SelectedPlanarFigureNodes = node;
	- m_CurrentFigureNodeInitialized = selectedPlanar->IsPlaced();
	-
	- m_SelectedMaskNode = nullptr;
	- m_SelectedImageMask = nullptr;
	-
	- m_PlanarFigureObserverTag = m_SelectedPlanarFigure->AddObserver(
	- mitk::EndInteractionPlanarFigureEvent(), changeListener );
	-
	- if(!m_CurrentFigureNodeInitialized)
	- {
	- typedef itk::SimpleMemberCommand< QmitkPartialVolumeAnalysisView > ITKCommandType;
	- ITKCommandType::Pointer initializationCommand;
	- initializationCommand = ITKCommandType::New();
	-
	- // set the callback function of the member command
	- initializationCommand->SetCallbackFunction( this, &QmitkPartialVolumeAnalysisView::PlanarFigureInitialized );
	-
	- // add an observer
	- m_InitializedObserverTag = selectedPlanar->AddObserver( mitk::EndPlacementPlanarFigureEvent(), initializationCommand );
	-
	- }
	-
	- m_Controls->m_SelectedMaskLabel->setText( m_SelectedPlanarFigureNodes->GetNode()->GetName().c_str() );
	- PlanarFigureFocus(node);
	- }
	- }
	-
	- //mask
	- this->m_Controls->m_EstimateCircle->setEnabled(isMask && selectedImage->GetDimension()==3);
	- if(isMask && selectedImage->GetDimension()==3)
	- {
	- if(selectedImage != m_SelectedImage.GetPointer())
	- {
	- somethingChanged = true;
	-
	- if ( (m_SelectedImageMask.IsNotNull()) && (m_ImageMaskObserverTag >= 0) )
	- {
	- m_SelectedImageMask->RemoveObserver( m_ImageMaskObserverTag );
	- m_ImageMaskObserverTag = -1;
	- }
	-
	- m_SelectedMaskNode = node;
	- m_SelectedImageMask = selectedImage;
	- m_SelectedPlanarFigure = nullptr;
	- m_SelectedPlanarFigureNodes->RemoveAllNodes();
	-
	- m_ImageMaskObserverTag = m_SelectedImageMask->AddObserver(
	- itk::ModifiedEvent(), changeListener );
	-
	- m_Controls->m_SelectedMaskLabel->setText( m_SelectedMaskNode->GetName().c_str() );
	-
	- }
	- }
	-
	- //tensor image
	- if(isTensorImage && selectedTensorImage->GetDimension()==3)
	- {
	- if(selectedImage != m_SelectedImage.GetPointer())
	- {
	- somethingChanged = true;
	-
	- if ( (m_SelectedImage.IsNotNull()) && (m_ImageObserverTag >= 0) )
	- {
	- m_SelectedImage->RemoveObserver( m_ImageObserverTag );
	- m_ImageObserverTag = -1;
	- }
	-
	- *m_SelectedImageNodes = node;
	- m_SelectedImage = selectedImage;
	-
	- m_IsTensorImage = true;
	-
	- ExtractTensorImages(selectedImage);
	-
	- // Add change listeners to selected objects
	- m_ImageObserverTag = m_SelectedImage->AddObserver(
	- itk::ModifiedEvent(), changeListener );
	-
	- m_Controls->m_SimilarAnglesFrame->setVisible(true);
	- m_Controls->m_SimilarAnglesLabel->setVisible(true);
	-
	- m_Controls->m_SelectedImageLabel->setText( m_SelectedImageNodes->GetNode()->GetName().c_str() );
	- }
	- }
	- }
	-
	- if(somethingChanged)
	- {
	- this->SetMeasurementInfoToRenderWindow("");
	-
	- if(m_SelectedPlanarFigure.IsNull() && m_SelectedImageMask.IsNull() )
	- {
	- m_Controls->m_SelectedMaskLabel->setText("<font color='red'>mandatory</font>");
	- m_Controls->m_ResampleOptionsFrame->setEnabled(false);
	- m_Controls->m_HistogramWidget->setEnabled(false);
	- m_Controls->m_ClassSelector->setEnabled(false);
	- m_Controls->m_DisplayHistogramCheckbox->setEnabled(false);
	- m_Controls->m_AdvancedCheckbox->setEnabled(false);
	- m_Controls->frame_7->setEnabled(false);
	- }
	- else
	- {
	- m_Controls->m_ResampleOptionsFrame->setEnabled(true);
	- m_Controls->m_HistogramWidget->setEnabled(true);
	- m_Controls->m_ClassSelector->setEnabled(true);
	- m_Controls->m_DisplayHistogramCheckbox->setEnabled(true);
	- m_Controls->m_AdvancedCheckbox->setEnabled(true);
	- m_Controls->frame_7->setEnabled(true);
	- }
	-
	- // Clear statistics / histogram GUI if nothing is selected
	- if ( m_SelectedImage.IsNull() )
	- {
	- m_Controls->m_PlanarFigureButtonsFrame->setEnabled(false);
	- m_Controls->m_OpacityFrame->setEnabled(false);
	- m_Controls->m_SelectedImageLabel->setText("<font color='red'>mandatory</font>");
	- }
	- else
	- {
	- m_Controls->m_PlanarFigureButtonsFrame->setEnabled(true);
	- m_Controls->m_OpacityFrame->setEnabled(true);
	- }
	-
	- if( !m_Visible \|\| m_SelectedImage.IsNull()
	- \|\| (m_SelectedPlanarFigure.IsNull() && m_SelectedImageMask.IsNull()) )
	- {
	- m_Controls->m_InputData->setTitle("Please Select Input Data");
	- m_Controls->m_HistogramWidget->ClearItemModel();
	- m_CurrentStatisticsValid = false;
	- }
	- else
	- {
	- m_Controls->m_InputData->setTitle("Input Data");
	- this->RequestStatisticsUpdate();
	- }
	- }
	-}
	-
	-
	-void QmitkPartialVolumeAnalysisView::ShowClusteringResults()
	-{
	-
	- typedef itk::Image<unsigned char, 3> MaskImageType;
	- mitk::Image::Pointer mask = 0;
	- MaskImageType::Pointer itkmask = 0;
	-
	- if(m_IsTensorImage && m_Controls->m_SimilarAnglesSlider->value() != 0)
	- {
	- typedef itk::Image<float, 3> AngularErrorImageType;
	- typedef mitk::ImageToItk<AngularErrorImageType> CastType;
	- CastType::Pointer caster = CastType::New();
	- caster->SetInput(m_AngularErrorImage);
	- caster->Update();
	-
	- typedef itk::BinaryThresholdImageFilter< AngularErrorImageType, MaskImageType > ThreshType;
	- ThreshType::Pointer thresh = ThreshType::New();
	- thresh->SetUpperThreshold((90-m_Controls->m_SimilarAnglesSlider->value())*(itk::Math::pi/180.0));
	- thresh->SetInsideValue(1.0);
	- thresh->SetInput(caster->GetOutput());
	- thresh->Update();
	- itkmask = thresh->GetOutput();
	-
	- mask = mitk::Image::New();
	- mask->InitializeByItk(itkmask.GetPointer());
	- mask->SetVolume(itkmask->GetBufferPointer());
	-
	- // GetDataStorage()->Remove(m_newnode);
	- // m_newnode = mitk::DataNode::New();
	- // m_newnode->SetData(mask);
	- // m_newnode->SetName("masking node");
	- // m_newnode->SetIntProperty( "layer", 1002 );
	- // GetDataStorage()->Add(m_newnode, m_SelectedImageNodes->GetNode());
	-
	- }
	-
	- mitk::Image::Pointer clusteredImage;
	- ClusteringType::Pointer clusterer = ClusteringType::New();
	-
	- if(m_QuantifyClass==3)
	- {
	-
	- if(m_IsTensorImage)
	- {
	- double green_fa, green_rd, green_ad, green_md;
	- //double greengray_fa, greengray_rd, greengray_ad, greengray_md;
	- double gray_fa, gray_rd, gray_ad, gray_md;
	- //double redgray_fa, redgray_rd, redgray_ad, redgray_md;
	- double red_fa, red_rd, red_ad, red_md;
	-
	- mitk::Image* tmpImg = m_CurrentStatisticsCalculator->GetInternalAdditionalResampledImage(0);
	- mitk::Image::ConstPointer imgToCluster = tmpImg;
	-
	- red_fa = clusterer->PerformQuantification(imgToCluster, m_CurrentRGBClusteringResults->rgbChannels->r, mask);
	- green_fa = clusterer->PerformQuantification(imgToCluster, m_CurrentRGBClusteringResults->rgbChannels->g, mask);
	- gray_fa = clusterer->PerformQuantification(imgToCluster, m_CurrentRGBClusteringResults->rgbChannels->b, mask);
	-
	- tmpImg = m_CurrentStatisticsCalculator->GetInternalAdditionalResampledImage(3);
	- mitk::Image::ConstPointer imgToCluster3 = tmpImg;
	-
	- red_rd = clusterer->PerformQuantification(imgToCluster3, m_CurrentRGBClusteringResults->rgbChannels->r, mask);
	- green_rd = clusterer->PerformQuantification(imgToCluster3, m_CurrentRGBClusteringResults->rgbChannels->g, mask);
	- gray_rd = clusterer->PerformQuantification(imgToCluster3, m_CurrentRGBClusteringResults->rgbChannels->b, mask);
	-
	- tmpImg = m_CurrentStatisticsCalculator->GetInternalAdditionalResampledImage(4);
	- mitk::Image::ConstPointer imgToCluster4 = tmpImg;
	-
	- red_ad = clusterer->PerformQuantification(imgToCluster4, m_CurrentRGBClusteringResults->rgbChannels->r, mask);
	- green_ad = clusterer->PerformQuantification(imgToCluster4, m_CurrentRGBClusteringResults->rgbChannels->g, mask);
	- gray_ad = clusterer->PerformQuantification(imgToCluster4, m_CurrentRGBClusteringResults->rgbChannels->b, mask);
	-
	- tmpImg = m_CurrentStatisticsCalculator->GetInternalAdditionalResampledImage(5);
	- mitk::Image::ConstPointer imgToCluster5 = tmpImg;
	-
	- red_md = clusterer->PerformQuantification(imgToCluster5, m_CurrentRGBClusteringResults->rgbChannels->r, mask);
	- green_md = clusterer->PerformQuantification(imgToCluster5, m_CurrentRGBClusteringResults->rgbChannels->g, mask);
	- gray_md = clusterer->PerformQuantification(imgToCluster5, m_CurrentRGBClusteringResults->rgbChannels->b, mask);
	-
	- // clipboard
	- QString clipboardText("FA\t%1\t%2\t\t%3\t%4\t\t%5\t%6\t");
	- clipboardText = clipboardText
	- .arg(red_fa[0]).arg(red_fa[1])
	- .arg(gray_fa[0]).arg(gray_fa[1])
	- .arg(green_fa[0]).arg(green_fa[1]);
	- QString clipboardText3("RD\t%1\t%2\t\t%3\t%4\t\t%5\t%6\t");
	- clipboardText3 = clipboardText3
	- .arg(red_rd[0]).arg(red_rd[1])
	- .arg(gray_rd[0]).arg(gray_rd[1])
	- .arg(green_rd[0]).arg(green_rd[1]);
	- QString clipboardText4("AD\t%1\t%2\t\t%3\t%4\t\t%5\t%6\t");
	- clipboardText4 = clipboardText4
	- .arg(red_ad[0]).arg(red_ad[1])
	- .arg(gray_ad[0]).arg(gray_ad[1])
	- .arg(green_ad[0]).arg(green_ad[1]);
	- QString clipboardText5("MD\t%1\t%2\t\t%3\t%4\t\t%5\t%6");
	- clipboardText5 = clipboardText5
	- .arg(red_md[0]).arg(red_md[1])
	- .arg(gray_md[0]).arg(gray_md[1])
	- .arg(green_md[0]).arg(green_md[1]);
	-
	- QApplication::clipboard()->setText(clipboardText+clipboardText3+clipboardText4+clipboardText5, QClipboard::Clipboard);
	-
	- // now paint infos also on renderwindow
	- QString plainInfoText("%1 %2 %3 \n");
	- plainInfoText = plainInfoText
	- .arg("Red ", 20)
	- .arg("Gray ", 20)
	- .arg("Green", 20);
	-
	- QString plainInfoText0("FA:%1 ± %2%3 ± %4%5 ± %6\n");
	- plainInfoText0 = plainInfoText0
	- .arg(red_fa[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(red_fa[1], -10, 'g', 2, QLatin1Char( ' ' ))
	- .arg(gray_fa[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(gray_fa[1], -10, 'g', 2, QLatin1Char( ' ' ))
	- .arg(green_fa[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(green_fa[1], -10, 'g', 2, QLatin1Char( ' ' ));
	-
	- QString plainInfoText3("RDx10³:%1 ± %2%3 ± %4%5 ± %6\n");
	- plainInfoText3 = plainInfoText3
	- .arg(1000.0 * red_rd[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * red_rd[1], -10, 'g', 2, QLatin1Char( ' ' ))
	- .arg(1000.0 * gray_rd[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * gray_rd[1], -10, 'g', 2, QLatin1Char( ' ' ))
	- .arg(1000.0 * green_rd[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * green_rd[1], -10, 'g', 2, QLatin1Char( ' ' ));
	-
	- QString plainInfoText4("ADx10³:%1 ± %2%3 ± %4%5 ± %6\n");
	- plainInfoText4 = plainInfoText4
	- .arg(1000.0 * red_ad[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * red_ad[1], -10, 'g', 2, QLatin1Char( ' ' ))
	- .arg(1000.0 * gray_ad[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * gray_ad[1], -10, 'g', 2, QLatin1Char( ' ' ))
	- .arg(1000.0 * green_ad[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * green_ad[1], -10, 'g', 2, QLatin1Char( ' ' ));
	-
	- QString plainInfoText5("MDx10³:%1 ± %2%3 ± %4%5 ± %6");
	- plainInfoText5 = plainInfoText5
	- .arg(1000.0 * red_md[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * red_md[1], -10, 'g', 2, QLatin1Char( ' ' ))
	- .arg(1000.0 * gray_md[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * gray_md[1], -10, 'g', 2, QLatin1Char( ' ' ))
	- .arg(1000.0 * green_md[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * green_md[1], -10, 'g', 2, QLatin1Char( ' ' ));
	-
	- this->SetMeasurementInfoToRenderWindow(plainInfoText+plainInfoText0+plainInfoText3+plainInfoText4+plainInfoText5);
	-
	- }
	- else
	- {
	- double* green;
	- double* gray;
	- double* red;
	-
	- mitk::Image* tmpImg = m_CurrentStatisticsCalculator->GetInternalImage();
	- mitk::Image::ConstPointer imgToCluster = tmpImg;
	-
	- red = clusterer->PerformQuantification(imgToCluster, m_CurrentRGBClusteringResults->rgbChannels->r);
	- green = clusterer->PerformQuantification(imgToCluster, m_CurrentRGBClusteringResults->rgbChannels->g);
	- gray = clusterer->PerformQuantification(imgToCluster, m_CurrentRGBClusteringResults->rgbChannels->b);
	-
	- // clipboard
	- QString clipboardText("%1\t%2\t\t%3\t%4\t\t%5\t%6");
	- clipboardText = clipboardText.arg(red[0]).arg(red[1])
	- .arg(gray[0]).arg(gray[1])
	- .arg(green[0]).arg(green[1]);
	- QApplication::clipboard()->setText(clipboardText, QClipboard::Clipboard);
	-
	- // now paint infos also on renderwindow
	- QString plainInfoText("Red: %1 ± %2\nGray: %3 ± %4\nGreen: %5 ± %6");
	- plainInfoText = plainInfoText.arg(red[0]).arg(red[1])
	- .arg(gray[0]).arg(gray[1])
	- .arg(green[0]).arg(green[1]);
	-
	- this->SetMeasurementInfoToRenderWindow(plainInfoText);
	-
	- }
	-
	-
	- clusteredImage = m_CurrentRGBClusteringResults->rgb;
	-
	- }
	- else
	- {
	- if(m_IsTensorImage)
	- {
	- double red_fa, red_rd, red_ad, red_md;
	-
	- mitk::Image* tmpImg = m_CurrentStatisticsCalculator->GetInternalAdditionalResampledImage(0);
	- mitk::Image::ConstPointer imgToCluster = tmpImg;
	- red_fa = clusterer->PerformQuantification(imgToCluster, m_CurrentPerformClusteringResults->clusteredImage, mask);
	-
	- tmpImg = m_CurrentStatisticsCalculator->GetInternalAdditionalResampledImage(3);
	- mitk::Image::ConstPointer imgToCluster3 = tmpImg;
	- red_rd = clusterer->PerformQuantification(imgToCluster3, m_CurrentPerformClusteringResults->clusteredImage, mask);
	-
	- tmpImg = m_CurrentStatisticsCalculator->GetInternalAdditionalResampledImage(4);
	- mitk::Image::ConstPointer imgToCluster4 = tmpImg;
	- red_ad = clusterer->PerformQuantification(imgToCluster4, m_CurrentPerformClusteringResults->clusteredImage, mask);
	-
	- tmpImg = m_CurrentStatisticsCalculator->GetInternalAdditionalResampledImage(5);
	- mitk::Image::ConstPointer imgToCluster5 = tmpImg;
	- red_md = clusterer->PerformQuantification(imgToCluster5, m_CurrentPerformClusteringResults->clusteredImage, mask);
	-
	- // clipboard
	- QString clipboardText("FA\t%1\t%2\t");
	- clipboardText = clipboardText
	- .arg(red_fa[0]).arg(red_fa[1]);
	- QString clipboardText3("RD\t%1\t%2\t");
	- clipboardText3 = clipboardText3
	- .arg(red_rd[0]).arg(red_rd[1]);
	- QString clipboardText4("AD\t%1\t%2\t");
	- clipboardText4 = clipboardText4
	- .arg(red_ad[0]).arg(red_ad[1]);
	- QString clipboardText5("MD\t%1\t%2\t");
	- clipboardText5 = clipboardText5
	- .arg(red_md[0]).arg(red_md[1]);
	-
	- QApplication::clipboard()->setText(clipboardText+clipboardText3+clipboardText4+clipboardText5, QClipboard::Clipboard);
	-
	- // now paint infos also on renderwindow
	- QString plainInfoText("%1 \n");
	- plainInfoText = plainInfoText
	- .arg("Red ", 20);
	-
	- QString plainInfoText0("FA:%1 ± %2\n");
	- plainInfoText0 = plainInfoText0
	- .arg(red_fa[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(red_fa[1], -10, 'g', 2, QLatin1Char( ' ' ));
	-
	- QString plainInfoText3("RDx10³:%1 ± %2\n");
	- plainInfoText3 = plainInfoText3
	- .arg(1000.0 * red_rd[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * red_rd[1], -10, 'g', 2, QLatin1Char( ' ' ));
	-
	- QString plainInfoText4("ADx10³:%1 ± %2\n");
	- plainInfoText4 = plainInfoText4
	- .arg(1000.0 * red_ad[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * red_ad[1], -10, 'g', 2, QLatin1Char( ' ' ));
	-
	- QString plainInfoText5("MDx10³:%1 ± %2");
	- plainInfoText5 = plainInfoText5
	- .arg(1000.0 * red_md[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * red_md[1], -10, 'g', 2, QLatin1Char( ' ' ));
	-
	- this->SetMeasurementInfoToRenderWindow(plainInfoText+plainInfoText0+plainInfoText3+plainInfoText4+plainInfoText5);
	-
	- }
	- else
	- {
	- double* quant;
	-
	- mitk::Image* tmpImg = m_CurrentStatisticsCalculator->GetInternalImage();
	- mitk::Image::ConstPointer imgToCluster = tmpImg;
	- quant = clusterer->PerformQuantification(imgToCluster, m_CurrentPerformClusteringResults->clusteredImage);
	-
	- // clipboard
	- QString clipboardText("%1\t%2");
	- clipboardText = clipboardText.arg(quant[0]).arg(quant[1]);
	- QApplication::clipboard()->setText(clipboardText, QClipboard::Clipboard);
	-
	- // now paint infos also on renderwindow
	- QString plainInfoText("Measurement: %1 ± %2");
	- plainInfoText = plainInfoText.arg(quant[0]).arg(quant[1]);
	-
	- this->SetMeasurementInfoToRenderWindow(plainInfoText);
	- }
	-
	- clusteredImage = m_CurrentPerformClusteringResults->displayImage;
	-
	- }
	-
	- if(mask.IsNotNull())
	- {
	- typedef itk::Image<itk::RGBAPixel<unsigned char>,3> RGBImageType;
	- typedef mitk::ImageToItk<RGBImageType> ClusterCasterType;
	- ClusterCasterType::Pointer clCaster = ClusterCasterType::New();
	- clCaster->SetInput(clusteredImage);
	- clCaster->Update();
	- clCaster->GetOutput();
	-
	- typedef itk::MaskImageFilter< RGBImageType, MaskImageType, RGBImageType > MaskType;
	- MaskType::Pointer masker = MaskType::New();
	- masker->SetInput1(clCaster->GetOutput());
	- masker->SetInput2(itkmask);
	- masker->Update();
	-
	- clusteredImage = mitk::Image::New();
	- clusteredImage->InitializeByItk(masker->GetOutput());
	- clusteredImage->SetVolume(masker->GetOutput()->GetBufferPointer());
	- }
	-
	- if(m_ClusteringResult.IsNotNull())
	- {
	- this->GetDataStorage()->Remove(m_ClusteringResult);
	- }
	-
	- m_ClusteringResult = mitk::DataNode::New();
	- m_ClusteringResult->SetBoolProperty("helper object", true);
	- m_ClusteringResult->SetIntProperty( "layer", 1000 );
	- m_ClusteringResult->SetBoolProperty("texture interpolation", m_TexIsOn);
	- m_ClusteringResult->SetData(clusteredImage);
	- m_ClusteringResult->SetName("Clusterprobs");
	- this->GetDataStorage()->Add(m_ClusteringResult, m_SelectedImageNodes->GetNode());
	-
	- if(m_SelectedPlanarFigure.IsNotNull() && m_SelectedPlanarFigureNodes->GetNode().IsNotNull())
	- {
	- m_SelectedPlanarFigureNodes->GetNode()->SetIntProperty( "layer", 1001 );
	- }
	-
	- this->RequestRenderWindowUpdate();
	-
	-}
	-
	-
	-void QmitkPartialVolumeAnalysisView::UpdateStatistics()
	-{
	- if(!m_CurrentFigureNodeInitialized && m_SelectedPlanarFigure.IsNotNull())
	- {
	- MITK_DEBUG << "Selected planar figure not initialized. No stats calculation performed.";
	- return;
	- }
	-
	- // Remove any cached images that are no longer referenced elsewhere
	- this->RemoveOrphanImages();
	-
	- if ( m_SelectedImage.IsNotNull() )
	- {
	- // Check if a the selected image is a multi-channel image. If yes, statistics
	- // cannot be calculated currently.
	- if ( !m_IsTensorImage && m_SelectedImage->GetPixelType().GetNumberOfComponents() > 1 )
	- {
	- QMessageBox::information( nullptr, "Warning", "Non-tensor multi-component images not supported.");
	-
	- m_Controls->m_HistogramWidget->ClearItemModel();
	- m_CurrentStatisticsValid = false;
	- return;
	- }
	-
	- m_CurrentStatisticsCalculator = nullptr;
	- if(!m_IsTensorImage)
	- {
	- // Retrieve HistogramStatisticsCalculator from has map (or create a new one
	- // for this image if non-existant)
	- PartialVolumeAnalysisMapType::iterator it =
	- m_PartialVolumeAnalysisMap.find( m_SelectedImage );
	-
	- if ( it != m_PartialVolumeAnalysisMap.end() )
	- {
	- m_CurrentStatisticsCalculator = it->second;
	- }
	- }
	- if(m_CurrentStatisticsCalculator.IsNull())
	- {
	- m_CurrentStatisticsCalculator = mitk::PartialVolumeAnalysisHistogramCalculator::New();
	- m_CurrentStatisticsCalculator->SetPlanarFigureThickness(m_Controls->m_PlanarFiguresThickness->value());
	- if(m_IsTensorImage)
	- {
	- m_CurrentStatisticsCalculator->SetImage( m_CAImage );
	- m_CurrentStatisticsCalculator->AddAdditionalResamplingImage( m_FAImage );
	- m_CurrentStatisticsCalculator->AddAdditionalResamplingImage( m_DirectionComp1Image );
	- m_CurrentStatisticsCalculator->AddAdditionalResamplingImage( m_DirectionComp2Image );
	- m_CurrentStatisticsCalculator->AddAdditionalResamplingImage( m_RDImage );
	- m_CurrentStatisticsCalculator->AddAdditionalResamplingImage( m_ADImage );
	- m_CurrentStatisticsCalculator->AddAdditionalResamplingImage( m_MDImage );
	- }
	- else
	- {
	- m_CurrentStatisticsCalculator->SetImage( m_SelectedImage );
	- }
	- m_PartialVolumeAnalysisMap[m_SelectedImage] = m_CurrentStatisticsCalculator;
	- MITK_DEBUG << "Creating StatisticsCalculator";
	- }
	-
	- std::string maskName;
	- std::string maskType;
	- unsigned int maskDimension;
	-
	- if ( m_SelectedImageMask.IsNotNull() )
	- {
	-
	- mitk::PixelType pixelType = m_SelectedImageMask->GetPixelType();
	- MITK_DEBUG << pixelType.GetPixelTypeAsString();
	-
	-
	- if(pixelType.GetComponentTypeAsString() == "char")
	- {
	- MITK_DEBUG << "Pixel type is char instead of uchar";
	- return;
	- }
	-
	-
	- if(pixelType.GetBitsPerComponent() == 16)
	- {
	- //convert from ushort to uchar
	- typedef itk::Image<unsigned char, 3> UCharImageType;
	- UCharImageType::Pointer charImage;
	-
	-
	- if(pixelType.GetComponentTypeAsString() == "short" )
	- {
	- typedef itk::Image<short, 3> ShortImageType;
	-
	- ShortImageType::Pointer shortImage;
	- mitk::CastToItkImage( m_SelectedImageMask, shortImage );
	-
	- typedef itk::ImageDuplicator< ShortImageType > DuplicatorType;
	- DuplicatorType::Pointer duplicator = DuplicatorType::New();
	- duplicator->SetInputImage( shortImage );
	- duplicator->Update();
	-
	- typedef itk::CastImageFilter<ShortImageType, UCharImageType> ImageCasterType;
	-
	- ImageCasterType::Pointer caster = ImageCasterType::New();
	- caster->SetInput( duplicator->GetOutput() );
	- caster->Update();
	- charImage = caster->GetOutput();
	-
	- }
	- else
	- {
	- typedef itk::Image<unsigned short, 3> UShortImageType;
	-
	- UShortImageType::Pointer shortImage;
	- mitk::CastToItkImage( m_SelectedImageMask, shortImage );
	-
	- typedef itk::ImageDuplicator< UShortImageType > DuplicatorType;
	- DuplicatorType::Pointer duplicator = DuplicatorType::New();
	- duplicator->SetInputImage( shortImage );
	- duplicator->Update();
	-
	- typedef itk::CastImageFilter<UShortImageType, UCharImageType> ImageCasterType;
	-
	- ImageCasterType::Pointer caster = ImageCasterType::New();
	- caster->SetInput( duplicator->GetOutput() );
	- caster->Update();
	- charImage = caster->GetOutput();
	- }
	-
	- m_SelectedImageMask = nullptr;
	- m_SelectedImageMask = mitk::Image::New();
	- m_SelectedImageMask->InitializeByItk( charImage.GetPointer() );
	- m_SelectedImageMask->SetVolume( charImage->GetBufferPointer() );
	-
	- mitk::CastToMitkImage(charImage, m_SelectedImageMask);
	- }
	-
	-
	- m_CurrentStatisticsCalculator->SetImageMask( m_SelectedImageMask );
	-
	-
	- m_CurrentStatisticsCalculator->SetMaskingModeToImage();
	-
	- maskName = m_SelectedMaskNode->GetName();
	- maskType = m_SelectedImageMask->GetNameOfClass();
	- maskDimension = 3;
	-
	- std::stringstream maskLabel;
	- maskLabel << maskName;
	- if ( maskDimension > 0 )
	- {
	- maskLabel << " [" << maskDimension << "D " << maskType << "]";
	- }
	- m_Controls->m_SelectedMaskLabel->setText( maskLabel.str().c_str() );
	- }
	- else if ( m_SelectedPlanarFigure.IsNotNull() && m_SelectedPlanarFigureNodes->GetNode().IsNotNull())
	- {
	- m_CurrentStatisticsCalculator->SetPlanarFigure( m_SelectedPlanarFigure );
	- m_CurrentStatisticsCalculator->SetMaskingModeToPlanarFigure();
	-
	- maskName = m_SelectedPlanarFigureNodes->GetNode()->GetName();
	- maskType = m_SelectedPlanarFigure->GetNameOfClass();
	- maskDimension = 2;
	- }
	- else
	- {
	- m_CurrentStatisticsCalculator->SetMaskingModeToNone();
	-
	- maskName = "-";
	- maskType = "";
	- maskDimension = 0;
	- }
	-
	- bool statisticsChanged = false;
	- bool statisticsCalculationSuccessful = false;
	-
	- // Initialize progress bar
	- mitk::ProgressBar::GetInstance()->AddStepsToDo( 100 );
	-
	- // Install listener for progress events and initialize progress bar
	- typedef itk::SimpleMemberCommand< QmitkPartialVolumeAnalysisView > ITKCommandType;
	- ITKCommandType::Pointer progressListener;
	- progressListener = ITKCommandType::New();
	- progressListener->SetCallbackFunction( this, &QmitkPartialVolumeAnalysisView::UpdateProgressBar );
	- unsigned long progressObserverTag = m_CurrentStatisticsCalculator
	- ->AddObserver( itk::ProgressEvent(), progressListener );
	-
	- ClusteringType::ParamsType *cparams = 0;
	- ClusteringType::ClusterResultType *cresult = 0;
	- ClusteringType::HistType *chist = 0;
	-
	- try
	- {
	- m_CurrentStatisticsCalculator->SetNumberOfBins(m_Controls->m_NumberBins->text().toInt());
	- m_CurrentStatisticsCalculator->SetUpsamplingFactor(m_Controls->m_Upsampling->text().toDouble());
	- m_CurrentStatisticsCalculator->SetGaussianSigma(m_Controls->m_GaussianSigma->text().toDouble());
	-
	- // Compute statistics
	- statisticsChanged =
	- m_CurrentStatisticsCalculator->ComputeStatistics( );
	-
	- mitk::Image* tmpImg = m_CurrentStatisticsCalculator->GetInternalImage();
	- mitk::Image::ConstPointer imgToCluster = tmpImg;
	- if(imgToCluster.IsNotNull())
	- {
	-
	- // perform clustering
	- const HistogramType *histogram = m_CurrentStatisticsCalculator->GetHistogram( );
	-
	- if(histogram != nullptr)
	- {
	- ClusteringType::Pointer clusterer = ClusteringType::New();
	- clusterer->SetStepsNumIntegration(200);
	- clusterer->SetMaxIt(1000);
	-
	- mitk::Image::Pointer pFiberImg;
	- if(m_QuantifyClass==3)
	- {
	- if(m_Controls->m_Quantiles->isChecked())
	- {
	- m_CurrentRGBClusteringResults = clusterer->PerformRGBQuantiles(imgToCluster, histogram, m_Controls->m_q1->value(),m_Controls->m_q2->value());
	- }
	- else
	- {
	- m_CurrentRGBClusteringResults = clusterer->PerformRGBClustering(imgToCluster, histogram);
	- }
	-
	- pFiberImg = m_CurrentRGBClusteringResults->rgbChannels->r;
	- cparams = m_CurrentRGBClusteringResults->params;
	- cresult = m_CurrentRGBClusteringResults->result;
	- chist = m_CurrentRGBClusteringResults->hist;
	- }
	- else
	- {
	- if(m_Controls->m_Quantiles->isChecked())
	- {
	- m_CurrentPerformClusteringResults =
	- clusterer->PerformQuantiles(imgToCluster, histogram, m_Controls->m_q1->value(),m_Controls->m_q2->value());
	- }
	- else
	- {
	- m_CurrentPerformClusteringResults =
	- clusterer->PerformClustering(imgToCluster, histogram, m_QuantifyClass);
	- }
	-
	- pFiberImg = m_CurrentPerformClusteringResults->clusteredImage;
	- cparams = m_CurrentPerformClusteringResults->params;
	- cresult = m_CurrentPerformClusteringResults->result;
	- chist = m_CurrentPerformClusteringResults->hist;
	- }
	-
	- if(m_IsTensorImage)
	- {
	- m_AngularErrorImage = clusterer->CaculateAngularErrorImage(
	- m_CurrentStatisticsCalculator->GetInternalAdditionalResampledImage(1),
	- m_CurrentStatisticsCalculator->GetInternalAdditionalResampledImage(2),
	- pFiberImg);
	-
	- // GetDataStorage()->Remove(m_newnode2);
	- // m_newnode2 = mitk::DataNode::New();
	- // m_newnode2->SetData(m_AngularErrorImage);
	- // m_newnode2->SetName(("AngularError"));
	- // m_newnode2->SetIntProperty( "layer", 1003 );
	- // GetDataStorage()->Add(m_newnode2, m_SelectedImageNodes->GetNode());
	-
	- // newnode = mitk::DataNode::New();
	- // newnode->SetData(m_CurrentStatisticsCalculator->GetInternalAdditionalResampledImage(1));
	- // newnode->SetName(("Comp1"));
	- // GetDataStorage()->Add(newnode, m_SelectedImageNodes->GetNode());
	-
	- // newnode = mitk::DataNode::New();
	- // newnode->SetData(m_CurrentStatisticsCalculator->GetInternalAdditionalResampledImage(2));
	- // newnode->SetName(("Comp2"));
	- // GetDataStorage()->Add(newnode, m_SelectedImageNodes->GetNode());
	- }
	- ShowClusteringResults();
	- }
	-
	- }
	-
	- statisticsCalculationSuccessful = true;
	- }
	- catch ( const std::runtime_error &e )
	- {
	- QMessageBox::information( nullptr, "Warning", e.what());
	- }
	- catch ( const std::exception &e )
	- {
	- MITK_ERROR << "Caught exception: " << e.what();
	-
	- QMessageBox::information( nullptr, "Warning", e.what());
	- }
	-
	- m_CurrentStatisticsCalculator->RemoveObserver( progressObserverTag );
	-
	- // Make sure that progress bar closes
	- mitk::ProgressBar::GetInstance()->Progress( 100 );
	-
	- if ( statisticsCalculationSuccessful )
	- {
	- if ( statisticsChanged )
	- {
	- // Do not show any error messages
	- m_CurrentStatisticsValid = true;
	- }
	-
	- // m_Controls->m_HistogramWidget->SetHistogramModeToDirectHistogram();
	- m_Controls->m_HistogramWidget->SetParameters(
	- cparams, cresult, chist );
	- // m_Controls->m_HistogramWidget->UpdateItemModelFromHistogram();
	-
	- }
	- else
	- {
	- m_Controls->m_SelectedMaskLabel->setText("<font color='red'>mandatory</font>");
	-
	- // Clear statistics and histogram
	- m_Controls->m_HistogramWidget->ClearItemModel();
	- m_CurrentStatisticsValid = false;
	-
	-
	- // If a (non-closed) PlanarFigure is selected, display a line profile widget
	- if ( m_SelectedPlanarFigure.IsNotNull() )
	- {
	- // TODO: enable line profile widget
	- //m_Controls->m_StatisticsWidgetStack->setCurrentIndex( 1 );
	- //m_Controls->m_LineProfileWidget->SetImage( m_SelectedImage );
	- //m_Controls->m_LineProfileWidget->SetPlanarFigure( m_SelectedPlanarFigure );
	- //m_Controls->m_LineProfileWidget->UpdateItemModelFromPath();
	- }
	- }
	- }
	-
	-}
	-
	-void QmitkPartialVolumeAnalysisView::SetMeasurementInfoToRenderWindow(const QString& text)
	-{
	-
	- FindRenderWindow(m_SelectedPlanarFigureNodes->GetNode());
	-
	- if(m_LastRenderWindow != m_SelectedRenderWindow)
	- {
	-
	- if(m_LastRenderWindow)
	- {
	- QObject::disconnect( m_LastRenderWindow, SIGNAL( destroyed(QObject*) )
	- , this, SLOT( OnRenderWindowDelete(QObject*) ) );
	- }
	- m_LastRenderWindow = m_SelectedRenderWindow;
	- if(m_LastRenderWindow)
	- {
	- QObject::connect( m_LastRenderWindow, SIGNAL( destroyed(QObject*) )
	- , this, SLOT( OnRenderWindowDelete(QObject*) ) );
	- }
	- }
	-
	- if(m_LastRenderWindow && m_SelectedPlanarFigureNodes->GetNode().IsNotNull())
	- {
	- if (!text.isEmpty())
	- {
	- m_MeasurementInfoAnnotation->SetText(1, text.toLatin1().data());
	- mitk::VtkLayerController::GetInstance(m_LastRenderWindow->GetRenderWindow())->InsertForegroundRenderer(
	- m_MeasurementInfoRenderer, true);
	- }
	- else
	- {
	- if (mitk::VtkLayerController::GetInstance(
	- m_LastRenderWindow->GetRenderWindow()) ->IsRendererInserted(
	- m_MeasurementInfoRenderer))
	- mitk::VtkLayerController::GetInstance(m_LastRenderWindow->GetRenderWindow())->RemoveRenderer(
	- m_MeasurementInfoRenderer);
	- }
	- }
	- else
	- {
	- mitk::IRenderWindowPart* renderWindowPart = this->GetRenderWindowPart();
	-
	- if ( renderWindowPart == nullptr )
	- {
	- return;
	- }
	-
	- if (!text.isEmpty())
	- {
	- m_MeasurementInfoAnnotation->SetText(1, text.toLatin1().data());
	- mitk::VtkLayerController::GetInstance(renderWindowPart->GetQmitkRenderWindow("axial")->GetRenderWindow())->InsertForegroundRenderer(
	- m_MeasurementInfoRenderer, true);
	- }
	- else
	- {
	- if (mitk::VtkLayerController::GetInstance(
	- renderWindowPart->GetQmitkRenderWindow("axial")->GetRenderWindow()) ->IsRendererInserted(
	- m_MeasurementInfoRenderer))
	- mitk::VtkLayerController::GetInstance(renderWindowPart->GetQmitkRenderWindow("axial")->GetRenderWindow())->RemoveRenderer(
	- m_MeasurementInfoRenderer);
	- }
	- }
	-}
	-
	-void QmitkPartialVolumeAnalysisView::UpdateProgressBar()
	-{
	- mitk::ProgressBar::GetInstance()->Progress();
	-}
	-
	-void QmitkPartialVolumeAnalysisView::RequestStatisticsUpdate()
	-{
	- if ( !m_StatisticsUpdatePending )
	- {
	- QApplication::postEvent( this, new QmitkRequestStatisticsUpdateEvent );
	- m_StatisticsUpdatePending = true;
	- }
	-}
	-
	-
	-void QmitkPartialVolumeAnalysisView::RemoveOrphanImages()
	-{
	- PartialVolumeAnalysisMapType::iterator it = m_PartialVolumeAnalysisMap.begin();
	-
	- while ( it != m_PartialVolumeAnalysisMap.end() )
	- {
	- mitk::Image *image = it->first;
	- mitk::PartialVolumeAnalysisHistogramCalculator *calculator = it->second;
	- ++it;
	-
	- mitk::NodePredicateData::Pointer hasImage = mitk::NodePredicateData::New( image );
	- if ( this->GetDataStorage()->GetNode( hasImage ) == nullptr )
	- {
	- if ( m_SelectedImage == image )
	- {
	- m_SelectedImage = nullptr;
	- m_SelectedImageNodes->RemoveAllNodes();
	- }
	- if ( m_CurrentStatisticsCalculator == calculator )
	- {
	- m_CurrentStatisticsCalculator = nullptr;
	- }
	- m_PartialVolumeAnalysisMap.erase( image );
	- it = m_PartialVolumeAnalysisMap.begin();
	- }
	- }
	-}
	-
	-void QmitkPartialVolumeAnalysisView::ExtractTensorImages(
	- mitk::Image::Pointer tensorimage)
	-{
	- typedef itk::Image< itk::DiffusionTensor3D<float>, 3> TensorImageType;
	-
	- typedef mitk::ImageToItk<TensorImageType> CastType;
	- CastType::Pointer caster = CastType::New();
	- caster->SetInput(tensorimage);
	- caster->Update();
	- TensorImageType::Pointer image = caster->GetOutput();
	-
	- typedef itk::TensorDerivedMeasurementsFilter<float> MeasurementsType;
	- MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New();
	- measurementsCalculator->SetInput(image );
	- measurementsCalculator->SetMeasure(MeasurementsType::FA);
	- measurementsCalculator->Update();
	- MeasurementsType::OutputImageType::Pointer fa = measurementsCalculator->GetOutput();
	-
	- m_FAImage = mitk::Image::New();
	- m_FAImage->InitializeByItk(fa.GetPointer());
	- m_FAImage->SetVolume(fa->GetBufferPointer());
	-
	- // mitk::DataNode::Pointer node = mitk::DataNode::New();
	- // node->SetData(m_FAImage);
	- // GetDataStorage()->Add(node);
	-
	- measurementsCalculator = MeasurementsType::New();
	- measurementsCalculator->SetInput(image );
	- measurementsCalculator->SetMeasure(MeasurementsType::CA);
	- measurementsCalculator->Update();
	- MeasurementsType::OutputImageType::Pointer ca = measurementsCalculator->GetOutput();
	-
	- m_CAImage = mitk::Image::New();
	- m_CAImage->InitializeByItk(ca.GetPointer());
	- m_CAImage->SetVolume(ca->GetBufferPointer());
	-
	- // node = mitk::DataNode::New();
	- // node->SetData(m_CAImage);
	- // GetDataStorage()->Add(node);
	-
	- measurementsCalculator = MeasurementsType::New();
	- measurementsCalculator->SetInput(image );
	- measurementsCalculator->SetMeasure(MeasurementsType::RD);
	- measurementsCalculator->Update();
	- MeasurementsType::OutputImageType::Pointer rd = measurementsCalculator->GetOutput();
	-
	- m_RDImage = mitk::Image::New();
	- m_RDImage->InitializeByItk(rd.GetPointer());
	- m_RDImage->SetVolume(rd->GetBufferPointer());
	-
	- // node = mitk::DataNode::New();
	- // node->SetData(m_CAImage);
	- // GetDataStorage()->Add(node);
	-
	- measurementsCalculator = MeasurementsType::New();
	- measurementsCalculator->SetInput(image );
	- measurementsCalculator->SetMeasure(MeasurementsType::AD);
	- measurementsCalculator->Update();
	- MeasurementsType::OutputImageType::Pointer ad = measurementsCalculator->GetOutput();
	-
	- m_ADImage = mitk::Image::New();
	- m_ADImage->InitializeByItk(ad.GetPointer());
	- m_ADImage->SetVolume(ad->GetBufferPointer());
	-
	- // node = mitk::DataNode::New();
	- // node->SetData(m_CAImage);
	- // GetDataStorage()->Add(node);
	-
	- measurementsCalculator = MeasurementsType::New();
	- measurementsCalculator->SetInput(image );
	- measurementsCalculator->SetMeasure(MeasurementsType::RA);
	- measurementsCalculator->Update();
	- MeasurementsType::OutputImageType::Pointer md = measurementsCalculator->GetOutput();
	-
	- m_MDImage = mitk::Image::New();
	- m_MDImage->InitializeByItk(md.GetPointer());
	- m_MDImage->SetVolume(md->GetBufferPointer());
	-
	- // node = mitk::DataNode::New();
	- // node->SetData(m_CAImage);
	- // GetDataStorage()->Add(node);
	-
	- typedef DirectionsFilterType::PeakImageType DirImageType;
	- DirectionsFilterType::Pointer dirFilter = DirectionsFilterType::New();
	- dirFilter->SetInput(image );
	- dirFilter->SetUsePolarCoordinates(true);
	- dirFilter->Update();
	- ItkUcharImgType::Pointer numDirImage = dirFilter->GetOutput();
	- DirImageType::Pointer dirImage = dirFilter->GetPeakImage();
	-
	- itk::ImageRegionIterator<DirImageType> itd(dirImage, dirImage->GetLargestPossibleRegion());
	- itd.GoToBegin();
	- while( !itd.IsAtEnd() )
	- {
	- DirImageType::PixelType direction = itd.Get();
	- direction = fabs(direction);
	- itd.Set(direction);
	- ++itd;
	- }
	-
	- typedef itk::Image<float, 3> CompImageType;
	- CompImageType::Pointer comp1 = CompImageType::New();
	- comp1->SetSpacing( numDirImage->GetSpacing() ); // Set the image spacing
	- comp1->SetOrigin( numDirImage->GetOrigin() ); // Set the image origin
	- comp1->SetDirection( numDirImage->GetDirection() ); // Set the image direction
	- comp1->SetRegions( numDirImage->GetLargestPossibleRegion() );
	- comp1->Allocate();
	-
	- CompImageType::Pointer comp2 = CompImageType::New();
	- comp2->SetSpacing( numDirImage->GetSpacing() ); // Set the image spacing
	- comp2->SetOrigin( numDirImage->GetOrigin() ); // Set the image origin
	- comp2->SetDirection( numDirImage->GetDirection() ); // Set the image direction
	- comp2->SetRegions( numDirImage->GetLargestPossibleRegion() );
	- comp2->Allocate();
	-
	- itk::ImageRegionIterator<CompImageType> it1(comp1, comp1->GetLargestPossibleRegion());
	- itk::ImageRegionIterator<CompImageType> it2(comp2, comp2->GetLargestPossibleRegion());
	-
	- it1.GoToBegin();
	- it2.GoToBegin();
	-
	- while( !it2.IsAtEnd() )
	- {
	- DirImageType::IndexType peakIndex;
	- peakIndex[0] = it1.GetIndex()[0];
	- peakIndex[1] = it1.GetIndex()[1];
	- peakIndex[2] = it1.GetIndex()[2];
	- peakIndex[3] = 1;
	-
	- it1.Set(dirImage->GetPixel(peakIndex));
	- peakIndex[3] = 2;
	- it2.Set(dirImage->GetPixel(peakIndex));
	- ++it1;
	- ++it2;
	- }
	-
	- m_DirectionComp1Image = mitk::Image::New();
	- m_DirectionComp1Image->InitializeByItk(comp1.GetPointer());
	- m_DirectionComp1Image->SetVolume(comp1->GetBufferPointer());
	-
	- m_DirectionComp2Image = mitk::Image::New();
	- m_DirectionComp2Image->InitializeByItk(comp2.GetPointer());
	- m_DirectionComp2Image->SetVolume(comp2->GetBufferPointer());
	-
	-}
	-
	-void QmitkPartialVolumeAnalysisView::OnRenderWindowDelete(QObject * obj)
	-{
	- if(obj == m_LastRenderWindow)
	- m_LastRenderWindow = 0;
	- if(obj == m_SelectedRenderWindow)
	- m_SelectedRenderWindow = 0;
	-}
	-
	-bool QmitkPartialVolumeAnalysisView::event( QEvent *event )
	-{
	- if ( event->type() == (QEvent::Type) QmitkRequestStatisticsUpdateEvent::StatisticsUpdateRequest )
	- {
	- // Update statistics
	-
	- m_StatisticsUpdatePending = false;
	-
	- this->UpdateStatistics();
	- return true;
	- }
	-
	- return false;
	-}
	-
	-
	-void QmitkPartialVolumeAnalysisView::Activated()
	-{
	- mitk::DataStorage::SetOfObjects::ConstPointer _NodeSet = this->GetDataStorage()->GetAll();
	- mitk::DataNode* node = 0;
	- mitk::PlanarFigure* figure = 0;
	- mitk::PlanarFigureInteractor::Pointer figureInteractor = 0;
	-
	- // finally add all nodes to the model
	- for(mitk::DataStorage::SetOfObjects::ConstIterator it=_NodeSet->Begin(); it!=_NodeSet->End()
	- ; it++)
	- {
	- node = const_cast<mitk::DataNode*>(it->Value().GetPointer());
	- figure = dynamic_cast<mitk::PlanarFigure*>(node->GetData());
	-
	- if(figure)
	- {
	- figureInteractor = dynamic_cast<mitk::PlanarFigureInteractor*>(node->GetDataInteractor().GetPointer());
	-
	- if(figureInteractor.IsNull())
	- {
	- figureInteractor = mitk::PlanarFigureInteractor::New();
	- us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "MitkPlanarFigure" );
	- figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule );
	- figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule );
	- figureInteractor->SetDataNode( node );
	- }
	- }
	- }
	-}
	-
	-void QmitkPartialVolumeAnalysisView::Deactivated()
	-{
	-
	-}
	-
	-void QmitkPartialVolumeAnalysisView::ActivatedZombieView(berry::IWorkbenchPartReference::Pointer)
	-{
	- this->SetMeasurementInfoToRenderWindow("");
	-
	- mitk::DataStorage::SetOfObjects::ConstPointer _NodeSet = this->GetDataStorage()->GetAll();
	- mitk::DataNode* node = 0;
	- mitk::PlanarFigure* figure = 0;
	- mitk::PlanarFigureInteractor::Pointer figureInteractor = 0;
	-
	- // finally add all nodes to the model
	- for(mitk::DataStorage::SetOfObjects::ConstIterator it=_NodeSet->Begin(); it!=_NodeSet->End()
	- ; it++)
	- {
	- node = const_cast<mitk::DataNode*>(it->Value().GetPointer());
	- figure = dynamic_cast<mitk::PlanarFigure*>(node->GetData());
	-
	- if(figure)
	- {
	- figureInteractor = dynamic_cast<mitk::PlanarFigureInteractor*>(node->GetDataInteractor().GetPointer());
	-
	- if(figureInteractor)
	- figureInteractor->SetDataNode( nullptr );
	- }
	- }
	-}
	-
	-void QmitkPartialVolumeAnalysisView::Hidden()
	-{
	- if (m_ClusteringResult.IsNotNull())
	- {
	- this->GetDataStorage()->Remove(m_ClusteringResult);
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- }
	- Select(nullptr, true, true);
	- m_Visible = false;
	-}
	-
	-void QmitkPartialVolumeAnalysisView::Visible()
	-{
	- m_Visible = true;
	- berry::IWorkbenchPart::Pointer bla;
	- if (!this->GetCurrentSelection().empty())
	- {
	- this->OnSelectionChanged(bla, this->GetCurrentSelection());
	- }
	- else
	- {
	- this->OnSelectionChanged(bla, this->GetDataManagerSelection());
	- }
	-}
	-
	-void QmitkPartialVolumeAnalysisView::GreenRadio(bool checked)
	-{
	- if(checked)
	- {
	- m_Controls->m_PartialVolumeRadio->setChecked(false);
	- m_Controls->m_BlueRadio->setChecked(false);
	- m_Controls->m_AllRadio->setChecked(false);
	- m_Controls->m_ExportClusteringResultsButton->setEnabled(true);
	- }
	-
	- m_QuantifyClass = 0;
	-
	- RequestStatisticsUpdate();
	-}
	-
	-
	-void QmitkPartialVolumeAnalysisView::PartialVolumeRadio(bool checked)
	-{
	- if(checked)
	- {
	- m_Controls->m_GreenRadio->setChecked(false);
	- m_Controls->m_BlueRadio->setChecked(false);
	- m_Controls->m_AllRadio->setChecked(false);
	- m_Controls->m_ExportClusteringResultsButton->setEnabled(true);
	- }
	-
	- m_QuantifyClass = 1;
	-
	- RequestStatisticsUpdate();
	-}
	-
	-void QmitkPartialVolumeAnalysisView::BlueRadio(bool checked)
	-{
	- if(checked)
	- {
	- m_Controls->m_PartialVolumeRadio->setChecked(false);
	- m_Controls->m_GreenRadio->setChecked(false);
	- m_Controls->m_AllRadio->setChecked(false);
	- m_Controls->m_ExportClusteringResultsButton->setEnabled(true);
	- }
	-
	- m_QuantifyClass = 2;
	-
	- RequestStatisticsUpdate();
	-}
	-
	-void QmitkPartialVolumeAnalysisView::AllRadio(bool checked)
	-{
	- if(checked)
	- {
	- m_Controls->m_BlueRadio->setChecked(false);
	- m_Controls->m_PartialVolumeRadio->setChecked(false);
	- m_Controls->m_GreenRadio->setChecked(false);
	- m_Controls->m_ExportClusteringResultsButton->setEnabled(false);
	- }
	-
	- m_QuantifyClass = 3;
	-
	- RequestStatisticsUpdate();
	-}
	-
	-void QmitkPartialVolumeAnalysisView::NumberBinsChangedSlider(int)
	-{
	- m_Controls->m_NumberBins->setText(QString("%1").arg(m_Controls->m_NumberBinsSlider->value()*5.0));
	-}
	-
	-void QmitkPartialVolumeAnalysisView::UpsamplingChangedSlider(int)
	-{
	- m_Controls->m_Upsampling->setText(QString("%1").arg(m_Controls->m_UpsamplingSlider->value()/10.0));
	-}
	-
	-void QmitkPartialVolumeAnalysisView::GaussianSigmaChangedSlider(int)
	-{
	- m_Controls->m_GaussianSigma->setText(QString("%1").arg(m_Controls->m_GaussianSigmaSlider->value()/100.0));
	-}
	-
	-void QmitkPartialVolumeAnalysisView::SimilarAnglesChangedSlider(int)
	-{
	- m_Controls->m_SimilarAngles->setText(QString("%1°").arg(90-m_Controls->m_SimilarAnglesSlider->value()));
	- ShowClusteringResults();
	-}
	-
	-void QmitkPartialVolumeAnalysisView::OpacityChangedSlider(int v )
	-{
	-
	- if(m_SelectedImageNodes->GetNode().IsNotNull())
	- {
	- float opacImag = 1.0f-(v-5)/5.0f;
	- opacImag = opacImag < 0 ? 0 : opacImag;
	- m_SelectedImageNodes->GetNode()->SetFloatProperty("opacity", opacImag);
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- }
	-
	- if(m_ClusteringResult.IsNotNull())
	- {
	- float opacClust = v/5.0f;
	- opacClust = opacClust > 1 ? 1 : opacClust;
	- m_ClusteringResult->SetFloatProperty("opacity", opacClust);
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- }
	-}
	-
	-void QmitkPartialVolumeAnalysisView::NumberBinsReleasedSlider( )
	-{
	- RequestStatisticsUpdate();
	-}
	-
	-void QmitkPartialVolumeAnalysisView::UpsamplingReleasedSlider( )
	-{
	- RequestStatisticsUpdate();
	-}
	-
	-void QmitkPartialVolumeAnalysisView::GaussianSigmaReleasedSlider( )
	-{
	- RequestStatisticsUpdate();
	-}
	-
	-void QmitkPartialVolumeAnalysisView::SimilarAnglesReleasedSlider( )
	-{
	-
	-}
	-
	-void QmitkPartialVolumeAnalysisView::ToClipBoard()
	-{
	-
	- std::vector<std::vector<double>* > vals = m_Controls->m_HistogramWidget->m_Vals;
	- QString clipboardText;
	- for (std::vector<std::vector<double>* >::iterator it = vals.begin(); it
	- != vals.end(); ++it)
	- {
	- for (std::vector<double>::iterator it2 = (it).begin(); it2 != (it).end(); ++it2)
	- {
	- clipboardText.append(QString("%1 \t").arg(*it2));
	- }
	- clipboardText.append(QString("\n"));
	- }
	-
	- QApplication::clipboard()->setText(clipboardText, QClipboard::Clipboard);
	-}
	-
	-void QmitkPartialVolumeAnalysisView::PropertyChanged(const mitk::DataNode* /node/, const mitk::BaseProperty* /prop/)
	-{
	-}
	-
	-void QmitkPartialVolumeAnalysisView::NodeChanged(const mitk::DataNode* /node/)
	-{
	-}
	-
	-void QmitkPartialVolumeAnalysisView::NodeRemoved(const mitk::DataNode* node)
	-{
	- if (dynamic_cast<mitk::PlanarFigure*>(node->GetData()))
	- this->GetDataStorage()->Remove(m_ClusteringResult);
	-
	- if( node == m_SelectedPlanarFigureNodes->GetNode().GetPointer()
	- \|\| node == m_SelectedMaskNode.GetPointer() )
	- {
	- this->Select(nullptr,true,false);
	- SetMeasurementInfoToRenderWindow("");
	- }
	-
	- if( node == m_SelectedImageNodes->GetNode().GetPointer() )
	- {
	- this->Select(nullptr,false,true);
	- SetMeasurementInfoToRenderWindow("");
	- }
	-}
	-
	-void QmitkPartialVolumeAnalysisView::NodeAddedInDataStorage(const mitk::DataNode* node)
	-{
	- if(!m_Visible)
	- return;
	-
	- mitk::DataNode* nonConstNode = const_cast<mitk::DataNode*>(node);
	- mitk::PlanarFigure* figure = dynamic_cast<mitk::PlanarFigure*>(nonConstNode->GetData());
	-
	- if(figure)
	- {
	-
	- // set interactor for new node (if not already set)
	- mitk::PlanarFigureInteractor::Pointer figureInteractor
	- = dynamic_cast<mitk::PlanarFigureInteractor*>(node->GetDataInteractor().GetPointer());
	-
	- if(figureInteractor.IsNull())
	- {
	- figureInteractor = mitk::PlanarFigureInteractor::New();
	- us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "MitkPlanarFigure" );
	- figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule );
	- figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule );
	- figureInteractor->SetDataNode( nonConstNode );
	- }
	-
	- // remove uninitialized old planars
	- if( m_SelectedPlanarFigureNodes->GetNode().IsNotNull() && m_CurrentFigureNodeInitialized == false )
	- {
	- this->GetDataStorage()->Remove(m_SelectedPlanarFigureNodes->GetNode());
	- }
	-
	- }
	-}
	-
	-void QmitkPartialVolumeAnalysisView::TextIntON()
	-{
	- if(m_ClusteringResult.IsNotNull())
	- {
	- if(m_TexIsOn)
	- {
	- m_Controls->m_TextureIntON->setIcon(*m_IconTexOFF);
	- }
	- else
	- {
	- m_Controls->m_TextureIntON->setIcon(*m_IconTexON);
	- }
	-
	- m_ClusteringResult->SetBoolProperty("texture interpolation", !m_TexIsOn);
	- m_TexIsOn = !m_TexIsOn;
	- this->RequestRenderWindowUpdate();
	- }
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/src/internal/QmitkPartialVolumeAnalysisView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/src/internal/QmitkPartialVolumeAnalysisView.h
	deleted file mode 100644
	index 3a01e75b75..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/src/internal/QmitkPartialVolumeAnalysisView.h
	+++ /dev/null
	@@ -1,269 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#if !defined(QmitkPartialVolumeAnalysisView_H__INCLUDED)
	-#define QmitkPartialVolumeAnalysisView_H__INCLUDED
	-
	-#include "ui_QmitkPartialVolumeAnalysisViewControls.h"
	-
	-#include <QmitkAbstractView.h>
	-#include <berryIWorkbenchPartReference.h>
	-#include <mitkIZombieViewPart.h>
	-
	-// berry
	-#include <berryISelectionListener.h>
	-#include <berryIStructuredSelection.h>
	-
	-// itk
	-#include <itkTimeStamp.h>
	-#include <itkDiffusionTensorPrincipalDirectionImageFilter.h>
	-#include <itkExtractChannelFromRgbaImageFilter.h>
	-
	-// qmitk
	-#include "QmitkStepperAdapter.h"
	-#include "QmitkRenderWindow.h"
	-
	-// mitk
	-#include "mitkPartialVolumeAnalysisHistogramCalculator.h"
	-#include "mitkPlanarLine.h"
	-#include "mitkDataStorageSelection.h"
	-#include <mitkVtkLayerController.h>
	-
	-// vtk
	-#include <vtkTextProperty.h>
	-#include <vtkRenderer.h>
	-#include <vtkCornerAnnotation.h>
	-//#include "itkProcessObject.h"
	-
	-/*!
	-\brief QmitkPartialVolumeAnalysis
	-*/
	-class QmitkPartialVolumeAnalysisView : public QmitkAbstractView, public mitk::IZombieViewPart//, public itk::ProcessObject
	-{
	- Q_OBJECT
	-
	-public:
	-
	- /*!
	- \ Convenient typedefs
	- */
	- typedef mitk::DataStorage::SetOfObjects ConstVector;
	- typedef ConstVector::ConstPointer ConstVectorPointer;
	- typedef ConstVector::ConstIterator ConstVectorIterator;
	- typedef mitk::PartialVolumeAnalysisHistogramCalculator HistogramCalculatorType;
	- typedef HistogramCalculatorType::HistogramType HistogramType;
	- typedef mitk::PartialVolumeAnalysisClusteringCalculator ClusteringType;
	- typedef itk::DiffusionTensorPrincipalDirectionImageFilter<float> DirectionsFilterType;
	- typedef itk::Image<unsigned char, 3> ItkUcharImgType;
	-
	- /*!
	- \brief default constructor
	- */
	- QmitkPartialVolumeAnalysisView(QObject parent=0, const char name=0);
	-
	- /*!
	- \brief default destructor
	- */
	- virtual ~QmitkPartialVolumeAnalysisView();
	-
	- /*!
	- \brief method for creating the widget containing the application controls, like sliders, buttons etc.
	- */
	- virtual void CreateQtPartControl(QWidget *parent) override;
	-
	- /*!
	- \brief method for creating the connections of main and control widget
	- */
	- virtual void CreateConnections();
	-
	- virtual bool event( QEvent *event ) override;
	-
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- virtual void Activated() override;
	-
	- virtual void Deactivated() override;
	-
	- virtual void ActivatedZombieView(berry::IWorkbenchPartReference::Pointer reference) override;
	-
	- virtual void Hidden() override;
	-
	- virtual void Visible() override;
	-
	- virtual void SetFocus() override;
	-
	- bool AssertDrawingIsPossible(bool checked);
	-
	- virtual void NodeChanged(const mitk::DataNode* node) override;
	- virtual void PropertyChanged(const mitk::DataNode* node, const mitk::BaseProperty* prop);
	- virtual void NodeRemoved(const mitk::DataNode* node) override;
	- virtual void NodeAddedInDataStorage(const mitk::DataNode* node);
	-
	- virtual void AddFigureToDataStorage(mitk::PlanarFigure* figure, const QString& name,
	- const char propertyKey = nullptr, mitk::BaseProperty property = nullptr );
	-
	- void PlanarFigureInitialized();
	-
	- void PlanarFigureFocus(mitk::DataNode* node);
	-
	- void ShowClusteringResults();
	-
	- static const std::string VIEW_ID;
	-
	-protected slots:
	-
	- void EstimateCircle();
	- void SetHistogramVisibility();
	- void SetAdvancedVisibility();
	-
	- void NumberBinsChangedSlider(int v );
	- void UpsamplingChangedSlider( int v );
	- void GaussianSigmaChangedSlider( int v );
	- void SimilarAnglesChangedSlider(int v );
	-
	- void OpacityChangedSlider(int v );
	-
	- void NumberBinsReleasedSlider( );
	- void UpsamplingReleasedSlider( );
	- void GaussianSigmaReleasedSlider( );
	- void SimilarAnglesReleasedSlider( );
	-
	- void ActionDrawEllipseTriggered();
	- void ActionDrawRectangleTriggered();
	- void ActionDrawPolygonTriggered();
	-
	- void ToClipBoard();
	-
	- void GreenRadio(bool checked);
	- void PartialVolumeRadio(bool checked);
	- void BlueRadio(bool checked);
	- void AllRadio(bool checked);
	-
	- void OnRenderWindowDelete(QObject * obj);
	-
	- void TextIntON();
	- void ExportClusteringResults();
	-
	-protected:
	-
	- /** \brief Issues a request to update statistics by sending an event to the
	- * Qt event processing queue.
	- *
	- * Statistics update should only be executed after program execution returns
	- * to the Qt main loop. This mechanism also prevents multiple execution of
	- * updates where only one is required.*/
	- void RequestStatisticsUpdate();
	-
	- /** \brief Recalculate statistics for currently selected image and mask and
	- * update the GUI. */
	- void UpdateStatistics();
	-
	- /** \brief Listener for progress events to update progress bar. */
	- void UpdateProgressBar();
	-
	- /** \brief Removes any cached images which are no longer referenced elsewhere. */
	- void RemoveOrphanImages();
	-
	- void Select( mitk::DataNode::Pointer node, bool clearMaskOnFirstArgnullptr=false, bool clearImageOnFirstArgnullptr=false );
	-
	- void SetMeasurementInfoToRenderWindow(const QString& text);
	-
	- void FindRenderWindow(mitk::DataNode* node);
	-
	- void ExtractTensorImages(
	- mitk::Image::Pointer tensorimage);
	-
	- typedef std::map< mitk::Image *, mitk::PartialVolumeAnalysisHistogramCalculator::Pointer >
	- PartialVolumeAnalysisMapType;
	-
	- /*!
	- * controls containing sliders for scrolling through the slices
	- */
	- Ui::QmitkPartialVolumeAnalysisViewControls *m_Controls;
	-
	- QmitkStepperAdapter* m_TimeStepperAdapter;
	- unsigned int m_CurrentTime;
	-
	- QString m_Clipboard;
	-
	- // result text rendering
	- vtkRenderer * m_MeasurementInfoRenderer;
	- vtkCornerAnnotation *m_MeasurementInfoAnnotation;
	-
	- // Image and mask data
	- mitk::DataStorageSelection::Pointer m_SelectedImageNodes;
	- mitk::Image::Pointer m_SelectedImage;
	-
	- mitk::DataNode::Pointer m_SelectedMaskNode;
	- mitk::Image::Pointer m_SelectedImageMask;
	-
	- mitk::DataStorageSelection::Pointer m_SelectedPlanarFigureNodes;
	- mitk::PlanarFigure::Pointer m_SelectedPlanarFigure;
	-
	- bool m_IsTensorImage;
	- mitk::Image::Pointer m_FAImage;
	- mitk::Image::Pointer m_CAImage;
	- mitk::Image::Pointer m_RDImage;
	- mitk::Image::Pointer m_ADImage;
	- mitk::Image::Pointer m_MDImage;
	- mitk::Image::Pointer m_DirectionComp1Image;
	- mitk::Image::Pointer m_DirectionComp2Image;
	- mitk::Image::Pointer m_AngularErrorImage;
	-
	- QmitkRenderWindow* m_SelectedRenderWindow;
	- QmitkRenderWindow* m_LastRenderWindow;
	-
	- long m_ImageObserverTag;
	- long m_ImageMaskObserverTag;
	- long m_PlanarFigureObserverTag;
	-
	- // Hash map for associating one image statistics calculator with each iamge
	- // (so that previously calculated histograms / statistics can be recovered
	- // if a recalculation is not required)
	- PartialVolumeAnalysisMapType m_PartialVolumeAnalysisMap;
	-
	- HistogramCalculatorType::Pointer m_CurrentStatisticsCalculator;
	-
	- bool m_CurrentStatisticsValid;
	-
	- bool m_StatisticsUpdatePending;
	-
	- bool m_GaussianSigmaChangedSliding;
	- bool m_NumberBinsSliding;
	- bool m_UpsamplingChangedSliding;
	-
	- mitk::DataNode::Pointer m_ClusteringResult;
	-
	- int m_EllipseCounter;
	- int m_RectangleCounter;
	- int m_PolygonCounter;
	- long m_InitializedObserverTag;
	- bool m_CurrentFigureNodeInitialized;
	-
	- int m_QuantifyClass;
	-
	- ClusteringType::HelperStructPerformRGBClusteringRetval* m_CurrentRGBClusteringResults;
	- ClusteringType::HelperStructPerformClusteringRetval *m_CurrentPerformClusteringResults;
	-
	- QIcon* m_IconTexOFF;
	- QIcon* m_IconTexON;
	- bool m_TexIsOn;
	-
	- bool m_Visible;
	-};
	-
	-
	-#endif
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/src/internal/QmitkPartialVolumeAnalysisViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/src/internal/QmitkPartialVolumeAnalysisViewControls.ui
	deleted file mode 100644
	index 418ffce5e5..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/src/internal/QmitkPartialVolumeAnalysisViewControls.ui
	+++ /dev/null
	@@ -1,858 +0,0 @@
	-<?xml version="1.0" encoding="utf-8"?>
	-<ui version="4.0">
	- <class>QmitkPartialVolumeAnalysisViewControls</class>
	- <widget class="QWidget" name="QmitkPartialVolumeAnalysisViewControls">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>360</width>
	- <height>565</height>
	- </rect>
	- </property>
	- <property name="windowTitle">
	- <string>Form</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QVBoxLayout" name="verticalLayout">
	- <property name="spacing">
	- <number>0</number>
	- </property>
	- <property name="leftMargin">
	- <number>9</number>
	- </property>
	- <property name="topMargin">
	- <number>3</number>
	- </property>
	- <property name="rightMargin">
	- <number>9</number>
	- </property>
	- <property name="bottomMargin">
	- <number>3</number>
	- </property>
	- <item>
	- <widget class="QGroupBox" name="m_InputData">
	- <property name="title">
	- <string>Data</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_4">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Fixed" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="text">
	- <string>Tensor/Scalar Image:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label_2">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Fixed" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="text">
	- <string>Mask Image:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QLabel" name="m_SelectedImageLabel">
	- <property name="text">
	- <string><html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QLabel" name="m_SelectedMaskLabel">
	- <property name="text">
	- <string><html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html></string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <widget class="QGroupBox" name="groupBox_2">
	- <property name="title">
	- <string>Parameters</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QFrame" name="frame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QVBoxLayout" name="verticalLayout_2">
	- <property name="margin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QFrame" name="frame_2">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QHBoxLayout" name="horizontalLayout_4">
	- <property name="spacing">
	- <number>0</number>
	- </property>
	- <property name="margin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QFrame" name="m_PlanarFigureButtonsFrame">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QHBoxLayout" name="horizontalLayout_5">
	- <property name="margin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QPushButton" name="m_CircleButton">
	- <property name="maximumSize">
	- <size>
	- <width>30</width>
	- <height>30</height>
	- </size>
	- </property>
	- <property name="toolTip">
	- <string>Draw circular ROI</string>
	- </property>
	- <property name="text">
	- <string></string>
	- </property>
	- <property name="icon">
	- <iconset resource="../../resources/QmitkDiffusionImaging.qrc">
	- <normaloff>:/QmitkDiffusionImaging/circle.png</normaloff>
	-:/QmitkDiffusionImaging/circle.png </iconset>
	- </property>
	- <property name="iconSize">
	- <size>
	- <width>32</width>
	- <height>32</height>
	- </size>
	- </property>
	- <property name="checkable">
	- <bool>true</bool>
	- </property>
	- <property name="flat">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QPushButton" name="m_RectangleButton">
	- <property name="maximumSize">
	- <size>
	- <width>30</width>
	- <height>30</height>
	- </size>
	- </property>
	- <property name="toolTip">
	- <string>Draw quadratic ROI</string>
	- </property>
	- <property name="text">
	- <string></string>
	- </property>
	- <property name="icon">
	- <iconset resource="../../resources/QmitkDiffusionImaging.qrc">
	- <normaloff>:/QmitkDiffusionImaging/rectangle.png</normaloff>
	-:/QmitkDiffusionImaging/rectangle.png </iconset>
	- </property>
	- <property name="iconSize">
	- <size>
	- <width>32</width>
	- <height>32</height>
	- </size>
	- </property>
	- <property name="checkable">
	- <bool>true</bool>
	- </property>
	- <property name="flat">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QPushButton" name="m_PolygonButton">
	- <property name="maximumSize">
	- <size>
	- <width>30</width>
	- <height>30</height>
	- </size>
	- </property>
	- <property name="toolTip">
	- <string>Draw polygonal ROI</string>
	- </property>
	- <property name="text">
	- <string></string>
	- </property>
	- <property name="icon">
	- <iconset resource="../../resources/QmitkDiffusionImaging.qrc">
	- <normaloff>:/QmitkDiffusionImaging/polygon.png</normaloff>
	-:/QmitkDiffusionImaging/polygon.png </iconset>
	- </property>
	- <property name="iconSize">
	- <size>
	- <width>32</width>
	- <height>32</height>
	- </size>
	- </property>
	- <property name="checkable">
	- <bool>true</bool>
	- </property>
	- <property name="flat">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <spacer name="horizontalSpacer">
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>40</width>
	- <height>20</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <widget class="QFrame" name="m_ResampleOptionsFrame">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QFormLayout" name="formLayout_2">
	- <property name="fieldGrowthPolicy">
	- <enum>QFormLayout::AllNonFixedFieldsGrow</enum>
	- </property>
	- <property name="margin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label">
	- <property name="text">
	- <string>Upsampling</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QFrame" name="frame_bla">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QHBoxLayout" name="horizontalLayout">
	- <property name="margin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QSlider" name="m_UpsamplingSlider">
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>50</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>25</number>
	- </property>
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QLabel" name="m_Upsampling">
	- <property name="minimumSize">
	- <size>
	- <width>50</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="text">
	- <string>2.5</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="m_SimilarAnglesLabel">
	- <property name="text">
	- <string>Similar angles</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QFrame" name="m_SimilarAnglesFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <layout class="QHBoxLayout" name="horizontalLayout_7">
	- <property name="margin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QSlider" name="m_SimilarAnglesSlider">
	- <property name="maximum">
	- <number>90</number>
	- </property>
	- <property name="value">
	- <number>0</number>
	- </property>
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- <property name="tickPosition">
	- <enum>QSlider::NoTicks</enum>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QLabel" name="m_SimilarAngles">
	- <property name="minimumSize">
	- <size>
	- <width>50</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="text">
	- <string>90°</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <widget class="QFrame" name="frame_5">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QVBoxLayout" name="verticalLayout_4">
	- <property name="spacing">
	- <number>0</number>
	- </property>
	- <property name="margin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QCheckBox" name="m_DisplayHistogramCheckbox">
	- <property name="text">
	- <string>display histogram</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QmitkPartialVolumeAnalysisWidget" name="m_HistogramWidget" native="true">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <widget class="QFrame" name="m_BottomControls">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QVBoxLayout" name="verticalLayout_3">
	- <property name="margin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QFrame" name="m_ClassSelector">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QHBoxLayout" name="horizontalLayout_6">
	- <property name="margin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QPushButton" name="m_TextureIntON">
	- <property name="maximumSize">
	- <size>
	- <width>20</width>
	- <height>20</height>
	- </size>
	- </property>
	- <property name="text">
	- <string></string>
	- </property>
	- <property name="checkable">
	- <bool>true</bool>
	- </property>
	- <property name="flat">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QRadioButton" name="m_GreenRadio">
	- <property name="text">
	- <string>Green</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QRadioButton" name="m_PartialVolumeRadio">
	- <property name="toolTip">
	- <string comment="Partial Volume" extracomment="Partial Volume">Partial Volume</string>
	- </property>
	- <property name="statusTip">
	- <string comment="Partial Volume" extracomment="Partial Volume">Partial Volume</string>
	- </property>
	- <property name="whatsThis">
	- <string>Partial Volume</string>
	- </property>
	- <property name="accessibleName">
	- <string comment="Partial Volume" extracomment="Partial Volume">Partial Volume</string>
	- </property>
	- <property name="text">
	- <string>PV</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QRadioButton" name="m_BlueRadio">
	- <property name="text">
	- <string>Red</string>
	- </property>
	- <property name="checked">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QRadioButton" name="m_AllRadio">
	- <property name="text">
	- <string>All</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QToolButton" name="m_ExportClusteringResultsButton">
	- <property name="toolTip">
	- <string>Export clustering result as float image.</string>
	- </property>
	- <property name="text">
	- <string>...</string>
	- </property>
	- <property name="icon">
	- <iconset resource="../../../../../MITK-Superbuild-gcc/MITK-build/Plugins/org.mitk.gui.qt.diffusionimaging/org_mitk_gui_qt_diffusionimaging_cached.qrc">
	- <normaloff>:/org.mitk.gui.qt.diffusionimaging/resources/arrow.png</normaloff>
	-:/org.mitk.gui.qt.diffusionimaging/resources/arrow.png </iconset>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <widget class="QFrame" name="m_OpacityFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <layout class="QHBoxLayout" name="horizontalLayout_8">
	- <property name="margin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QLabel" name="m_OpacityLabel">
	- <property name="text">
	- <string>Opacity</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QSlider" name="m_OpacitySlider">
	- <property name="maximum">
	- <number>10</number>
	- </property>
	- <property name="value">
	- <number>5</number>
	- </property>
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- <property name="tickPosition">
	- <enum>QSlider::TicksBelow</enum>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <layout class="QGridLayout" name="gridLayout_7">
	- <item row="2" column="0">
	- <spacer name="verticalSpacer_2">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeType">
	- <enum>QSizePolicy::Fixed</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>10</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_7">
	- <property name="text">
	- <string>The computed class values (median, variance of the gaussians) are automatically copied to clipboard.</string>
	- </property>
	- <property name="textFormat">
	- <enum>Qt::AutoText</enum>
	- </property>
	- <property name="wordWrap">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <spacer name="verticalSpacer_3">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeType">
	- <enum>QSizePolicy::Fixed</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>10</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- </layout>
	- </item>
	- <item>
	- <widget class="QPushButton" name="m_ButtonCopyHistogramToClipboard">
	- <property name="text">
	- <string>Histogram to Clipboard</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QCheckBox" name="m_AdvancedCheckbox">
	- <property name="text">
	- <string>Advanced</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <spacer name="spacer2">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeType">
	- <enum>QSizePolicy::Preferred</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>10</width>
	- <height>1</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item>
	- <widget class="QFrame" name="frame_7">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QFormLayout" name="formLayout_3">
	- <property name="fieldGrowthPolicy">
	- <enum>QFormLayout::AllNonFixedFieldsGrow</enum>
	- </property>
	- <property name="margin">
	- <number>0</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_5">
	- <property name="text">
	- <string>Blurring</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QFrame" name="frame_3">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QHBoxLayout" name="horizontalLayout_2">
	- <property name="margin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QSlider" name="m_GaussianSigmaSlider">
	- <property name="maximum">
	- <number>200</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>0</number>
	- </property>
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QLabel" name="m_GaussianSigma">
	- <property name="minimumSize">
	- <size>
	- <width>50</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="text">
	- <string>0.0</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label_3">
	- <property name="text">
	- <string># Bins</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QFrame" name="frame_4">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <layout class="QHBoxLayout" name="horizontalLayout_3">
	- <property name="margin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QSlider" name="m_NumberBinsSlider">
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>100</number>
	- </property>
	- <property name="value">
	- <number>10</number>
	- </property>
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- <property name="tickPosition">
	- <enum>QSlider::NoTicks</enum>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QLabel" name="m_NumberBins">
	- <property name="minimumSize">
	- <size>
	- <width>50</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="text">
	- <string>50</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <widget class="QCheckBox" name="m_Quantiles">
	- <property name="text">
	- <string>quantiles</string>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="1">
	- <widget class="QFrame" name="frame_8">
	- <property name="frameShape">
	- <enum>QFrame::StyledPanel</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QHBoxLayout" name="horizontalLayout_9">
	- <property name="margin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QDoubleSpinBox" name="m_q1">
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.010000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.250000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QDoubleSpinBox" name="m_q2">
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.010000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.750000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="4" column="1">
	- <widget class="QPushButton" name="m_EstimateCircle">
	- <property name="text">
	- <string>Estimate circle from binary image</string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="1">
	- <widget class="QSpinBox" name="m_PlanarFiguresThickness"></widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QLabel" name="label_6">
	- <property name="text">
	- <string>"Thick" PFs</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <spacer name="verticalSpacer">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- </layout>
	- </widget>
	- <customwidgets>
	- <customwidget>
	- <class>QmitkPartialVolumeAnalysisWidget</class>
	- <extends>QWidget</extends>
	- <header>QmitkPartialVolumeAnalysisWidget.h</header>
	- <container>1</container>
	- </customwidget>
	- </customwidgets>
	- <resources>
	- <include location="../../../../../MITK-Superbuild-gcc/MITK-build/Plugins/org.mitk.gui.qt.diffusionimaging/org_mitk_gui_qt_diffusionimaging_cached.qrc"></include>
	- <include location="../../resources/QmitkDiffusionImaging.qrc"></include>
	- </resources>
	- <connections></connections>
	-</ui>
	\ No newline at end of file
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/src/internal/mitkPluginActivator.cpp
	deleted file mode 100644
	index 77ceef57e3..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/src/internal/mitkPluginActivator.cpp
	+++ /dev/null
	@@ -1,38 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkPluginActivator.h"
	-
	-#include "src/internal/QmitkPartialVolumeAnalysisView.h"
	-
	-ctkPluginContext* mitk::PluginActivator::m_Context = nullptr;
	-
	-ctkPluginContext* mitk::PluginActivator::GetContext()
	-{
	- return m_Context;
	-}
	-
	-void mitk::PluginActivator::start(ctkPluginContext* context)
	-{
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkPartialVolumeAnalysisView, context)
	- m_Context = context;
	-}
	-
	-void mitk::PluginActivator::stop(ctkPluginContext* context)
	-{
	- Q_UNUSED(context)
	- m_Context = nullptr;
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/src/internal/mitkPluginActivator.h b/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/src/internal/mitkPluginActivator.h
	deleted file mode 100644
	index 5809ae91f2..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.partialvolume/src/internal/mitkPluginActivator.h
	+++ /dev/null
	@@ -1,40 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef MITKPLUGINACTIVATOR_H
	-#define MITKPLUGINACTIVATOR_H
	-
	-#include <ctkPluginActivator.h>
	-
	-namespace mitk
	-{
	- class PluginActivator : public QObject, public ctkPluginActivator
	- {
	- Q_OBJECT
	- Q_PLUGIN_METADATA(IID "org.mitk.gui.qt.diffusionimaging.partialvolume")
	- Q_INTERFACES(ctkPluginActivator)
	-
	- public:
	- static ctkPluginContext* GetContext();
	-
	- void start(ctkPluginContext* context) override;
	- void stop(ctkPluginContext* context) override;
	-
	- private:
	- static ctkPluginContext* m_Context;
	- };
	-}
	-
	-#endif
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/CMakeLists.txt
	deleted file mode 100644
	index 341222ae5d..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/CMakeLists.txt
	+++ /dev/null
	@@ -1,11 +0,0 @@
	-# The project name must correspond to the directory name of your plug-in
	-# and must not contain periods.
	-project(org_mitk_gui_qt_diffusionimaging_preprocessing)
	-
	-mitk_create_plugin(
	- SUBPROJECTS MITK-DTI
	- EXPORT_DIRECTIVE DIFFUSIONIMAGING_PREPROCESSING_EXPORT
	- EXPORTED_INCLUDE_SUFFIXES src
	- MODULE_DEPENDS MitkDiffusionCore
	- PACKAGE_DEPENDS Qt5\|Network
	-)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/documentation/UserManual/PreprocessingGUI_1.png b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/documentation/UserManual/PreprocessingGUI_1.png
	deleted file mode 100644
	index 7ca7625fe0..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/documentation/UserManual/PreprocessingGUI_1.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/documentation/UserManual/PreprocessingGUI_2.png b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/documentation/UserManual/PreprocessingGUI_2.png
	deleted file mode 100644
	index 9e0ad6a952..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/documentation/UserManual/PreprocessingGUI_2.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/documentation/UserManual/PreprocessingGUI_3.png b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/documentation/UserManual/PreprocessingGUI_3.png
	deleted file mode 100644
	index 35be653437..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/documentation/UserManual/PreprocessingGUI_3.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/documentation/UserManual/PreprocessingGUI_4.png b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/documentation/UserManual/PreprocessingGUI_4.png
	deleted file mode 100644
	index 5bee685263..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/documentation/UserManual/PreprocessingGUI_4.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/documentation/UserManual/QmitkDiffusionImagingPreprocessingPage.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/documentation/UserManual/QmitkDiffusionImagingPreprocessingPage.dox
	deleted file mode 100644
	index f01bbeb40f..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/documentation/UserManual/QmitkDiffusionImagingPreprocessingPage.dox
	+++ /dev/null
	@@ -1,27 +0,0 @@
	-/**
	-\page org_mitk_views_diffusionpreprocessing Preprocessing of Diffusion Images
	-
	-\section QmitkDiffusionImagingPreprocessingPagePreprocessing Preprocessing
	-
	-The Preprocessing View bundles a selection of features and tools for dealing with diffusion weighted MR images. It can be used to modify header and geometry information, manipulate gradients and gradient images as well as calculating ADC maps.
	-
	-\section QmitkDiffusionImagingPreprocessingPageDetails Details
	-
	-\imageMacro{PreprocessingGUI_1.png,"Gradients tab",9.97}
	-
	-
	-The Gradients tab allows you to examine the number of b values and how many gradients were acquired for each. Here you can also visualize the gradients as points on a sphere, mirror opposite gradients so all are oriented within the same half sphere, round b values and merge similar gradients.
	-
	-\imageMacro{PreprocessingGUI_2.png,"Image values tab",9.97}
	-
	-The Image values tab enables you to manipulate the voxel values by e.g. resampling images, averaging repetitions of the same gradient, normalizing the image values or merging several DWIs into one.
	-
	-\imageMacro{PreprocessingGUI_3.png,"Header tab",9.97}
	-
	-In the Header tab you can selectively change geometry information of the image and delete or extract specific gradient volumes.
	-
	-\imageMacro{PreprocessingGUI_4.png,"Other tab",9.97}
	-
	-Miscellaneous tools in the Other tab allow for ADC map calculation and the extraction of the b0 image with the possibility of averaging all b0 images.
	-
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/documentation/doxygen/modules.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/documentation/doxygen/modules.dox
	deleted file mode 100644
	index c0a9180de7..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/documentation/doxygen/modules.dox
	+++ /dev/null
	@@ -1,16 +0,0 @@
	-/**
	- \defgroup org_mitk_gui_qt_diffusionimaging_preprocessing org.mitk.gui.qt.diffusionimaging.preprocessing
	- \ingroup MITKPlugins
	-
	- \brief This is the diffusionimaging.preprocessing plugin.
	-
	-*/
	-
	-/**
	- \defgroup org_mitk_gui_qt_diffusionimaging_preprocessing_internal Internal
	- \ingroup org_mitk_gui_qt_diffusionimaging_preprocessing
	-
	- \brief This subcategory includes the internal classes of the org.mitk.gui.qt.diffusionimaging.preprocessing plugin. Other
	- plugins must not rely on these classes. They contain implementation details and their interface
	- may change at any time. We mean it.
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/files.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/files.cmake
	deleted file mode 100644
	index f24fdc236a..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/files.cmake
	+++ /dev/null
	@@ -1,43 +0,0 @@
	-set(SRC_CPP_FILES
	-
	-
	-)
	-
	-set(INTERNAL_CPP_FILES
	- mitkPluginActivator.cpp
	-
	- QmitkPreprocessingView.cpp
	- QmitkDwiPreprocessingPerspective.cpp
	-)
	-
	-set(UI_FILES
	- src/internal/QmitkPreprocessingViewControls.ui
	-)
	-
	-set(MOC_H_FILES
	- src/internal/mitkPluginActivator.h
	-
	- src/internal/QmitkPreprocessingView.h
	- src/internal/QmitkDwiPreprocessingPerspective.h
	-)
	-
	-set(CACHED_RESOURCE_FILES
	- plugin.xml
	-
	- resources/dwi2.png
	-)
	-
	-set(QRC_FILES
	-
	-)
	-
	-
	-set(CPP_FILES )
	-
	-foreach(file ${SRC_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/${file})
	-endforeach(file ${SRC_CPP_FILES})
	-
	-foreach(file ${INTERNAL_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/internal/${file})
	-endforeach(file ${INTERNAL_CPP_FILES})
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/manifest_headers.cmake
	deleted file mode 100644
	index 223766b673..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/manifest_headers.cmake
	+++ /dev/null
	@@ -1,5 +0,0 @@
	-set(Plugin-Name "MITK Preprocessing")
	-set(Plugin-Version "1.0.0")
	-set(Plugin-Vendor "DKFZ, Medical and Biological Informatics")
	-set(Plugin-ContactAddress "http://www.mitk.org")
	-set(Require-Plugin org.mitk.gui.qt.diffusionimaging org.mitk.gui.qt.common)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/plugin.xml b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/plugin.xml
	deleted file mode 100644
	index cc085d4be1..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/plugin.xml
	+++ /dev/null
	@@ -1,28 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<?BlueBerry version="0.1"?>
	-<plugin>
	-
	- <extension point="org.blueberry.ui.views">
	-
	- <view id="org.mitk.views.diffusionpreprocessing"
	- name="Preprocessing"
	- category="Preprocessing"
	- class="QmitkPreprocessingView"
	- icon="resources/dwi2.png">
	- <keywordReference id="org.mitk.views.diffusionpreprocessing.Keyword"/>
	- </view>
	-
	- </extension>
	-
	- <extension point="org.blueberry.ui.perspectives">
	-
	- <perspective id="org.mitk.perspectives.dwipreprocessing"
	- name="Preprocessing"
	- class="QmitkDwiPreprocessingPerspective"
	- icon="resources/dwi2.png">
	- <description>This perspective contains views for diffusion-weighted image preprocessing such as head motion correction, registration, denoising and gradient manipulation.</description>
	- </perspective>
	-
	- </extension>
	-
	-</plugin>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/resources/dwi2.png b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/resources/dwi2.png
	deleted file mode 100644
	index c2087367ce..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/resources/dwi2.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/resources/prprocessing.svg b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/resources/prprocessing.svg
	deleted file mode 100644
	index f999c4dd3a..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/resources/prprocessing.svg
	+++ /dev/null
	@@ -1,149 +0,0 @@
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	-
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkDwiPreprocessingPerspective.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkDwiPreprocessingPerspective.cpp
	deleted file mode 100644
	index 776da102c1..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkDwiPreprocessingPerspective.cpp
	+++ /dev/null
	@@ -1,52 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkDwiPreprocessingPerspective.h"
	-#include "berryIViewLayout.h"
	-
	-void QmitkDwiPreprocessingPerspective::CreateInitialLayout(berry::IPageLayout::Pointer layout)
	-{
	- /////////////////////////////////////////////////////
	- // all di-app perspectives should have the following:
	- /////////////////////////////////////////////////////
	-
	- QString editorArea = layout->GetEditorArea();
	-
	- layout->AddStandaloneViewPlaceholder("org.mitk.views.viewnavigatorview", berry::IPageLayout::LEFT, 0.3f, editorArea, false);
	-
	- layout->AddStandaloneView("org.mitk.views.datamanager",
	- false, berry::IPageLayout::LEFT, 0.3f, editorArea);
	-
	- layout->AddStandaloneView("org.mitk.views.controlvisualizationpropertiesview",
	- false, berry::IPageLayout::BOTTOM, .15f, "org.mitk.views.datamanager");
	-
	- berry::IFolderLayout::Pointer left =
	- layout->CreateFolder("org.mbi.diffusionimaginginternal.leftcontrols",
	- berry::IPageLayout::BOTTOM, 0.15f, "org.mitk.views.controlvisualizationpropertiesview");
	-
	- layout->AddStandaloneViewPlaceholder("org.mitk.views.imagenavigator",
	- berry::IPageLayout::BOTTOM, .7f, "org.mbi.diffusionimaginginternal.leftcontrols", false);
	-
	- /////////////////////////////////////////////
	- // here goes the perspective specific stuff
	- /////////////////////////////////////////////
	-
	- left->AddView("org.mitk.views.diffusionpreprocessing");
	- left->AddView("org.mitk.views.brainextraction");
	- left->AddView("org.mitk.views.denoisingview");
	- left->AddView("org.mitk.views.simpleregistrationview");
	- left->AddView("org.mitk.views.headmotioncorrectionview");
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkDwiPreprocessingPerspective.h b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkDwiPreprocessingPerspective.h
	deleted file mode 100644
	index bdfc1cf04f..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkDwiPreprocessingPerspective.h
	+++ /dev/null
	@@ -1,36 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef QmitkDwiPreprocessingPerspective_H_
	-#define QmitkDwiPreprocessingPerspective_H_
	-
	-#include <berryIPerspectiveFactory.h>
	-
	-class QmitkDwiPreprocessingPerspective : public QObject, public berry::IPerspectiveFactory
	-{
	- Q_OBJECT
	- Q_INTERFACES(berry::IPerspectiveFactory)
	-
	-public:
	-
	- QmitkDwiPreprocessingPerspective() {}
	- ~QmitkDwiPreprocessingPerspective() {}
	-
	- void CreateInitialLayout(berry::IPageLayout::Pointer layout) override;
	-};
	-
	-#endif /* QmitkFiberProcessingPerspective_H_ */
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingView.cpp
	deleted file mode 100644
	index 838dd6d580..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingView.cpp
	+++ /dev/null
	@@ -1,1951 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-//#define MBILOG_ENABLE_DEBUG
	-
	-#include "QmitkPreprocessingView.h"
	-#include "mitkDiffusionImagingConfigure.h"
	-
	-// qt includes
	-#include <QMessageBox>
	-
	-// itk includes
	-#include "itkTimeProbe.h"
	-#include "itkB0ImageExtractionImageFilter.h"
	-#include "itkB0ImageExtractionToSeparateImageFilter.h"
	-#include "itkBrainMaskExtractionImageFilter.h"
	-#include "itkCastImageFilter.h"
	-#include "itkVectorContainer.h"
	-#include <itkElectrostaticRepulsionDiffusionGradientReductionFilter.h>
	-#include <itkMergeDiffusionImagesFilter.h>
	-#include <itkDwiGradientLengthCorrectionFilter.h>
	-#include <itkDwiNormilzationFilter.h>
	-#include <mitkTensorImage.h>
	-#include <mitkOdfImage.h>
	-
	-// Multishell includes
	-#include <itkRadialMultishellToSingleshellImageFilter.h>
	-
	-// Multishell Functors
	-#include <itkADCAverageFunctor.h>
	-#include <itkKurtosisFitFunctor.h>
	-#include <itkBiExpFitFunctor.h>
	-#include <itkADCFitFunctor.h>
	-
	-// mitk includes
	-#include "QmitkDataStorageComboBox.h"
	-#include "mitkProgressBar.h"
	-#include "mitkStatusBar.h"
	-#include "mitkNodePredicateDataType.h"
	-#include "mitkProperties.h"
	-#include "mitkVtkResliceInterpolationProperty.h"
	-#include "mitkLookupTable.h"
	-#include "mitkLookupTableProperty.h"
	-#include "mitkTransferFunction.h"
	-#include "mitkTransferFunctionProperty.h"
	-#include "mitkDataNodeObject.h"
	-#include "mitkOdfNormalizationMethodProperty.h"
	-#include "mitkOdfScaleByProperty.h"
	-#include <mitkPointSet.h>
	-#include <itkAdcImageFilter.h>
	-#include <itkBrainMaskExtractionImageFilter.h>
	-#include <mitkImageCast.h>
	-#include <mitkRotationOperation.h>
	-#include <QTableWidgetItem>
	-#include <QTableWidget>
	-#include <mitkInteractionConst.h>
	-#include <mitkImageAccessByItk.h>
	-#include <itkResampleDwiImageFilter.h>
	-#include <itkResampleImageFilter.h>
	-#include <itkImageDuplicator.h>
	-#include <itkMaskImageFilter.h>
	-#include <mitkNodePredicateProperty.h>
	-#include <mitkNodePredicateAnd.h>
	-#include <mitkNodePredicateNot.h>
	-#include <mitkNodePredicateOr.h>
	-#include <itkCropImageFilter.h>
	-#include <itkDiffusionTensor3DReconstructionImageFilter.h>
	-#include <itkRemoveDwiChannelFilter.h>
	-#include <itkExtractDwiChannelFilter.h>
	-#include <mitkBValueMapProperty.h>
	-#include <mitkGradientDirectionsProperty.h>
	-#include <mitkMeasurementFrameProperty.h>
	-#include <itkImageDuplicator.h>
	-#include <itkFlipImageFilter.h>
	-#include <mitkITKImageImport.h>
	-
	-const std::string QmitkPreprocessingView::VIEW_ID =
	- "org.mitk.views.diffusionpreprocessing";
	-
	-#define DI_INFO MITK_INFO("DiffusionImaging")
	-
	-
	-typedef float TTensorPixelType;
	-
	-
	-QmitkPreprocessingView::QmitkPreprocessingView()
	- : QmitkAbstractView(),
	- m_Controls(nullptr)
	-{
	-}
	-
	-QmitkPreprocessingView::~QmitkPreprocessingView()
	-{
	-
	-}
	-
	-void QmitkPreprocessingView::CreateQtPartControl(QWidget *parent)
	-{
	- if (!m_Controls)
	- {
	- // create GUI widgets
	- m_Controls = new Ui::QmitkPreprocessingViewControls;
	- m_Controls->setupUi(parent);
	- this->CreateConnections();
	-
	- m_Controls->m_MeasurementFrameTable->horizontalHeader()->setSectionResizeMode(QHeaderView::Stretch);
	- m_Controls->m_MeasurementFrameTable->verticalHeader()->setSectionResizeMode(QHeaderView::Stretch);
	- m_Controls->m_DirectionMatrixTable->horizontalHeader()->setSectionResizeMode(QHeaderView::Stretch);
	- m_Controls->m_DirectionMatrixTable->verticalHeader()->setSectionResizeMode(QHeaderView::Stretch);
	- }
	-}
	-
	-void QmitkPreprocessingView::SetFocus()
	-{
	- m_Controls->m_MirrorGradientToHalfSphereButton->setFocus();
	-}
	-
	-void QmitkPreprocessingView::CreateConnections()
	-{
	- if ( m_Controls )
	- {
	- m_Controls->m_NormalizationMaskBox->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_SelctedImageComboBox->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_MergeDwiBox->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_AlignImageBox->SetDataStorage(this->GetDataStorage());
	-
	- mitk::TNodePredicateDataType<mitk::Image>::Pointer isMitkImage = mitk::TNodePredicateDataType<mitk::Image>::New();
	-
	- mitk::NodePredicateDataType::Pointer isDti = mitk::NodePredicateDataType::New("TensorImage");
	- mitk::NodePredicateDataType::Pointer isOdf = mitk::NodePredicateDataType::New("OdfImage");
	- mitk::NodePredicateOr::Pointer isDiffusionImage = mitk::NodePredicateOr::New(isOdf, isDti);
	-
	- mitk::NodePredicateAnd::Pointer noDiffusionImage = mitk::NodePredicateAnd::New(isMitkImage, mitk::NodePredicateNot::New(isDiffusionImage));
	- mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true));
	- mitk::NodePredicateAnd::Pointer binaryNoDiffusionImage = mitk::NodePredicateAnd::New(noDiffusionImage, isBinaryPredicate);
	-
	- m_Controls->m_NormalizationMaskBox->SetPredicate(binaryNoDiffusionImage);
	- m_Controls->m_SelctedImageComboBox->SetPredicate(isMitkImage);
	- m_Controls->m_MergeDwiBox->SetPredicate(isMitkImage);
	- m_Controls->m_AlignImageBox->SetPredicate(isMitkImage);
	-
	- m_Controls->m_ExtractBrainMask->setVisible(false);
	- m_Controls->m_BrainMaskIterationsBox->setVisible(false);
	- m_Controls->m_ResampleIntFrame->setVisible(false);
	- connect( (QObject*)(m_Controls->m_ButtonAverageGradients), SIGNAL(clicked()), this, SLOT(AverageGradients()) );
	- connect( (QObject*)(m_Controls->m_ButtonExtractB0), SIGNAL(clicked()), this, SLOT(ExtractB0()) );
	- connect( (QObject*)(m_Controls->m_ReduceGradientsButton), SIGNAL(clicked()), this, SLOT(DoReduceGradientDirections()) );
	- connect( (QObject*)(m_Controls->m_ShowGradientsButton), SIGNAL(clicked()), this, SLOT(DoShowGradientDirections()) );
	- connect( (QObject*)(m_Controls->m_MirrorGradientToHalfSphereButton), SIGNAL(clicked()), this, SLOT(DoHalfSphereGradientDirections()) );
	- connect( (QObject*)(m_Controls->m_MergeDwisButton), SIGNAL(clicked()), this, SLOT(MergeDwis()) );
	- connect( (QObject*)(m_Controls->m_ProjectSignalButton), SIGNAL(clicked()), this, SLOT(DoProjectSignal()) );
	- connect( (QObject*)(m_Controls->m_B_ValueMap_Rounder_SpinBox), SIGNAL(valueChanged(int)), this, SLOT(UpdateDwiBValueMapRounder(int)));
	- connect( (QObject*)(m_Controls->m_CreateLengthCorrectedDwi), SIGNAL(clicked()), this, SLOT(DoLengthCorrection()) );
	- connect( (QObject*)(m_Controls->m_NormalizeImageValuesButton), SIGNAL(clicked()), this, SLOT(DoDwiNormalization()) );
	- connect( (QObject*)(m_Controls->m_ResampleImageButton), SIGNAL(clicked()), this, SLOT(DoResampleImage()) );
	- connect( (QObject*)(m_Controls->m_ResampleTypeBox), SIGNAL(currentIndexChanged(int)), this, SLOT(DoUpdateInterpolationGui(int)) );
	- connect( (QObject*)(m_Controls->m_CropImageButton), SIGNAL(clicked()), this, SLOT(DoCropImage()) );
	- connect( (QObject*)(m_Controls->m_RemoveGradientButton), SIGNAL(clicked()), this, SLOT(DoRemoveGradient()) );
	- connect( (QObject*)(m_Controls->m_ExtractGradientButton), SIGNAL(clicked()), this, SLOT(DoExtractGradient()) );
	- connect( (QObject*)(m_Controls->m_FlipAxis), SIGNAL(clicked()), this, SLOT(DoFlipAxis()) );
	- connect( (QObject*)(m_Controls->m_FlipGradientsButton), SIGNAL(clicked()), this, SLOT(DoFlipGradientDirections()) );
	- connect( (QObject*)(m_Controls->m_ClearRotationButton), SIGNAL(clicked()), this, SLOT(DoClearRotationOfGradients()) );
	- connect( (QObject*)(m_Controls->m_ModifyHeader), SIGNAL(clicked()), this, SLOT(DoApplyHeader()) );
	- connect( (QObject*)(m_Controls->m_AlignImageButton), SIGNAL(clicked()), this, SLOT(DoAlignImages()) );
	- connect( (QObject)(m_Controls->m_SelctedImageComboBox), SIGNAL(OnSelectionChanged(const mitk::DataNode)), this, SLOT(OnImageSelectionChanged()) );
	-
	- m_Controls->m_NormalizationMaskBox->SetZeroEntryText("--");
	-
	- QFont f("monospace");
	- f.setStyleHint(QFont::Monospace);
	- m_Controls->m_OriginalGradientsText->setFont(f);
	- m_Controls->m_WorkingGradientsText->setFont(f);
	- }
	-}
	-
	-void QmitkPreprocessingView::DoAlignImages()
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	- if (node.IsNull()) { return; }
	-
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	- if ( image == nullptr ) { return; }
	-
	-
	- mitk::DataNode::Pointer target_node = m_Controls->m_AlignImageBox->GetSelectedNode();
	- if (target_node.IsNull()) { return; }
	-
	- mitk::Image::Pointer target_image = dynamic_cast<mitk::Image*>(target_node->GetData());
	- if ( target_image == nullptr ) { return; }
	-
	- image->SetOrigin(target_image->GetGeometry()->GetOrigin());
	- mitk::RenderingManager::GetInstance()->InitializeViews( image->GetTimeGeometry(),
	- mitk::RenderingManager::REQUEST_UPDATE_ALL,
	- true );
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-void QmitkPreprocessingView::DoFlipAxis()
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	- if (node.IsNull()) { return; }
	-
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	- if ( image == nullptr ) { return; }
	-
	- bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(node) );
	-
	- if (isDiffusionImage)
	- {
	- ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New();
	- mitk::CastToItkImage(image, itkVectorImagePointer);
	-
	- itk::FixedArray<bool, 3> flipAxes;
	- flipAxes[0] = m_Controls->m_FlipX->isChecked();
	- flipAxes[1] = m_Controls->m_FlipY->isChecked();
	- flipAxes[2] = m_Controls->m_FlipZ->isChecked();
	-
	- itk::FlipImageFilter< ItkDwiType >::Pointer flipper = itk::FlipImageFilter< ItkDwiType >::New();
	- flipper->SetInput(itkVectorImagePointer);
	- flipper->SetFlipAxes(flipAxes);
	- flipper->Update();
	-
	- auto oldGradients = PropHelper::GetGradientContainer(image);
	- auto newGradients = GradProp::GradientDirectionsContainerType::New();
	-
	- for (unsigned int i=0; i<oldGradients->Size(); i++)
	- {
	- GradProp::GradientDirectionType g = oldGradients->GetElement(i);
	- GradProp::GradientDirectionType newG = g;
	- if (flipAxes[0]) { newG[0] *= -1; }
	-
	- if (flipAxes[1]) { newG[1] *= -1; }
	-
	- if (flipAxes[2]) { newG[2] *= -1; }
	-
	- newGradients->InsertElement(i, newG);
	- }
	-
	- mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( flipper->GetOutput() );
	- PropHelper::CopyProperties(image, newImage, true);
	- PropHelper::SetGradientContainer(newImage, newGradients);
	- PropHelper::InitializeImage(newImage);
	- newImage->GetGeometry()->SetOrigin(image->GetGeometry()->GetOrigin());
	-
	- mitk::DataNode::Pointer imageNode = mitk::DataNode::New();
	- imageNode->SetData( newImage );
	- QString name = node->GetName().c_str();
	-
	- imageNode->SetName((name+"_flipped").toStdString().c_str());
	- GetDataStorage()->Add(imageNode, node);
	-
	- mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true );
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- }
	- else if( image->GetPixelType().GetNumberOfComponents() == 1 )
	- {
	- AccessFixedDimensionByItk(image, TemplatedFlipAxis,3);
	- }
	- else
	- {
	- QMessageBox::warning(nullptr,"Warning", QString("Operation not supported in multi-component images") );
	- }
	-}
	-
	-
	-template < typename TPixel, unsigned int VImageDimension >
	-void QmitkPreprocessingView::TemplatedFlipAxis(itk::Image<TPixel, VImageDimension>* itkImage)
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	- if (node.IsNull()) { return; }
	-
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	- if ( image == nullptr ) { return; }
	-
	- itk::FixedArray<bool, 3> flipAxes;
	- flipAxes[0] = m_Controls->m_FlipX->isChecked();
	- flipAxes[1] = m_Controls->m_FlipY->isChecked();
	- flipAxes[2] = m_Controls->m_FlipZ->isChecked();
	-
	- typename itk::FlipImageFilter< itk::Image<TPixel, VImageDimension> >::Pointer flipper
	- = itk::FlipImageFilter< itk::Image<TPixel, VImageDimension> >::New();
	- flipper->SetInput(itkImage);
	- flipper->SetFlipAxes(flipAxes);
	- flipper->Update();
	-
	- mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( flipper->GetOutput() );
	- newImage->GetGeometry()->SetOrigin(image->GetGeometry()->GetOrigin());
	-
	- mitk::DataNode::Pointer imageNode = mitk::DataNode::New();
	- imageNode->SetData( newImage );
	- QString name = node->GetName().c_str();
	-
	- imageNode->SetName((name+"_flipped").toStdString().c_str());
	- GetDataStorage()->Add(imageNode, node);
	-
	- mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(),
	- mitk::RenderingManager::REQUEST_UPDATE_ALL,
	- true );
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-void QmitkPreprocessingView::DoRemoveGradient()
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	- if (node.IsNull()) { return; }
	-
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	- if ( image == nullptr ) { return; }
	-
	- bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) );
	- if ( !isDiffusionImage )
	- {
	- return;
	- }
	-
	- std::vector< unsigned int > channelsToRemove;
	- channelsToRemove.push_back(m_Controls->m_RemoveGradientBox->value());
	-
	- ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New();
	- mitk::CastToItkImage(image, itkVectorImagePointer);
	-
	- itk::RemoveDwiChannelFilter< short >::Pointer filter = itk::RemoveDwiChannelFilter< short >::New();
	- filter->SetInput(itkVectorImagePointer);
	- filter->SetChannelIndices(channelsToRemove);
	- filter->SetDirections(PropHelper::GetGradientContainer(image));
	- filter->Update();
	-
	- mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( filter->GetOutput() );
	- PropHelper::CopyProperties(image, newImage, true);
	- PropHelper::SetGradientContainer(newImage, filter->GetNewDirections());
	- PropHelper::InitializeImage( newImage );
	-
	- mitk::DataNode::Pointer imageNode = mitk::DataNode::New();
	- imageNode->SetData( newImage );
	- QString name = node->GetName().c_str();
	-
	- imageNode->SetName((name+"_removedgradients").toStdString().c_str());
	- GetDataStorage()->Add(imageNode, node);
	-
	- mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(),
	- mitk::RenderingManager::REQUEST_UPDATE_ALL,
	- true );
	-
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-void QmitkPreprocessingView::DoExtractGradient()
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	- if (node.IsNull()) { return; }
	-
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	- if ( image == nullptr ) { return; }
	-
	- bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) );
	- if ( !isDiffusionImage ) { return; }
	-
	- ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New();
	- mitk::CastToItkImage(image, itkVectorImagePointer);
	-
	- unsigned int channel = m_Controls->m_ExtractGradientBox->value();
	- itk::ExtractDwiChannelFilter< short >::Pointer filter = itk::ExtractDwiChannelFilter< short >::New();
	- filter->SetInput( itkVectorImagePointer);
	- filter->SetChannelIndex(channel);
	- filter->Update();
	-
	- mitk::Image::Pointer newImage = mitk::Image::New();
	- newImage->InitializeByItk( filter->GetOutput() );
	- newImage->SetImportChannel( filter->GetOutput()->GetBufferPointer() );
	-
	- mitk::DataNode::Pointer imageNode = mitk::DataNode::New();
	- imageNode->SetData( newImage );
	-
	- QString name = node->GetName().c_str();
	- imageNode->SetName( (name+"_direction-"+QString::number(channel)).toStdString().c_str() );
	- GetDataStorage()->Add(imageNode, node);
	-
	- mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(),
	- mitk::RenderingManager::REQUEST_UPDATE_ALL,
	- true);
	-}
	-
	-void QmitkPreprocessingView::DoCropImage()
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	- if (node.IsNull()) { return; }
	-
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	- if ( image == nullptr ) { return; }
	-
	- bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) );
	- if ( isDiffusionImage )
	- {
	- ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New();
	- mitk::CastToItkImage(image, itkVectorImagePointer);
	-
	- ItkDwiType::SizeType lower;
	- ItkDwiType::SizeType upper;
	- lower[0] = m_Controls->m_XstartBox->value();
	- lower[1] = m_Controls->m_YstartBox->value();
	- lower[2] = m_Controls->m_ZstartBox->value();
	- upper[0] = m_Controls->m_XendBox->value();
	- upper[1] = m_Controls->m_YendBox->value();
	- upper[2] = m_Controls->m_ZendBox->value();
	-
	- itk::CropImageFilter< ItkDwiType, ItkDwiType >::Pointer cropper = itk::CropImageFilter< ItkDwiType, ItkDwiType >::New();
	- cropper->SetLowerBoundaryCropSize(lower);
	- cropper->SetUpperBoundaryCropSize(upper);
	- cropper->SetInput( itkVectorImagePointer );
	- cropper->Update();
	-
	- ItkDwiType::Pointer itkOutImage = cropper->GetOutput();
	- ItkDwiType::DirectionType dir = itkOutImage->GetDirection();
	- itk::Point<double,3> origin = itkOutImage->GetOrigin();
	-
	- itk::Point<double,3> t; t[0] = lower[0]itkOutImage->GetSpacing()[0]; t[1] = lower[1]itkOutImage->GetSpacing()[1]; t[2] = lower[2]*itkOutImage->GetSpacing()[2];
	- t= dir*t;
	-
	- origin[0] += t[0];
	- origin[1] += t[1];
	- origin[2] += t[2];
	-
	- itkOutImage->SetOrigin(origin);
	-
	- mitk::Image::Pointer newimage = mitk::GrabItkImageMemory( itkOutImage );
	- PropHelper::CopyProperties(image, newimage, false);
	- PropHelper::InitializeImage( newimage );
	-
	- mitk::DataNode::Pointer imageNode = mitk::DataNode::New();
	- imageNode->SetData( newimage );
	- QString name = node->GetName().c_str();
	- imageNode->SetName((name+"_cropped").toStdString().c_str());
	- GetDataStorage()->Add(imageNode, node);
	- mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(),
	- mitk::RenderingManager::REQUEST_UPDATE_ALL,
	- true );
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	-
	- mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(),
	- mitk::RenderingManager::REQUEST_UPDATE_ALL,
	- true );
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- }
	- else if( image->GetPixelType().GetNumberOfComponents() )
	- {
	- AccessFixedDimensionByItk(image, TemplatedCropImage,3);
	- }
	- else
	- {
	- QMessageBox::warning(nullptr,"Warning", QString("Operation not supported in multi-component images") );
	- }
	-}
	-
	-template < typename TPixel, unsigned int VImageDimension >
	-void QmitkPreprocessingView::TemplatedCropImage( itk::Image<TPixel, VImageDimension>* itkImage)
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	- if (node.IsNull()) { return; }
	-
	- ItkDwiType::SizeType lower;
	- ItkDwiType::SizeType upper;
	- lower[0] = m_Controls->m_XstartBox->value();
	- lower[1] = m_Controls->m_YstartBox->value();
	- lower[2] = m_Controls->m_ZstartBox->value();
	- upper[0] = m_Controls->m_XendBox->value();
	- upper[1] = m_Controls->m_YendBox->value();
	- upper[2] = m_Controls->m_ZendBox->value();
	-
	- typedef itk::Image<TPixel, VImageDimension> ImageType;
	- typename itk::CropImageFilter< ImageType, ImageType >::Pointer cropper
	- = itk::CropImageFilter< ImageType, ImageType >::New();
	- cropper->SetLowerBoundaryCropSize(lower);
	- cropper->SetUpperBoundaryCropSize(upper);
	- cropper->SetInput(itkImage);
	- cropper->Update();
	-
	- typename ImageType::Pointer itkOutImage = cropper->GetOutput();
	- typename ImageType::DirectionType dir = itkOutImage->GetDirection();
	- itk::Point<double,3> origin = itkOutImage->GetOrigin();
	-
	- itk::Point<double,3> t; t[0] = lower[0]itkOutImage->GetSpacing()[0]; t[1] = lower[1]itkOutImage->GetSpacing()[1]; t[2] = lower[2]*itkOutImage->GetSpacing()[2];
	- t= dir*t;
	-
	- origin[0] += t[0];
	- origin[1] += t[1];
	- origin[2] += t[2];
	-
	- itkOutImage->SetOrigin(origin);
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk( itkOutImage.GetPointer() );
	- image->SetVolume( itkOutImage->GetBufferPointer() );
	- mitk::DataNode::Pointer imageNode = mitk::DataNode::New();
	- imageNode->SetData( image );
	- QString name = node->GetName().c_str();
	-
	- imageNode->SetName((name+"_cropped").toStdString().c_str());
	- GetDataStorage()->Add(imageNode, node);
	-
	- mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(),
	- mitk::RenderingManager::REQUEST_UPDATE_ALL,
	- true );
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-void QmitkPreprocessingView::DoUpdateInterpolationGui(int i)
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	- if (node.IsNull()) { return; }
	-
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	- if ( image == nullptr ) { return; }
	-
	- switch (i)
	- {
	- case 0:
	- {
	- m_Controls->m_ResampleIntFrame->setVisible(false);
	- m_Controls->m_ResampleDoubleFrame->setVisible(true);
	- break;
	- }
	- case 1:
	- {
	- m_Controls->m_ResampleIntFrame->setVisible(false);
	- m_Controls->m_ResampleDoubleFrame->setVisible(true);
	-
	- mitk::BaseGeometry* geom = image->GetGeometry();
	- m_Controls->m_ResampleDoubleX->setValue(geom->GetSpacing()[0]);
	- m_Controls->m_ResampleDoubleY->setValue(geom->GetSpacing()[1]);
	- m_Controls->m_ResampleDoubleZ->setValue(geom->GetSpacing()[2]);
	- break;
	- }
	- case 2:
	- {
	- m_Controls->m_ResampleIntFrame->setVisible(true);
	- m_Controls->m_ResampleDoubleFrame->setVisible(false);
	-
	- mitk::BaseGeometry* geom = image->GetGeometry();
	- m_Controls->m_ResampleIntX->setValue(geom->GetExtent(0));
	- m_Controls->m_ResampleIntY->setValue(geom->GetExtent(1));
	- m_Controls->m_ResampleIntZ->setValue(geom->GetExtent(2));
	- break;
	- }
	- default:
	- {
	- m_Controls->m_ResampleIntFrame->setVisible(false);
	- m_Controls->m_ResampleDoubleFrame->setVisible(true);
	- }
	- }
	-}
	-
	-void QmitkPreprocessingView::DoExtractBrainMask()
	-{
	-}
	-
	-void QmitkPreprocessingView::DoResampleImage()
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	- if (node.IsNull()) { return; }
	-
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	- if ( image == nullptr ) { return; }
	-
	- bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) );
	- if ( isDiffusionImage )
	- {
	- ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New();
	- mitk::CastToItkImage(image, itkVectorImagePointer);
	-
	- typedef itk::ResampleDwiImageFilter< short > ResampleFilter;
	- ResampleFilter::Pointer resampler = ResampleFilter::New();
	- resampler->SetInput( itkVectorImagePointer );
	-
	- switch (m_Controls->m_ResampleTypeBox->currentIndex())
	- {
	- case 0:
	- {
	- itk::Vector< double, 3 > samplingFactor;
	- samplingFactor[0] = m_Controls->m_ResampleDoubleX->value();
	- samplingFactor[1] = m_Controls->m_ResampleDoubleY->value();
	- samplingFactor[2] = m_Controls->m_ResampleDoubleZ->value();
	- resampler->SetSamplingFactor(samplingFactor);
	- break;
	- }
	- case 1:
	- {
	- itk::Vector< double, 3 > newSpacing;
	- newSpacing[0] = m_Controls->m_ResampleDoubleX->value();
	- newSpacing[1] = m_Controls->m_ResampleDoubleY->value();
	- newSpacing[2] = m_Controls->m_ResampleDoubleZ->value();
	- resampler->SetNewSpacing(newSpacing);
	- break;
	- }
	- case 2:
	- {
	- itk::ImageRegion<3> newRegion;
	- newRegion.SetSize(0, m_Controls->m_ResampleIntX->value());
	- newRegion.SetSize(1, m_Controls->m_ResampleIntY->value());
	- newRegion.SetSize(2, m_Controls->m_ResampleIntZ->value());
	- resampler->SetNewImageSize(newRegion);
	- break;
	- }
	- default:
	- {
	- MITK_WARN << "Unknown resampling parameters!";
	- return;
	- }
	- }
	-
	- QString outAdd;
	- switch (m_Controls->m_InterpolatorBox->currentIndex())
	- {
	- case 0:
	- {
	- resampler->SetInterpolation(ResampleFilter::Interpolate_NearestNeighbour);
	- outAdd = "NearestNeighbour";
	- break;
	- }
	- case 1:
	- {
	- resampler->SetInterpolation(ResampleFilter::Interpolate_Linear);
	- outAdd = "Linear";
	- break;
	- }
	- case 2:
	- {
	- resampler->SetInterpolation(ResampleFilter::Interpolate_BSpline);
	- outAdd = "BSpline";
	- break;
	- }
	- case 3:
	- {
	- resampler->SetInterpolation(ResampleFilter::Interpolate_WindowedSinc);
	- outAdd = "WindowedSinc";
	- break;
	- }
	- default:
	- {
	- resampler->SetInterpolation(ResampleFilter::Interpolate_NearestNeighbour);
	- outAdd = "NearestNeighbour";
	- }
	- }
	-
	- resampler->Update();
	-
	- mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( resampler->GetOutput() );
	- PropHelper::CopyProperties(image, newImage, false);
	- PropHelper::InitializeImage( newImage );
	-
	- mitk::DataNode::Pointer imageNode = mitk::DataNode::New();
	- imageNode->SetData( newImage );
	- QString name = node->GetName().c_str();
	-
	- imageNode->SetName((name+"_resampled_"+outAdd).toStdString().c_str());
	- imageNode->SetVisibility(false);
	- GetDataStorage()->Add(imageNode, node);
	- }
	- else if( image->GetPixelType().GetNumberOfComponents() )
	- {
	- AccessFixedDimensionByItk(image, TemplatedResampleImage,3);
	- }
	- else
	- {
	- QMessageBox::warning(nullptr,"Warning", QString("Operation not supported in multi-component images") );
	- }
	-}
	-
	-
	-template < typename TPixel, unsigned int VImageDimension >
	-void QmitkPreprocessingView::TemplatedResampleImage( itk::Image<TPixel, VImageDimension>* itkImage)
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	- if (node.IsNull()) { return; }
	-
	- itk::Vector< double, 3 > newSpacing;
	- itk::ImageRegion<3> newRegion;
	-
	- switch (m_Controls->m_ResampleTypeBox->currentIndex())
	- {
	- case 0:
	- {
	- itk::Vector< double, 3 > sampling;
	- sampling[0] = m_Controls->m_ResampleDoubleX->value();
	- sampling[1] = m_Controls->m_ResampleDoubleY->value();
	- sampling[2] = m_Controls->m_ResampleDoubleZ->value();
	-
	- newSpacing = itkImage->GetSpacing();
	- newSpacing[0] /= sampling[0];
	- newSpacing[1] /= sampling[1];
	- newSpacing[2] /= sampling[2];
	- newRegion = itkImage->GetLargestPossibleRegion();
	- newRegion.SetSize(0, newRegion.GetSize(0)*sampling[0]);
	- newRegion.SetSize(1, newRegion.GetSize(1)*sampling[1]);
	- newRegion.SetSize(2, newRegion.GetSize(2)*sampling[2]);
	-
	- break;
	- }
	- case 1:
	- {
	- newSpacing[0] = m_Controls->m_ResampleDoubleX->value();
	- newSpacing[1] = m_Controls->m_ResampleDoubleY->value();
	- newSpacing[2] = m_Controls->m_ResampleDoubleZ->value();
	-
	- itk::Vector< double, 3 > oldSpacing = itkImage->GetSpacing();
	- itk::Vector< double, 3 > sampling;
	- sampling[0] = oldSpacing[0]/newSpacing[0];
	- sampling[1] = oldSpacing[1]/newSpacing[1];
	- sampling[2] = oldSpacing[2]/newSpacing[2];
	- newRegion = itkImage->GetLargestPossibleRegion();
	- newRegion.SetSize(0, newRegion.GetSize(0)*sampling[0]);
	- newRegion.SetSize(1, newRegion.GetSize(1)*sampling[1]);
	- newRegion.SetSize(2, newRegion.GetSize(2)*sampling[2]);
	- break;
	- }
	- case 2:
	- {
	- newRegion.SetSize(0, m_Controls->m_ResampleIntX->value());
	- newRegion.SetSize(1, m_Controls->m_ResampleIntY->value());
	- newRegion.SetSize(2, m_Controls->m_ResampleIntZ->value());
	-
	- itk::ImageRegion<3> oldRegion = itkImage->GetLargestPossibleRegion();
	- itk::Vector< double, 3 > sampling;
	- sampling[0] = (double)newRegion.GetSize(0)/oldRegion.GetSize(0);
	- sampling[1] = (double)newRegion.GetSize(1)/oldRegion.GetSize(1);
	- sampling[2] = (double)newRegion.GetSize(2)/oldRegion.GetSize(2);
	-
	- newSpacing = itkImage->GetSpacing();
	- newSpacing[0] /= sampling[0];
	- newSpacing[1] /= sampling[1];
	- newSpacing[2] /= sampling[2];
	- break;
	- }
	- default:
	- {
	- MITK_WARN << "Unknown resampling parameters!";
	- return;
	- }
	- }
	-
	- itk::Point<double,3> origin = itkImage->GetOrigin();
	- origin[0] -= itkImage->GetSpacing()[0]/2;
	- origin[1] -= itkImage->GetSpacing()[1]/2;
	- origin[2] -= itkImage->GetSpacing()[2]/2;
	- origin[0] += newSpacing[0]/2;
	- origin[1] += newSpacing[1]/2;
	- origin[2] += newSpacing[2]/2;
	-
	- typedef itk::Image<TPixel, VImageDimension> ImageType;
	- typename ImageType::Pointer outImage = ImageType::New();
	- outImage->SetSpacing( newSpacing );
	- outImage->SetOrigin( origin );
	- outImage->SetDirection( itkImage->GetDirection() );
	- outImage->SetLargestPossibleRegion( newRegion );
	- outImage->SetBufferedRegion( newRegion );
	- outImage->SetRequestedRegion( newRegion );
	- outImage->Allocate();
	-
	- typedef itk::ResampleImageFilter<ImageType, ImageType> ResampleFilter;
	- typename ResampleFilter::Pointer resampler = ResampleFilter::New();
	- resampler->SetInput(itkImage);
	- resampler->SetOutputParametersFromImage(outImage);
	-
	- QString outAdd;
	- switch (m_Controls->m_InterpolatorBox->currentIndex())
	- {
	- case 0:
	- {
	- typename itk::NearestNeighborInterpolateImageFunction<ImageType>::Pointer interp
	- = itk::NearestNeighborInterpolateImageFunction<ImageType>::New();
	- resampler->SetInterpolator(interp);
	- outAdd = "NearestNeighbour";
	- break;
	- }
	- case 1:
	- {
	- typename itk::LinearInterpolateImageFunction<ImageType>::Pointer interp
	- = itk::LinearInterpolateImageFunction<ImageType>::New();
	- resampler->SetInterpolator(interp);
	- outAdd = "Linear";
	- break;
	- }
	- case 2:
	- {
	- typename itk::BSplineInterpolateImageFunction<ImageType>::Pointer interp
	- = itk::BSplineInterpolateImageFunction<ImageType>::New();
	- resampler->SetInterpolator(interp);
	- outAdd = "BSpline";
	- break;
	- }
	- case 3:
	- {
	- typename itk::WindowedSincInterpolateImageFunction<ImageType, 3>::Pointer interp
	- = itk::WindowedSincInterpolateImageFunction<ImageType, 3>::New();
	- resampler->SetInterpolator(interp);
	- outAdd = "WindowedSinc";
	- break;
	- }
	- default:
	- {
	- typename itk::NearestNeighborInterpolateImageFunction<ImageType>::Pointer interp
	- = itk::NearestNeighborInterpolateImageFunction<ImageType>::New();
	- resampler->SetInterpolator(interp);
	- outAdd = "NearestNeighbour";
	- }
	- }
	-
	- resampler->Update();
	-
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk( resampler->GetOutput() );
	- image->SetVolume( resampler->GetOutput()->GetBufferPointer() );
	- mitk::DataNode::Pointer imageNode = mitk::DataNode::New();
	- imageNode->SetData( image );
	- QString name = node->GetName().c_str();
	-
	- imageNode->SetName((name+"_resampled_"+outAdd).toStdString().c_str());
	- GetDataStorage()->Add(imageNode, node);
	-}
	-
	-void QmitkPreprocessingView::DoApplyHeader()
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	- if (node.IsNull()) { return; }
	-
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	- if ( image == nullptr ) { return; }
	-
	- bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) );
	-
	- bool isDti = false;
	- bool isOdf = false;
	- bool isPeak = false;
	- if (!isDiffusionImage)
	- {
	- if ( dynamic_cast<mitk::TensorImage*>(node->GetData()) )
	- isDti = true;
	- else if ( dynamic_cast<mitk::OdfImage*>(node->GetData()) )
	- isOdf = true;
	- else if ( dynamic_cast<mitk::PeakImage*>(node->GetData()) )
	- isPeak = true;
	- }
	- mitk::Image::Pointer newImage = image->Clone();
	-
	- mitk::Vector3D spacing;
	- spacing[0] = m_Controls->m_HeaderSpacingX->value();
	- spacing[1] = m_Controls->m_HeaderSpacingY->value();
	- spacing[2] = m_Controls->m_HeaderSpacingZ->value();
	- newImage->GetGeometry()->SetSpacing( spacing );
	-
	- mitk::Point3D origin;
	- origin[0] = m_Controls->m_HeaderOriginX->value();
	- origin[1] = m_Controls->m_HeaderOriginY->value();
	- origin[2] = m_Controls->m_HeaderOriginZ->value();
	- newImage->GetGeometry()->SetOrigin(origin);
	-
	- vtkSmartPointer< vtkMatrix4x4 > matrix = vtkSmartPointer< vtkMatrix4x4 >::New();
	- matrix->SetElement(0,3,newImage->GetGeometry()->GetOrigin()[0]);
	- matrix->SetElement(1,3,newImage->GetGeometry()->GetOrigin()[1]);
	- matrix->SetElement(2,3,newImage->GetGeometry()->GetOrigin()[2]);
	- for (int r=0; r<3; r++)
	- {
	- for (int c=0; c<3; c++)
	- {
	- QTableWidgetItem* item = m_Controls->m_DirectionMatrixTable->item(r,c);
	- if (!item)
	- continue;
	- matrix->SetElement(r,c,item->text().toDouble());
	- }
	- }
	- newImage->GetGeometry()->SetIndexToWorldTransformByVtkMatrixWithoutChangingSpacing(matrix);
	-
	- if ( isDiffusionImage )
	- {
	- vnl_matrix_fixed< double, 3, 3 > mf;
	- for (int r=0; r<3; r++)
	- {
	- for (int c=0; c<3; c++)
	- {
	- QTableWidgetItem* item = m_Controls->m_MeasurementFrameTable->item(r,c);
	- if (!item)
	- continue;
	- mf[r][c] = item->text().toDouble();
	- }
	- }
	- PropHelper::SetMeasurementFrame(newImage, mf);
	- PropHelper::InitializeImage( newImage );
	- }
	-
	- mitk::DataNode::Pointer imageNode = mitk::DataNode::New();
	- if (isOdf)
	- {
	- mitk::OdfImage::ItkOdfImageType::Pointer itk_img = mitk::OdfImage::ItkOdfImageType::New();
	- mitk::CastToItkImage(newImage, itk_img);
	-
	- mitk::Image::Pointer odfImage = dynamic_cast<mitk::Image*>(mitk::OdfImage::New().GetPointer());
	- mitk::CastToMitkImage(itk_img, odfImage);
	- odfImage->SetVolume(itk_img->GetBufferPointer());
	- imageNode->SetData( odfImage );
	- }
	- else if (isDti)
	- {
	- mitk::TensorImage::ItkTensorImageType::Pointer itk_img = mitk::ImageToItkImage<mitk::TensorImage::PixelType,3>(newImage);
	- mitk::Image::Pointer tensorImage = dynamic_cast<mitk::Image*>(mitk::TensorImage::New().GetPointer());
	- mitk::CastToMitkImage(itk_img, tensorImage);
	- tensorImage->SetVolume(itk_img->GetBufferPointer());
	- imageNode->SetData( tensorImage );
	- }
	- else if (isPeak)
	- {
	- mitk::PeakImage::ItkPeakImageType::Pointer itk_img = mitk::ImageToItkImage<float,4>(newImage);
	- mitk::Image::Pointer peakImage = dynamic_cast<mitk::Image*>(mitk::PeakImage::New().GetPointer());
	- mitk::CastToMitkImage(itk_img, peakImage);
	- peakImage->SetVolume(itk_img->GetBufferPointer());
	- imageNode->SetData( peakImage );
	- }
	- else
	- imageNode->SetData( newImage );
	-
	- QString name = node->GetName().c_str();
	- imageNode->SetName((name+"_newheader").toStdString().c_str());
	- GetDataStorage()->Add(imageNode, node);
	- mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(),
	- mitk::RenderingManager::REQUEST_UPDATE_ALL,
	- true );
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-void QmitkPreprocessingView::DoProjectSignal()
	-{
	- switch(m_Controls->m_ProjectionMethodBox->currentIndex())
	- {
	- case 0:
	- DoADCAverage();
	- break;
	- case 1:
	- DoAKCFit();
	- break;
	- case 2:
	- DoBiExpFit();
	- break;
	- default:
	- DoADCAverage();
	- }
	-}
	-
	-void QmitkPreprocessingView::DoDwiNormalization()
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	- if (node.IsNull()) { return; }
	-
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	- if ( image == nullptr ) { return; }
	-
	- bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) );
	- if ( ! isDiffusionImage ) { return; }
	-
	- auto gradientContainer = PropHelper::GetGradientContainer(image);
	-
	- int b0Index = -1;
	- for (unsigned int i=0; i<gradientContainer->size(); i++)
	- {
	- GradientDirectionType g = gradientContainer->GetElement(i);
	- if (g.magnitude()<0.001)
	- {
	- b0Index = i;
	- break;
	- }
	- }
	- if (b0Index==-1) { return; }
	-
	- typedef itk::DwiNormilzationFilter<short> FilterType;
	-
	- ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New();
	- mitk::CastToItkImage(image, itkVectorImagePointer);
	-
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetInput( itkVectorImagePointer );
	- filter->SetGradientDirections(PropHelper::GetGradientContainer(image));
	- filter->SetNewMean(m_Controls->m_NewMean->value());
	- filter->SetNewStdev(m_Controls->m_NewStdev->value());
	-
	- UcharImageType::Pointer itkImage = nullptr;
	- if (m_Controls->m_NormalizationMaskBox->GetSelectedNode().IsNotNull())
	- {
	- itkImage = UcharImageType::New();
	- if ( dynamic_cast<mitk::Image*>(m_Controls->m_NormalizationMaskBox->GetSelectedNode()->GetData()) != nullptr )
	- {
	- mitk::CastToItkImage( dynamic_cast<mitk::Image*>(m_Controls->m_NormalizationMaskBox->GetSelectedNode()->GetData()), itkImage );
	- }
	- filter->SetMaskImage(itkImage);
	- }
	- filter->Update();
	-
	- mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( filter->GetOutput() );
	- PropHelper::CopyProperties(image, newImage, false);
	- PropHelper::InitializeImage( newImage );
	-
	- mitk::DataNode::Pointer imageNode = mitk::DataNode::New();
	- imageNode->SetData( newImage );
	- QString name = node->GetName().c_str();
	-
	- imageNode->SetName((name+"_normalized").toStdString().c_str());
	- GetDataStorage()->Add(imageNode, node);
	-}
	-
	-void QmitkPreprocessingView::DoLengthCorrection()
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	- if (node.IsNull())
	- return;
	-
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	- if (image == nullptr )
	- return;
	-
	- if (!PropHelper::IsDiffusionWeightedImage(image))
	- return;
	-
	- typedef itk::DwiGradientLengthCorrectionFilter FilterType;
	-
	- ItkDwiType::Pointer itkVectorImagePointer = PropHelper::GetItkVectorImage(image);
	-
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetRoundingValue( m_Controls->m_B_ValueMap_Rounder_SpinBox->value());
	- filter->SetReferenceBValue(PropHelper::GetReferenceBValue(image));
	- filter->SetReferenceGradientDirectionContainer(PropHelper::GetGradientContainer(image));
	- filter->Update();
	-
	- mitk::Image::Pointer newImage = mitk::Image::New();
	- newImage->InitializeByItk( itkVectorImagePointer.GetPointer() );
	- newImage->SetImportVolume( itkVectorImagePointer->GetBufferPointer(), 0, 0, mitk::Image::CopyMemory);
	- itkVectorImagePointer->GetPixelContainer()->ContainerManageMemoryOff();
	-
	- PropHelper::CopyProperties(image, newImage, true);
	- PropHelper::SetGradientContainer(newImage, filter->GetOutputGradientDirectionContainer());
	- PropHelper::SetReferenceBValue(newImage, filter->GetNewBValue());
	- PropHelper::InitializeImage( newImage );
	-
	- mitk::DataNode::Pointer imageNode = mitk::DataNode::New();
	- imageNode->SetData( newImage );
	- QString name = node->GetName().c_str();
	-
	- imageNode->SetName((name+"_rounded").toStdString().c_str());
	- GetDataStorage()->Add(imageNode, node);
	-}
	-
	-void QmitkPreprocessingView::UpdateDwiBValueMapRounder(int i)
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	- if (node.IsNull()) { return; }
	-
	- bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(node) );
	- if ( ! isDiffusionImage ) { return; }
	-
	- UpdateBValueTableWidget(i);
	- UpdateGradientDetails();
	-}
	-
	-void QmitkPreprocessingView::
	-CallMultishellToSingleShellFilter( itk::DWIVoxelFunctor * functor,
	- mitk::Image::Pointer image,
	- QString imageName,
	- mitk::DataNode* parent )
	-{
	- typedef itk::RadialMultishellToSingleshellImageFilter<DiffusionPixelType, DiffusionPixelType> FilterType;
	-
	- // filter input parameter
	- const mitk::BValueMapProperty::BValueMap& originalShellMap = PropHelper::GetBValueMap(image);
	-
	- ItkDwiType::Pointer itkVectorImagePointer = PropHelper::GetItkVectorImage(image);
	- ItkDwiType* vectorImage = itkVectorImagePointer.GetPointer();
	- const GradProp::GradientDirectionsContainerType::Pointer gradientContainer = PropHelper::GetGradientContainer(image);
	- const unsigned int& bValue = PropHelper::GetReferenceBValue(image);
	-
	- mitk::DataNode::Pointer imageNode = 0;
	-
	- // filter call
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetInput(vectorImage);
	- filter->SetOriginalGradientDirections(gradientContainer);
	- filter->SetOriginalBValueMap(originalShellMap);
	- filter->SetOriginalBValue(bValue);
	- filter->SetFunctor(functor);
	- filter->Update();
	-
	- // create new DWI image
	- mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( filter->GetOutput() );
	- PropHelper::CopyProperties(image, outImage, true);
	-
	- PropHelper::SetGradientContainer(outImage, filter->GetTargetGradientDirections());
	- PropHelper::SetReferenceBValue(outImage, m_Controls->m_targetBValueSpinBox->value());
	- PropHelper::InitializeImage( outImage );
	-
	- imageNode = mitk::DataNode::New();
	- imageNode->SetData( outImage );
	- imageNode->SetName(imageName.toStdString().c_str());
	- GetDataStorage()->Add(imageNode, parent);
	-}
	-
	-void QmitkPreprocessingView::DoBiExpFit()
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	- if (node.IsNull()) { return; }
	-
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	- if ( image == nullptr ) { return; }
	-
	- bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) );
	- if ( ! isDiffusionImage ) { return; }
	-
	- itk::BiExpFitFunctor::Pointer functor = itk::BiExpFitFunctor::New();
	-
	- QString name(node->GetName().c_str());
	-
	- const mitk::BValueMapProperty::BValueMap& originalShellMap = PropHelper::GetBValueMap(image);
	-
	- mitk::BValueMapProperty::BValueMap::const_iterator it = originalShellMap.begin();
	- ++it;/* skip b=0/ unsigned int s = 0; /shell index */
	- vnl_vector<double> bValueList(originalShellMap.size()-1);
	-
	- while( it != originalShellMap.end() ) { bValueList.put(s++,(it++)->first); }
	-
	- const double targetBValue = m_Controls->m_targetBValueSpinBox->value();
	- functor->setListOfBValues(bValueList);
	- functor->setTargetBValue(targetBValue);
	- CallMultishellToSingleShellFilter(functor,image,name + "_BiExp", node);
	-}
	-
	-void QmitkPreprocessingView::DoAKCFit()
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	- if (node.IsNull()) { return; }
	-
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	- if ( image == nullptr ) { return; }
	-
	- bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) );
	- if ( ! isDiffusionImage ) { return; }
	-
	- itk::KurtosisFitFunctor::Pointer functor = itk::KurtosisFitFunctor::New();
	-
	- QString name(node->GetName().c_str());
	-
	- const mitk::BValueMapProperty::BValueMap& originalShellMap = PropHelper::GetBValueMap(image);
	-
	- mitk::BValueMapProperty::BValueMap::const_iterator it = originalShellMap.begin();
	- ++it;/* skip b=0/ unsigned int s = 0; /shell index */
	- vnl_vector<double> bValueList(originalShellMap.size()-1);
	- while(it != originalShellMap.end())
	- bValueList.put(s++,(it++)->first);
	-
	- const double targetBValue = m_Controls->m_targetBValueSpinBox->value();
	- functor->setListOfBValues(bValueList);
	- functor->setTargetBValue(targetBValue);
	- CallMultishellToSingleShellFilter(functor,image,name + "_AKC", node);
	-}
	-
	-void QmitkPreprocessingView::DoADCFit()
	-{
	- // later
	-}
	-
	-void QmitkPreprocessingView::DoADCAverage()
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	- if (node.IsNull()) { return; }
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	- if ( image == nullptr ) { return; }
	-
	- bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) );
	- if ( ! isDiffusionImage )
	- return;
	-
	- itk::ADCAverageFunctor::Pointer functor = itk::ADCAverageFunctor::New();
	-
	- QString name(node->GetName().c_str());
	-
	- const mitk::BValueMapProperty::BValueMap &originalShellMap = PropHelper::GetBValueMap(image);
	-
	- mitk::BValueMapProperty::BValueMap::const_iterator it = originalShellMap.begin();
	- ++it;/* skip b=0/ unsigned int s = 0; /shell index */
	- vnl_vector<double> bValueList(originalShellMap.size()-1);
	- while(it != originalShellMap.end())
	- bValueList.put(s++,(it++)->first);
	-
	- const double targetBValue = m_Controls->m_targetBValueSpinBox->value();
	- functor->setListOfBValues(bValueList);
	- functor->setTargetBValue(targetBValue);
	- CallMultishellToSingleShellFilter(functor,image,name + "_ADC", node);
	-}
	-
	-void QmitkPreprocessingView::CleanBValueTableWidget()
	-{
	- m_Controls->m_B_ValueMap_TableWidget->clear();
	- m_Controls->m_B_ValueMap_TableWidget->setRowCount(1);
	- QStringList headerList;
	- headerList << "b-Value" << "Number of gradients";
	- m_Controls->m_B_ValueMap_TableWidget->setHorizontalHeaderLabels(headerList);
	- m_Controls->m_B_ValueMap_TableWidget->setItem(0,0,new QTableWidgetItem("-"));
	- m_Controls->m_B_ValueMap_TableWidget->setItem(0,1,new QTableWidgetItem("-"));
	-}
	-
	-void QmitkPreprocessingView::UpdateGradientDetails()
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	- if ( image == nullptr ) { return; }
	-
	- bool isDiffusionImage(false);
	-
	- isDiffusionImage = PropHelper::IsDiffusionWeightedImage(image);
	-
	- if ( ! isDiffusionImage )
	- {
	- m_Controls->m_WorkingGradientsText->clear();
	- m_Controls->m_OriginalGradientsText->clear();
	- return;
	- }
	-
	- auto gradientContainer = PropHelper::GetGradientContainer(image);
	- QString text = "";
	- for (unsigned int j=0; j<gradientContainer->Size(); j++)
	- {
	- auto g = gradientContainer->at(j);
	- g = g.normalize();
	- if (g[0]>=0)
	- text += " ";
	- text += QString::number(g[0]);
	- if (j<gradientContainer->Size()-1)
	- text += " ";
	- else
	- text += "\n";
	- }
	- for (unsigned int j=0; j<gradientContainer->Size(); j++)
	- {
	- auto g = gradientContainer->at(j);
	- g = g.normalize();
	- if (g[1]>=0)
	- text += " ";
	- text += QString::number(g[1]);
	- if (j<gradientContainer->Size()-1)
	- text += " ";
	- else
	- text += "\n";
	- }
	- for (unsigned int j=0; j<gradientContainer->Size(); j++)
	- {
	- auto g = gradientContainer->at(j);
	- g = g.normalize();
	- if (g[2]>=0)
	- text += " ";
	- text += QString::number(g[2]);
	- if (j<gradientContainer->Size()-1)
	- text += " ";
	- else
	- text += "\n";
	- }
	-
	- m_Controls->m_WorkingGradientsText->setPlainText(text);
	-
	- gradientContainer = PropHelper::GetOriginalGradientContainer(image);
	- text = "";
	- for (unsigned int j=0; j<gradientContainer->Size(); j++)
	- {
	- auto g = gradientContainer->at(j);
	- g = g.normalize();
	- if (g[0]>=0)
	- text += " ";
	- text += QString::number(g[0]);
	- if (j<gradientContainer->Size()-1)
	- text += " ";
	- else
	- text += "\n";
	- }
	- for (unsigned int j=0; j<gradientContainer->Size(); j++)
	- {
	- auto g = gradientContainer->at(j);
	- g = g.normalize();
	- if (g[1]>=0)
	- text += " ";
	- text += QString::number(g[1]);
	- if (j<gradientContainer->Size()-1)
	- text += " ";
	- else
	- text += "\n";
	- }
	- for (unsigned int j=0; j<gradientContainer->Size(); j++)
	- {
	- auto g = gradientContainer->at(j);
	- g = g.normalize();
	- if (g[2]>=0)
	- text += " ";
	- text += QString::number(g[2]);
	- if (j<gradientContainer->Size()-1)
	- text += " ";
	- else
	- text += "\n";
	- }
	- m_Controls->m_OriginalGradientsText->setPlainText(text);
	-}
	-
	-void QmitkPreprocessingView::UpdateBValueTableWidget(int)
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	-
	- if (node.IsNull())
	- {
	- CleanBValueTableWidget();
	- return;
	- }
	-
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	- if ( image == nullptr ) { return; }
	-
	- bool isDiffusionImage(false);
	-
	- isDiffusionImage = PropHelper::IsDiffusionWeightedImage(image);
	-
	- if ( ! isDiffusionImage )
	- {
	- CleanBValueTableWidget();
	- }
	- else
	- {
	- typedef mitk::BValueMapProperty::BValueMap BValueMap;
	- typedef mitk::BValueMapProperty::BValueMap::iterator BValueMapIterator;
	-
	- BValueMapIterator it;
	-
	- BValueMap roundedBValueMap = PropHelper::GetBValueMap(image);
	-
	- m_Controls->m_B_ValueMap_TableWidget->clear();
	- m_Controls->m_B_ValueMap_TableWidget->setRowCount(roundedBValueMap.size() );
	- QStringList headerList;
	- headerList << "b-Value" << "Number of gradients";
	- m_Controls->m_B_ValueMap_TableWidget->setHorizontalHeaderLabels(headerList);
	-
	- int i = 0 ;
	- for(it = roundedBValueMap.begin() ;it != roundedBValueMap.end(); it++)
	- {
	- m_Controls->m_B_ValueMap_TableWidget->setItem(i,0,new QTableWidgetItem(QString::number(it->first)));
	- QTableWidgetItem* item = m_Controls->m_B_ValueMap_TableWidget->item(i,0);
	- item->setFlags(item->flags() & ~Qt::ItemIsEditable);
	- m_Controls->m_B_ValueMap_TableWidget->setItem(i,1,new QTableWidgetItem(QString::number(it->second.size())));
	- i++;
	- }
	- }
	-}
	-
	-void QmitkPreprocessingView::OnSelectionChanged(berry::IWorkbenchPart::Pointer , const QList<mitk::DataNode::Pointer>& nodes)
	-{
	- (void) nodes;
	- this->OnImageSelectionChanged();
	-}
	-
	-void QmitkPreprocessingView::OnImageSelectionChanged()
	-{
	- for (int r=0; r<3; r++)
	- for (int c=0; c<3; c++)
	- {
	- {
	- QTableWidgetItem* item = m_Controls->m_MeasurementFrameTable->item( r, c );
	- delete item;
	- item = new QTableWidgetItem();
	- m_Controls->m_MeasurementFrameTable->setItem( r, c, item );
	- }
	- {
	- QTableWidgetItem* item = m_Controls->m_DirectionMatrixTable->item( r, c );
	- delete item;
	- item = new QTableWidgetItem();
	- m_Controls->m_DirectionMatrixTable->setItem( r, c, item );
	- }
	- }
	-
	- bool foundImageVolume = true;
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	- if (node.IsNull()) { return; }
	-
	- bool foundDwiVolume( PropHelper::IsDiffusionWeightedImage( node ) );
	-
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	- if ( image == nullptr ) { return; }
	-
	- bool multiComponentVolume = (image->GetPixelType().GetNumberOfComponents() > 1);
	- bool threeDplusTVolume = (image->GetTimeSteps() > 1);
	-
	- m_Controls->m_ButtonAverageGradients->setEnabled(foundDwiVolume);
	- m_Controls->m_ButtonExtractB0->setEnabled(foundDwiVolume);
	- m_Controls->m_CheckExtractAll->setEnabled(foundDwiVolume);
	- m_Controls->m_MeasurementFrameTable->setEnabled(foundDwiVolume);
	- m_Controls->m_ReduceGradientsButton->setEnabled(foundDwiVolume);
	- m_Controls->m_ShowGradientsButton->setEnabled(foundDwiVolume);
	- m_Controls->m_MirrorGradientToHalfSphereButton->setEnabled(foundDwiVolume);
	- m_Controls->m_MergeDwisButton->setEnabled(foundDwiVolume);
	- m_Controls->m_B_ValueMap_Rounder_SpinBox->setEnabled(foundDwiVolume);
	- m_Controls->m_ProjectSignalButton->setEnabled(foundDwiVolume);
	- m_Controls->m_CreateLengthCorrectedDwi->setEnabled(foundDwiVolume);
	- m_Controls->m_targetBValueSpinBox->setEnabled(foundDwiVolume);
	- m_Controls->m_NormalizeImageValuesButton->setEnabled(foundDwiVolume);
	- m_Controls->m_RemoveGradientButton->setEnabled(foundDwiVolume);
	- m_Controls->m_ExtractGradientButton->setEnabled(foundDwiVolume);
	- m_Controls->m_FlipGradientsButton->setEnabled(foundDwiVolume);
	- m_Controls->m_ClearRotationButton->setEnabled(foundDwiVolume);
	-
	- m_Controls->m_DirectionMatrixTable->setEnabled(foundImageVolume);
	- m_Controls->m_ModifyHeader->setEnabled(foundImageVolume);
	- m_Controls->m_AlignImageBox->setEnabled(foundImageVolume);
	-
	- // we do not support multi-component and 3D+t images for certain operations
	- bool foundSingleImageVolume = foundDwiVolume \|\| (foundImageVolume && !(multiComponentVolume \|\| threeDplusTVolume));
	- m_Controls->m_FlipAxis->setEnabled(foundSingleImageVolume);
	- m_Controls->m_CropImageButton->setEnabled(foundSingleImageVolume);
	- m_Controls->m_ExtractBrainMask->setEnabled(foundSingleImageVolume);
	- m_Controls->m_ResampleImageButton->setEnabled(foundSingleImageVolume);
	-
	- // reset sampling frame to 1 and update all ealted components
	- m_Controls->m_B_ValueMap_Rounder_SpinBox->setValue(1);
	-
	- UpdateBValueTableWidget(m_Controls->m_B_ValueMap_Rounder_SpinBox->value());
	- DoUpdateInterpolationGui(m_Controls->m_ResampleTypeBox->currentIndex());
	- UpdateGradientDetails();
	-
	- m_Controls->m_HeaderSpacingX->setValue(image->GetGeometry()->GetSpacing()[0]);
	- m_Controls->m_HeaderSpacingY->setValue(image->GetGeometry()->GetSpacing()[1]);
	- m_Controls->m_HeaderSpacingZ->setValue(image->GetGeometry()->GetSpacing()[2]);
	- m_Controls->m_HeaderOriginX->setValue(image->GetGeometry()->GetOrigin()[0]);
	- m_Controls->m_HeaderOriginY->setValue(image->GetGeometry()->GetOrigin()[1]);
	- m_Controls->m_HeaderOriginZ->setValue(image->GetGeometry()->GetOrigin()[2]);
	- m_Controls->m_XstartBox->setMaximum(image->GetGeometry()->GetExtent(0)-1);
	- m_Controls->m_YstartBox->setMaximum(image->GetGeometry()->GetExtent(1)-1);
	- m_Controls->m_ZstartBox->setMaximum(image->GetGeometry()->GetExtent(2)-1);
	- m_Controls->m_XendBox->setMaximum(image->GetGeometry()->GetExtent(0)-1);
	- m_Controls->m_YendBox->setMaximum(image->GetGeometry()->GetExtent(1)-1);
	- m_Controls->m_ZendBox->setMaximum(image->GetGeometry()->GetExtent(2)-1);
	-
	- for (int r=0; r<3; r++)
	- for (int c=0; c<3; c++)
	- {
	- // Direction matrix
	- QTableWidgetItem* item = m_Controls->m_DirectionMatrixTable->item( r, c );
	- delete item;
	- item = new QTableWidgetItem();
	- item->setTextAlignment(Qt::AlignCenter \| Qt::AlignVCenter);
	- double val = image->GetGeometry()->GetVtkMatrix()->GetElement(r,c)/image->GetGeometry()->GetSpacing()[c];
	- item->setText(QString::number(val));
	- m_Controls->m_DirectionMatrixTable->setItem( r, c, item );
	- }
	-
	- if (foundDwiVolume)
	- {
	- m_Controls->m_InputData->setTitle("Input Data");
	- vnl_matrix_fixed< double, 3, 3 > mf = PropHelper::GetMeasurementFrame(image);
	-
	- for (int r=0; r<3; r++)
	- for (int c=0; c<3; c++)
	- {
	- // Measurement frame
	- QTableWidgetItem* item = m_Controls->m_MeasurementFrameTable->item( r, c );
	- delete item;
	- item = new QTableWidgetItem();
	- item->setTextAlignment(Qt::AlignCenter \| Qt::AlignVCenter);
	- item->setText(QString::number(mf.get(r,c)));
	- m_Controls->m_MeasurementFrameTable->setItem( r, c, item );
	- }
	-
	- //calculate target bValue for MultishellToSingleShellfilter
	- const mitk::BValueMapProperty::BValueMap & bValMap = PropHelper::GetBValueMap(image);
	-
	- mitk::BValueMapProperty::BValueMap::const_iterator it = bValMap.begin();
	- unsigned int targetBVal = 0;
	- while(it != bValMap.end()) { targetBVal += (it++)->first; }
	-
	- targetBVal /= (float)bValMap.size()-1;
	- m_Controls->m_targetBValueSpinBox->setValue(targetBVal);
	-
	- m_Controls->m_RemoveGradientBox->setMaximum(PropHelper::GetGradientContainer(image)->Size()-1);
	- m_Controls->m_ExtractGradientBox->setMaximum(PropHelper::GetGradientContainer(image)->Size()-1);
	- }
	-
	-}
	-
	-
	-void QmitkPreprocessingView::Activated()
	-{
	-}
	-
	-void QmitkPreprocessingView::Deactivated()
	-{
	- OnImageSelectionChanged();
	-}
	-
	-void QmitkPreprocessingView::Visible()
	-{
	- OnImageSelectionChanged();
	-}
	-
	-void QmitkPreprocessingView::Hidden()
	-{
	-}
	-
	-void QmitkPreprocessingView::DoClearRotationOfGradients()
	-{
	-
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	- if (node.IsNull())
	- return;
	-
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	- if (image == nullptr)
	- return;
	-
	- if(!PropHelper::IsDiffusionWeightedImage(image))
	- return;
	-
	- mitk::Image::Pointer newDwi = image->Clone();
	-
	- PropHelper::SetApplyMatrixToGradients(newDwi, false);
	-
	- mitk::DataNode::Pointer imageNode = mitk::DataNode::New();
	- imageNode->SetData( newDwi );
	-
	- QString name = node->GetName().c_str();
	- imageNode->SetName( (name+"_OriginalGradients").toStdString().c_str() );
	- GetDataStorage()->Add( imageNode, node );
	-
	-}
	-
	-void QmitkPreprocessingView::DoFlipGradientDirections()
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	- if (node.IsNull()) { return; }
	-
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	- if ( image == nullptr ) { return; }
	-
	- mitk::Image::Pointer newDwi = image->Clone();
	-
	- auto gradientContainer = PropHelper::GetGradientContainer(newDwi);
	-
	- for (unsigned int j=0; j<gradientContainer->Size(); j++)
	- {
	- if (m_Controls->m_FlipGradBoxX->isChecked()) { gradientContainer->at(j)[0] *= -1; }
	- if (m_Controls->m_FlipGradBoxY->isChecked()) { gradientContainer->at(j)[1] *= -1; }
	- if (m_Controls->m_FlipGradBoxZ->isChecked()) { gradientContainer->at(j)[2] *= -1; }
	- }
	-
	- PropHelper::CopyProperties(image, newDwi, true);
	- PropHelper::SetGradientContainer(newDwi, gradientContainer);
	- PropHelper::InitializeImage( newDwi );
	-
	- mitk::DataNode::Pointer imageNode = mitk::DataNode::New();
	- imageNode->SetData( newDwi );
	-
	- QString name = node->GetName().c_str();
	- imageNode->SetName( (name+"_GradientFlip").toStdString().c_str() );
	- GetDataStorage()->Add( imageNode, node );
	-}
	-
	-void QmitkPreprocessingView::DoHalfSphereGradientDirections()
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	- if (node.IsNull()) { return; }
	-
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	- if ( image == nullptr ) { return; }
	-
	- mitk::Image::Pointer newDwi = image->Clone();
	- auto gradientContainer = PropHelper::GetGradientContainer(newDwi);
	-
	- for (unsigned int j=0; j<gradientContainer->Size(); j++)
	- {
	- if (gradientContainer->at(j)[0]<0) { gradientContainer->at(j) = -gradientContainer->at(j); }
	- }
	-
	- PropHelper::CopyProperties(image, newDwi, true);
	- PropHelper::SetGradientContainer(newDwi, gradientContainer);
	- PropHelper::InitializeImage( newDwi );
	-
	- mitk::DataNode::Pointer imageNode = mitk::DataNode::New();
	- imageNode->SetData( newDwi );
	-
	- QString name = node->GetName().c_str();
	- imageNode->SetName( (name+"_halfsphere").toStdString().c_str() );
	- GetDataStorage()->Add( imageNode, node );
	-}
	-
	-void QmitkPreprocessingView::DoShowGradientDirections()
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	- if (node.IsNull()) { return; }
	-
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	- if ( image == nullptr ) { return; }
	-
	- bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) );
	- if ( !isDiffusionImage ) { return; }
	-
	- int maxIndex = 0;
	- unsigned int maxSize = image->GetDimension(0);
	- if (maxSize<image->GetDimension(1))
	- {
	- maxSize = image->GetDimension(1);
	- maxIndex = 1;
	- }
	- if (maxSize<image->GetDimension(2))
	- {
	- maxSize = image->GetDimension(2);
	- maxIndex = 2;
	- }
	-
	- mitk::Point3D origin = image->GetGeometry()->GetOrigin();
	- mitk::PointSet::Pointer originSet = mitk::PointSet::New();
	-
	- typedef mitk::BValueMapProperty::BValueMap BValueMap;
	- typedef mitk::BValueMapProperty::BValueMap::iterator BValueMapIterator;
	- BValueMap bValMap = PropHelper::GetBValueMap(image);
	- auto gradientContainer = PropHelper::GetGradientContainer(image);
	-
	- mitk::BaseGeometry::Pointer geometry = image->GetGeometry();
	- int shellCount = 1;
	-
	- for(BValueMapIterator it = bValMap.begin(); it!=bValMap.end(); ++it)
	- {
	- mitk::PointSet::Pointer pointset = mitk::PointSet::New();
	- for (unsigned int j=0; j<it->second.size(); j++)
	- {
	- mitk::Point3D ip;
	- vnl_vector_fixed< double, 3 > v = gradientContainer->at(it->second[j]);
	- if (v.magnitude()>mitk::eps)
	- {
	- ip[0] = v[0]maxSizegeometry->GetSpacing()[maxIndex]/2
	- + origin[0]-0.5*geometry->GetSpacing()[0]
	- + geometry->GetSpacing()[0]*image->GetDimension(0)/2;
	-
	- ip[1] = v[1]maxSizegeometry->GetSpacing()[maxIndex]/2
	- + origin[1]-0.5*geometry->GetSpacing()[1]
	- + geometry->GetSpacing()[1]*image->GetDimension(1)/2;
	-
	- ip[2] = v[2]maxSizegeometry->GetSpacing()[maxIndex]/2
	- + origin[2]-0.5*geometry->GetSpacing()[2]
	- + geometry->GetSpacing()[2]*image->GetDimension(2)/2;
	-
	- pointset->InsertPoint(j, ip);
	- }
	- else if (originSet->IsEmpty())
	- {
	- ip[0] = v[0]maxSizegeometry->GetSpacing()[maxIndex]/2
	- + origin[0]-0.5*geometry->GetSpacing()[0]
	- + geometry->GetSpacing()[0]*image->GetDimension(0)/2;
	-
	- ip[1] = v[1]maxSizegeometry->GetSpacing()[maxIndex]/2
	- + origin[1]-0.5*geometry->GetSpacing()[1]
	- + geometry->GetSpacing()[1]*image->GetDimension(1)/2;
	-
	- ip[2] = v[2]maxSizegeometry->GetSpacing()[maxIndex]/2
	- + origin[2]-0.5*geometry->GetSpacing()[2]
	- + geometry->GetSpacing()[2]*image->GetDimension(2)/2;
	-
	- originSet->InsertPoint(j, ip);
	- }
	- }
	- if ( it->first < mitk::eps ) { continue; }
	-
	- // add shell to datastorage
	- mitk::DataNode::Pointer newNode = mitk::DataNode::New();
	- newNode->SetData(pointset);
	-
	- QString name = node->GetName().c_str();
	- name += "_Shell_";
	- name += QString::number( it->first );
	- newNode->SetName( name.toStdString().c_str() );
	- newNode->SetProperty( "pointsize", mitk::FloatProperty::New((float)maxSize / 50) );
	-
	- int b0 = shellCount % 2;
	- int b1 = 0;
	- int b2 = 0;
	- if (shellCount>4) { b2 = 1; }
	-
	- if (shellCount%4 >= 2) { b1 = 1; }
	-
	- newNode->SetProperty("color", mitk::ColorProperty::New( b2, b1, b0 ));
	- GetDataStorage()->Add( newNode, node );
	- shellCount++;
	- }
	-
	- // add origin to datastorage
	- mitk::DataNode::Pointer newNode = mitk::DataNode::New();
	- newNode->SetData(originSet);
	-
	- QString name = node->GetName().c_str();
	- name += "_Origin";
	- newNode->SetName(name.toStdString().c_str());
	- newNode->SetProperty("pointsize", mitk::FloatProperty::New((float)maxSize/50));
	- newNode->SetProperty("color", mitk::ColorProperty::New(1,1,1));
	- GetDataStorage()->Add(newNode, node);
	-}
	-
	-void QmitkPreprocessingView::DoReduceGradientDirections()
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	- if (node.IsNull()) { return; }
	-
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	- if ( image == nullptr ) { return; }
	-
	- bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) );
	- if ( !isDiffusionImage ) { return; }
	-
	- typedef itk::ElectrostaticRepulsionDiffusionGradientReductionFilter<DiffusionPixelType, DiffusionPixelType> FilterType;
	- typedef mitk::BValueMapProperty::BValueMap BValueMap;
	-
	- // GetShellSelection from GUI
	- BValueMap shellSlectionMap;
	- BValueMap originalShellMap = PropHelper::GetBValueMap(image);
	-
	- std::vector<unsigned int> newNumGradientDirections;
	- int shellCounter = 0;
	-
	- QString name = node->GetName().c_str();
	- for (int i=0; i<m_Controls->m_B_ValueMap_TableWidget->rowCount(); i++)
	- {
	- double BValue = m_Controls->m_B_ValueMap_TableWidget->item(i,0)->text().toDouble();
	- shellSlectionMap[BValue] = originalShellMap[BValue];
	- unsigned int num = m_Controls->m_B_ValueMap_TableWidget->item(i,1)->text().toUInt();
	- newNumGradientDirections.push_back(num);
	- name += "_";
	- name += QString::number(num);
	- shellCounter++;
	- }
	-
	- if (newNumGradientDirections.empty()) { return; }
	-
	- auto gradientContainer = PropHelper::GetGradientContainer(image);
	-
	- ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New();
	- mitk::CastToItkImage(image, itkVectorImagePointer);
	-
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetInput( itkVectorImagePointer );
	- filter->SetOriginalGradientDirections(gradientContainer);
	- filter->SetNumGradientDirections(newNumGradientDirections);
	- filter->SetOriginalBValueMap(originalShellMap);
	- filter->SetShellSelectionBValueMap(shellSlectionMap);
	- filter->SetUseFirstN(m_Controls->m_KeepFirstNBox->isChecked());
	- filter->Update();
	-
	- mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( filter->GetOutput() );
	- PropHelper::CopyProperties(image, newImage, true);
	- PropHelper::SetGradientContainer(newImage, filter->GetGradientDirections());
	- PropHelper::InitializeImage(newImage);
	-
	- mitk::DataNode::Pointer imageNode = mitk::DataNode::New();
	- imageNode->SetData( newImage );
	-
	- imageNode->SetName(name.toStdString().c_str());
	- GetDataStorage()->Add(imageNode, node);
	-
	- // update the b-value widget to remove the modified number of gradients used for extraction
	- this->CleanBValueTableWidget();
	- this->UpdateBValueTableWidget(0);
	- this->UpdateGradientDetails();
	-}
	-
	-void QmitkPreprocessingView::MergeDwis()
	-{
	- typedef GradProp::GradientDirectionsContainerType GradientContainerType;
	-
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	- if (node.IsNull()) { return; }
	-
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	- if ( image == nullptr ) { return; }
	-
	- bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) );
	- if ( !isDiffusionImage ) { return; }
	-
	- mitk::DataNode::Pointer node2 = m_Controls->m_MergeDwiBox->GetSelectedNode();
	- if (node2.IsNull()) { return; }
	-
	- mitk::Image::Pointer image2 = dynamic_cast<mitk::Image*>(node2->GetData());
	- if ( image2 == nullptr ) { return; }
	-
	- typedef itk::VectorImage<DiffusionPixelType,3> DwiImageType;
	- typedef std::vector< DwiImageType::Pointer > DwiImageContainerType;
	-
	- typedef std::vector< GradientContainerType::Pointer > GradientListContainerType;
	-
	- DwiImageContainerType imageContainer;
	- GradientListContainerType gradientListContainer;
	- std::vector< double > bValueContainer;
	-
	- QString name = "";
	- {
	- ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New();
	- mitk::CastToItkImage(image, itkVectorImagePointer);
	-
	- imageContainer.push_back( itkVectorImagePointer );
	- gradientListContainer.push_back(PropHelper::GetGradientContainer(image));
	- bValueContainer.push_back(PropHelper::GetReferenceBValue(image));
	-
	- name += node->GetName().c_str();
	- }
	-
	- {
	- ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New();
	- mitk::CastToItkImage(image2, itkVectorImagePointer);
	-
	- imageContainer.push_back( itkVectorImagePointer );
	- gradientListContainer.push_back(PropHelper::GetGradientContainer(image2));
	- bValueContainer.push_back(PropHelper::GetReferenceBValue(image2));
	-
	- name += "+";
	- name += node2->GetName().c_str();
	- }
	-
	- typedef itk::MergeDiffusionImagesFilter<short> FilterType;
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetImageVolumes(imageContainer);
	- filter->SetGradientLists(gradientListContainer);
	- filter->SetBValues(bValueContainer);
	- filter->Update();
	-
	- vnl_matrix_fixed< double, 3, 3 > mf; mf.set_identity();
	- mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( filter->GetOutput() );
	-
	- PropHelper::SetGradientContainer(newImage, filter->GetOutputGradients());
	- PropHelper::SetMeasurementFrame(newImage, mf);
	- PropHelper::SetReferenceBValue(newImage, filter->GetB_Value());
	- PropHelper::InitializeImage( newImage );
	-
	- mitk::DataNode::Pointer imageNode = mitk::DataNode::New();
	- imageNode->SetData( newImage );
	- imageNode->SetName(name.toStdString().c_str());
	- GetDataStorage()->Add(imageNode);
	-}
	-
	-void QmitkPreprocessingView::ExtractB0()
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	- if (node.IsNull()) { return; }
	-
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	- if ( image == nullptr ) { return; }
	-
	- bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) );
	- if ( !isDiffusionImage ) { return; }
	-
	- // call the extraction withou averaging if the check-box is checked
	- if( this->m_Controls->m_CheckExtractAll->isChecked() )
	- {
	- DoExtractBOWithoutAveraging();
	- return;
	- }
	-
	- ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New();
	- mitk::CastToItkImage(image, itkVectorImagePointer);
	-
	- // Extract image using found index
	- typedef itk::B0ImageExtractionImageFilter<short, short> FilterType;
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetInput( itkVectorImagePointer );
	- filter->SetDirections(PropHelper::GetGradientContainer(image));
	-
	- filter->Update();
	-
	- mitk::Image::Pointer mitkImage = mitk::Image::New();
	- mitkImage->InitializeByItk( filter->GetOutput() );
	- mitkImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
	- mitk::DataNode::Pointer newNode=mitk::DataNode::New();
	- newNode->SetData( mitkImage );
	- newNode->SetProperty( "name", mitk::StringProperty::New(node->GetName() + "_B0"));
	-
	- GetDataStorage()->Add(newNode, node);
	-}
	-
	-void QmitkPreprocessingView::DoExtractBOWithoutAveraging()
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	- if (node.IsNull()) { return; }
	-
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	- if ( image == nullptr ) { return; }
	-
	- bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) );
	- if ( !isDiffusionImage ) { return; }
	-
	- // typedefs
	- typedef itk::B0ImageExtractionToSeparateImageFilter< short, short> FilterType;
	-
	- ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New();
	- mitk::CastToItkImage(image, itkVectorImagePointer);
	-
	- // Extract image using found index
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetInput( itkVectorImagePointer );
	- filter->SetDirections(PropHelper::GetGradientContainer(image));
	-
	- filter->Update();
	-
	- mitk::Image::Pointer mitkImage = mitk::Image::New();
	- mitkImage->InitializeByItk( filter->GetOutput() );
	- mitkImage->SetImportChannel( filter->GetOutput()->GetBufferPointer() );
	- mitk::DataNode::Pointer newNode=mitk::DataNode::New();
	- newNode->SetData( mitkImage );
	- newNode->SetProperty( "name", mitk::StringProperty::New(node->GetName() + "_B0_ALL"));
	-
	- GetDataStorage()->Add(newNode, node);
	-
	- /*A reinitialization is needed to access the time channels via the ImageNavigationController
	- The Global-Geometry can not recognize the time channel without a re-init.
	- (for a new selection in datamanger a automatically updated of the Global-Geometry should be done
	- - if it contains the time channel)*/
	- mitk::RenderingManager::GetInstance()->InitializeViews( newNode->GetData()->GetTimeGeometry(),
	- mitk::RenderingManager::REQUEST_UPDATE_ALL,
	- true);
	-}
	-
	-void QmitkPreprocessingView::AverageGradients()
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode();
	- if (node.IsNull()) { return; }
	-
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	- if ( image == nullptr ) { return; }
	-
	- bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) );
	- if ( !isDiffusionImage )
	- return;
	-
	- mitk::Image::Pointer newDwi = image->Clone();
	- PropHelper::AverageRedundantGradients(newDwi, m_Controls->m_Blur->value());
	- PropHelper::InitializeImage(newDwi);
	-
	- mitk::DataNode::Pointer imageNode = mitk::DataNode::New();
	- imageNode->SetData( newDwi );
	- QString name = node->GetName().c_str();
	- imageNode->SetName((name+"_averaged").toStdString().c_str());
	- GetDataStorage()->Add(imageNode, node);
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingView.h
	deleted file mode 100644
	index eb6690bf5b..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingView.h
	+++ /dev/null
	@@ -1,159 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _QMITKPREPROCESSINGVIEW_H_INCLUDED
	-#define _QMITKPREPROCESSINGVIEW_H_INCLUDED
	-
	-#include <QmitkAbstractView.h>
	-#include <mitkILifecycleAwarePart.h>
	-
	-#include "ui_QmitkPreprocessingViewControls.h"
	-
	-// st includes
	-#include <string>
	-
	-// itk includes
	-#include <itkImage.h>
	-#include <itkVectorImage.h>
	-
	-// mitk includes
	-#include <mitkImage.h>
	-#include "itkDWIVoxelFunctor.h"
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <vtkMatrix4x4.h>
	-#include <vtkSmartPointer.h>
	-#include <mitkPeakImage.h>
	-#include <mitkImageToItk.h>
	-
	-typedef short DiffusionPixelType;
	-
	-struct PrpSelListener;
	-
	-/*!
	- * \ingroup org_mitk_gui_qt_preprocessing_internal
	- *
	- * \brief Viewing and modifying diffusion weighted images (gradient reduction, resampling, b-value projection, ...)
	- *
	- */
	-class QmitkPreprocessingView : public QmitkAbstractView, public mitk::ILifecycleAwarePart
	-{
	-
	- friend struct PrpSelListener;
	-
	- // this is needed for all Qt objects that should have a MOC object (everything that derives from QObject)
	- Q_OBJECT
	-
	- public:
	-
	- static const std::string VIEW_ID;
	-
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionType GradientDirectionType;
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionsContainerType GradientDirectionContainerType;
	- typedef itk::VectorImage< short, 3 > ItkDwiType;
	- typedef itk::Image< unsigned char, 3 > UcharImageType;
	- typedef itk::Image< double, 3 > ItkDoubleImageType;
	- typedef mitk::DiffusionPropertyHelper PropHelper;
	- typedef mitk::GradientDirectionsProperty GradProp;
	-
	- QmitkPreprocessingView();
	- virtual ~QmitkPreprocessingView();
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	-
	- /// \brief Creation of the connections of main and control widget
	- virtual void CreateConnections();
	-
	- virtual void Activated() override;
	-
	- virtual void Deactivated() override;
	-
	- virtual void Visible() override;
	-
	- virtual void Hidden() override;
	-
	- ///
	- /// Sets the focus to an internal widget.
	- ///
	- virtual void SetFocus() override;
	-
	- static const int nrconvkernels;
	-
	-protected slots:
	-
	- void AverageGradients();
	- void ExtractB0();
	- void MergeDwis();
	- void DoApplyHeader();
	- void DoReduceGradientDirections();
	- void DoShowGradientDirections();
	- void DoHalfSphereGradientDirections();
	- void UpdateDwiBValueMapRounder(int i);
	- void DoLengthCorrection();
	- void DoDwiNormalization();
	- void DoProjectSignal();
	- void DoExtractBrainMask();
	- void DoResampleImage();
	- void DoCropImage();
	- void DoUpdateInterpolationGui(int i);
	- void DoRemoveGradient();
	- void DoExtractGradient();
	- void DoFlipAxis();
	- void OnImageSelectionChanged();
	- void DoFlipGradientDirections();
	- void DoClearRotationOfGradients();
	- void DoAlignImages();
	-
	-protected:
	-
	- void DoADCFit();
	- void DoAKCFit();
	- void DoBiExpFit();
	- void DoADCAverage();
	-
	- template < typename TPixel, unsigned int VImageDimension >
	- void TemplatedFlipAxis( itk::Image<TPixel, VImageDimension>* itkImage);
	-
	- template < typename TPixel, unsigned int VImageDimension >
	- void TemplatedCropImage( itk::Image<TPixel, VImageDimension>* itkImage);
	-
	- template < typename TPixel, unsigned int VImageDimension >
	- void TemplatedResampleImage( itk::Image<TPixel, VImageDimension>* itkImage);
	-
	- /** Called by ExtractB0 if check-box activated, extracts all b0 images without averaging */
	- void DoExtractBOWithoutAveraging();
	-
	- void UpdateBValueTableWidget(int);
	- void UpdateGradientDetails();
	-
	- /// \brief called by QmitkAbstractView when DataManager's selection has changed
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- Ui::QmitkPreprocessingViewControls* m_Controls;
	-
	- void SetDefaultNodeProperties(mitk::DataNode::Pointer node, std::string name);
	- void CallMultishellToSingleShellFilter( itk::DWIVoxelFunctor * functor,
	- mitk::Image::Pointer ImPtr, QString imageName,
	- mitk::DataNode* parent );
	-
	- void CleanBValueTableWidget();
	-
	-};
	-
	-
	-
	-
	-#endif // _QMITKPREPROCESSINGVIEW_H_INCLUDED
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingViewControls.ui
	deleted file mode 100644
	index dbcdfbf628..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingViewControls.ui
	+++ /dev/null
	@@ -1,1807 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<ui version="4.0">
	- <class>QmitkPreprocessingViewControls</class>
	- <widget class="QWidget" name="QmitkPreprocessingViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>503</width>
	- <height>1001</height>
	- </rect>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="acceptDrops">
	- <bool>false</bool>
	- </property>
	- <property name="windowTitle">
	- <string>QmitkPreprocessingViewControls</string>
	- </property>
	- <property name="autoFillBackground">
	- <bool>true</bool>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_18">
	- <property name="verticalSpacing">
	- <number>25</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QGroupBox" name="m_InputData">
	- <property name="title">
	- <string>Please Select Input Data</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_2">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_5">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Image:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_SelctedImageComboBox">
	- <property name="sizeAdjustPolicy">
	- <enum>QComboBox::AdjustToMinimumContentsLength</enum>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QTabWidget" name="tabWidget">
	- <property name="currentIndex">
	- <number>0</number>
	- </property>
	- <widget class="QWidget" name="tab_4">
	- <attribute name="title">
	- <string>Gradients</string>
	- </attribute>
	- <layout class="QGridLayout" name="gridLayout_6">
	- <property name="verticalSpacing">
	- <number>25</number>
	- </property>
	- <item row="5" column="0">
	- <widget class="QGroupBox" name="groupBox_6">
	- <property name="title">
	- <string>Remove or extract gradient volumes</string>
	- </property>
	- <layout class="QFormLayout" name="formLayout_3">
	- <property name="horizontalSpacing">
	- <number>6</number>
	- </property>
	- <property name="verticalSpacing">
	- <number>6</number>
	- </property>
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QCommandLinkButton" name="m_RemoveGradientButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="text">
	- <string>Remove gradient volume</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_RemoveGradientBox"/>
	- </item>
	- <item row="1" column="0">
	- <widget class="QCommandLinkButton" name="m_ExtractGradientButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="text">
	- <string>Extract gradient volume</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QSpinBox" name="m_ExtractGradientBox"/>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="3" column="0" rowspan="2">
	- <widget class="QFrame" name="frame_2">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_10">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="horizontalSpacing">
	- <number>6</number>
	- </property>
	- <item row="3" column="1">
	- <layout class="QFormLayout" name="formLayout">
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_2">
	- <property name="toolTip">
	- <string><html><head/><body><p>Define the sampling frame the b-Values are rounded with.</p></body></html></string>
	- </property>
	- <property name="text">
	- <string>Sampling frame:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_B_ValueMap_Rounder_SpinBox">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string><html><head/><body><p>Round b-values to nearest multiple of this value (click &quot;Round b-value&quot; to create new image with these values).</p></body></html></string>
	- </property>
	- <property name="correctionMode">
	- <enum>QAbstractSpinBox::CorrectToNearestValue</enum>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>10000</number>
	- </property>
	- <property name="singleStep">
	- <number>10</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </item>
	- <item row="6" column="0">
	- <widget class="QCommandLinkButton" name="m_MirrorGradientToHalfSphereButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string>Sometimes the gradient directions are not located on one half sphere.</string>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string notr="true"/>
	- </property>
	- <property name="text">
	- <string>Mirror gradients to half sphere</string>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <widget class="QCommandLinkButton" name="m_ShowGradientsButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string>Generate pointset displaying the gradient vectors (applied measurement frame).</string>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string notr="true"/>
	- </property>
	- <property name="text">
	- <string>Show gradients</string>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QCommandLinkButton" name="m_FlipGradientsButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string>Generate pointset displaying the gradient vectors (applied measurement frame).</string>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string notr="true"/>
	- </property>
	- <property name="text">
	- <string>Flip gradients</string>
	- </property>
	- </widget>
	- </item>
	- <item row="8" column="0">
	- <widget class="QCommandLinkButton" name="m_ReduceGradientsButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string>Retain only the specified number of gradient directions and according image volumes. The retained directions are spread equally over the half sphere using an iterative energy repulsion strategy.</string>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string notr="true"/>
	- </property>
	- <property name="text">
	- <string>Reduce number of gradients</string>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="1">
	- <widget class="QFrame" name="frame_8">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Plain</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_21">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QCheckBox" name="m_FlipGradBoxX">
	- <property name="text">
	- <string>x</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QCheckBox" name="m_FlipGradBoxY">
	- <property name="text">
	- <string>y</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="2">
	- <widget class="QCheckBox" name="m_FlipGradBoxZ">
	- <property name="text">
	- <string>z</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QCommandLinkButton" name="m_CreateLengthCorrectedDwi">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="text">
	- <string>Round b-values</string>
	- </property>
	- </widget>
	- </item>
	- <item row="9" column="0">
	- <widget class="QCommandLinkButton" name="m_ClearRotationButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string>By default, the image matrix is applied to the image gradients. This button removes this additional rotation.</string>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string notr="true"/>
	- </property>
	- <property name="text">
	- <string>Clear rotation of gradients</string>
	- </property>
	- </widget>
	- </item>
	- <item row="8" column="1">
	- <widget class="QCheckBox" name="m_KeepFirstNBox">
	- <property name="toolTip">
	- <string>Don't optimize gradients to retain, simply keep first n gradients per b-value.</string>
	- </property>
	- <property name="text">
	- <string>first n</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="6" column="0">
	- <widget class="QTabWidget" name="tabWidget_2">
	- <property name="currentIndex">
	- <number>0</number>
	- </property>
	- <widget class="QWidget" name="tab">
	- <attribute name="title">
	- <string>Original Gradients</string>
	- </attribute>
	- <layout class="QGridLayout" name="gridLayout_24">
	- <item row="0" column="0">
	- <widget class="QPlainTextEdit" name="m_OriginalGradientsText">
	- <property name="verticalScrollBarPolicy">
	- <enum>Qt::ScrollBarAsNeeded</enum>
	- </property>
	- <property name="horizontalScrollBarPolicy">
	- <enum>Qt::ScrollBarAsNeeded</enum>
	- </property>
	- <property name="sizeAdjustPolicy">
	- <enum>QAbstractScrollArea::AdjustIgnored</enum>
	- </property>
	- <property name="lineWrapMode">
	- <enum>QPlainTextEdit::NoWrap</enum>
	- </property>
	- <property name="readOnly">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <widget class="QWidget" name="tab_6">
	- <attribute name="title">
	- <string>Working Gradients</string>
	- </attribute>
	- <layout class="QGridLayout" name="gridLayout_23">
	- <item row="0" column="0">
	- <widget class="QPlainTextEdit" name="m_WorkingGradientsText">
	- <property name="verticalScrollBarPolicy">
	- <enum>Qt::ScrollBarAsNeeded</enum>
	- </property>
	- <property name="horizontalScrollBarPolicy">
	- <enum>Qt::ScrollBarAsNeeded</enum>
	- </property>
	- <property name="sizeAdjustPolicy">
	- <enum>QAbstractScrollArea::AdjustIgnored</enum>
	- </property>
	- <property name="lineWrapMode">
	- <enum>QPlainTextEdit::NoWrap</enum>
	- </property>
	- <property name="readOnly">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </widget>
	- </item>
	- <item row="7" column="0">
	- <spacer name="verticalSpacer_5">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="0" column="0">
	- <widget class="QTableWidget" name="m_B_ValueMap_TableWidget">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Minimum" vsizetype="Minimum">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="verticalScrollBarPolicy">
	- <enum>Qt::ScrollBarAsNeeded</enum>
	- </property>
	- <property name="horizontalScrollBarPolicy">
	- <enum>Qt::ScrollBarAlwaysOff</enum>
	- </property>
	- <attribute name="horizontalHeaderCascadingSectionResizes">
	- <bool>true</bool>
	- </attribute>
	- <attribute name="horizontalHeaderDefaultSectionSize">
	- <number>100</number>
	- </attribute>
	- <attribute name="horizontalHeaderStretchLastSection">
	- <bool>true</bool>
	- </attribute>
	- <attribute name="verticalHeaderVisible">
	- <bool>false</bool>
	- </attribute>
	- <attribute name="verticalHeaderCascadingSectionResizes">
	- <bool>true</bool>
	- </attribute>
	- <column>
	- <property name="text">
	- <string>b-Value</string>
	- </property>
	- </column>
	- <column>
	- <property name="text">
	- <string>Number of gradients</string>
	- </property>
	- </column>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <widget class="QWidget" name="tab_5">
	- <attribute name="title">
	- <string>Image Values</string>
	- </attribute>
	- <layout class="QGridLayout" name="gridLayout_8">
	- <property name="verticalSpacing">
	- <number>25</number>
	- </property>
	- <item row="3" column="0">
	- <spacer name="verticalSpacer">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="0" column="0">
	- <widget class="QFrame" name="frame_3">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_11">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="horizontalSpacing">
	- <number>6</number>
	- </property>
	- <item row="1" column="1">
	- <widget class="QFrame" name="frame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QFormLayout" name="formLayout_2">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="1">
	- <widget class="QDoubleSpinBox" name="m_Blur">
	- <property name="toolTip">
	- <string comment="Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured." extracomment="Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured.">Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured.</string>
	- </property>
	- <property name="statusTip">
	- <string comment="Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured." extracomment="Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured.">Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured.</string>
	- </property>
	- <property name="whatsThis">
	- <string comment="Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured." extracomment="Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured.">Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured.</string>
	- </property>
	- <property name="decimals">
	- <number>6</number>
	- </property>
	- <property name="maximum">
	- <double>2.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.000100000000000</double>
	- </property>
	- <property name="value">
	- <double>0.001000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label">
	- <property name="toolTip">
	- <string comment="Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured." extracomment="Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured.">Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured.</string>
	- </property>
	- <property name="statusTip">
	- <string comment="Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured." extracomment="Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured.">Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured.</string>
	- </property>
	- <property name="whatsThis">
	- <string comment="Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured." extracomment="Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured.">Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured.</string>
	- </property>
	- <property name="text">
	- <string>Merge radius</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="6" column="0">
	- <widget class="QCommandLinkButton" name="m_MergeDwisButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string>Merges selected DWIs of same dimension. If several b-values are present, the resulting image will contain multiple b-shells.</string>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string notr="true"/>
	- </property>
	- <property name="text">
	- <string>Merge selected DWIs</string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QCommandLinkButton" name="m_NormalizeImageValuesButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string>Normalizes the diffusion-weighted image values across all weighted volumes to the given mean and standard deviation.</string>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string notr="true"/>
	- </property>
	- <property name="text">
	- <string>Normalize image values</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QFrame" name="frame_4">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_4">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QSpinBox" name="m_targetBValueSpinBox">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string>Target b-value</string>
	- </property>
	- <property name="maximum">
	- <number>100000</number>
	- </property>
	- <property name="singleStep">
	- <number>500</number>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QComboBox" name="m_ProjectionMethodBox">
	- <property name="toolTip">
	- <string>Select projection method.</string>
	- </property>
	- <property name="sizeAdjustPolicy">
	- <enum>QComboBox::AdjustToMinimumContentsLength</enum>
	- </property>
	- <item>
	- <property name="text">
	- <string>ADC Average</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>AKC</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Bi-Exponential</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QCommandLinkButton" name="m_ButtonAverageGradients">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string>Multiple acquistions of one gradient direction can be averaged. Due to rounding errors, similar gradients often differ in the last decimal positions. The Merge radius allows to average them by taking all directions within a certain radius into account.</string>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string notr="true"/>
	- </property>
	- <property name="text">
	- <string>Average repetitions</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QCommandLinkButton" name="m_ProjectSignalButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string>Project image values onto one b-shell.</string>
	- </property>
	- <property name="text">
	- <string>Project onto shell</string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="1">
	- <widget class="QFrame" name="frame_6">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_19">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="verticalSpacing">
	- <number>0</number>
	- </property>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_NewStdev">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="toolTip">
	- <string>New stdev</string>
	- </property>
	- <property name="maximum">
	- <number>100000</number>
	- </property>
	- <property name="singleStep">
	- <number>100</number>
	- </property>
	- <property name="value">
	- <number>500</number>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="2">
	- <widget class="QmitkDataStorageComboBoxWithSelectNone" name="m_NormalizationMaskBox">
	- <property name="toolTip">
	- <string>Select binary mask image. The mask is used to calculate the old mean and standard deviation.</string>
	- </property>
	- <property name="sizeAdjustPolicy">
	- <enum>QComboBox::AdjustToMinimumContentsLength</enum>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QSpinBox" name="m_NewMean">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="toolTip">
	- <string>New mean value</string>
	- </property>
	- <property name="maximum">
	- <number>100000</number>
	- </property>
	- <property name="singleStep">
	- <number>100</number>
	- </property>
	- <property name="value">
	- <number>1000</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QCommandLinkButton" name="m_FlipAxis">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string>Merges selected DWIs of same dimension. If several b-values are present, the resulting image will contain multiple b-shells.</string>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string notr="true"/>
	- </property>
	- <property name="text">
	- <string>Flip axis</string>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="1">
	- <widget class="QFrame" name="frame_7">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_20">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="2">
	- <widget class="QCheckBox" name="m_FlipY">
	- <property name="text">
	- <string>Y</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="4">
	- <spacer name="horizontalSpacer_4">
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>40</width>
	- <height>20</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="0" column="1">
	- <widget class="QCheckBox" name="m_FlipX">
	- <property name="text">
	- <string>X</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="3">
	- <widget class="QCheckBox" name="m_FlipZ">
	- <property name="text">
	- <string>Z</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_8">
	- <property name="text">
	- <string>Axis:</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="6" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_MergeDwiBox">
	- <property name="sizeAdjustPolicy">
	- <enum>QComboBox::AdjustToMinimumContentsLength</enum>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QGroupBox" name="groupBox_2">
	- <property name="title">
	- <string>Resample image</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_12">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <property name="spacing">
	- <number>6</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QFrame" name="m_ResampleDoubleFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_5">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>0</number>
	- </property>
	- <item row="0" column="1">
	- <widget class="QDoubleSpinBox" name="m_ResampleDoubleY">
	- <property name="minimum">
	- <double>0.010000000000000</double>
	- </property>
	- <property name="value">
	- <double>2.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QDoubleSpinBox" name="m_ResampleDoubleX">
	- <property name="minimum">
	- <double>0.010000000000000</double>
	- </property>
	- <property name="value">
	- <double>2.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="2">
	- <widget class="QDoubleSpinBox" name="m_ResampleDoubleZ">
	- <property name="minimum">
	- <double>0.010000000000000</double>
	- </property>
	- <property name="value">
	- <double>2.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QComboBox" name="m_ResampleTypeBox">
	- <item>
	- <property name="text">
	- <string>Sampling factor</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>New image spacing</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>New image size</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QFrame" name="frame_5">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_14">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_3">
	- <property name="text">
	- <string>Interpolator:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QComboBox" name="m_InterpolatorBox">
	- <item>
	- <property name="text">
	- <string>Nearest neighbour</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Linear</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>B-spline</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Windowed sinc</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QCommandLinkButton" name="m_ResampleImageButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string notr="true"/>
	- </property>
	- <property name="text">
	- <string>Resample image</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QFrame" name="m_ResampleIntFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_13">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QSpinBox" name="m_ResampleIntX">
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>10000</number>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_ResampleIntY">
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>10000</number>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="2">
	- <widget class="QSpinBox" name="m_ResampleIntZ">
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>10000</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QGroupBox" name="groupBox_8">
	- <property name="title">
	- <string>Crop Image</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_22">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <property name="spacing">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_9">
	- <property name="text">
	- <string>x:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_XstartBox"/>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_10">
	- <property name="text">
	- <string>y:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label_11">
	- <property name="text">
	- <string>z:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QCommandLinkButton" name="m_CropImageButton">
	- <property name="text">
	- <string>Crop Image</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="2">
	- <widget class="QSpinBox" name="m_XendBox"/>
	- </item>
	- <item row="1" column="1">
	- <widget class="QSpinBox" name="m_YstartBox"/>
	- </item>
	- <item row="1" column="2">
	- <widget class="QSpinBox" name="m_YendBox"/>
	- </item>
	- <item row="2" column="1">
	- <widget class="QSpinBox" name="m_ZstartBox"/>
	- </item>
	- <item row="2" column="2">
	- <widget class="QSpinBox" name="m_ZendBox"/>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <widget class="QWidget" name="tab_3">
	- <attribute name="title">
	- <string>Header</string>
	- </attribute>
	- <layout class="QGridLayout" name="gridLayout_7">
	- <property name="verticalSpacing">
	- <number>25</number>
	- </property>
	- <item row="2" column="0">
	- <widget class="QGroupBox" name="groupBox_3">
	- <property name="title">
	- <string>Voxel size</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_16">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="2">
	- <widget class="QDoubleSpinBox" name="m_HeaderSpacingZ">
	- <property name="decimals">
	- <number>4</number>
	- </property>
	- <property name="minimum">
	- <double>0.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>99.989999999999995</double>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QDoubleSpinBox" name="m_HeaderSpacingX">
	- <property name="decimals">
	- <number>4</number>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QDoubleSpinBox" name="m_HeaderSpacingY">
	- <property name="decimals">
	- <number>4</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QCommandLinkButton" name="m_ModifyHeader">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string notr="true"/>
	- </property>
	- <property name="text">
	- <string>Apply new header information</string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QGroupBox" name="groupBox">
	- <property name="title">
	- <string>Direction matrix</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_3">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QTableWidget" name="m_DirectionMatrixTable">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Minimum" vsizetype="Minimum">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="cursor" stdset="0">
	- <cursorShape>IBeamCursor</cursorShape>
	- </property>
	- <property name="autoFillBackground">
	- <bool>true</bool>
	- </property>
	- <property name="verticalScrollBarPolicy">
	- <enum>Qt::ScrollBarAlwaysOff</enum>
	- </property>
	- <property name="horizontalScrollBarPolicy">
	- <enum>Qt::ScrollBarAlwaysOff</enum>
	- </property>
	- <property name="showGrid">
	- <bool>true</bool>
	- </property>
	- <property name="cornerButtonEnabled">
	- <bool>false</bool>
	- </property>
	- <attribute name="horizontalHeaderVisible">
	- <bool>false</bool>
	- </attribute>
	- <attribute name="horizontalHeaderCascadingSectionResizes">
	- <bool>true</bool>
	- </attribute>
	- <attribute name="horizontalHeaderHighlightSections">
	- <bool>true</bool>
	- </attribute>
	- <attribute name="horizontalHeaderMinimumSectionSize">
	- <number>0</number>
	- </attribute>
	- <attribute name="verticalHeaderVisible">
	- <bool>false</bool>
	- </attribute>
	- <attribute name="verticalHeaderCascadingSectionResizes">
	- <bool>true</bool>
	- </attribute>
	- <attribute name="verticalHeaderHighlightSections">
	- <bool>true</bool>
	- </attribute>
	- <row>
	- <property name="text">
	- <string>New Row</string>
	- </property>
	- </row>
	- <row>
	- <property name="text">
	- <string>New Row</string>
	- </property>
	- </row>
	- <row>
	- <property name="text">
	- <string>New Row</string>
	- </property>
	- </row>
	- <column>
	- <property name="text">
	- <string>New Column</string>
	- </property>
	- </column>
	- <column>
	- <property name="text">
	- <string>New Column</string>
	- </property>
	- </column>
	- <column>
	- <property name="text">
	- <string>New Column</string>
	- </property>
	- </column>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <spacer name="horizontalSpacer_2">
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>40</width>
	- <height>20</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QGroupBox" name="groupBox_4">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="title">
	- <string>Measurment frame</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QTableWidget" name="m_MeasurementFrameTable">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Minimum" vsizetype="Minimum">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="cursor" stdset="0">
	- <cursorShape>IBeamCursor</cursorShape>
	- </property>
	- <property name="autoFillBackground">
	- <bool>true</bool>
	- </property>
	- <property name="verticalScrollBarPolicy">
	- <enum>Qt::ScrollBarAlwaysOff</enum>
	- </property>
	- <property name="horizontalScrollBarPolicy">
	- <enum>Qt::ScrollBarAlwaysOff</enum>
	- </property>
	- <property name="showGrid">
	- <bool>true</bool>
	- </property>
	- <property name="cornerButtonEnabled">
	- <bool>false</bool>
	- </property>
	- <attribute name="horizontalHeaderVisible">
	- <bool>false</bool>
	- </attribute>
	- <attribute name="horizontalHeaderCascadingSectionResizes">
	- <bool>true</bool>
	- </attribute>
	- <attribute name="horizontalHeaderHighlightSections">
	- <bool>true</bool>
	- </attribute>
	- <attribute name="horizontalHeaderMinimumSectionSize">
	- <number>0</number>
	- </attribute>
	- <attribute name="verticalHeaderVisible">
	- <bool>false</bool>
	- </attribute>
	- <attribute name="verticalHeaderCascadingSectionResizes">
	- <bool>true</bool>
	- </attribute>
	- <attribute name="verticalHeaderHighlightSections">
	- <bool>true</bool>
	- </attribute>
	- <row>
	- <property name="text">
	- <string>New Row</string>
	- </property>
	- </row>
	- <row>
	- <property name="text">
	- <string>New Row</string>
	- </property>
	- </row>
	- <row>
	- <property name="text">
	- <string>New Row</string>
	- </property>
	- </row>
	- <column>
	- <property name="text">
	- <string>New Column</string>
	- </property>
	- </column>
	- <column>
	- <property name="text">
	- <string>New Column</string>
	- </property>
	- </column>
	- <column>
	- <property name="text">
	- <string>New Column</string>
	- </property>
	- </column>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <spacer name="horizontalSpacer">
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>40</width>
	- <height>20</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="7" column="0">
	- <spacer name="verticalSpacer_2">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="1" column="0">
	- <widget class="QGroupBox" name="groupBox_5">
	- <property name="title">
	- <string>Origin</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_17">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="2">
	- <widget class="QDoubleSpinBox" name="m_HeaderOriginZ">
	- <property name="decimals">
	- <number>4</number>
	- </property>
	- <property name="minimum">
	- <double>-999999999.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>999999999.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QDoubleSpinBox" name="m_HeaderOriginY">
	- <property name="decimals">
	- <number>4</number>
	- </property>
	- <property name="minimum">
	- <double>-99999999.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>999999999.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QDoubleSpinBox" name="m_HeaderOriginX">
	- <property name="decimals">
	- <number>4</number>
	- </property>
	- <property name="minimum">
	- <double>-999999999.000000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>999999999.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="8" column="0">
	- <widget class="QGroupBox" name="groupBox_7">
	- <property name="title">
	- <string>Align origins</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_15">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_AlignImageBox">
	- <property name="sizeAdjustPolicy">
	- <enum>QComboBox::AdjustToMinimumContentsLength</enum>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QCommandLinkButton" name="m_AlignImageButton">
	- <property name="text">
	- <string>Align to</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <widget class="QWidget" name="tab_2">
	- <attribute name="title">
	- <string>Other</string>
	- </attribute>
	- <layout class="QGridLayout" name="gridLayout_9">
	- <item row="1" column="0">
	- <widget class="QCommandLinkButton" name="m_ExtractBrainMask">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string>If multiple baseline acquisitions are present, the default behaviour is to output an averaged image.</string>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string notr="true"/>
	- </property>
	- <property name="text">
	- <string>Estimate binary brain mask</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QSpinBox" name="m_BrainMaskIterationsBox">
	- <property name="toolTip">
	- <string>Maximum number of iterations.</string>
	- </property>
	- <property name="maximum">
	- <number>10000</number>
	- </property>
	- <property name="value">
	- <number>10000</number>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <spacer name="verticalSpacer_3">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="0" column="0">
	- <widget class="QCommandLinkButton" name="m_ButtonExtractB0">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string>If multiple baseline acquisitions are present, the default behaviour is to output an averaged image.</string>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string notr="true"/>
	- </property>
	- <property name="text">
	- <string>Extract baseline image</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QCheckBox" name="m_CheckExtractAll">
	- <property name="toolTip">
	- <string>Create a 3D+t data set containing all b0 images as timesteps</string>
	- </property>
	- <property name="text">
	- <string>Disable averaging</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <layoutdefault spacing="6" margin="11"/>
	- <customwidgets>
	- <customwidget>
	- <class>QmitkDataStorageComboBox</class>
	- <extends>QComboBox</extends>
	- <header location="global">QmitkDataStorageComboBox.h</header>
	- </customwidget>
	- <customwidget>
	- <class>QmitkDataStorageComboBoxWithSelectNone</class>
	- <extends>QComboBox</extends>
	- <header>QmitkDataStorageComboBoxWithSelectNone.h</header>
	- </customwidget>
	- </customwidgets>
	- <tabstops>
	- <tabstop>m_SelctedImageComboBox</tabstop>
	- <tabstop>tabWidget</tabstop>
	- <tabstop>m_B_ValueMap_TableWidget</tabstop>
	- <tabstop>m_CreateLengthCorrectedDwi</tabstop>
	- <tabstop>m_B_ValueMap_Rounder_SpinBox</tabstop>
	- <tabstop>m_FlipGradientsButton</tabstop>
	- <tabstop>m_FlipGradBoxX</tabstop>
	- <tabstop>m_FlipGradBoxY</tabstop>
	- <tabstop>m_FlipGradBoxZ</tabstop>
	- <tabstop>m_ShowGradientsButton</tabstop>
	- <tabstop>m_MirrorGradientToHalfSphereButton</tabstop>
	- <tabstop>m_ReduceGradientsButton</tabstop>
	- <tabstop>m_ClearRotationButton</tabstop>
	- <tabstop>m_RemoveGradientButton</tabstop>
	- <tabstop>m_RemoveGradientBox</tabstop>
	- <tabstop>m_ExtractGradientButton</tabstop>
	- <tabstop>m_ExtractGradientBox</tabstop>
	- <tabstop>m_ButtonAverageGradients</tabstop>
	- <tabstop>m_Blur</tabstop>
	- <tabstop>m_ProjectSignalButton</tabstop>
	- <tabstop>m_targetBValueSpinBox</tabstop>
	- <tabstop>m_ProjectionMethodBox</tabstop>
	- <tabstop>m_NormalizeImageValuesButton</tabstop>
	- <tabstop>m_NewMean</tabstop>
	- <tabstop>m_NewStdev</tabstop>
	- <tabstop>m_NormalizationMaskBox</tabstop>
	- <tabstop>m_FlipAxis</tabstop>
	- <tabstop>m_FlipX</tabstop>
	- <tabstop>m_FlipY</tabstop>
	- <tabstop>m_FlipZ</tabstop>
	- <tabstop>m_MergeDwisButton</tabstop>
	- <tabstop>m_MergeDwiBox</tabstop>
	- <tabstop>m_ResampleTypeBox</tabstop>
	- <tabstop>m_ResampleDoubleX</tabstop>
	- <tabstop>m_ResampleDoubleY</tabstop>
	- <tabstop>m_ResampleDoubleZ</tabstop>
	- <tabstop>m_ResampleIntX</tabstop>
	- <tabstop>m_ResampleIntY</tabstop>
	- <tabstop>m_ResampleIntZ</tabstop>
	- <tabstop>m_InterpolatorBox</tabstop>
	- <tabstop>m_ResampleImageButton</tabstop>
	- <tabstop>m_XstartBox</tabstop>
	- <tabstop>m_XendBox</tabstop>
	- <tabstop>m_YstartBox</tabstop>
	- <tabstop>m_YendBox</tabstop>
	- <tabstop>m_ZstartBox</tabstop>
	- <tabstop>m_ZendBox</tabstop>
	- <tabstop>m_CropImageButton</tabstop>
	- <tabstop>m_ModifyHeader</tabstop>
	- <tabstop>m_HeaderOriginX</tabstop>
	- <tabstop>m_HeaderOriginY</tabstop>
	- <tabstop>m_HeaderOriginZ</tabstop>
	- <tabstop>m_HeaderSpacingX</tabstop>
	- <tabstop>m_HeaderSpacingY</tabstop>
	- <tabstop>m_HeaderSpacingZ</tabstop>
	- <tabstop>m_DirectionMatrixTable</tabstop>
	- <tabstop>m_MeasurementFrameTable</tabstop>
	- <tabstop>m_ButtonExtractB0</tabstop>
	- <tabstop>m_CheckExtractAll</tabstop>
	- <tabstop>m_ExtractBrainMask</tabstop>
	- <tabstop>m_BrainMaskIterationsBox</tabstop>
	- </tabstops>
	- <resources/>
	- <connections/>
	-</ui>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/mitkPluginActivator.cpp
	deleted file mode 100644
	index 56d175c7d5..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/mitkPluginActivator.cpp
	+++ /dev/null
	@@ -1,44 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkPluginActivator.h"
	-
	-#include "src/internal/QmitkPreprocessingView.h"
	-#include "src/internal/QmitkDwiPreprocessingPerspective.h"
	-#include <usModuleInitialization.h>
	-
	-
	-ctkPluginContext* mitk::PluginActivator::m_Context = nullptr;
	-
	-US_INITIALIZE_MODULE
	-
	-ctkPluginContext* mitk::PluginActivator::GetContext()
	-{
	- return m_Context;
	-}
	-
	-void mitk::PluginActivator::start(ctkPluginContext* context)
	-{
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkDwiPreprocessingPerspective, context)
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkPreprocessingView, context)
	- m_Context = context;
	-}
	-
	-void mitk::PluginActivator::stop(ctkPluginContext* context)
	-{
	- Q_UNUSED(context)
	- m_Context = nullptr;
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/mitkPluginActivator.h b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/mitkPluginActivator.h
	deleted file mode 100644
	index 2867726397..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/mitkPluginActivator.h
	+++ /dev/null
	@@ -1,40 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef MITKPLUGINACTIVATOR_H
	-#define MITKPLUGINACTIVATOR_H
	-
	-#include <ctkPluginActivator.h>
	-
	-namespace mitk
	-{
	- class PluginActivator : public QObject, public ctkPluginActivator
	- {
	- Q_OBJECT
	- Q_PLUGIN_METADATA(IID "org.mitk.gui.qt.diffusionimaging.preprocessing")
	- Q_INTERFACES(ctkPluginActivator)
	-
	- public:
	- static ctkPluginContext* GetContext();
	-
	- void start(ctkPluginContext* context) override;
	- void stop(ctkPluginContext* context) override;
	-
	- private:
	- static ctkPluginContext* m_Context;
	- };
	-}
	-
	-#endif
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.python/CMakeLists.txt
	deleted file mode 100644
	index 7ab1179c26..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/CMakeLists.txt
	+++ /dev/null
	@@ -1,18 +0,0 @@
	-if(MITK_USE_Python)
	-
	-# The project name must correspond to the directory name of your plug-in
	-# and must not contain periods.
	-project(org_mitk_gui_qt_diffusionimaging_python)
	-
	-mitk_create_plugin(
	- SUBPROJECTS MITK-DTI
	- EXPORT_DIRECTIVE DIFFUSIONIMAGING_PREPROCESSING_EXPORT
	- EXPORTED_INCLUDE_SUFFIXES src
	- MODULE_DEPENDS MitkDiffusionCore MitkPython
	- PACKAGE_DEPENDS Qt5\|Network BetData
	-)
	-
	-#set(_install_DESTINATION "BetData")
	-MITK_INSTALL(DIRECTORY ${BetData_DIR}/)
	-
	-endif()
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/documentation/doxygen/modules.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.python/documentation/doxygen/modules.dox
	deleted file mode 100644
	index c0a9180de7..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/documentation/doxygen/modules.dox
	+++ /dev/null
	@@ -1,16 +0,0 @@
	-/**
	- \defgroup org_mitk_gui_qt_diffusionimaging_preprocessing org.mitk.gui.qt.diffusionimaging.preprocessing
	- \ingroup MITKPlugins
	-
	- \brief This is the diffusionimaging.preprocessing plugin.
	-
	-*/
	-
	-/**
	- \defgroup org_mitk_gui_qt_diffusionimaging_preprocessing_internal Internal
	- \ingroup org_mitk_gui_qt_diffusionimaging_preprocessing
	-
	- \brief This subcategory includes the internal classes of the org.mitk.gui.qt.diffusionimaging.preprocessing plugin. Other
	- plugins must not rely on these classes. They contain implementation details and their interface
	- may change at any time. We mean it.
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/files.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.python/files.cmake
	deleted file mode 100644
	index 736c7682d6..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/files.cmake
	+++ /dev/null
	@@ -1,49 +0,0 @@
	-set(SRC_CPP_FILES
	-
	-
	-)
	-
	-set(INTERNAL_CPP_FILES
	- mitkPluginActivator.cpp
	-
	- QmitkBrainExtractionView.cpp
	- QmitkDipyReconstructionsView.cpp
	- QmitkTractSegView.cpp
	-)
	-
	-set(UI_FILES
	- src/internal/QmitkBrainExtractionViewControls.ui
	- src/internal/QmitkDipyReconstructionsViewControls.ui
	- src/internal/QmitkTractSegViewControls.ui
	-)
	-
	-set(MOC_H_FILES
	- src/internal/mitkPluginActivator.h
	-
	- src/internal/QmitkBrainExtractionView.h
	- src/internal/QmitkDipyReconstructionsView.h
	- src/internal/QmitkTractSegView.h
	-)
	-
	-set(CACHED_RESOURCE_FILES
	- plugin.xml
	-
	- resources/tract_seg.png
	- resources/brain_extraction.png
	- resources/dipy.png
	-)
	-
	-set(QRC_FILES
	- resources/QmitkDiffusionPython.qrc
	-)
	-
	-
	-set(CPP_FILES )
	-
	-foreach(file ${SRC_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/${file})
	-endforeach(file ${SRC_CPP_FILES})
	-
	-foreach(file ${INTERNAL_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/internal/${file})
	-endforeach(file ${INTERNAL_CPP_FILES})
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.python/manifest_headers.cmake
	deleted file mode 100644
	index 223766b673..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/manifest_headers.cmake
	+++ /dev/null
	@@ -1,5 +0,0 @@
	-set(Plugin-Name "MITK Preprocessing")
	-set(Plugin-Version "1.0.0")
	-set(Plugin-Vendor "DKFZ, Medical and Biological Informatics")
	-set(Plugin-ContactAddress "http://www.mitk.org")
	-set(Require-Plugin org.mitk.gui.qt.diffusionimaging org.mitk.gui.qt.common)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/plugin.xml b/Plugins/org.mitk.gui.qt.diffusionimaging.python/plugin.xml
	deleted file mode 100644
	index 74b3161e1c..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/plugin.xml
	+++ /dev/null
	@@ -1,48 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<?BlueBerry version="0.1"?>
	-<plugin>
	-
	- <extension point="org.blueberry.ui.views">
	-
	- <view id="org.mitk.views.brainextraction"
	- name="Brain Extraction"
	- category="Preprocessing"
	- class="QmitkBrainExtractionView"
	- icon="resources/brain_extraction.png">
	- <keywordReference id="org.mitk.views.brainextraction.Keyword"/>
	- </view>
	-
	- <view id="org.mitk.views.dipyreconstruction"
	- name="Dipy ODF Reconstructions"
	- category="Signal modeling"
	- class="QmitkDipyReconstructionsView"
	- icon="resources/dipy.png">
	- <keywordReference id="org.mitk.views.dipyreconstruction.Keyword"/>
	- </view>
	-
	- <view id="org.mitk.views.tractseg"
	- name="TractSeg"
	- category="Segmentation"
	- class="QmitkTractSegView"
	- icon="resources/tract_seg.png">
	- <keywordReference id="org.mitk.views.dipyreconstruction.Keyword"/>
	- </view>
	-
	- </extension>
	-
	-
	-
	- <extension point="org.blueberry.ui.keywords">
	-
	- <keyword label="segmentation" id="org.mitk.views.brainextraction.Keyword"/>
	- <keyword label="segmentation" id="org.mitk.views.tractseg.Keyword"/>
	- <keyword label="fiber" id="org.mitk.views.tractseg.Keyword"/>
	- <keyword label="bundle" id="org.mitk.views.tractseg.Keyword"/>
	- <keyword label="tract" id="org.mitk.views.tractseg.Keyword"/>
	- <keyword label="TOM" id="org.mitk.views.tractseg.Keyword"/>
	- <keyword label="map" id="org.mitk.views.tractseg.Keyword"/>
	- <keyword label="orientation" id="org.mitk.views.tractseg.Keyword"/>
	-
	- </extension>
	-
	-</plugin>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/QmitkDiffusionPython.qrc b/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/QmitkDiffusionPython.qrc
	deleted file mode 100644
	index d966a74575..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/QmitkDiffusionPython.qrc
	+++ /dev/null
	@@ -1,6 +0,0 @@
	-<RCC>
	- <qresource prefix="/QmitkDiffusionPython">
	- <file>dipy_reconstructions.py</file>
	- <file>tractseg.py</file>
	- </qresource>
	-</RCC>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/brain_extraction.png b/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/brain_extraction.png
	deleted file mode 100644
	index 23b5bc8322..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/brain_extraction.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/dipy.png b/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/dipy.png
	deleted file mode 100644
	index 7994e2e0b2..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/dipy.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/dipy_reconstructions.py b/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/dipy_reconstructions.py
	deleted file mode 100644
	index c9792c2e5c..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/dipy_reconstructions.py
	+++ /dev/null
	@@ -1,424 +0,0 @@
	-import sys
	-
	-
	-def get_mitk_sphere():
	- """ Return MITK compliant dipy Sphere object.
	- MITK stores ODFs as 252 values spherically sampled from the continuous ODF.
	- The sampling directions are generate by a 5-fold subdivisions of an icosahedron.
	- """
	- xyz = np.array([
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	- 0.9817040172417226, 0.9870396762453547, 0.9325589150767597,
	- 0.8173592116492303, 0.6708930871960926, 0.9399233672993689,
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	- 0.5232435944036425, 0.3889403678268736, 0.2135250052622625,
	- 0.02420694871807206, -0.1448539951504302, 0.5971534158422009,
	- 0.4482053228282282, 0.2597018771197477, 0.06677517278138323,
	- 0.6404616222418184, 0.4782876117785159, 0.2868761951248767,
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	- -0.03496843048443223, -0.2252069693946209, -0.4261053308619027,
	- -0.5992598174372795, -0.720136706807033, -0.2236017161594696,
	- -0.4317330442416767, -0.6250530132529536, -0.7675317913865697,
	- -0.4101898771205939, -0.6101488498350025, -0.7728099228904255,
	- -0.5638041319099237, -0.7350961954485662, 0.6411372723067146,
	- 0.6002931843810706, 0.5219523372221417, 0.4191004905746099,
	- 0.4596949806286311, 0.3916338931244087, 0.2980734064957148,
	- 0.226741584116328, 0.1432114770939381, -0.02097489882147943,
	- 0.8608164411414747, 0.7207644427956729, 0.5303678926086439,
	- 0.3211867913977836, 0.9015721838250796, 0.7879881821713033,
	- 0.6114960278478284, 0.3951892122332402, 0.1820657113417612,
	- 0.8070430398170311, 0.6574928275930984, 0.4544842943197335,
	- 0.2358529185889448, 0.6597856586149884, 0.4841878538357612,
	- 0.2789921022280572, 0.4842093252521232, 0.3043325272261384,
	- 0.5992589358516202, 0.4261046359672609, 0.2252066549797059,
	- 0.6250522113657903, 0.4317325950511361, 0.6101482870567641,
	- 0.9096403689902206, 0.9275522217134882, 0.8909112253661301,
	- 0.796262827475376, 0.6691520068054228, 0.8241233338640371,
	- 0.810859375773786, 0.7430057321681839, 0.6332085061147845,
	- 0.6854064426268304, 0.6413714065577412, 0.5581299045184589,
	- 0.5164832226272315, 0.4563611494403301, 0.3496833143594963,
	- -0.3951892821849063, -0.6114960336943951, -0.787988199289983,
	- -0.4544844137443082, -0.657492739431111, -0.484187939006181,
	- 0.4936478319326018, 0.2653148405479006, 0.01970714938077021,
	- -0.1989850169013517, 0.4302075642722875, 0.1852629793843341,
	- -0.0559739158243807, 0.3387563694841473, 0.09867487876932232,
	- 0.2393267951217032, -0.999553621201999, -0.9653354239158236,
	- -0.8682642090770526, -0.9597077173597477, -0.8918540989344099,
	- -0.8573751662344773, -0.2980738893651726, -0.3916343988495664,
	- -0.4596955428592778, -0.4950341577852201, -0.1432117197792371,
	- -0.2267418620329016, -0.2909964852939082, 0.02097514873862574,
	- -0.05800679989935065, 0.1653145532988453, -0.3786231842883476,
	- -0.1464197032303796, 0.09531724619007391, -0.1924163631703616,
	- 0.05252803743712917, 0.006318730357784829, -0.3534800054422614,
	- -0.1720548071373146, 0.02057294660420643, 0.190134278339324,
	- -0.1169519894866824, 0.07636807502743861, 0.2529338262925594,
	- 0.1271908635410245, 0.3046134343217798, 0.3366066958443542,
	- 0.6094980941008995, 0.7135382519498201, 0.7711196978950583,
	- 0.7870198804193677, 0.8705500304441893, 0.9132984713369965,
	- 0.403998910419839, 0.62060207699311, 0.7967976318501995,
	- 0.4726965405256068, 0.6757048258462731, 0.5106167801856609])
	-
	- n = int(xyz.shape[0] / 3)
	- x = xyz[:n]
	- y = xyz[n:2 * n]
	- z = xyz[2 * n:]
	-
	- for i in range(n):
	- v = np.array([x[i], y[i], z[i]])
	- norm = np.linalg.norm(v)
	- if norm > 0:
	- v /= norm
	- x[i] = v[0]
	- y[i] = v[1]
	- z[i] = v[2]
	-
	- s = sphere.Sphere(x=x, y=y, z=z)
	- return s
	-
	-
	-error_string = None
	-del error_string
	-try:
	- import dipy.direction.peaks as dpp
	- from dipy.reconst.shore import ShoreModel
	- from dipy.reconst.shm import CsaOdfModel, OpdtModel, SphHarmModel
	- import dipy.reconst.sfm as sfm
	- from dipy.reconst.csdeconv import auto_response, ConstrainedSphericalDeconvModel
	- from dipy.core import sphere
	- import numpy as np
	- from dipy.core.gradients import gradient_table
	- import SimpleITK as sitk
	-
	- print('DIPY Reconstructions')
	- data = sitk.GetArrayFromImage(in_image)
	- bvals = np.array(bvals)
	- bvecs = np.array(bvecs)
	-
	- # create dipy Sphere
	- sphere = get_mitk_sphere()
	- odf = None
	- model = None
	- gtab = gradient_table(bvals, bvecs)
	-
	- if mask is not None:
	- mask = sitk.GetArrayFromImage(mask)
	- print(mask.shape)
	-
	-
	- # fit selected model
	- sh_coeffs = None
	- odf = None
	- if model_type == '3D-SHORE':
	- print('Fitting 3D-SHORE')
	- print("radial_order: ", radial_order)
	- print("zeta: ", zeta)
	- print("lambdaN: ", lambdaN)
	- print("lambdaL: ", lambdaL)
	- model = ShoreModel(gtab, radial_order=radial_order, zeta=zeta, lambdaN=lambdaN, lambdaL=lambdaL)
	- asmfit = model.fit(data)
	- odf = asmfit.odf(sphere)
	- elif model_type == 'CSA-QBALL':
	- print('Fitting CSA-QBALL')
	- print("sh_order: ", sh_order)
	- print("smooth: ", smooth)
	- model = CsaOdfModel(gtab=gtab, sh_order=sh_order, smooth=smooth)
	- sh_coeffs = model.fit(data, mask=mask).shm_coeff
	- elif model_type == 'SFM':
	- print('Fitting SFM')
	- print("fa_thr: ", fa_thr)
	- response, ratio = auto_response(gtab, data, roi_radius=10, fa_thr=fa_thr)
	- model = sfm.SparseFascicleModel(gtab, sphere=sphere,
	- l1_ratio=0.5, alpha=0.001,
	- response=response[0])
	- odf = model.fit(data, mask=mask).odf(sphere)
	- elif model_type == 'CSD':
	- print('Fitting CSD')
	- print("sh_order: ", sh_order)
	- print("fa_thr: ", fa_thr)
	- response, ratio = auto_response(gtab, data, roi_radius=10, fa_thr=fa_thr)
	- model = ConstrainedSphericalDeconvModel(gtab, response, sh_order=sh_order)
	- sh_coeffs = model.fit(data).shm_coeff
	- elif model_type == 'Opdt':
	- print('Orientation Probability Density Transform')
	- print("sh_order: ", sh_order)
	- print("smooth: ", smooth)
	- model = OpdtModel(gtab=gtab, sh_order=sh_order, smooth=smooth)
	- sh_coeffs = model.fit(data, mask=mask).shm_coeff
	- else:
	- raise ValueError('Model type not supported. Available models: 3D-SHORE, CSA-QBALL, SFM, CSD, Opdt')
	-
	- if odf is not None:
	- odf = np.nan_to_num(odf)
	- print('Preparing ODF image')
	- odf_image = sitk.Image([data.shape[2], data.shape[1], data.shape[0]], sitk.sitkVectorFloat32, len(sphere.vertices))
	- for x in range(data.shape[2]):
	- for y in range(data.shape[1]):
	- for z in range(data.shape[0]):
	- if mask is not None and mask[z, y, x] == 0:
	- continue
	- odf_image.SetPixel(x, y, z, odf[z, y, x, :])
	- odf_image.SetOrigin(in_image.GetOrigin())
	- odf_image.SetSpacing(in_image.GetSpacing())
	- odf_image.SetDirection(in_image.GetDirection())
	- elif sh_coeffs is not None:
	- sh_coeffs = np.nan_to_num(sh_coeffs)
	- print('Preparing SH image')
	- sh_image = sitk.Image([sh_coeffs.shape[2], sh_coeffs.shape[1], sh_coeffs.shape[0]], sitk.sitkVectorFloat32, sh_coeffs.shape[3])
	- for x in range(sh_coeffs.shape[2]):
	- for y in range(sh_coeffs.shape[1]):
	- for z in range(sh_coeffs.shape[0]):
	- if mask is not None and mask[z, y, x] == 0:
	- continue
	- sh_image.SetPixel(x, y, z, sh_coeffs[z, y, x, :])
	- sh_image.SetOrigin(in_image.GetOrigin())
	- sh_image.SetSpacing(in_image.GetSpacing())
	- sh_image.SetDirection(in_image.GetDirection())
	-
	- if num_peaks > 0:
	-
	- print('Calculating peaks')
	- sys.stdout.flush()
	- # calculate peak image
	- data = np.nan_to_num(data)
	- sf_peaks = dpp.peaks_from_model(model,
	- data,
	- sphere,
	- relative_peak_threshold=relative_peak_threshold,
	- min_separation_angle=min_separation_angle,
	- return_sh=False, npeaks=num_peaks, parallel=True,
	- mask=mask)
	-
	- # reshape to be MITK/MRtrix compliant
	- s = sf_peaks.peak_dirs.shape
	- peaks = sf_peaks.peak_dirs.reshape((s[0], s[1], s[2], num_peaks * 3), order='C')
	- peaks = np.nan_to_num(peaks)
	- peak_image = sitk.Image([data.shape[2], data.shape[1], data.shape[0]], sitk.sitkVectorFloat32, num_peaks * 3)
	-
	- # scale peaks
	- max_peak = 1.0
	- if normalize_peaks:
	- max_peak = np.max(sf_peaks.peak_values)
	- if max_peak <= 0:
	- max_peak = 1.0
	- for x in range(s[0]):
	- for y in range(s[1]):
	- for z in range(s[2]):
	- for i in range(num_peaks):
	- peaks[x, y, z, i * 3] *= sf_peaks.peak_values[x, y, z, i] / max_peak
	- peaks[x, y, z, i * 3 + 1] *= sf_peaks.peak_values[x, y, z, i] / max_peak
	- peaks[x, y, z, i * 3 + 2] *= sf_peaks.peak_values[x, y, z, i] / max_peak
	-
	- peak_image.SetPixel(z, y, x, peaks[x, y, z, :])
	-
	- peak_image.SetOrigin(in_image.GetOrigin())
	- peak_image.SetSpacing(in_image.GetSpacing())
	- peak_image.SetDirection(in_image.GetDirection())
	-
	-
	-except Exception as e:
	- error_string = str(e)
	- print(error_string)
	-
	-sys.stdout.flush()
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/tract_seg.png b/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/tract_seg.png
	deleted file mode 100755
	index 4462301d22..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/tract_seg.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/tractseg.py b/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/tractseg.py
	deleted file mode 100644
	index 8acde177b5..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/resources/tractseg.py
	+++ /dev/null
	@@ -1,115 +0,0 @@
	-error_string = None
	-del error_string
	-try:
	- import nibabel as nib
	- import numpy as np
	- from tractseg.python_api import run_tractseg
	- from tractseg.python_api import img_utils
	-
	- data = sitk.GetArrayFromImage(in_image)
	- data = np.nan_to_num(data)
	- swapaxes = False
	- if data.shape != (sx, sy, sz):
	- print("Swapping axes!")
	- data = np.swapaxes(data, 0, 2)
	- swapaxes = True
	-
	- affine = np.zeros((4, 4))
	- affine[0, 0] = in_image.GetDirection()[0] * in_image.GetSpacing()[0]
	- affine[1, 0] = in_image.GetDirection()[1] * in_image.GetSpacing()[0]
	- affine[2, 0] = in_image.GetDirection()[2] * in_image.GetSpacing()[0]
	- affine[0, 1] = in_image.GetDirection()[3] * in_image.GetSpacing()[1]
	- affine[1, 1] = in_image.GetDirection()[4] * in_image.GetSpacing()[1]
	- affine[2, 1] = in_image.GetDirection()[5] * in_image.GetSpacing()[1]
	- affine[0, 2] = in_image.GetDirection()[6] * in_image.GetSpacing()[2]
	- affine[1, 2] = in_image.GetDirection()[7] * in_image.GetSpacing()[2]
	- affine[2, 2] = in_image.GetDirection()[8] * in_image.GetSpacing()[2]
	- affine[0, 3] = in_image.GetOrigin()[0]
	- affine[1, 3] = in_image.GetOrigin()[1]
	- affine[2, 3] = in_image.GetOrigin()[2]
	- affine[3, 3] = 1
	-
	- data, flip_axis = img_utils.flip_peaks_to_correct_orientation_if_needed(nib.Nifti1Image(data, affine=affine),
	- do_flip=True)
	- print('flip_axis', flip_axis)
	-
	- print('output_type', output_type)
	- print('get_probs', get_probs)
	- print('dropout_sampling', dropout_sampling)
	- print('threshold', threshold)
	-
	- seg = run_tractseg(data=data, output_type=output_type, input_type="peaks", verbose=verbose, get_probs=get_probs,
	- dropout_sampling=dropout_sampling, threshold=threshold, postprocess=False)
	-
	- # bla = nib.Nifti1Image(seg, affine)
	- # nib.save(bla, '/home/neher/test.nii.gz')
	- if swapaxes:
	- print("Swapping axes back!")
	- seg = np.swapaxes(seg, 0, 2)
	-
	- print('Output shape: ' + str(seg.shape))
	- if output_type == "tract_segmentation":
	-
	- if not get_probs and not dropout_sampling:
	- if collapse:
	- temp = np.zeros((seg.shape[0], seg.shape[1], seg.shape[2]))
	- for l in range(seg.shape[3]):
	- temp[np.where(seg[:, :, :, l] > 0)] = l + 1
	- seg = temp
	- segmentation = sitk.GetImageFromArray(seg.astype(np.uint8))
	- else:
	- segmentation = sitk.GetImageFromArray(seg)
	-
	- segmentation.SetOrigin(in_image.GetOrigin())
	- segmentation.SetSpacing(in_image.GetSpacing())
	- segmentation.SetDirection(in_image.GetDirection())
	-
	- elif output_type == "endings_segmentation":
	-
	- print("endings_segmentation", get_probs, dropout_sampling)
	- if not get_probs and not dropout_sampling:
	-
	- # merge start and end into labelmap
	- temp = np.zeros((seg.shape[0], seg.shape[1], seg.shape[2], seg.shape[3] // 2))
	- for l in range(temp.shape[3]):
	- temp[:, :, :, l][np.where(seg[:, :, :, l * 2] > 0)] = 1
	- temp[:, :, :, l][np.where(seg[:, :, :, l * 2 + 1] > 0)] = 2
	- seg = temp
	-
	- if collapse:
	- temp = np.zeros((seg.shape[0], seg.shape[1], seg.shape[2]))
	- for l in range(seg.shape[3]):
	- temp[np.where(seg[:, :, :, l] == 1)] = 2*l + 1
	- temp[np.where(seg[:, :, :, l] == 2)] = 2*l + 2
	- seg = temp
	- segmentation = sitk.GetImageFromArray(seg.astype(np.uint8))
	- else:
	-
	- temp = np.zeros((seg.shape[0], seg.shape[1], seg.shape[2], seg.shape[3] // 2))
	- for l in range(temp.shape[3]):
	- temp[:, :, :, l] += seg[:, :, :, l * 2]
	- temp[:, :, :, l] += seg[:, :, :, l * 2 + 1]
	- seg = temp
	- segmentation = sitk.GetImageFromArray(seg)
	-
	- segmentation.SetOrigin(in_image.GetOrigin())
	- segmentation.SetSpacing(in_image.GetSpacing())
	- segmentation.SetDirection(in_image.GetDirection())
	-
	- elif output_type == "TOM":
	- if not collapse:
	- for x in range(0, 72):
	- tom = sitk.GetImageFromArray(seg[:, :, :, x * 3:x * 3 + 3])
	- tom.SetOrigin(in_image.GetOrigin())
	- tom.SetSpacing(in_image.GetSpacing())
	- tom.SetDirection(in_image.GetDirection())
	- globals()['tom%s' % x] = tom
	- else:
	- tom0 = sitk.GetImageFromArray(seg)
	- tom0.SetOrigin(in_image.GetOrigin())
	- tom0.SetSpacing(in_image.GetSpacing())
	- tom0.SetDirection(in_image.GetDirection())
	-
	-except Exception as e:
	- error_string = str(e)
	- print(error_string)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkBrainExtractionView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkBrainExtractionView.cpp
	deleted file mode 100644
	index 740e63ed10..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkBrainExtractionView.cpp
	+++ /dev/null
	@@ -1,253 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-//misc
	-#define _USE_MATH_DEFINES
	-#include <math.h>
	-
	-// Blueberry
	-#include <berryISelectionService.h>
	-#include <berryIWorkbenchWindow.h>
	-
	-// Qmitk
	-#include "QmitkBrainExtractionView.h"
	-
	-// MITK
	-#include <mitkNodePredicateDataType.h>
	-
	-// Qt
	-#include <QMessageBox>
	-#include <QFileDialog>
	-#include <QDir>
	-#include <QDirIterator>
	-#include <QTimer>
	-
	-#include <mitkNodePredicateDimension.h>
	-#include <mitkNodePredicateAnd.h>
	-#include <mitkIOUtil.h>
	-#include <mitkIPythonService.h>
	-#include <itkResampleImageFilter.h>
	-#include <mitkImageCast.h>
	-#include <itkBSplineInterpolateImageFunction.h>
	-#include <itkLinearInterpolateImageFunction.h>
	-#include <itkThresholdImageFilter.h>
	-#include <itksys/SystemTools.hxx>
	-#include <itkB0ImageExtractionToSeparateImageFilter.h>
	-
	-#include <usGetModuleContext.h>
	-#include <usModuleContext.h>
	-#include <usModule.h>
	-#include <usModuleResource.h>
	-#include <usModuleResourceStream.h>
	-#include <boost/algorithm/string.hpp>
	-
	-#include <BetData.h>
	-
	-#define _USE_MATH_DEFINES
	-#include <math.h>
	-
	-typedef itksys::SystemTools ist;
	-
	-const std::string QmitkBrainExtractionView::VIEW_ID = "org.mitk.views.brainextraction";
	-
	-QmitkBrainExtractionView::QmitkBrainExtractionView()
	- : QmitkAbstractView()
	- , m_Controls( nullptr )
	- , m_DiffusionImage( nullptr )
	-{
	-
	-}
	-
	-// Destructor
	-QmitkBrainExtractionView::~QmitkBrainExtractionView()
	-{
	-}
	-
	-void QmitkBrainExtractionView::CreateQtPartControl( QWidget *parent )
	-{
	- // build up qt view, unless already done
	- if ( !m_Controls )
	- {
	- // create GUI widgets from the Qt Designer's .ui file
	- m_Controls = new Ui::QmitkBrainExtractionViewControls;
	- m_Controls->setupUi( parent );
	- connect( m_Controls->m_ImageBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGUI()) );
	- connect( m_Controls->m_StartButton, SIGNAL(clicked()), this, SLOT(StartBrainExtraction()) );
	- this->m_Parent = parent;
	-
	- m_Controls->m_ImageBox->SetDataStorage(this->GetDataStorage());
	- mitk::NodePredicateDimension::Pointer dimPred = mitk::NodePredicateDimension::New(3);
	- mitk::TNodePredicateDataType<mitk::Image>::Pointer isImagePredicate = mitk::TNodePredicateDataType<mitk::Image>::New();
	- m_Controls->m_ImageBox->SetPredicate(isImagePredicate);
	-
	- UpdateGUI();
	- }
	-}
	-
	-void QmitkBrainExtractionView::OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList<mitk::DataNode::Pointer>& )
	-{
	-}
	-
	-void QmitkBrainExtractionView::UpdateGUI()
	-{
	- if (m_Controls->m_ImageBox->GetSelectedNode().IsNotNull())
	- m_Controls->m_StartButton->setEnabled(true);
	- else
	- m_Controls->m_StartButton->setEnabled(false);
	-}
	-
	-void QmitkBrainExtractionView::SetFocus()
	-{
	- UpdateGUI();
	- m_Controls->m_StartButton->setFocus();
	-}
	-
	-std::string QmitkBrainExtractionView::GetPythonFile(std::string filename)
	-{
	- std::string out = "";
	- std::string exec_dir = QCoreApplication::applicationDirPath().toStdString();
	- for (auto dir : mitk::bet::relative_search_dirs)
	- {
	- if ( ist::FileExists( ist::GetCurrentWorkingDirectory() + dir + filename) )
	- {
	- out = ist::GetCurrentWorkingDirectory() + dir + filename;
	- return out;
	- }
	- if ( ist::FileExists( exec_dir + dir + filename) )
	- {
	- out = exec_dir + dir + filename;
	- return out;
	- }
	- }
	- for (auto dir : mitk::bet::absolute_search_dirs)
	- {
	- if ( ist::FileExists( dir + filename) )
	- {
	- out = dir + filename;
	- return out;
	- }
	- }
	-
	- return out;
	-}
	-
	-void QmitkBrainExtractionView::StartBrainExtraction()
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_ImageBox->GetSelectedNode();
	- mitk::Image::Pointer mitk_image = dynamic_cast<mitk::Image*>(node->GetData());
	-
	- bool missing_file = false;
	- std::string missing_file_string = "";
	- if ( GetPythonFile("run_mitk.py").empty() )
	- {
	- missing_file_string += "Brain extraction script file missing: run_mitk.py\n\n";
	- missing_file = true;
	- }
	-
	- if ( GetPythonFile("model_final.model").empty() )
	- {
	- missing_file_string += "Brain extraction model file missing: model_final.model\n\n";
	- missing_file = true;
	- }
	-
	- if ( GetPythonFile("basic_config_just_like_braintumor.py").empty() )
	- {
	- missing_file_string += "Config file missing: basic_config_just_like_braintumor.py\n\n";
	- missing_file = true;
	- }
	-
	- if (missing_file)
	- {
	- QMessageBox::warning(nullptr, "Error", (missing_file_string).c_str(), QMessageBox::Ok);
	- return;
	- }
	-
	- try
	- {
	- us::ModuleContext* context = us::GetModuleContext();
	- us::ServiceReference<mitk::IPythonService> m_PythonServiceRef = context->GetServiceReference<mitk::IPythonService>();
	- mitk::IPythonService* m_PythonService = dynamic_cast<mitk::IPythonService*> ( context->GetService<mitk::IPythonService>(m_PythonServiceRef) );
	- mitk::IPythonService::ForceLoadModule();
	-
	- // extend python search path
	- m_PythonService->AddAbsoluteSearchDirs(mitk::bet::absolute_search_dirs);
	- m_PythonService->AddRelativeSearchDirs(mitk::bet::relative_search_dirs);
	-
	- // legacy (can be romved when BetData is updated accordingly)
	- m_PythonService->Execute("paths=list()");
	-
	- // set input files (model and config)
	- m_PythonService->Execute("model_file=\""+GetPythonFile("model_final.model")+"\"");
	- m_PythonService->Execute("config_file=\""+GetPythonFile("basic_config_just_like_braintumor.py")+"\"");
	-
	- // copy input image to python
	- m_PythonService->CopyToPythonAsSimpleItkImage( mitk_image, "in_image");
	-
	- // run segmentation script
	- m_PythonService->ExecuteScript( GetPythonFile("run_mitk.py") );
	-
	- // clean up after running script (better way than deleting individual variables?)
	- if(m_PythonService->DoesVariableExist("in_image"))
	- m_PythonService->Execute("del in_image");
	-
	- // check for errors
	- if(!m_PythonService->GetVariable("error_string").empty())
	- {
	- QMessageBox::warning(nullptr, "Error", QString(m_PythonService->GetVariable("error_string").c_str()), QMessageBox::Ok);
	- return;
	- }
	-
	- // get output images and add to datastorage
	- std::string output_variables = m_PythonService->GetVariable("output_variables");
	- std::vector<std::string> outputs;
	- boost::split(outputs, output_variables, boost::is_any_of(","));
	-
	- std::string output_types = m_PythonService->GetVariable("output_types");
	- std::vector<std::string> types;
	- boost::split(types, output_types, boost::is_any_of(","));
	-
	- for (unsigned int i=0; i<outputs.size(); ++i)
	- {
	- if (m_PythonService->DoesVariableExist(outputs.at(i)))
	- {
	- mitk::Image::Pointer image = m_PythonService->CopySimpleItkImageFromPython(outputs.at(i));
	-
	- if(types.at(i)=="input" && mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(mitk_image))
	- {
	- mitk::DiffusionPropertyHelper::CopyProperties(mitk_image, image, true);
	- mitk::DiffusionPropertyHelper::InitializeImage(image);
	- }
	-
	- mitk::DataNode::Pointer corrected_node = mitk::DataNode::New();
	- corrected_node->SetData( image );
	- std::string name = node->GetName();
	- name += "_";
	- name += outputs.at(i);
	- corrected_node->SetName(name);
	- GetDataStorage()->Add(corrected_node, node);
	- m_PythonService->Execute("del " + outputs.at(i));
	-
	- mitk::RenderingManager::GetInstance()->InitializeViews( corrected_node->GetData()->GetTimeGeometry(),
	- mitk::RenderingManager::REQUEST_UPDATE_ALL,
	- true);
	- }
	- }
	- }
	- catch(...)
	- {
	- QMessageBox::warning(nullptr, "Error", "File could not be processed.\nIs pytorch installed on your system?\nDoes your script use the correct input and output variable names (in: in_image & model, out: brain_mask & brain_extracted)?", QMessageBox::Ok);
	- }
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkBrainExtractionView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkBrainExtractionView.h
	deleted file mode 100644
	index 9630c8d601..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkBrainExtractionView.h
	+++ /dev/null
	@@ -1,77 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-
	-#include <berryISelectionListener.h>
	-#include <berryIStructuredSelection.h>
	-
	-#include <QmitkAbstractView.h>
	-#include "ui_QmitkBrainExtractionViewControls.h"
	-#include <mitkImage.h>
	-
	-#include <mitkDiffusionPropertyHelper.h>
	-
	-
	-/*!
	-\brief
	-*/
	-class QmitkBrainExtractionView : public QmitkAbstractView
	-{
	-
	- // this is needed for all Qt objects that should have a Qt meta-object
	- // (everything that derives from QObject and wants to have signal/slots)
	- Q_OBJECT
	-
	-public:
	-
	- static const std::string VIEW_ID;
	-
	- typedef itk::VectorImage< short, 3 > ItkDwiType;
	- typedef mitk::GradientDirectionsProperty GradProp;
	-
	- QmitkBrainExtractionView();
	- virtual ~QmitkBrainExtractionView();
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	- void SetFocus() override;
	-
	-protected slots:
	-
	- void StartBrainExtraction();
	- void UpdateGUI(); ///< update button activity etc. dpending on current datamanager selection
	-
	- std::string GetPythonFile(std::string filename);
	-
	-
	-protected:
	-
	- /// \brief called by QmitkAbstractView when DataManager's selection has changed
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- Ui::QmitkBrainExtractionViewControls* m_Controls;
	-
	- mitk::Image::Pointer m_DiffusionImage;
	- std::vector< mitk::DataNode::Pointer > m_SelectedDiffusionNodes;
	-
	-private:
	-
	- void UpdateRegistrationStatus(); ///< update textual status display of the Registration process
	-
	- // the Qt parent of our GUI (NOT of this object)
	- QWidget* m_Parent;
	-
	-};
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkBrainExtractionViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkBrainExtractionViewControls.ui
	deleted file mode 100644
	index 6c6eadc387..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkBrainExtractionViewControls.ui
	+++ /dev/null
	@@ -1,97 +0,0 @@
	-<?xml version="1.0" encoding="utf-8"?>
	-<ui version="4.0">
	- <class>QmitkBrainExtractionViewControls</class>
	- <widget class="QWidget" name="QmitkBrainExtractionViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>435</width>
	- <height>744</height>
	- </rect>
	- </property>
	- <property name="windowTitle">
	- <string>Form</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_2">
	- <item row="1" column="0">
	- <widget class="QCommandLinkButton" name="m_StartButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>Start Brain Extraction</string>
	- </property>
	- </widget>
	- </item>
	- <item row="10" column="0">
	- <spacer name="verticalSpacer">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="0" column="0">
	- <widget class="QFrame" name="frame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_ImageBox"></widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label">
	- <property name="text">
	- <string>Input Image:</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <customwidgets>
	- <customwidget>
	- <class>QmitkDataStorageComboBox</class>
	- <extends>QComboBox</extends>
	- <header>QmitkDataStorageComboBox.h</header>
	- </customwidget>
	- </customwidgets>
	- <resources></resources>
	- <connections></connections>
	-</ui>
	\ No newline at end of file
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkDipyReconstructionsView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkDipyReconstructionsView.cpp
	deleted file mode 100644
	index 9b639bf059..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkDipyReconstructionsView.cpp
	+++ /dev/null
	@@ -1,409 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-// Blueberry
	-#include <berryISelectionService.h>
	-#include <berryIWorkbenchWindow.h>
	-
	-// Qmitk
	-#include "QmitkDipyReconstructionsView.h"
	-
	-#include <mitkNodePredicateIsDWI.h>
	-#include <mitkIPythonService.h>
	-#include <boost/lexical_cast.hpp>
	-#include <QFile>
	-#include <QMessageBox>
	-#include <usModuleContext.h>
	-#include <usGetModuleContext.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <mitkOdfImage.h>
	-#include <mitkShImage.h>
	-#include <mitkImageCast.h>
	-#include <itkVectorImageToFourDImageFilter.h>
	-#include <mitkPeakImage.h>
	-#include <mitkNodePredicateAnd.h>
	-#include <mitkNodePredicateDataType.h>
	-#include <mitkNodePredicateProperty.h>
	-#include <mitkNodePredicateDimension.h>
	-#include <itkShCoefficientImageImporter.h>
	-
	-const std::string QmitkDipyReconstructionsView::VIEW_ID = "org.mitk.views.dipyreconstruction";
	-
	-QmitkDipyReconstructionsView::QmitkDipyReconstructionsView()
	- : QmitkAbstractView()
	- , m_Controls( 0 )
	-{
	-
	-}
	-
	-// Destructor
	-QmitkDipyReconstructionsView::~QmitkDipyReconstructionsView()
	-{
	-}
	-
	-void QmitkDipyReconstructionsView::CreateQtPartControl( QWidget *parent )
	-{
	- // build up qt view, unless already done
	- if ( !m_Controls )
	- {
	- // create GUI widgets from the Qt Designer's .ui file
	- m_Controls = new Ui::QmitkDipyReconstructionsViewControls;
	- m_Controls->setupUi( parent );
	- connect( m_Controls->m_ImageBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGUI()) );
	- connect( m_Controls->m_StartButton, SIGNAL(clicked()), this, SLOT(StartFit()) );
	- connect( m_Controls->m_ModelBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGUI()) );
	- this->m_Parent = parent;
	-
	- m_Controls->m_ImageBox->SetDataStorage(this->GetDataStorage());
	- mitk::NodePredicateIsDWI::Pointer isDwi = mitk::NodePredicateIsDWI::New();
	- m_Controls->m_ImageBox->SetPredicate( isDwi );
	-
	- mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true));
	- mitk::TNodePredicateDataType<mitk::Image>::Pointer isImagePredicate = mitk::TNodePredicateDataType<mitk::Image>::New();
	- mitk::NodePredicateAnd::Pointer isBinary3dImage = mitk::NodePredicateAnd::New( mitk::NodePredicateAnd::New( isImagePredicate, isBinaryPredicate ), mitk::NodePredicateDimension::New(3));
	-
	- m_Controls->m_MaskBox->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_MaskBox->SetPredicate( isBinary3dImage );
	- m_Controls->m_MaskBox->SetZeroEntryText("--");
	-
	- UpdateGUI();
	- }
	-}
	-
	-void QmitkDipyReconstructionsView::OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList<mitk::DataNode::Pointer>& )
	-{
	-}
	-
	-void QmitkDipyReconstructionsView::UpdateGUI()
	-{
	- if (m_Controls->m_ImageBox->GetSelectedNode().IsNotNull())
	- m_Controls->m_StartButton->setEnabled(true);
	- else
	- m_Controls->m_StartButton->setEnabled(false);
	-
	- m_Controls->m_ShoreBox->setVisible(false);
	- m_Controls->m_SfmBox->setVisible(false);
	- m_Controls->m_CsdBox->setVisible(false);
	- m_Controls->m_CsaBox->setVisible(false);
	- m_Controls->m_OpdtBox->setVisible(false);
	- switch(m_Controls->m_ModelBox->currentIndex())
	- {
	- case 0:
	- {
	- m_Controls->m_ShoreBox->setVisible(true);
	- break;
	- }
	- case 1:
	- {
	- m_Controls->m_SfmBox->setVisible(true);
	- break;
	- }
	- case 2:
	- {
	- m_Controls->m_CsdBox->setVisible(true);
	- break;
	- }
	- case 3:
	- {
	- m_Controls->m_CsaBox->setVisible(true);
	- break;
	- }
	- case 4:
	- {
	- m_Controls->m_OpdtBox->setVisible(true);
	- break;
	- }
	- }
	-}
	-
	-void QmitkDipyReconstructionsView::SetFocus()
	-{
	- UpdateGUI();
	- m_Controls->m_StartButton->setFocus();
	-}
	-
	-void QmitkDipyReconstructionsView::StartFit()
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_ImageBox->GetSelectedNode();
	- mitk::Image::Pointer input_image = dynamic_cast<mitk::Image*>(node->GetData());
	-
	- // get python script as string
	- QString data;
	- QString fileName(":/QmitkDiffusionImaging/dipy_reconstructions.py");
	- QFile file(fileName);
	- if(!file.open(QIODevice::ReadOnly)) {
	- qDebug()<<"filenot opened"<<endl;
	- }
	- else
	- {
	- qDebug()<<"file opened"<<endl;
	- data = file.readAll();
	- }
	- file.close();
	-
	- // get bvals and bvecs
	- std::locale::global(std::locale::classic());
	- std::string bvals = "[";
	- std::string bvecs = "[";
	- auto gcont = mitk::DiffusionPropertyHelper::GetGradientContainer(input_image);
	- auto bvaluevector = mitk::DiffusionPropertyHelper::GetBValueVector(input_image);
	- int b0_count = 0;
	- for (unsigned int i=0; i<gcont->Size(); ++i)
	- {
	- bvals += boost::lexical_cast<std::string>(bvaluevector.at(i));
	- if (bvaluevector.at(i)==0)
	- b0_count++;
	- auto g = gcont->GetElement(i);
	-
	- if (g.two_norm()>0.000001)
	- g /= g.two_norm();
	- bvecs += "[" + boost::lexical_cast<std::string>(g[0]) + "," + boost::lexical_cast<std::string>(g[1]) + "," + boost::lexical_cast<std::string>(g[2]) + "]";
	-
	- if (i<gcont->Size()-1)
	- {
	- bvals += ", ";
	- bvecs += ", ";
	- }
	- }
	- bvals += "]";
	- bvecs += "]";
	- if (b0_count==0)
	- {
	- QMessageBox::warning(nullptr, "Error", "No b=0 volume found. Do your b-values need rounding? Use the Preprocessing View for rounding b-values,", QMessageBox::Ok);
	- return;
	- }
	-
	-
	- us::ModuleContext* context = us::GetModuleContext();
	- us::ServiceReference<mitk::IPythonService> m_PythonServiceRef = context->GetServiceReference<mitk::IPythonService>();
	- mitk::IPythonService* m_PythonService = dynamic_cast<mitk::IPythonService*> ( context->GetService<mitk::IPythonService>(m_PythonServiceRef) );
	- mitk::IPythonService::ForceLoadModule();
	-
	- m_PythonService->CopyToPythonAsSimpleItkImage( input_image, "in_image");
	- m_PythonService->Execute("mask=None");
	- if (m_Controls->m_MaskBox->GetSelectedNode().IsNotNull())
	- {
	- auto mitk_mask = dynamic_cast<mitk::Image*>(m_Controls->m_MaskBox->GetSelectedNode()->GetData());
	- if (mitk_mask->GetLargestPossibleRegion().GetSize()==input_image->GetLargestPossibleRegion().GetSize())
	- m_PythonService->CopyToPythonAsSimpleItkImage( mitk_mask, "mask");
	- else
	- MITK_INFO << "Mask image not used. Does not match data size: " << mitk_mask->GetLargestPossibleRegion().GetSize() << " vs. "
	- << input_image->GetLargestPossibleRegion().GetSize();
	- }
	-
	- m_PythonService->Execute("normalize_peaks=False");
	- if (m_Controls->m_NormalizePeaks->isChecked())
	- m_PythonService->Execute("normalize_peaks=True");
	-
	- std::string model = "3D-SHORE";
	- int sh_order = 0;
	- switch(m_Controls->m_ModelBox->currentIndex())
	- {
	- case 0:
	- {
	- model = "3D-SHORE";
	- m_PythonService->Execute("radial_order=" + boost::lexical_cast<std::string>(m_Controls->m_RadialOrder->value()));
	- m_PythonService->Execute("zeta=" + boost::lexical_cast<std::string>(m_Controls->m_Zeta->value()));
	- m_PythonService->Execute("lambdaN=" + m_Controls->m_LambdaN->text().toStdString());
	- m_PythonService->Execute("lambdaL=" + m_Controls->m_LambdaL->text().toStdString());
	- break;
	- }
	- case 1:
	- {
	- model = "SFM";
	- m_PythonService->Execute("fa_thr=" + boost::lexical_cast<std::string>(m_Controls->m_FaThresholdSfm->value()));
	- break;
	- }
	- case 2:
	- {
	- model = "CSD";
	- sh_order = m_Controls->m_ShOrderCsd->value();
	- m_PythonService->Execute("sh_order=" + boost::lexical_cast<std::string>(sh_order));
	- m_PythonService->Execute("fa_thr=" + boost::lexical_cast<std::string>(m_Controls->m_FaThresholdCsd->value()));
	- break;
	- }
	- case 3:
	- {
	- model = "CSA-QBALL";
	- sh_order = m_Controls->m_ShOrderCsa->value();
	- m_PythonService->Execute("sh_order=" + boost::lexical_cast<std::string>(sh_order));
	- m_PythonService->Execute("smooth=" + boost::lexical_cast<std::string>(m_Controls->m_LambdaCsa->value()));
	- break;
	- }
	- case 4:
	- {
	- model = "Opdt";
	- sh_order = m_Controls->m_ShOrderOpdt->value();
	- m_PythonService->Execute("sh_order=" + boost::lexical_cast<std::string>(sh_order));
	- m_PythonService->Execute("smooth=" + boost::lexical_cast<std::string>(m_Controls->m_LambdaOpdt->value()));
	- break;
	- }
	- }
	- m_PythonService->Execute("model_type='"+model+"'");
	-
	- m_PythonService->Execute("num_peaks=0");
	- if (m_Controls->m_DoCalculatePeaks->isChecked())
	- {
	- m_PythonService->Execute("num_peaks=" + boost::lexical_cast<std::string>(m_Controls->m_NumPeaks->value()));
	- m_PythonService->Execute("min_separation_angle=" + boost::lexical_cast<std::string>(m_Controls->m_SepAngle->value()));
	- m_PythonService->Execute("relative_peak_threshold=" + boost::lexical_cast<std::string>(m_Controls->m_RelativeThreshold->value()));
	- }
	-
	- m_PythonService->Execute("data=False");
	- m_PythonService->Execute("bvals=" + bvals);
	- m_PythonService->Execute("bvecs=" + bvecs);
	- m_PythonService->Execute(data.toStdString(), mitk::IPythonService::MULTI_LINE_COMMAND);
	-
	- // clean up after running script (better way than deleting individual variables?)
	- if(m_PythonService->DoesVariableExist("in_image"))
	- m_PythonService->Execute("del in_image");
	-
	- // check for errors
	- if(!m_PythonService->GetVariable("error_string").empty())
	- {
	- QMessageBox::warning(nullptr, "Error", QString(m_PythonService->GetVariable("error_string").c_str()), QMessageBox::Ok);
	- return;
	- }
	-
	- if (m_PythonService->DoesVariableExist("odf_image"))
	- {
	- mitk::OdfImage::ItkOdfImageType::Pointer itkImg = mitk::OdfImage::ItkOdfImageType::New();
	-
	- mitk::Image::Pointer out_image = m_PythonService->CopySimpleItkImageFromPython("odf_image");
	- mitk::CastToItkImage(out_image, itkImg);
	-
	- mitk::OdfImage::Pointer image = mitk::OdfImage::New();
	- image->InitializeByItk( itkImg.GetPointer() );
	- image->SetVolume( itkImg->GetBufferPointer() );
	-
	- mitk::DataNode::Pointer odfs = mitk::DataNode::New();
	- odfs->SetData( image );
	- QString name(node->GetName().c_str());
	- odfs->SetName(name.toStdString() + "_" + model);
	- GetDataStorage()->Add(odfs, node);
	- m_PythonService->Execute("del odf_image");
	- }
	- else if (m_PythonService->DoesVariableExist("sh_image"))
	- {
	- mitk::Image::Pointer out_image = m_PythonService->CopySimpleItkImageFromPython("sh_image");
	- itk::VectorImage<float>::Pointer vectorImage = itk::VectorImage<float>::New();
	- mitk::CastToItkImage(out_image, vectorImage);
	-
	- itk::VectorImageToFourDImageFilter< float >::Pointer converter = itk::VectorImageToFourDImageFilter< float >::New();
	- converter->SetInputImage(vectorImage);
	- converter->GenerateData();
	- mitk::ShImage::ShOnDiskType::Pointer itkImg = converter->GetOutputImage();
	-
	- mitk::ShImage::Pointer shImage = mitk::ShImage::New();
	- mitk::Image::Pointer mitkImage = dynamic_cast<mitk::Image*>(shImage.GetPointer());
	-
	- switch(sh_order)
	- {
	- case 2:
	- {
	- typedef itk::ShCoefficientImageImporter< float, 2 > ImporterType;
	- typename ImporterType::Pointer importer = ImporterType::New();
	- importer->SetInputImage(itkImg);
	- importer->GenerateData();
	- mitk::CastToMitkImage(importer->GetCoefficientImage(), mitkImage);
	- mitkImage->SetVolume(importer->GetCoefficientImage()->GetBufferPointer());
	- break;
	- }
	- case 4:
	- {
	- typedef itk::ShCoefficientImageImporter< float, 4 > ImporterType;
	- typename ImporterType::Pointer importer = ImporterType::New();
	- importer->SetInputImage(itkImg);
	- importer->GenerateData();
	- mitk::CastToMitkImage(importer->GetCoefficientImage(), mitkImage);
	- mitkImage->SetVolume(importer->GetCoefficientImage()->GetBufferPointer());
	- break;
	- }
	- case 6:
	- {
	- typedef itk::ShCoefficientImageImporter< float, 6 > ImporterType;
	- typename ImporterType::Pointer importer = ImporterType::New();
	- importer->SetInputImage(itkImg);
	- importer->GenerateData();
	- mitk::CastToMitkImage(importer->GetCoefficientImage(), mitkImage);
	- mitkImage->SetVolume(importer->GetCoefficientImage()->GetBufferPointer());
	- break;
	- }
	- case 8:
	- {
	- typedef itk::ShCoefficientImageImporter< float, 8 > ImporterType;
	- typename ImporterType::Pointer importer = ImporterType::New();
	- importer->SetInputImage(itkImg);
	- importer->GenerateData();
	- mitk::CastToMitkImage(importer->GetCoefficientImage(), mitkImage);
	- mitkImage->SetVolume(importer->GetCoefficientImage()->GetBufferPointer());
	- break;
	- }
	- case 10:
	- {
	- typedef itk::ShCoefficientImageImporter< float, 10 > ImporterType;
	- typename ImporterType::Pointer importer = ImporterType::New();
	- importer->SetInputImage(itkImg);
	- importer->GenerateData();
	- mitk::CastToMitkImage(importer->GetCoefficientImage(), mitkImage);
	- mitkImage->SetVolume(importer->GetCoefficientImage()->GetBufferPointer());
	- break;
	- }
	- case 12:
	- {
	- typedef itk::ShCoefficientImageImporter< float, 12 > ImporterType;
	- typename ImporterType::Pointer importer = ImporterType::New();
	- importer->SetInputImage(itkImg);
	- importer->GenerateData();
	- mitk::CastToMitkImage(importer->GetCoefficientImage(), mitkImage);
	- mitkImage->SetVolume(importer->GetCoefficientImage()->GetBufferPointer());
	- break;
	- }
	- default:
	- mitkThrow() << "SH order not supported";
	- }
	-
	- mitk::DataNode::Pointer shNode = mitk::DataNode::New();
	- shNode->SetData( mitkImage );
	- QString name(node->GetName().c_str());
	- shNode->SetName(name.toStdString() + "_" + model);
	- GetDataStorage()->Add(shNode, node);
	- m_PythonService->Execute("del sh_image");
	- }
	-
	- if (m_Controls->m_DoCalculatePeaks->isChecked() && m_PythonService->DoesVariableExist("peak_image"))
	- {
	- mitk::Image::Pointer out_image = m_PythonService->CopySimpleItkImageFromPython("peak_image");
	- itk::VectorImage<float>::Pointer vectorImage = itk::VectorImage<float>::New();
	- mitk::CastToItkImage(out_image, vectorImage);
	-
	- itk::VectorImageToFourDImageFilter< float >::Pointer converter = itk::VectorImageToFourDImageFilter< float >::New();
	- converter->SetInputImage(vectorImage);
	- converter->GenerateData();
	- mitk::PeakImage::ItkPeakImageType::Pointer itk_peaks = converter->GetOutputImage();
	-
	- mitk::Image::Pointer mitk_peaks = dynamic_cast<mitk::Image*>(mitk::PeakImage::New().GetPointer());
	- mitk::CastToMitkImage(itk_peaks, mitk_peaks);
	- mitk_peaks->SetVolume(itk_peaks->GetBufferPointer());
	-
	- mitk::DataNode::Pointer seg = mitk::DataNode::New();
	- seg->SetData( mitk_peaks );
	- seg->SetName("Peaks");
	- GetDataStorage()->Add(seg, node);
	- m_PythonService->Execute("del peak_image");
	- }
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkDipyReconstructionsView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkDipyReconstructionsView.h
	deleted file mode 100644
	index f9186b3db9..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkDipyReconstructionsView.h
	+++ /dev/null
	@@ -1,72 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-
	-#include <berryISelectionListener.h>
	-#include <berryIStructuredSelection.h>
	-
	-#include <QmitkAbstractView.h>
	-#include "ui_QmitkDipyReconstructionsViewControls.h"
	-#include <mitkImage.h>
	-
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <QmitkDataStorageComboBoxWithSelectNone.h>
	-
	-/*!
	-\brief
	-*/
	-class QmitkDipyReconstructionsView : public QmitkAbstractView
	-{
	-
	- // this is needed for all Qt objects that should have a Qt meta-object
	- // (everything that derives from QObject and wants to have signal/slots)
	- Q_OBJECT
	-
	-public:
	-
	- static const std::string VIEW_ID;
	-
	- typedef itk::VectorImage< short, 3 > ItkDwiType;
	- typedef mitk::GradientDirectionsProperty GradProp;
	-
	- QmitkDipyReconstructionsView();
	- virtual ~QmitkDipyReconstructionsView();
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	- void SetFocus() override;
	-
	-protected slots:
	-
	- void StartFit();
	- void UpdateGUI(); ///< update button activity etc. dpending on current datamanager selection
	-
	-
	-protected:
	-
	- /// \brief called by QmitkAbstractView when DataManager's selection has changed
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- Ui::QmitkDipyReconstructionsViewControls* m_Controls;
	-
	-private:
	-
	- void UpdateRegistrationStatus(); ///< update textual status display of the Registration process
	-
	- // the Qt parent of our GUI (NOT of this object)
	- QWidget* m_Parent;
	-
	-};
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkDipyReconstructionsViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkDipyReconstructionsViewControls.ui
	deleted file mode 100644
	index 50c9d025a6..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkDipyReconstructionsViewControls.ui
	+++ /dev/null
	@@ -1,669 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<ui version="4.0">
	- <class>QmitkDipyReconstructionsViewControls</class>
	- <widget class="QWidget" name="QmitkDipyReconstructionsViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>435</width>
	- <height>1036</height>
	- </rect>
	- </property>
	- <property name="windowTitle">
	- <string>Form</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_2">
	- <property name="verticalSpacing">
	- <number>25</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QFrame" name="frame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="2" column="1">
	- <widget class="QComboBox" name="m_ModelBox">
	- <item>
	- <property name="text">
	- <string>3D-SHORE</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Sparse Fascicle Model</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Constrained Spherical Deconvolution</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>CSA-QBALL</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Orientation Probability Density Transform</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label">
	- <property name="text">
	- <string>Input Image:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label_2">
	- <property name="text">
	- <string>Model:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_ImageBox"/>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_7">
	- <property name="text">
	- <string>Mask Image:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QmitkDataStorageComboBoxWithSelectNone" name="m_MaskBox"/>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QGroupBox" name="m_ShoreBox">
	- <property name="title">
	- <string>3D-SHORE Parameters</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_3">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_RadialOrder">
	- <property name="minimum">
	- <number>2</number>
	- </property>
	- <property name="maximum">
	- <number>100</number>
	- </property>
	- <property name="singleStep">
	- <number>2</number>
	- </property>
	- <property name="value">
	- <number>6</number>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_4">
	- <property name="text">
	- <string>Zeta:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_3">
	- <property name="text">
	- <string>Radial Order:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label_5">
	- <property name="text">
	- <string>LambdaN:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QLabel" name="label_6">
	- <property name="text">
	- <string>LambdaL:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QSpinBox" name="m_Zeta">
	- <property name="maximum">
	- <number>9999</number>
	- </property>
	- <property name="value">
	- <number>700</number>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QLineEdit" name="m_LambdaN">
	- <property name="text">
	- <string>1e-8</string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="1">
	- <widget class="QLineEdit" name="m_LambdaL">
	- <property name="text">
	- <string>1e-8</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <widget class="QGroupBox" name="m_OpdtBox">
	- <property name="title">
	- <string>Orientation Probability Density Transform Parameters</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_14">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="2" column="1">
	- <widget class="QFrame" name="frame_9">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_15">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>0</number>
	- </property>
	- </layout>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_ShOrderOpdt">
	- <property name="minimum">
	- <number>2</number>
	- </property>
	- <property name="maximum">
	- <number>12</number>
	- </property>
	- <property name="singleStep">
	- <number>2</number>
	- </property>
	- <property name="value">
	- <number>6</number>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_24">
	- <property name="text">
	- <string>Lambda:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_25">
	- <property name="text">
	- <string>SH Order:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QDoubleSpinBox" name="m_LambdaOpdt">
	- <property name="decimals">
	- <number>4</number>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.001000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.006000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="7" column="0">
	- <widget class="QCommandLinkButton" name="m_StartButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Start Reconstruction</string>
	- </property>
	- </widget>
	- </item>
	- <item row="16" column="0">
	- <spacer name="verticalSpacer">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="2" column="0">
	- <widget class="QGroupBox" name="m_SfmBox">
	- <property name="title">
	- <string>Sparse Fascicle Model Parameters</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_6">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_11">
	- <property name="text">
	- <string>FA Threshold:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QDoubleSpinBox" name="m_FaThresholdSfm">
	- <property name="decimals">
	- <number>3</number>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.700000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QGroupBox" name="m_CsaBox">
	- <property name="title">
	- <string>CSA-QBALL Parameters</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_12">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="2" column="1">
	- <widget class="QFrame" name="frame_8">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_13">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>0</number>
	- </property>
	- </layout>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_ShOrderCsa">
	- <property name="minimum">
	- <number>2</number>
	- </property>
	- <property name="maximum">
	- <number>12</number>
	- </property>
	- <property name="singleStep">
	- <number>2</number>
	- </property>
	- <property name="value">
	- <number>6</number>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_23">
	- <property name="text">
	- <string>Lambda:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_22">
	- <property name="text">
	- <string>SH Order:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QDoubleSpinBox" name="m_LambdaCsa">
	- <property name="decimals">
	- <number>4</number>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.001000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.006000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QGroupBox" name="m_CsdBox">
	- <property name="title">
	- <string>Constrained Spherical Deconvolution Parameters</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_9">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_16">
	- <property name="text">
	- <string>SH Order:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QFrame" name="frame_7">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_11">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>0</number>
	- </property>
	- </layout>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_ShOrderCsd">
	- <property name="minimum">
	- <number>2</number>
	- </property>
	- <property name="maximum">
	- <number>12</number>
	- </property>
	- <property name="singleStep">
	- <number>2</number>
	- </property>
	- <property name="value">
	- <number>6</number>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label_18">
	- <property name="text">
	- <string>FA Threshold:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QDoubleSpinBox" name="m_FaThresholdCsd">
	- <property name="decimals">
	- <number>3</number>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.700000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="6" column="0">
	- <widget class="QGroupBox" name="groupBox">
	- <property name="title">
	- <string>Extract Peaks</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_4">
	- <item row="2" column="1">
	- <widget class="QSpinBox" name="m_NumPeaks">
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>100</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>3</number>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QLabel" name="label_28">
	- <property name="text">
	- <string>Relative Threshold:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QLabel" name="label_27">
	- <property name="text">
	- <string>Min. Separation Angle:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QCheckBox" name="m_DoCalculatePeaks">
	- <property name="text">
	- <string/>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="1">
	- <widget class="QSpinBox" name="m_SepAngle">
	- <property name="minimum">
	- <number>0</number>
	- </property>
	- <property name="maximum">
	- <number>90</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>15</number>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="1">
	- <widget class="QDoubleSpinBox" name="m_RelativeThreshold">
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.400000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_29">
	- <property name="text">
	- <string>Calculate Peaks:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label_26">
	- <property name="text">
	- <string>Max. Peaks:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_30">
	- <property name="text">
	- <string>Normalize Peaks:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QCheckBox" name="m_NormalizePeaks">
	- <property name="text">
	- <string/>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <customwidgets>
	- <customwidget>
	- <class>QmitkDataStorageComboBox</class>
	- <extends>QComboBox</extends>
	- <header location="global">QmitkDataStorageComboBox.h</header>
	- </customwidget>
	- <customwidget>
	- <class>QmitkDataStorageComboBoxWithSelectNone</class>
	- <extends>QComboBox</extends>
	- <header>QmitkDataStorageComboBoxWithSelectNone.h</header>
	- </customwidget>
	- </customwidgets>
	- <resources/>
	- <connections/>
	-</ui>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkTractSegView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkTractSegView.cpp
	deleted file mode 100644
	index dc3d54808d..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkTractSegView.cpp
	+++ /dev/null
	@@ -1,355 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-// Blueberry
	-#include <berryISelectionService.h>
	-#include <berryIWorkbenchWindow.h>
	-
	-// Qmitk
	-#include "QmitkTractSegView.h"
	-
	-#include <mitkNodePredicateDataType.h>
	-#include <mitkIPythonService.h>
	-#include <boost/lexical_cast.hpp>
	-#include <QFile>
	-#include <QMessageBox>
	-#include <usModuleContext.h>
	-#include <usGetModuleContext.h>
	-#include <mitkPeakImage.h>
	-#include <mitkImageCast.h>
	-#include <mitkImageToItk.h>
	-#include <mitkITKImageImport.h>
	-#include <itkFourDToVectorImageFilter.h>
	-#include <itkVectorImageToFourDImageFilter.h>
	-#include <itkSplitVectorImageFilter.h>
	-#include <itkFlipPeaksFilter.h>
	-#include <mitkLookupTable.h>
	-#include <mitkLookupTableProperty.h>
	-#include <mitkLevelWindow.h>
	-#include <mitkLevelWindowProperty.h>
	-
	-const std::string QmitkTractSegView::VIEW_ID = "org.mitk.views.tractseg";
	-
	-QmitkTractSegView::QmitkTractSegView()
	- : QmitkAbstractView()
	- , m_Controls( 0 )
	-{
	-
	-}
	-
	-// Destructor
	-QmitkTractSegView::~QmitkTractSegView()
	-{
	-}
	-
	-void QmitkTractSegView::CreateQtPartControl( QWidget *parent )
	-{
	- // build up qt view, unless already done
	- if ( !m_Controls )
	- {
	- // create GUI widgets from the Qt Designer's .ui file
	- m_Controls = new Ui::QmitkTractSegViewControls;
	- m_Controls->setupUi( parent );
	- connect( m_Controls->m_ImageBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGUI()) );
	- connect( m_Controls->m_StartButton, SIGNAL(clicked()), this, SLOT(Start()) );
	- connect( m_Controls->m_OutputBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGUI()) );
	- connect( m_Controls->m_ModeBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGUI()) );
	- this->m_Parent = parent;
	-
	- m_Controls->m_ImageBox->SetDataStorage(this->GetDataStorage());
	- mitk::NodePredicateDataType::Pointer isDwi = mitk::NodePredicateDataType::New("PeakImage");
	- m_Controls->m_ImageBox->SetPredicate( isDwi );
	-
	- UpdateGUI();
	- }
	-}
	-
	-void QmitkTractSegView::OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList<mitk::DataNode::Pointer>& )
	-{
	-}
	-
	-void QmitkTractSegView::UpdateGUI()
	-{
	- if (m_Controls->m_ImageBox->GetSelectedNode().IsNotNull())
	- m_Controls->m_StartButton->setEnabled(true);
	- else
	- m_Controls->m_StartButton->setEnabled(false);
	-
	- m_Controls->m_CollapseBox->setVisible(true);
	- m_Controls->m_thresholdFrame->setVisible(true);
	-
	- if (m_Controls->m_OutputBox->currentIndex()==3 \|\| m_Controls->m_OutputBox->currentIndex()==1)
	- m_Controls->m_thresholdFrame->setVisible(false);
	-
	- if (m_Controls->m_OutputBox->currentIndex()>0)
	- m_Controls->m_CollapseBox->setVisible(false);
	-}
	-
	-void QmitkTractSegView::SetFocus()
	-{
	- UpdateGUI();
	- m_Controls->m_StartButton->setFocus();
	-}
	-
	-void QmitkTractSegView::Start()
	-{
	- std::locale::global(std::locale::classic());
	- mitk::DataNode::Pointer node = m_Controls->m_ImageBox->GetSelectedNode();
	- mitk::Image::Pointer input_image = dynamic_cast<mitk::Image*>(node->GetData());
	-
	- // get python script as string
	- QString data;
	- QString fileName(":/QmitkDiffusionImaging/tractseg.py");
	- QFile file(fileName);
	- if(!file.open(QIODevice::ReadOnly)) {
	- qDebug()<<"filenot opened"<<endl;
	- }
	- else
	- {
	- qDebug()<<"file opened"<<endl;
	- data = file.readAll();
	- }
	- file.close();
	-
	- us::ModuleContext* context = us::GetModuleContext();
	- us::ServiceReference<mitk::IPythonService> m_PythonServiceRef = context->GetServiceReference<mitk::IPythonService>();
	- mitk::IPythonService* m_PythonService = dynamic_cast<mitk::IPythonService*> ( context->GetService<mitk::IPythonService>(m_PythonServiceRef) );
	- mitk::IPythonService::ForceLoadModule();
	-
	- typedef mitk::ImageToItk< mitk::PeakImage::ItkPeakImageType > CasterType;
	- CasterType::Pointer caster = CasterType::New();
	- caster->SetInput(input_image);
	- caster->Update();
	- mitk::PeakImage::ItkPeakImageType::Pointer itk_peaks = caster->GetOutput();
	- if (itk_peaks->GetLargestPossibleRegion().GetSize()[3]!=9)
	- {
	- QMessageBox::warning(nullptr, "Error", "TractSeg only works with 3-peak images!", QMessageBox::Ok);
	- return;
	- }
	-
	- itk::FlipPeaksFilter< float >::Pointer flipper = itk::FlipPeaksFilter< float >::New();
	- flipper->SetInput(itk_peaks);
	- flipper->SetFlipX(false);
	- flipper->SetFlipY(false);
	- flipper->SetFlipZ(true);
	- flipper->Update();
	-
	- itk::FourDToVectorImageFilter< float >::Pointer converter = itk::FourDToVectorImageFilter< float >::New();
	- converter->SetInputImage(flipper->GetOutput());
	- converter->GenerateData();
	- mitk::Image::Pointer mitk_vec_img = mitk::GrabItkImageMemory( converter->GetOutputImage().GetPointer() );
	-
	- m_PythonService->CopyToPythonAsSimpleItkImage( mitk_vec_img, "in_image");
	-
	- m_PythonService->Execute("sx=" + boost::lexical_cast<std::string>(itk_peaks->GetLargestPossibleRegion().GetSize()[0]));
	- m_PythonService->Execute("sy=" + boost::lexical_cast<std::string>(itk_peaks->GetLargestPossibleRegion().GetSize()[1]));
	- m_PythonService->Execute("sz=" + boost::lexical_cast<std::string>(itk_peaks->GetLargestPossibleRegion().GetSize()[2]));
	-
	- if (m_PythonService->DoesVariableExist("segmentation"))
	- m_PythonService->Execute("del segmentation");
	-
	- if(m_Controls->m_ModeBox->currentIndex()==0)
	- m_PythonService->Execute("output_type=\"tract_segmentation\"");
	- else if(m_Controls->m_ModeBox->currentIndex()==1)
	- m_PythonService->Execute("output_type=\"endings_segmentation\"");
	-
	- if(m_Controls->m_OutputBox->currentIndex()==3)
	- m_PythonService->Execute("output_type=\"TOM\"");
	-
	-
	- if (m_Controls->m_CollapseBox->isChecked() && m_Controls->m_OutputBox->currentIndex()==0)
	- m_PythonService->Execute("collapse=True");
	- else
	- m_PythonService->Execute("collapse=False");
	-
	- m_PythonService->Execute("get_probs=False");
	- m_PythonService->Execute("dropout_sampling=False");
	-
	- if (m_Controls->m_OutputBox->currentIndex()==1)
	- m_PythonService->Execute("get_probs=True");
	- else if (m_Controls->m_OutputBox->currentIndex()==2)
	- m_PythonService->Execute("dropout_sampling=True");
	-
	- m_PythonService->Execute("threshold=" + boost::lexical_cast<std::string>(m_Controls->m_SegThresholdBox->value()));
	-
	- m_PythonService->Execute("verbose=False");
	- m_PythonService->Execute(data.toStdString(), mitk::IPythonService::MULTI_LINE_COMMAND);
	-
	- // clean up after running script (better way than deleting individual variables?)
	- if(m_PythonService->DoesVariableExist("in_image"))
	- m_PythonService->Execute("del in_image");
	- if(m_PythonService->DoesVariableExist("collapse"))
	- m_PythonService->Execute("del collapse");
	-
	- // check for errors
	- if(!m_PythonService->GetVariable("error_string").empty())
	- {
	- QMessageBox::warning(nullptr, "Error", QString(m_PythonService->GetVariable("error_string").c_str()), QMessageBox::Ok);
	- return;
	- }
	-
	- std::vector<std::string> small_name_list = {"AF_left", "AF_right", "CA", "CST_left", "CST_right", "CG_left", "CG_right",
	- "ICP_left", "ICP_right", "MCP", "SCP_left", "SCP_right", "ILF_left", "ILF_right",
	- "IFO_left", "IFO_right", "OR_left", "OR_right", "UF_left", "UF_right"};
	-
	- std::vector<std::string> large_name_list = {"AF_left", "AF_right", "ATR_left", "ATR_right", "CA", "CC_1", "CC_2", "CC_3", "CC_4", "CC_5",
	- "CC_6", "CC_7","CG_left","CG_right","CST_left","CST_right" ,"MLF_left","MLF_right","FPT_left"
	- ,"FPT_right","FX_left","FX_right","ICP_left","ICP_right","IFO_left","IFO_right"
	- ,"ILF_left" ,"ILF_right","MCP","OR_left","OR_right","POPT_left","POPT_right"
	- ,"SCP_left","SCP_right","SLF_I_left","SLF_I_right","SLF_II_left","SLF_II_right"
	- ,"SLF_III_left","SLF_III_right","STR_left","STR_right","UF_left","UF_right"
	- ,"CC","T_PREF_left","T_PREF_right","T_PREM_left","T_PREM_right","T_PREC_left"
	- ,"T_PREC_right","T_POSTC_left","T_POSTC_right","T_PAR_left","T_PAR_right","T_OCC_left"
	- ,"T_OCC_right","ST_FO_left","ST_FO_right","ST_PREF_left","ST_PREF_right","ST_PREM_left"
	- ,"ST_PREM_right","ST_PREC_left","ST_PREC_right","ST_POSTC_left","ST_POSTC_right"
	- ,"ST_PAR_left","ST_PAR_right","ST_OCC_left","ST_OCC_right"};
	-
	- if (m_PythonService->DoesVariableExist("segmentation"))
	- {
	- mitk::Image::Pointer out_image = m_PythonService->CopySimpleItkImageFromPython("segmentation");
	-
	- if (!m_Controls->m_CollapseBox->isChecked() \|\| m_Controls->m_OutputBox->currentIndex()>0)
	- {
	- if (m_Controls->m_OutputBox->currentIndex()>0)
	- {
	- itk::VectorImage<float>::Pointer vectorImage = itk::VectorImage<float>::New();
	- mitk::CastToItkImage(out_image, vectorImage);
	- itk::SplitVectorImageFilter<float>::Pointer splitter = itk::SplitVectorImageFilter<float>::New();
	- splitter->SetInputImage(vectorImage);
	- splitter->GenerateData();
	- int c = 0;
	- for (auto itk_seg : splitter->GetOutputImages())
	- {
	- mitk::DataNode::Pointer seg = mitk::DataNode::New();
	- seg->SetData( mitk::GrabItkImageMemory(itk_seg) );
	- seg->SetName(large_name_list.at(c));
	-
	- mitk::LookupTable::Pointer lut = mitk::LookupTable::New();
	- lut->SetType( mitk::LookupTable::JET_TRANSPARENT );
	- mitk::LookupTableProperty::Pointer lut_prop = mitk::LookupTableProperty::New();
	- lut_prop->SetLookupTable( lut );
	- seg->SetProperty("LookupTable", lut_prop );
	- mitk::LevelWindow lw; lw.SetRangeMinMax(0.0,1.0);
	- seg->SetProperty( "levelwindow", mitk::LevelWindowProperty::New( lw ) );
	-
	- GetDataStorage()->Add(seg, node);
	- ++c;
	- }
	- }
	- else
	- {
	- itk::VectorImage<unsigned char>::Pointer vectorImage = itk::VectorImage<unsigned char>::New();
	- mitk::CastToItkImage(out_image, vectorImage);
	- itk::SplitVectorImageFilter<unsigned char>::Pointer splitter = itk::SplitVectorImageFilter<unsigned char>::New();
	- splitter->SetInputImage(vectorImage);
	- splitter->GenerateData();
	- int c = 0;
	- for (auto itk_seg : splitter->GetOutputImages())
	- {
	- mitk::DataNode::Pointer seg = mitk::DataNode::New();
	- seg->SetData( mitk::GrabItkImageMemory(itk_seg) );
	- if (m_Controls->m_ModeBox->currentIndex()==0)
	- {
	- seg->SetName(large_name_list.at(c));
	- seg->SetBoolProperty("binary", true);
	- }
	- else
	- {
	- mitk::LookupTable::Pointer lut = mitk::LookupTable::New();
	- lut->SetType( mitk::LookupTable::MULTILABEL );
	- mitk::LookupTableProperty::Pointer lut_prop = mitk::LookupTableProperty::New();
	- lut_prop->SetLookupTable( lut );
	- seg->SetProperty("LookupTable", lut_prop );
	- mitk::LevelWindow lw; lw.SetRangeMinMax(0,2);
	- seg->SetProperty( "levelwindow", mitk::LevelWindowProperty::New( lw ) );
	-
	- seg->SetName(large_name_list.at(c));
	- }
	- GetDataStorage()->Add(seg, node);
	- ++c;
	- }
	- }
	- }
	- else
	- {
	- mitk::DataNode::Pointer seg = mitk::DataNode::New();
	- seg->SetData(out_image);
	-
	- mitk::LevelWindow lw;
	- if (m_Controls->m_ModeBox->currentIndex()==0)
	- {
	- seg->SetName("TractLabels");
	- lw.SetRangeMinMax(0, 72);
	- }
	- else
	- {
	- seg->SetName("TractEndpointRegionLabels");
	- lw.SetRangeMinMax(0, 144);
	- }
	-
	- if (m_Controls->m_OutputBox->currentIndex()==0)
	- {
	- mitk::LookupTable::Pointer lut = mitk::LookupTable::New();
	- lut->SetType( mitk::LookupTable::MULTILABEL );
	- mitk::LookupTableProperty::Pointer lut_prop = mitk::LookupTableProperty::New();
	- lut_prop->SetLookupTable( lut );
	- seg->SetProperty("LookupTable", lut_prop );
	- seg->SetProperty( "levelwindow", mitk::LevelWindowProperty::New( lw ) );
	- }
	-
	- GetDataStorage()->Add(seg, node);
	- }
	-
	- m_PythonService->Execute("del segmentation");
	- }
	- else
	- {
	- for (int i=0; i<72; ++i)
	- if (m_PythonService->DoesVariableExist("tom" + boost::lexical_cast<std::string>(i)))
	- {
	- mitk::Image::Pointer out_image = m_PythonService->CopySimpleItkImageFromPython("tom" + boost::lexical_cast<std::string>(i));
	- itk::VectorImage<float>::Pointer vectorImage = itk::VectorImage<float>::New();
	- mitk::CastToItkImage(out_image, vectorImage);
	-
	- itk::VectorImageToFourDImageFilter< float >::Pointer converter = itk::VectorImageToFourDImageFilter< float >::New();
	- converter->SetInputImage(vectorImage);
	- converter->GenerateData();
	- mitk::PeakImage::ItkPeakImageType::Pointer itk_peaks = converter->GetOutputImage();
	-
	- itk::FlipPeaksFilter< float >::Pointer flipper = itk::FlipPeaksFilter< float >::New();
	- flipper->SetInput(itk_peaks);
	- flipper->SetFlipX(false);
	- flipper->SetFlipY(false);
	- flipper->SetFlipZ(true);
	- flipper->Update();
	- itk_peaks = flipper->GetOutput();
	-
	- mitk::Image::Pointer mitk_peaks = dynamic_cast<mitk::Image*>(mitk::PeakImage::New().GetPointer());
	- mitk::CastToMitkImage(itk_peaks, mitk_peaks);
	- mitk_peaks->SetVolume(itk_peaks->GetBufferPointer());
	-
	- mitk::DataNode::Pointer seg = mitk::DataNode::New();
	- seg->SetData( mitk_peaks );
	- if (!m_Controls->m_CollapseBox->isChecked())
	- seg->SetName(large_name_list.at(i) + "_TOM");
	- else
	- seg->SetName("Collapsed_TOM");
	- GetDataStorage()->Add(seg, node);
	- m_PythonService->Execute("del tom" + boost::lexical_cast<std::string>(i));
	- }
	- }
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkTractSegView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkTractSegView.h
	deleted file mode 100644
	index 3a8888d970..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkTractSegView.h
	+++ /dev/null
	@@ -1,65 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-
	-#include <berryISelectionListener.h>
	-#include <berryIStructuredSelection.h>
	-
	-#include <QmitkAbstractView.h>
	-#include "ui_QmitkTractSegViewControls.h"
	-
	-/*!
	-\brief
	-*/
	-class QmitkTractSegView : public QmitkAbstractView
	-{
	-
	- // this is needed for all Qt objects that should have a Qt meta-object
	- // (everything that derives from QObject and wants to have signal/slots)
	- Q_OBJECT
	-
	-public:
	-
	- static const std::string VIEW_ID;
	-
	- QmitkTractSegView();
	- virtual ~QmitkTractSegView();
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	- void SetFocus() override;
	-
	-protected slots:
	-
	- void Start();
	- void UpdateGUI(); ///< update button activity etc. dpending on current datamanager selection
	-
	-
	-protected:
	-
	- /// \brief called by QmitkAbstractView when DataManager's selection has changed
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- Ui::QmitkTractSegViewControls* m_Controls;
	-
	-private:
	-
	- void UpdateRegistrationStatus(); ///< update textual status display of the Registration process
	-
	- // the Qt parent of our GUI (NOT of this object)
	- QWidget* m_Parent;
	-
	-};
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkTractSegViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkTractSegViewControls.ui
	deleted file mode 100644
	index 1d701069b0..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkTractSegViewControls.ui
	+++ /dev/null
	@@ -1,233 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<ui version="4.0">
	- <class>QmitkTractSegViewControls</class>
	- <widget class="QWidget" name="QmitkTractSegViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>435</width>
	- <height>803</height>
	- </rect>
	- </property>
	- <property name="windowTitle">
	- <string>Form</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_2">
	- <property name="verticalSpacing">
	- <number>25</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QFrame" name="frame_2">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_3">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="2" column="0">
	- <widget class="QCheckBox" name="m_CollapseBox">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Collapse tracts into single 3D volume</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QFrame" name="frame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_2">
	- <property name="text">
	- <string>Mode:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_ImageBox"/>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label">
	- <property name="text">
	- <string>Input Peaks:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QComboBox" name="m_ModeBox">
	- <item>
	- <property name="text">
	- <string>Tracts</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Tract Endpoint Regions</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label_3">
	- <property name="text">
	- <string>Output:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QComboBox" name="m_OutputBox">
	- <item>
	- <property name="text">
	- <string>Segmentations</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Probability Maps</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Uncertainty Maps</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Tract Orientation Maps</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QFrame" name="m_thresholdFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_4">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="verticalSpacing">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_4">
	- <property name="text">
	- <string>Segmentation Threshold:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QDoubleSpinBox" name="m_SegThresholdBox">
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.500000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QCommandLinkButton" name="m_StartButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Start TractSeg</string>
	- </property>
	- </widget>
	- </item>
	- <item row="11" column="0">
	- <spacer name="verticalSpacer">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- </layout>
	- </widget>
	- <customwidgets>
	- <customwidget>
	- <class>QmitkDataStorageComboBox</class>
	- <extends>QComboBox</extends>
	- <header location="global">QmitkDataStorageComboBox.h</header>
	- </customwidget>
	- </customwidgets>
	- <resources/>
	- <connections/>
	-</ui>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/mitkPluginActivator.cpp
	deleted file mode 100644
	index 6d4bd857d3..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/mitkPluginActivator.cpp
	+++ /dev/null
	@@ -1,46 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkPluginActivator.h"
	-
	-#include "src/internal/QmitkBrainExtractionView.h"
	-#include "src/internal/QmitkDipyReconstructionsView.h"
	-#include "src/internal/QmitkTractSegView.h"
	-#include <usModuleInitialization.h>
	-
	-
	-ctkPluginContext* mitk::PluginActivator::m_Context = nullptr;
	-
	-US_INITIALIZE_MODULE
	-
	-ctkPluginContext* mitk::PluginActivator::GetContext()
	-{
	- return m_Context;
	-}
	-
	-void mitk::PluginActivator::start(ctkPluginContext* context)
	-{
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkBrainExtractionView, context)
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkDipyReconstructionsView, context)
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkTractSegView, context)
	- m_Context = context;
	-}
	-
	-void mitk::PluginActivator::stop(ctkPluginContext* context)
	-{
	- Q_UNUSED(context)
	- m_Context = nullptr;
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/mitkPluginActivator.h b/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/mitkPluginActivator.h
	deleted file mode 100644
	index 2867726397..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/mitkPluginActivator.h
	+++ /dev/null
	@@ -1,40 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef MITKPLUGINACTIVATOR_H
	-#define MITKPLUGINACTIVATOR_H
	-
	-#include <ctkPluginActivator.h>
	-
	-namespace mitk
	-{
	- class PluginActivator : public QObject, public ctkPluginActivator
	- {
	- Q_OBJECT
	- Q_PLUGIN_METADATA(IID "org.mitk.gui.qt.diffusionimaging.preprocessing")
	- Q_INTERFACES(ctkPluginActivator)
	-
	- public:
	- static ctkPluginContext* GetContext();
	-
	- void start(ctkPluginContext* context) override;
	- void stop(ctkPluginContext* context) override;
	-
	- private:
	- static ctkPluginContext* m_Context;
	- };
	-}
	-
	-#endif
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/CMakeLists.txt
	deleted file mode 100644
	index 5f0e2f510b..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/CMakeLists.txt
	+++ /dev/null
	@@ -1,10 +0,0 @@
	-# The project name must correspond to the directory name of your plug-in
	-# and must not contain periods.
	-project(org_mitk_gui_qt_diffusionimaging_reconstruction)
	-
	-mitk_create_plugin(
	- SUBPROJECTS MITK-DTI
	- EXPORT_DIRECTIVE DIFFUSIONIMAGING_RECONSTRUCTION_EXPORT
	- EXPORTED_INCLUDE_SUFFIXES src
	- MODULE_DEPENDS MitkQtWidgetsExt MitkQuantification
	-)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/QmitkDiffusionImagingQuantificationPage.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/QmitkDiffusionImagingQuantificationPage.dox
	deleted file mode 100644
	index 831dc92e9d..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/QmitkDiffusionImagingQuantificationPage.dox
	+++ /dev/null
	@@ -1,7 +0,0 @@
	-/**
	-
	-\page org_mitk_views_diffusionquantification Scalar Indices
	-
	-The scalar indices view allows the calculation of different scalar measures for raw diffusion-weighted images (MD, ADC), tensors (Fractional Anisotropy, Relative Anisotropy, Axial Diffusivity, Radial Diffusivity) or ODFs (Generalized Fractional Anisotropy).
	-
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/QmitkOdfDetailsViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/QmitkOdfDetailsViewUserManual.dox
	deleted file mode 100644
	index 79b928c33b..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/QmitkOdfDetailsViewUserManual.dox
	+++ /dev/null
	@@ -1,8 +0,0 @@
	-/**
	-\page org_mitk_views_odfdetails ODF Details
	-
	-This view provides detailed information about the orentation distribution function at the current crosshair position (if a Tensor/ODF image is selected). A visualization of the ODF as well as statistical information are displayed.
	-
	-\imageMacro{odfdetails.png,"The ODF Details View",10.01}
	-
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/QmitkQBallReconstructionViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/QmitkQBallReconstructionViewUserManual.dox
	deleted file mode 100644
	index c2da0829be..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/QmitkQBallReconstructionViewUserManual.dox
	+++ /dev/null
	@@ -1,21 +0,0 @@
	-/**
	-\page org_mitk_views_qballreconstruction Q-Ball Reconstruction
	-
	-The q-ball reonstruction view implements a variety of reconstruction methods. The different reconstruction methods are described in the following:
	-\li <b>Numerical:</b> The original, numerical q-ball reconstruction presented by Tuch et al. [5]
	-\li <b>Standard (SH):</b> Descoteaux's reconstruction based on spherical harmonic basis functions [6]
	-\li <b>Solid Angle (SH):</b> Aganj's reconstruction with solid angle consideration [7]
	-\li <b>ADC-profile only:</b> The ADC-profile reconstructed with spherical harmonic basis functions
	-\li <b>Raw signal only:</b> The raw signal reconstructed with spherical harmonic basis functions
	-
	-\imageMacro{qballs1.png,"The q-ball resonstruction view",9.99}
	-
	-B0 threshold works the same as in tensor reconstruction. The maximum l-level configures the size of the spherical harmonics basis. Larger l-values (e.g. l=8) allow higher levels of detail, lower levels are more stable against noise (e.g. l=4). Lambda is a regularisation parameter. Set it to 0 for no regularisation. lambda = 0.006 has proven to be a stable choice under various settings.
	-
	-\imageMacro{qballs2.png,"Advanced q-ball reconstruction settings",8.00}
	-
	-This is how a q-ball image should initially look after reconstruction. Standard q-balls feature a relatively low GFA and thus appear rather dark. Adjust the level-window to solve this.
	-
	-\imageMacro{qballs3.png,"q-ball image after reconstruction",16.00}
	-
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/QmitkTensorReconstructionViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/QmitkTensorReconstructionViewUserManual.dox
	deleted file mode 100644
	index 935571e18d..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/QmitkTensorReconstructionViewUserManual.dox
	+++ /dev/null
	@@ -1,18 +0,0 @@
	-/**
	-\page org_mitk_views_tensorreconstruction Tensor Reconstruction
	-
	-The tensor reconstruction view allows ITK based tensor reconstruction [3]. The advanced settings for ITK reconstruction let you configure a manual threshold on the non-diffusion weighted image. All voxels below this threshold will not be reconstructed and left blank. It is also possible to check for negative eigenvalues. The according voxels are also left blank.
	-
	-\imageMacro{tensor1.png,"ITK tensor reconstruction", 9.97}
	-
	-A few seconds (depending on the image size) after the reconstruction button is hit, a colored image should appear in the main window.
	-
	-\imageMacro{tensor4.png,"Tensor image after reconstruction",16.00}
	-
	-To assess the quality of the tensor fit it has been proposed to calculate the model residual [9]. This calculates the residual between the measured signal and the signal predicted by the model. Large residuals indicate an inadequacy of the model or the presence of artefacts in the signal intensity (noise, head motion, etc.). To use this option: Select a DWI dataset, estimate a tensor, select both the DWI node and the tensor node in the datamanager and press Residual Image Calculation. MITK Diffusion can show the residual for every voxel averaged over all volumes or (in the plot widget) summarized per volume or for every slice in every volume. Clicking in the widget where the residual is shown per slice will automatically let the cross-hair jump to that position in the DWI dataset. If Percentage of outliers is checked, the per volume plot will show the percentage of outliers per volume. Otherwise it will show the mean together with the first and third quantile of residuals. See [9] for more information.
	-
	-\imageMacro{residuals.png,"The residual widget",16.00}
	-
	-The view also allows the generation of artificial diffusion weighted or ODF images from the selected tensor image. The ODFs of the Q-Ball image are directly initialized from the tensor values and afterwards normalized. The diffusion weighted image is estimated using the l2-norm image of the tensor image as B0. The gradient images are afterwards generated using the standard tensor equation.
	-
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/ScalarIndicesGUI.png b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/ScalarIndicesGUI.png
	deleted file mode 100644
	index 3496bdb82a..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/ScalarIndicesGUI.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/odfdetails.png b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/odfdetails.png
	deleted file mode 100644
	index ff0586832c..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/odfdetails.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/qballs1.png b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/qballs1.png
	deleted file mode 100644
	index 51a7484688..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/qballs1.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/qballs2.png b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/qballs2.png
	deleted file mode 100644
	index 62a5f22018..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/qballs2.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/qballs3.png b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/qballs3.png
	deleted file mode 100644
	index fa42db11cb..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/qballs3.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/residuals.png b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/residuals.png
	deleted file mode 100644
	index 1cdc10a10e..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/residuals.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/tensor1.png b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/tensor1.png
	deleted file mode 100644
	index d3457ee469..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/tensor1.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/tensor4.png b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/tensor4.png
	deleted file mode 100644
	index ef434ed162..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/UserManual/tensor4.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/doxygen/modules.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/doxygen/modules.dox
	deleted file mode 100644
	index 27227615ca..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/documentation/doxygen/modules.dox
	+++ /dev/null
	@@ -1,16 +0,0 @@
	-/**
	- \defgroup org_mitk_gui_qt_diffusionimaging_reconstruction org.mitk.gui.qt.diffusionimaging.reconstruction
	- \ingroup MITKPlugins
	-
	- \brief This is the diffusionimaging.reconstruction plugin.
	-
	-*/
	-
	-/**
	- \defgroup org_mitk_gui_qt_diffusionimaging_reconstruction_internal Internal
	- \ingroup org_mitk_gui_qt_diffusionimaging_reconstruction
	-
	- \brief This subcategory includes the internal classes of the org.mitk.gui.qt.diffusionimaging.reconstruction plugin. Other
	- plugins must not rely on these classes. They contain implementation details and their interface
	- may change at any time. We mean it.
	-*/
	\ No newline at end of file
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/files.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/files.cmake
	deleted file mode 100644
	index a871219250..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/files.cmake
	+++ /dev/null
	@@ -1,66 +0,0 @@
	-set(SRC_CPP_FILES
	- QmitkODFDetailsWidget.cpp
	- QmitkODFRenderWidget.cpp
	- QmitkResidualAnalysisWidget.cpp
	- QmitkResidualViewWidget.cpp
	-)
	-
	-set(INTERNAL_CPP_FILES
	- mitkPluginActivator.cpp
	-
	- Perspectives/QmitkReconstructionPerspective.cpp
	- Perspectives/QmitkQuantificationPerspective.cpp
	-
	- QmitkQBallReconstructionView.cpp
	- QmitkDiffusionQuantificationView.cpp
	- QmitkTensorReconstructionView.cpp
	- QmitkODFDetailsView.cpp
	-)
	-
	-set(UI_FILES
	- src/internal/QmitkQBallReconstructionViewControls.ui
	- src/internal/QmitkDiffusionQuantificationViewControls.ui
	- src/internal/QmitkTensorReconstructionViewControls.ui
	- src/internal/QmitkODFDetailsViewControls.ui
	-)
	-
	-set(MOC_H_FILES
	- src/internal/mitkPluginActivator.h
	-
	- src/internal/Perspectives/QmitkReconstructionPerspective.h
	- src/internal/Perspectives/QmitkQuantificationPerspective.h
	-
	- src/internal/QmitkQBallReconstructionView.h
	- src/internal/QmitkDiffusionQuantificationView.h
	- src/internal/QmitkTensorReconstructionView.h
	- src/internal/QmitkODFDetailsView.h
	-
	- src/QmitkODFRenderWidget.h
	- src/QmitkODFDetailsWidget.h
	- src/QmitkResidualAnalysisWidget.h
	- src/QmitkResidualViewWidget.h
	-)
	-
	-set(CACHED_RESOURCE_FILES
	- plugin.xml
	-
	- resources/quantification.png
	- resources/OdfDetails.png
	- resources/tensor.png
	- resources/odf.png
	-)
	-
	-set(QRC_FILES
	-
	-)
	-
	-
	-set(CPP_FILES )
	-
	-foreach(file ${SRC_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/${file})
	-endforeach(file ${SRC_CPP_FILES})
	-
	-foreach(file ${INTERNAL_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/internal/${file})
	-endforeach(file ${INTERNAL_CPP_FILES})
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/manifest_headers.cmake
	deleted file mode 100644
	index 649136a2f4..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/manifest_headers.cmake
	+++ /dev/null
	@@ -1,5 +0,0 @@
	-set(Plugin-Name "MITK Reconstruction")
	-set(Plugin-Version "1.0.0")
	-set(Plugin-Vendor "DKFZ, Medical and Biological Informatics")
	-set(Plugin-ContactAddress "http://www.mitk.org")
	-set(Require-Plugin org.mitk.gui.qt.diffusionimaging org.mitk.gui.qt.common)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/plugin.xml b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/plugin.xml
	deleted file mode 100644
	index 4fae3638b9..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/plugin.xml
	+++ /dev/null
	@@ -1,112 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<?BlueBerry version="0.1"?>
	-<plugin>
	-
	- <extension point="org.blueberry.ui.views">
	-
	- <view id="org.mitk.views.qballreconstruction"
	- name="Q-Balls"
	- category="Signal modeling"
	- icon="resources/odf.png"
	- class="QmitkQBallReconstructionView">
	- <description>Q-Ball reconstruction view</description>
	- <keywordReference id="org.mitk.views.reconstruction.Keyword"/>
	- </view>
	-
	- <view id="org.mitk.views.diffusionquantification"
	- name="Diffusion Indices"
	- category="Quantification"
	- class="QmitkDiffusionQuantificationView"
	- icon="resources/quantification.png">
	- <description>Calculation of tensor, ODF and raw signal scalar maps.</description>
	- <keywordReference id="org.mitk.views.diffusionquantification.Keyword"/>
	- </view>
	-
	- <view id="org.mitk.views.tensorreconstruction"
	- name="Tensors"
	- category="Signal modeling"
	- icon="resources/tensor.png"
	- class="QmitkTensorReconstructionView">
	- <keywordReference id="org.mitk.views.reconstruction.Keyword"/>
	- </view>
	-
	- <view id="org.mitk.views.odfdetails"
	- name="ODF Details"
	- category="Quantification"
	- class="QmitkODFDetailsView"
	- icon="resources/OdfDetails.png">
	- <keywordReference id="org.mitk.views.odfdetails.Keyword"/>
	- </view>
	-
	- </extension>
	-
	- <extension point="org.blueberry.ui.keywords">
	-
	- <keyword label="signal" id="org.mitk.views.reconstruction.Keyword"/>
	- <keyword label="reconstruction" id="org.mitk.views.reconstruction.Keyword"/>
	- <keyword label="ball" id="org.mitk.views.reconstruction.Keyword"/>
	- <keyword label="diffusion" id="org.mitk.views.reconstruction.Keyword"/>
	- <keyword label="qball" id="org.mitk.views.reconstruction.Keyword"/>
	- <keyword label="q-ball" id="org.mitk.views.reconstruction.Keyword"/>
	- <keyword label="propagator" id="org.mitk.views.reconstruction.Keyword"/>
	- <keyword label="modeling" id="org.mitk.views.reconstruction.Keyword"/>
	- <keyword label="ODF" id="org.mitk.views.diffusionquantification.Keyword"/>
	- <keyword label="dODF" id="org.mitk.views.diffusionquantification.Keyword"/>
	-
	- <keyword label="signal" id="org.mitk.views.reconstruction.Keyword"/>
	- <keyword label="reconstruction" id="org.mitk.views.reconstruction.Keyword"/>
	- <keyword label="tensor" id="org.mitk.views.reconstruction.Keyword"/>
	- <keyword label="diffusion" id="org.mitk.views.reconstruction.Keyword"/>
	- <keyword label="second order" id="org.mitk.views.reconstruction.Keyword"/>
	- <keyword label="propagator" id="org.mitk.views.reconstruction.Keyword"/>
	- <keyword label="modeling" id="org.mitk.views.reconstruction.Keyword"/>
	- <keyword label="DTI" id="org.mitk.views.reconstruction.Keyword"/>
	-
	- <keyword label="ADC" id="org.mitk.views.diffusionquantification.Keyword"/>
	- <keyword label="GFA" id="org.mitk.views.diffusionquantification.Keyword"/>
	- <keyword label="RA" id="org.mitk.views.diffusionquantification.Keyword"/>
	- <keyword label="AD" id="org.mitk.views.diffusionquantification.Keyword"/>
	- <keyword label="RD" id="org.mitk.views.diffusionquantification.Keyword"/>
	- <keyword label="MD" id="org.mitk.views.diffusionquantification.Keyword"/>
	- <keyword label="anisotropy" id="org.mitk.views.diffusionquantification.Keyword"/>
	- <keyword label="fractional" id="org.mitk.views.diffusionquantification.Keyword"/>
	- <keyword label="radial" id="org.mitk.views.diffusionquantification.Keyword"/>
	- <keyword label="axial" id="org.mitk.views.diffusionquantification.Keyword"/>
	- <keyword label="diffusivity" id="org.mitk.views.diffusionquantification.Keyword"/>
	- <keyword label="mean" id="org.mitk.views.diffusionquantification.Keyword"/>
	- <keyword label="generalized" id="org.mitk.views.diffusionquantification.Keyword"/>
	- <keyword label="derived" id="org.mitk.views.diffusionquantification.Keyword"/>
	- <keyword label="index" id="org.mitk.views.diffusionquantification.Keyword"/>
	- <keyword label="indices" id="org.mitk.views.diffusionquantification.Keyword"/>
	- <keyword label="diffusion" id="org.mitk.views.diffusionquantification.Keyword"/>
	-
	- <keyword label="ODF" id="org.mitk.views.odfdetails.Keyword"/>
	- <keyword label="dODF" id="org.mitk.views.odfdetails.Keyword"/>
	- <keyword label="fODF" id="org.mitk.views.odfdetails.Keyword"/>
	- <keyword label="FOD" id="org.mitk.views.odfdetails.Keyword"/>
	- <keyword label="statistics" id="org.mitk.views.odfdetails.Keyword"/>
	- <keyword label="values" id="org.mitk.views.odfdetails.Keyword"/>
	- <keyword label="shape" id="org.mitk.views.odfdetails.Keyword"/>
	-
	- </extension>
	-
	-
	- <extension point="org.blueberry.ui.perspectives">
	-
	- <perspective id="org.mitk.perspectives.reconstruction1"
	- name="ODF Reconstruction/Signal Modelling"
	- class="QmitkReconstructionPerspective"
	- icon="resources/odf.png">
	- <keywordReference id="org.mitk.views.reconstruction.Keyword"/>
	- </perspective>
	-
	- <perspective id="org.mitk.perspectives.quantification"
	- name="Diffusion Indices"
	- class="QmitkQuantificationPerspective"
	- icon="resources/quantification.png">
	- <keywordReference id="org.mitk.views.diffusionquantification.Keyword"/>
	- </perspective>
	-
	- </extension>
	-
	-</plugin>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/resources/OdfDetails.png b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/resources/OdfDetails.png
	deleted file mode 100644
	index 7792adbe4f..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/resources/OdfDetails.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/resources/odf.png b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/resources/odf.png
	deleted file mode 100644
	index d99423e16e..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/resources/odf.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/resources/quantification.png b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/resources/quantification.png
	deleted file mode 100644
	index 0b05b683ee..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/resources/quantification.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/resources/tensor.png b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/resources/tensor.png
	deleted file mode 100644
	index 22c5433a60..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/resources/tensor.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/QmitkODFDetailsWidget.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/QmitkODFDetailsWidget.cpp
	deleted file mode 100644
	index 333567d9bd..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/QmitkODFDetailsWidget.cpp
	+++ /dev/null
	@@ -1,39 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkODFDetailsWidget.h"
	-
	-#include <qwt_scale_engine.h>
	-
	-QmitkODFDetailsWidget::QmitkODFDetailsWidget( QWidget * parent )
	- : QmitkPlotWidget(parent)
	-{
	- QFrame* canvas = qobject_cast<QFrame*>(m_Plot->canvas());
	- if (canvas)
	- {
	- canvas->setLineWidth(0);
	- canvas->setContentsMargins(0,0,0,0);
	- }
	-
	- auto scale = new QwtLinearScaleEngine();
	- m_Plot->setAxisScaleEngine(0, scale);
	-
	- m_Plot->setAxisScale ( 0, -0.5, 0.5 );
	-}
	-
	-QmitkODFDetailsWidget::~QmitkODFDetailsWidget()
	-{
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/QmitkODFDetailsWidget.h b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/QmitkODFDetailsWidget.h
	deleted file mode 100644
	index 07f8606d01..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/QmitkODFDetailsWidget.h
	+++ /dev/null
	@@ -1,74 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef QmitkODFDetailsWidget_H_
	-#define QmitkODFDetailsWidget_H_
	-
	-#include "QmitkPlotWidget.h"
	-#include <org_mitk_gui_qt_diffusionimaging_reconstruction_Export.h>
	-#include <itkOrientationDistributionFunction.h>
	-
	-
	-/**
	- * \brief Widget for displaying image histograms based on the vtkQtChart
	- * framework
	- */
	-class DIFFUSIONIMAGING_RECONSTRUCTION_EXPORT QmitkODFDetailsWidget : public QmitkPlotWidget
	-{
	-Q_OBJECT
	-
	-public:
	-
	- template< unsigned int ODF_SIZE=ODF_SAMPLING_SIZE >
	- void SetParameters( itk::OrientationDistributionFunction<float, ODF_SIZE> odf )
	- {
	- this->Clear();
	-
	- std::vector<double> xVals;
	- std::vector<double> yVals;
	- double max = itk::NumericTraits<double>::NonpositiveMin();
	- double min = itk::NumericTraits<double>::max();
	-
	- for (unsigned int i=0; i<ODF_SIZE; i++){
	- xVals.push_back(i);
	- yVals.push_back(odf[i]);
	- if (odf[i]>max)
	- max = odf[i];
	- if (odf[i]<min)
	- min = odf[i];
	- }
	-
	- if(min>0)
	- m_Plot->setAxisScale ( 0, 0, max );
	- else
	- m_Plot->setAxisScale ( 0, min, max );
	-
	- auto curveId = this->InsertCurve( "ODF Values" );
	- this->SetCurveData( curveId, xVals, yVals );
	- this->SetCurvePen( curveId, QPen(Qt::blue, 0.5, Qt::SolidLine, Qt::RoundCap, Qt::RoundJoin) );
	- this->Replot();
	- }
	-
	- QmitkODFDetailsWidget( QWidget * /parent = 0 /);
	- virtual ~QmitkODFDetailsWidget();
	-
	- std::vector<double> m_Vals;
	-
	-private:
	-
	-};
	-
	-#endif /* QmitkODFDetailsWidget_H_ */
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/QmitkODFRenderWidget.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/QmitkODFRenderWidget.cpp
	deleted file mode 100644
	index 9d5a0a6b5d..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/QmitkODFRenderWidget.cpp
	+++ /dev/null
	@@ -1,44 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkODFRenderWidget.h"
	-#include <mitkLookupTable.h>
	-#include <mitkLookupTableProperty.h>
	-#include <vtkSmartPointer.h>
	-#include <mitkPlaneGeometry.h>
	-
	-QmitkODFRenderWidget::QmitkODFRenderWidget(QWidget* parent, Qt::WindowFlags f): QWidget(parent, f)
	-{
	- //create Layouts
	- QmitkODFRenderWidgetLayout = new QHBoxLayout( this );
	-
	- //Set Layout to widget
	- this->setLayout(QmitkODFRenderWidgetLayout);
	-
	- //Create RenderWindow
	- m_RenderWindow = new QmitkRenderWindow(this, "odf render widget");
	- m_RenderWindow->setMaximumSize(300,300);
	- m_RenderWindow->GetRenderer()->SetMapperID( mitk::BaseRenderer::Standard3D );
	-
	- //m_RenderWindow->SetLayoutIndex( 3 );
	- QmitkODFRenderWidgetLayout->addWidget( m_RenderWindow );
	-}
	-
	-
	-QmitkODFRenderWidget::~QmitkODFRenderWidget()
	-{
	-}
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/QmitkODFRenderWidget.h b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/QmitkODFRenderWidget.h
	deleted file mode 100644
	index 31c2ec4328..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/QmitkODFRenderWidget.h
	+++ /dev/null
	@@ -1,168 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef QmitkODFRenderWidget_H_
	-#define QmitkODFRenderWidget_H_
	-
	-
	-#include <org_mitk_gui_qt_diffusionimaging_reconstruction_Export.h>
	-
	-#include <QWidget>
	-#include <QmitkRenderWindow.h>
	-#include <QBoxLayout>
	-#include <vtkPolyData.h>
	-#include <mitkSurface.h>
	-#include <mitkDataNode.h>
	-#include <itkOrientationDistributionFunction.h>
	-#include <mitkStandaloneDataStorage.h>
	-#include <vtkFloatArray.h>
	-#include <vtkPointData.h>
	-#include <vtkLookupTable.h>
	-#include <vtkDoubleArray.h>
	-#include <vtkCellData.h>
	-#include <vtkSphereSource.h>
	-#include <vtkPolyDataMapper.h>
	-#include <vtkCamera.h>
	-#include <mitkLookupTable.h>
	-#include <mitkLookupTableProperty.h>
	-
	-class DIFFUSIONIMAGING_RECONSTRUCTION_EXPORT QmitkODFRenderWidget : public QWidget
	-{
	- Q_OBJECT
	-
	-public:
	-
	- QmitkODFRenderWidget( QWidget* parent = nullptr, Qt::WindowFlags f = nullptr );
	- virtual ~QmitkODFRenderWidget();
	-
	- template<unsigned int ODF_SIZE=ODF_SAMPLING_SIZE>
	- void GenerateODF( itk::OrientationDistributionFunction<float, ODF_SIZE> odf, int normalization, bool dir_color)
	- {
	- try
	- {
	- switch(normalization)
	- {
	- case 0:
	- odf = odf.MinMaxNormalize();
	- break;
	- case 1:
	- odf = odf.MaxNormalize();
	- break;
	- case 2:
	- odf = odf.MaxNormalize();
	- break;
	- default:
	- odf = odf.MinMaxNormalize();
	- }
	-
	- m_Surface = mitk::Surface::New();
	- m_ds = mitk::StandaloneDataStorage::New();
	- m_Node = mitk::DataNode::New();
	-
	- vtkPolyData* m_TemplateOdf = itk::OrientationDistributionFunction<float,ODF_SIZE>::GetBaseMesh();
	-
	- vtkPolyData *polyData = vtkPolyData::New();
	- vtkPoints *points = vtkPoints::New();
	- vtkFloatArray *scalars = vtkFloatArray::New();
	-
	- for (unsigned int i=0; i<ODF_SIZE; i++){
	- double p[3];
	- m_TemplateOdf->GetPoints()->GetPoint(i,p);
	- double val = odf[i];
	-
	- p[0] *= val;
	- p[1] *= val;
	- p[2] *= val;
	- points->InsertPoint(i,p);
	-
	- scalars->InsertTuple1(i, 1-val);
	- }
	-
	- polyData->SetPoints(points);
	- vtkCellArray* polys = m_TemplateOdf->GetPolys();
	- polyData->SetPolys(polys);
	- polyData->GetPointData()->SetScalars(scalars);
	-
	- polys->Delete();
	- scalars->Delete();
	- points->Delete();
	-
	- m_Surface->SetVtkPolyData(polyData);
	- m_Node->SetData(m_Surface);
	-
	- mitk::LookupTable::Pointer mitkLut = mitk::LookupTable::New();
	-
	- // assign an empty vtk lookup table to the odf renderer, it is the same
	- // the ODF 2D Mapper has
	- vtkSmartPointer<vtkLookupTable> lut = vtkSmartPointer<vtkLookupTable>::New();
	- mitkLut->SetVtkLookupTable( lut );
	-
	- mitk::LookupTableProperty::Pointer mitkLutProp = mitk::LookupTableProperty::New();
	- mitkLutProp->SetLookupTable(mitkLut);
	- m_Node->SetProperty( "LookupTable", mitkLutProp );
	-
	- m_Node->SetProperty("scalar visibility", mitk::BoolProperty::New(true));
	- m_Node->SetProperty("color mode", mitk::BoolProperty::New(true));
	- m_Node->SetProperty("material.specularCoefficient", mitk::FloatProperty::New(0.5));
	-
	- if (dir_color)
	- {
	- m_Node->SetProperty("scalar visibility", mitk::BoolProperty::New(false));
	- m_Node->SetProperty("color mode", mitk::BoolProperty::New(false));
	- vnl_vector_fixed<double,3> d = odf.GetPrincipalDiffusionDirection();
	- mitk::Color c;
	- c.SetRed(fabs(static_cast<float>(d[0])));
	- c.SetGreen(fabs(static_cast<float>(d[1])));
	- c.SetBlue(fabs(static_cast<float>(d[2])));
	- m_Node->SetColor(c);
	- }
	-
	- m_ds->Add(m_Node);
	-
	- m_RenderWindow->GetRenderer()->SetDataStorage( m_ds );
	-
	- // adjust camera to current plane rotation
	- mitk::PlaneGeometry::ConstPointer worldPlaneGeometry = mitk::BaseRenderer::GetInstance(m_RenderWindow->GetVtkRenderWindow())->GetCurrentWorldPlaneGeometry();
	- mitk::Vector3D normal = worldPlaneGeometry->GetNormal();
	- mitk::Vector3D up = worldPlaneGeometry->GetAxisVector(1);
	- normal.Normalize();
	- up.Normalize();
	-
	- vtkSmartPointer<vtkCamera> cam = vtkSmartPointer<vtkCamera>::New();
	- const double camPos[3] = {normal[0],normal[1],normal[2]};
	- const double camUp[3] = {up[0],up[1],up[2]};
	- cam->SetPosition(camPos);
	- cam->SetViewUp(camUp);
	- cam->SetParallelProjection(1);
	- m_RenderWindow->GetRenderer()->GetVtkRenderer()->SetActiveCamera(cam);
	- m_RenderWindow->update();
	- }
	- catch (...)
	- {
	-
	- }
	- }
	-
	-protected:
	-
	- QHBoxLayout* QmitkODFRenderWidgetLayout;
	- QmitkRenderWindow* m_RenderWindow;
	-
	- mitk::Surface::Pointer m_Surface;
	- mitk::StandaloneDataStorage::Pointer m_ds;
	- mitk::DataNode::Pointer m_Node;
	-};
	-#endif /QmitkODFRenderWidget_H_/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/QmitkResidualAnalysisWidget.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/QmitkResidualAnalysisWidget.cpp
	deleted file mode 100644
	index 2b3e73e909..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/QmitkResidualAnalysisWidget.cpp
	+++ /dev/null
	@@ -1,117 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkResidualAnalysisWidget.h"
	-
	-#include <QPen>
	-
	-#include <qwt_legend.h>
	-#include <qwt_plot_picker.h>
	-#include <qwt_picker_machine.h>
	-
	-
	-QmitkResidualAnalysisWidget::QmitkResidualAnalysisWidget( QWidget * parent )
	- : QmitkPlotWidget(parent)
	-{
	- m_PlotPicker = new QwtPlotPicker(m_Plot->canvas());
	- m_PlotPicker->setStateMachine(new QwtPickerDragPointMachine());
	- m_PlotPicker->setTrackerMode(QwtPicker::ActiveOnly);
	-}
	-
	-
	-
	-QmitkResidualAnalysisWidget::~QmitkResidualAnalysisWidget()
	-{
	- delete m_PlotPicker;
	-}
	-
	-
	-void QmitkResidualAnalysisWidget::DrawMeans()
	-{
	- this->Clear();
	- this->SetPlotTitle("mean residual per volume");
	- QPen pen( Qt::SolidLine );
	- pen.setWidth(1);
	-
	-
	- // Create values for x-axis
	- std::vector<double> xAxis;
	- for(unsigned int i=0; i<m_Means.size(); ++i)
	- {
	- xAxis.push_back((double)i);
	- }
	-
	- pen.setColor(Qt::black);
	- int curveId = this->InsertCurve( "Mean" );
	- this->SetCurveData( curveId, xAxis, m_Means );
	- this->SetCurvePen( curveId, pen );
	- this->SetCurveStyle( curveId, QwtPlotCurve::Dots);
	-
	- pen.setColor(Qt::blue);
	- curveId = this->InsertCurve( "Q1" );
	- this->SetCurveData( curveId, xAxis, m_Q1 );
	- this->SetCurvePen( curveId, pen );
	- this->SetCurveStyle( curveId, QwtPlotCurve::Dots);
	-
	- pen.setColor(Qt::red);
	- curveId = this->InsertCurve( "Q3" );
	- this->SetCurveData( curveId, xAxis, m_Q3 );
	- this->SetCurvePen( curveId, pen );
	- this->SetCurveStyle( curveId, QwtPlotCurve::Dots);
	-
	-
	- this->m_Plot->setAxisTitle(0, "Residual");
	- this->m_Plot->setAxisTitle(3, "DWI Volume");
	-
	-
	- auto legend = new QwtLegend;
	- this->SetLegend(legend, QwtPlot::RightLegend, 0.5);
	-
	- this->Replot();
	-
	-}
	-
	-void QmitkResidualAnalysisWidget::DrawPercentagesOfOutliers()
	-{
	- this->Clear();
	-
	-
	- this->SetPlotTitle("Percentage of outliers");
	- QPen pen( Qt::SolidLine );
	- pen.setWidth(1);
	-
	-
	- // Create values for x-axis
	- std::vector<double> xAxis;
	- for(unsigned int i=0; i<m_PercentagesOfOutliers.size(); ++i)
	- {
	- xAxis.push_back((double)i);
	- }
	-
	- pen.setColor(Qt::black);
	- int curveId = this->InsertCurve( "Outliers" );
	- this->SetCurveData( curveId, xAxis, m_PercentagesOfOutliers );
	- this->SetCurvePen( curveId, pen );
	- //this->SetCurveStyle( curveId, QwtPlotCurve::Fitted);
	-
	- this->m_Plot->setAxisTitle(0, "Percentage of outliers");
	- this->m_Plot->setAxisTitle(3, "DWI Volume");
	-
	- auto legend = new QwtLegend;
	- this->SetLegend(legend, QwtPlot::RightLegend, 0.5);
	-
	- this->Replot();
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/QmitkResidualAnalysisWidget.h b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/QmitkResidualAnalysisWidget.h
	deleted file mode 100644
	index 57858d985f..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/QmitkResidualAnalysisWidget.h
	+++ /dev/null
	@@ -1,84 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef QmitkResidualAnalysisWidget_H_
	-#define QmitkResidualAnalysisWidget_H_
	-
	-#include "QmitkPlotWidget.h"
	-
	-#include <org_mitk_gui_qt_diffusionimaging_reconstruction_Export.h>
	-
	-class QwtPlotPicker;
	-
	-/**
	- * \brief Widget for displaying boxplots
	- * framework
	- */
	-class DIFFUSIONIMAGING_RECONSTRUCTION_EXPORT QmitkResidualAnalysisWidget : public QmitkPlotWidget
	-{
	-
	-Q_OBJECT
	-
	-public:
	-
	-
	- QmitkResidualAnalysisWidget( QWidget * parent);
	- virtual ~QmitkResidualAnalysisWidget();
	-
	-
	-
	-
	- QwtPlot* GetPlot()
	- {
	- return m_Plot;
	- }
	-
	- QwtPlotPicker* m_PlotPicker;
	-
	-
	- void SetMeans(std::vector< double > means)
	- {
	- m_Means = means;
	- }
	-
	- void SetQ1(std::vector< double > q1)
	- {
	- m_Q1 = q1;
	- }
	-
	- void SetQ3(std::vector< double > q3)
	- {
	- m_Q3 = q3;
	- }
	-
	- void SetPercentagesOfOutliers(std::vector< double > perc)
	- {
	- m_PercentagesOfOutliers = perc;
	- }
	-
	-
	- void DrawMeans();
	- void DrawPercentagesOfOutliers();
	-
	-
	-protected:
	- std::vector< double > m_Means;
	- std::vector< double > m_Q1;
	- std::vector< double > m_Q3;
	- std::vector< double > m_PercentagesOfOutliers;
	-};
	-
	-#endif
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/QmitkResidualViewWidget.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/QmitkResidualViewWidget.cpp
	deleted file mode 100644
	index e2aa1cd6f0..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/QmitkResidualViewWidget.cpp
	+++ /dev/null
	@@ -1,170 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkResidualViewWidget.h"
	-#include <iostream>
	-#include <QToolTip>
	-
	-
	-QmitkResidualViewWidget::QmitkResidualViewWidget( QWidget * parent )
	- : QGraphicsView(parent)
	-{
	-
	-
	-}
	-
	-
	-QmitkResidualViewWidget::QmitkResidualViewWidget(QGraphicsScene scene, QWidget parent)
	- : QGraphicsView(scene, parent)
	-{
	-
	-}
	-
	-
	-void QmitkResidualViewWidget::mousePressEvent(QMouseEvent* event) {
	- // Panning
	- m_LastPanPoint = event->pos();
	- setCursor(Qt::ClosedHandCursor);
	-
	-
	-
	- QGraphicsItem *item = this->itemAt(event->pos());
	- if(item == m_ResidualPixmapItem)
	- {
	- QPointF sceneCoord(mapToScene(event->pos()));
	- QPointF imageCoord(item->mapFromParent(sceneCoord));
	-
	- int volume = (int)imageCoord.y();
	- int slice = (int)imageCoord.x();
	-
	- emit pointSelected(slice, volume);
	-
	- }
	-}
	-
	-
	-void QmitkResidualViewWidget::mouseReleaseEvent(QMouseEvent*) {
	- setCursor(Qt::OpenHandCursor);
	- m_LastPanPoint = QPoint();
	-}
	-
	-void QmitkResidualViewWidget::mouseMoveEvent(QMouseEvent *event)
	-{
	- if(!m_LastPanPoint.isNull()) {
	- QPointF delta = mapToScene(m_LastPanPoint) - mapToScene(event->pos());
	- m_LastPanPoint = event->pos();
	- SetCenter(m_CurrentCenterPoint + delta);
	- }
	-}
	-
	-void QmitkResidualViewWidget::wheelEvent(QWheelEvent *event)
	-{
	-
	- // Position of the mouse in scene coordinates
	- QPointF before(mapToScene(event->pos()));
	-
	- QPointF screenCenter = m_CurrentCenterPoint;
	-
	- double factor = 1.15;
	- if(event->delta() > 0)
	- {
	- scale(factor, factor);
	- }
	- else
	- {
	- scale(1.0 / factor, 1.0 / factor);
	- }
	-
	- //Get the position after scaling, in scene coords
	- QPointF after(mapToScene(event->pos()));
	-
	- //Get the offset of how the screen moved
	- QPointF offset = before - after;
	-
	- //Adjust to the new center for correct zooming
	- QPointF newCenter = screenCenter + offset;
	- SetCenter(newCenter);
	-
	-}
	-
	-
	-/**
	- * Sets the current centerpoint. Also updates the scene's center point.
	- * Unlike centerOn, which has no way of getting the floating point center
	- * back, SetCenter() stores the center point. It also handles the special
	- * sidebar case. This function will claim the centerPoint to sceneRec ie.
	- * the centerPoint must be within the sceneRec.
	- */
	-
	-void QmitkResidualViewWidget::SetCenter(const QPointF& center) {
	-
	- QRectF visibleArea = mapToScene(rect()).boundingRect();
	- QRectF sceneBounds = sceneRect();
	-
	- double boundX = visibleArea.width() / 2.0 ;
	- double boundY = visibleArea.height() / 2.0;
	- double boundWidth = sceneBounds.width() -2.0 * boundX;
	- double boundHeight = sceneBounds.height() - 2.0 * boundY;
	-
	- //The max boundary that the centerPoint can be to
	- QRectF bounds(boundX, boundY, boundWidth, boundHeight);
	-
	- if(bounds.contains(center))
	- {
	- m_CurrentCenterPoint = center;
	- }
	- else
	- {
	- //We need to clamp or use the center of the screen
	- if(visibleArea.contains(sceneBounds))
	- {
	- //Use the center of scene ie. we can see the whole scene
	- m_CurrentCenterPoint = sceneBounds.center();
	- }
	- else{
	-
	- m_CurrentCenterPoint = center;
	-
	- //We need to clamp the center. The centerPoint is too large
	- if(center.x() > bounds.x() + bounds.width())
	- {
	- m_CurrentCenterPoint.setX(bounds.x() + bounds.width());
	- }
	- else if(center.x() < bounds.x()) {
	- m_CurrentCenterPoint.setX(bounds.x());
	- }
	-
	- if(center.y() > bounds.y() + bounds.height())
	- {
	- m_CurrentCenterPoint.setY(bounds.y() + bounds.height());
	- }
	- else if(center.y() < bounds.y())
	- {
	- m_CurrentCenterPoint.setY(bounds.y());
	- }
	-
	- }
	- }
	-
	- // Update the scrollbars
	- centerOn(m_CurrentCenterPoint);
	-}
	-
	-
	-
	-
	-
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/QmitkResidualViewWidget.h b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/QmitkResidualViewWidget.h
	deleted file mode 100644
	index 60aa329575..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/QmitkResidualViewWidget.h
	+++ /dev/null
	@@ -1,80 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef QmitkResidualViewWidget_H_
	-#define QmitkResidualViewWidget_H_
	-
	-//#include <QObject>
	-#include <QGraphicsView>
	-#include <QWheelEvent>
	-#include <QMouseEvent>
	-#include <QGraphicsPixmapItem>
	-
	-#include <org_mitk_gui_qt_diffusionimaging_reconstruction_Export.h>
	-
	-
	-/**
	- * \brief Widget for displaying the residual between an original dwi image and the dwi estimated from a tensor image
	- *
	- */
	-class DIFFUSIONIMAGING_RECONSTRUCTION_EXPORT QmitkResidualViewWidget : public QGraphicsView
	-{
	-
	-Q_OBJECT
	-
	-public:
	-
	-
	- QmitkResidualViewWidget(QWidget *parent = nullptr);
	-
	- QmitkResidualViewWidget(QGraphicsScene scene, QWidget parent = nullptr);
	-
	-
	- // ~QmitkResidualViewWidget();
	-
	-
	- void SetResidualPixmapItem(QGraphicsPixmapItem* item)
	- {
	- m_ResidualPixmapItem = item;
	- }
	-
	-signals:
	-
	- void pointSelected(int slice, int volume);
	-
	-protected:
	-
	- void wheelEvent(QWheelEvent *event) override;
	-
	- void mouseMoveEvent(QMouseEvent* event) override;
	-
	- void mousePressEvent(QMouseEvent* event) override;
	-
	- void mouseReleaseEvent(QMouseEvent* event) override;
	-
	- QPointF m_CurrentCenterPoint;
	-
	- QGraphicsPixmapItem* m_ResidualPixmapItem;
	-
	- QPoint m_LastPanPoint;
	-
	- void SetCenter(const QPointF& centerPoint);
	-
	-
	-
	-};
	-
	-#endif
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/Perspectives/QmitkQuantificationPerspective.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/Perspectives/QmitkQuantificationPerspective.cpp
	deleted file mode 100644
	index f99d4cabbc..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/Perspectives/QmitkQuantificationPerspective.cpp
	+++ /dev/null
	@@ -1,51 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkQuantificationPerspective.h"
	-#include "berryIViewLayout.h"
	-
	-void QmitkQuantificationPerspective::CreateInitialLayout(berry::IPageLayout::Pointer layout)
	-{
	- /////////////////////////////////////////////////////
	- // all di-app perspectives should have the following:
	- /////////////////////////////////////////////////////
	-
	- QString editorArea = layout->GetEditorArea();
	-
	- layout->AddStandaloneViewPlaceholder("org.mitk.views.viewnavigatorview", berry::IPageLayout::LEFT, 0.3f, editorArea, false);
	-
	- layout->AddStandaloneView("org.mitk.views.datamanager",
	- false, berry::IPageLayout::LEFT, 0.3f, editorArea);
	-
	- layout->AddStandaloneView("org.mitk.views.controlvisualizationpropertiesview",
	- false, berry::IPageLayout::BOTTOM, .15f, "org.mitk.views.datamanager");
	-
	- berry::IFolderLayout::Pointer left =
	- layout->CreateFolder("org.mbi.diffusionimaginginternal.leftcontrols",
	- berry::IPageLayout::BOTTOM, 0.15f, "org.mitk.views.controlvisualizationpropertiesview");
	-
	- layout->AddStandaloneViewPlaceholder("org.mitk.views.imagenavigator",
	- berry::IPageLayout::BOTTOM, .7f, "org.mbi.diffusionimaginginternal.leftcontrols", false);
	-
	- /////////////////////////////////////////////
	- // here goes the perspective specific stuff
	- /////////////////////////////////////////////
	-
	- left->AddView("org.mitk.views.diffusionquantification");
	- left->AddView("org.mitk.views.imagestatisticsReloaded");
	- left->AddView("org.mitk.views.segmentation");
	- left->AddView("org.mitk.views.odfdetails");
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/Perspectives/QmitkQuantificationPerspective.h b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/Perspectives/QmitkQuantificationPerspective.h
	deleted file mode 100644
	index 8ea0b75a8a..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/Perspectives/QmitkQuantificationPerspective.h
	+++ /dev/null
	@@ -1,36 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef QmitkQuantificationPerspective_H_
	-#define QmitkQuantificationPerspective_H_
	-
	-#include <berryIPerspectiveFactory.h>
	-
	-class QmitkQuantificationPerspective : public QObject, public berry::IPerspectiveFactory
	-{
	- Q_OBJECT
	- Q_INTERFACES(berry::IPerspectiveFactory)
	-
	-public:
	-
	- QmitkQuantificationPerspective() {}
	- ~QmitkQuantificationPerspective() {}
	-
	- void CreateInitialLayout(berry::IPageLayout::Pointer layout) override;
	-};
	-
	-#endif /* QmitkQuantificationPerspective_H_ */
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/Perspectives/QmitkReconstructionPerspective.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/Perspectives/QmitkReconstructionPerspective.cpp
	deleted file mode 100644
	index 68d2b4c969..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/Perspectives/QmitkReconstructionPerspective.cpp
	+++ /dev/null
	@@ -1,52 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkReconstructionPerspective.h"
	-#include "berryIViewLayout.h"
	-
	-void QmitkReconstructionPerspective::CreateInitialLayout(berry::IPageLayout::Pointer layout)
	-{
	- /////////////////////////////////////////////////////
	- // all di-app perspectives should have the following:
	- /////////////////////////////////////////////////////
	-
	- QString editorArea = layout->GetEditorArea();
	-
	- layout->AddStandaloneViewPlaceholder("org.mitk.views.viewnavigatorview", berry::IPageLayout::LEFT, 0.3f, editorArea, false);
	-
	- layout->AddStandaloneView("org.mitk.views.datamanager",
	- false, berry::IPageLayout::LEFT, 0.3f, editorArea);
	-
	- layout->AddStandaloneView("org.mitk.views.controlvisualizationpropertiesview",
	- false, berry::IPageLayout::BOTTOM, .15f, "org.mitk.views.datamanager");
	-
	- berry::IFolderLayout::Pointer left =
	- layout->CreateFolder("org.mbi.diffusionimaginginternal.leftcontrols",
	- berry::IPageLayout::BOTTOM, 0.15f, "org.mitk.views.controlvisualizationpropertiesview");
	-
	- layout->AddStandaloneViewPlaceholder("org.mitk.views.imagenavigator",
	- berry::IPageLayout::BOTTOM, .7f, "org.mbi.diffusionimaginginternal.leftcontrols", false);
	-
	- /////////////////////////////////////////////
	- // here goes the perspective specific stuff
	- /////////////////////////////////////////////
	-
	- left->AddView("org.mitk.views.tensorreconstruction");
	- left->AddView("org.mitk.views.qballreconstruction");
	- left->AddView("org.mitk.views.odfmaximaextraction");
	- left->AddView("org.mitk.views.dipyreconstruction");
	- left->AddView("org.mitk.views.odfdetails");
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/Perspectives/QmitkReconstructionPerspective.h b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/Perspectives/QmitkReconstructionPerspective.h
	deleted file mode 100644
	index f0f64719c5..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/Perspectives/QmitkReconstructionPerspective.h
	+++ /dev/null
	@@ -1,36 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef QmitkReconstructionPerspective_H_
	-#define QmitkReconstructionPerspective_H_
	-
	-#include <berryIPerspectiveFactory.h>
	-
	-class QmitkReconstructionPerspective : public QObject, public berry::IPerspectiveFactory
	-{
	- Q_OBJECT
	- Q_INTERFACES(berry::IPerspectiveFactory)
	-
	-public:
	-
	- QmitkReconstructionPerspective() {}
	- ~QmitkReconstructionPerspective() {}
	-
	- void CreateInitialLayout(berry::IPageLayout::Pointer layout) override;
	-};
	-
	-#endif /* QmitkReconstructionPerspective_H_ */
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkDiffusionQuantificationView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkDiffusionQuantificationView.cpp
	deleted file mode 100644
	index d5792ee0c7..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkDiffusionQuantificationView.cpp
	+++ /dev/null
	@@ -1,606 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkDiffusionQuantificationView.h"
	-#include "mitkDiffusionImagingConfigure.h"
	-#include "itkTimeProbe.h"
	-#include "itkImage.h"
	-#include "mitkNodePredicateDataType.h"
	-#include "mitkDataNodeObject.h"
	-#include "mitkOdfImage.h"
	-#include <mitkTensorImage.h>
	-#include "mitkImageCast.h"
	-#include "mitkStatusBar.h"
	-#include "itkDiffusionOdfGeneralizedFaImageFilter.h"
	-#include "itkShiftScaleImageFilter.h"
	-#include "itkTensorFractionalAnisotropyImageFilter.h"
	-#include "itkTensorRelativeAnisotropyImageFilter.h"
	-#include "itkTensorDerivedMeasurementsFilter.h"
	-#include "QmitkDataStorageComboBox.h"
	-#include <QMessageBox>
	-#include "berryIWorkbenchWindow.h"
	-#include "berryISelectionService.h"
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <itkAdcImageFilter.h>
	-#include <itkBallAndSticksImageFilter.h>
	-#include <itkMultiTensorImageFilter.h>
	-#include <mitkLookupTable.h>
	-#include <mitkLookupTableProperty.h>
	-#include <mitkITKImageImport.h>
	-#include <mitkLexicalCast.h>
	-#include <mitkNodePredicateIsDWI.h>
	-#include <mitkNodePredicateDataType.h>
	-#include <mitkNodePredicateOr.h>
	-#include <QmitkStyleManager.h>
	-#include <mitkLevelWindowProperty.h>
	-#include <mitkDiffusionFunctionCollection.h>
	-
	-const std::string QmitkDiffusionQuantificationView::VIEW_ID = "org.mitk.views.diffusionquantification";
	-
	-
	-QmitkDiffusionQuantificationView::QmitkDiffusionQuantificationView()
	- : QmitkAbstractView(),
	- m_Controls(nullptr)
	-{
	-
	-}
	-
	-QmitkDiffusionQuantificationView::~QmitkDiffusionQuantificationView()
	-{
	-
	-}
	-
	-void QmitkDiffusionQuantificationView::CreateQtPartControl(QWidget *parent)
	-{
	- if (!m_Controls)
	- {
	- // create GUI widgets
	- m_Controls = new Ui::QmitkDiffusionQuantificationViewControls;
	- m_Controls->setupUi(parent);
	-
	- m_Controls->m_BallStickButton->setVisible(false);
	- m_Controls->m_MultiTensorButton->setVisible(false);
	-
	- connect( static_cast<QObject*>(m_Controls->m_GFAButton), SIGNAL(clicked()), this, SLOT(GFA()) );
	- connect( static_cast<QObject*>(m_Controls->m_FAButton), SIGNAL(clicked()), this, SLOT(FA()) );
	- connect( static_cast<QObject*>(m_Controls->m_RAButton), SIGNAL(clicked()), this, SLOT(RA()) );
	- connect( static_cast<QObject*>(m_Controls->m_ADButton), SIGNAL(clicked()), this, SLOT(AD()) );
	- connect( static_cast<QObject*>(m_Controls->m_RDButton), SIGNAL(clicked()), this, SLOT(RD()) );
	- connect( static_cast<QObject*>(m_Controls->m_MDButton), SIGNAL(clicked()), this, SLOT(MD()) );
	- connect( static_cast<QObject*>(m_Controls->m_MdDwiButton), SIGNAL(clicked()), this, SLOT(MD_DWI()) );
	- connect( static_cast<QObject*>(m_Controls->m_AdcDwiButton), SIGNAL(clicked()), this, SLOT(ADC_DWI()) );
	- connect( static_cast<QObject*>(m_Controls->m_ClusteringAnisotropy), SIGNAL(clicked()), this, SLOT(ClusterAnisotropy()) );
	- connect( static_cast<QObject*>(m_Controls->m_BallStickButton), SIGNAL(clicked()), this, SLOT(DoBallStickCalculation()) );
	- connect( static_cast<QObject*>(m_Controls->m_MultiTensorButton), SIGNAL(clicked()), this, SLOT(DoMultiTensorCalculation()) );
	-
	- m_Controls->m_ImageBox->SetDataStorage(this->GetDataStorage());
	- mitk::TNodePredicateDataType<mitk::TensorImage>::Pointer isDti = mitk::TNodePredicateDataType<mitk::TensorImage>::New();
	- mitk::TNodePredicateDataType<mitk::OdfImage>::Pointer isOdf = mitk::TNodePredicateDataType<mitk::OdfImage>::New();
	- mitk::TNodePredicateDataType<mitk::ShImage>::Pointer isSh = mitk::TNodePredicateDataType<mitk::ShImage>::New();
	- mitk::NodePredicateIsDWI::Pointer isDwi = mitk::NodePredicateIsDWI::New();
	- m_Controls->m_ImageBox->SetPredicate( mitk::NodePredicateOr::New(isSh, mitk::NodePredicateOr::New(isDti, mitk::NodePredicateOr::New(isOdf, isDwi))) );
	-
	- connect( static_cast<QObject*>(m_Controls->m_ImageBox), SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui()));
	- }
	-}
	-
	-void QmitkDiffusionQuantificationView::SetFocus()
	-{
	- m_Controls->m_ScaleImageValuesBox->setFocus();
	-}
	-
	-void QmitkDiffusionQuantificationView::UpdateGui()
	-{
	- bool foundOdfVolume = false;
	- bool foundTensorVolume = false;
	- bool foundDwVolume = false;
	- mitk::DataNode::Pointer selNode = m_Controls->m_ImageBox->GetSelectedNode();
	-
	- if( selNode.IsNotNull() && (dynamic_cast<mitk::OdfImage>(selNode->GetData()) \|\| dynamic_cast<mitk::ShImage>(selNode->GetData())) )
	- foundOdfVolume = true;
	- else if( selNode.IsNotNull() && dynamic_cast<mitk::TensorImage*>(selNode->GetData()) )
	- foundTensorVolume = true;
	- else if( selNode.IsNotNull())
	- foundDwVolume = true;
	-
	- m_Controls->m_GFAButton->setEnabled(foundOdfVolume);
	- m_Controls->m_FAButton->setEnabled(foundTensorVolume);
	- m_Controls->m_RAButton->setEnabled(foundTensorVolume);
	- m_Controls->m_ADButton->setEnabled(foundTensorVolume);
	- m_Controls->m_RDButton->setEnabled(foundTensorVolume);
	- m_Controls->m_MDButton->setEnabled(foundTensorVolume);
	- m_Controls->m_ClusteringAnisotropy->setEnabled(foundTensorVolume);
	- m_Controls->m_AdcDwiButton->setEnabled(foundDwVolume);
	- m_Controls->m_MdDwiButton->setEnabled(foundDwVolume);
	- m_Controls->m_BallStickButton->setEnabled(foundDwVolume);
	- m_Controls->m_MultiTensorButton->setEnabled(foundDwVolume);
	-}
	-
	-void QmitkDiffusionQuantificationView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /part/, const QList<mitk::DataNode::Pointer>& )
	-{
	- UpdateGui();
	-}
	-
	-void QmitkDiffusionQuantificationView::ADC_DWI()
	-{
	- DoAdcCalculation(true);
	-}
	-
	-void QmitkDiffusionQuantificationView::MD_DWI()
	-{
	- DoAdcCalculation(false);
	-}
	-
	-void QmitkDiffusionQuantificationView::DoBallStickCalculation()
	-{
	- if (m_Controls->m_ImageBox->GetSelectedNode().IsNotNull())
	- {
	- mitk::DataNode* node = m_Controls->m_ImageBox->GetSelectedNode();
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	-
	- typedef itk::BallAndSticksImageFilter< short, double > FilterType;
	-
	- ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New();
	- mitk::CastToItkImage(image, itkVectorImagePointer);
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetInput( itkVectorImagePointer );
	- filter->SetGradientDirections(mitk::DiffusionPropertyHelper::GetGradientContainer(image));
	- filter->SetB_value(static_cast<double>(mitk::DiffusionPropertyHelper::GetReferenceBValue(image)));
	- filter->Update();
	-
	- mitk::Image::Pointer newImage = mitk::Image::New();
	- newImage->InitializeByItk( filter->GetOutput() );
	- newImage->SetVolume( filter->GetOutput()->GetBufferPointer() );
	- mitk::DataNode::Pointer imageNode = mitk::DataNode::New();
	- imageNode->SetData( newImage );
	- QString name = node->GetName().c_str();
	-
	- imageNode->SetName((name+"_f").toStdString().c_str());
	- GetDataStorage()->Add(imageNode, node);
	-
	- {
	- FilterType::PeakImageType::Pointer itkImg = filter->GetPeakImage();
	- mitk::Image::Pointer newImage = mitk::Image::New();
	- CastToMitkImage(itkImg, newImage);
	-
	- mitk::DataNode::Pointer imageNode = mitk::DataNode::New();
	- imageNode->SetData( newImage );
	- QString name = node->GetName().c_str();
	-
	- imageNode->SetName((name+"_Sticks").toStdString().c_str());
	- GetDataStorage()->Add(imageNode, node);
	- }
	-
	- {
	- mitk::Image::Pointer dOut = mitk::GrabItkImageMemory( filter->GetOutDwi().GetPointer() );
	-
	- mitk::DiffusionPropertyHelper::SetGradientContainer(dOut, mitk::DiffusionPropertyHelper::GetGradientContainer(image) );
	- mitk::DiffusionPropertyHelper::SetReferenceBValue(dOut, mitk::DiffusionPropertyHelper::GetReferenceBValue(image) );
	- mitk::DiffusionPropertyHelper::InitializeImage(dOut);
	-
	- mitk::DataNode::Pointer imageNode = mitk::DataNode::New();
	- imageNode->SetData(dOut);
	- QString name = node->GetName().c_str();
	- imageNode->SetName((name+"_Estimated-DWI").toStdString().c_str());
	- GetDataStorage()->Add(imageNode, node);
	- }
	- }
	-}
	-
	-void QmitkDiffusionQuantificationView::DoMultiTensorCalculation()
	-{
	- if (m_Controls->m_ImageBox->GetSelectedNode().IsNotNull()) // for all items
	- {
	- mitk::DataNode* node = m_Controls->m_ImageBox->GetSelectedNode();
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	-
	- typedef itk::MultiTensorImageFilter< short, double > FilterType;
	-
	- ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New();
	- mitk::CastToItkImage(image, itkVectorImagePointer);
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetInput( itkVectorImagePointer );
	- filter->SetGradientDirections(mitk::DiffusionPropertyHelper::GetGradientContainer(image));
	- filter->SetB_value(static_cast<double>(mitk::DiffusionPropertyHelper::GetReferenceBValue(image)));
	- filter->Update();
	-
	- typedef mitk::TensorImage::ItkTensorImageType TensorImageType;
	- for (unsigned int i=0; i<NUM_TENSORS; i++)
	- {
	- TensorImageType::Pointer tensorImage = filter->GetTensorImages().at(i);
	- mitk::TensorImage::Pointer image = mitk::TensorImage::New();
	- image->InitializeByItk( tensorImage.GetPointer() );
	- image->SetVolume( tensorImage->GetBufferPointer() );
	-
	- mitk::DataNode::Pointer imageNode = mitk::DataNode::New();
	- imageNode->SetData( image );
	- QString name = node->GetName().c_str();
	- name.append("_Tensor");
	- name.append(boost::lexical_cast<std::string>(i).c_str());
	- imageNode->SetName(name.toStdString().c_str());
	- GetDataStorage()->Add(imageNode, node);
	- }
	- }
	-}
	-
	-void QmitkDiffusionQuantificationView::DoAdcCalculation(bool fit)
	-{
	- if (m_Controls->m_ImageBox->GetSelectedNode().IsNotNull())
	- {
	- mitk::DataNode* node = m_Controls->m_ImageBox->GetSelectedNode();
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
	-
	- typedef itk::AdcImageFilter< short, double > FilterType;
	-
	- ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New();
	- mitk::CastToItkImage(image, itkVectorImagePointer);
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetInput( itkVectorImagePointer );
	-
	- filter->SetGradientDirections( mitk::DiffusionPropertyHelper::GetGradientContainer(image) );
	- filter->SetB_value( static_cast<double>(mitk::DiffusionPropertyHelper::GetReferenceBValue(image)) );
	-
	- filter->SetFitSignal(fit);
	- filter->Update();
	-
	- typedef itk::ShiftScaleImageFilter<itk::AdcImageFilter< short, double >::OutputImageType, itk::AdcImageFilter< short, double >::OutputImageType> ShiftScaleFilterType;
	- ShiftScaleFilterType::Pointer multi = ShiftScaleFilterType::New();
	- multi->SetShift(0.0);
	- multi->SetScale(m_Controls->m_ScaleImageValuesBox->value());
	- multi->SetInput(filter->GetOutput());
	- multi->Update();
	-
	- mitk::Image::Pointer newImage = mitk::Image::New();
	- newImage->InitializeByItk( multi->GetOutput() );
	- newImage->SetVolume( multi->GetOutput()->GetBufferPointer() );
	- mitk::DataNode::Pointer imageNode = mitk::DataNode::New();
	- imageNode->SetData( newImage );
	- QString name = node->GetName().c_str();
	-
	- mitk::LookupTable::Pointer lut = mitk::LookupTable::New();
	- lut->SetType( mitk::LookupTable::JET_TRANSPARENT );
	- mitk::LookupTableProperty::Pointer lut_prop = mitk::LookupTableProperty::New();
	- lut_prop->SetLookupTable( lut );
	-
	- imageNode->SetProperty("LookupTable", lut_prop );
	- if (fit)
	- imageNode->SetName((name+"_ADC").toStdString().c_str());
	- else
	- imageNode->SetName((name+"_MD").toStdString().c_str());
	-
	- mitk::LevelWindow lw;
	- lw.SetLevelWindow(0.0015, 0.003);
	- imageNode->SetProperty( "levelwindow", mitk::LevelWindowProperty::New( lw ) );
	- GetDataStorage()->Add(imageNode, node);
	- }
	-}
	-
	-void QmitkDiffusionQuantificationView::GFA()
	-{
	- OdfQuantify(0);
	-}
	-
	-void QmitkDiffusionQuantificationView::FA()
	-{
	- TensorQuantify(0);
	-}
	-
	-void QmitkDiffusionQuantificationView::RA()
	-{
	- TensorQuantify(1);
	-}
	-
	-void QmitkDiffusionQuantificationView::AD()
	-{
	- TensorQuantify(2);
	-}
	-
	-void QmitkDiffusionQuantificationView::RD()
	-{
	- TensorQuantify(3);
	-}
	-
	-void QmitkDiffusionQuantificationView::ClusterAnisotropy()
	-{
	- TensorQuantify(4);
	-}
	-
	-void QmitkDiffusionQuantificationView::MD()
	-{
	- TensorQuantify(5);
	-}
	-
	-void QmitkDiffusionQuantificationView::OdfQuantify(int method)
	-{
	- OdfQuantification(method);
	-}
	-
	-void QmitkDiffusionQuantificationView::TensorQuantify(int method)
	-{
	- TensorQuantification(method);
	-}
	-
	-void QmitkDiffusionQuantificationView::OdfQuantification(int method)
	-{
	- QString status;
	-
	- if (m_Controls->m_ImageBox->GetSelectedNode().IsNotNull())
	- {
	- mitk::DataNode* node = m_Controls->m_ImageBox->GetSelectedNode();
	-
	- typedef float TOdfPixelType;
	- typedef itk::Vector<TOdfPixelType,ODF_SAMPLING_SIZE> OdfVectorType;
	- typedef itk::Image<OdfVectorType,3> OdfVectorImgType;
	- mitk::Image::Pointer vol = dynamic_cast<mitk::Image*>(node->GetData());
	-
	- OdfVectorImgType::Pointer itkvol;
	- if (dynamic_cast<mitk::ShImage*>(vol.GetPointer()))
	- itkvol = mitk::convert::GetItkOdfFromShImage(vol);
	- else
	- itkvol = mitk::convert::GetItkOdfFromOdfImage(vol);
	- std::string nodename = node->GetName();
	-
	- mitk::StatusBar::GetInstance()->DisplayText(status.sprintf("Computing GFA for %s", nodename.c_str()).toLatin1());
	- typedef itk::DiffusionOdfGeneralizedFaImageFilter<TOdfPixelType,TOdfPixelType,ODF_SAMPLING_SIZE> GfaFilterType;
	- GfaFilterType::Pointer gfaFilter = GfaFilterType::New();
	- gfaFilter->SetInput(itkvol);
	-
	- std::string newname;
	- newname.append(nodename);
	- switch(method)
	- {
	- case 0:
	- {
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_STANDARD);
	- newname.append("GFA");
	- break;
	- }
	- case 1:
	- {
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_QUANTILES_HIGH_LOW);
	- newname.append("01");
	- break;
	- }
	- case 2:
	- {
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_QUANTILE_HIGH);
	- newname.append("02");
	- break;
	- }
	- case 3:
	- {
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_MAX_ODF_VALUE);
	- newname.append("03");
	- break;
	- }
	- case 4:
	- {
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_DECONVOLUTION_COEFFS);
	- newname.append("04");
	- break;
	- }
	- case 5:
	- {
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_MIN_MAX_NORMALIZED_STANDARD);
	- newname.append("05");
	- break;
	- }
	- case 6:
	- {
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_NORMALIZED_ENTROPY);
	- newname.append("06");
	- break;
	- }
	- case 7:
	- {
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_NEMATIC_ORDER_PARAMETER);
	- newname.append("07");
	- break;
	- }
	- case 8:
	- {
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_QUANTILES_LOW_HIGH);
	- newname.append("08");
	- break;
	- }
	- case 9:
	- {
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_QUANTILE_LOW);
	- newname.append("09");
	- break;
	- }
	- case 10:
	- {
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_MIN_ODF_VALUE);
	- newname.append("10");
	- break;
	- }
	- case 11:
	- {
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_STD_BY_MAX);
	- newname.append("11");
	- break;
	- }
	- default:
	- {
	- newname.append("0");
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_STANDARD);
	- }
	- }
	- gfaFilter->Update();
	-
	- typedef itk::Image<TOdfPixelType, 3> ImgType;
	- ImgType::Pointer img = ImgType::New();
	- img->SetSpacing( gfaFilter->GetOutput()->GetSpacing() ); // Set the image spacing
	- img->SetOrigin( gfaFilter->GetOutput()->GetOrigin() ); // Set the image origin
	- img->SetDirection( gfaFilter->GetOutput()->GetDirection() ); // Set the image direction
	- img->SetLargestPossibleRegion( gfaFilter->GetOutput()->GetLargestPossibleRegion());
	- img->SetBufferedRegion( gfaFilter->GetOutput()->GetLargestPossibleRegion() );
	- img->Allocate();
	- itk::ImageRegionIterator<ImgType> ot (img, img->GetLargestPossibleRegion() );
	- ot.GoToBegin();
	- itk::ImageRegionConstIterator<GfaFilterType::OutputImageType> it
	- (gfaFilter->GetOutput(), gfaFilter->GetOutput()->GetLargestPossibleRegion() );
	-
	- for (it.GoToBegin(); !it.IsAtEnd(); ++it)
	- {
	- GfaFilterType::OutputImageType::PixelType val = it.Get();
	- ot.Set(val * m_Controls->m_ScaleImageValuesBox->value());
	- ++ot;
	- }
	-
	-
	- // GFA TO DATATREE
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk( img.GetPointer() );
	- image->SetVolume( img->GetBufferPointer() );
	- mitk::DataNode::Pointer new_node=mitk::DataNode::New();
	- new_node->SetData( image );
	- new_node->SetProperty( "name", mitk::StringProperty::New(newname) );
	-
	- mitk::LookupTable::Pointer lut = mitk::LookupTable::New();
	- lut->SetType( mitk::LookupTable::JET_TRANSPARENT );
	- mitk::LookupTableProperty::Pointer lut_prop = mitk::LookupTableProperty::New();
	- lut_prop->SetLookupTable( lut );
	- new_node->SetProperty("LookupTable", lut_prop );
	-
	- mitk::LevelWindow lw;
	- lw.SetLevelWindow(0.5, 1.0);
	- new_node->SetProperty( "levelwindow", mitk::LevelWindowProperty::New( lw ) );
	-
	- GetDataStorage()->Add(new_node, node);
	-
	- mitk::StatusBar::GetInstance()->DisplayText("Computation complete.");
	- }
	-
	- this->GetRenderWindowPart()->RequestUpdate();
	-
	-}
	-
	-void QmitkDiffusionQuantificationView::TensorQuantification(int method)
	-{
	- QString status;
	-
	- if (m_Controls->m_ImageBox->GetSelectedNode().IsNotNull())
	- {
	- mitk::DataNode* node = m_Controls->m_ImageBox->GetSelectedNode();
	-
	- typedef mitk::TensorImage::ScalarPixelType TTensorPixelType;
	- typedef mitk::TensorImage::ItkTensorImageType TensorImageType;
	-
	- mitk::Image* vol = static_cast<mitk::Image*>(node->GetData());
	- TensorImageType::Pointer itkvol = TensorImageType::New();
	- mitk::CastToItkImage(vol, itkvol);
	-
	- std::string nodename = node->GetName();
	-
	- mitk::StatusBar::GetInstance()->DisplayText(status.sprintf("Computing FA for %s", nodename.c_str()).toLatin1());
	- typedef itk::Image< TTensorPixelType, 3 > FAImageType;
	-
	- typedef itk::ShiftScaleImageFilter<FAImageType, FAImageType> ShiftScaleFilterType;
	- ShiftScaleFilterType::Pointer multi = ShiftScaleFilterType::New();
	- multi->SetShift(0.0);
	- multi->SetScale(m_Controls->m_ScaleImageValuesBox->value());
	-
	- typedef itk::TensorDerivedMeasurementsFilter<TTensorPixelType> MeasurementsType;
	-
	- mitk::LevelWindow lw;
	- if(method == 0) //FA
	- {
	- MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New();
	- measurementsCalculator->SetInput(itkvol.GetPointer() );
	- measurementsCalculator->SetMeasure(MeasurementsType::FA);
	- measurementsCalculator->Update();
	- multi->SetInput(measurementsCalculator->GetOutput());
	- nodename = QString(nodename.c_str()).append("_FA").toStdString();
	- lw.SetLevelWindow(0.5, 1.0);
	- }
	- else if(method == 1) //RA
	- {
	- MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New();
	- measurementsCalculator->SetInput(itkvol.GetPointer() );
	- measurementsCalculator->SetMeasure(MeasurementsType::RA);
	- measurementsCalculator->Update();
	- multi->SetInput(measurementsCalculator->GetOutput());
	- nodename = QString(nodename.c_str()).append("_RA").toStdString();
	- lw.SetLevelWindow(0.015, 0.03);
	- }
	- else if(method == 2) // AD (Axial diffusivity)
	- {
	- MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New();
	- measurementsCalculator->SetInput(itkvol.GetPointer() );
	- measurementsCalculator->SetMeasure(MeasurementsType::AD);
	- measurementsCalculator->Update();
	- multi->SetInput(measurementsCalculator->GetOutput());
	- nodename = QString(nodename.c_str()).append("_AD").toStdString();
	- lw.SetLevelWindow(0.0015, 0.003);
	- }
	- else if(method == 3) // RD (Radial diffusivity, (Lambda2+Lambda3)/2
	- {
	- MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New();
	- measurementsCalculator->SetInput(itkvol.GetPointer() );
	- measurementsCalculator->SetMeasure(MeasurementsType::RD);
	- measurementsCalculator->Update();
	- multi->SetInput(measurementsCalculator->GetOutput());
	- nodename = QString(nodename.c_str()).append("_RD").toStdString();
	- lw.SetLevelWindow(0.0015, 0.003);
	- }
	- else if(method == 4) // 1-(Lambda2+Lambda3)/(2*Lambda1)
	- {
	- MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New();
	- measurementsCalculator->SetInput(itkvol.GetPointer() );
	- measurementsCalculator->SetMeasure(MeasurementsType::CA);
	- measurementsCalculator->Update();
	- multi->SetInput(measurementsCalculator->GetOutput());
	- nodename = QString(nodename.c_str()).append("_CA").toStdString();
	- lw.SetLevelWindow(0.5, 1.0);
	- }
	- else if(method == 5) // MD (Mean Diffusivity, (Lambda1+Lambda2+Lambda3)/3 )
	- {
	- MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New();
	- measurementsCalculator->SetInput(itkvol.GetPointer() );
	- measurementsCalculator->SetMeasure(MeasurementsType::MD);
	- measurementsCalculator->Update();
	- multi->SetInput(measurementsCalculator->GetOutput());
	- nodename = QString(nodename.c_str()).append("_MD").toStdString();
	- lw.SetLevelWindow(0.0015, 0.003);
	- }
	-
	- multi->Update();
	-
	- // FA TO DATATREE
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk( multi->GetOutput() );
	- image->SetVolume( multi->GetOutput()->GetBufferPointer() );
	- mitk::DataNode::Pointer new_node=mitk::DataNode::New();
	- new_node->SetData( image );
	- new_node->SetProperty( "name", mitk::StringProperty::New(nodename) );
	-
	- mitk::LookupTable::Pointer lut = mitk::LookupTable::New();
	- lut->SetType( mitk::LookupTable::JET_TRANSPARENT );
	- mitk::LookupTableProperty::Pointer lut_prop = mitk::LookupTableProperty::New();
	- lut_prop->SetLookupTable( lut );
	- new_node->SetProperty("LookupTable", lut_prop );
	- new_node->SetProperty( "levelwindow", mitk::LevelWindowProperty::New( lw ) );
	-
	- GetDataStorage()->Add(new_node, node);
	-
	- mitk::StatusBar::GetInstance()->DisplayText("Computation complete.");
	- }
	-
	- this->GetRenderWindowPart()->RequestUpdate();
	-
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkDiffusionQuantificationView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkDiffusionQuantificationView.h
	deleted file mode 100644
	index 5f7b4873e1..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkDiffusionQuantificationView.h
	+++ /dev/null
	@@ -1,90 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _QMITKDIFFUSIONQUANTIFICATIONVIEW_H_INCLUDED
	-#define _QMITKDIFFUSIONQUANTIFICATIONVIEW_H_INCLUDED
	-
	-#include <QmitkAbstractView.h>
	-#include <string>
	-#include <itkVectorImage.h>
	-
	-#include "ui_QmitkDiffusionQuantificationViewControls.h"
	-/*!
	- * \ingroup org_mitk_gui_qt_diffusionquantification_internal
	- *
	- * \brief QmitkDiffusionQuantificationView
	- *
	- * Document your class here.
	- */
	-class QmitkDiffusionQuantificationView : public QmitkAbstractView
	-{
	-
	- friend struct DqSelListener;
	-
	- // this is needed for all Qt objects that should have a MOC object (everything that derives from QObject)
	- Q_OBJECT
	-
	- public:
	-
	- static const std::string VIEW_ID;
	-
	- QmitkDiffusionQuantificationView();
	- virtual ~QmitkDiffusionQuantificationView();
	-
	- typedef itk::VectorImage< short, 3 > ItkDwiType;
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	- virtual void SetFocus() override;
	-
	-protected slots:
	-
	- void GFA();
	- void FA();
	- void RA();
	- void AD();
	- void RD();
	- void ClusterAnisotropy();
	- void MD();
	-
	- void ADC_DWI();
	- void MD_DWI();
	-
	- void OdfQuantify(int method);
	- void OdfQuantification(int method) ;
	-
	- void TensorQuantify(int method);
	- void TensorQuantification(int method) ;
	-
	- void DoBallStickCalculation();
	- void DoMultiTensorCalculation();
	- void UpdateGui();
	-
	-protected:
	-
	- void DoAdcCalculation(bool fit);
	-
	- /// \brief called by QmitkAbstractView when DataManager's selection has changed
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- Ui::QmitkDiffusionQuantificationViewControls* m_Controls;
	- static const float m_ScaleDAIValues;
	-};
	-
	-
	-
	-
	-#endif // _QMITKDIFFUSIONQUANTIFICATIONVIEW_H_INCLUDED
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkDiffusionQuantificationViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkDiffusionQuantificationViewControls.ui
	deleted file mode 100644
	index c3a9115d0a..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkDiffusionQuantificationViewControls.ui
	+++ /dev/null
	@@ -1,284 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<ui version="4.0">
	- <class>QmitkDiffusionQuantificationViewControls</class>
	- <widget class="QWidget" name="QmitkDiffusionQuantificationViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>343</width>
	- <height>858</height>
	- </rect>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="windowTitle">
	- <string>QmitkTemplate</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_2">
	- <property name="verticalSpacing">
	- <number>25</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QGroupBox" name="groupBox_3">
	- <property name="title">
	- <string>Raw diffusion-weighted image</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_5">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QCommandLinkButton" name="m_AdcDwiButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="text">
	- <string>ADC</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QCommandLinkButton" name="m_MdDwiButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="text">
	- <string>MD</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QCommandLinkButton" name="m_BallStickButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="text">
	- <string>Ball-Stick</string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QCommandLinkButton" name="m_MultiTensorButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="text">
	- <string>Multi-Tensor Fit</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QGroupBox" name="groupBox_2">
	- <property name="title">
	- <string>Tensor image</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_4">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QCommandLinkButton" name="m_FAButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="text">
	- <string>FA (Fractional Anisotropy)</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QCommandLinkButton" name="m_RAButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="text">
	- <string>RA (Relative Anisotropy)</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QCommandLinkButton" name="m_ADButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="text">
	- <string>AD (Axial Diffusivity)</string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QCommandLinkButton" name="m_RDButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="text">
	- <string>RD (Radial Diffusivity)</string>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QCommandLinkButton" name="m_MDButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="text">
	- <string>MD (Mean Diffusivity)</string>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <widget class="QCommandLinkButton" name="m_ClusteringAnisotropy">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="text">
	- <string>1-(λ2+λ3)/(2*λ1)</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QGroupBox" name="m_InputData">
	- <property name="title">
	- <string>Input Data</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label">
	- <property name="text">
	- <string>Image</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_2">
	- <property name="text">
	- <string>Scale Image Values:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QDoubleSpinBox" name="m_ScaleImageValuesBox">
	- <property name="maximum">
	- <double>9999999.000000000000000</double>
	- </property>
	- <property name="value">
	- <double>1.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_ImageBox"/>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QGroupBox" name="groupBox">
	- <property name="title">
	- <string>ODF image</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_3">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QCommandLinkButton" name="m_GFAButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="text">
	- <string>GFA</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <spacer name="verticalSpacer">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- </layout>
	- </widget>
	- <layoutdefault spacing="6" margin="11"/>
	- <customwidgets>
	- <customwidget>
	- <class>QmitkDataStorageComboBox</class>
	- <extends>QComboBox</extends>
	- <header location="global">QmitkDataStorageComboBox.h</header>
	- </customwidget>
	- </customwidgets>
	- <includes>
	- <include location="local">QmitkDataStorageComboBox.h</include>
	- </includes>
	- <resources/>
	- <connections/>
	-</ui>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkODFDetailsView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkODFDetailsView.cpp
	deleted file mode 100644
	index c0906f0f77..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkODFDetailsView.cpp
	+++ /dev/null
	@@ -1,405 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include <berryISelectionService.h>
	-#include <berryIWorkbenchWindow.h>
	-#include "QmitkODFDetailsView.h"
	-#include <QTableWidgetItem>
	-#include <vtkFloatArray.h>
	-#include <vtkPointData.h>
	-#include <vtkCellData.h>
	-#include <vtkLookupTable.h>
	-#include <mitkOdfNormalizationMethodProperty.h>
	-#include <QTextEdit>
	-#include <mitkTensorImage.h>
	-#include <QMessageBox>
	-#include <QmitkRenderingManager.h>
	-#include <mitkShImage.h>
	-#include <mitkImageReadAccessor.h>
	-#include <mitkImagePixelReadAccessor.h>
	-#include <mitkDiffusionFunctionCollection.h>
	-#include <vtkRenderWindowInteractor.h>
	-
	-const std::string QmitkODFDetailsView::VIEW_ID = "org.mitk.views.odfdetails";
	-
	-QmitkODFDetailsView::QmitkODFDetailsView()
	- : QmitkAbstractView()
	- , m_Controls(nullptr)
	- , m_OdfNormalization(0)
	- , m_ImageNode(nullptr)
	-{
	-
	-}
	-
	-QmitkODFDetailsView::~QmitkODFDetailsView()
	-{
	-}
	-
	-void QmitkODFDetailsView::Activated()
	-{
	-}
	-
	-void QmitkODFDetailsView::Deactivated()
	-{
	-}
	-
	-void QmitkODFDetailsView::Visible()
	-{
	-
	-}
	-
	-void QmitkODFDetailsView::Hidden()
	-{
	-
	-}
	-
	-void QmitkODFDetailsView::SetFocus()
	-{
	- this->m_Controls->m_OverviewTextEdit->setFocus();
	-}
	-
	-void QmitkODFDetailsView::CreateQtPartControl( QWidget *parent )
	-{
	- // build up qt view, unless already done
	- if ( !m_Controls )
	- {
	- // create GUI widgets from the Qt Designer's .ui file
	- m_Controls = new Ui::QmitkODFDetailsViewControls;
	- m_Controls->setupUi( parent );
	- m_Controls->m_OdfBox->setVisible(false);
	- m_Controls->m_ODFRenderWidget->setVisible(false);
	-
	- m_SliceChangeListener.RenderWindowPartActivated(this->GetRenderWindowPart());
	- connect(&m_SliceChangeListener, SIGNAL(SliceChanged()), this, SLOT(OnSliceChanged()));
	- }
	-}
	-
	-void QmitkODFDetailsView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /part/, const QList<mitk::DataNode::Pointer>& nodes)
	-{
	- m_Controls->m_InputData->setTitle("Please Select Input Data");
	- m_Controls->m_InputImageLabel->setText("<font color='red'>mandatory</font>");
	-
	- m_ImageNode = nullptr;
	-
	- // iterate selection
	- for (mitk::DataNode::Pointer node: nodes)
	- {
	- if( node.IsNotNull() && (dynamic_cast<mitk::OdfImage>(node->GetData()) \|\| dynamic_cast<mitk::TensorImage>(node->GetData()) \|\| dynamic_cast<mitk::ShImage*>(node->GetData())) )
	- {
	- m_Controls->m_InputImageLabel->setText(node->GetName().c_str());
	- m_ImageNode = node;
	- }
	- }
	-
	- UpdateOdf();
	- if (m_ImageNode.IsNotNull())
	- {
	- m_Controls->m_InputData->setTitle("Input Data");
	- }
	-}
	-
	-void QmitkODFDetailsView::UpdateOdf()
	-{
	- try
	- {
	- m_Controls->m_OverviewBox->setVisible(true);
	- if (m_ImageNode.IsNull() \|\| !this->GetRenderWindowPart())
	- {
	- m_Controls->m_ODFRenderWidget->setVisible(false);
	- m_Controls->m_OdfBox->setVisible(false);
	- m_Controls->m_OverviewBox->setVisible(false);
	- return;
	- }
	-
	- // restore the input image label ( needed in case the last run resulted into an exception )
	- m_Controls->m_InputImageLabel->setText(m_ImageNode->GetName().c_str());
	-
	- // ODF Normalization Property
	- mitk::OdfNormalizationMethodProperty* nmp = dynamic_cast<mitk::OdfNormalizationMethodProperty*>(m_ImageNode->GetProperty( "Normalization" ));
	- if(nmp)
	- m_OdfNormalization = nmp->GetNormalization();
	-
	- bool dir_color = false;
	- m_ImageNode->GetBoolProperty( "DiffusionCore.Rendering.OdfVtkMapper.ColourisationModeBit", dir_color );
	-
	- bool toggle_tensor = false;
	- m_ImageNode->GetBoolProperty( "DiffusionCore.Rendering.OdfVtkMapper.SwitchTensorView", toggle_tensor );
	-
	- mitk::Point3D world = this->GetRenderWindowPart()->GetSelectedPosition();
	- mitk::Point3D cont_index;
	- mitk::Image::Pointer img = dynamic_cast<mitk::Image*>(m_ImageNode->GetData());
	- img->GetGeometry()->WorldToIndex(world, cont_index);
	- itk::Index<3> index;
	- index[0] = static_cast<int>(cont_index[0]+0.5);
	- index[1] = static_cast<int>(cont_index[1]+0.5);
	- index[2] = static_cast<int>(cont_index[2]+0.5);
	-
	- float sum = 0;
	- float max = itk::NumericTraits<float>::NonpositiveMin();
	- float min = itk::NumericTraits<float>::max();
	- QString values;
	- QString overviewText;
	-
	- // check if dynamic_cast successfull and if the crosshair position is inside of the geometry of the ODF data
	- // otherwise possible crash for a scenario with multiple nodes
	- if (dynamic_cast<mitk::OdfImage*>(m_ImageNode->GetData()) && ( m_ImageNode->GetData()->GetGeometry()->IsInside(world) ) )
	- {
	- itk::OrientationDistributionFunction<float, ODF_SAMPLING_SIZE> odf;
	- m_Controls->m_ODFRenderWidget->setVisible(true);
	- m_Controls->m_OdfBox->setVisible(true);
	-
	- try
	- {
	- const mitk::OdfImage* Odf_image = dynamic_cast< mitk::OdfImage* >( m_ImageNode->GetData() );
	-
	- mitk::ImagePixelReadAccessor<mitk::OdfImage::PixelType, 3> pixel_read(Odf_image, Odf_image->GetVolumeData(0));
	- auto pixel_data = pixel_read.GetPixelByIndex(index);
	-
	- for (unsigned int i=0; i<odf.GetNumberOfComponents(); i++)
	- {
	- auto val = pixel_data[i];
	- odf[i] = val;
	- values += QString::number(i)+": "+QString::number(static_cast<double>(val))+"\n";
	- sum += val;
	- if (val>max)
	- max = val;
	- if (val<min)
	- min = val;
	- }
	- float mean = sum/odf.GetNumberOfComponents();
	-
	- float stdev = 0;
	- for (unsigned int i=0; i<odf.GetNumberOfComponents(); i++)
	- {
	- float diff = odf[i] - mean;
	- stdev += diff*diff;
	- }
	- stdev = std::sqrt(stdev/(odf.GetNumberOfComponents()-1));
	-
	- QString pos = QString::number(index[0])+", "+QString::number(index[1])+", "+QString::number(index[2]);
	- overviewText += "Coordinates: "+pos+"\n";
	- overviewText += "GFA: "+QString::number(static_cast<double>(odf.GetGeneralizedFractionalAnisotropy()))+"\n";
	- overviewText += "Sum: "+QString::number(static_cast<double>(sum))+"\n";
	- overviewText += "Mean: "+QString::number(static_cast<double>(mean))+"\n";
	- overviewText += "Stdev: "+QString::number(static_cast<double>(stdev))+"\n";
	- overviewText += "Min: "+QString::number(static_cast<double>(min))+"\n";
	- overviewText += "Max: "+QString::number(static_cast<double>(max))+"\n";
	- vnl_vector_fixed<double, 3> pd = odf.GetDirection(odf.GetPrincipalDiffusionDirectionIndex());
	- overviewText += "Main Diffusion:\n "+QString::number(pd[0])+"\n "+QString::number(pd[1])+"\n "+QString::number(pd[2])+"\n";
	-
	- m_Controls->m_OdfValuesTextEdit->setText(values);
	- m_Controls->m_OverviewTextEdit->setVisible(true);
	- m_Controls->m_ODFDetailsWidget->SetParameters<ODF_SAMPLING_SIZE>(odf);
	- m_Controls->m_ODFRenderWidget->GenerateODF<ODF_SAMPLING_SIZE>(odf, m_OdfNormalization, dir_color);
	- m_Controls->m_OverviewTextEdit->setText(overviewText.toStdString().c_str());
	- }
	- catch( mitk::Exception &e )
	- {
	- MITK_WARN << "LOCKED : " << e.what();
	- m_Controls->m_ODFRenderWidget->setVisible(false);
	- m_Controls->m_OdfBox->setVisible(false);
	- m_Controls->m_OverviewTextEdit->setVisible(false);
	-
	- // reset the selection
	- m_Controls->m_InputImageLabel->setText("<font color='green'>Click image to restore rendering!</font>");
	- }
	- }
	- else if (dynamic_cast<mitk::TensorImage*>(m_ImageNode->GetData()) && ( m_ImageNode->GetData()->GetGeometry()->IsInside(world) ) )
	- {
	- itk::OrientationDistributionFunction<float, 5000> odf;
	- m_Controls->m_ODFRenderWidget->setVisible(true);
	- m_Controls->m_OdfBox->setVisible(false);
	- const mitk::TensorImage* Odf_image = dynamic_cast< mitk::TensorImage*>(m_ImageNode->GetData());
	-
	- // pixel access block
	- try
	- {
	- mitk::ImagePixelReadAccessor<mitk::TensorImage::PixelType, 3> pixel_read(Odf_image, Odf_image->GetVolumeData(0));
	- auto tensorelems = pixel_read.GetPixelByIndex(index);
	-
	- TensorPixelType tensor(tensorelems);
	- if (!toggle_tensor)
	- odf.InitFromTensor(tensor);
	- else
	- {
	- odf.InitFromEllipsoid(tensor);
	- m_OdfNormalization = 1;
	- }
	-
	- /** Array of eigen-values. */
	- typedef itk::FixedArray<float, 3> EigenValuesArrayType;
	- /** Matrix of eigen-vectors. */
	- typedef itk::Matrix<float, 3, 3> EigenVectorsMatrixType;
	-
	- EigenValuesArrayType eigenValues;
	- EigenVectorsMatrixType eigenvectors;
	-
	- QString pos = QString::number(index[0])+", "+QString::number(index[1])+", "+QString::number(index[2]);
	- overviewText += "Coordinates: "+pos+"\n";
	- overviewText += "FA: "+QString::number(tensor.GetFractionalAnisotropy())+"\n";
	- overviewText += "RA: "+QString::number(tensor.GetRelativeAnisotropy())+"\n";
	- overviewText += "Trace: "+QString::number(tensor.GetTrace())+"\n";
	- tensor.ComputeEigenAnalysis(eigenValues,eigenvectors);
	- overviewText += "Eigenvalues:\n "+QString::number(static_cast<double>(eigenValues[2]))+"\n "+QString::number(static_cast<double>(eigenValues[1]))+"\n "+QString::number(static_cast<double>(eigenValues[0]))+"\n";
	- overviewText += "Main Diffusion:\n "+QString::number(static_cast<double>(eigenvectors(2, 0)))+"\n "+QString::number(static_cast<double>(eigenvectors(2, 1)))+"\n "+QString::number(static_cast<double>(eigenvectors(2, 2)))+"\n";
	- overviewText += "Values:\n "+QString::number(static_cast<double>(tensorelems[0]))+"\n "+QString::number(static_cast<double>(tensorelems[1]))+"\n "+QString::number(static_cast<double>(tensorelems[2]))+"\n "+QString::number(static_cast<double>(tensorelems[3]))+"\n "+QString::number(static_cast<double>(tensorelems[4]))+"\n "+QString::number(static_cast<double>(tensorelems[5]))+"\n "+"\n";
	- m_Controls->m_OverviewTextEdit->setVisible(true);
	-
	- m_Controls->m_ODFDetailsWidget->SetParameters<5000>(odf);
	- m_Controls->m_ODFRenderWidget->GenerateODF<5000>(odf, m_OdfNormalization, dir_color);
	- m_Controls->m_OverviewTextEdit->setText(overviewText.toStdString().c_str());
	- }
	- // end pixel access block
	- catch(mitk::Exception &e )
	- {
	- MITK_WARN << "LOCKED : " << e.what();
	- m_Controls->m_ODFRenderWidget->setVisible(false);
	- m_Controls->m_OdfBox->setVisible(false);
	- m_Controls->m_OverviewTextEdit->setVisible(false);
	-
	- // reset the selection
	- m_Controls->m_InputImageLabel->setText("<font color='green'>Click image to restore rendering!</font>");
	- }
	- }
	- else if (dynamic_cast<mitk::ShImage*>(m_ImageNode->GetData()) && ( m_ImageNode->GetData()->GetGeometry()->IsInside(world) ) )
	- {
	- itk::OrientationDistributionFunction<float, 5000> odf;
	- m_Controls->m_ODFRenderWidget->setVisible(true);
	- m_Controls->m_OdfBox->setVisible(false);
	-
	- mitk::ShImage::Pointer Odf_image = dynamic_cast< mitk::ShImage*>(m_ImageNode->GetData());
	- mitk::Image::Pointer image = dynamic_cast< mitk::ShImage*>(m_ImageNode->GetData());
	- QString coeff_string = "";
	- switch (Odf_image->ShOrder())
	- {
	- case 2:
	- {
	- auto img = mitk::convert::GetItkShFromShImage<6>(image);
	- auto coeffs = img->GetPixel(index);
	- for (unsigned int i=0; i<coeffs.Size(); ++i)
	- coeff_string += QString::number(static_cast<double>(coeffs[i])) + " ";
	- mitk::sh::SampleOdf(coeffs.GetVnlVector(), odf);
	- break;
	- }
	- case 4:
	- {
	- auto img = mitk::convert::GetItkShFromShImage<15>(image);
	- auto coeffs = img->GetPixel(index);
	- for (unsigned int i=0; i<coeffs.Size(); ++i)
	- coeff_string += QString::number(static_cast<double>(coeffs[i])) + " ";
	- mitk::sh::SampleOdf(coeffs.GetVnlVector(), odf);
	- break;
	- }
	- case 6:
	- {
	- auto img = mitk::convert::GetItkShFromShImage<28>(image);
	- auto coeffs = img->GetPixel(index);
	- for (unsigned int i=0; i<coeffs.Size(); ++i)
	- coeff_string += QString::number(static_cast<double>(coeffs[i])) + " ";
	- mitk::sh::SampleOdf(coeffs.GetVnlVector(), odf);
	- break;
	- }
	- case 8:
	- {
	- auto img = mitk::convert::GetItkShFromShImage<45>(image);
	- auto coeffs = img->GetPixel(index);
	- for (unsigned int i=0; i<coeffs.Size(); ++i)
	- coeff_string += QString::number(static_cast<double>(coeffs[i])) + " ";
	- mitk::sh::SampleOdf(coeffs.GetVnlVector(), odf);
	- break;
	- }
	- case 10:
	- {
	- auto img = mitk::convert::GetItkShFromShImage<66>(image);
	- auto coeffs = img->GetPixel(index);
	- for (unsigned int i=0; i<coeffs.Size(); ++i)
	- coeff_string += QString::number(static_cast<double>(coeffs[i])) + " ";
	- mitk::sh::SampleOdf(coeffs.GetVnlVector(), odf);
	- break;
	- }
	- case 12:
	- {
	- auto img = mitk::convert::GetItkShFromShImage<91>(image);
	- auto coeffs = img->GetPixel(index);
	- for (unsigned int i=0; i<coeffs.Size(); ++i)
	- coeff_string += QString::number(static_cast<double>(coeffs[i])) + " ";
	- mitk::sh::SampleOdf(coeffs.GetVnlVector(), odf);
	- break;
	- }
	- default :
	- mitkThrow() << "SH order larger 12 not supported";
	- }
	-
	- for (unsigned int i=0; i<odf.GetNumberOfComponents(); i++)
	- {
	- auto val = odf[i];
	- values += QString::number(i)+": "+QString::number(static_cast<double>(val))+"\n";
	- sum += val;
	- if (val>max)
	- max = val;
	- if (val<min)
	- min = val;
	- }
	- float mean = sum/odf.GetNumberOfComponents();
	-
	- float stdev = 0;
	- for (unsigned int i=0; i<odf.GetNumberOfComponents(); i++)
	- {
	- float val = odf[i];
	- float diff = val - mean;
	- stdev += diff*diff;
	- }
	- stdev = std::sqrt(stdev/(odf.GetNumberOfComponents()-1));
	-
	- QString pos = QString::number(index[0])+", "+QString::number(index[1])+", "+QString::number(index[2]);
	- overviewText += "Coordinates: "+pos+"\n";
	- overviewText += "SH order: "+QString::number(static_cast<double>(Odf_image->ShOrder()))+"\n";
	- overviewText += "Num. Coefficients: "+QString::number(static_cast<double>(Odf_image->NumCoefficients()))+"\n";
	- overviewText += "Coefficients: "+coeff_string+"\n";
	- overviewText += "GFA: "+QString::number(static_cast<double>(odf.GetGeneralizedFractionalAnisotropy()))+"\n";
	- overviewText += "Sum: "+QString::number(static_cast<double>(sum))+"\n";
	- overviewText += "Mean: "+QString::number(static_cast<double>(mean))+"\n";
	- overviewText += "Stdev: "+QString::number(static_cast<double>(stdev))+"\n";
	- overviewText += "Min: "+QString::number(static_cast<double>(min))+"\n";
	- overviewText += "Max: "+QString::number(static_cast<double>(max))+"\n";
	- vnl_vector_fixed<double, 3> pd = odf.GetDirection(odf.GetPrincipalDiffusionDirectionIndex());
	- overviewText += "Main Diffusion:\n "+QString::number(pd[0])+"\n "+QString::number(pd[1])+"\n "+QString::number(pd[2])+"\n";
	-
	- m_Controls->m_OdfValuesTextEdit->setText(values);
	- m_Controls->m_OverviewTextEdit->setVisible(true);
	- m_Controls->m_ODFDetailsWidget->SetParameters<5000>(odf);
	- m_Controls->m_ODFRenderWidget->GenerateODF<5000>(odf, m_OdfNormalization, dir_color);
	- m_Controls->m_OverviewTextEdit->setText(overviewText.toStdString().c_str());
	- }
	- else
	- {
	- m_Controls->m_ODFRenderWidget->setVisible(false);
	- m_Controls->m_OdfBox->setVisible(false);
	- overviewText += "Please reinit image geometry.\n";
	- }
	-
	-
	- }
	- catch(...)
	- {
	- QMessageBox::critical(nullptr, "Error", "Data could not be analyzed. The image might be corrupted.");
	- }
	-}
	-
	-void QmitkODFDetailsView::OnSliceChanged()
	-{
	- UpdateOdf();
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkODFDetailsView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkODFDetailsView.h
	deleted file mode 100644
	index 8ad5a1020a..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkODFDetailsView.h
	+++ /dev/null
	@@ -1,98 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _QMITKQmitkODFDetailsView_H_INCLUDED
	-#define _QMITKQmitkODFDetailsView_H_INCLUDED
	-
	-#include <berryISelectionListener.h>
	-
	-#include <QmitkAbstractView.h>
	-#include "mitkILifecycleAwarePart.h"
	-
	-#include "ui_QmitkODFDetailsViewControls.h"
	-
	-#include <itkVectorImage.h>
	-#include <itkImage.h>
	-#include <itkOrientationDistributionFunction.h>
	-#include <mitkOdfImage.h>
	-#include <vtkTransform.h>
	-#include <vtkDoubleArray.h>
	-#include <vtkOdfSource.h>
	-#include <vtkSmartPointer.h>
	-#include <QmitkRenderWindow.h>
	-#include <vtkPolyDataMapper.h>
	-#include <vtkRenderer.h>
	-#include <vtkCamera.h>
	-#include <itkDiffusionTensor3D.h>
	-#include <QmitkSliceNavigationListener.h>
	-#include <mitkTensorImage.h>
	-
	-/*!
	- \brief View displaying details of the orientation distribution function in the voxel at the current crosshair position.
	-*/
	-
	-class QmitkODFDetailsView : public QmitkAbstractView, public mitk::ILifecycleAwarePart
	-{
	- // this is needed for all Qt objects that should have a Qt meta-object
	- // (everything that derives from QObject and wants to have signal/slots)
	- Q_OBJECT
	-
	-public:
	-
	- static const std::string VIEW_ID;
	-
	- QmitkODFDetailsView();
	- virtual ~QmitkODFDetailsView();
	-
	- typedef mitk::OdfImage::ScalarPixelType TOdfPixelType;
	- typedef mitk::OdfImage::PixelType OdfVectorType;
	- typedef mitk::OdfImage::ItkOdfImageType OdfVectorImgType;
	-
	- typedef mitk::TensorImage::PixelType TensorPixelType;
	- typedef mitk::TensorImage::ItkTensorImageType TensorImageType;
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	-
	-
	-protected slots:
	-
	- void OnSliceChanged();
	-
	-protected:
	-
	- /// \brief called by QmitkAbstractView when DataManager's selection has changed
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- virtual void SetFocus() override;
	-
	- virtual void Activated() override;
	- virtual void Deactivated() override;
	- virtual void Visible() override;
	- virtual void Hidden() override;
	-
	- void UpdateOdf(); ///< called if slice position or datamanager selection has changed
	-
	- Ui::QmitkODFDetailsViewControls* m_Controls;
	-
	- int m_OdfNormalization; ///< normalization method defined in the visualization view
	- mitk::DataNode::Pointer m_ImageNode;
	- QmitkSliceNavigationListener m_SliceChangeListener;
	-};
	-
	-
	-
	-#endif // _QmitkODFDetailsView_H_INCLUDED
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkODFDetailsViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkODFDetailsViewControls.ui
	deleted file mode 100644
	index 84a4354f48..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkODFDetailsViewControls.ui
	+++ /dev/null
	@@ -1,259 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<ui version="4.0">
	- <class>QmitkODFDetailsViewControls</class>
	- <widget class="QWidget" name="QmitkODFDetailsViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>351</width>
	- <height>734</height>
	- </rect>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="windowTitle">
	- <string>QmitkTemplate</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QVBoxLayout" name="verticalLayout_2">
	- <property name="spacing">
	- <number>6</number>
	- </property>
	- <property name="leftMargin">
	- <number>9</number>
	- </property>
	- <property name="topMargin">
	- <number>9</number>
	- </property>
	- <property name="rightMargin">
	- <number>9</number>
	- </property>
	- <property name="bottomMargin">
	- <number>9</number>
	- </property>
	- <item>
	- <widget class="QGroupBox" name="m_InputData">
	- <property name="title">
	- <string>Please Select Input Data</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_3">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label">
	- <property name="text">
	- <string>DTI/ODF/SH:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QLabel" name="m_InputImageLabel">
	- <property name="text">
	- <string><html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html></string>
	- </property>
	- <property name="wordWrap">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <widget class="QGroupBox" name="m_OverviewBox">
	- <property name="title">
	- <string>Overview</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_4">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QTextEdit" name="m_OverviewTextEdit">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="readOnly">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QmitkODFRenderWidget" name="m_ODFRenderWidget" native="true">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>200</width>
	- <height>200</height>
	- </size>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <widget class="QFrame" name="frame_2">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>0</number>
	- </property>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <widget class="QGroupBox" name="m_OdfBox">
	- <property name="title">
	- <string>ODF Values</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_2">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="2" column="0">
	- <widget class="QTextEdit" name="m_OdfValuesTextEdit">
	- <property name="readOnly">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QmitkODFDetailsWidget" name="m_ODFDetailsWidget" native="true">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>200</height>
	- </size>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <spacer name="spacer1">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeType">
	- <enum>QSizePolicy::Expanding</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>220</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- </layout>
	- </widget>
	- <layoutdefault spacing="6" margin="11"/>
	- <customwidgets>
	- <customwidget>
	- <class>QmitkODFDetailsWidget</class>
	- <extends>QWidget</extends>
	- <header>QmitkODFDetailsWidget.h</header>
	- <container>1</container>
	- </customwidget>
	- <customwidget>
	- <class>QmitkODFRenderWidget</class>
	- <extends>QWidget</extends>
	- <header>QmitkODFRenderWidget.h</header>
	- <container>1</container>
	- </customwidget>
	- </customwidgets>
	- <resources/>
	- <connections/>
	-</ui>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkQBallReconstructionView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkQBallReconstructionView.cpp
	deleted file mode 100644
	index b12fb0d210..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkQBallReconstructionView.cpp
	+++ /dev/null
	@@ -1,808 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-//#define MBILOG_ENABLE_DEBUG
	-
	-#include "QmitkQBallReconstructionView.h"
	-
	-// qt includes
	-#include <QMessageBox>
	-
	-// itk includes
	-#include "itkTimeProbe.h"
	-
	-// mitk includes
	-#include "mitkProgressBar.h"
	-#include "mitkStatusBar.h"
	-
	-#include "mitkNodePredicateDataType.h"
	-#include "QmitkDataStorageComboBox.h"
	-
	-#include "itkDiffusionQballReconstructionImageFilter.h"
	-#include "itkAnalyticalDiffusionQballReconstructionImageFilter.h"
	-#include "itkDiffusionMultiShellQballReconstructionImageFilter.h"
	-#include "itkVectorContainer.h"
	-#include "itkB0ImageExtractionImageFilter.h"
	-#include <itkBinaryThresholdImageFilter.h>
	-
	-#include "mitkOdfImage.h"
	-#include "mitkProperties.h"
	-#include "mitkVtkResliceInterpolationProperty.h"
	-#include "mitkLookupTable.h"
	-#include "mitkLookupTableProperty.h"
	-#include "mitkTransferFunction.h"
	-#include "mitkTransferFunctionProperty.h"
	-#include "mitkDataNodeObject.h"
	-#include "mitkOdfNormalizationMethodProperty.h"
	-#include "mitkOdfScaleByProperty.h"
	-#include <mitkImageCast.h>
	-#include "mitkDiffusionImagingConfigure.h"
	-#include <mitkNodePredicateIsDWI.h>
	-
	-#include "berryIStructuredSelection.h"
	-#include "berryIWorkbenchWindow.h"
	-#include "berryISelectionService.h"
	-#include <mitkShImage.h>
	-#include <boost/version.hpp>
	-#include <itkShToOdfImageFilter.h>
	-#include <mitkImageCast.h>
	-#include <mitkDiffusionFunctionCollection.h>
	-
	-const std::string QmitkQBallReconstructionView::VIEW_ID = "org.mitk.views.qballreconstruction";
	-
	-
	-typedef float TTensorPixelType;
	-
	-const int QmitkQBallReconstructionView::nrconvkernels = 252;
	-
	-
	-struct QbrShellSelection
	-{
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionType GradientDirectionType;
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionsContainerType GradientDirectionContainerType;
	- typedef mitk::DiffusionPropertyHelper::BValueMapType BValueMapType;
	- typedef itk::VectorImage< DiffusionPixelType, 3 > ITKDiffusionImageType;
	-
	- QmitkQBallReconstructionView* m_View;
	- mitk::DataNode * m_Node;
	- std::string m_NodeName;
	-
	- std::vector<QCheckBox *> m_CheckBoxes;
	- QLabel * m_Label;
	-
	- mitk::Image * m_Image;
	-
	- QbrShellSelection(QmitkQBallReconstructionView* view, mitk::DataNode * node)
	- : m_View(view),
	- m_Node(node),
	- m_NodeName(node->GetName())
	- {
	- m_Image = dynamic_cast<mitk::Image * > (node->GetData());
	-
	- if(!m_Image)
	- {
	- MITK_ERROR << "QmitkQBallReconstructionView::QbrShellSelection : no image selected";
	- return;
	- }
	- bool isDiffusionImage( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast<mitk::Image *>(m_Node->GetData())) );
	-
	- if( !isDiffusionImage )
	- {
	- MITK_ERROR <<
	- "QmitkQBallReconstructionView::QbrShellSelection : selected image contains no diffusion information";
	- return;
	- }
	-
	- GenerateCheckboxes();
	-
	- }
	-
	- void GenerateCheckboxes()
	- {
	- BValueMapType origMap = mitk::DiffusionPropertyHelper::GetBValueMap(m_Image);
	- BValueMapType::iterator itStart = origMap.begin();
	- itStart++;
	- BValueMapType::iterator itEnd = origMap.end();
	-
	- m_Label = new QLabel(m_NodeName.c_str());
	- m_Label->setVisible(true);
	- m_View->m_Controls->m_QBallSelectionBox->layout()->addWidget(m_Label);
	-
	- for(BValueMapType::iterator it = itStart ; it!= itEnd; it++)
	- {
	- QCheckBox * box = new QCheckBox(QString::number(it->first));
	- m_View->m_Controls->m_QBallSelectionBox->layout()->addWidget(box);
	-
	- box->setChecked(true);
	- box->setCheckable(true);
	- // box->setVisible(true);
	- m_CheckBoxes.push_back(box);
	- }
	- }
	-
	- void SetVisible(bool vis)
	- {
	- foreach(QCheckBox * box, m_CheckBoxes)
	- {
	- box->setVisible(vis);
	- }
	- }
	-
	- BValueMapType GetBValueSelctionMap()
	- {
	- BValueMapType inputMap = mitk::DiffusionPropertyHelper::GetBValueMap(m_Image);
	- BValueMapType outputMap;
	-
	- unsigned int val = 0;
	-
	- if(inputMap.find(0) == inputMap.end()){
	- return outputMap;
	- }else{
	- outputMap[val] = inputMap[val];
	- }
	-
	- foreach(QCheckBox * box, m_CheckBoxes)
	- {
	- if(box->isChecked()){
	- val = box->text().toUInt();
	- outputMap[val] = inputMap[val];
	- MITK_INFO << val;
	- }
	- }
	-
	- return outputMap;
	- }
	-
	- ~QbrShellSelection()
	- {
	- m_View->m_Controls->m_QBallSelectionBox->layout()->removeWidget(m_Label);
	- delete m_Label;
	-
	- for(std::vector<QCheckBox *>::iterator it = m_CheckBoxes.begin() ; it!= m_CheckBoxes.end(); it++)
	- {
	- m_View->m_Controls->m_QBallSelectionBox->layout()->removeWidget((*it));
	- delete (*it);
	- }
	- m_CheckBoxes.clear();
	- }
	-};
	-
	-QmitkQBallReconstructionView::QmitkQBallReconstructionView()
	- : QmitkAbstractView(),
	- m_Controls(nullptr)
	-{
	-}
	-
	-QmitkQBallReconstructionView::~QmitkQBallReconstructionView()
	-{
	-
	-}
	-
	-void QmitkQBallReconstructionView::CreateQtPartControl(QWidget *parent)
	-{
	- if (!m_Controls)
	- {
	- // create GUI widgets
	- m_Controls = new Ui::QmitkQBallReconstructionViewControls;
	- m_Controls->setupUi(parent);
	- this->CreateConnections();
	-
	- QStringList items;
	- items << "2" << "4" << "6" << "8" << "10" << "12";
	- m_Controls->m_QBallReconstructionMaxLLevelComboBox->addItems(items);
	- m_Controls->m_QBallReconstructionMaxLLevelComboBox->setCurrentIndex(1);
	- MethodChoosen(m_Controls->m_QBallReconstructionMethodComboBox->currentIndex());
	- }
	-}
	-
	-void QmitkQBallReconstructionView::SetFocus()
	-{
	-}
	-
	-void QmitkQBallReconstructionView::CreateConnections()
	-{
	- if ( m_Controls )
	- {
	- connect( static_cast<QObject*>(m_Controls->m_ButtonStandard), SIGNAL(clicked()), this, SLOT(ReconstructStandard()) );
	- connect( static_cast<QObject*>(m_Controls->m_QBallReconstructionMethodComboBox), SIGNAL(currentIndexChanged(int)), this, SLOT(MethodChoosen(int)) );
	- connect( static_cast<QObject*>(m_Controls->m_QBallReconstructionThreasholdEdit), SIGNAL(valueChanged(int)), this, SLOT(PreviewThreshold(int)) );
	- connect( static_cast<QObject*>(m_Controls->m_ConvertButton), SIGNAL(clicked()), this, SLOT(ConvertShImage()) );
	-
	- m_Controls->m_ImageBox->SetDataStorage(this->GetDataStorage());
	- mitk::NodePredicateIsDWI::Pointer isDwi = mitk::NodePredicateIsDWI::New();
	- m_Controls->m_ImageBox->SetPredicate( isDwi );
	-
	- m_Controls->m_ShImageBox->SetDataStorage(this->GetDataStorage());
	- mitk::TNodePredicateDataType<mitk::ShImage>::Pointer isSh = mitk::TNodePredicateDataType<mitk::ShImage>::New();
	- m_Controls->m_ShImageBox->SetPredicate( isSh );
	-
	- connect( static_cast<QObject*>(m_Controls->m_ImageBox), SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui()));
	- connect( static_cast<QObject*>(m_Controls->m_ShImageBox), SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui()));
	-
	- UpdateGui();
	- }
	-}
	-
	-void QmitkQBallReconstructionView::ConvertShImage()
	-{
	- if (m_Controls->m_ShImageBox->GetSelectedNode().IsNotNull())
	- {
	- mitk::Image::Pointer mitkImg = dynamic_cast<mitk::Image*>(m_Controls->m_ShImageBox->GetSelectedNode()->GetData());
	- auto img = mitk::convert::GetOdfFromShImage(mitkImg);
	- mitk::DataNode::Pointer node= mitk::DataNode::New();
	- node->SetData( img );
	- node->SetName(m_Controls->m_ShImageBox->GetSelectedNode()->GetName());
	- GetDataStorage()->Add(node, m_Controls->m_ShImageBox->GetSelectedNode());
	- }
	-}
	-
	-void QmitkQBallReconstructionView::UpdateGui()
	-{
	- m_Controls->m_ButtonStandard->setEnabled(false);
	- if (m_Controls->m_ImageBox->GetSelectedNode().IsNotNull())
	- {
	- m_Controls->m_ButtonStandard->setEnabled(true);
	- GenerateShellSelectionUI(m_Controls->m_ImageBox->GetSelectedNode());
	- }
	-
	- m_Controls->m_ConvertButton->setEnabled(m_Controls->m_ShImageBox->GetSelectedNode().IsNotNull());
	-}
	-
	-void QmitkQBallReconstructionView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /part/, const QList<mitk::DataNode::Pointer>& /nodes/)
	-{
	- UpdateGui();
	-}
	-
	-void QmitkQBallReconstructionView::Activated()
	-{
	-}
	-
	-void QmitkQBallReconstructionView::Deactivated()
	-{
	-}
	-
	-void QmitkQBallReconstructionView::Visible()
	-{
	-}
	-
	-void QmitkQBallReconstructionView::Hidden()
	-{
	-}
	-
	-void QmitkQBallReconstructionView::ReconstructStandard()
	-{
	- int index = m_Controls->m_QBallReconstructionMethodComboBox->currentIndex();
	-
	- switch(index)
	- {
	- case 0:
	- {
	- // Numerical
	- Reconstruct(0,0);
	- break;
	- }
	- case 1:
	- {
	- // Standard
	- Reconstruct(1,0);
	- break;
	- }
	- case 2:
	- {
	- // Solid Angle
	- Reconstruct(1,6);
	- break;
	- }
	- case 3:
	- {
	- // ADC
	- Reconstruct(1,4);
	- break;
	- }
	- case 4:
	- {
	- // Raw Signal
	- Reconstruct(1,5);
	- break;
	- }
	- case 5:
	- {
	- // Q-Ball reconstruction
	- Reconstruct(2,0);
	- break;
	- }
	- }
	-}
	-
	-void QmitkQBallReconstructionView::MethodChoosen(int method)
	-{
	- m_Controls->m_QBallSelectionBox->setHidden(true);
	- m_Controls->m_OutputOdfImage->setHidden(true);
	-
	- if (method==0)
	- m_Controls->m_ShFrame->setVisible(false);
	- else
	- m_Controls->m_ShFrame->setVisible(true);
	-
	- switch(method)
	- {
	- case 0:
	- m_Controls->m_Description->setText("Numerical recon. (Tuch 2004)");
	- break;
	- case 1:
	- m_Controls->m_Description->setText("Spherical harmonics recon. (Descoteaux 2007)");
	- m_Controls->m_OutputOdfImage->setHidden(false);
	- break;
	- case 2:
	- m_Controls->m_Description->setText("SH recon. with solid angle consideration (Aganj 2009)");
	- m_Controls->m_OutputOdfImage->setHidden(false);
	- break;
	- case 3:
	- m_Controls->m_Description->setText("SH solid angle with non-neg. constraint (Goh 2009)");
	- m_Controls->m_OutputOdfImage->setHidden(false);
	- break;
	- case 4:
	- m_Controls->m_Description->setText("SH recon. of the plain ADC-profiles");
	- m_Controls->m_OutputOdfImage->setHidden(false);
	- break;
	- case 5:
	- m_Controls->m_Description->setText("SH recon. of the raw diffusion signal");
	- m_Controls->m_OutputOdfImage->setHidden(false);
	- break;
	- case 6:
	- m_Controls->m_Description->setText("SH recon. of the multi shell diffusion signal (Aganj 2010)");
	- m_Controls->m_QBallSelectionBox->setHidden(false);
	- m_Controls->m_OutputOdfImage->setHidden(false);
	- break;
	- }
	-}
	-
	-void QmitkQBallReconstructionView::Reconstruct(int method, int normalization)
	-{
	- if (m_Controls->m_ImageBox->GetSelectedNode().IsNotNull())
	- {
	- if(method == 0)
	- {
	- NumericalQBallReconstruction(m_Controls->m_ImageBox->GetSelectedNode(), normalization);
	- }
	- else if(method == 1)
	- {
	- AnalyticalQBallReconstruction(m_Controls->m_ImageBox->GetSelectedNode(), normalization);
	- }
	- else if(method == 2)
	- {
	- MultiQBallReconstruction(m_Controls->m_ImageBox->GetSelectedNode());
	- }
	- }
	-}
	-
	-void QmitkQBallReconstructionView::NumericalQBallReconstruction(mitk::DataNode::Pointer node, int normalization)
	-{
	- try
	- {
	- mitk::Image* vols = static_cast<mitk::Image*>(node->GetData());
	-
	- std::string nodename = node->GetName();
	-
	- typedef itk::DiffusionQballReconstructionImageFilter
	- <DiffusionPixelType, DiffusionPixelType, TTensorPixelType, ODF_SAMPLING_SIZE>
	- QballReconstructionImageFilterType;
	-
	- ITKDiffusionImageType::Pointer itkVectorImagePointer = ITKDiffusionImageType::New();
	- mitk::CastToItkImage(vols, itkVectorImagePointer);
	-
	- QballReconstructionImageFilterType::Pointer filter = QballReconstructionImageFilterType::New();
	- filter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(vols));
	- filter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(vols), itkVectorImagePointer);
	- filter->SetThreshold( static_cast<short>(m_Controls->m_QBallReconstructionThreasholdEdit->value()) );
	-
	- std::string nodePostfix;
	- switch(normalization)
	- {
	- case 0:
	- {
	- filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_STANDARD);
	- nodePostfix = "_Numerical_Qball";
	- break;
	- }
	- case 1:
	- {
	- filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_B_ZERO_B_VALUE);
	- nodePostfix = "_Numerical_ZeroBvalueNormalization_Qball";
	- break;
	- }
	- case 2:
	- {
	- filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_B_ZERO);
	- nodePostfix = "_NumericalQball_ZeroNormalization_Qball";
	- break;
	- }
	- case 3:
	- {
	- filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_NONE);
	- nodePostfix = "_NumericalQball_NoNormalization_Qball";
	- break;
	- }
	- default:
	- {
	- filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_STANDARD);
	- nodePostfix = "_NumericalQball_Qball";
	- }
	- }
	-
	- filter->Update();
	-
	- // ODFs TO DATATREE
	- mitk::OdfImage::Pointer image = mitk::OdfImage::New();
	- image->InitializeByItk( filter->GetOutput() );
	- image->SetVolume( filter->GetOutput()->GetBufferPointer() );
	- mitk::DataNode::Pointer new_node = mitk::DataNode::New();
	- new_node->SetData( image );
	- new_node->SetName(nodename+nodePostfix);
	- mitk::ProgressBar::GetInstance()->Progress();
	-
	- GetDataStorage()->Add(new_node, node);
	-
	- this->GetRenderWindowPart()->RequestUpdate();
	- }
	- catch (itk::ExceptionObject &ex)
	- {
	- MITK_INFO << ex ;
	- QMessageBox::information(nullptr, "Reconstruction not possible:", ex.GetDescription());
	- return ;
	- }
	-}
	-
	-void QmitkQBallReconstructionView::AnalyticalQBallReconstruction( mitk::DataNode::Pointer node, int normalization)
	-{
	- try
	- {
	- auto lambda = m_Controls->m_QBallReconstructionLambdaLineEdit->value();
	- switch(m_Controls->m_QBallReconstructionMaxLLevelComboBox->currentIndex())
	- {
	- case 0:
	- {
	- TemplatedAnalyticalQBallReconstruction<2>(node, lambda, normalization);
	- break;
	- }
	- case 1:
	- {
	- TemplatedAnalyticalQBallReconstruction<4>(node, lambda, normalization);
	- break;
	- }
	- case 2:
	- {
	- TemplatedAnalyticalQBallReconstruction<6>(node, lambda, normalization);
	- break;
	- }
	- case 3:
	- {
	- TemplatedAnalyticalQBallReconstruction<8>(node, lambda, normalization);
	- break;
	- }
	- case 4:
	- {
	- TemplatedAnalyticalQBallReconstruction<10>(node, lambda, normalization);
	- break;
	- }
	- case 5:
	- {
	- TemplatedAnalyticalQBallReconstruction<12>(node, lambda, normalization);
	- break;
	- }
	- }
	-
	- this->GetRenderWindowPart()->RequestUpdate();
	- }
	- catch (itk::ExceptionObject &ex)
	- {
	- MITK_INFO << ex;
	- QMessageBox::information(nullptr, "Reconstruction not possible:", ex.GetDescription());
	- return;
	- }
	-}
	-
	-template<int L>
	-void QmitkQBallReconstructionView::TemplatedAnalyticalQBallReconstruction(mitk::DataNode* dataNodePointer, double lambda, int normalization)
	-{
	- typedef itk::AnalyticalDiffusionQballReconstructionImageFilter
	- <DiffusionPixelType,DiffusionPixelType,TTensorPixelType,L,ODF_SAMPLING_SIZE> FilterType;
	- typename FilterType::Pointer filter = FilterType::New();
	-
	- mitk::Image* vols = dynamic_cast<mitk::Image*>(dataNodePointer->GetData());
	-
	- ITKDiffusionImageType::Pointer itkVectorImagePointer = ITKDiffusionImageType::New();
	- mitk::CastToItkImage(vols, itkVectorImagePointer);
	-
	- filter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(vols));
	- filter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(vols), itkVectorImagePointer);
	- filter->SetThreshold( static_cast<short>(m_Controls->m_QBallReconstructionThreasholdEdit->value()) );
	- filter->SetLambda(lambda);
	-
	- std::string nodePostfix;
	- switch(normalization)
	- {
	- case 0:
	- {
	- filter->SetNormalizationMethod(FilterType::QBAR_STANDARD);
	- nodePostfix = "_Qball";
	- break;
	- }
	- case 1:
	- {
	- filter->SetNormalizationMethod(FilterType::QBAR_B_ZERO_B_VALUE);
	- nodePostfix = "_1_Qball";
	- break;
	- }
	- case 2:
	- {
	- filter->SetNormalizationMethod(FilterType::QBAR_B_ZERO);
	- nodePostfix = "_2_Qball";
	- break;
	- }
	- case 3:
	- {
	- filter->SetNormalizationMethod(FilterType::QBAR_NONE);
	- nodePostfix = "_3_Qball";
	- break;
	- }
	- case 4:
	- {
	- filter->SetNormalizationMethod(FilterType::QBAR_ADC_ONLY);
	- nodePostfix = "_AdcProfile";
	- break;
	- }
	- case 5:
	- {
	- filter->SetNormalizationMethod(FilterType::QBAR_RAW_SIGNAL);
	- nodePostfix = "_RawSignal";
	- break;
	- }
	- case 6:
	- {
	- filter->SetNormalizationMethod(FilterType::QBAR_SOLID_ANGLE);
	- nodePostfix = "_CSA_Qball";
	- break;
	- }
	- case 7:
	- {
	- filter->SetNormalizationMethod(FilterType::QBAR_NONNEG_SOLID_ANGLE);
	- nodePostfix = "_NonNegCSA_Qball";
	- break;
	- }
	- default:
	- {
	- filter->SetNormalizationMethod(FilterType::QBAR_STANDARD);
	- }
	- }
	-
	- filter->Update();
	-
	- mitk::Image::Pointer coeffsImage = dynamic_cast<mitk::Image*>(mitk::ShImage::New().GetPointer());
	- coeffsImage->InitializeByItk( filter->GetCoefficientImage().GetPointer() );
	- coeffsImage->SetVolume( filter->GetCoefficientImage()->GetBufferPointer() );
	-
	- mitk::DataNode::Pointer coeffsNode = mitk::DataNode::New();
	- coeffsNode->SetData( coeffsImage );
	- coeffsNode->SetProperty( "name", mitk::StringProperty::New(dataNodePointer->GetName() + nodePostfix + "_SH") );
	- GetDataStorage()->Add(coeffsNode, dataNodePointer);
	-
	- // ODFs TO DATATREE
	- if(m_Controls->m_OutputOdfImage->isChecked())
	- {
	- mitk::OdfImage::Pointer image = mitk::OdfImage::New();
	- image->InitializeByItk( filter->GetOutput() );
	- image->SetVolume( filter->GetOutput()->GetBufferPointer() );
	- mitk::DataNode::Pointer node=mitk::DataNode::New();
	- node->SetData( image );
	- node->SetName(dataNodePointer->GetName() + nodePostfix + "_Sampeld");
	-
	- GetDataStorage()->Add(node, coeffsNode);
	- }
	-}
	-
	-void QmitkQBallReconstructionView::MultiQBallReconstruction(mitk::DataNode::Pointer node)
	-{
	- try
	- {
	- auto lambda = m_Controls->m_QBallReconstructionLambdaLineEdit->value();
	- switch(m_Controls->m_QBallReconstructionMaxLLevelComboBox->currentIndex())
	- {
	- case 0:
	- {
	- TemplatedMultiQBallReconstruction<2>(lambda, node);
	- break;
	- }
	- case 1:
	- {
	- TemplatedMultiQBallReconstruction<4>(lambda, node);
	- break;
	- }
	- case 2:
	- {
	- TemplatedMultiQBallReconstruction<6>(lambda, node);
	- break;
	- }
	- case 3:
	- {
	- TemplatedMultiQBallReconstruction<8>(lambda, node);
	- break;
	- }
	- case 4:
	- {
	- TemplatedMultiQBallReconstruction<10>(lambda, node);
	- break;
	- }
	- case 5:
	- {
	- TemplatedMultiQBallReconstruction<12>(lambda, node);
	- break;
	- }
	- }
	- }
	- catch (itk::ExceptionObject &ex)
	- {
	- MITK_INFO << ex ;
	- QMessageBox::information(nullptr, "Reconstruction not possible:", ex.GetDescription());
	- return ;
	- }
	-}
	-
	-template<int L>
	-void QmitkQBallReconstructionView::TemplatedMultiQBallReconstruction(double lambda, mitk::DataNode* dataNodePointer)
	-{
	- typedef itk::DiffusionMultiShellQballReconstructionImageFilter
	- <DiffusionPixelType,DiffusionPixelType,TTensorPixelType,L,ODF_SAMPLING_SIZE> FilterType;
	- typename FilterType::Pointer filter = FilterType::New();
	-
	- std::string nodename;
	- dataNodePointer->GetStringProperty("name",nodename);
	-
	- mitk::Image* dwi = dynamic_cast<mitk::Image*>(dataNodePointer->GetData());
	- BValueMapType currSelectionMap = m_ShellSelectorMap[dataNodePointer]->GetBValueSelctionMap();
	-
	- if(currSelectionMap.size() != 4)// \|\| currSelectionMap.find(0) != currSelectionMap.end())
	- {
	- QMessageBox::information(nullptr, "Reconstruction not possible:" ,QString("Only three equidistant shells are supported. (ImageName: " + QString(nodename.c_str()) + ")"));
	- return;
	- }
	-
	- BValueMapType::reverse_iterator it1 = currSelectionMap.rbegin();
	- BValueMapType::reverse_iterator it2 = currSelectionMap.rbegin();
	- ++it2;
	-
	- // Get average distance
	- int avdistance = 0;
	- for(; it2 != currSelectionMap.rend(); ++it1,++it2)
	- avdistance += static_cast<int>(it1->first - it2->first);
	- avdistance /= currSelectionMap.size()-1;
	-
	- // Check if all shells are using the same averae distance
	- it1 = currSelectionMap.rbegin();
	- it2 = currSelectionMap.rbegin();
	- ++it2;
	- for(; it2 != currSelectionMap.rend(); ++it1,++it2)
	- {
	- if(avdistance != static_cast<int>(it1->first - it2->first))
	- {
	- QMessageBox::information(nullptr, "Reconstruction not possible:" ,QString("Selected Shells are not in a equidistant configuration. (ImageName: " + QString(nodename.c_str()) + ")"));
	- return;
	- }
	- }
	- ITKDiffusionImageType::Pointer itkVectorImagePointer = ITKDiffusionImageType::New();
	- mitk::CastToItkImage(dwi, itkVectorImagePointer);
	-
	- filter->SetBValueMap(m_ShellSelectorMap[dataNodePointer]->GetBValueSelctionMap());
	- filter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(dwi), itkVectorImagePointer, mitk::DiffusionPropertyHelper::GetReferenceBValue(dwi));
	- filter->SetThreshold( static_cast<short>(m_Controls->m_QBallReconstructionThreasholdEdit->value()) );
	- filter->SetLambda(lambda);
	- filter->Update();
	-
	-
	- mitk::Image::Pointer coeffsImage = dynamic_cast<mitk::Image*>(mitk::ShImage::New().GetPointer());
	- coeffsImage->InitializeByItk( filter->GetCoefficientImage().GetPointer() );
	- coeffsImage->SetVolume( filter->GetCoefficientImage()->GetBufferPointer() );
	-
	- mitk::DataNode::Pointer coeffsNode=mitk::DataNode::New();
	- coeffsNode->SetData( coeffsImage );
	- coeffsNode->SetProperty( "name", mitk::StringProperty::New(dataNodePointer->GetName() + "_SH_MultiShell_Qball_SH") );
	- GetDataStorage()->Add(coeffsNode, dataNodePointer);
	-
	- if(m_Controls->m_OutputOdfImage->isChecked())
	- {
	- // ODFs TO DATATREE
	- mitk::OdfImage::Pointer image = mitk::OdfImage::New();
	- image->InitializeByItk( filter->GetOutput() );
	- image->SetVolume( filter->GetOutput()->GetBufferPointer() );
	- mitk::DataNode::Pointer node=mitk::DataNode::New();
	- node->SetData( image );
	- node->SetName(dataNodePointer->GetName() + "_SH_MultiShell_Qball_Sampled");
	-
	- GetDataStorage()->Add(node, coeffsNode);
	- }
	-}
	-
	-void QmitkQBallReconstructionView::GenerateShellSelectionUI(mitk::DataNode::Pointer node)
	-{
	- std::map<const mitk::DataNode * , QbrShellSelection * > tempMap;
	-
	- if(m_ShellSelectorMap.find( node.GetPointer() ) != m_ShellSelectorMap.end())
	- {
	- tempMap[node.GetPointer()] = m_ShellSelectorMap[node.GetPointer()];
	- m_ShellSelectorMap.erase(node.GetPointer());
	- }
	- else
	- {
	- tempMap[node.GetPointer()] = new QbrShellSelection(this, node );
	- tempMap[node.GetPointer()]->SetVisible(true);
	- }
	-
	- for(std::map<const mitk::DataNode * , QbrShellSelection * >::iterator it = m_ShellSelectorMap.begin(); it != m_ShellSelectorMap.end();it ++)
	- {
	- delete it->second;
	- }
	- m_ShellSelectorMap.clear();
	- m_ShellSelectorMap = tempMap;
	-}
	-
	-void QmitkQBallReconstructionView::PreviewThreshold(short threshold)
	-{
	- if (m_Controls->m_ImageBox->GetSelectedNode().IsNotNull())
	- {
	- mitk::Image* vols = static_cast<mitk::Image*>(m_Controls->m_ImageBox->GetSelectedNode()->GetData());
	-
	- // Extract b0 image
	- ITKDiffusionImageType::Pointer itkVectorImagePointer = ITKDiffusionImageType::New();
	- mitk::CastToItkImage(vols, itkVectorImagePointer);
	-
	- typedef itk::B0ImageExtractionImageFilter<short, short> FilterType;
	- FilterType::Pointer filterB0 = FilterType::New();
	- filterB0->SetInput( itkVectorImagePointer );
	- filterB0->SetDirections(mitk::DiffusionPropertyHelper::GetGradientContainer(vols));
	- filterB0->Update();
	-
	- mitk::Image::Pointer mitkImage = mitk::Image::New();
	-
	- typedef itk::Image<short, 3> ImageType;
	- typedef itk::Image<short, 3> SegmentationType;
	- typedef itk::BinaryThresholdImageFilter<ImageType, SegmentationType> ThresholdFilterType;
	- // apply threshold
	- ThresholdFilterType::Pointer filterThreshold = ThresholdFilterType::New();
	- filterThreshold->SetInput(filterB0->GetOutput());
	- filterThreshold->SetLowerThreshold(threshold);
	- filterThreshold->SetInsideValue(0);
	- filterThreshold->SetOutsideValue(1); // mark cut off values red
	- filterThreshold->Update();
	-
	- mitkImage->InitializeByItk( filterThreshold->GetOutput() );
	- mitkImage->SetVolume( filterThreshold->GetOutput()->GetBufferPointer() );
	- mitk::DataNode::Pointer node;
	- if (this->GetDataStorage()->GetNamedDerivedNode("ThresholdOverlay", m_Controls->m_ImageBox->GetSelectedNode()))
	- {
	- node = this->GetDataStorage()->GetNamedDerivedNode("ThresholdOverlay", m_Controls->m_ImageBox->GetSelectedNode());
	- }
	- else
	- {
	- // create a new node, to show thresholded values
	- node = mitk::DataNode::New();
	- GetDataStorage()->Add( node, m_Controls->m_ImageBox->GetSelectedNode() );
	- node->SetProperty( "name", mitk::StringProperty::New("ThresholdOverlay"));
	- node->SetBoolProperty("helper object", true);
	- }
	- node->SetData( mitkImage );
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- }
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkQBallReconstructionView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkQBallReconstructionView.h
	deleted file mode 100644
	index b913e147cd..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkQBallReconstructionView.h
	+++ /dev/null
	@@ -1,133 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _QMITKQBALLRECONSTRUCTIONVIEW_H_INCLUDED
	-#define _QMITKQBALLRECONSTRUCTIONVIEW_H_INCLUDED
	-
	-#include <QmitkAbstractView.h>
	-#include <mitkILifecycleAwarePart.h>
	-
	-#include <string>
	-
	-#include "ui_QmitkQBallReconstructionViewControls.h"
	-
	-#include <mitkImage.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <itkVectorImage.h>
	-#include <mitkShImage.h>
	-
	-typedef short DiffusionPixelType;
	-
	-struct QbrSelListener;
	-
	-struct QbrShellSelection;
	-
	-/*!
	- * \ingroup org_mitk_gui_qt_qballreconstruction_internal
	- *
	- * \brief QmitkQBallReconstructionView
	- *
	- * Document your class here.
	- */
	-class QmitkQBallReconstructionView : public QmitkAbstractView, public mitk::ILifecycleAwarePart
	-{
	-
	- friend struct QbrSelListener;
	-
	- friend struct QbrShellSelection;
	-
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionType GradientDirectionType;
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionsContainerType GradientDirectionContainerType;
	- typedef mitk::DiffusionPropertyHelper::BValueMapType BValueMapType;
	- typedef itk::VectorImage< DiffusionPixelType, 3 > ITKDiffusionImageType;
	-
	- // this is needed for all Qt objects that should have a MOC object (everything that derives from QObject)
	- Q_OBJECT
	-
	- public:
	-
	- static const std::string VIEW_ID;
	-
	- QmitkQBallReconstructionView();
	- virtual ~QmitkQBallReconstructionView();
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	-
	- /// \brief Creation of the connections of main and control widget
	- virtual void CreateConnections();
	-
	- ///
	- /// Sets the focus to an internal widget.
	- ///
	- virtual void SetFocus() override;
	-
	- /// \brief Called when the view gets activated
	- virtual void Activated() override;
	-
	- /// \brief Called when the view gets deactivated
	- virtual void Deactivated() override;
	-
	- /// \brief Called when the view becomes visible
	- virtual void Visible() override;
	-
	- /// \brief Called when the view becomes hidden
	- virtual void Hidden() override;
	-
	- static const int nrconvkernels;
	-
	-protected slots:
	-
	- void UpdateGui();
	- void ReconstructStandard();
	- void ConvertShImage();
	- void MethodChoosen(int method);
	- void Reconstruct(int method, int normalization);
	-
	- void NumericalQBallReconstruction(mitk::DataNode::Pointer node, int normalization);
	- void AnalyticalQBallReconstruction(mitk::DataNode::Pointer node, int normalization);
	- void MultiQBallReconstruction(mitk::DataNode::Pointer node);
	-
	-
	- /**
	- * @brief PreviewThreshold Generates a preview of the values that are cut off by the thresholds
	- * @param threshold
	- */
	- void PreviewThreshold(short threshold);
	-
	-protected:
	-
	- /// \brief called by QmitkAbstractView when DataManager's selection has changed
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- Ui::QmitkQBallReconstructionViewControls* m_Controls;
	-
	- template<int L>
	- void TemplatedAnalyticalQBallReconstruction(mitk::DataNode* dataNodePointer, double lambda, int normalization);
	-
	- template<int L>
	- void TemplatedMultiQBallReconstruction(double lambda, mitk::DataNode*);
	-
	-private:
	-
	- std::map< const mitk::DataNode , QbrShellSelection > m_ShellSelectorMap;
	- void GenerateShellSelectionUI(mitk::DataNode::Pointer node);
	-};
	-
	-
	-
	-
	-#endif // _QMITKQBALLRECONSTRUCTIONVIEW_H_INCLUDED
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkQBallReconstructionViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkQBallReconstructionViewControls.ui
	deleted file mode 100644
	index d73a88cf59..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkQBallReconstructionViewControls.ui
	+++ /dev/null
	@@ -1,424 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<ui version="4.0">
	- <class>QmitkQBallReconstructionViewControls</class>
	- <widget class="QWidget" name="QmitkQBallReconstructionViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>372</width>
	- <height>844</height>
	- </rect>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="acceptDrops">
	- <bool>true</bool>
	- </property>
	- <property name="windowTitle">
	- <string>QmitkQBallReconstructionViewControls</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_4">
	- <property name="verticalSpacing">
	- <number>25</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QGroupBox" name="groupBox_3">
	- <property name="title">
	- <string>Parameters</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_5">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QComboBox" name="m_QBallReconstructionMethodComboBox">
	- <property name="currentIndex">
	- <number>2</number>
	- </property>
	- <item>
	- <property name="text">
	- <string>Numerical</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Standard</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Solid Angle</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>ADC-Profile only</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Raw Signal only</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Multi-Shell</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="m_Description">
	- <property name="text">
	- <string>TextLabel</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QFrame" name="m_ShFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_3">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QFrame" name="frame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_2">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="4" column="0">
	- <widget class="QLabel" name="m_QBallReconstructionLambdaTextLabel_2">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="toolTip">
	- <string>Regularization Parameter</string>
	- </property>
	- <property name="text">
	- <string>Lambda:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="1">
	- <widget class="QDoubleSpinBox" name="m_QBallReconstructionLambdaLineEdit">
	- <property name="toolTip">
	- <string>Regularization factor</string>
	- </property>
	- <property name="decimals">
	- <number>3</number>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.001000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.006000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="m_QBallReconstructionMaxLLevelTextLabel_2">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="text">
	- <string>SH-Order:</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QComboBox" name="m_QBallReconstructionMaxLLevelComboBox">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="currentIndex">
	- <number>-1</number>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="m_QBallReconstructionThresholdLabel_2">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="text">
	- <string>B0 Threshold</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QSpinBox" name="m_QBallReconstructionThreasholdEdit">
	- <property name="maximum">
	- <number>10000</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QCheckBox" name="m_OutputOdfImage">
	- <property name="text">
	- <string>Output Sampled ODF Image</string>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QCommandLinkButton" name="m_ButtonStandard">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string notr="true"/>
	- </property>
	- <property name="text">
	- <string>Start Reconstruction</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QGroupBox" name="m_InputData">
	- <property name="title">
	- <string>Input Data</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label">
	- <property name="toolTip">
	- <string>Input for Q-Ball reconstruction.</string>
	- </property>
	- <property name="text">
	- <string>Raw DWI:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_ImageBox"/>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QGroupBox" name="m_QBallSelectionBox">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="layoutDirection">
	- <enum>Qt::LeftToRight</enum>
	- </property>
	- <property name="autoFillBackground">
	- <bool>false</bool>
	- </property>
	- <property name="title">
	- <string>Multi-Shell Reconstruction</string>
	- </property>
	- <layout class="QVBoxLayout" name="verticalLayout_2">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- </layout>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <spacer name="verticalSpacer">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>0</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="3" column="0">
	- <widget class="QGroupBox" name="groupBox">
	- <property name="title">
	- <string>Convert SH to sampled ODF image</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_6">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="3" column="0">
	- <widget class="QCommandLinkButton" name="m_ConvertButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string notr="true"/>
	- </property>
	- <property name="text">
	- <string>Convert</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QFrame" name="frame_2">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_7">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_2">
	- <property name="toolTip">
	- <string>Input for Q-Ball reconstruction.</string>
	- </property>
	- <property name="text">
	- <string>SH Image:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_ShImageBox"/>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <layoutdefault spacing="6" margin="11"/>
	- <customwidgets>
	- <customwidget>
	- <class>QmitkDataStorageComboBox</class>
	- <extends>QComboBox</extends>
	- <header location="global">QmitkDataStorageComboBox.h</header>
	- </customwidget>
	- </customwidgets>
	- <resources/>
	- <connections/>
	-</ui>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkTensorReconstructionView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkTensorReconstructionView.cpp
	deleted file mode 100644
	index ac8cd5167f..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkTensorReconstructionView.cpp
	+++ /dev/null
	@@ -1,931 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkTensorReconstructionView.h"
	-#include "mitkDiffusionImagingConfigure.h"
	-
	-// qt includes
	-#include <QMessageBox>
	-#include <QImage>
	-#include <QGraphicsScene>
	-#include <QGraphicsPixmapItem>
	-#include <QGraphicsLinearLayout>
	-
	-
	-// itk includes
	-#include "itkTimeProbe.h"
	-//#include "itkTensor.h"
	-
	-// mitk includes
	-#include "mitkProgressBar.h"
	-#include "mitkStatusBar.h"
	-
	-#include "mitkNodePredicateDataType.h"
	-#include "QmitkDataStorageComboBox.h"
	-
	-#include "mitkTeemDiffusionTensor3DReconstructionImageFilter.h"
	-#include "itkDiffusionTensor3DReconstructionImageFilter.h"
	-#include "itkTensorImageToDiffusionImageFilter.h"
	-#include "itkPointShell.h"
	-#include "itkVector.h"
	-#include "itkB0ImageExtractionImageFilter.h"
	-#include "itkTensorReconstructionWithEigenvalueCorrectionFilter.h"
	-
	-#include "mitkImageCast.h"
	-#include "mitkImageAccessByItk.h"
	-#include <itkBinaryThresholdImageFilter.h>
	-#include <mitkImageVtkMapper2D.h>
	-
	-#include "mitkProperties.h"
	-#include "mitkDataNodeObject.h"
	-#include "mitkOdfNormalizationMethodProperty.h"
	-#include "mitkOdfScaleByProperty.h"
	-#include "mitkLookupTableProperty.h"
	-#include "mitkLookupTable.h"
	-#include "mitkImageStatisticsHolder.h"
	-#include <mitkITKImageImport.h>
	-
	-#include <itkTensorImageToOdfImageFilter.h>
	-#include <itkResidualImageFilter.h>
	-
	-#include <berryIWorkbenchWindow.h>
	-#include <berryISelectionService.h>
	-#include <mitkImageVtkMapper2D.h>
	-#include <mitkNodePredicateIsDWI.h>
	-#include <mitkNodePredicateDataType.h>
	-
	-const std::string QmitkTensorReconstructionView::VIEW_ID = "org.mitk.views.tensorreconstruction";
	-
	-typedef mitk::TensorImage::ScalarPixelType TTensorPixelType;
	-typedef mitk::TensorImage::PixelType TensorPixelType;
	-typedef mitk::TensorImage::ItkTensorImageType TensorImageType;
	-
	-using namespace berry;
	-
	-QmitkTensorReconstructionView::QmitkTensorReconstructionView()
	- : QmitkAbstractView(),
	- m_Controls(nullptr)
	-{
	-
	-}
	-
	-QmitkTensorReconstructionView::~QmitkTensorReconstructionView()
	-{
	-
	-}
	-
	-void QmitkTensorReconstructionView::CreateQtPartControl(QWidget *parent)
	-{
	- if (!m_Controls)
	- {
	- // create GUI widgets
	- m_Controls = new Ui::QmitkTensorReconstructionViewControls;
	- m_Controls->setupUi(parent);
	- this->CreateConnections();
	-
	- Advanced1CheckboxClicked();
	- }
	-}
	-
	-void QmitkTensorReconstructionView::SetFocus()
	-{
	- m_Controls->m_Advanced1->setFocus();
	-}
	-
	-void QmitkTensorReconstructionView::CreateConnections()
	-{
	- if ( m_Controls )
	- {
	- connect( (QObject*)(m_Controls->m_StartReconstruction), SIGNAL(clicked()), this, SLOT(Reconstruct()) );
	- connect( (QObject*)(m_Controls->m_Advanced1), SIGNAL(clicked()), this, SLOT(Advanced1CheckboxClicked()) );
	- connect( (QObject*)(m_Controls->m_TensorsToDWIButton), SIGNAL(clicked()), this, SLOT(TensorsToDWI()) );
	- connect( (QObject*)(m_Controls->m_TensorsToOdfButton), SIGNAL(clicked()), this, SLOT(TensorsToOdf()) );
	- connect( (QObject*)(m_Controls->m_ResidualButton), SIGNAL(clicked()), this, SLOT(ResidualCalculation()) );
	- connect( (QObject*)(m_Controls->m_PerSliceView), SIGNAL(pointSelected(int, int)), this, SLOT(ResidualClicked(int, int)) );
	- connect( (QObject*)(m_Controls->m_TensorReconstructionThreshold), SIGNAL(valueChanged(int)), this, SLOT(PreviewThreshold(int)) );
	-
	- m_Controls->m_ResidualTab->setVisible(false);
	- m_Controls->m_PercentagesOfOutliers->setVisible(false);
	-
	- m_Controls->m_DwiBox->SetDataStorage(this->GetDataStorage());
	- mitk::NodePredicateIsDWI::Pointer isDwi = mitk::NodePredicateIsDWI::New();
	- m_Controls->m_DwiBox->SetPredicate( isDwi );
	- connect( (QObject*)(m_Controls->m_DwiBox), SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui()));
	-
	- m_Controls->m_OdfBox->SetDataStorage(this->GetDataStorage());
	- mitk::TNodePredicateDataType<mitk::TensorImage>::Pointer isDti = mitk::TNodePredicateDataType<mitk::TensorImage>::New();
	- m_Controls->m_OdfBox->SetPredicate( isDti );
	- connect( (QObject*)(m_Controls->m_OdfBox), SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui()));
	-
	- m_Controls->m_DtiBox->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_DtiBox->SetPredicate( isDti );
	- connect( (QObject*)(m_Controls->m_DtiBox), SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui()));
	-
	- m_Controls->m_ResBox1->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_ResBox1->SetPredicate( isDwi );
	- connect( (QObject*)(m_Controls->m_ResBox1), SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui()));
	-
	- m_Controls->m_ResBox2->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_ResBox2->SetPredicate( isDti );
	- connect( (QObject*)(m_Controls->m_ResBox2), SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui()));
	- }
	-}
	-
	-void QmitkTensorReconstructionView::ResidualClicked(int slice, int volume)
	-{
	- mitk::Image* diffImage;
	- mitk::DataNode::Pointer correctNode;
	- mitk::BaseGeometry* geometry;
	-
	- if (m_Controls->m_ResBox1->GetSelectedNode().IsNotNull())
	- {
	- diffImage = static_cast<mitk::Image*>(m_Controls->m_ResBox1->GetSelectedNode()->GetData());
	-
	- geometry = m_Controls->m_ResBox1->GetSelectedNode()->GetData()->GetGeometry();
	-
	- // Remember the node whose display index must be updated
	- correctNode = mitk::DataNode::New();
	- correctNode = m_Controls->m_ResBox1->GetSelectedNode();
	-
	- GradientDirectionContainerType::Pointer dirs = mitk::DiffusionPropertyHelper::GetGradientContainer(diffImage);
	-
	- for(itk::SizeValueType i=0; i<dirs->Size() && i<=(itk::SizeValueType)volume; i++)
	- {
	- GradientDirectionType grad = dirs->ElementAt(i);
	-
	- // check if image is b0 weighted
	- if(fabs(grad[0]) < 0.001 && fabs(grad[1]) < 0.001 && fabs(grad[2]) < 0.001)
	- {
	- volume++;
	- }
	- }
	-
	- QString pos = "Volume: ";
	- pos.append(QString::number(volume));
	- pos.append(", Slice: ");
	- pos.append(QString::number(slice));
	- m_Controls->m_PositionLabel->setText(pos);
	-
	- if(correctNode)
	- {
	- int oldDisplayVal;
	- correctNode->GetIntProperty("DisplayChannel", oldDisplayVal);
	- QString oldVal = QString::number(oldDisplayVal);
	- QString newVal = QString::number(volume);
	- correctNode->SetIntProperty("DisplayChannel",volume);
	- correctNode->SetSelected(true);
	- this->FirePropertyChanged("DisplayChannel", oldVal, newVal);
	- correctNode->UpdateOutputInformation();
	-
	-
	- mitk::Point3D p3 = this->GetRenderWindowPart()->GetSelectedPosition();
	- itk::Index<3> ix;
	- geometry->WorldToIndex(p3, ix);
	- // ix[2] = slice;
	-
	- mitk::Vector3D vec;
	- vec[0] = ix[0];
	- vec[1] = ix[1];
	- vec[2] = slice;
	-
	- mitk::Vector3D v3New;
	- geometry->IndexToWorld(vec, v3New);
	- mitk::Point3D origin = geometry->GetOrigin();
	- mitk::Point3D p3New;
	- p3New[0] = v3New[0] + origin[0];
	- p3New[1] = v3New[1] + origin[1];
	- p3New[2] = v3New[2] + origin[2];
	-
	- this->GetRenderWindowPart()->SetSelectedPosition(p3New);
	- this->GetRenderWindowPart()->RequestUpdate();
	- }
	- }
	-}
	-
	-void QmitkTensorReconstructionView::Advanced1CheckboxClicked()
	-{
	- bool check = m_Controls->
	- m_Advanced1->isChecked();
	-
	- m_Controls->frame->setVisible(check);
	-}
	-
	-void QmitkTensorReconstructionView::Activated()
	-{
	-}
	-
	-void QmitkTensorReconstructionView::Deactivated()
	-{
	-
	- // Get all current nodes
	-
	- mitk::DataStorage::SetOfObjects::ConstPointer objects = this->GetDataStorage()->GetAll();
	- mitk::DataStorage::SetOfObjects::const_iterator itemiter( objects->begin() );
	- mitk::DataStorage::SetOfObjects::const_iterator itemiterend( objects->end() );
	- while ( itemiter != itemiterend ) // for all items
	- {
	- mitk::DataNode::Pointer node = *itemiter;
	- if (node.IsNull())
	- continue;
	-
	- // only look at interesting types
	- if( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(dynamic_cast<mitk::Image*>(node->GetData())))
	- {
	- if (this->GetDataStorage()->GetNamedDerivedNode("ThresholdOverlay", *itemiter))
	- {
	- node = this->GetDataStorage()->GetNamedDerivedNode("ThresholdOverlay", *itemiter);
	- this->GetDataStorage()->Remove(node);
	- }
	- }
	- itemiter++;
	- }
	-
	-
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-void QmitkTensorReconstructionView::Visible()
	-{
	-}
	-
	-void QmitkTensorReconstructionView::Hidden()
	-{
	-}
	-
	-void QmitkTensorReconstructionView::ResidualCalculation()
	-{
	- // Extract dwi and dti from current selection
	- // In case of multiple selections, take the first one, since taking all combinations is not meaningful
	-
	- mitk::DataStorage::SetOfObjects::Pointer set =
	- mitk::DataStorage::SetOfObjects::New();
	-
	- mitk::Image::Pointer diffImage
	- = mitk::Image::New();
	-
	- TensorImageType::Pointer tensorImage;
	-
	- std::string nodename;
	-
	- if(m_Controls->m_ResBox1->GetSelectedNode())
	- {
	- diffImage = static_cast<mitk::Image*>(m_Controls->m_ResBox1->GetSelectedNode()->GetData());
	- }
	- else
	- return;
	- if(m_Controls->m_ResBox2->GetSelectedNode().IsNotNull())
	- {
	- mitk::TensorImage* mitkVol;
	- mitkVol = static_cast<mitk::TensorImage*>(m_Controls->m_ResBox2->GetSelectedNode()->GetData());
	- mitk::CastToItkImage(mitkVol, tensorImage);
	- m_Controls->m_ResBox2->GetSelectedNode()->GetStringProperty("name", nodename);
	- }
	- else
	- return;
	-
	- typedef itk::TensorImageToDiffusionImageFilter<
	- TTensorPixelType, DiffusionPixelType > FilterType;
	-
	- GradientDirectionContainerType* gradients
	- = mitk::DiffusionPropertyHelper::GetGradientContainer(diffImage);
	-
	- // Find the min and the max values from a baseline image
	- mitk::ImageStatisticsHolder *stats = diffImage->GetStatistics();
	-
	- //Initialize filter that calculates the modeled diffusion weighted signals
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetInput( tensorImage );
	- filter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImage));
	- filter->SetGradientList(gradients);
	- filter->SetMin(stats->GetScalarValueMin());
	- filter->SetMax(stats->GetScalarValueMax());
	- filter->Update();
	-
	-
	- // TENSORS TO DATATREE
	- mitk::Image::Pointer image = mitk::GrabItkImageMemory( filter->GetOutput() );
	- mitk::DiffusionPropertyHelper::CopyProperties(diffImage, image, true);
	- mitk::DiffusionPropertyHelper::SetGradientContainer(image, gradients);
	- mitk::DiffusionPropertyHelper::InitializeImage( image );
	-
	- mitk::DataNode::Pointer node = mitk::DataNode::New();
	- node->SetData( image );
	- mitk::ImageVtkMapper2D::SetDefaultProperties(node);
	-
	- QString newname;
	- newname = newname.append(nodename.c_str());
	- newname = newname.append("_Estimated DWI");
	- node->SetName(newname.toLatin1());
	-
	- GetDataStorage()->Add(node, m_Controls->m_ResBox2->GetSelectedNode());
	-
	- BValueMapType map = mitk::DiffusionPropertyHelper::GetBValueMap(image);
	- std::vector< unsigned int > b0Indices = map[0];
	-
	-
	- typedef itk::ResidualImageFilter<DiffusionPixelType, float> ResidualImageFilterType;
	-
	- ITKDiffusionImageType::Pointer itkVectorImagePointer = ITKDiffusionImageType::New();
	- mitk::CastToItkImage(diffImage, itkVectorImagePointer);
	- ITKDiffusionImageType::Pointer itkSecondVectorImagePointer = ITKDiffusionImageType::New();
	- mitk::CastToItkImage(image, itkSecondVectorImagePointer);
	-
	- ResidualImageFilterType::Pointer residualFilter = ResidualImageFilterType::New();
	- residualFilter->SetInput( itkVectorImagePointer );
	- residualFilter->SetSecondDiffusionImage( itkSecondVectorImagePointer );
	- residualFilter->SetGradients(gradients);
	- residualFilter->SetB0Index(b0Indices[0]);
	- residualFilter->SetB0Threshold(30);
	- residualFilter->Update();
	-
	- itk::Image<float, 3>::Pointer residualImage = itk::Image<float, 3>::New();
	- residualImage = residualFilter->GetOutput();
	-
	- mitk::Image::Pointer mitkResImg = mitk::Image::New();
	-
	- mitk::CastToMitkImage(residualImage, mitkResImg);
	-
	- stats = mitkResImg->GetStatistics();
	- float min = stats->GetScalarValueMin();
	- float max = stats->GetScalarValueMax();
	-
	- mitk::LookupTableProperty::Pointer lutProp = mitk::LookupTableProperty::New();
	- mitk::LookupTable::Pointer lut = mitk::LookupTable::New();
	-
	-
	- vtkSmartPointer<vtkLookupTable> lookupTable =
	- vtkSmartPointer<vtkLookupTable>::New();
	-
	- lookupTable->SetTableRange(min, max);
	-
	-
	- // If you don't want to use the whole color range, you can use
	- // SetValueRange, SetHueRange, and SetSaturationRange
	- lookupTable->Build();
	-
	- vtkSmartPointer<vtkLookupTable> reversedlookupTable =
	- vtkSmartPointer<vtkLookupTable>::New();
	- reversedlookupTable->SetTableRange(min+1, max);
	- reversedlookupTable->Build();
	-
	- for(int i=0; i<256; i++)
	- {
	- double* rgba = reversedlookupTable->GetTableValue(255-i);
	-
	- lookupTable->SetTableValue(i, rgba[0], rgba[1], rgba[2], rgba[3]);
	- }
	-
	- lut->SetVtkLookupTable(lookupTable);
	- lutProp->SetLookupTable(lut);
	-
	- // Create lookuptable
	-
	- mitk::DataNode::Pointer resNode=mitk::DataNode::New();
	- resNode->SetData( mitkResImg );
	- resNode->SetName("Residuals");
	-
	- resNode->SetProperty("LookupTable", lutProp);
	-
	- bool b;
	- resNode->GetBoolProperty("use color", b);
	- resNode->SetBoolProperty("use color", false);
	-
	- GetDataStorage()->Add(resNode, m_Controls->m_ResBox2->GetSelectedNode());
	-
	- this->GetRenderWindowPart()->RequestUpdate();
	-
	-
	-
	- // Draw Graph
	- std::vector<double> means = residualFilter->GetMeans();
	- std::vector<double> q1s = residualFilter->GetQ1();
	- std::vector<double> q3s = residualFilter->GetQ3();
	- std::vector<double> percentagesOfOUtliers = residualFilter->GetPercentagesOfOutliers();
	-
	- m_Controls->m_ResidualAnalysis->SetMeans(means);
	- m_Controls->m_ResidualAnalysis->SetQ1(q1s);
	- m_Controls->m_ResidualAnalysis->SetQ3(q3s);
	- m_Controls->m_ResidualAnalysis->SetPercentagesOfOutliers(percentagesOfOUtliers);
	-
	- if(m_Controls->m_PercentagesOfOutliers->isChecked())
	- {
	- m_Controls->m_ResidualAnalysis->DrawPercentagesOfOutliers();
	- }
	- else
	- {
	- m_Controls->m_ResidualAnalysis->DrawMeans();
	- }
	-
	-
	-
	- // Draw Graph for volumes per slice in the QGraphicsView
	- std::vector< std::vector<double> > outliersPerSlice = residualFilter->GetOutliersPerSlice();
	- int xSize = outliersPerSlice.size();
	- if(xSize == 0)
	- {
	- return;
	- }
	- int ySize = outliersPerSlice[0].size();
	-
	-
	- // Find maximum in outliersPerSlice
	- double maxOutlier= 0.0;
	- for(int i=0; i<xSize; i++)
	- {
	- for(int j=0; j<ySize; j++)
	- {
	- if(outliersPerSlice[i][j]>maxOutlier)
	- {
	- maxOutlier = outliersPerSlice[i][j];
	- }
	- }
	- }
	-
	-
	- // Create some QImage
	- QImage qImage(xSize, ySize, QImage::Format_RGB32);
	- QImage legend(1, 256, QImage::Format_RGB32);
	- QRgb value;
	-
	- vtkSmartPointer<vtkLookupTable> lookup =
	- vtkSmartPointer<vtkLookupTable>::New();
	-
	- lookup->SetTableRange(0.0, maxOutlier);
	- lookup->Build();
	-
	- reversedlookupTable->SetTableRange(0, maxOutlier);
	- reversedlookupTable->Build();
	-
	- for(int i=0; i<256; i++)
	- {
	- double* rgba = reversedlookupTable->GetTableValue(255-i);
	- lookup->SetTableValue(i, rgba[0], rgba[1], rgba[2], rgba[3]);
	- }
	-
	-
	- // Fill qImage
	- for(int i=0; i<xSize; i++)
	- {
	- for(int j=0; j<ySize; j++)
	- {
	- double out = outliersPerSlice[i][j];
	-
	- unsigned char *_rgba = lookup->MapValue(out);
	- int r, g, b;
	- r = _rgba[0];
	- g = _rgba[1];
	- b = _rgba[2];
	-
	- value = qRgb(r, g, b);
	-
	- qImage.setPixel(i,j,value);
	-
	- }
	- }
	-
	- for(int i=0; i<256; i++)
	- {
	- double* rgba = lookup->GetTableValue(i);
	- int r, g, b;
	- r = rgba[0]*255;
	- g = rgba[1]*255;
	- b = rgba[2]*255;
	- value = qRgb(r, g, b);
	- legend.setPixel(0,255-i,value);
	- }
	-
	- QString upper = QString::number(maxOutlier, 'g', 3);
	- upper.append(" %");
	- QString lower = QString::number(0.0);
	- lower.append(" %");
	- m_Controls->m_UpperLabel->setText(upper);
	- m_Controls->m_LowerLabel->setText(lower);
	-
	- QPixmap pixmap(QPixmap::fromImage(qImage));
	- QGraphicsPixmapItem *item = new QGraphicsPixmapItem(pixmap);
	- item->setTransform(QTransform::fromScale(10.0, 3.0), true);
	-
	- QPixmap pixmap2(QPixmap::fromImage(legend));
	- QGraphicsPixmapItem *item2 = new QGraphicsPixmapItem(pixmap2);
	- item2->setTransform(QTransform::fromScale(20.0, 1.0), true);
	-
	- m_Controls->m_PerSliceView->SetResidualPixmapItem(item);
	-
	- QGraphicsScene* scene = new QGraphicsScene;
	- QGraphicsScene* scene2 = new QGraphicsScene;
	-
	- scene->addItem(item);
	- scene2->addItem(item2);
	-
	- m_Controls->m_PerSliceView->setScene(scene);
	- m_Controls->m_LegendView->setScene(scene2);
	- m_Controls->m_PerSliceView->show();
	- m_Controls->m_PerSliceView->repaint();
	-
	- m_Controls->m_LegendView->setHorizontalScrollBarPolicy ( Qt::ScrollBarAlwaysOff );
	- m_Controls->m_LegendView->setVerticalScrollBarPolicy ( Qt::ScrollBarAlwaysOff );
	- m_Controls->m_LegendView->show();
	- m_Controls->m_LegendView->repaint();
	-}
	-
	-void QmitkTensorReconstructionView::Reconstruct()
	-{
	- int method = m_Controls->m_ReconctructionMethodBox->currentIndex();
	-
	- switch (method)
	- {
	- case 0:
	- ItkTensorReconstruction();
	- break;
	- case 1:
	- TensorReconstructionWithCorr();
	- break;
	- default:
	- ItkTensorReconstruction();
	- }
	-}
	-
	-void QmitkTensorReconstructionView::TensorReconstructionWithCorr()
	-{
	- try
	- {
	- if ( m_Controls->m_DwiBox->GetSelectedNode().IsNotNull() ) // for all items
	- {
	- mitk::Image* vols = static_cast<mitk::Image*>(m_Controls->m_DwiBox->GetSelectedNode()->GetData());
	- std::string nodename = m_Controls->m_DwiBox->GetSelectedNode()->GetName();
	-
	- typedef itk::TensorReconstructionWithEigenvalueCorrectionFilter< DiffusionPixelType, TTensorPixelType > ReconstructionFilter;
	-
	- float b0Threshold = m_Controls->m_TensorReconstructionThreshold->value();
	- mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer gradientContainerCopy = mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::New();
	- for(auto it = mitk::DiffusionPropertyHelper::GetGradientContainer(vols)->Begin(); it != mitk::DiffusionPropertyHelper::GetGradientContainer(vols)->End(); it++)
	- gradientContainerCopy->push_back(it.Value());
	-
	- ITKDiffusionImageType::Pointer itkVectorImagePointer = ITKDiffusionImageType::New();
	- mitk::CastToItkImage(vols, itkVectorImagePointer);
	-
	- ReconstructionFilter::Pointer reconFilter = ReconstructionFilter::New();
	- reconFilter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(vols));
	- reconFilter->SetGradientImage( gradientContainerCopy, itkVectorImagePointer);
	- reconFilter->SetB0Threshold(b0Threshold);
	- reconFilter->Update();
	-
	- typedef mitk::TensorImage::ItkTensorImageType TensorImageType;
	- TensorImageType::Pointer outputTensorImg = reconFilter->GetOutput();
	-
	- typedef itk::ImageRegionIterator<TensorImageType> TensorImageIteratorType;
	- TensorImageIteratorType tensorIt(outputTensorImg, outputTensorImg->GetRequestedRegion());
	- tensorIt.GoToBegin();
	-
	- int negatives = 0;
	- while(!tensorIt.IsAtEnd())
	- {
	- typedef mitk::TensorImage::PixelType TensorType;
	- TensorType tensor = tensorIt.Get();
	-
	- TensorType::EigenValuesArrayType ev;
	- tensor.ComputeEigenValues(ev);
	-
	- for(unsigned int i=0; i<ev.Size(); i++)
	- {
	- if(ev[i] < 0.0)
	- {
	- tensor.Fill(0.0);
	- tensorIt.Set(tensor);
	- negatives++;
	- break;
	- }
	- }
	- ++tensorIt;
	- }
	- MITK_INFO << negatives << " tensors with negative eigenvalues" << std::endl;
	-
	- mitk::TensorImage::Pointer image = mitk::TensorImage::New();
	- image->InitializeByItk( outputTensorImg.GetPointer() );
	- image->SetVolume( outputTensorImg->GetBufferPointer() );
	- mitk::DataNode::Pointer node=mitk::DataNode::New();
	- node->SetData( image );
	- node->SetName(nodename+"_EigenvalueCorrected_DT");
	- GetDataStorage()->Add(node, m_Controls->m_DwiBox->GetSelectedNode());
	- }
	-
	- this->GetRenderWindowPart()->RequestUpdate();
	- }
	- catch (itk::ExceptionObject &ex)
	- {
	- MITK_INFO << ex ;
	- QMessageBox::information(0, "Reconstruction not possible:", ex.GetDescription());
	- }
	-}
	-
	-void QmitkTensorReconstructionView::ItkTensorReconstruction()
	-{
	- try
	- {
	- if ( m_Controls->m_DwiBox->GetSelectedNode().IsNotNull() ) // for all items
	- {
	- mitk::Image* vols = static_cast<mitk::Image*>(m_Controls->m_DwiBox->GetSelectedNode()->GetData());
	-
	- std::string nodename = m_Controls->m_DwiBox->GetSelectedNode()->GetName();
	-
	-
	- typedef itk::DiffusionTensor3DReconstructionImageFilter<DiffusionPixelType, DiffusionPixelType, TTensorPixelType > TensorReconstructionImageFilterType;
	- TensorReconstructionImageFilterType::Pointer tensorReconstructionFilter = TensorReconstructionImageFilterType::New();
	-
	- GradientDirectionContainerType::Pointer gradientContainerCopy = GradientDirectionContainerType::New();
	- for(GradientDirectionContainerType::ConstIterator it = mitk::DiffusionPropertyHelper::GetGradientContainer(vols)->Begin();
	- it != mitk::DiffusionPropertyHelper::GetGradientContainer(vols)->End(); it++)
	- {
	- gradientContainerCopy->push_back(it.Value());
	- }
	-
	- ITKDiffusionImageType::Pointer itkVectorImagePointer = ITKDiffusionImageType::New();
	- mitk::CastToItkImage(vols, itkVectorImagePointer);
	-
	- tensorReconstructionFilter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(vols));
	- tensorReconstructionFilter->SetGradientImage( gradientContainerCopy, itkVectorImagePointer );
	- tensorReconstructionFilter->SetThreshold( m_Controls->m_TensorReconstructionThreshold->value() );
	- tensorReconstructionFilter->Update();
	-
	- // TENSORS TO DATATREE
	- mitk::TensorImage::Pointer image = mitk::TensorImage::New();
	-
	- typedef mitk::TensorImage::ItkTensorImageType TensorImageType;
	- TensorImageType::Pointer tensorImage;
	- tensorImage = tensorReconstructionFilter->GetOutput();
	-
	- // Check the tensor for negative eigenvalues
	- if(m_Controls->m_CheckNegativeEigenvalues->isChecked())
	- {
	- typedef itk::ImageRegionIterator<TensorImageType> TensorImageIteratorType;
	- TensorImageIteratorType tensorIt(tensorImage, tensorImage->GetRequestedRegion());
	- tensorIt.GoToBegin();
	-
	- while(!tensorIt.IsAtEnd())
	- {
	-
	- typedef mitk::TensorImage::PixelType TensorType;
	- //typedef itk::Tensor<TTensorPixelType, 3> TensorType2;
	-
	- TensorType tensor = tensorIt.Get();
	-
	- TensorType::EigenValuesArrayType ev;
	- tensor.ComputeEigenValues(ev);
	- for(unsigned int i=0; i<ev.Size(); i++)
	- {
	- if(ev[i] < 0.0)
	- {
	- tensor.Fill(0.0);
	- tensorIt.Set(tensor);
	- break;
	- }
	- }
	- ++tensorIt;
	- }
	- }
	-
	- tensorImage->SetDirection( itkVectorImagePointer->GetDirection() );
	- image->InitializeByItk( tensorImage.GetPointer() );
	- image->SetVolume( tensorReconstructionFilter->GetOutput()->GetBufferPointer() );
	- mitk::DataNode::Pointer node=mitk::DataNode::New();
	- node->SetData( image );
	- node->SetName(nodename+"_LinearLeastSquares_DT");
	- GetDataStorage()->Add(node, m_Controls->m_DwiBox->GetSelectedNode());
	- }
	-
	- this->GetRenderWindowPart()->RequestUpdate();
	- }
	- catch (itk::ExceptionObject &ex)
	- {
	- MITK_INFO << ex ;
	- QMessageBox::information(0, "Reconstruction not possible:", ex.GetDescription());
	- return;
	- }
	-}
	-
	-void QmitkTensorReconstructionView::TensorsToDWI()
	-{
	- DoTensorsToDWI();
	-}
	-
	-void QmitkTensorReconstructionView::TensorsToOdf()
	-{
	- if (m_Controls->m_OdfBox->GetSelectedNode().IsNotNull())
	- {
	- mitk::DataNode::Pointer tensorImageNode = m_Controls->m_OdfBox->GetSelectedNode();
	-
	- typedef mitk::TensorImage::ScalarPixelType TTensorPixelType;
	- typedef mitk::TensorImage::ItkTensorImageType TensorImageType;
	-
	- TensorImageType::Pointer itkvol = TensorImageType::New();
	- mitk::CastToItkImage(dynamic_cast<mitk::TensorImage*>(tensorImageNode->GetData()), itkvol);
	-
	- typedef itk::TensorImageToOdfImageFilter< TTensorPixelType, TTensorPixelType > FilterType;
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetInput( itkvol );
	- filter->Update();
	-
	- typedef itk::Vector<TTensorPixelType,ODF_SAMPLING_SIZE> OutputPixelType;
	- typedef itk::Image<OutputPixelType,3> OutputImageType;
	-
	- mitk::OdfImage::Pointer image = mitk::OdfImage::New();
	- OutputImageType::Pointer outimg = filter->GetOutput();
	- image->InitializeByItk( outimg.GetPointer() );
	- image->SetVolume( outimg->GetBufferPointer() );
	- mitk::DataNode::Pointer node = mitk::DataNode::New();
	- node->SetData( image );
	- node->SetName(tensorImageNode->GetName()+"_Odf");
	- GetDataStorage()->Add(node, tensorImageNode);
	- }
	-}
	-
	-void QmitkTensorReconstructionView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /part/, const QList<mitk::DataNode::Pointer>& )
	-{
	- UpdateGui();
	-}
	-
	-void QmitkTensorReconstructionView::UpdateGui()
	-{
	- m_Controls->m_StartReconstruction->setEnabled(m_Controls->m_DwiBox->GetSelectedNode().IsNotNull());
	-
	- m_Controls->m_TensorsToDWIButton->setEnabled(m_Controls->m_DtiBox->GetSelectedNode().IsNotNull());
	- m_Controls->m_TensorsToOdfButton->setEnabled(m_Controls->m_OdfBox->GetSelectedNode().IsNotNull());
	-
	- m_Controls->m_ResidualButton->setEnabled(m_Controls->m_ResBox1->GetSelectedNode().IsNotNull() && m_Controls->m_ResBox2->GetSelectedNode().IsNotNull());
	- m_Controls->m_PercentagesOfOutliers->setEnabled(m_Controls->m_ResBox1->GetSelectedNode().IsNotNull() && m_Controls->m_ResBox2->GetSelectedNode().IsNotNull());
	- m_Controls->m_PerSliceView->setEnabled(m_Controls->m_ResBox1->GetSelectedNode().IsNotNull() && m_Controls->m_ResBox2->GetSelectedNode().IsNotNull());
	-}
	-
	-template<int ndirs>
	-itk::VectorContainer<unsigned int, vnl_vector_fixed<double, 3> >::Pointer
	-QmitkTensorReconstructionView::MakeGradientList()
	-{
	- itk::VectorContainer<unsigned int, vnl_vector_fixed<double,3> >::Pointer retval =
	- itk::VectorContainer<unsigned int, vnl_vector_fixed<double,3> >::New();
	- vnl_matrix_fixed<double, 3, ndirs>* U =
	- itk::PointShell<ndirs, vnl_matrix_fixed<double, 3, ndirs> >::DistributePointShell();
	-
	- for(int i=0; i<ndirs;i++)
	- {
	- vnl_vector_fixed<double,3> v;
	- v[0] = U->get(0,i); v[1] = U->get(1,i); v[2] = U->get(2,i);
	- retval->push_back(v);
	- }
	- // Add 0 vector for B0
	- vnl_vector_fixed<double,3> v;
	- v.fill(0.0);
	- retval->push_back(v);
	-
	- return retval;
	-}
	-
	-void QmitkTensorReconstructionView::DoTensorsToDWI()
	-{
	- try
	- {
	- if (m_Controls->m_DtiBox->GetSelectedNode().IsNotNull())
	- {
	- std::string nodename = m_Controls->m_DtiBox->GetSelectedNode()->GetName();
	-
	- mitk::TensorImage* vol = static_cast<mitk::TensorImage*>(m_Controls->m_DtiBox->GetSelectedNode()->GetData());
	-
	- typedef mitk::TensorImage::ScalarPixelType TTensorPixelType;
	- typedef mitk::TensorImage::ItkTensorImageType TensorImageType;
	-
	-
	- TensorImageType::Pointer itkvol = TensorImageType::New();
	- mitk::CastToItkImage(vol, itkvol);
	-
	- typedef itk::TensorImageToDiffusionImageFilter<
	- TTensorPixelType, DiffusionPixelType > FilterType;
	-
	- FilterType::GradientListPointerType gradientList = FilterType::GradientListType::New();
	-
	- switch(m_Controls->m_TensorsToDWINumDirsSelect->currentIndex())
	- {
	- case 0:
	- gradientList = MakeGradientList<12>();
	- break;
	- case 1:
	- gradientList = MakeGradientList<42>();
	- break;
	- case 2:
	- gradientList = MakeGradientList<92>();
	- break;
	- case 3:
	- gradientList = MakeGradientList<162>();
	- break;
	- case 4:
	- gradientList = MakeGradientList<252>();
	- break;
	- case 5:
	- gradientList = MakeGradientList<362>();
	- break;
	- case 6:
	- gradientList = MakeGradientList<492>();
	- break;
	- case 7:
	- gradientList = MakeGradientList<642>();
	- break;
	- case 8:
	- gradientList = MakeGradientList<812>();
	- break;
	- case 9:
	- gradientList = MakeGradientList<1002>();
	- break;
	- default:
	- gradientList = MakeGradientList<92>();
	-
	- }
	- double bVal = m_Controls->m_TensorsToDWIBValueEdit->text().toDouble();
	-
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetInput( itkvol );
	- filter->SetBValue(bVal);
	- filter->SetGradientList(gradientList);
	- filter->Update();
	-
	- mitk::Image::Pointer image = mitk::GrabItkImageMemory( filter->GetOutput() );
	-
	- mitk::DiffusionPropertyHelper::SetGradientContainer(image, gradientList);
	- mitk::DiffusionPropertyHelper::SetReferenceBValue(image, bVal);
	- mitk::DiffusionPropertyHelper::InitializeImage( image );
	-
	- mitk::DataNode::Pointer node=mitk::DataNode::New();
	- node->SetData( image );
	- mitk::ImageVtkMapper2D::SetDefaultProperties(node);
	- node->SetName(nodename+"_DWI");
	- GetDataStorage()->Add(node, m_Controls->m_DtiBox->GetSelectedNode());
	- }
	- this->GetRenderWindowPart()->RequestUpdate();
	- }
	- catch (itk::ExceptionObject &ex)
	- {
	- MITK_INFO << ex ;
	- QMessageBox::information(0, "DWI estimation failed:", ex.GetDescription());
	- return ;
	- }
	-}
	-
	-
	-void QmitkTensorReconstructionView::PreviewThreshold(int threshold)
	-{
	- if (m_Controls->m_DwiBox->GetSelectedNode().IsNotNull())
	- {
	- mitk::Image* vols = static_cast<mitk::Image*>(m_Controls->m_DwiBox->GetSelectedNode()->GetData());
	-
	- ITKDiffusionImageType::Pointer itkVectorImagePointer = ITKDiffusionImageType::New();
	- mitk::CastToItkImage(vols, itkVectorImagePointer);
	-
	- // Extract b0 image
	- typedef itk::B0ImageExtractionImageFilter<short, short> FilterType;
	- FilterType::Pointer filterB0 = FilterType::New();
	- filterB0->SetInput(itkVectorImagePointer);
	- filterB0->SetDirections(mitk::DiffusionPropertyHelper::GetGradientContainer(vols));
	- filterB0->Update();
	-
	- mitk::Image::Pointer mitkImage = mitk::Image::New();
	-
	- typedef itk::Image<short, 3> ImageType;
	- typedef itk::Image<short, 3> SegmentationType;
	- typedef itk::BinaryThresholdImageFilter<ImageType, SegmentationType> ThresholdFilterType;
	- // apply threshold
	- ThresholdFilterType::Pointer filterThreshold = ThresholdFilterType::New();
	- filterThreshold->SetInput(filterB0->GetOutput());
	- filterThreshold->SetLowerThreshold(threshold);
	- filterThreshold->SetInsideValue(0);
	- filterThreshold->SetOutsideValue(1); // mark cut off values red
	- filterThreshold->Update();
	-
	- mitkImage->InitializeByItk( filterThreshold->GetOutput() );
	- mitkImage->SetVolume( filterThreshold->GetOutput()->GetBufferPointer() );
	- mitk::DataNode::Pointer node;
	- if (this->GetDataStorage()->GetNamedDerivedNode("ThresholdOverlay", m_Controls->m_DwiBox->GetSelectedNode()))
	- {
	- node = this->GetDataStorage()->GetNamedDerivedNode("ThresholdOverlay", m_Controls->m_DwiBox->GetSelectedNode());
	- }
	- else
	- {
	- // create a new node, to show thresholded values
	- node = mitk::DataNode::New();
	- GetDataStorage()->Add( node, m_Controls->m_DwiBox->GetSelectedNode() );
	- node->SetProperty( "name", mitk::StringProperty::New("ThresholdOverlay"));
	- node->SetBoolProperty("helper object", true);
	- }
	- node->SetData( mitkImage );
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- }
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkTensorReconstructionView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkTensorReconstructionView.h
	deleted file mode 100644
	index 7155e04e8a..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkTensorReconstructionView.h
	+++ /dev/null
	@@ -1,124 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _QMITKTENSORRECONSTRUCTIONVIEW_H_INCLUDED
	-#define _QMITKTENSORRECONSTRUCTIONVIEW_H_INCLUDED
	-
	-#include <QmitkAbstractView.h>
	-#include <mitkILifecycleAwarePart.h>
	-
	-#include <string>
	-
	-#include "ui_QmitkTensorReconstructionViewControls.h"
	-
	-#include <mitkTensorImage.h>
	-#include <mitkImage.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <itkVectorImage.h>
	-
	-typedef short DiffusionPixelType;
	-
	-struct TrSelListener;
	-
	-/*!
	- * \ingroup org_mitk_gui_qt_tensorreconstruction_internal
	- *
	- * \brief QmitkTensorReconstructionView
	- *
	- * Document your class here.
	- */
	-class QmitkTensorReconstructionView : public QmitkAbstractView, public mitk::ILifecycleAwarePart
	-{
	-
	- friend struct TrSelListener;
	-
	- // this is needed for all Qt objects that should have a MOC object (everything that derives from QObject)
	- Q_OBJECT
	-
	- public:
	-
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionType GradientDirectionType;
	- typedef mitk::DiffusionPropertyHelper::GradientDirectionsContainerType GradientDirectionContainerType;
	- typedef mitk::DiffusionPropertyHelper::BValueMapType BValueMapType;
	- typedef itk::VectorImage< DiffusionPixelType, 3 > ITKDiffusionImageType;
	-
	- static const std::string VIEW_ID;
	-
	- QmitkTensorReconstructionView();
	- virtual ~QmitkTensorReconstructionView();
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	-
	- /// \brief Creation of the connections of main and control widget
	- virtual void CreateConnections();
	-
	- ///
	- /// Sets the focus to an internal widget.
	- ///
	- virtual void SetFocus() override;
	-
	- /// \brief Called when the view gets activated
	- virtual void Activated() override;
	-
	- /// \brief Called when the view gets deactivated
	- virtual void Deactivated() override;
	-
	- /// \brief Called when the view becomes visible
	- virtual void Visible() override;
	-
	- /// \brief Called when the view becomes hidden
	- virtual void Hidden() override;
	-
	- static const int nrconvkernels;
	-
	-protected slots:
	-
	- void UpdateGui();
	- void TensorsToOdf();
	- void TensorsToDWI();
	- void DoTensorsToDWI();
	- void Advanced1CheckboxClicked();
	- void Reconstruct();
	- void ResidualCalculation();
	- void ResidualClicked(int slice, int volume);
	- /**
	- * @brief PreviewThreshold Generates a preview of the values that are cut off by the thresholds
	- * @param threshold
	- */
	- void PreviewThreshold(int threshold);
	-
	-protected:
	-
	- void ItkTensorReconstruction();
	- void TeemTensorReconstruction();
	- void TensorReconstructionWithCorr();
	-
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- Ui::QmitkTensorReconstructionViewControls* m_Controls;
	-
	- template<int ndirs> itk::VectorContainer<unsigned int, vnl_vector_fixed<double,3> >::Pointer MakeGradientList();
	-
	- template<int L>
	- void TemplatedAnalyticalTensorReconstruction(mitk::Image* vols,
	- float lambda, std::string nodename, std::vector<mitk::DataNode::Pointer>* nodes, int normalization);
	-};
	-
	-
	-
	-
	-#endif // _QMITKTENSORRECONSTRUCTIONVIEW_H_INCLUDED
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkTensorReconstructionViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkTensorReconstructionViewControls.ui
	deleted file mode 100644
	index 1650d5269f..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/QmitkTensorReconstructionViewControls.ui
	+++ /dev/null
	@@ -1,757 +0,0 @@
	-<?xml version="1.0" encoding="utf-8"?>
	-<ui version="4.0">
	- <class>QmitkTensorReconstructionViewControls</class>
	- <widget class="QWidget" name="QmitkTensorReconstructionViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>368</width>
	- <height>1019</height>
	- </rect>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="acceptDrops">
	- <bool>true</bool>
	- </property>
	- <property name="windowTitle">
	- <string>QmitkTensorReconstructionViewControls</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_5">
	- <property name="verticalSpacing">
	- <number>25</number>
	- </property>
	- <item row="2" column="0">
	- <widget class="QGroupBox" name="groupBox_4">
	- <property name="title">
	- <string>ODF Image from Tensors</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_8">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QCommandLinkButton" name="m_TensorsToOdfButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string comment="Calculate ODF value as tensor value in the according direction" extracomment="Calculate ODF value as tensor value in the according direction">Calculate ODF value as tensor value in the according direction</string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string notr="true"></string>
	- </property>
	- <property name="text">
	- <string>Start</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QFrame" name="frame_7">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_10">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_OdfBox"></widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_4">
	- <property name="text">
	- <string>Tensor Image:</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QGroupBox" name="groupBox">
	- <property name="title">
	- <string>Diffusion-weighted Image from Tensors</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_6">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="2" column="0">
	- <widget class="QCommandLinkButton" name="m_TensorsToDWIButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string>Estimates the original diffusion weighted image based on a reconstructed tensor image.</string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string notr="true"></string>
	- </property>
	- <property name="text">
	- <string>Estimate DWI based on Tensor Image</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QFrame" name="m_TensorsToDWIFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QFormLayout" name="formLayout_3">
	- <property name="fieldGrowthPolicy">
	- <enum>QFormLayout::AllNonFixedFieldsGrow</enum>
	- </property>
	- <property name="horizontalSpacing">
	- <number>6</number>
	- </property>
	- <property name="verticalSpacing">
	- <number>6</number>
	- </property>
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_TensorsToDWIBValueLabel">
	- <property name="toolTip">
	- <string comment='how fuzzy the confidence boundary should be. By default, confidence boundary is perfectly sharp (float); default: "0"' extracomment='how fuzzy the confidence boundary should be. By default, confidence boundary is perfectly sharp (float); default: "0"'>how fuzzy the confidence boundary should be. By default, confidence boundary is perfectly sharp (float); default: "0"</string>
	- </property>
	- <property name="statusTip">
	- <string comment='how fuzzy the confidence boundary should be. By default, confidence boundary is perfectly sharp (float); default: "0"' extracomment='how fuzzy the confidence boundary should be. By default, confidence boundary is perfectly sharp (float); default: "0"'>how fuzzy the confidence boundary should be. By default, confidence boundary is perfectly sharp (float); default: "0"</string>
	- </property>
	- <property name="whatsThis">
	- <string comment='how fuzzy the confidence boundary should be. By default, confidence boundary is perfectly sharp (float); default: "0"' extracomment='how fuzzy the confidence boundary should be. By default, confidence boundary is perfectly sharp (float); default: "0"'>how fuzzy the confidence boundary should be. By default, confidence boundary is perfectly sharp (float); default: "0"</string>
	- </property>
	- <property name="text">
	- <string>B-Value</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="m_TensorsToDWINumDirsLabel">
	- <property name="text">
	- <string>#Gradient Directions</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QComboBox" name="m_TensorsToDWINumDirsSelect">
	- <property name="currentIndex">
	- <number>3</number>
	- </property>
	- <item>
	- <property name="text">
	- <string>12</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>42</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>92</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>162</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>252</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>362</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>492</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>642</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>812</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>1002</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_TensorsToDWIBValueEdit">
	- <property name="maximum">
	- <number>10000</number>
	- </property>
	- <property name="singleStep">
	- <number>100</number>
	- </property>
	- <property name="value">
	- <number>1000</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QFrame" name="frame_6">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_9">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_DtiBox"></widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_3">
	- <property name="text">
	- <string>Tensor Image:</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QGroupBox" name="groupBox_5">
	- <property name="title">
	- <string>Calculate Residuals</string>
	- </property>
	- <property name="checkable">
	- <bool>false</bool>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_2">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <property name="horizontalSpacing">
	- <number>6</number>
	- </property>
	- <item row="2" column="0">
	- <widget class="QCheckBox" name="m_PercentagesOfOutliers">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="text">
	- <string>percentages of error</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QTabWidget" name="m_ResidualTab">
	- <property name="currentIndex">
	- <number>0</number>
	- </property>
	- <widget class="QWidget" name="tab">
	- <attribute name="title">
	- <string>Per volume</string>
	- </attribute>
	- <layout class="QVBoxLayout" name="verticalLayout_8">
	- <item>
	- <widget class="QmitkResidualAnalysisWidget" name="m_ResidualAnalysis" native="true">
	- <property name="minimumSize">
	- <size>
	- <width>200</width>
	- <height>300</height>
	- </size>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <widget class="QWidget" name="tab_2">
	- <attribute name="title">
	- <string>Per slice</string>
	- </attribute>
	- <layout class="QVBoxLayout" name="verticalLayout_10">
	- <item>
	- <widget class="QLabel" name="label_2">
	- <property name="text">
	- <string>outliers per slice</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QFrame" name="frame_5">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QHBoxLayout" name="horizontalLayout_2">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QmitkResidualViewWidget" name="m_PerSliceView">
	- <property name="maximumSize">
	- <size>
	- <width>300</width>
	- <height>400</height>
	- </size>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QFrame" name="frame_4">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QVBoxLayout" name="verticalLayout_9">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QLabel" name="m_UpperLabel">
	- <property name="text">
	- <string></string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QGraphicsView" name="m_LegendView">
	- <property name="maximumSize">
	- <size>
	- <width>20</width>
	- <height>255</height>
	- </size>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QLabel" name="m_LowerLabel">
	- <property name="text">
	- <string></string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <widget class="QLabel" name="m_PositionLabel">
	- <property name="text">
	- <string>Volume: .., Slice:..</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QCommandLinkButton" name="m_ResidualButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string>Calculate the residual from a dti and a dwi image</string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string notr="true"></string>
	- </property>
	- <property name="text">
	- <string>Start</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QFrame" name="frame_8">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_11">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_ResBox1"></widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_5">
	- <property name="text">
	- <string>Diffusion-weighted Image:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_7">
	- <property name="text">
	- <string>Tensor Image:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_ResBox2"></widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <spacer name="verticalSpacer">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="0" column="0">
	- <widget class="QGroupBox" name="groupBox_2">
	- <property name="title">
	- <string>Tensor Reconstruction</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_7">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="2" column="1">
	- <widget class="QCheckBox" name="m_Advanced1">
	- <property name="text">
	- <string>Advanced Settings</string>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="1">
	- <widget class="QCommandLinkButton" name="m_StartReconstruction">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string>Select raw DWI!</string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string notr="true"></string>
	- </property>
	- <property name="text">
	- <string>Start Reconstruction</string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="1">
	- <widget class="QFrame" name="frame">
	- <property name="frameShape">
	- <enum>QFrame::StyledPanel</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_4">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QFrame" name="frame_3">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_3">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QLabel" name="m_TensorReconstructionThresholdLabel_2">
	- <property name="text">
	- <string>B0 Threshold</string>
	- </property>
	- <property name="wordWrap">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QSpinBox" name="m_TensorReconstructionThreshold">
	- <property name="maximum">
	- <number>10000</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QCheckBox" name="m_CheckNegativeEigenvalues">
	- <property name="toolTip">
	- <string>Only influences WLS reconstruction</string>
	- </property>
	- <property name="text">
	- <string>Ignore voxels with negative eigenvalues</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QComboBox" name="m_ReconctructionMethodBox">
	- <property name="currentIndex">
	- <number>0</number>
	- </property>
	- <item>
	- <property name="text">
	- <string>ITK Linear Least Squares</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>With correction for negative eigenvalues</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QFrame" name="frame_2">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_DwiBox"></widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label">
	- <property name="text">
	- <string>Diffusion-weighted Image:</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <layoutdefault spacing="6" margin="11"></layoutdefault>
	- <customwidgets>
	- <customwidget>
	- <class>QmitkDataStorageComboBox</class>
	- <extends>QComboBox</extends>
	- <header location="global">QmitkDataStorageComboBox.h</header>
	- </customwidget>
	- <customwidget>
	- <class>QmitkResidualAnalysisWidget</class>
	- <extends>QWidget</extends>
	- <header>QmitkResidualAnalysisWidget.h</header>
	- <container>1</container>
	- </customwidget>
	- <customwidget>
	- <class>QmitkResidualViewWidget</class>
	- <extends>QGraphicsView</extends>
	- <header>QmitkResidualViewWidget.h</header>
	- </customwidget>
	- </customwidgets>
	- <resources></resources>
	- <connections></connections>
	-</ui>
	\ No newline at end of file
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/mitkPluginActivator.cpp
	deleted file mode 100644
	index 8f1c0a3c84..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/mitkPluginActivator.cpp
	+++ /dev/null
	@@ -1,49 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkPluginActivator.h"
	-
	-#include "src/internal/QmitkQBallReconstructionView.h"
	-#include "src/internal/QmitkTensorReconstructionView.h"
	-#include "src/internal/QmitkDiffusionQuantificationView.h"
	-#include "src/internal/QmitkODFDetailsView.h"
	-#include "src/internal/Perspectives/QmitkReconstructionPerspective.h"
	-#include "src/internal/Perspectives/QmitkQuantificationPerspective.h"
	-
	-ctkPluginContext* mitk::PluginActivator::m_Context = nullptr;
	-
	-ctkPluginContext* mitk::PluginActivator::GetContext()
	-{
	- return m_Context;
	-}
	-
	-void mitk::PluginActivator::start(ctkPluginContext* context)
	-{
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkReconstructionPerspective, context)
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkQuantificationPerspective, context)
	-
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkQBallReconstructionView, context)
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkDiffusionQuantificationView, context)
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkTensorReconstructionView, context)
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkODFDetailsView, context)
	- m_Context = context;
	-}
	-
	-void mitk::PluginActivator::stop(ctkPluginContext* context)
	-{
	- Q_UNUSED(context)
	- m_Context = nullptr;
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/mitkPluginActivator.h b/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/mitkPluginActivator.h
	deleted file mode 100644
	index caea06327d..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.reconstruction/src/internal/mitkPluginActivator.h
	+++ /dev/null
	@@ -1,40 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef MITKPLUGINACTIVATOR_H
	-#define MITKPLUGINACTIVATOR_H
	-
	-#include <ctkPluginActivator.h>
	-
	-namespace mitk
	-{
	- class PluginActivator : public QObject, public ctkPluginActivator
	- {
	- Q_OBJECT
	- Q_PLUGIN_METADATA(IID "org.mitk.gui.qt.diffusionimaging.reconstruction")
	- Q_INTERFACES(ctkPluginActivator)
	-
	- public:
	- static ctkPluginContext* GetContext();
	-
	- void start(ctkPluginContext* context) override;
	- void stop(ctkPluginContext* context) override;
	-
	- private:
	- static ctkPluginContext* m_Context;
	- };
	-}
	-
	-#endif
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/CMakeLists.txt
	deleted file mode 100644
	index a0dd6267f4..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/CMakeLists.txt
	+++ /dev/null
	@@ -1,10 +0,0 @@
	-# The project name must correspond to the directory name of your plug-in
	-# and must not contain periods.
	-project(org_mitk_gui_qt_diffusionimaging_registration)
	-
	-mitk_create_plugin(
	- SUBPROJECTS MITK-DTI
	- EXPORT_DIRECTIVE DIFFUSIONIMAGING_REGISTRATION_EXPORT
	- EXPORTED_INCLUDE_SUFFIXES src
	- MODULE_DEPENDS MitkDiffusionCore MitkMatchPointRegistration MitkMatchPointRegistrationUI
	-)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/UserManual/QmitkHeadMotionCorrection.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/UserManual/QmitkHeadMotionCorrection.dox
	deleted file mode 100644
	index 0b98310a5f..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/UserManual/QmitkHeadMotionCorrection.dox
	+++ /dev/null
	@@ -1,5 +0,0 @@
	-/**
	-\page org_mitk_views_headmotioncorrectionview Head-Motion Correction
	-
	-This view allows head-motion and eddy-current correction by affinely registering all volumes to the first unweighted volume of the complete diffusion-weighted image. The individual gradient directions are roated accordingly.
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/UserManual/QmitkSimpleRegistration.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/UserManual/QmitkSimpleRegistration.dox
	deleted file mode 100644
	index b6fc0bb470..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/UserManual/QmitkSimpleRegistration.dox
	+++ /dev/null
	@@ -1,6 +0,0 @@
	-/**
	-\page org_mitk_views_simpleregistrationview Registration
	-
	-This view enables the simple rigid or affine registration of two images. It is also possible to transform a tractogram with a registration object obtained from a previous registration of two images.
	-
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/UserManual/registration_basic.png b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/UserManual/registration_basic.png
	deleted file mode 100644
	index c031d56e3f..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/UserManual/registration_basic.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/UserManual/registration_batch.png b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/UserManual/registration_batch.png
	deleted file mode 100644
	index b1647ff48d..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/UserManual/registration_batch.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/doxygen/modules.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/doxygen/modules.dox
	deleted file mode 100644
	index c6573fdaf0..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/documentation/doxygen/modules.dox
	+++ /dev/null
	@@ -1,16 +0,0 @@
	-/**
	- \defgroup org_mitk_gui_qt_diffusionimaging_registration org.mitk.gui.qt.diffusionimaging.registration
	- \ingroup MITKPlugins
	-
	- \brief This is the diffusionimaging.registration plugin.
	-
	-*/
	-
	-/**
	- \defgroup org_mitk_gui_qt_diffusionimaging_registration_internal Internal
	- \ingroup org_mitk_gui_qt_diffusionimaging_registration
	-
	- \brief This subcategory includes the internal classes of the org.mitk.gui.qt.diffusionimaging.registration plugin. Other
	- plugins must not rely on these classes. They contain implementation details and their interface
	- may change at any time. We mean it.
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/files.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/files.cmake
	deleted file mode 100644
	index 0c53c6ac2e..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/files.cmake
	+++ /dev/null
	@@ -1,44 +0,0 @@
	-set(SRC_CPP_FILES
	-
	-
	-)
	-
	-set(INTERNAL_CPP_FILES
	- mitkPluginActivator.cpp
	-
	- QmitkHeadMotionCorrectionView.cpp
	- QmitkSimpleRegistrationView.cpp
	-)
	-
	-set(UI_FILES
	- src/internal/QmitkHeadMotionCorrectionViewControls.ui
	- src/internal/QmitkSimpleRegistrationViewControls.ui
	-)
	-
	-set(MOC_H_FILES
	- src/internal/mitkPluginActivator.h
	-
	- src/internal/QmitkHeadMotionCorrectionView.h
	- src/internal/QmitkSimpleRegistrationView.h
	-)
	-
	-set(CACHED_RESOURCE_FILES
	- plugin.xml
	-
	- resources/diffusionregistration.png
	-)
	-
	-set(QRC_FILES
	-
	-)
	-
	-
	-set(CPP_FILES )
	-
	-foreach(file ${SRC_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/${file})
	-endforeach(file ${SRC_CPP_FILES})
	-
	-foreach(file ${INTERNAL_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/internal/${file})
	-endforeach(file ${INTERNAL_CPP_FILES})
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/manifest_headers.cmake
	deleted file mode 100644
	index 226f6402e8..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/manifest_headers.cmake
	+++ /dev/null
	@@ -1,5 +0,0 @@
	-set(Plugin-Name "MITK dMRI Registration")
	-set(Plugin-Version "1.0.0")
	-set(Plugin-Vendor "DKFZ, Medical and Biological Informatics")
	-set(Plugin-ContactAddress "http://www.mitk.org")
	-set(Require-Plugin org.mitk.gui.qt.diffusionimaging org.mitk.gui.qt.common)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/plugin.xml b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/plugin.xml
	deleted file mode 100644
	index 91e656626c..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/plugin.xml
	+++ /dev/null
	@@ -1,40 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<?BlueBerry version="0.1"?>
	-<plugin>
	-
	- <extension point="org.blueberry.ui.views">
	-
	- <view id="org.mitk.views.headmotioncorrectionview"
	- name="Head-Motion Correction"
	- category="Registration"
	- class="QmitkHeadMotionCorrectionView"
	- icon="resources/diffusionregistration.png">
	- <keywordReference id="org.mitk.views.headmotioncorrectionview.Keyword"/>
	- </view>
	-
	- <view id="org.mitk.views.simpleregistrationview"
	- name="Registration"
	- category="Registration"
	- class="QmitkSimpleRegistrationView"
	- icon="resources/diffusionregistration.png">
	- <keywordReference id="org.mitk.views.simpleregistrationview.Keyword"/>
	- </view>
	-
	- </extension>
	-
	- <extension point="org.blueberry.ui.keywords">
	-
	- <keyword label="registration" id="org.mitk.views.simpleregistrationview.Keyword"/>
	- <keyword label="registration" id="org.mitk.views.headmotioncorrectionview.Keyword"/>
	- <keyword label="motion" id="org.mitk.views.simpleregistrationview.Keyword"/>
	- <keyword label="motion" id="org.mitk.views.headmotioncorrectionview.Keyword"/>
	- <keyword label="head" id="org.mitk.views.simpleregistrationview.Keyword"/>
	- <keyword label="head" id="org.mitk.views.headmotioncorrectionview.Keyword"/>
	- <keyword label="align" id="org.mitk.views.simpleregistrationview.Keyword"/>
	- <keyword label="align" id="org.mitk.views.headmotioncorrectionview.Keyword"/>
	- <keyword label="register" id="org.mitk.views.simplerigidregistrationview.Keyword"/>
	- <keyword label="register" id="org.mitk.views.headmotioncorrectionview.Keyword"/>
	-
	- </extension>
	-
	-</plugin>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/resources/diffusionregistration.png b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/resources/diffusionregistration.png
	deleted file mode 100644
	index e10f5ab85e..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/resources/diffusionregistration.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkHeadMotionCorrectionView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkHeadMotionCorrectionView.cpp
	deleted file mode 100644
	index 614dd6531e..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkHeadMotionCorrectionView.cpp
	+++ /dev/null
	@@ -1,124 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-//misc
	-#define _USE_MATH_DEFINES
	-#include <math.h>
	-
	-// Blueberry
	-#include <berryISelectionService.h>
	-#include <berryIWorkbenchWindow.h>
	-
	-// Qmitk
	-#include "QmitkHeadMotionCorrectionView.h"
	-
	-// MITK
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <mitkNodePredicateDataType.h>
	-
	-// Qt
	-#include <QMessageBox>
	-#include <QFileDialog>
	-#include <QDir>
	-#include <QDirIterator>
	-#include <QTimer>
	-
	-#include <mitkDWIHeadMotionCorrectionFilter.h>
	-
	-#define _USE_MATH_DEFINES
	-#include <math.h>
	-
	-const std::string QmitkHeadMotionCorrectionView::VIEW_ID = "org.mitk.views.headmotioncorrectionview";
	-
	-QmitkHeadMotionCorrectionView::QmitkHeadMotionCorrectionView()
	- : QmitkAbstractView()
	- , m_Controls( 0 )
	- , m_DiffusionImage( nullptr )
	-{
	-
	-}
	-
	-// Destructor
	-QmitkHeadMotionCorrectionView::~QmitkHeadMotionCorrectionView()
	-{
	-}
	-
	-void QmitkHeadMotionCorrectionView::CreateQtPartControl( QWidget *parent )
	-{
	- // build up qt view, unless already done
	- if ( !m_Controls )
	- {
	- // create GUI widgets from the Qt Designer's .ui file
	- m_Controls = new Ui::QmitkHeadMotionCorrectionViewControls;
	- m_Controls->setupUi( parent );
	- connect( m_Controls->m_ImageBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGUI()) );
	- connect( m_Controls->m_RegistrationStartButton, SIGNAL(clicked()), this, SLOT(StartCorrection()) );
	- this->m_Parent = parent;
	-
	- m_Controls->m_ImageBox->SetDataStorage(this->GetDataStorage());
	- mitk::TNodePredicateDataType<mitk::Image>::Pointer isImagePredicate = mitk::TNodePredicateDataType<mitk::Image>::New();
	- m_Controls->m_ImageBox->SetPredicate(isImagePredicate);
	- UpdateGUI();
	- }
	-}
	-
	-void QmitkHeadMotionCorrectionView::OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList<mitk::DataNode::Pointer>& )
	-{
	-
	-}
	-
	-void QmitkHeadMotionCorrectionView::UpdateGUI()
	-{
	- if (m_Controls->m_ImageBox->GetSelectedNode().IsNotNull())
	- {
	- m_Controls->m_RegistrationStartButton->setEnabled(true);
	- m_Controls->m_RegistrationStartButton->setToolTip("Start Registration");
	- }
	- else
	- {
	- m_Controls->m_RegistrationStartButton->setEnabled(false);
	- m_Controls->m_RegistrationStartButton->setToolTip("No Diffusion image selected.");
	- }
	-}
	-
	-void QmitkHeadMotionCorrectionView::SetFocus()
	-{
	- UpdateGUI();
	- m_Controls->m_RegistrationStartButton->setFocus();
	-}
	-
	-void QmitkHeadMotionCorrectionView::StartCorrection()
	-{
	- mitk::DataNode::Pointer node = m_Controls->m_ImageBox->GetSelectedNode();
	- mitk::Image::Pointer inImage = dynamic_cast<mitk::Image*>(node->GetData());
	-
	- if (!mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(inImage))
	- {
	- QMessageBox::warning(nullptr, "Image not processed", "Input is not a diffusion-weighted image!");
	- return;
	- }
	-
	- mitk::DWIHeadMotionCorrectionFilter::Pointer registerer = mitk::DWIHeadMotionCorrectionFilter::New();
	- registerer->SetInput(inImage);
	- registerer->Update();
	- mitk::Image::Pointer image = registerer->GetCorrectedImage();
	- mitk::DataNode::Pointer corrected_node = mitk::DataNode::New();
	- corrected_node->SetData( image );
	- QString name(node->GetName().c_str());
	- name += "_Corrected";
	- corrected_node->SetName(name.toStdString());
	- GetDataStorage()->Add(corrected_node, node);
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkHeadMotionCorrectionView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkHeadMotionCorrectionView.h
	deleted file mode 100644
	index 338cc0a131..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkHeadMotionCorrectionView.h
	+++ /dev/null
	@@ -1,75 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-
	-#include <berryISelectionListener.h>
	-#include <berryIStructuredSelection.h>
	-
	-#include <QmitkAbstractView.h>
	-#include "ui_QmitkHeadMotionCorrectionViewControls.h"
	-
	-#include <mitkImage.h>
	-
	-#include <QThread>
	-#include <QTime>
	-
	-typedef short DiffusionPixelType;
	-
	-/*!
	-\brief View for diffusion image registration / head motion correction
	-*/
	-class QmitkHeadMotionCorrectionView : public QmitkAbstractView
	-{
	-
	- // this is needed for all Qt objects that should have a Qt meta-object
	- // (everything that derives from QObject and wants to have signal/slots)
	- Q_OBJECT
	-
	-public:
	-
	- static const std::string VIEW_ID;
	-
	- QmitkHeadMotionCorrectionView();
	- virtual ~QmitkHeadMotionCorrectionView();
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	- void SetFocus() override;
	-
	-protected slots:
	-
	- void StartCorrection();
	- void UpdateGUI(); ///< update button activity etc. dpending on current datamanager selection
	-
	-
	-protected:
	-
	- /// \brief called by QmitkAbstractView when DataManager's selection has changed
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- Ui::QmitkHeadMotionCorrectionViewControls* m_Controls;
	-
	- mitk::Image::Pointer m_DiffusionImage;
	- std::vector< mitk::DataNode::Pointer > m_SelectedDiffusionNodes;
	-
	-private:
	-
	- void UpdateRegistrationStatus(); ///< update textual status display of the Registration process
	-
	- // the Qt parent of our GUI (NOT of this object)
	- QWidget* m_Parent;
	-
	-};
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkHeadMotionCorrectionViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkHeadMotionCorrectionViewControls.ui
	deleted file mode 100644
	index e919050341..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkHeadMotionCorrectionViewControls.ui
	+++ /dev/null
	@@ -1,97 +0,0 @@
	-<?xml version="1.0" encoding="utf-8"?>
	-<ui version="4.0">
	- <class>QmitkHeadMotionCorrectionViewControls</class>
	- <widget class="QWidget" name="QmitkHeadMotionCorrectionViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>435</width>
	- <height>744</height>
	- </rect>
	- </property>
	- <property name="windowTitle">
	- <string>Form</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_2">
	- <item row="1" column="0">
	- <widget class="QCommandLinkButton" name="m_RegistrationStartButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string>Start DWI registration/Head Motion Correction</string>
	- </property>
	- <property name="text">
	- <string>Start Head Motion Correction</string>
	- </property>
	- </widget>
	- </item>
	- <item row="10" column="0">
	- <spacer name="verticalSpacer">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="0" column="0">
	- <widget class="QFrame" name="frame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_ImageBox"></widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label">
	- <property name="text">
	- <string>Input Image:</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <customwidgets>
	- <customwidget>
	- <class>QmitkDataStorageComboBox</class>
	- <extends>QComboBox</extends>
	- <header location="global">QmitkDataStorageComboBox.h</header>
	- </customwidget>
	- </customwidgets>
	- <resources></resources>
	- <connections></connections>
	-</ui>
	\ No newline at end of file
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkSimpleRegistrationView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkSimpleRegistrationView.cpp
	deleted file mode 100644
	index e28dd5db5e..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkSimpleRegistrationView.cpp
	+++ /dev/null
	@@ -1,403 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-//misc
	-#define _USE_MATH_DEFINES
	-#include <math.h>
	-
	-// Blueberry
	-#include <berryISelectionService.h>
	-#include <berryIWorkbenchWindow.h>
	-
	-// Qmitk
	-#include "QmitkSimpleRegistrationView.h"
	-
	-// MITK
	-#include <mitkNodePredicateDataType.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <mitkImageMappingHelper.h>
	-#include <mitkITKImageImport.h>
	-#include <mitkImageCast.h>
	-#include <itkExtractDwiChannelFilter.h>
	-#include <mitkMultiModalRigidDefaultRegistrationAlgorithm.h>
	-#include <mitkMultiModalAffineDefaultRegistrationAlgorithm.h>
	-#include <itkComposeImageFilter.h>
	-#include <mitkFiberBundle.h>
	-#include <mitkRegistrationHelper.h>
	-#include <mitkDiffusionImageCorrectionFilter.h>
	-
	-// Qt
	-#include <QThreadPool>
	-
	-#define _USE_MATH_DEFINES
	-#include <math.h>
	-
	-const std::string QmitkSimpleRegistrationView::VIEW_ID = "org.mitk.views.simpleregistrationview";
	-
	-QmitkSimpleRegistrationView::QmitkSimpleRegistrationView()
	- : QmitkAbstractView()
	- , m_Controls( 0 )
	- , m_RegistrationType(0)
	-{
	-
	-}
	-
	-// Destructor
	-QmitkSimpleRegistrationView::~QmitkSimpleRegistrationView()
	-{
	-
	-}
	-
	-void QmitkSimpleRegistrationView::StartRegistration()
	-{
	- QmitkRegistrationJob* pJob;
	-
	- if (m_Controls->m_RegBox->currentIndex()==0)
	- {
	- mitk::MultiModalRigidDefaultRegistrationAlgorithm< ItkFloatImageType >::Pointer algo = mitk::MultiModalRigidDefaultRegistrationAlgorithm< ItkFloatImageType >::New();
	- pJob = new QmitkRegistrationJob(algo);
	- m_RegistrationType = 0;
	- }
	- else
	- {
	- mitk::MultiModalAffineDefaultRegistrationAlgorithm< ItkFloatImageType >::Pointer algo = mitk::MultiModalAffineDefaultRegistrationAlgorithm< ItkFloatImageType >::New();
	- pJob = new QmitkRegistrationJob(algo);
	- m_RegistrationType = 1;
	- }
	-
	- pJob->setAutoDelete(true);
	-
	- m_MovingImageNode = m_Controls->m_MovingImageBox->GetSelectedNode();
	- mitk::Image::Pointer movingImage = dynamic_cast<mitk::Image*>(m_MovingImageNode->GetData());
	- if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(movingImage))
	- {
	- ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New();
	- mitk::CastToItkImage(movingImage, itkVectorImagePointer);
	-
	- itk::ExtractDwiChannelFilter< short >::Pointer filter = itk::ExtractDwiChannelFilter< short >::New();
	- filter->SetInput( itkVectorImagePointer);
	- filter->SetChannelIndex(m_Controls->m_MovingChannelBox->value());
	- filter->Update();
	-
	- mitk::Image::Pointer newImage = mitk::Image::New();
	- newImage->InitializeByItk( filter->GetOutput() );
	- newImage->SetImportChannel( filter->GetOutput()->GetBufferPointer() );
	-
	- pJob->m_spMovingData = newImage;
	- }
	- else
	- pJob->m_spMovingData = movingImage;
	-
	-
	- mitk::Image::Pointer fixedImage = dynamic_cast<mitk::Image*>(m_Controls->m_FixedImageBox->GetSelectedNode()->GetData());
	- if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(fixedImage))
	- {
	- ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New();
	- mitk::CastToItkImage(fixedImage, itkVectorImagePointer);
	-
	- itk::ExtractDwiChannelFilter< short >::Pointer filter = itk::ExtractDwiChannelFilter< short >::New();
	- filter->SetInput( itkVectorImagePointer);
	- filter->SetChannelIndex(m_Controls->m_MovingChannelBox->value());
	- filter->Update();
	-
	- mitk::Image::Pointer newImage = mitk::Image::New();
	- newImage->InitializeByItk( filter->GetOutput() );
	- newImage->SetImportChannel( filter->GetOutput()->GetBufferPointer() );
	-
	- pJob->m_spTargetData = newImage;
	- }
	- else
	- pJob->m_spTargetData = fixedImage;
	-
	- pJob->m_TargetDataUID = mitk::EnsureUID(m_Controls->m_FixedImageBox->GetSelectedNode()->GetData());
	- pJob->m_MovingDataUID = mitk::EnsureUID(m_Controls->m_MovingImageBox->GetSelectedNode()->GetData());
	-
	- connect(pJob, SIGNAL(RegResultIsAvailable(mitk::MAPRegistrationWrapper::Pointer, const QmitkRegistrationJob*)), this,
	- SLOT(OnRegResultIsAvailable(mitk::MAPRegistrationWrapper::Pointer, const QmitkRegistrationJob*)),
	- Qt::BlockingQueuedConnection);
	-
	- QThreadPool* threadPool = QThreadPool::globalInstance();
	- threadPool->start(pJob);
	-
	- m_Controls->m_RegistrationStartButton->setEnabled(false);
	- m_Controls->m_RegistrationStartButton->setText("Registration in progress ...");
	-}
	-
	-void QmitkSimpleRegistrationView::OnRegResultIsAvailable(mitk::MAPRegistrationWrapper::Pointer spResultRegistration, const QmitkRegistrationJob* job)
	-{
	- mitk::Image::Pointer movingImage = dynamic_cast<mitk::Image*>(m_MovingImageNode->GetData());
	- mitk::Image::Pointer image;
	-
	- if (m_RegistrationType==0 && !m_Controls->m_ResampleBox->isChecked())
	- {
	- image = mitk::ImageMappingHelper::refineGeometry(movingImage, spResultRegistration, true);
	-
	- mitk::DiffusionPropertyHelper::CopyProperties(movingImage, image, true);
	- auto reg = spResultRegistration->GetRegistration();
	- typedef mitk::DiffusionImageCorrectionFilter CorrectionFilterType;
	- CorrectionFilterType::Pointer corrector = CorrectionFilterType::New();
	- corrector->SetImage( image );
	- corrector->CorrectDirections( mitk::MITKRegistrationHelper::getAffineMatrix(reg, false)->GetMatrix().GetVnlMatrix() );
	- }
	- else
	- {
	- if (!mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(movingImage))
	- {
	- image = mitk::ImageMappingHelper::map(movingImage, spResultRegistration, false, 0, job->m_spTargetData->GetGeometry(), false, 0, mitk::ImageMappingInterpolator::BSpline_3);
	- }
	- else
	- {
	- typedef itk::ComposeImageFilter < ITKDiffusionVolumeType > ComposeFilterType;
	- ComposeFilterType::Pointer composer = ComposeFilterType::New();
	-
	- ItkDwiType::Pointer itkVectorImagePointer = mitk::DiffusionPropertyHelper::GetItkVectorImage(movingImage);
	- for (unsigned int i=0; i<itkVectorImagePointer->GetVectorLength(); ++i)
	- {
	- itk::ExtractDwiChannelFilter< short >::Pointer filter = itk::ExtractDwiChannelFilter< short >::New();
	- filter->SetInput( itkVectorImagePointer);
	- filter->SetChannelIndex(i);
	- filter->Update();
	-
	- mitk::Image::Pointer gradientVolume = mitk::Image::New();
	- gradientVolume->InitializeByItk( filter->GetOutput() );
	- gradientVolume->SetImportChannel( filter->GetOutput()->GetBufferPointer() );
	-
	- mitk::Image::Pointer registered_mitk_image = mitk::ImageMappingHelper::map(gradientVolume, spResultRegistration, false, 0, job->m_spTargetData->GetGeometry(), false, 0, mitk::ImageMappingInterpolator::BSpline_3);
	-
	- ITKDiffusionVolumeType::Pointer registered_itk_image = ITKDiffusionVolumeType::New();
	- mitk::CastToItkImage(registered_mitk_image, registered_itk_image);
	- composer->SetInput(i, registered_itk_image);
	- }
	-
	- composer->Update();
	-
	- image = mitk::GrabItkImageMemory( composer->GetOutput() );
	- mitk::DiffusionPropertyHelper::CopyProperties(movingImage, image, true);
	-
	- auto reg = spResultRegistration->GetRegistration();
	- typedef mitk::DiffusionImageCorrectionFilter CorrectionFilterType;
	- CorrectionFilterType::Pointer corrector = CorrectionFilterType::New();
	- corrector->SetImage( image );
	- corrector->CorrectDirections( mitk::MITKRegistrationHelper::getAffineMatrix(reg, false)->GetMatrix().GetVnlMatrix() );
	- }
	- }
	-
	- if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(image))
	- mitk::DiffusionPropertyHelper::InitializeImage( image );
	-
	- mitk::DataNode::Pointer resultNode = mitk::DataNode::New();
	- resultNode->SetData(image);
	-
	- if (m_MovingImageNode.IsNotNull())
	- {
	- m_MovingImageNode->SetVisibility(false);
	- QString name = m_MovingImageNode->GetName().c_str();
	- if (m_RegistrationType==0)
	- resultNode->SetName((name+"_registered (rigid)").toStdString().c_str());
	- else
	- resultNode->SetName((name+"_registered (affine)").toStdString().c_str());
	- }
	- else
	- {
	- if (m_RegistrationType==0)
	- resultNode->SetName("Registered (rigid)");
	- else
	- resultNode->SetName("Registered (affine)");
	- }
	-// resultNode->SetOpacity(0.6);
	-// resultNode->SetColor(0.0, 0.0, 1.0);
	- GetDataStorage()->Add(resultNode);
	-
	- mitk::RenderingManager::GetInstance()->InitializeViews( resultNode->GetData()->GetTimeGeometry(),
	- mitk::RenderingManager::REQUEST_UPDATE_ALL,
	- true);
	-
	- if (m_Controls->m_RegOutputBox->isChecked())
	- {
	- mitk::DataNode::Pointer registration_node = mitk::DataNode::New();
	- registration_node->SetData(spResultRegistration);
	- if (m_RegistrationType==0)
	- registration_node->SetName("Registration Object (rigid)");
	- else
	- registration_node->SetName("Registration Object (affine)");
	- GetDataStorage()->Add(registration_node, resultNode);
	- }
	-
	- this->GetRenderWindowPart()->RequestUpdate();
	-
	- m_Controls->m_RegistrationStartButton->setEnabled(true);
	- m_Controls->m_RegistrationStartButton->setText("Start Registration");
	-
	- m_MovingImageNode = nullptr;
	-
	- TractoChanged();
	-}
	-
	-void QmitkSimpleRegistrationView::CreateQtPartControl( QWidget *parent )
	-{
	- // build up qt view, unless already done
	- if ( !m_Controls )
	- {
	- // create GUI widgets from the Qt Designer's .ui file
	- m_Controls = new Ui::QmitkSimpleRegistrationViewControls;
	- m_Controls->setupUi( parent );
	-
	- m_Controls->m_FixedImageBox->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_MovingImageBox->SetDataStorage(this->GetDataStorage());
	-
	- mitk::TNodePredicateDataType<mitk::Image>::Pointer isImagePredicate = mitk::TNodePredicateDataType<mitk::Image>::New();
	- m_Controls->m_FixedImageBox->SetPredicate(isImagePredicate);
	- m_Controls->m_MovingImageBox->SetPredicate(isImagePredicate);
	-
	- mitk::TNodePredicateDataType<mitk::FiberBundle>::Pointer isFib = mitk::TNodePredicateDataType<mitk::FiberBundle>::New();
	- mitk::TNodePredicateDataType<mitk::MAPRegistrationWrapper>::Pointer isReg = mitk::TNodePredicateDataType<mitk::MAPRegistrationWrapper>::New();
	-
	- m_Controls->m_TractoBox->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_RegObjectBox->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_TractoBox->SetPredicate(isFib);
	- m_Controls->m_RegObjectBox->SetPredicate(isReg);
	-
	- connect( m_Controls->m_FixedImageBox, SIGNAL(currentIndexChanged(int)), this, SLOT(FixedImageChanged()) );
	- connect( m_Controls->m_MovingImageBox, SIGNAL(currentIndexChanged(int)), this, SLOT(MovingImageChanged()) );
	-
	- connect( m_Controls->m_TractoBox, SIGNAL(currentIndexChanged(int)), this, SLOT(TractoChanged()) );
	- connect( m_Controls->m_RegObjectBox, SIGNAL(currentIndexChanged(int)), this, SLOT(TractoChanged()) );
	-
	- connect( m_Controls->m_RegistrationStartButton, SIGNAL(clicked()), this, SLOT(StartRegistration()) );
	- connect( m_Controls->m_TractoRegistrationStartButton, SIGNAL(clicked()), this, SLOT(StartTractoRegistration()) );
	-
	- FixedImageChanged();
	- MovingImageChanged();
	- TractoChanged();
	- }
	-}
	-
	-void QmitkSimpleRegistrationView::StartTractoRegistration()
	-{
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(m_Controls->m_TractoBox->GetSelectedNode()->GetData());
	- mitk::MAPRegistrationWrapper::Pointer reg = dynamic_cast<mitk::MAPRegistrationWrapper*>(m_Controls->m_RegObjectBox->GetSelectedNode()->GetData());
	-
	- mitk::MITKRegistrationHelper::Affine3DTransformType::Pointer affine = mitk::MITKRegistrationHelper::getAffineMatrix(reg, false);
	-
	- mitk::FiberBundle::Pointer fib_copy = fib->GetDeepCopy();
	- fib_copy->TransformFibers(affine);
	-
	- mitk::DataNode::Pointer registration_node = mitk::DataNode::New();
	- registration_node->SetData(fib_copy);
	- QString name = m_Controls->m_TractoBox->GetSelectedNode()->GetName().c_str();
	- registration_node->SetName((name+"_registered").toStdString().c_str());
	- GetDataStorage()->Add(registration_node, m_Controls->m_TractoBox->GetSelectedNode());
	-}
	-
	-void QmitkSimpleRegistrationView::TractoChanged()
	-{
	- if (m_Controls->m_RegObjectBox->GetSelectedNode().IsNotNull() && m_Controls->m_TractoBox->GetSelectedNode().IsNotNull())
	- m_Controls->m_TractoRegistrationStartButton->setEnabled(true);
	- else
	- m_Controls->m_TractoRegistrationStartButton->setEnabled(false);
	-}
	-
	-void QmitkSimpleRegistrationView::FixedImageChanged()
	-{
	- if (m_Controls->m_FixedImageBox->GetSelectedNode().IsNotNull())
	- {
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(m_Controls->m_FixedImageBox->GetSelectedNode()->GetData());
	- int channels = image->GetNumberOfChannels();
	- int dims = image->GetDimension();
	- int fourth_dim_size = image->GetTimeSteps();
	- bool isdiff = mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(image);
	-
	- if (dims==4 \|\| channels>1)
	- {
	- m_Controls->m_FixedChannelBox->setEnabled(false);
	- m_Controls->m_RegistrationStartButton->setEnabled(false);
	- }
	-
	- if (isdiff)
	- {
	- m_Controls->m_FixedChannelBox->setEnabled(true);
	- if (fourth_dim_size>1)
	- m_Controls->m_FixedChannelBox->setMaximum(fourth_dim_size-1);
	- else if (isdiff)
	- m_Controls->m_FixedChannelBox->setMaximum(mitk::DiffusionPropertyHelper::GetGradientContainer(image)->Size()-1);
	- }
	- else
	- {
	- m_Controls->m_FixedChannelBox->setEnabled(false);
	- }
	-
	- m_Controls->m_RegistrationStartButton->setEnabled(true);
	- }
	- else
	- {
	- m_Controls->m_FixedChannelBox->setEnabled(false);
	- m_Controls->m_RegistrationStartButton->setEnabled(false);
	- }
	-}
	-
	-void QmitkSimpleRegistrationView::MovingImageChanged()
	-{
	- if (m_Controls->m_MovingImageBox->GetSelectedNode().IsNotNull())
	- {
	- mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(m_Controls->m_MovingImageBox->GetSelectedNode()->GetData());
	- int channels = image->GetNumberOfChannels();
	- int dims = image->GetDimension();
	- int fourth_dim_size = image->GetTimeSteps();
	- bool isdiff = mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(image);
	-
	- if (dims==4 \|\| channels>1)
	- {
	- m_Controls->m_MovingChannelBox->setEnabled(false);
	- m_Controls->m_RegistrationStartButton->setEnabled(false);
	- }
	-
	- if (isdiff)
	- {
	- m_Controls->m_MovingChannelBox->setEnabled(true);
	- if (fourth_dim_size>1)
	- m_Controls->m_MovingChannelBox->setMaximum(fourth_dim_size-1);
	- else if (isdiff)
	- m_Controls->m_MovingChannelBox->setMaximum(mitk::DiffusionPropertyHelper::GetGradientContainer(image)->Size()-1);
	- }
	- else
	- {
	- m_Controls->m_MovingChannelBox->setEnabled(false);
	- }
	-
	- m_Controls->m_RegistrationStartButton->setEnabled(true);
	- }
	- else
	- {
	- m_Controls->m_MovingChannelBox->setEnabled(false);
	- m_Controls->m_RegistrationStartButton->setEnabled(false);
	- }
	-}
	-
	-void QmitkSimpleRegistrationView::OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList<mitk::DataNode::Pointer>& )
	-{
	- FixedImageChanged();
	- MovingImageChanged();
	- TractoChanged();
	-}
	-
	-
	-void QmitkSimpleRegistrationView::SetFocus()
	-{
	- m_Controls->m_RegistrationStartButton->setFocus();
	- FixedImageChanged();
	- MovingImageChanged();
	-}
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkSimpleRegistrationView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkSimpleRegistrationView.h
	deleted file mode 100644
	index 777508b956..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkSimpleRegistrationView.h
	+++ /dev/null
	@@ -1,75 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-
	-#include <berryISelectionListener.h>
	-#include <berryIStructuredSelection.h>
	-#include <QmitkAbstractView.h>
	-#include "ui_QmitkSimpleRegistrationViewControls.h"
	-
	-#include <mitkImage.h>
	-#include <QmitkRegistrationJob.h>
	-
	-typedef short DiffusionPixelType;
	-
	-/*!
	-\brief View for diffusion image registration / head motion correction
	-*/
	-
	-// Forward Qt class declarations
	-
	-class QmitkSimpleRegistrationView : public QmitkAbstractView
	-{
	-
	- // this is needed for all Qt objects that should have a Qt meta-object
	- // (everything that derives from QObject and wants to have signal/slots)
	- Q_OBJECT
	-
	-public:
	-
	- typedef itk::Image< float, 3 > ItkFloatImageType;
	- typedef itk::Image<DiffusionPixelType, 3> ITKDiffusionVolumeType;
	- typedef itk::VectorImage< short, 3 > ItkDwiType;
	- static const std::string VIEW_ID;
	-
	- QmitkSimpleRegistrationView();
	- virtual ~QmitkSimpleRegistrationView();
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	- void SetFocus() override;
	-
	-protected slots:
	-
	- void MovingImageChanged();
	- void FixedImageChanged();
	- void TractoChanged();
	- void StartRegistration();
	- void StartTractoRegistration();
	- void OnRegResultIsAvailable(mitk::MAPRegistrationWrapper::Pointer spResultRegistration, const QmitkRegistrationJob* pRegJob);
	-
	-protected:
	-
	- /// \brief called by QmitkAbstractView when DataManager's selection has changed
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- Ui::QmitkSimpleRegistrationViewControls* m_Controls;
	- mitk::DataNode::Pointer m_MovingImageNode;
	- int m_RegistrationType;
	-
	-private:
	-
	-};
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkSimpleRegistrationViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkSimpleRegistrationViewControls.ui
	deleted file mode 100644
	index a61c2080ef..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkSimpleRegistrationViewControls.ui
	+++ /dev/null
	@@ -1,302 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<ui version="4.0">
	- <class>QmitkSimpleRegistrationViewControls</class>
	- <widget class="QWidget" name="QmitkSimpleRegistrationViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>435</width>
	- <height>744</height>
	- </rect>
	- </property>
	- <property name="windowTitle">
	- <string>Form</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_2">
	- <property name="verticalSpacing">
	- <number>25</number>
	- </property>
	- <item row="13" column="0">
	- <spacer name="verticalSpacer">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="3" column="0">
	- <widget class="QGroupBox" name="groupBox_2">
	- <property name="title">
	- <string>Image Registration</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_6">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="2" column="0">
	- <widget class="QCommandLinkButton" name="m_RegistrationStartButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Start Registration</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QFrame" name="frame_2">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_3">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_3">
	- <property name="text">
	- <string>Registration Type:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QComboBox" name="m_RegBox">
	- <item>
	- <property name="text">
	- <string>Rigid</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Affine</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QCheckBox" name="m_RegOutputBox">
	- <property name="text">
	- <string/>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_4">
	- <property name="text">
	- <string>Output Registration Object:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label_7">
	- <property name="text">
	- <string>Always Resample to Target:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QCheckBox" name="m_ResampleBox">
	- <property name="text">
	- <string/>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QFrame" name="frame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="1" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_MovingImageBox"/>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_2">
	- <property name="text">
	- <string>Moving Image:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_FixedImageBox"/>
	- </item>
	- <item row="1" column="2">
	- <widget class="QSpinBox" name="m_MovingChannelBox">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string>Select dMRI volume used to calculate transformation.</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="2">
	- <widget class="QSpinBox" name="m_FixedChannelBox">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string>Select dMRI volume used to calculate transformation.</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label">
	- <property name="text">
	- <string>Fixed Image:</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <widget class="QFrame" name="frame_3">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_5">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QCommandLinkButton" name="m_TractoRegistrationStartButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Start Tractography Registration</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QGroupBox" name="groupBox">
	- <property name="title">
	- <string>Tractography Registration</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_4">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_5">
	- <property name="text">
	- <string>Registration Object:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_RegObjectBox"/>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_6">
	- <property name="text">
	- <string>Tractogram:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_TractoBox"/>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <customwidgets>
	- <customwidget>
	- <class>QmitkDataStorageComboBox</class>
	- <extends>QComboBox</extends>
	- <header location="global">QmitkDataStorageComboBox.h</header>
	- </customwidget>
	- </customwidgets>
	- <resources/>
	- <connections/>
	-</ui>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/mitkPluginActivator.cpp
	deleted file mode 100644
	index 7432af3c10..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/mitkPluginActivator.cpp
	+++ /dev/null
	@@ -1,41 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkPluginActivator.h"
	-
	-#include "src/internal/QmitkHeadMotionCorrectionView.h"
	-#include "src/internal/QmitkSimpleRegistrationView.h"
	-
	-
	-ctkPluginContext* mitk::PluginActivator::m_Context = nullptr;
	-
	-ctkPluginContext* mitk::PluginActivator::GetContext()
	-{
	- return m_Context;
	-}
	-
	-void mitk::PluginActivator::start(ctkPluginContext* context)
	-{
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkHeadMotionCorrectionView, context)
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkSimpleRegistrationView, context)
	- m_Context = context;
	-}
	-
	-void mitk::PluginActivator::stop(ctkPluginContext* context)
	-{
	- Q_UNUSED(context)
	- m_Context = nullptr;
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/mitkPluginActivator.h b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/mitkPluginActivator.h
	deleted file mode 100644
	index d534f6a502..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/mitkPluginActivator.h
	+++ /dev/null
	@@ -1,40 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef MITKPLUGINACTIVATOR_H
	-#define MITKPLUGINACTIVATOR_H
	-
	-#include <ctkPluginActivator.h>
	-
	-namespace mitk
	-{
	- class PluginActivator : public QObject, public ctkPluginActivator
	- {
	- Q_OBJECT
	- Q_PLUGIN_METADATA(IID "org.mitk.gui.qt.diffusionimaging.registration")
	- Q_INTERFACES(ctkPluginActivator)
	-
	- public:
	- static ctkPluginContext* GetContext();
	-
	- void start(ctkPluginContext* context) override;
	- void stop(ctkPluginContext* context) override;
	-
	- private:
	- static ctkPluginContext* m_Context;
	- };
	-}
	-
	-#endif
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/CMakeLists.txt
	deleted file mode 100644
	index cda45e0351..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/CMakeLists.txt
	+++ /dev/null
	@@ -1,10 +0,0 @@
	-# The project name must correspond to the directory name of your plug-in
	-# and must not contain periods.
	-project(org_mitk_gui_qt_diffusionimaging_tbss)
	-
	-mitk_create_plugin(
	- SUBPROJECTS MITK-DTI
	- EXPORT_DIRECTIVE DIFFUSIONIMAGING_TBSS_EXPORT
	- EXPORTED_INCLUDE_SUFFIXES src
	- MODULE_DEPENDS MitkQtWidgetsExt MitkFiberTracking MitkQuantification
	-)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/documentation/UserManual/QmitkTbssViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/documentation/UserManual/QmitkTbssViewUserManual.dox
	deleted file mode 100644
	index b99b98232d..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/documentation/UserManual/QmitkTbssViewUserManual.dox
	+++ /dev/null
	@@ -1,58 +0,0 @@
	-/**
	-\page org_mitk_views_tractbasedspatialstatistics The TBSS View
	-
	-\imageMacro{tbss.png,"Icon of the TBSS View",2.00}
	-
	-\section QmitkTractbasedSpatialStatistics Summary
	-
	-This view can be used to locally explore data resulting from preprocessing with the TBSS view of FSL
	-
	-This document will tell you how to use this view, but it is assumed that you already know how to use MITK in general and how to work with the TBSS view of FSL.
	-
	-If you encounter problems using the view, please have a look at the \ref QmitkTractbasedSpatialStatisticsUserManualTroubleshooting page.
	-
	-\tableofcontents
	-
	-\section QmitkTractbasedSpatialStatisticsUserManualOverview Overview
	-
	-This view is currently under development and as such the interface as well as the capabilities are likely to change significantly between different versions.
	-
	-This documentation describes the features of this current version.
	-
	-
	-
	-\section QmitkTractbasedSpatialStatisticsUserManualFSLImport FSL Import
	-The FSL import allows to import data that has been preprocessed by FSL. FSL creates output images that typically have names like all_FA_skeletonized.nii.gz that are 4-dimensional images that contain registered images of all subjects. By loading this 4D image into the datamanager and listing the groups with the correct number of subjects, in the order of occurrence in the 4D image, in the TBSS-View using the Add button and clicking the import subject data a TBSS file is created that contains all the information needed for tract analysis. The diffusion measure of the image can be set as well.
	-
	-\imageMacro{fslimport.png,"FSL Import",16.00}
	-
	-\section QmitkTractbasedSpatialStatisticsUserManualRois Regions of Interest (ROIs)
	-To create a ROI the mean FA skeleton (typically called mean_FA_skeleton.nii.gz) that is created by FSL should be loaded in to the datamanager and selected. By using the Pointlistwidget points should be set on the skeleton (make sure to select points with relatively high FA values). Points are set by first selecting the button with the '+' and than shift-leftclick in the image. When the correct image is selected in the datamanager the Create ROI button is enabled. Clicking this will create a region of interest that passes through the previously selected points. The roi appears in the datamanager. Before doing so, the name of the roi and the information on the structure on which the ROI lies can be set. This will be saved as extra information in the roi-image. Before the ROI is calculated, a pop-up window will ask the user to provide a threshold value. This should be the same threshold that was previously used in FSL to create a binary mask of the FA skeleton. When this is not done correctly, the region of interest will possible contain zero-valued voxels.
	-
	-\imageMacro{tbssRoi.png,"Regions of Interest (ROIs)",16.00}
	-
	-
	-\section QmitkTractbasedSpatialStatisticsUserManualProfiles
	-
	-y selecting a tbss image with group information and a region of interest image (as was created in a previous stap). A profile plot is drawn in the plot canvas. By clicking in the graph the crosshairs jump to the corresponding location in the image.
	-
	-\imageMacro{profiles.png,"Profile plots",16.00}
	-
	-\section QmitkTractbasedSpatialStatisticsUserManualFiberPlotting
	-It is also possible to use fiber bundles to plot values in images. However, unlike TBSS this only works on 3D volumes (one subject only). To plot the values of a 3D volume using fiber tracking results, we need, fiber data and two planar circles as Regions of Interest that define the region that must be plotted. For every fiber that passes through both ROIs the values at the corresponding positions in the volume are plotted. Every fiber is resampled to the number of segments specified in the GUI. The average value can also be plotted. The subset of the fibers between the ROIs can be cut out by pressing the Cut button.
	-
	-\imageMacro{trackingplot.png,"Plot of fiber tracts",16.00}
	-
	-
	-\section QmitkTractbasedSpatialStatisticsUserManualTroubleshooting Troubleshooting
	-
	-Please report to the MITK mailing list.
	-See http://www.mitk.org/wiki/Mailinglist on how to do this.
	-
	-
	-
	-\section QmitkTractbasedSpatialStatisticsUserManualReferences References
	-1. S.M. Smith, M. Jenkinson, H. Johansen-Berg, D. Rueckert, T.E. Nichols, C.E. Mackay, K.E. Watkins, O. Ciccarelli, M.Z. Cader, P.M. Matthews, and T.E.J. Behrens. Tract-based spatial statistics: Voxelwise analysis of multi-subject diffusion data. NeuroImage, 31:1487-1505, 2006.
	-
	-2. S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 23(S1):208-219, 2004.
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/documentation/UserManual/fslimport.png b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/documentation/UserManual/fslimport.png
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	index aee5f25e98..0000000000
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/documentation/UserManual/profiles.png b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/documentation/UserManual/profiles.png
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	index fb4b4669f3..0000000000
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/documentation/UserManual/tbss.png b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/documentation/UserManual/tbss.png
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	index c1efc783a6..0000000000
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/documentation/UserManual/tbssRoi.png b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/documentation/UserManual/tbssRoi.png
	deleted file mode 100644
	index 9389813184..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/documentation/UserManual/tbssRoi.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/documentation/UserManual/trackingplot.png b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/documentation/UserManual/trackingplot.png
	deleted file mode 100644
	index 454c87e9a4..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/documentation/UserManual/trackingplot.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/documentation/doxygen/modules.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/documentation/doxygen/modules.dox
	deleted file mode 100644
	index 5b2e1a648f..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/documentation/doxygen/modules.dox
	+++ /dev/null
	@@ -1,16 +0,0 @@
	-/**
	- \defgroup org_mitk_gui_qt_diffusionimaging_tbss org.mitk.gui.qt.diffusionimaging.tbss
	- \ingroup MITKPlugins
	-
	- \brief This is the diffusionimaging.tbss plugin.
	-
	-*/
	-
	-/**
	- \defgroup org_mitk_gui_qt_diffusionimaging_tbss_internal Internal
	- \ingroup org_mitk_gui_qt_diffusionimaging_tbss
	-
	- \brief This subcategory includes the internal classes of the org.mitk.gui.qt.diffusionimaging.tbss plugin. Other
	- plugins must not rely on these classes. They contain implementation details and their interface
	- may change at any time. We mean it.
	-*/
	\ No newline at end of file
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/files.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/files.cmake
	deleted file mode 100644
	index 7dd8059646..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/files.cmake
	+++ /dev/null
	@@ -1,46 +0,0 @@
	-set(SRC_CPP_FILES
	- QmitkTbssRoiAnalysisWidget.cpp
	-)
	-
	-set(INTERNAL_CPP_FILES
	- QmitkTractbasedSpatialStatisticsView.cpp
	- QmitkTbssTableModel.cpp
	- QmitkTbssMetaTableModel.cpp
	- QmitkTbssSkeletonizationView.cpp
	-
	- mitkPluginActivator.cpp
	-)
	-
	-set(UI_FILES
	- src/internal/QmitkTractbasedSpatialStatisticsViewControls.ui
	- src/internal/QmitkTbssSkeletonizationViewControls.ui
	-)
	-
	-set(MOC_H_FILES
	- src/internal/mitkPluginActivator.h
	-
	- src/internal/QmitkTractbasedSpatialStatisticsView.h
	- src/internal/QmitkTbssSkeletonizationView.h
	- src/QmitkTbssRoiAnalysisWidget.h
	-)
	-
	-set(CACHED_RESOURCE_FILES
	- plugin.xml
	-
	- resources/tbss.png
	-)
	-
	-set(QRC_FILES
	-
	-)
	-
	-
	-set(CPP_FILES )
	-
	-foreach(file ${SRC_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/${file})
	-endforeach(file ${SRC_CPP_FILES})
	-
	-foreach(file ${INTERNAL_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/internal/${file})
	-endforeach(file ${INTERNAL_CPP_FILES})
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/manifest_headers.cmake
	deleted file mode 100644
	index 5c107a6272..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/manifest_headers.cmake
	+++ /dev/null
	@@ -1,5 +0,0 @@
	-set(Plugin-Name "MITK Tbss")
	-set(Plugin-Version "1.0.0")
	-set(Plugin-Vendor "DKFZ, Medical and Biological Informatics")
	-set(Plugin-ContactAddress "http://www.mitk.org")
	-set(Require-Plugin org.mitk.gui.qt.diffusionimaging org.mitk.gui.qt.common)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/plugin.xml b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/plugin.xml
	deleted file mode 100644
	index 768c5b184e..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/plugin.xml
	+++ /dev/null
	@@ -1,26 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<?eclipse version="3.0"?>
	-<plugin>
	-
	- <extension point="org.blueberry.ui.views">
	-
	- <view id="org.mitk.views.tbssskeletonization"
	- name="Tbss Skeletonization"
	- category="Quantification"
	- class="QmitkTbssSkeletonizationView"
	- icon="resources/tbss.png">
	- <keywordReference id="org.mitk.views.tbssskeletonization.Keyword"/>
	- </view>
	-
	- <view id="org.mitk.views.tractbasedspatialstatistics"
	- name="Tract-based spatial statistics"
	- category="Quantification"
	- class="QmitkTractbasedSpatialStatisticsView"
	- icon="resources/tbss.png">
	- <keywordReference id="org.mitk.views.tractbasedspatialstatistics.Keyword"/>
	- </view>
	-
	- </extension>
	-
	-
	-</plugin>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/resources/tbss.png b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/resources/tbss.png
	deleted file mode 100644
	index 61f1eef09e..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/resources/tbss.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/QmitkTbssRoiAnalysisWidget.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/QmitkTbssRoiAnalysisWidget.cpp
	deleted file mode 100644
	index 8d48e6f0f7..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/QmitkTbssRoiAnalysisWidget.cpp
	+++ /dev/null
	@@ -1,967 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkTbssRoiAnalysisWidget.h"
	-#include "mitkImagePixelReadAccessor.h"
	-#include "mitkPixelTypeMultiplex.h"
	-
	-#include <qwt_plot_marker.h>
	-#include <qwt_plot_picker.h>
	-#include <qwt_picker_machine.h>
	-
	-#include <vtkCellArray.h>
	-
	-QmitkTbssRoiAnalysisWidget::QmitkTbssRoiAnalysisWidget( QWidget * parent )
	- : QmitkPlotWidget(parent)
	-{
	- m_PlotPicker = new QwtPlotPicker(m_Plot->canvas());
	- m_PlotPicker->setStateMachine(new QwtPickerDragPointMachine());
	- m_PlotPicker->setTrackerMode(QwtPicker::ActiveOnly);
	-
	- m_PlottingFiberBundle = false;
	-}
	-
	-
	-
	-void QmitkTbssRoiAnalysisWidget::DoPlotFiberBundles(mitk::FiberBundle fib, mitk::Image img,
	- mitk::DataNode* startRoi, mitk::DataNode* endRoi, bool avg, int number)
	-{
	-
	- TractContainerType tracts = CreateTracts(fib, startRoi, endRoi);
	-
	- TractContainerType resampledTracts = ParameterizeTracts(tracts, number);
	-
	- // Now we have the resampled tracts. Next we should use these points to read out the values
	-
	-
	-
	- mitkPixelTypeMultiplex3(PlotFiberBundles,img->GetImageDescriptor()->GetChannelTypeById(0),resampledTracts, img, avg);
	- m_CurrentTracts = resampledTracts;
	-}
	-
	-
	-TractContainerType QmitkTbssRoiAnalysisWidget::CreateTracts(mitk::FiberBundle *fib,
	- mitk::DataNode *startRoi,
	- mitk::DataNode *endRoi)
	-{
	- mitk::PlaneGeometry* startGeometry2D = const_cast<mitk::PlaneGeometry>(dynamic_cast<mitk::PlanarFigure>(startRoi->GetData())->GetPlaneGeometry());
	- mitk::PlaneGeometry* endGeometry2D = const_cast<mitk::PlaneGeometry>(dynamic_cast<mitk::PlanarFigure>(endRoi->GetData())->GetPlaneGeometry());
	-
	-
	- mitk::Point3D startCenter = dynamic_cast<mitk::PlanarFigure*>(startRoi->GetData())->GetWorldControlPoint(0); //center Point of start roi
	- mitk::Point3D endCenter = dynamic_cast<mitk::PlanarFigure*>(startRoi->GetData())->GetWorldControlPoint(0); //center Point of end roi
	-
	- mitk::FiberBundle::Pointer inStart = fib->ExtractFiberSubset(startRoi, nullptr);
	- mitk::FiberBundle::Pointer inBoth = inStart->ExtractFiberSubset(endRoi, nullptr);
	-
	-
	-
	- int num = inBoth->GetNumFibers();
	-
	-
	- TractContainerType tracts;
	-
	-
	- vtkSmartPointer<vtkPolyData> fiberPolyData = inBoth->GetFiberPolyData();
	- vtkCellArray* lines = fiberPolyData->GetLines();
	- lines->InitTraversal();
	-
	-
	-
	- // Now find out for each fiber which ROI is encountered first. If this is the startRoi, the direction is ok
	- // Otherwise the plot should be in the reverse direction
	- for( int fiberID( 0 ); fiberID < num; fiberID++ )
	- {
	- vtkIdType numPointsInCell(0);
	- vtkIdType* pointsInCell(nullptr);
	- lines->GetNextCell ( numPointsInCell, pointsInCell );
	-
	- int startId = 0;
	- int endId = 0;
	-
	- mitk::ScalarType minDistStart = std::numeric_limits<mitk::ScalarType>::max();
	- mitk::ScalarType minDistEnd = std::numeric_limits<mitk::ScalarType>::max();
	-
	-
	-
	- for( int pointInCellID( 0 ); pointInCellID < numPointsInCell ; pointInCellID++)
	- {
	-
	-
	- mitk::ScalarType *p = fiberPolyData->GetPoint( pointsInCell[ pointInCellID ] );
	-
	- mitk::Point3D point;
	- point[0] = p[0];
	- point[1] = p[1];
	- point[2] = p[2];
	-
	- mitk::ScalarType distanceToStart = point.EuclideanDistanceTo(startCenter);
	- mitk::ScalarType distanceToEnd = point.EuclideanDistanceTo(endCenter);
	-
	- if(distanceToStart < minDistStart)
	- {
	- minDistStart = distanceToStart;
	- startId = pointInCellID;
	- }
	-
	- if(distanceToEnd < minDistEnd)
	- {
	- minDistEnd = distanceToEnd;
	- endId = pointInCellID;
	- }
	-
	-
	-
	- }
	-
	- /* We found the start and end points of of the part that should be plottet for
	- the current fiber. now we need to plot them. If the endId is smaller than the startId the plot order
	- must be reversed*/
	-
	- TractType singleTract;
	- PointType point;
	-
	- if(startId < endId)
	- {
	-
	- // Calculate the intersection of the ROI with the startRoi and decide if the startId is part of the roi or must be cut of
	- mitk::ScalarType *p = fiberPolyData->GetPoint( pointsInCell[ startId ] );
	- mitk::Vector3D p0;
	- p0[0] = p[0]; p0[1] = p[1]; p0[2] = p[2];
	-
	- p = fiberPolyData->GetPoint( pointsInCell[ startId+1 ] );
	- mitk::Vector3D p1;
	- p1[0] = p[0]; p1[1] = p[1]; p1[2] = p[2];
	-
	- // Check if p and p2 are both on the same side of the plane
	- mitk::Vector3D normal = startGeometry2D->GetNormal();
	-
	- mitk::Point3D pStart;
	- pStart[0] = p0[0]; pStart[1] = p0[1]; pStart[2] = p0[2];
	-
	- mitk::Point3D pSecond;
	- pSecond[0] = p1[0]; pSecond[1] = p1[1]; pSecond[2] = p1[2];
	-
	- bool startOnPositive = startGeometry2D->IsAbove(pStart);
	- bool secondOnPositive = startGeometry2D->IsAbove(pSecond);
	-
	-
	- mitk::Vector3D onPlane;
	- onPlane[0] = startCenter[0]; onPlane[1] = startCenter[1]; onPlane[2] = startCenter[2];
	-
	-
	-
	- if(! (secondOnPositive ^ startOnPositive) )
	- {
	- /* startId and startId+1 lie on the same side of the plane, so we need
	- need startId-1 to calculate the intersection with the planar figure*/
	- p = fiberPolyData->GetPoint( pointsInCell[ startId-1 ] );
	- p1[0] = p[0]; p1[1] = p[1]; p1[2] = p[2];
	- }
	-
	-
	- mitk::ScalarType d = ( (onPlane-p0)normal) / ( (p0-p1) normal );
	- mitk::Vector3D newPoint = (p0-p1);
	-
	- point[0] = d*newPoint[0] + p0[0];
	- point[1] = d*newPoint[1] + p0[1];
	- point[2] = d*newPoint[2] + p0[2];
	-
	- singleTract.push_back(point);
	-
	- if(! (secondOnPositive ^ startOnPositive) )
	- {
	- /* StartId and startId+1 lie on the same side of the plane
	- so startId is also part of the ROI*/
	-
	- mitk::ScalarType *start = fiberPolyData->GetPoint( pointsInCell[startId] );
	- point[0] = start[0]; point[1] = start[1]; point[2] = start[2];
	- singleTract.push_back(point);
	- }
	-
	-
	-
	- for( int pointInCellID( startId+1 ); pointInCellID < endId ; pointInCellID++)
	- {
	- // push back point
	- mitk::ScalarType *p = fiberPolyData->GetPoint( pointsInCell[ pointInCellID ] );
	- point[0] = p[0]; point[1] = p[1]; point[2] = p[2];
	- singleTract.push_back( point );
	-
	- }
	-
	- /* endId must be included if endId and endId-1 lie on the same side of the
	- plane defined by endRoi*/
	-
	-
	- p = fiberPolyData->GetPoint( pointsInCell[ endId ] );
	- p0[0] = p[0]; p0[1] = p[1]; p0[2] = p[2];
	-
	- p = fiberPolyData->GetPoint( pointsInCell[ endId-1 ] );
	- p1[0] = p[0]; p1[1] = p[1]; p1[2] = p[2];
	-
	- mitk::Point3D pLast;
	- pLast[0] = p0[0]; pLast[1] = p0[1]; pLast[2] = p0[2];
	-
	- mitk::Point3D pBeforeLast;
	- pBeforeLast[0] = p1[0]; pBeforeLast[1] = p1[1]; pBeforeLast[2] = p1[2];
	-
	- normal = endGeometry2D->GetNormal();
	- bool lastOnPositive = endGeometry2D->IsAbove(pLast);
	- bool secondLastOnPositive = endGeometry2D->IsAbove(pBeforeLast);
	-
	-
	- onPlane[0] = endCenter[0];
	- onPlane[1] = endCenter[1];
	- onPlane[2] = endCenter[2];
	-
	- if(! (lastOnPositive ^ secondLastOnPositive) )
	- {
	- /* endId and endId-1 lie on the same side of the plane, so we need
	- need endId+1 to calculate the intersection with the planar figure.
	- this should exist since we know that the fiber crosses the planar figure
	- endId is also part of the tract and can be inserted here */
	-
	- p = fiberPolyData->GetPoint( pointsInCell[ endId ] );
	- point[0] = p[0]; point[1] = p[1]; point[2] = p[2];
	- singleTract.push_back( point );
	-
	- p = fiberPolyData->GetPoint( pointsInCell[ endId+1 ] );
	- }
	-
	- d = ( (onPlane-p0)normal) / ( (p0-p1) normal );
	-
	- newPoint = (p0-p1);
	-
	- point[0] = d*newPoint[0] + p0[0];
	- point[1] = d*newPoint[1] + p0[1];
	- point[2] = d*newPoint[2] + p0[2];
	-
	- singleTract.push_back(point);
	-
	-
	-
	- }
	- else{
	-
	- // Calculate the intersection of the ROI with the startRoi and decide if the startId is part of the roi or must be cut of
	- mitk::ScalarType *p = fiberPolyData->GetPoint( pointsInCell[ startId ] );
	- mitk::Vector3D p0;
	- p0[0] = p[0]; p0[1] = p[1]; p0[2] = p[2];
	-
	- p = fiberPolyData->GetPoint( pointsInCell[ startId-1 ] );
	- mitk::Vector3D p1;
	- p1[0] = p[0]; p1[1] = p[1]; p1[2] = p[2];
	-
	- // Check if p and p2 are both on the same side of the plane
	- mitk::Vector3D normal = startGeometry2D->GetNormal();
	-
	- mitk::Point3D pStart;
	- pStart[0] = p0[0]; pStart[1] = p0[1]; pStart[2] = p0[2];
	-
	- mitk::Point3D pSecond;
	- pSecond[0] = p1[0]; pSecond[1] = p1[1]; pSecond[2] = p1[2];
	-
	- bool startOnPositive = startGeometry2D->IsAbove(pStart);
	- bool secondOnPositive = startGeometry2D->IsAbove(pSecond);
	-
	- mitk::Vector3D onPlane;
	- onPlane[0] = startCenter[0]; onPlane[1] = startCenter[1]; onPlane[2] = startCenter[2];
	-
	-
	- if(! (secondOnPositive ^ startOnPositive) )
	- {
	- /* startId and startId+1 lie on the same side of the plane, so we need
	- need startId-1 to calculate the intersection with the planar figure*/
	- p = fiberPolyData->GetPoint( pointsInCell[ startId-1 ] );
	- p1[0] = p[0]; p1[1] = p[1]; p1[2] = p[2];
	- }
	-
	-
	- mitk::ScalarType d = ( (onPlane-p0)normal) / ( (p0-p1) normal );
	- mitk::Vector3D newPoint = (p0-p1);
	-
	-
	- point[0] = d*newPoint[0] + p0[0];
	- point[1] = d*newPoint[1] + p0[1];
	- point[2] = d*newPoint[2] + p0[2];
	-
	-
	- singleTract.push_back(point);
	-
	- if(! (secondOnPositive ^ startOnPositive) )
	- {
	- /* StartId and startId+1 lie on the same side of the plane
	- so startId is also part of the ROI*/
	-
	- mitk::ScalarType *start = fiberPolyData->GetPoint( pointsInCell[startId] );
	- point[0] = start[0]; point[1] = start[1]; point[2] = start[2];
	- singleTract.push_back(point);
	- }
	-
	-
	-
	- for( int pointInCellID( startId-1 ); pointInCellID > endId ; pointInCellID--)
	- {
	- // push back point
	- mitk::ScalarType *p = fiberPolyData->GetPoint( pointsInCell[ pointInCellID ] );
	- point[0] = p[0]; point[1] = p[1]; point[2] = p[2];
	- singleTract.push_back( point );
	-
	- }
	-
	- /* endId must be included if endId and endI+1 lie on the same side of the
	- plane defined by endRoi*/
	-
	-
	- p = fiberPolyData->GetPoint( pointsInCell[ endId ] );
	- p0[0] = p[0]; p0[1] = p[1]; p0[2] = p[2];
	-
	- p = fiberPolyData->GetPoint( pointsInCell[ endId+1 ] );
	- p1[0] = p[0]; p1[1] = p[1]; p1[2] = p[2];
	-
	- mitk::Point3D pLast;
	- pLast[0] = p0[0]; pLast[1] = p0[1]; pLast[2] = p0[2];
	-
	- mitk::Point3D pBeforeLast;
	- pBeforeLast[0] = p1[0]; pBeforeLast[1] = p1[1]; pBeforeLast[2] = p1[2];
	-
	- bool lastOnPositive = endGeometry2D->IsAbove(pLast);
	- bool secondLastOnPositive = endGeometry2D->IsAbove(pBeforeLast);
	- normal = endGeometry2D->GetNormal();
	-
	-
	-
	- onPlane[0] = endCenter[0];
	- onPlane[1] = endCenter[1];
	- onPlane[2] = endCenter[2];
	-
	- if(! (lastOnPositive ^ secondLastOnPositive) )
	- {
	- /* endId and endId+1 lie on the same side of the plane, so we need
	- need endId-1 to calculate the intersection with the planar figure.
	- this should exist since we know that the fiber crosses the planar figure
	- endId is also part of the tract and can be inserted here */
	-
	- p = fiberPolyData->GetPoint( pointsInCell[ endId ] );
	- point[0] = p[0]; point[1] = p[1]; point[2] = p[2];
	- singleTract.push_back( point );
	-
	- p = fiberPolyData->GetPoint( pointsInCell[ endId-1 ] );
	- }
	-
	- d = ( (onPlane-p0)normal) / ( (p0-p1) normal );
	-
	- newPoint = (p0-p1);
	-
	- point[0] = d*newPoint[0] + p0[0];
	- point[1] = d*newPoint[1] + p0[1];
	- point[2] = d*newPoint[2] + p0[2];
	-
	- singleTract.push_back(point);
	-
	- }
	-
	-
	- tracts.push_back(singleTract);
	-
	-
	- }
	-
	- return tracts;
	-}
	-
	-void QmitkTbssRoiAnalysisWidget::PlotFiberBetweenRois(mitk::FiberBundle fib, mitk::Image img,
	- mitk::DataNode* startRoi, mitk::DataNode* endRoi, bool avg, int number)
	-{
	-
	- if(fib == nullptr \|\| img == nullptr \|\| startRoi == nullptr \|\| endRoi == nullptr)
	- return;
	-
	-
	- m_Fib = fib;
	- m_CurrentImage = img;
	- m_CurrentStartRoi = startRoi;
	- m_CurrentEndRoi = endRoi;
	-
	-
	- DoPlotFiberBundles(fib, img, startRoi, endRoi, avg, number);
	-}
	-
	-
	-
	-void QmitkTbssRoiAnalysisWidget::ModifyPlot(int number, bool avg)
	-{
	- if(m_Fib == nullptr \|\| m_CurrentTbssImage == nullptr \|\| m_CurrentStartRoi == nullptr \|\| m_CurrentEndRoi == nullptr)
	- return;
	-
	- if(m_PlottingFiberBundle)
	- {
	- DoPlotFiberBundles(m_Fib, m_CurrentImage, m_CurrentStartRoi, m_CurrentEndRoi, avg, number);
	- }
	- else
	- {
	- PlotFiber4D(m_CurrentTbssImage, m_Fib, m_CurrentStartRoi, m_CurrentEndRoi, number);
	- }
	-}
	-
	-
	-
	-TractContainerType QmitkTbssRoiAnalysisWidget::ParameterizeTracts(TractContainerType tracts, int number)
	-{
	- TractContainerType resampledTracts;
	-
	-
	-
	- for(auto it = tracts.begin(); it != tracts.end(); ++it)
	- {
	- TractType resampledTract;
	- TractType tract = *it;
	-
	- // Calculate the total length
	- mitk::ScalarType totalLength = 0;
	-
	- if(tract.size() < 2)
	- continue;
	-
	- PointType p0 = tract.at(0);
	- for(unsigned int i = 1; i<tract.size(); i++)
	- {
	- PointType p1 = tract.at(i);
	- mitk::ScalarType length = p0.EuclideanDistanceTo(p1);
	- totalLength += length;
	- p0 = p1;
	- }
	-
	- mitk::ScalarType stepSize = totalLength / number;
	-
	-
	-
	- p0 = tract.at(0);
	- PointType p1 = tract.at(1);
	- unsigned int tractCounter = 2;
	- mitk::ScalarType distance = p0.EuclideanDistanceTo(p1);
	- mitk::ScalarType locationBetween = 0;
	-
	- for(mitk::ScalarType position = 0;
	- position <= totalLength+0.001 && static_cast<int>(resampledTract.size()) <= (number+1);
	- position+=stepSize)
	- {
	-
	- /* In case we walked to far we need to find the next segment we are on and on what relative position on that
	- tract we are on. Small correction for rounding errors */
	- while(locationBetween > distance+0.001)
	- {
	-
	- if(tractCounter == tract.size())
	- std::cout << "problem";
	-
	- // Determine by what distance we are no on the next segment
	- locationBetween = locationBetween - distance;
	- p0 = p1;
	- p1 = tract.at(tractCounter);
	- tractCounter++;
	-
	- distance = p0.EuclideanDistanceTo(p1);
	-
	- }
	-
	- // Direction
	- PointType::VectorType direction = p1-p0;
	- direction.Normalize();
	-
	- PointType newSample = p0 + direction*locationBetween;
	- resampledTract.push_back(newSample);
	-
	-
	- locationBetween += stepSize;
	-
	-
	- }
	-
	- resampledTracts.push_back(resampledTract);
	-
	-
	- }
	- return resampledTracts;
	-}
	-
	-
	-mitk::Point3D QmitkTbssRoiAnalysisWidget::GetPositionInWorld(int index)
	-{
	-
	-
	- mitk::ScalarType xSum = 0.0;
	- mitk::ScalarType ySum = 0.0;
	- mitk::ScalarType zSum = 0.0;
	- for(auto it = m_CurrentTracts.begin();
	- it!=m_CurrentTracts.end(); ++it)
	- {
	- TractType tract = *it;
	- PointType p = tract.at(index);
	- xSum += p[0];
	- ySum += p[1];
	- zSum += p[2];
	- }
	-
	- int number = m_CurrentTracts.size();
	-
	- mitk::ScalarType xPos = xSum / number;
	- mitk::ScalarType yPos = ySum / number;
	- mitk::ScalarType zPos = zSum / number;
	-
	-
	- mitk::Point3D pos;
	- pos[0] = xPos;
	- pos[1] = yPos;
	- pos[2] = zPos;
	-
	- return pos;
	-}
	-
	-
	-std::vector< std::vector<mitk::ScalarType> > QmitkTbssRoiAnalysisWidget::CalculateGroupProfiles()
	-{
	- MITK_INFO << "make profiles!";
	- std::vector< std::vector<mitk::ScalarType> > profiles;
	-
	-
	- int size = m_Projections->GetVectorLength();
	- for(int s=0; s<size; s++)
	- {
	- // Iterate trough the roi
	- std::vector<mitk::ScalarType> profile;
	- RoiType::iterator it;
	- it = m_Roi.begin();
	- while(it != m_Roi.end())
	- {
	- itk::Index<3> ix = *it;
	- profile.push_back(m_Projections->GetPixel(ix).GetElement(s));
	- it++;
	- }
	-
	- profiles.push_back(profile);
	- }
	-
	-
	-
	- m_IndividualProfiles = profiles;
	- // Calculate the averages
	-
	- // Here a check could be build in to check whether all profiles have
	- // the same length, but this should normally be the case if the input
	- // data were corrected with the TBSS Module.
	-
	- std::vector< std::vector<mitk::ScalarType> > groupProfiles;
	-
	- std::vector< std::pair<std::string, int> >::iterator it;
	- it = m_Groups.begin();
	-
	- int c = 0; //the current profile number
	-
	- while(it != m_Groups.end() && profiles.size() > 0)
	- {
	- std::pair<std::string, int> p = *it;
	- int size = p.second;
	-
	- //initialize a vector of the right length with zeroes
	- std::vector<mitk::ScalarType> averageProfile;
	- for(unsigned int i=0; i<profiles.at(0).size(); i++)
	- {
	- averageProfile.push_back(0.0);
	- }
	-
	- // Average the right number of profiles
	-
	- for(int i=0; i<size; i++)
	- {
	- for(unsigned int j=0; j<averageProfile.size(); ++j)
	- {
	- averageProfile.at(j) = averageProfile.at(j) + profiles.at(c).at(j);
	- }
	- c++;
	- }
	-
	- // Divide by the number of profiles to get group average
	- for(unsigned int i=0; i<averageProfile.size(); i++)
	- {
	- averageProfile.at(i) = averageProfile.at(i) / size;
	- }
	-
	- groupProfiles.push_back(averageProfile);
	-
	- ++it;
	- }
	-
	- return groupProfiles;
	-}
	-
	-
	-void QmitkTbssRoiAnalysisWidget::DrawProfiles()
	-{
	- std::vector <std::vector<mitk::ScalarType> > groupProfiles = CalculateGroupProfiles();
	- Plot(groupProfiles);
	-}
	-
	-void QmitkTbssRoiAnalysisWidget::Plot(std::vector <std::vector<mitk::ScalarType> > groupProfiles)
	-{
	- this->Clear();
	- m_Vals.clear();
	- std::vector<mitk::ScalarType> v1;
	-
	-
	- std::vector<mitk::ScalarType> xAxis;
	- for(unsigned int i=0; i<groupProfiles.at(0).size(); ++i)
	- {
	- xAxis.push_back((mitk::ScalarType)i);
	- }
	-
	-
	- // fill m_Vals. This might be used by the user to copy data to the clipboard
	- for(unsigned int i=0; i<groupProfiles.size(); i++)
	- {
	-
	- v1.clear();
	-
	-
	- for(unsigned int j=0; j<groupProfiles.at(i).size(); j++)
	- {
	- v1.push_back(groupProfiles.at(i).at(j));
	- }
	-
	- m_Vals.push_back(v1);
	-
	- }
	-
	- std::string title = m_Measure + " profiles on the ";
	- title.append(m_Structure);
	- this->SetPlotTitle( title.c_str() );
	- QPen pen( Qt::SolidLine );
	- pen.setWidth(2);
	-
	-
	-
	- std::vector< std::pair<std::string, int> >::iterator it;
	- it = m_Groups.begin();
	-
	- int c = 0; //the current profile number
	-
	- QColor colors[4] = {Qt::green, Qt::blue, Qt::yellow, Qt::red};
	-
	- while(it != m_Groups.end() && groupProfiles.size() > 0)
	- {
	-
	- std::pair< std::string, int > group = *it;
	-
	- pen.setColor(colors[c]);
	- int curveId = this->InsertCurve( group.first.c_str() );
	- this->SetCurveData( curveId, xAxis, groupProfiles.at(c) );
	-
	-
	- this->SetCurvePen( curveId, pen );
	-
	- c++;
	- it++;
	-
	- }
	-
	-
	- auto legend = new QwtLegend;
	- this->SetLegend(legend, QwtPlot::RightLegend, 0.5);
	-
	-
	- std::cout << m_Measure << std::endl;
	- this->m_Plot->setAxisTitle(0, m_Measure.c_str());
	- this->m_Plot->setAxisTitle(3, "Position");
	-
	- this->Replot();
	-}
	-
	-
	-std::vector< std::vector<mitk::ScalarType> > QmitkTbssRoiAnalysisWidget::CalculateGroupProfilesFibers(mitk::TbssImage::Pointer tbssImage,
	- mitk::FiberBundle *fib,
	- mitk::DataNode* startRoi,
	- mitk::DataNode* endRoi,
	- int number)
	-{
	- TractContainerType tracts = CreateTracts(fib, startRoi, endRoi);
	-
	- TractContainerType resampledTracts = ParameterizeTracts(tracts, number);
	-
	- int nTracts = resampledTracts.size();
	-
	- this->Clear();
	-
	-
	- // For every group we have m fibers * n subjects of profiles to fill
	-
	- std::vector< std::vector<mitk::ScalarType> > profiles;
	-
	- // calculate individual profiles by going through all n subjects
	- int size = m_Projections->GetVectorLength();
	- for(int s=0; s<size; s++)
	- {
	-
	- // Iterate through all tracts
	-
	- for(int t=0; t<nTracts; t++)
	- {
	- // Iterate trough the tract
	- std::vector<mitk::ScalarType> profile;
	- auto it = resampledTracts[t].begin();
	- while(it != resampledTracts[t].end())
	- {
	- PointType p = *it;
	- PointType index;
	- tbssImage->GetGeometry()->WorldToIndex(p, index);
	-
	- itk::Index<3> ix;
	- ix[0] = index[0];
	- ix[1] = index[1];
	- ix[2] = index[2];
	- // Get value from image
	-
	- profile.push_back(m_Projections->GetPixel(ix).GetElement(s));
	-
	- it++;
	- }
	- profiles.push_back(profile);
	- }
	-
	-
	- }
	-
	- m_IndividualProfiles = profiles;
	-
	- // Now create the group averages (every group contains m fibers * n_i group members
	-
	- std::vector< std::pair<std::string, int> >::iterator it;
	- it = m_Groups.begin();
	- int c = 0; //the current profile number
	-
	- // Calculate the group averages
	- std::vector< std::vector<mitk::ScalarType> > groupProfiles;
	-
	- while(it != m_Groups.end() && profiles.size() > 0)
	- {
	- std::pair<std::string, int> p = *it;
	- int size = p.second;
	-
	- //initialize a vector of the right length with zeroes
	- std::vector<mitk::ScalarType> averageProfile;
	- for(unsigned int i=0; i<profiles.at(0).size(); i++)
	- {
	- averageProfile.push_back(0.0);
	- }
	-
	- // Average the right number of profiles
	-
	- for(int i=0; i<size*nTracts; i++)
	- {
	- for(unsigned int j=0; j<averageProfile.size(); ++j)
	- {
	- averageProfile.at(j) = averageProfile.at(j) + profiles.at(c).at(j);
	- }
	- c++;
	- }
	-
	- // Divide by the number of profiles to get group average
	- for(unsigned int i=0; i<averageProfile.size(); i++)
	- {
	- averageProfile.at(i) = averageProfile.at(i) / (size*nTracts);
	- }
	-
	- groupProfiles.push_back(averageProfile);
	-
	- ++it;
	- }
	-
	- return groupProfiles;
	-}
	-
	-
	-void QmitkTbssRoiAnalysisWidget::PlotFiber4D(mitk::TbssImage::Pointer tbssImage,
	- mitk::FiberBundle *fib,
	- mitk::DataNode* startRoi,
	- mitk::DataNode* endRoi,
	- int number)
	-{
	- m_PlottingFiberBundle = false;
	- m_Fib = fib;
	- m_CurrentStartRoi = startRoi;
	- m_CurrentEndRoi = endRoi;
	- m_CurrentTbssImage = tbssImage;
	- std::vector <std::vector<mitk::ScalarType> > groupProfiles = CalculateGroupProfilesFibers(tbssImage, fib, startRoi, endRoi, number);
	- Plot(groupProfiles);
	-
	-}
	-
	-
	-template <typename T>
	-void QmitkTbssRoiAnalysisWidget::PlotFiberBundles(const mitk::PixelType, TractContainerType tracts, mitk::Image *img, bool avg)
	-{
	-
	- m_PlottingFiberBundle = true;
	-
	- this->Clear();
	- auto it = tracts.begin();
	-
	-
	- std::vector< std::vector <mitk::ScalarType > > profiles;
	-
	- mitk::ImagePixelReadAccessor<T,3> imAccess(img,img->GetVolumeData(0));
	-
	- it = tracts.begin();
	- while(it != tracts.end())
	- {
	-
	- TractType tract = *it;
	- auto tractIt = tract.begin();
	-
	- std::vector<mitk::ScalarType> profile;
	-
	- while(tractIt != tract.end())
	- {
	- PointType p = *tractIt;
	-
	- // Get value from image
	- profile.push_back( (mitk::ScalarType) imAccess.GetPixelByWorldCoordinates(p) );
	-
	- ++tractIt;
	- }
	-
	- profiles.push_back(profile);
	- std::cout << std::endl;
	-
	- ++it;
	- }
	-
	-
	- if(profiles.size() == 0)
	- return;
	-
	- m_IndividualProfiles = profiles;
	-
	-
	- std::string title = "Fiber bundle plot";
	- this->SetPlotTitle( title.c_str() );
	-
	-
	- // initialize average profile
	- std::vector<mitk::ScalarType> averageProfile;
	- std::vector<mitk::ScalarType> profile = profiles.at(0); // can do this because we checked the size of profiles before
	- for(unsigned int i=0; i<profile.size(); ++i)
	- {
	- averageProfile.push_back(0.0);
	- }
	-
	-
	- auto profit = profiles.begin();
	-
	- int id=0;
	- while(profit != profiles.end())
	- {
	- std::vector<mitk::ScalarType> profile = *profit;
	-
	-
	-
	- std::vector<mitk::ScalarType> xAxis;
	- for(unsigned int i=0; i<profile.size(); ++i)
	- {
	- xAxis.push_back((mitk::ScalarType)i);
	- averageProfile.at(i) += profile.at(i) / profiles.size();
	- }
	-
	- int curveId = this->InsertCurve( "" );
	-
	- this->SetCurveData( curveId, xAxis, profile );
	-
	- ++profit;
	- id++;
	-
	-
	- }
	-
	- m_Average = averageProfile;
	-
	-
	- if(avg)
	- {
	-
	- // Draw the average profile
	- std::vector<mitk::ScalarType> xAxis;
	- for(unsigned int i=0; i<averageProfile.size(); ++i)
	- {
	- xAxis.push_back((mitk::ScalarType)i);
	- }
	-
	- int curveId = this->InsertCurve( "" );
	- this->SetCurveData( curveId, xAxis, averageProfile );
	-
	-
	-
	-
	- QPen pen( Qt::SolidLine );
	- pen.setWidth(3);
	- pen.setColor(Qt::red);
	-
	- this->SetCurvePen( curveId, pen );
	-
	-
	-
	- id++;
	-
	-
	- }
	-
	- this->Replot();
	-
	-
	-
	-
	-
	-}
	-
	-
	-void QmitkTbssRoiAnalysisWidget::drawBar(int x)
	-{
	-
	- m_Plot->detachItems(QwtPlotItem::Rtti_PlotMarker, true);
	-
	-
	- QwtPlotMarker *mX = new QwtPlotMarker();
	- //mX->setLabel(QString::fromLatin1("selected point"));
	- mX->setLabelAlignment(Qt::AlignLeft \| Qt::AlignBottom);
	- mX->setLabelOrientation(Qt::Vertical);
	- mX->setLineStyle(QwtPlotMarker::VLine);
	- mX->setLinePen(QPen(Qt::black, 0, Qt::SolidLine));
	- mX->setXValue(x);
	- mX->attach(m_Plot);
	-
	-
	- this->Replot();
	-
	-}
	-
	-QmitkTbssRoiAnalysisWidget::~QmitkTbssRoiAnalysisWidget()
	-{
	- delete m_PlotPicker;
	-
	-}
	-
	-
	-
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/QmitkTbssRoiAnalysisWidget.h b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/QmitkTbssRoiAnalysisWidget.h
	deleted file mode 100644
	index 746206cb0d..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/QmitkTbssRoiAnalysisWidget.h
	+++ /dev/null
	@@ -1,230 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef QmitkTbssRoiAnalysisWidget_H_
	-#define QmitkTbssRoiAnalysisWidget_H_
	-
	-#include "QmitkPlotWidget.h"
	-
	-#include <org_mitk_gui_qt_diffusionimaging_tbss_Export.h>
	-
	-#include <mitkFiberBundle.h>
	-#include <mitkTbssImage.h>
	-
	-#include <itkVectorImage.h>
	-
	-typedef itk::VectorImage<float,3> VectorImageType;
	-typedef std::vector< itk::Index<3> > RoiType;
	-
	-typedef mitk::Point3D PointType;
	-typedef std::vector< PointType> TractType;
	-typedef std::vector< TractType > TractContainerType;
	-
	-class QwtPlotPicker;
	-
	-/**
	- * \brief Plot widget for TBSS Data
	- * This widget can plot regions of interest on TBSS projection data. The projection data is created by importing FSL TBSS subject data and
	- * completing it with patient data using the QmitkTractbasedSpatialStatisticsView.
	- * The region of interest is a vector of indices from which data for plotting should be obtained.
	- */
	-
	-class DIFFUSIONIMAGING_TBSS_EXPORT QmitkTbssRoiAnalysisWidget : public QmitkPlotWidget
	-{
	-
	-Q_OBJECT
	-
	-public:
	-
	-
	- QmitkTbssRoiAnalysisWidget( QWidget * parent);
	- virtual ~QmitkTbssRoiAnalysisWidget();
	-
	-
	- /* \brief Set group information as a vector of pairs of group name and number of group members */
	- void SetGroups(std::vector< std::pair<std::string, int> > groups)
	- {
	- m_Groups = groups;
	- }
	-
	- /* \brief Draws the group averaged profiles */
	- void DrawProfiles();
	-
	-
	- void PlotFiber4D(mitk::TbssImage::Pointer tbssImage,
	- mitk::FiberBundle *fib,
	- mitk::DataNode *startRoi,
	- mitk::DataNode *endRoi,
	- int number);
	-
	-
	- template <typename T>
	- void PlotFiberBundles(const mitk::PixelType, TractContainerType tracts, mitk::Image* img, bool avg=false);
	-
	-
	- /* \brief Sets the projections of the individual subjects */
	- void SetProjections(VectorImageType::Pointer projections)
	- {
	- m_Projections = projections;
	- }
	-
	- /* \brief Set the region of interest*/
	- void SetRoi(RoiType roi)
	- {
	- m_Roi = roi;
	- }
	-
	- /* \brief Set structure information to display in the plot */
	- void SetStructure(std::string structure)
	- {
	- m_Structure = structure;
	- }
	-
	- /* \brief Set measurement type for display in the plot */
	- void SetMeasure(std::string measure)
	- {
	- m_Measure = measure;
	- }
	-
	- /* \brief Draws a bar to indicate were the user clicked in the plot */
	- void drawBar(int x);
	-
	-
	-
	- /* \brief Returns the values of the group averaged profiles */
	- std::vector <std::vector<double> > GetVals()
	- {
	- return m_Vals;
	- }
	-
	-
	- /* \brief Returns the values of the individual subjects profiles */
	- std::vector <std::vector<double> > GetIndividualProfiles()
	- {
	- return m_IndividualProfiles;
	- }
	-
	-
	- std::vector<double> GetAverageProfile()
	- {
	- return m_Average;
	- }
	-
	-
	- void SetPlottingFiber(bool b)
	- {
	- m_PlottingFiberBundle = b;
	- }
	-
	- bool IsPlottingFiber()
	- {
	- return m_PlottingFiberBundle;
	- }
	-
	-
	- void PlotFiberBetweenRois(mitk::FiberBundle fib, mitk::Image img,
	- mitk::DataNode startRoi, mitk::DataNode endRoi, bool avg=-1, int number=25);
	-
	-
	-
	-
	- // Takes an index which is an x coordinate from the plot and finds the corresponding position in world space
	- mitk::Point3D GetPositionInWorld(int index);
	- void ModifyPlot(int number, bool avg);
	-
	-
	-
	- QwtPlotPicker* m_PlotPicker;
	-
	-protected:
	-
	- mitk::FiberBundle* m_Fib;
	-
	-
	- std::vector< std::vector<double> > m_Vals;
	-
	- std::vector< std::vector<double> > m_IndividualProfiles;
	- std::vector< double > m_Average;
	-
	-
	-
	- std::vector< std::vector<double> > CalculateGroupProfiles();
	- std::vector< std::vector<double> > CalculateGroupProfilesFibers(mitk::TbssImage::Pointer tbssImage,
	- mitk::FiberBundle *fib,
	- mitk::DataNode* startRoi,
	- mitk::DataNode* endRoi,
	- int number);
	-
	- void Plot(std::vector <std::vector<double> > groupProfiles);
	-
	-
	- void Tokenize(const std::string& str,
	- std::vector<std::string>& tokens,
	- const std::string& delimiters = " ")
	- {
	- // Skip delimiters at beginning.
	- std::string::size_type lastPos = str.find_first_not_of(delimiters, 0);
	- // Find first "non-delimiter".
	- std::string::size_type pos = str.find_first_of(delimiters, lastPos);
	-
	- while (std::string::npos != pos \|\| std::string::npos != lastPos)
	- {
	- // Found a token, add it to the vector.
	- tokens.push_back(str.substr(lastPos, pos - lastPos));
	- // Skip delimiters. Note the "not_of"
	- lastPos = str.find_first_not_of(delimiters, pos);
	- // Find next "non-delimiter"
	- pos = str.find_first_of(delimiters, lastPos);
	- }
	- }
	-
	- std::vector< std::pair<std::string, int> > m_Groups;
	-
	- VectorImageType::Pointer m_Projections;
	- RoiType m_Roi;
	- std::string m_Structure;
	- std::string m_Measure;
	-
	- bool m_PlottingFiberBundle; // true when the plot results from a fiber tracking result (vtk .fib file)
	-
	-
	- // Resample a collection of tracts so that every tract contains #number equidistant samples
	- TractContainerType ParameterizeTracts(TractContainerType tracts, int number);
	-
	-
	- TractContainerType m_CurrentTracts;
	-
	-
	- mitk::Image* m_CurrentImage;
	- mitk::TbssImage* m_CurrentTbssImage;
	-
	- mitk::DataNode* m_CurrentStartRoi;
	- mitk::DataNode* m_CurrentEndRoi;
	-
	-
	- void DoPlotFiberBundles(mitk::FiberBundle fib, mitk::Image img,
	- mitk::DataNode* startRoi, mitk::DataNode* endRoi, bool avg=false, int number=25);
	-
	-
	-
	- /* \brief Creates tracts from a mitk::FiberBundle and two planar figures indicating the start end end point */
	- TractContainerType CreateTracts(mitk::FiberBundle fib, mitk::DataNode startRoi, mitk::DataNode* endRoi);
	-
	-
	-
	-};
	-
	-#endif
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTbssMetaTableModel.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTbssMetaTableModel.cpp
	deleted file mode 100644
	index 74fd270564..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTbssMetaTableModel.cpp
	+++ /dev/null
	@@ -1,149 +0,0 @@
	-
	-
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-
	-#include "QmitkTbssMetaTableModel.h"
	-
	-QmitkTbssMetaTableModel::QmitkTbssMetaTableModel(QObject *parent)
	- : QAbstractTableModel(parent)
	-{
	-}
	-
	-QmitkTbssMetaTableModel::QmitkTbssMetaTableModel(QList< QPair<QString, QString> > pairs, QObject *parent)
	- : QAbstractTableModel(parent)
	-{
	- listOfPairs=pairs;
	-}
	-
	-int QmitkTbssMetaTableModel::rowCount(const QModelIndex &parent) const
	-{
	- Q_UNUSED(parent);
	- return listOfPairs.size();
	-}
	-
	-int QmitkTbssMetaTableModel::columnCount(const QModelIndex &parent) const
	-{
	- Q_UNUSED(parent);
	- return 2;
	-}
	-
	-QVariant QmitkTbssMetaTableModel::data(const QModelIndex &index, int role) const
	-{
	- if (!index.isValid())
	- return QVariant();
	-
	- if (index.row() >= listOfPairs.size() \|\| index.row() < 0)
	- return QVariant();
	-
	- if (role == Qt::DisplayRole) {
	- QPair<QString, QString> pair = listOfPairs.at(index.row());
	-
	- if (index.column() == 0)
	- return pair.first;
	- else if (index.column() == 1)
	- return pair.second;
	- }
	- return QVariant();
	-}
	-
	-QVariant QmitkTbssMetaTableModel::headerData(int section, Qt::Orientation orientation, int role) const
	-{
	- if (role != Qt::DisplayRole)
	- return QVariant();
	-
	- if (orientation == Qt::Horizontal) {
	- switch (section) {
	- case 0:
	- return tr("Image");
	-
	- case 1:
	- return tr("Filename");
	-
	- default:
	- return QVariant();
	- }
	- }
	- return QVariant();
	-}
	-
	-bool QmitkTbssMetaTableModel::insertRows(int position, int rows, const QModelIndex &index)
	-{
	- Q_UNUSED(index);
	- beginInsertRows(QModelIndex(), position, position+rows-1);
	-
	- for (int row=0; row < rows; row++) {
	- QPair<QString, QString> pair("Image ", "Filename");
	- listOfPairs.insert(position, pair);
	- }
	-
	- endInsertRows();
	- return true;
	-}
	-
	-bool QmitkTbssMetaTableModel::removeRows(int position, int rows, const QModelIndex &index)
	-{
	- Q_UNUSED(index);
	- beginRemoveRows(QModelIndex(), position, position+rows-1);
	-
	- for (int row=0; row < rows; ++row) {
	- listOfPairs.removeAt(position);
	- }
	-
	- endRemoveRows();
	- return true;
	-}
	-
	-bool QmitkTbssMetaTableModel::setData(const QModelIndex &index, const QVariant &value, int role)
	-{
	- if (index.isValid() && role == Qt::EditRole) {
	- int row = index.row();
	-
	- QPair<QString, QString> p = listOfPairs.value(row);
	-
	- if (index.column() == 0)
	- p.first = value.toString();
	- else if (index.column() == 1)
	- p.second = value.toString();
	- else
	- return false;
	-
	- listOfPairs.replace(row, p);
	- emit(dataChanged(index, index));
	-
	- return true;
	- }
	-
	- return false;
	-}
	-
	-Qt::ItemFlags QmitkTbssMetaTableModel::flags(const QModelIndex &index) const
	-{
	- if (!index.isValid())
	- return Qt::ItemIsEnabled;
	-
	- return QAbstractTableModel::flags(index) \| Qt::ItemIsEditable;
	-}
	-
	-QList< QPair<QString, QString> > QmitkTbssMetaTableModel::getList()
	-{
	- return listOfPairs;
	-}
	-
	-
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTbssMetaTableModel.h b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTbssMetaTableModel.h
	deleted file mode 100644
	index ba6999bc26..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTbssMetaTableModel.h
	+++ /dev/null
	@@ -1,54 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-
	-#ifndef QmitkTbssMetaTableModel_h
	-#define QmitkTbssMetaTableModel_h
	-
	-
	-#include <QAbstractTableModel>
	-
	-#include <QPair>
	-#include <QList>
	-#include <QObject>
	-#include <QString>
	-
	-
	-class QmitkTbssMetaTableModel : public QAbstractTableModel
	-{
	-
	- // TableModel to model pairs of group description and group number
	-
	-public:
	- QmitkTbssMetaTableModel(QObject *parent=nullptr);
	- QmitkTbssMetaTableModel(QList< QPair<QString, QString> > listofPairs, QObject *parent=nullptr);
	-
	- int rowCount(const QModelIndex &parent) const override;
	- int columnCount(const QModelIndex &parent) const override;
	- QVariant data(const QModelIndex &index, int role) const override;
	- QVariant headerData(int section, Qt::Orientation orientation, int role) const override;
	- Qt::ItemFlags flags(const QModelIndex &index) const override;
	- bool setData(const QModelIndex &index, const QVariant &value, int role=Qt::EditRole) override;
	- bool insertRows(int position, int rows, const QModelIndex &index=QModelIndex()) override;
	- bool removeRows(int position, int rows, const QModelIndex &index=QModelIndex()) override;
	- QList< QPair<QString, QString> > getList();
	-
	-private:
	- QList< QPair<QString, QString> > listOfPairs;
	-};
	-
	-#endif
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTbssSkeletonizationView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTbssSkeletonizationView.cpp
	deleted file mode 100644
	index fd8444008f..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTbssSkeletonizationView.cpp
	+++ /dev/null
	@@ -1,502 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-// Qmitk
	-#include "QmitkTbssSkeletonizationView.h"
	-
	-
	-#include <itkSkeletonizationFilter.h>
	-#include <itkProjectionFilter.h>
	-#include <itkDistanceMapFilter.h>
	-#include <itkBinaryThresholdImageFilter.h>
	-
	-#include <itkImageFileReader.h>
	-
	-// mitk
	-#include <mitkImagePixelReadAccessor.h>
	-#include <mitkImagePixelWriteAccessor.h>
	-#include <mitkPixelTypeMultiplex.h>
	-#include <mitkImage.h>
	-
	-// Qt
	-#include <QInputDialog>
	-#include <QMessageBox>
	-
	-//vtk
	-#include <vtkLinearTransform.h>
	-#include <vtkMatrix4x4.h>
	-
	-// Boost
	-#include <mitkLexicalCast.h>
	-
	-
	-
	-const std::string QmitkTbssSkeletonizationView::VIEW_ID = "org.mitk.views.tbssskeletonization";
	-
	-using namespace berry;
	-
	-
	-QmitkTbssSkeletonizationView::QmitkTbssSkeletonizationView()
	- : QmitkAbstractView()
	- , m_Controls( 0 )
	- , m_Activated(false)
	-{
	-
	-}
	-
	-QmitkTbssSkeletonizationView::~QmitkTbssSkeletonizationView()
	-{
	-}
	-
	-void QmitkTbssSkeletonizationView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /part/, const QList<mitk::DataNode::Pointer>& nodes)
	-{
	-
	-
	- //datamanager selection changed
	- if (!this->IsActivated())
	- return;
	-
	- bool found3dImage = false;
	- bool found4dImage = false;
	-
	- this->m_Controls->m_TubularName->setText(QString("Tubular Structure Mask: "));
	- this->m_Controls->m_TubularName->setEnabled(false);
	- this->m_Controls->m_MeanLabel->setText(QString("Mean: "));
	- this->m_Controls->m_MeanLabel->setEnabled(false);
	- this->m_Controls->m_PatientDataLabel->setText(QString("Patient Data: "));
	- this->m_Controls->m_PatientDataLabel->setEnabled(false);
	-
	-
	- // iterate selection
	- for (mitk::DataNode::Pointer node: nodes)
	- {
	- // only look at interesting types from valid nodes
	- mitk::BaseData* nodeData = node->GetData();
	- std::string name = "";
	- node->GetStringProperty("name", name);
	-
	-
	- if(nodeData)
	- {
	- if(QString("Image").compare(nodeData->GetNameOfClass())==0)
	- {
	- mitk::Image* img = static_cast<mitk::Image*>(nodeData);
	-
	- if(img->GetDimension() == 3)
	- {
	- bool isBinary(false);
	- node->GetBoolProperty("binary", isBinary);
	-
	-
	- if(isBinary)
	- {
	- QString label("Tubular Structure Mask: ");
	- label.append(QString(name.c_str()));
	- this->m_Controls->m_TubularName->setText(label);
	- this->m_Controls->m_TubularName->setEnabled(true);
	- }
	- else
	- {
	- found3dImage = true;
	- QString label("Mean: ");
	- label.append(QString(name.c_str()));
	- this->m_Controls->m_MeanLabel->setText(label);
	- this->m_Controls->m_MeanLabel->setEnabled(true);
	- }
	- }
	- else if(img->GetDimension() == 4)
	- {
	- found4dImage = true;
	- QString label("Patient Data: ");
	- label.append(QString(name.c_str()));
	- this->m_Controls->m_PatientDataLabel->setText(label);
	- this->m_Controls->m_PatientDataLabel->setEnabled(true);
	- }
	- }
	- }
	-
	- }
	-
	- this->m_Controls->m_Skeletonize->setEnabled(found3dImage);
	- this->m_Controls->m_Project->setEnabled(found3dImage && found4dImage);
	- this->m_Controls->m_OutputMask->setEnabled(found3dImage && found4dImage);
	- this->m_Controls->m_OutputDistanceMap->setEnabled(found3dImage && found4dImage);
	-
	-}
	-
	-
	-
	-void QmitkTbssSkeletonizationView::CreateQtPartControl( QWidget *parent )
	-{
	- // build up qt view, unless already done
	- if ( !m_Controls )
	- {
	- // create GUI widgets from the Qt Designer's .ui file
	- m_Controls = new Ui::QmitkTbssSkeletonizationViewControls;
	- m_Controls->setupUi( parent );
	- this->CreateConnections();
	- }
	-
	-}
	-
	-void QmitkTbssSkeletonizationView::SetFocus()
	-{
	- m_Controls->m_Skeletonize->setFocus();
	-}
	-
	-void QmitkTbssSkeletonizationView::Activated()
	-{
	- m_Activated = true;
	-}
	-
	-void QmitkTbssSkeletonizationView::Deactivated()
	-{
	- m_Activated = false;
	-}
	-
	-bool QmitkTbssSkeletonizationView::IsActivated() const
	-{
	- return m_Activated;
	-}
	-
	-void QmitkTbssSkeletonizationView::Visible()
	-{
	-}
	-
	-void QmitkTbssSkeletonizationView::Hidden()
	-{
	-}
	-
	-void QmitkTbssSkeletonizationView::CreateConnections()
	-{
	- if ( m_Controls )
	- {
	- connect( (QObject*)(m_Controls->m_Skeletonize), SIGNAL(clicked()), this, SLOT(Skeletonize() ));
	- connect( (QObject*)(m_Controls->m_Project), SIGNAL(clicked()), this, SLOT(Project() ));
	- }
	-}
	-
	-
	-
	-void QmitkTbssSkeletonizationView::Skeletonize()
	-{
	-
	-
	-
	-
	- typedef itk::SkeletonizationFilter<FloatImageType, FloatImageType> SkeletonisationFilterType;
	- SkeletonisationFilterType::Pointer skeletonizer = SkeletonisationFilterType::New();
	-
	-
	- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
	-
	-
	- mitk::Image::Pointer meanImage = mitk::Image::New();
	- std::string name = "";
	-
	- for (auto node: nodes)
	- {
	- // process only on valid nodes
	- mitk::BaseData* nodeData = node->GetData();
	-
	- if(nodeData)
	- {
	- if(QString("Image").compare(nodeData->GetNameOfClass())==0)
	- {
	-
	- bool isBinary(false);
	- node->GetBoolProperty("binary", isBinary);
	-
	- mitk::Image* img = static_cast<mitk::Image*>(nodeData);
	- if(img->GetDimension() == 3 && !isBinary)
	- {
	- meanImage = img;
	- name = node->GetName();
	- }
	- }
	- }
	- }
	-
	-
	- // Calculate skeleton
	- FloatImageType::Pointer itkImg = FloatImageType::New();
	- mitk::CastToItkImage(meanImage, itkImg);
	- skeletonizer->SetInput(itkImg);
	- skeletonizer->Update();
	-
	-
	- FloatImageType::Pointer output = skeletonizer->GetOutput();
	- mitk::Image::Pointer mitkOutput = mitk::Image::New();
	- mitk::CastToMitkImage(output, mitkOutput);
	- name += "_skeleton";
	- AddToDataStorage(mitkOutput, name);
	-
	-
	-
	-}
	-
	-void QmitkTbssSkeletonizationView::Project()
	-{
	-
	- typedef itk::SkeletonizationFilter<FloatImageType, FloatImageType> SkeletonisationFilterType;
	- typedef itk::ProjectionFilter ProjectionFilterType;
	- typedef itk::DistanceMapFilter<FloatImageType, FloatImageType> DistanceMapFilterType;
	-
	- SkeletonisationFilterType::Pointer skeletonizer = SkeletonisationFilterType::New();
	-
	-
	-
	- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
	-
	-
	- mitk::Image::Pointer meanImage = mitk::Image::New();
	- mitk::Image::Pointer subjects = mitk::Image::New();
	- mitk::Image::Pointer tubular = mitk::Image::New();
	-
	- for (auto node: nodes)
	- {
	- // process only on valid nodes
	- mitk::BaseData* nodeData = node->GetData();
	-
	- if(nodeData)
	- {
	- if(QString("Image").compare(nodeData->GetNameOfClass())==0)
	- {
	- mitk::Image* img = static_cast<mitk::Image*>(nodeData);
	- if(img->GetDimension() == 3)
	- {
	-
	- bool isBinary(false);
	- node->GetBoolProperty("binary", isBinary);
	-
	-
	- if(isBinary)
	- {
	- tubular = img;
	- }
	- else
	- {
	- meanImage = img;
	- }
	- }
	-
	- else if(img->GetDimension() == 4)
	- {
	- subjects = img;
	- }
	- }
	- }
	-
	- }
	-
	- Float4DImageType::Pointer allFA;
	- mitkPixelTypeMultiplex2(ConvertToItk,subjects->GetChannelDescriptor().GetPixelType(),subjects, allFA);
	-
	- // Calculate skeleton
	- FloatImageType::Pointer itkImg = FloatImageType::New();
	- mitk::CastToItkImage(meanImage, itkImg);
	- skeletonizer->SetInput(itkImg);
	- skeletonizer->Update();
	-
	-
	- FloatImageType::Pointer output = skeletonizer->GetOutput();
	- mitk::Image::Pointer mitkOutput = mitk::Image::New();
	- mitk::CastToMitkImage(output, mitkOutput);
	- AddToDataStorage(mitkOutput, "mean_FA_skeletonised");
	-
	-
	-
	- // Retrieve direction image needed later by the projection filter
	- DirectionImageType::Pointer directionImg = skeletonizer->GetVectorImage();
	-
	-
	- // Calculate distance image
	- DistanceMapFilterType::Pointer distanceMapFilter = DistanceMapFilterType::New();
	- distanceMapFilter->SetInput(output);
	- distanceMapFilter->Update();
	- FloatImageType::Pointer distanceMap = distanceMapFilter->GetOutput();
	-
	- if(m_Controls->m_OutputDistanceMap->isChecked())
	- {
	- mitk::Image::Pointer mitkDistance = mitk::Image::New();
	- mitk::CastToMitkImage(distanceMap, mitkDistance);
	- AddToDataStorage(mitkDistance, "distance map");
	- }
	-
	- // Do projection
	-
	- // Ask a threshold to create a skeleton mask
	- double threshold = -1.0;
	- while(threshold == -1.0)
	- {
	- threshold = QInputDialog::getDouble(m_Controls->m_Skeletonize, tr("Specify the FA threshold"),
	- tr("Threshold:"), QLineEdit::Normal,
	- 0.2);
	-
	- if(threshold < 0.0 \|\| threshold > 1.0)
	- {
	- QMessageBox msgBox;
	- msgBox.setText("Please choose a value between 0 and 1");
	- msgBox.exec();
	- threshold = -1.0;
	- }
	- }
	-
	- typedef itk::BinaryThresholdImageFilter<FloatImageType, CharImageType> ThresholdFilterType;
	- ThresholdFilterType::Pointer thresholder = ThresholdFilterType::New();
	- thresholder->SetInput(output);
	- thresholder->SetLowerThreshold(threshold);
	- thresholder->SetUpperThreshold(std::numeric_limits<float>::max());
	- thresholder->SetOutsideValue(0);
	- thresholder->SetInsideValue(1);
	- thresholder->Update();
	-
	-
	- CharImageType::Pointer thresholdedImg = thresholder->GetOutput();
	-
	-
	- if(m_Controls->m_OutputMask->isChecked())
	- {
	- mitk::Image::Pointer mitkThresholded = mitk::Image::New();
	- mitk::CastToMitkImage(thresholdedImg, mitkThresholded);
	- std::string maskName = "skeleton_mask_at_" + boost::lexical_cast<std::string>(threshold);
	- AddToDataStorage(mitkThresholded, maskName);
	- }
	-
	-
	-
	-
	- CharImageType::Pointer itkTubular = CharImageType::New();
	- mitk::CastToItkImage(tubular, itkTubular);
	-
	-
	- ProjectionFilterType::Pointer projectionFilter = ProjectionFilterType::New();
	- projectionFilter->SetDistanceMap(distanceMap);
	- projectionFilter->SetDirections(directionImg);
	- projectionFilter->SetAllFA(allFA);
	- projectionFilter->SetTube(itkTubular);
	- projectionFilter->SetSkeleton(thresholdedImg);
	- projectionFilter->Project();
	-
	- Float4DImageType::Pointer projected = projectionFilter->GetProjections();
	-
	- mitk::Image::Pointer mitkProjections = mitk::Image::New();
	- mitk::CastToMitkImage(projected, mitkProjections);
	-
	- AddToDataStorage(mitkProjections, "all_FA_projected");
	-
	-
	-
	-}
	-
	-void QmitkTbssSkeletonizationView::AddToDataStorage(mitk::Image* img, std::string name)
	-{
	- mitk::DataNode::Pointer result = mitk::DataNode::New();
	- result->SetProperty( "name", mitk::StringProperty::New(name) );
	- result->SetData( img );
	-
	- // add new image to data storage and set as active to ease further processing
	- GetDataStorage()->Add( result );
	-}
	-
	-
	-
	-template <class TPixel>
	-void QmitkTbssSkeletonizationView::ConvertToItk(mitk::PixelType, mitk::Image* image, Float4DImageType::Pointer output)
	-{
	- output = Float4DImageType::New();
	-
	- mitk::BaseGeometry* geo = image->GetGeometry();
	- mitk::Vector3D mitkSpacing = geo->GetSpacing();
	- mitk::Point3D mitkOrigin = geo->GetOrigin();
	-
	- Float4DImageType::SpacingType spacing;
	- spacing[0] = mitkSpacing[0];
	- spacing[1] = mitkSpacing[1];
	- spacing[2] = mitkSpacing[2];
	- spacing[3] = 1.0; // todo: check if spacing has length 4
	-
	- Float4DImageType::PointType origin;
	- origin[0] = mitkOrigin[0];
	- origin[1] = mitkOrigin[1];
	- origin[2] = mitkOrigin[2];
	- origin[3] = 0;
	-
	- Float4DImageType::SizeType size;
	- size[0] = image->GetDimension(0);
	- size[1] = image->GetDimension(1);
	- size[2] = image->GetDimension(2);
	- size[3] = image->GetDimension(3);
	-
	- Float4DImageType::DirectionType dir;
	- vtkLinearTransform* lin = geo->GetVtkTransform();
	- vtkMatrix4x4 *m = lin->GetMatrix();
	-
	- dir.Fill(0.0);
	- for(int x=0; x<3; x++)
	- {
	- for(int y=0; y<3; y++)
	- {
	- dir[x][y] = m->GetElement(x,y);
	- }
	- }
	- dir[3][3] = 1;
	-
	-
	-
	- output->SetSpacing(spacing);
	- output->SetOrigin(origin);
	- output->SetRegions(size);
	- output->SetDirection(dir);
	- output->Allocate();
	-
	-
	- if(image->GetDimension() == 4)
	- {
	- unsigned int timesteps = image->GetDimension(3);
	-
	- try{
	- // REPLACE THIS METHODE()ConvertToItk) WITH mitk::CastToItk
	-
	- // iterate through the subjects and copy data to output
	- for(unsigned int t=0; t<timesteps; t++)
	- {
	- mitk::ImagePixelReadAccessor <TPixel,3> inAcc(image,image->GetVolumeData(t));
	-
	- for(unsigned int x=0; x<image->GetDimension(0); x++)
	- {
	- for(unsigned int y=0; y<image->GetDimension(1); y++)
	- {
	- for(unsigned int z=0; z<image->GetDimension(2); z++)
	- {
	- itk::Index<3> ix = {{x, y, z}};
	- itk::Index<4> ix4 = {{x, y, z, t}};
	-
	- output->SetPixel(ix4, inAcc.GetPixelByIndex(ix));
	-
	- }
	- }
	- }
	- }
	- }
	- catch(const std::exception & e)
	- {
	- MITK_INFO << e.what();
	- }
	-
	- }
	-
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTbssSkeletonizationView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTbssSkeletonizationView.h
	deleted file mode 100644
	index a0b2c88cc6..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTbssSkeletonizationView.h
	+++ /dev/null
	@@ -1,114 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef QmitkTbssSkeletonizationView_h
	-#define QmitkTbssSkeletonizationView_h
	-
	-
	-#include <QmitkAbstractView.h>
	-#include <mitkILifecycleAwarePart.h>
	-
	-#include "ui_QmitkTbssSkeletonizationViewControls.h"
	-#include "itkImage.h"
	-#include "mitkPixelType.h"
	-
	-namespace mitk {
	- class Image;
	-}
	-
	-typedef itk::Image<float, 3> FloatImageType;
	-typedef itk::Image<char, 3> CharImageType;
	-typedef itk::Image<float, 4> Float4DImageType;
	-
	-typedef itk::CovariantVector<int,3> VectorType;
	-typedef itk::Image<VectorType, 3> DirectionImageType;
	-
	-
	-/*!
	- * \brief Implementation of the core functionality of TBSS.
	- * This plugin provides the core functionality of TBSS (see Smith et al., 2009. http://dx.doi.org/10.1016/j.neuroimage.2006.02.024)
	- * It can skeletonize a mean FA image and calculate the projection of all individual subjects to this skeleton.
	-*/
	-
	-class QmitkTbssSkeletonizationView : public QmitkAbstractView, public mitk::ILifecycleAwarePart
	-{
	-
	- Q_OBJECT
	-
	- public:
	-
	- static const std::string VIEW_ID;
	-
	- QmitkTbssSkeletonizationView();
	- virtual ~QmitkTbssSkeletonizationView();
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	-
	- //Creation of the connections of main and control widget
	- virtual void CreateConnections();
	-
	- ///
	- /// Sets the focus to an internal widget.
	- ///
	- virtual void SetFocus() override;
	-
	- /// \brief Called when the view gets activated
	- virtual void Activated() override;
	-
	- /// \brief Called when the view gets deactivated
	- virtual void Deactivated() override;
	-
	- bool IsActivated() const;
	-
	- /// \brief Called when the view gets visible
	- virtual void Visible() override;
	-
	- /// \brief Called when the view gets hidden
	- virtual void Hidden() override;
	-
	- protected slots:
	-
	-
	- /* \brief Perform skeletonization only */
	- void Skeletonize();
	-
	- // Perform skeletonization and Projection of subject data to the skeleton
	- void Project();
	-
	-
	-
	- protected:
	-
	- //brief called by QmitkAbstractView when DataManager's selection has changed
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- Ui::QmitkTbssSkeletonizationViewControls* m_Controls;
	-
	- void AddToDataStorage(mitk::Image* img, std::string name);
	-
	- template <class TPixel>
	- void ConvertToItk(mitk::PixelType, mitk::Image* image, Float4DImageType::Pointer);
	-
	- private:
	-
	- bool m_Activated;
	-
	-};
	-
	-
	-
	-#endif // _QMITKTbssSkeletonizationVIEW_H_INCLUDED
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTbssSkeletonizationViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTbssSkeletonizationViewControls.ui
	deleted file mode 100644
	index cfcacb84f6..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTbssSkeletonizationViewControls.ui
	+++ /dev/null
	@@ -1,137 +0,0 @@
	-<?xml version="1.0" encoding="utf-8"?>
	-<ui version="4.0">
	- <class>QmitkTbssSkeletonizationViewControls</class>
	- <widget class="QWidget" name="QmitkTbssSkeletonizationViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>431</width>
	- <height>811</height>
	- </rect>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="windowTitle">
	- <string>QmitkTemplate</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QVBoxLayout" name="verticalLayout_9">
	- <item>
	- <widget class="QFrame" name="frame">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>80</height>
	- </size>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::StyledPanel</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QVBoxLayout" name="verticalLayout">
	- <item>
	- <widget class="QLabel" name="m_MeanLabel">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="text">
	- <string>Mean:</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QLabel" name="m_PatientDataLabel">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="text">
	- <string>Patient Data:</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QLabel" name="m_TubularName">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="text">
	- <string>Tubular Structure Mask:</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <widget class="QPushButton" name="m_Skeletonize">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="text">
	- <string>Skeletonize</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QPushButton" name="m_Project">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="text">
	- <string>Skeletonize and Project</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QCheckBox" name="m_OutputMask">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="text">
	- <string>Output binary mask</string>
	- </property>
	- <property name="checked">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QCheckBox" name="m_OutputDistanceMap">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="text">
	- <string>Output distance map</string>
	- </property>
	- <property name="checked">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <layoutdefault spacing="6" margin="11"></layoutdefault>
	- <resources></resources>
	- <connections></connections>
	-</ui>
	\ No newline at end of file
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTbssTableModel.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTbssTableModel.cpp
	deleted file mode 100644
	index b68e4a1c4b..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTbssTableModel.cpp
	+++ /dev/null
	@@ -1,149 +0,0 @@
	-
	-
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-
	-#include "QmitkTbssTableModel.h"
	-
	-QmitkTbssTableModel::QmitkTbssTableModel(QObject *parent)
	- : QAbstractTableModel(parent)
	-{
	-}
	-
	-QmitkTbssTableModel::QmitkTbssTableModel(QList< QPair<QString, int> > pairs, QObject *parent)
	- : QAbstractTableModel(parent)
	-{
	- listOfPairs=pairs;
	-}
	-
	-int QmitkTbssTableModel::rowCount(const QModelIndex &parent) const
	-{
	- Q_UNUSED(parent);
	- return listOfPairs.size();
	-}
	-
	-int QmitkTbssTableModel::columnCount(const QModelIndex &parent) const
	-{
	- Q_UNUSED(parent);
	- return 2;
	-}
	-
	-QVariant QmitkTbssTableModel::data(const QModelIndex &index, int role) const
	-{
	- if (!index.isValid())
	- return QVariant();
	-
	- if (index.row() >= listOfPairs.size() \|\| index.row() < 0)
	- return QVariant();
	-
	- if (role == Qt::DisplayRole) {
	- QPair<QString, int> pair = listOfPairs.at(index.row());
	-
	- if (index.column() == 0)
	- return pair.first;
	- else if (index.column() == 1)
	- return pair.second;
	- }
	- return QVariant();
	-}
	-
	-QVariant QmitkTbssTableModel::headerData(int section, Qt::Orientation orientation, int role) const
	-{
	- if (role != Qt::DisplayRole)
	- return QVariant();
	-
	- if (orientation == Qt::Horizontal) {
	- switch (section) {
	- case 0:
	- return tr("Group");
	-
	- case 1:
	- return tr("Size");
	-
	- default:
	- return QVariant();
	- }
	- }
	- return QVariant();
	-}
	-
	-bool QmitkTbssTableModel::insertRows(int position, int rows, const QModelIndex &index)
	-{
	- Q_UNUSED(index);
	- beginInsertRows(QModelIndex(), position, position+rows-1);
	-
	- for (int row=0; row < rows; row++) {
	- QPair<QString, int> pair(" ", 0);
	- listOfPairs.insert(position, pair);
	- }
	-
	- endInsertRows();
	- return true;
	-}
	-
	-bool QmitkTbssTableModel::removeRows(int position, int rows, const QModelIndex &index)
	-{
	- Q_UNUSED(index);
	- beginRemoveRows(QModelIndex(), position, position+rows-1);
	-
	- for (int row=0; row < rows; ++row) {
	- listOfPairs.removeAt(position);
	- }
	-
	- endRemoveRows();
	- return true;
	-}
	-
	-bool QmitkTbssTableModel::setData(const QModelIndex &index, const QVariant &value, int role)
	-{
	- if (index.isValid() && role == Qt::EditRole) {
	- int row = index.row();
	-
	- QPair<QString, int> p = listOfPairs.value(row);
	-
	- if (index.column() == 0)
	- p.first = value.toString();
	- else if (index.column() == 1)
	- p.second = value.toInt();
	- else
	- return false;
	-
	- listOfPairs.replace(row, p);
	- emit(dataChanged(index, index));
	-
	- return true;
	- }
	-
	- return false;
	-}
	-
	-Qt::ItemFlags QmitkTbssTableModel::flags(const QModelIndex &index) const
	-{
	- if (!index.isValid())
	- return Qt::ItemIsEnabled;
	-
	- return QAbstractTableModel::flags(index) \| Qt::ItemIsEditable;
	-}
	-
	-QList< QPair<QString, int> > QmitkTbssTableModel::getList()
	-{
	- return listOfPairs;
	-}
	-
	-
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTbssTableModel.h b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTbssTableModel.h
	deleted file mode 100644
	index 3388058e56..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTbssTableModel.h
	+++ /dev/null
	@@ -1,52 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-
	-#ifndef QmitkTbssTableModel_h
	-#define QmitkTbssTableModel_h
	-
	-
	-#include <QAbstractTableModel>
	-
	-#include <QPair>
	-#include <QList>
	-#include <QObject>
	-
	-class QmitkTbssTableModel : public QAbstractTableModel
	-{
	-
	- //Q_OBJECT
	-
	-public:
	- QmitkTbssTableModel(QObject *parent=nullptr);
	- QmitkTbssTableModel(QList< QPair<QString, int> > listofPairs, QObject *parent=nullptr);
	-
	- int rowCount(const QModelIndex &parent) const override;
	- int columnCount(const QModelIndex &parent) const override;
	- QVariant data(const QModelIndex &index, int role) const override;
	- QVariant headerData(int section, Qt::Orientation orientation, int role) const override;
	- Qt::ItemFlags flags(const QModelIndex &index) const override;
	- bool setData(const QModelIndex &index, const QVariant &value, int role=Qt::EditRole) override;
	- bool insertRows(int position, int rows, const QModelIndex &index=QModelIndex()) override;
	- bool removeRows(int position, int rows, const QModelIndex &index=QModelIndex()) override;
	- QList< QPair<QString, int> > getList();
	-
	-private:
	- QList< QPair<QString, int> > listOfPairs;
	-};
	-
	-#endif
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTractbasedSpatialStatisticsView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTractbasedSpatialStatisticsView.cpp
	deleted file mode 100644
	index 1901085a8d..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTractbasedSpatialStatisticsView.cpp
	+++ /dev/null
	@@ -1,1142 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-// Qmitk
	-#include "QmitkTractbasedSpatialStatisticsView.h"
	-
	-#include "mitkDataNodeObject.h"
	-#include <itkCastImageFilter.h>
	-
	-// Qt
	-#include <QMessageBox>
	-#include <QInputDialog>
	-#include <QClipboard>
	-
	-#include <qwt_plot_picker.h>
	-
	-#include <mitkTractAnalyzer.h>
	-#include <mitkTbssImporter.h>
	-#include <mitkPlanarCircle.h>
	-#include <mitkPlanarFigureInteractor.h>
	-
	-
	-#include "vtkPoints.h"
	-#include <vtkCellArray.h>
	-#include <vtkPolyLine.h>
	-#include <mitkWorkbenchUtil.h>
	-
	-
	-const std::string QmitkTractbasedSpatialStatisticsView::VIEW_ID = "org.mitk.views.tractbasedspatialstatistics";
	-
	-using namespace berry;
	-
	-
	-QmitkTractbasedSpatialStatisticsView::QmitkTractbasedSpatialStatisticsView()
	-: QmitkAbstractView()
	-, m_Controls( 0 )
	-, m_Activated(false)
	-{
	-
	-}
	-
	-QmitkTractbasedSpatialStatisticsView::~QmitkTractbasedSpatialStatisticsView()
	-{
	-}
	-
	-
	-void QmitkTractbasedSpatialStatisticsView::PerformChange()
	-{
	- m_Controls->m_RoiPlotWidget->ModifyPlot(m_Controls->m_Segments->value(), m_Controls->m_Average->isChecked());
	-}
	-
	-void QmitkTractbasedSpatialStatisticsView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /part/, const QList<mitk::DataNode::Pointer>& nodes)
	-{
	- //datamanager selection changed
	- if (!this->IsActivated())
	- return;
	-
	-
	- // Check which datatypes are selected in the datamanager and enable/disable widgets accordingly
	-
	- bool foundTbssRoi = false;
	- bool foundTbss = false;
	- bool found3dImage = false;
	- bool found4dImage = false;
	- bool foundFiberBundle = false;
	- bool foundStartRoi = false;
	- bool foundEndRoi = false;
	-
	- mitk::TbssRoiImage* roiImage = nullptr;
	- mitk::TbssImage* image = nullptr;
	- mitk::Image* img = nullptr;
	- mitk::FiberBundle* fib = nullptr;
	- mitk::DataNode* start = nullptr;
	- mitk::DataNode* end = nullptr;
	-
	- m_CurrentStartRoi = nullptr;
	- m_CurrentEndRoi = nullptr;
	-
	-
	-
	- for (mitk::DataNode::Pointer node: nodes)
	- {
	- // only look at interesting types
	- // check for valid data
	- mitk::BaseData* nodeData = node->GetData();
	- if( nodeData )
	- {
	- if(QString("TbssRoiImage").compare(nodeData->GetNameOfClass())==0)
	- {
	- foundTbssRoi = true;
	- roiImage = static_cast<mitk::TbssRoiImage*>(nodeData);
	- }
	- else if (QString("TbssImage").compare(nodeData->GetNameOfClass())==0)
	- {
	- foundTbss = true;
	- image = static_cast<mitk::TbssImage*>(nodeData);
	- }
	- else if(QString("Image").compare(nodeData->GetNameOfClass())==0)
	- {
	- img = static_cast<mitk::Image*>(nodeData);
	- if(img->GetDimension() == 3)
	- {
	- found3dImage = true;
	- }
	- else if(img->GetDimension() == 4)
	- {
	- found4dImage = true;
	- }
	- }
	-
	- else if (QString("FiberBundle").compare(nodeData->GetNameOfClass())==0)
	- {
	- foundFiberBundle = true;
	- fib = static_cast<mitk::FiberBundle*>(nodeData);
	- this->m_CurrentFiberNode = node;
	- }
	-
	-
	- if(QString("PlanarCircle").compare(nodeData->GetNameOfClass())==0)
	- {
	- if(!foundStartRoi)
	- {
	- start = node;
	- this->m_CurrentStartRoi = node;
	- foundStartRoi = true;
	- }
	- else
	- {
	- end = node;
	- this->m_CurrentEndRoi = node;
	- foundEndRoi = true;
	- }
	- }
	- }
	- }
	-
	-
	- this->m_Controls->m_CreateRoi->setEnabled(found3dImage);
	- this->m_Controls->m_ImportFsl->setEnabled(found4dImage);
	-
	-
	-
	- if(foundTbss && foundTbssRoi)
	- {
	- this->Plot(image, roiImage);
	- }
	-
	- else if(found3dImage && foundFiberBundle && foundStartRoi && foundEndRoi)
	- {
	- this->PlotFiberBundle(fib, img, start, end);
	- }
	-
	- else if(found3dImage && foundFiberBundle)
	- {
	- this->PlotFiberBundle(fib, img);
	- }
	-
	- else if(foundTbss && foundStartRoi && foundEndRoi && foundFiberBundle)
	- {
	- this->PlotFiber4D(image, fib, start, end);
	- }
	-
	- if(found3dImage)
	- {
	- this->InitPointsets();
	- }
	-
	- this->m_Controls->m_Cut->setEnabled(foundFiberBundle && foundStartRoi && foundEndRoi);
	- this->m_Controls->m_SegmentLabel->setEnabled(foundFiberBundle && foundStartRoi && foundEndRoi && (found3dImage \|\| foundTbss));
	- this->m_Controls->m_Segments->setEnabled(foundFiberBundle && foundStartRoi && foundEndRoi && (found3dImage \|\| foundTbss));
	- this->m_Controls->m_Average->setEnabled(foundFiberBundle && foundStartRoi && foundEndRoi && found3dImage);
	-
	-}
	-
	-void QmitkTractbasedSpatialStatisticsView::InitPointsets()
	-{
	- // Check if PointSetStart exsits, if not create it.
	- m_P1 = this->GetDataStorage()->GetNamedNode("PointSetNode");
	-
	- if (m_PointSetNode)
	- {
	- //m_PointSetNode = dynamic_cast<mitk::PointSet*>(m_P1->GetData());
	- return;
	- }
	-
	- if ((!m_P1) \|\| (!m_PointSetNode))
	- {
	- // create new ones
	- m_PointSetNode = mitk::PointSet::New();
	- m_P1 = mitk::DataNode::New();
	- m_P1->SetData( m_PointSetNode );
	- m_P1->SetProperty( "name", mitk::StringProperty::New( "PointSet" ) );
	- m_P1->SetProperty( "opacity", mitk::FloatProperty::New( 1 ) );
	- m_P1->SetProperty( "helper object", mitk::BoolProperty::New(true) ); // CHANGE if wanted
	- m_P1->SetProperty( "pointsize", mitk::FloatProperty::New( 0.1 ) );
	- m_P1->SetColor( 1.0, 0.0, 0.0 );
	- this->GetDataStorage()->Add(m_P1);
	- m_Controls->m_PointWidget->SetPointSetNode(m_P1);
	- auto renderWindowPart = this->GetRenderWindowPart(mitk::WorkbenchUtil::IRenderWindowPartStrategy::OPEN);
	- auto axialSnc = renderWindowPart->GetQmitkRenderWindow("axial")->GetSliceNavigationController();
	- auto sagittalSnc = renderWindowPart->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController();
	- auto coronalSnc = renderWindowPart->GetQmitkRenderWindow("coronal")->GetSliceNavigationController();
	- m_Controls->m_PointWidget->AddSliceNavigationController(axialSnc);
	- m_Controls->m_PointWidget->AddSliceNavigationController(sagittalSnc);
	- m_Controls->m_PointWidget->AddSliceNavigationController(coronalSnc);
	- }
	-}
	-
	-void QmitkTractbasedSpatialStatisticsView::CreateQtPartControl( QWidget *parent )
	-{
	- // build up qt view, unless already done
	- if ( !m_Controls )
	- {
	- // create GUI widgets from the Qt Designer's .ui file
	- m_Controls = new Ui::QmitkTractbasedSpatialStatisticsViewControls;
	- m_Controls->setupUi( parent );
	- this->CreateConnections();
	- }
	-
	-
	- // Table for the FSL TBSS import
	- m_GroupModel = new QmitkTbssTableModel();
	- m_Controls->m_GroupInfo->setModel(m_GroupModel);
	-
	-
	-}
	-
	-void QmitkTractbasedSpatialStatisticsView::SetFocus()
	-{
	- m_Controls->m_AddGroup->setFocus();
	-}
	-
	-void QmitkTractbasedSpatialStatisticsView::Activated()
	-{
	- m_Activated = true;
	-}
	-
	-void QmitkTractbasedSpatialStatisticsView::Deactivated()
	-{
	- m_Activated = false;
	-}
	-
	-bool QmitkTractbasedSpatialStatisticsView::IsActivated() const
	-{
	- return m_Activated;
	-}
	-
	-void QmitkTractbasedSpatialStatisticsView::Visible()
	-{
	-}
	-
	-void QmitkTractbasedSpatialStatisticsView::Hidden()
	-{
	-}
	-
	-void QmitkTractbasedSpatialStatisticsView::CreateConnections()
	-{
	- if ( m_Controls )
	- {
	- connect( (QObject*)(m_Controls->m_CreateRoi), SIGNAL(clicked()), this, SLOT(CreateRoi()) );
	- connect( (QObject*)(m_Controls->m_ImportFsl), SIGNAL(clicked()), this, SLOT(TbssImport()) );
	- connect( (QObject*)(m_Controls->m_AddGroup), SIGNAL(clicked()), this, SLOT(AddGroup()) );
	- connect( (QObject*)(m_Controls->m_RemoveGroup), SIGNAL(clicked()), this, SLOT(RemoveGroup()) );
	- connect( (QObject*)(m_Controls->m_Clipboard), SIGNAL(clicked()), this, SLOT(CopyToClipboard()) );
	- connect( m_Controls->m_RoiPlotWidget->m_PlotPicker, SIGNAL(selected(const QPointF&)), SLOT(Clicked(const QPointF&) ) );
	- connect( m_Controls->m_RoiPlotWidget->m_PlotPicker, SIGNAL(moved(const QPointF&)), SLOT(Clicked(const QPointF&) ) );
	- connect( (QObject*)(m_Controls->m_Cut), SIGNAL(clicked()), this, SLOT(Cut()) );
	- connect( (QObject*)(m_Controls->m_Average), SIGNAL(stateChanged(int)), this, SLOT(PerformChange()) );
	- connect( (QObject*)(m_Controls->m_Segments), SIGNAL(valueChanged(int)), this, SLOT(PerformChange()) );
	-
	- }
	-}
	-
	-
	-void QmitkTractbasedSpatialStatisticsView::CopyToClipboard()
	-{
	-
	-
	-
	- if(m_Controls->m_RoiPlotWidget->IsPlottingFiber())
	- {
	- // Working with fiber bundles
	- std::vector <std::vector<double> > profiles = m_Controls->m_RoiPlotWidget->GetIndividualProfiles();
	-
	- QString clipboardText;
	- for (std::vector<std::vector<double> >::iterator it = profiles.begin(); it
	- != profiles.end(); ++it)
	- {
	- for (std::vector<double>::iterator it2 = (*it).begin(); it2 !=
	- (*it).end(); ++it2)
	- {
	- clipboardText.append(QString("%1 \t").arg(*it2));
	- }
	- clipboardText.append(QString("\n"));
	- }
	-
	-
	-
	- if(m_Controls->m_Average->isChecked())
	- {
	- std::vector<double> averages = m_Controls->m_RoiPlotWidget->GetAverageProfile();
	- clipboardText.append(QString("\nAverage\n"));
	-
	- for (std::vector<double>::iterator it2 = averages.begin(); it2 !=
	- averages.end(); ++it2)
	- {
	- clipboardText.append(QString("%1 \t").arg(*it2));
	-
	- }
	- }
	-
	- QApplication::clipboard()->setText(clipboardText, QClipboard::Clipboard);
	-
	- }
	-
	- else{
	-
	- // Working with TBSS Data
	- if(m_Controls->m_Average->isChecked())
	- {
	- std::vector<std::vector<double> > vals = m_Controls->m_RoiPlotWidget->GetVals();
	- QString clipboardText;
	- for (std::vector<std::vector<double> >::iterator it = vals.begin(); it
	- != vals.end(); ++it)
	- {
	- for (std::vector<double>::iterator it2 = (*it).begin(); it2 !=
	- (*it).end(); ++it2)
	- {
	- clipboardText.append(QString("%1 \t").arg(*it2));
	-
	- double d = *it2;
	- std::cout << d <<std::endl;
	- }
	- clipboardText.append(QString("\n"));
	- }
	-
	- QApplication::clipboard()->setText(clipboardText, QClipboard::Clipboard);
	- }
	- else
	- {
	- std::vector<std::vector<double> > vals = m_Controls->m_RoiPlotWidget->GetIndividualProfiles();
	- QString clipboardText;
	- for (std::vector<std::vector<double> >::iterator it = vals.begin(); it
	- != vals.end(); ++it)
	- {
	- for (std::vector<double>::iterator it2 = (*it).begin(); it2 !=
	- (*it).end(); ++it2)
	- {
	- clipboardText.append(QString("%1 \t").arg(*it2));
	-
	- double d = *it2;
	- std::cout << d <<std::endl;
	- }
	- clipboardText.append(QString("\n"));
	- }
	- QApplication::clipboard()->setText(clipboardText, QClipboard::Clipboard);
	- }
	-
	- }
	-
	-
	-}
	-
	-void QmitkTractbasedSpatialStatisticsView::RemoveGroup()
	-{
	-
	- QTableView temp = static_cast<QTableView>(m_Controls->m_GroupInfo);
	-
	- QItemSelectionModel *selectionModel = temp->selectionModel();
	-
	- QModelIndexList indices = selectionModel->selectedRows();
	-
	- QModelIndex index;
	-
	- foreach(index, indices)
	- {
	- int row = index.row();
	- m_GroupModel->removeRows(row, 1, QModelIndex());
	- }
	-
	-}
	-
	-
	-
	-void QmitkTractbasedSpatialStatisticsView::AddGroup()
	-{
	- QString group("Group");
	- int number = 0;
	- QPair<QString, int> pair(group, number);
	- QList< QPair<QString, int> >list = m_GroupModel->getList();
	-
	-
	- if(!list.contains(pair))
	- {
	- m_GroupModel->insertRows(0, 1, QModelIndex());
	-
	- QModelIndex index = m_GroupModel->index(0, 0, QModelIndex());
	- m_GroupModel->setData(index, group, Qt::EditRole);
	- index = m_GroupModel->index(0, 1, QModelIndex());
	- m_GroupModel->setData(index, number, Qt::EditRole);
	-
	- }
	-}
	-
	-
	-void QmitkTractbasedSpatialStatisticsView::TbssImport()
	-{
	-
	- // Read groups from the interface
	- mitk::TbssImporter::Pointer importer = mitk::TbssImporter::New();
	-
	- QList< QPair<QString, int> >list = m_GroupModel->getList();
	-
	-
	- if(list.size() == 0)
	- {
	- QMessageBox msgBox;
	- msgBox.setText("No study group information has been set yet.");
	- msgBox.exec();
	- return;
	- }
	-
	-
	- std::vector < std::pair<std::string, int> > groups;
	- for(int i=0; i<list.size(); i++)
	- {
	- QPair<QString, int> pair = list.at(i);
	- std::string s = pair.first.toStdString();
	- int n = pair.second;
	-
	- std::pair<std::string, int> p;
	- p.first = s;
	- p.second = n;
	- groups.push_back(p);
	- }
	-
	- importer->SetGroupInfo(groups);
	-
	- std::string minfo = m_Controls->m_MeasurementInfo->text().toStdString();
	- importer->SetMeasurementInfo(minfo);
	-
	-
	- std::string name = "";
	-
	- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
	-
	- for (auto node: nodes)
	- {
	- if(QString("Image").compare(node->GetData()->GetNameOfClass())==0)
	- {
	- mitk::Image* img = static_cast<mitk::Image*>(node->GetData());
	- if(img->GetDimension() == 4)
	- {
	- importer->SetImportVolume(img);
	- name = node->GetName();
	- }
	- }
	- }
	-
	-
	- mitk::TbssImage::Pointer tbssImage;
	-
	- tbssImage = importer->Import();
	- name += "_tbss";
	- AddTbssToDataStorage(tbssImage, name);
	-
	-
	-}
	-
	-
	-void QmitkTractbasedSpatialStatisticsView::AddTbssToDataStorage(mitk::Image* image, std::string name)
	-{
	- mitk::LevelWindow levelwindow;
	- levelwindow.SetAuto( image );
	- mitk::LevelWindowProperty::Pointer levWinProp = mitk::LevelWindowProperty::New();
	- levWinProp->SetLevelWindow( levelwindow );
	-
	- mitk::DataNode::Pointer result = mitk::DataNode::New();
	- result->SetProperty( "name", mitk::StringProperty::New(name) );
	- result->SetData( image );
	- result->SetProperty( "levelwindow", levWinProp );
	-
	-
	- // add new image to data storage and set as active to ease further processing
	- GetDataStorage()->Add( result );
	-
	- // show the results
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-
	-void QmitkTractbasedSpatialStatisticsView::Clicked(const QPointF& pos)
	-{
	- int index = (int)pos.x();
	-
	- if(m_Roi.size() > 0 && m_CurrentGeometry != nullptr && !m_Controls->m_RoiPlotWidget->IsPlottingFiber() )
	- {
	-
	- index = std::min( (int)m_Roi.size()-1, std::max(0, index) );
	- itk::Index<3> ix = m_Roi.at(index);
	-
	- mitk::Vector3D i;
	- i[0] = ix[0];
	- i[1] = ix[1];
	- i[2] = ix[2];
	-
	- mitk::Vector3D w;
	-
	- m_CurrentGeometry->IndexToWorld(i, w);
	-
	- mitk::Point3D origin = m_CurrentGeometry->GetOrigin();
	-
	- mitk::Point3D p;
	- p[0] = w[0] + origin[0];
	- p[1] = w[1] + origin[1];
	- p[2] = w[2] + origin[2];
	-
	- this->GetRenderWindowPart()->SetSelectedPosition(p);
	- m_Controls->m_RoiPlotWidget->drawBar(index);
	- }
	-
	- else if(m_Controls->m_RoiPlotWidget->IsPlottingFiber() )
	- {
	-
	- mitk::Point3D point = m_Controls->m_RoiPlotWidget->GetPositionInWorld(index);
	- this->GetRenderWindowPart()->SetSelectedPosition(point);
	-
	-
	- }
	-
	-
	-}
	-
	-void QmitkTractbasedSpatialStatisticsView::Cut()
	-{
	- mitk::BaseData* fibData = m_CurrentFiberNode->GetData();
	- mitk::FiberBundle* fib = static_cast<mitk::FiberBundle*>(fibData);
	-
	- mitk::PlaneGeometry* startGeometry2D = const_cast<mitk::PlaneGeometry>(dynamic_cast<mitk::PlanarFigure>(m_CurrentStartRoi->GetData())->GetPlaneGeometry());
	- mitk::PlaneGeometry* endGeometry2D = const_cast<mitk::PlaneGeometry>(dynamic_cast<mitk::PlanarFigure>(m_CurrentEndRoi->GetData())->GetPlaneGeometry());
	-
	- mitk::Point3D startCenter = dynamic_cast<mitk::PlanarFigure*>(m_CurrentStartRoi->GetData())->GetWorldControlPoint(0); //center Point of start roi
	- mitk::Point3D endCenter = dynamic_cast<mitk::PlanarFigure*>(m_CurrentEndRoi->GetData())->GetWorldControlPoint(0); //center Point of end roi
	-
	- mitk::FiberBundle::Pointer inStart = fib->ExtractFiberSubset(m_CurrentStartRoi, nullptr);
	- mitk::FiberBundle::Pointer inBoth = inStart->ExtractFiberSubset(m_CurrentEndRoi, nullptr);
	-
	- int num = inBoth->GetNumFibers();
	-
	- vtkSmartPointer<vtkPolyData> fiberPolyData = inBoth->GetFiberPolyData();
	- vtkCellArray* lines = fiberPolyData->GetLines();
	- lines->InitTraversal();
	-
	-
	- // initialize new vtk polydata
	- vtkSmartPointer<vtkPoints> points = vtkSmartPointer<vtkPoints>::New();
	- vtkSmartPointer<vtkPolyData> polyData = vtkSmartPointer<vtkPolyData>::New();
	- vtkSmartPointer<vtkCellArray> cells = vtkSmartPointer<vtkCellArray>::New();
	-
	- int pointIndex=0;
	-
	-
	- // find start and endpoint
	- for( int fiberID( 0 ); fiberID < num; fiberID++ )
	- {
	- vtkIdType numPointsInCell(0);
	- vtkIdType* pointsInCell(nullptr);
	- lines->GetNextCell ( numPointsInCell, pointsInCell );
	-
	- int startId = 0;
	- int endId = 0;
	-
	- float minDistStart = std::numeric_limits<float>::max();
	- float minDistEnd = std::numeric_limits<float>::max();
	-
	-
	- vtkSmartPointer<vtkPolyLine> polyLine = vtkSmartPointer<vtkPolyLine>::New();
	- int lineIndex=0;
	-
	-
	- for( int pointInCellID( 0 ); pointInCellID < numPointsInCell ; pointInCellID++)
	- {
	- double *p = fiberPolyData->GetPoint( pointsInCell[ pointInCellID ] );
	-
	- mitk::Point3D point;
	- point[0] = p[0];
	- point[1] = p[1];
	- point[2] = p[2];
	-
	- float distanceToStart = point.EuclideanDistanceTo(startCenter);
	- float distanceToEnd = point.EuclideanDistanceTo(endCenter);
	-
	- if(distanceToStart < minDistStart)
	- {
	- minDistStart = distanceToStart;
	- startId = pointInCellID;
	- }
	-
	- if(distanceToEnd < minDistEnd)
	- {
	- minDistEnd = distanceToEnd;
	- endId = pointInCellID;
	- }
	-
	-
	-
	- }
	-
	-
	-
	- /* We found the start and end points of of the part that should be plottet for
	- the current fiber. now we need to plot them. If the endId is smaller than the startId the plot order
	- must be reversed*/
	-
	- if(startId < endId)
	- {
	-
	- double *p = fiberPolyData->GetPoint( pointsInCell[ startId ] );
	-
	- mitk::Vector3D p0;
	- p0[0] = p[0];
	- p0[1] = p[1];
	- p0[2] = p[2];
	-
	- p = fiberPolyData->GetPoint( pointsInCell[ startId+1 ] );
	-
	- mitk::Vector3D p1;
	- p1[0] = p[0];
	- p1[1] = p[1];
	- p1[2] = p[2];
	-
	-
	- // Check if p and p2 are both on the same side of the plane
	- mitk::Vector3D normal = startGeometry2D->GetNormal();
	-
	- mitk::Point3D pStart;
	- pStart[0] = p0[0];
	- pStart[1] = p0[1];
	- pStart[2] = p0[2];
	-
	- bool startOnPositive = startGeometry2D->IsAbove(pStart);
	-
	- mitk::Point3D pSecond;
	- pSecond[0] = p1[0];
	- pSecond[1] = p1[1];
	- pSecond[2] = p1[2];
	-
	- bool secondOnPositive = startGeometry2D->IsAbove(pSecond);
	-
	-
	- // Calculate intersection with the plane
	-
	- mitk::Vector3D onPlane;
	- onPlane[0] = startCenter[0];
	- onPlane[1] = startCenter[1];
	- onPlane[2] = startCenter[2];
	-
	-
	- if(! (secondOnPositive ^ startOnPositive) )
	- {
	- /* startId and startId+1 lie on the same side of the plane, so we need
	- need startId-1 to calculate the intersection with the planar figure*/
	- p = fiberPolyData->GetPoint( pointsInCell[ startId-1 ] );
	- p1[0] = p[0];
	- p1[1] = p[1];
	- p1[2] = p[2];
	- }
	-
	-
	- double d = ( (onPlane-p0)normal) / ( (p0-p1) normal );
	-
	- mitk::Vector3D newPoint = (p0-p1);
	-
	- newPoint[0] = d*newPoint[0] + p0[0];
	- newPoint[1] = d*newPoint[1] + p0[1];
	- newPoint[2] = d*newPoint[2] + p0[2];
	-
	-
	- double insertPoint[3];
	- insertPoint[0] = newPoint[0];
	- insertPoint[1] = newPoint[1];
	- insertPoint[2] = newPoint[2];
	-
	-
	- // First insert the intersection with the start roi
	- points->InsertNextPoint(insertPoint);
	- polyLine->GetPointIds()->InsertId(lineIndex,pointIndex);
	- lineIndex++;
	- pointIndex++;
	-
	- if(! (secondOnPositive ^ startOnPositive) )
	- {
	- /* StartId and startId+1 lie on the same side of the plane
	- so startId is also part of the ROI*/
	-
	- double *start = fiberPolyData->GetPoint( pointsInCell[startId] );
	- points->InsertNextPoint(start);
	- polyLine->GetPointIds()->InsertId(lineIndex,pointIndex);
	- lineIndex++;
	- pointIndex++;
	-
	-
	- }
	-
	- // Insert the rest up and to including endId-1
	- for( int pointInCellID( startId+1 ); pointInCellID < endId ; pointInCellID++)
	- {
	- // create new polyline for new polydata
	- double *p = fiberPolyData->GetPoint( pointsInCell[ pointInCellID ] );
	- points->InsertNextPoint(p);
	-
	-
	- // add point to line
	- polyLine->GetPointIds()->InsertId(lineIndex,pointIndex);
	- lineIndex++;
	- pointIndex++;
	-
	- }
	-
	-
	-
	- /* endId must be included if endId and endId-1 lie on the same side of the
	- plane defined by endRoi*/
	-
	-
	- p = fiberPolyData->GetPoint( pointsInCell[ endId ] );
	- p0[0] = p[0]; p0[1] = p[1]; p0[2] = p[2];
	-
	-
	- p = fiberPolyData->GetPoint( pointsInCell[ endId-1 ] );
	- p1[0] = p[0]; p1[1] = p[1]; p1[2] = p[2];
	-
	-
	- mitk::Point3D pLast;
	- pLast[0] = p0[0]; pLast[1] = p0[1]; pLast[2] = p0[2];
	-
	- mitk::Point3D pBeforeLast;
	- pBeforeLast[0] = p1[0]; pBeforeLast[1] = p1[1]; pBeforeLast[2] = p1[2];
	-
	- bool lastOnPositive = endGeometry2D->IsAbove(pLast);
	- bool secondLastOnPositive = endGeometry2D->IsAbove(pBeforeLast);
	- normal = endGeometry2D->GetNormal();
	-
	-
	- onPlane[0] = endCenter[0];
	- onPlane[1] = endCenter[1];
	- onPlane[2] = endCenter[2];
	-
	-
	-
	- if(! (lastOnPositive ^ secondLastOnPositive) )
	- {
	- /* endId and endId-1 lie on the same side of the plane, so we need
	- need endId+1 to calculate the intersection with the planar figure.
	- this should exist since we know that the fiber crosses the planar figure
	- endId is part of the roi so can also be included here*/
	- p = fiberPolyData->GetPoint( pointsInCell[ endId+1 ] );
	- p1[0] = p[0];
	- p1[1] = p[1];
	- p1[2] = p[2];
	-
	-
	- double *end = fiberPolyData->GetPoint( pointsInCell[endId] );
	- points->InsertNextPoint(end);
	- polyLine->GetPointIds()->InsertId(lineIndex,pointIndex);
	- lineIndex++;
	- pointIndex++;
	- }
	-
	- d = ( (onPlane-p0)normal) / ( (p0-p1) normal );
	-
	- newPoint = (p0-p1);
	-
	- newPoint[0] = d*newPoint[0] + p0[0];
	- newPoint[1] = d*newPoint[1] + p0[1];
	- newPoint[2] = d*newPoint[2] + p0[2];
	-
	- insertPoint[0] = newPoint[0];
	- insertPoint[1] = newPoint[1];
	- insertPoint[2] = newPoint[2];
	-
	- //Insert the Last Point (intersection with the end roi)
	-
	- points->InsertNextPoint(insertPoint);
	- polyLine->GetPointIds()->InsertId(lineIndex,pointIndex);
	- lineIndex++;
	- pointIndex++;
	-
	-
	- }
	-
	- // Need to reverse walking order
	- else{
	- double *p = fiberPolyData->GetPoint( pointsInCell[ startId ] );
	-
	- mitk::Vector3D p0;
	- p0[0] = p[0];
	- p0[1] = p[1];
	- p0[2] = p[2];
	-
	- p = fiberPolyData->GetPoint( pointsInCell[ startId-1 ] );
	-
	- mitk::Vector3D p1;
	- p1[0] = p[0];
	- p1[1] = p[1];
	- p1[2] = p[2];
	-
	-
	- // Check if p and p2 are both on the same side of the plane
	- mitk::Vector3D normal = startGeometry2D->GetNormal();
	-
	- mitk::Point3D pStart;
	- pStart[0] = p0[0];
	- pStart[1] = p0[1];
	- pStart[2] = p0[2];
	-
	- bool startOnPositive = startGeometry2D->IsAbove(pStart);
	-
	- mitk::Point3D pSecond;
	- pSecond[0] = p1[0];
	- pSecond[1] = p1[1];
	- pSecond[2] = p1[2];
	-
	- bool secondOnPositive = startGeometry2D->IsAbove(pSecond);
	-
	-
	- // Calculate intersection with the plane
	-
	- mitk::Vector3D onPlane;
	- onPlane[0] = startCenter[0];
	- onPlane[1] = startCenter[1];
	- onPlane[2] = startCenter[2];
	-
	-
	- if(! (secondOnPositive ^ startOnPositive) )
	- {
	- /* startId and startId-1 lie on the same side of the plane, so we need
	- need startId+1 to calculate the intersection with the planar figure*/
	- p = fiberPolyData->GetPoint( pointsInCell[ startId+1 ] );
	- p1[0] = p[0];
	- p1[1] = p[1];
	- p1[2] = p[2];
	- }
	-
	-
	- double d = ( (onPlane-p0)normal) / ( (p0-p1) normal );
	-
	- mitk::Vector3D newPoint = (p0-p1);
	-
	- newPoint[0] = d*newPoint[0] + p0[0];
	- newPoint[1] = d*newPoint[1] + p0[1];
	- newPoint[2] = d*newPoint[2] + p0[2];
	-
	-
	- double insertPoint[3];
	- insertPoint[0] = newPoint[0];
	- insertPoint[1] = newPoint[1];
	- insertPoint[2] = newPoint[2];
	-
	-
	- // First insert the intersection with the start roi
	- points->InsertNextPoint(insertPoint);
	- polyLine->GetPointIds()->InsertId(lineIndex,pointIndex);
	- lineIndex++;
	- pointIndex++;
	-
	- if(! (secondOnPositive ^ startOnPositive) )
	- {
	- /* startId and startId-1 lie on the same side of the plane
	- so endId is also part of the ROI*/
	-
	- double *start = fiberPolyData->GetPoint( pointsInCell[startId] );
	- points->InsertNextPoint(start);
	- polyLine->GetPointIds()->InsertId(lineIndex,pointIndex);
	- lineIndex++;
	- pointIndex++;
	-
	-
	- }
	-
	- // Insert the rest up and to including endId-1
	- for( int pointInCellID( startId-1 ); pointInCellID > endId ; pointInCellID--)
	- {
	- // create new polyline for new polydata
	- double *p = fiberPolyData->GetPoint( pointsInCell[ pointInCellID ] );
	- points->InsertNextPoint(p);
	-
	-
	- // add point to line
	- polyLine->GetPointIds()->InsertId(lineIndex,pointIndex);
	- lineIndex++;
	- pointIndex++;
	-
	- }
	-
	-
	-
	- /* startId must be included if startId and startId+ lie on the same side of the
	- plane defined by endRoi*/
	-
	-
	- p = fiberPolyData->GetPoint( pointsInCell[ endId ] );
	- p0[0] = p[0];
	- p0[1] = p[1];
	- p0[2] = p[2];
	-
	-
	- p = fiberPolyData->GetPoint( pointsInCell[ endId+1 ] );
	- p1[0] = p[0];
	- p1[1] = p[1];
	- p1[2] = p[2];
	-
	-
	- mitk::Point3D pLast;
	- pLast[0] = p0[0];
	- pLast[1] = p0[1];
	- pLast[2] = p0[2];
	-
	- bool lastOnPositive = endGeometry2D->IsAbove(pLast);
	-
	- mitk::Point3D pBeforeLast;
	- pBeforeLast[0] = p1[0];
	- pBeforeLast[1] = p1[1];
	- pBeforeLast[2] = p1[2];
	-
	- bool secondLastOnPositive = endGeometry2D->IsAbove(pBeforeLast);
	-
	- onPlane[0] = endCenter[0];
	- onPlane[1] = endCenter[1];
	- onPlane[2] = endCenter[2];
	-
	-
	-
	- if(! (lastOnPositive ^ secondLastOnPositive) )
	- {
	- /* endId and endId+1 lie on the same side of the plane, so we need
	- need endId-1 to calculate the intersection with the planar figure.
	- this should exist since we know that the fiber crosses the planar figure*/
	- p = fiberPolyData->GetPoint( pointsInCell[ endId-1 ] );
	- p1[0] = p[0];
	- p1[1] = p[1];
	- p1[2] = p[2];
	-
	-
	- /* endId and endId+1 lie on the same side of the plane
	- so startId is also part of the ROI*/
	-
	- double *end = fiberPolyData->GetPoint( pointsInCell[endId] );
	- points->InsertNextPoint(end);
	- polyLine->GetPointIds()->InsertId(lineIndex,pointIndex);
	- lineIndex++;
	- pointIndex++;
	- }
	-
	- d = ( (onPlane-p0)normal) / ( (p0-p1) normal );
	-
	- newPoint = (p0-p1);
	-
	- newPoint[0] = d*newPoint[0] + p0[0];
	- newPoint[1] = d*newPoint[1] + p0[1];
	- newPoint[2] = d*newPoint[2] + p0[2];
	-
	-
	- insertPoint[0] = newPoint[0];
	- insertPoint[1] = newPoint[1];
	- insertPoint[2] = newPoint[2];
	-
	-
	-
	- //Insert the Last Point (intersection with the end roi)
	- points->InsertNextPoint(insertPoint);
	- polyLine->GetPointIds()->InsertId(lineIndex,pointIndex);
	- lineIndex++;
	- pointIndex++;
	-
	-
	-
	- }
	-
	-
	- // add polyline to vtk cell array
	- cells->InsertNextCell(polyLine);
	-
	- }
	-
	-
	- // Add the points to the dataset
	- polyData->SetPoints(points);
	-
	- // Add the lines to the dataset
	- polyData->SetLines(cells);
	-
	- mitk::FiberBundle::Pointer cutBundle = mitk::FiberBundle::New(polyData);
	-
	-
	- mitk::DataNode::Pointer cutNode = mitk::DataNode::New();
	- cutNode->SetData(cutBundle);
	- std::string name = "fiberCut";
	- cutNode->SetName(name);
	- GetDataStorage()->Add(cutNode);
	-
	-
	-
	-}
	-
	-
	-void QmitkTractbasedSpatialStatisticsView::CreateRoi()
	-{
	- bool ok;
	- double threshold = QInputDialog::getDouble(m_Controls->m_CreateRoi, tr("Set an FA threshold"),
	- tr("Threshold:"), 0.2, 0.0, 1.0, 2, &ok);
	-
	- if(!ok)
	- return;
	-
	- mitk::Image::Pointer image;
	-
	- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
	-
	- for (auto node: nodes)
	- {
	- if(QString("Image").compare(node->GetData()->GetNameOfClass())==0)
	- {
	- mitk::Image* img = static_cast<mitk::Image*>(node->GetData());
	- if(img->GetDimension() == 3)
	- {
	- image = img;
	- }
	- }
	- }
	-
	- if(image.IsNull())
	- {
	- return;
	- }
	-
	- mitk::TractAnalyzer analyzer;
	- analyzer.SetInputImage(image);
	- analyzer.SetThreshold(threshold);
	-
	- m_PointSetNode = this->m_Controls->m_PointWidget->GetPointSet();
	-
	- // Set Pointset to analyzer
	- analyzer.SetPointSet(m_PointSetNode);
	-
	- // Run Analyzer
	- try
	- {
	- analyzer.MakeRoi();
	- }
	- catch (const mitk::Exception& e)
	- {
	- QMessageBox msgBox;
	- msgBox.setText(QString::fromStdString(e.what()));
	- msgBox.exec();
	- }
	-
	- // Obtain tbss roi image from analyzer
	- mitk::TbssRoiImage::Pointer tbssRoi = analyzer.GetRoiImage();
	-
	- tbssRoi->SetStructure(m_Controls->m_Structure->text().toStdString());
	-
	- // get path description and set to interface
	- std::string pathDescription = analyzer.GetPathDescription();
	- m_Controls->m_PathTextEdit->setPlainText(QString(pathDescription.c_str()));
	-
	-
	- // Add roi image to datastorage
	- AddTbssToDataStorage(tbssRoi, m_Controls->m_RoiName->text().toStdString());
	-
	-
	-
	-
	-}
	-
	-void QmitkTractbasedSpatialStatisticsView::PlotFiber4D(mitk::TbssImage* image,
	- mitk::FiberBundle* fib,
	- mitk::DataNode* startRoi,
	- mitk::DataNode* endRoi)
	-{
	-
	-
	- if(m_Controls->m_TabWidget->currentWidget() == m_Controls->m_MeasureTAB)
	- {
	- m_CurrentGeometry = image->GetGeometry();
	-
	- m_Controls->m_RoiPlotWidget->SetGroups(image->GetGroupInfo());
	- m_Controls->m_RoiPlotWidget->SetProjections(image->GetImage());
	- m_Controls->m_RoiPlotWidget->SetMeasure( image->GetMeasurementInfo() );
	- m_Controls->m_RoiPlotWidget->PlotFiber4D(image, fib, startRoi, endRoi, m_Controls->m_Segments->value());
	- }
	-
	-
	-}
	-
	-void QmitkTractbasedSpatialStatisticsView:: PlotFiberBundle(mitk::FiberBundle fib, mitk::Image img,
	- mitk::DataNode* startRoi, mitk::DataNode* endRoi)
	-{
	- bool avg = m_Controls->m_Average->isChecked();
	- int segments = m_Controls->m_Segments->value();
	- m_Controls->m_RoiPlotWidget->PlotFiberBetweenRois(fib, img, startRoi ,endRoi, avg, segments);
	- m_Controls->m_RoiPlotWidget->SetPlottingFiber(true);
	- mitk::RenderingManager::GetInstance()->ForceImmediateUpdateAll();
	-}
	-
	-
	-void QmitkTractbasedSpatialStatisticsView::Plot(mitk::TbssImage* image, mitk::TbssRoiImage* roiImage)
	-{
	- if(m_Controls->m_TabWidget->currentWidget() == m_Controls->m_MeasureTAB)
	- {
	-
	- std::vector< itk::Index<3> > roi = roiImage->GetRoi();
	- m_Roi = roi;
	- m_CurrentGeometry = image->GetGeometry();
	-
	-
	- std::string structure = roiImage->GetStructure();
	-
	- m_Controls->m_RoiPlotWidget->SetGroups(image->GetGroupInfo());
	- m_Controls->m_RoiPlotWidget->SetProjections(image->GetImage());
	- m_Controls->m_RoiPlotWidget->SetRoi(roi);
	- m_Controls->m_RoiPlotWidget->SetStructure(structure);
	- m_Controls->m_RoiPlotWidget->SetMeasure( image->GetMeasurementInfo() );
	- m_Controls->m_RoiPlotWidget->DrawProfiles();
	- }
	-
	- m_Controls->m_RoiPlotWidget->SetPlottingFiber(false);
	-
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTractbasedSpatialStatisticsView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTractbasedSpatialStatisticsView.h
	deleted file mode 100644
	index eedae2854e..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTractbasedSpatialStatisticsView.h
	+++ /dev/null
	@@ -1,184 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef QmitkTractbasedSpatialStatisticsView_h
	-#define QmitkTractbasedSpatialStatisticsView_h
	-
	-
	-#include <QmitkAbstractView.h>
	-#include <mitkILifecycleAwarePart.h>
	-
	-#include "ui_QmitkTractbasedSpatialStatisticsViewControls.h"
	-#include <QListWidgetItem>
	-
	-#include <itkImageFileReader.h>
	-#include <itkImageFileWriter.h>
	-
	-#include <itkDiffusionTensor3D.h>
	-
	-#include <mitkTbssImage.h>
	-#include <mitkTbssRoiImage.h>
	-
	-#include "QmitkTbssTableModel.h"
	-#include "QmitkTbssMetaTableModel.h"
	-
	-#include <mitkFiberBundle.h>
	-
	-
	-// Image types
	-typedef short DiffusionPixelType;
	-typedef itk::Image<char, 3> CharImageType;
	-typedef itk::Image<unsigned char, 3> UCharImageType;
	-typedef itk::Image<float, 4> Float4DImageType;
	-typedef itk::Image<float, 3> FloatImageType;
	-typedef itk::VectorImage<float, 3> VectorImageType;
	-
	-// Readers/Writers
	-typedef itk::ImageFileReader< CharImageType > CharReaderType;
	-typedef itk::ImageFileReader< UCharImageType > UCharReaderType;
	-typedef itk::ImageFileWriter< CharImageType > CharWriterType;
	-typedef itk::ImageFileReader< FloatImageType > FloatReaderType;
	-typedef itk::ImageFileWriter< FloatImageType > FloatWriterType;
	-typedef itk::ImageFileReader< Float4DImageType > Float4DReaderType;
	-typedef itk::ImageFileWriter< Float4DImageType > Float4DWriterType;
	-
	-
	-
	-/*!
	- * \brief This plugin provides an extension for Tract-based spatial statistics (see Smith et al., 2009. http://dx.doi.org/10.1016/j.neuroimage.2006.02.024)
	- * TBSS enables analyzing the brain by a pipeline of registration, skeletonization, and projection that results in a white matter skeleton
	- * for all subjects that are analyzed statistically in a whole-brain manner.
	- * This plugin provides functionality to select single tracts and analyze them separately.
	- *
	- * Prerequisites: the mean_FA_skeleton and all_FA_skeletonised datasets produced by the FSL TBSS pipeline: http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/tbss/index
	-*/
	-
	-class QmitkTractbasedSpatialStatisticsView : public QmitkAbstractView, public mitk::ILifecycleAwarePart
	-{
	-
	- Q_OBJECT
	-
	- public:
	-
	- static const std::string VIEW_ID;
	-
	- QmitkTractbasedSpatialStatisticsView();
	- virtual ~QmitkTractbasedSpatialStatisticsView();
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	-
	- /// \brief Creation of the connections of main and control widget
	- virtual void CreateConnections();
	-
	- ///
	- /// Sets the focus to an internal widget.
	- ///
	- virtual void SetFocus() override;
	-
	- /// \brief Called when the view gets activated
	- virtual void Activated() override;
	-
	- /// \brief Called when the view gets deactivated
	- virtual void Deactivated() override;
	-
	- bool IsActivated() const;
	-
	- /// \brief Called when the view gets visible
	- virtual void Visible() override;
	-
	- /// \brief Called when the view gets hidden
	- virtual void Hidden() override;
	-
	- protected slots:
	-
	- // Creates Roi
	- void CreateRoi();
	-
	- void Clicked(const QPointF& pos);
	-
	- // Import of FSL TBSS data
	- void TbssImport();
	-
	- // Add a group as metadata. This metadata is required by the plotting functionality
	- void AddGroup();
	-
	- // Remove a group
	- void RemoveGroup();
	-
	- // Copies the values displayed in the plot widget to clipboard, i.e. exports the data
	- void CopyToClipboard();
	-
	- // Method to cut away parts of fiber bundles that should not be plotted.
	- void Cut();
	-
	- // Adjust plot widget
	- void PerformChange();
	-
	-
	- protected:
	-
	-
	- /// \brief called by QmitkAbstractView when DataManager's selection has changed
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- // Creates a plot using a 4D image containing the projections of all subjects and a region of interest
	- void Plot(mitk::TbssImage, mitk::TbssRoiImage);
	-
	-
	- void PlotFiberBundle(mitk::FiberBundle* fib, mitk::Image* img, mitk::DataNode* startRoi=nullptr, mitk::DataNode* endRoi=nullptr);
	-
	-
	- void PlotFiber4D(mitk::TbssImage, mitk::FiberBundle fib, mitk::DataNode startRoi=nullptr, mitk::DataNode endRoi=nullptr);
	-
	- // Create a point set. This point set defines the points through which a region of interest should go
	- void InitPointsets();
	-
	- // Pointset and DataNode to contain the PointSet used in ROI creation
	- mitk::PointSet::Pointer m_PointSetNode;
	- mitk::DataNode::Pointer m_P1;
	-
	- // GUI widgets
	- Ui::QmitkTractbasedSpatialStatisticsViewControls* m_Controls;
	-
	- // Used to save the region of interest in a vector of itk::index.
	- std::vector< itk::Index<3> > m_Roi;
	-
	- mitk::FiberBundle* m_Fib;
	-
	- mitk::BaseGeometry* m_CurrentGeometry;
	-
	- // A table model for saving group information in a name,number pair.
	- QmitkTbssTableModel* m_GroupModel;
	-
	- // Convenience function for adding a new image to the datastorage and giving it a name.
	- void AddTbssToDataStorage(mitk::Image* image, std::string name);
	-
	- mitk::DataNode::Pointer m_CurrentFiberNode; // needed for the index property when interacting with the plot widget
	-
	- // needed when a plot should only show values between a start end end roi
	- mitk::DataNode::Pointer m_CurrentStartRoi;
	- mitk::DataNode::Pointer m_CurrentEndRoi;
	-
	-private:
	-
	- bool m_Activated;
	-
	-};
	-
	-
	-
	-#endif // _QMITKTRACTBASEDSPATIALSTATISTICSVIEW_H_INCLUDED
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTractbasedSpatialStatisticsViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTractbasedSpatialStatisticsViewControls.ui
	deleted file mode 100644
	index 2fe7b197fa..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/QmitkTractbasedSpatialStatisticsViewControls.ui
	+++ /dev/null
	@@ -1,474 +0,0 @@
	-<?xml version="1.0" encoding="utf-8"?>
	-<ui version="4.0">
	- <class>QmitkTractbasedSpatialStatisticsViewControls</class>
	- <widget class="QWidget" name="QmitkTractbasedSpatialStatisticsViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>265</width>
	- <height>811</height>
	- </rect>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="windowTitle">
	- <string>QmitkTemplate</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QVBoxLayout" name="verticalLayout_5">
	- <item>
	- <widget class="QGroupBox" name="m_ImportGroupBox">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="title">
	- <string>FSL import Subject Data</string>
	- </property>
	- <property name="checkable">
	- <bool>false</bool>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- <layout class="QVBoxLayout" name="verticalLayout_4">
	- <item>
	- <widget class="QFrame" name="frame_7">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QHBoxLayout" name="horizontalLayout_4">
	- <property name="margin">
	- <number>0</number>
	- </property>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <widget class="QFrame" name="frame_6">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QHBoxLayout" name="horizontalLayout_2">
	- <item>
	- <widget class="QTableView" name="m_GroupInfo">
	- <property name="toolTip">
	- <string>Group information</string>
	- </property>
	- <property name="selectionBehavior">
	- <enum>QAbstractItemView::SelectRows</enum>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QFrame" name="frame_5">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="maximumSize">
	- <size>
	- <width>110</width>
	- <height>100</height>
	- </size>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QVBoxLayout" name="verticalLayout_2">
	- <item>
	- <widget class="QPushButton" name="m_AddGroup">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="toolTip">
	- <string>Add group entry. After that give the group a name and the correct number</string>
	- </property>
	- <property name="text">
	- <string>Add</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QPushButton" name="m_RemoveGroup">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="toolTip">
	- <string>Remove selected entries</string>
	- </property>
	- <property name="text">
	- <string>Remove</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QPushButton" name="m_ImportFsl">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="toolTip">
	- <string>Import a 4D image containing group data after group information has been set</string>
	- </property>
	- <property name="text">
	- <string>Import data</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <widget class="QFrame" name="frame">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::StyledPanel</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QHBoxLayout" name="horizontalLayout_3">
	- <item>
	- <widget class="QLabel" name="label_2">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="text">
	- <string>Measure</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QLineEdit" name="m_MeasurementInfo">
	- <property name="toolTip">
	- <string>Measurement in the to be imported 4D image</string>
	- </property>
	- <property name="text">
	- <string>FA</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <widget class="QGroupBox" name="m_Workspace">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="title">
	- <string>Tract-specific analysis</string>
	- </property>
	- <layout class="QVBoxLayout" name="verticalLayout">
	- <item>
	- <widget class="QTabWidget" name="m_TabWidget">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="toolTip">
	- <string>To create a roi first load a tbss meta image into the datamanager</string>
	- </property>
	- <property name="currentIndex">
	- <number>0</number>
	- </property>
	- <widget class="QWidget" name="m_RoiTab">
	- <attribute name="title">
	- <string>ROIs</string>
	- </attribute>
	- <layout class="QFormLayout" name="formLayout">
	- <item row="2" column="0">
	- <widget class="QLabel" name="label">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="text">
	- <string>Points on Roi</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QmitkPointListWidget" name="m_PointWidget" native="true">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
	- <horstretch>100</horstretch>
	- <verstretch>100</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>100</height>
	- </size>
	- </property>
	- <property name="toolTip">
	- <string>Use this widget to create points on the ROI by shift-leftclick on the right positions on the skeleton. Then click Create Roi. The Roi that will be created will pass through the points in the order of occurence in this list</string>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QPushButton" name="m_CreateRoi">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="toolTip">
	- <string>No suitable tbss meta image selected yet. The meta image needs to contain a mean FA skeleton and a skeleton mask</string>
	- </property>
	- <property name="text">
	- <string>Create ROI</string>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="1">
	- <widget class="QPlainTextEdit" name="m_PathTextEdit">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="toolTip">
	- <string>Points on the ROI</string>
	- </property>
	- </widget>
	- </item>
	- <item row="6" column="0">
	- <widget class="QLabel" name="label_3">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="text">
	- <string>Name</string>
	- </property>
	- </widget>
	- </item>
	- <item row="6" column="1">
	- <widget class="QLineEdit" name="m_RoiName">
	- <property name="toolTip">
	- <string>Give a name to the region of interest</string>
	- </property>
	- <property name="text">
	- <string>roiname</string>
	- </property>
	- </widget>
	- </item>
	- <item row="8" column="0">
	- <widget class="QLabel" name="label_4">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="text">
	- <string>Structure info</string>
	- </property>
	- </widget>
	- </item>
	- <item row="8" column="1">
	- <widget class="QLineEdit" name="m_Structure">
	- <property name="toolTip">
	- <string>On what anatomical structure lies the ROI?</string>
	- </property>
	- <property name="text">
	- <string>Structure</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_TbssImageLabel">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="toolTip">
	- <string>current selection</string>
	- </property>
	- <property name="text">
	- <string>mean FA skeleton:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <spacer name="horizontalSpacer">
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>253</width>
	- <height>20</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- </layout>
	- </widget>
	- <widget class="QWidget" name="m_MeasureTAB">
	- <attribute name="title">
	- <string>Measuring</string>
	- </attribute>
	- <layout class="QVBoxLayout" name="verticalLayout_3">
	- <item>
	- <widget class="QWidget" name="widget" native="true">
	- <property name="maximumSize">
	- <size>
	- <width>16777215</width>
	- <height>50</height>
	- </size>
	- </property>
	- <layout class="QHBoxLayout" name="horizontalLayout">
	- <item>
	- <widget class="QLabel" name="m_SegmentLabel">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="text">
	- <string>#segments</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QSpinBox" name="m_Segments">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="maximum">
	- <number>100</number>
	- </property>
	- <property name="value">
	- <number>25</number>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QCheckBox" name="m_Average">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="text">
	- <string>Average</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QPushButton" name="m_Cut">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="text">
	- <string>Cut</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <widget class="QmitkTbssRoiAnalysisWidget" name="m_RoiPlotWidget" native="true">
	- <property name="toolTip">
	- <string>To plot, load a tbss image with subject information and a region of interest corresponding to the study and select them both</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QPushButton" name="m_Clipboard">
	- <property name="text">
	- <string>Copy to clipboard</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <layoutdefault spacing="6" margin="11"></layoutdefault>
	- <customwidgets>
	- <customwidget>
	- <class>QmitkPointListWidget</class>
	- <extends>QWidget</extends>
	- <header location="global">QmitkPointListWidget.h</header>
	- </customwidget>
	- <customwidget>
	- <class>QmitkTbssRoiAnalysisWidget</class>
	- <extends>QWidget</extends>
	- <header>QmitkTbssRoiAnalysisWidget.h</header>
	- <container>1</container>
	- </customwidget>
	- </customwidgets>
	- <resources></resources>
	- <connections></connections>
	-</ui>
	\ No newline at end of file
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/mitkPluginActivator.cpp
	deleted file mode 100644
	index ca8680a525..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/mitkPluginActivator.cpp
	+++ /dev/null
	@@ -1,40 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkPluginActivator.h"
	-
	-#include "src/internal/QmitkTractbasedSpatialStatisticsView.h"
	-#include "src/internal/QmitkTbssSkeletonizationView.h"
	-
	-ctkPluginContext* mitk::PluginActivator::m_Context = nullptr;
	-
	-ctkPluginContext* mitk::PluginActivator::GetContext()
	-{
	- return m_Context;
	-}
	-
	-void mitk::PluginActivator::start(ctkPluginContext* context)
	-{
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkTractbasedSpatialStatisticsView, context)
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkTbssSkeletonizationView, context)
	- m_Context = context;
	-}
	-
	-void mitk::PluginActivator::stop(ctkPluginContext* context)
	-{
	- Q_UNUSED(context)
	- m_Context = nullptr;
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/mitkPluginActivator.h b/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/mitkPluginActivator.h
	deleted file mode 100644
	index 26b5989119..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tbss/src/internal/mitkPluginActivator.h
	+++ /dev/null
	@@ -1,40 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef MITKPLUGINACTIVATOR_H
	-#define MITKPLUGINACTIVATOR_H
	-
	-#include <ctkPluginActivator.h>
	-
	-namespace mitk
	-{
	- class PluginActivator : public QObject, public ctkPluginActivator
	- {
	- Q_OBJECT
	- Q_PLUGIN_METADATA(IID "org.mitk.gui.qt.diffusionimaging.tbss")
	- Q_INTERFACES(ctkPluginActivator)
	-
	- public:
	- static ctkPluginContext* GetContext();
	-
	- void start(ctkPluginContext* context) override;
	- void stop(ctkPluginContext* context) override;
	-
	- private:
	- static ctkPluginContext* m_Context;
	- };
	-}
	-
	-#endif
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/CMakeLists.txt
	deleted file mode 100644
	index 095d4e206a..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/CMakeLists.txt
	+++ /dev/null
	@@ -1,11 +0,0 @@
	-# The project name must correspond to the directory name of your plug-in
	-# and must not contain periods.
	-project(org_mitk_gui_qt_diffusionimaging_tractography)
	-
	-mitk_create_plugin(
	- SUBPROJECTS MITK-DTI
	- EXPORT_DIRECTIVE DIFFUSIONIMAGING_TRACTOGRAPHY_EXPORT
	- EXPORTED_INCLUDE_SUFFIXES src
	- MODULE_DEPENDS MitkFiberTracking
	- PACKAGE_DEPENDS Vigra HDF5
	-)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/UserManual/QmitkGibbsTrackingViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/UserManual/QmitkGibbsTrackingViewUserManual.dox
	deleted file mode 100644
	index 802ad0d4d5..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/UserManual/QmitkGibbsTrackingViewUserManual.dox
	+++ /dev/null
	@@ -1,38 +0,0 @@
	-/**
	-\page org_mitk_views_gibbstracking Global Gibbs Tractography
	-
	-This view provides the user interface for the global Gibbs tractography algorithm, a global fiber tracking algorithm, originally proposed by Reisert et.al. [1].
	-
	-The corresponding comman line application is named "MitkGlobalTractography".
	-
	-\tableofcontents
	-
	-\section QmitkGibbsTrackingUserManualInputData Input Data
	-
	-Mandatory Input:
	-\li One ODF or tensor image selected in the datamanager
	-
	-Optional Input:
	-\li Mask Image: White matter probability mask. Corresponds to the probability to generate fiber segments in the respective voxel.
	-
	-\section QmitkGibbsTrackingUserManualParameters Parameters
	-
	-\li Number of iterations: More iterations causes the algorithm to be more stable but also to take longer to finish the tracking. Recommended: minimum 10^8 iterations for full brain tractography.
	-\li Particle length/width/weight controlling the contribution of each particle to the model M
	-\li Start and end temperature controlling how fast the process reaches a stable state. (usually no change needed)
	-\li Weighting between the internal (affinity of the model to long and straigt fibers) and external energy (affinity of the model towards the data). (usually no change needed).
	-\li Minimum fiber length constraint (in mm). Shorter fibers are discarded after the tracking.
	-
	-The automatic selection of parameters for the particle length/width and weight are determined directly from the input image using information about the image spacing and GFA.
	-
	-\section QmitkGibbsTrackingUserManualTrackingSurveillance Surveilance of the tracking process
	-
	-Once started, the tracking can be monitored via the textual output that informs about the tracking progress and several stats of the current state of the algorithm.
	-If enabled, the intermediate tracking results are displayed in the renderwindows each second. This live visualization should usually be disabled for performance reasons. It can be turned on and off during the tracking process via the according checkbox. The button next to this checkbox allows the visualization of only the next iteration step.
	-
	-\section QmitkGibbsTrackingUserManualReferences References
	-
	-[1] Reisert, M., Mader, I., Anastasopoulos, C., Weigel, M., Schnell, S., Kiselev, V.: Global fiber reconstruction becomes practical. Neuroimage 54 (2011) 955-962
	-
	-
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/UserManual/QmitkMLBTViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/UserManual/QmitkMLBTViewUserManual.dox
	deleted file mode 100644
	index 018dd3b0e5..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/UserManual/QmitkMLBTViewUserManual.dox
	+++ /dev/null
	@@ -1,22 +0,0 @@
	-/**
	-\page org_mitk_views_mlbtview Machine Learning Based Streamline Tractography
	-
	-This view provides a user interface to train random-forest classifiers used for machine learning based tractography tractography [1]. The corresponding command line application is named "MitkRfTraining".
	-Tractography with the trained classifier can be performed using the "Streamline Tractography View".
	-
	-\section MlbstUserManualTraining Training
	-
	-Parameters:
	-
	-\li Num. Trees: Number of trees that constitute the random forest. The default of 30 works well for most cases.
	-\li Max. Depth: Maximum tree depth.
	-\li Sample Fraction: Fraction of randomly drawn samples used to train each tree.
	-\li Non-WM Sampling Points: Number of randomly placed sampling points in each non-white-matter voxel. These sampling points are needed to train the classifier for non-fiber tissue.
	-\li Fiber Sampling: The fibers are resampled equidistantly. This influences the number of white-matter sampling ponts. Defaul is 0.5*min. voxel size.
	-
	-
	-\section MlbstUserManualReferences References
	-
	-[1] Neher, Peter F., Marc-Alexandre Côté, Jean-Christophe Houde, Maxime Descoteaux, and Klaus H. Maier-Hein. “Fiber Tractography Using Machine Learning.” NeuroImage. Accessed July 17, 2017. doi:10.1016/j.neuroimage.2017.07.028.
	-
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/UserManual/QmitkStreamlineTrackingViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/UserManual/QmitkStreamlineTrackingViewUserManual.dox
	deleted file mode 100644
	index 6cc4616fd8..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/UserManual/QmitkStreamlineTrackingViewUserManual.dox
	+++ /dev/null
	@@ -1,105 +0,0 @@
	-/**
	-\page org_mitk_views_streamlinetracking Streamline Tractography
	-
	-This view enables streamline tractography on various input data. The corresponding command line application is named "MitkStreamlineTractography".
	-
	-Available sections:
	-- \ref StrTrackUserManualInputData
	-- \ref StrTrackUserManualSeeding
	-- \ref StrTrackUserManualConstraints
	-- \ref StrTrackUserManualParameters
	-- \ref StrTrackUserManualNeighbourhoodSampling
	-- \ref StrTrackUserManualDataHandling
	-- \ref StrTrackUserManualPostprocessing
	-- \ref StrTrackUserManualReferences
	-
	-\section StrTrackUserManualInputData Input Data
	-
	-Select the data you want to track on in the datamanager. Supported file types are:
	-- One or multiple DTI images selected in the datamanager.
	-- One ODF image, e.g. obtained using MITK Q-ball reconstruction or MRtrix CSD (tractography similar to [6]).
	-- One peak image (4D float image).
	-- One raw diffusion-weighted image for machine learning based tractography [1].
	--- Tractography Forest: Needed for machine learning based tractography [1].
	-
	-\section StrTrackUserManualSeeding Seeding
	-
	-Specify how, where and how many tractography seed points are placed. This can be either done statically using a seed image or in an interactive fashion. Interactive tractography enables the dynamic placement of spherical seed regions simply by clicking into the image (similar to [5]).
	-
	-Image based seeding:
	-- Seed Image: ROI image used to define the seed voxels. If no seed mask is specified, the whole image volume is seeded.
	-- Seeds per voxel: If set to 1, the seed is defined as the voxel center. If > 1 the seeds are distributet randomly inside the voxel.
	-
	-Interactive seeding:
	-- Update on Parameter Change: When "Update on Parameter Change" is checked, each parameter change causes an instant retracking with the new parameters. This enables an intuitive exploration of the effects that the other tractography parameters have on the resulting tractogram.
	-- Radius: Radius of the manually placed spherical seed region.
	-- Num.Seeds: Number of seeds placed randomly inside the spherical seed region.
	-
	-Parameters for both seeding modes:
	-- Trials Per Seed: Try each seed N times until a valid streamline is obtained (only for probabilistic tractography).
	-- Max. Num. Fibers: Tractography is stopped after the desired number of fibers is reached, even before all seed points are processed.
	-
	-\section StrTrackUserManualConstraints ROI Constraints
	-
	-Specify various ROI and mask images to constrain the tractography process.
	-
	-- Mask Image: ROI image used to constrain the generated streamlines, typically a brain mask. Streamlines that leave the regions defined in this image will stop immediately.
	-- Stop ROI Image: ROI image used to define stopping regions. Streamlines that enter the regions defined in this image will stop immediately.
	-- Exclusion ROI Image: Fibers that enter a region defined in this image will be discarded.
	-- Endpoint Constraints: Determines which fibers are accepted based on their endpoint location. Options are:
	- - No constraints on endpoint locations (command line option NONE)
	- - Both EPs are required to be located in the target image (command line option EPS_IN_TARGET)
	- - Both EPs are required to be located in the target image and the image values at the respective position needs to be distinct (command line option EPS_IN_TARGET_LABELDIFF)
	- - One EP is required to be located in the seed image and one in the target image (command line option EPS_IN_SEED_AND_TARGET)
	- - At least one EP is required to be located in the target image (command line option MIN_ONE_EP_IN_TARGET)
	- - Exactly one EP is required to be located in the target image (command line option ONE_EP_IN_TARGET)
	- - No EP is allowed to be located in the target image (command line option NO_EP_IN_TARGET)
	-- Target Image: ROI image needed for endpoint constraints.
	-
	-\section StrTrackUserManualParameters Tractography Parameters
	-
	-- Mode: Toggle between deterministic and probabilistic tractography (also affects tracking prior proposals). The probabilistic method simply samples the output direction from the discrete probability ditribution provided by the discretized ODF. Probabilistic peak tracking does not derive probabilities from the data but simply adds a normally distributed jitter to the proposed direction.
	-- Sharpen ODFs: If you are using dODF images as input, it is advisable to sharpen the ODFs (min-max normalize and raise to the power of 4). This is not necessary (and not recommended) for CSD fODFs, since they are naturally much sharper.
	-- Cutoff: If the streamline reaches a position with an FA value or peak magnitude lower than the speciefied threshold, tracking is terminated. Typical values are 0.2 for FA/GFA and 0.1 for CSD peaks.
	-- FA/GFA image used to determine streamline termination. If no image is specified, the FA/GFA image is automatically calculated from the input image. If multiple tensor images are used as input, it is recommended to provide such an image since the FA maps calculated from the individual input tensor images can not provide a suitable termination criterion.
	-- ODF Cutoff: Additional threshold on the ODF magnitude. This is useful in case of CSD fODF tractography. For fODFs a good default value is 0.1, for normalized dODFs, e.g. Q-ball ODFs, this threshold should be very low (0.00025) or 0.
	-- Step Size: The algorithm proceeds along the streamline with a fixed stepsize. Default is 0.5*minSpacing.
	-- Min. Tract Length: Shorter fibers are discarded.
	-- Max. Tract Length: Longer fibers are discarded.
	-- Angular Threshold: Maximum angle between two successive steps (in degree). Default is 90° * step_size. For probabilistic tractography, candidate directions exceeding this threshold have probability 0, i.e. the respective ODF value is set to zero. The probabilities of the valid directions are normalized to sum to 1.
	-- Loop Check: Stop streamline if the threshold on the angular stdev over the last 4 voxel lengths is exceeded. -1 = no loop check.
	-- f and g values to balance between FACT [2] and TEND [3,4] tracking (only for tensor based tractography). For further information please refer to [2,3]
	-- Peak Jitter: Used for probabilistic peak tractography. Since no probability are provided by the data, a gausian jitter is added to the peaks. The value influences the standard deviataion of the gaussian (dir[i] += normal(0, peak_jitter*\|dir[i]\|)).
	-
	-\section StrTrackUserManualTractographyPrior Tractography Prior
	-It is possible to use a peak image as prior for tractography on arbitrary other input images. The local progression direction is determined as the weighted average between the direction obtained from the prior and the input data.
	-- Weight: Weighting factor between prior and input data directions. A weight of zero means that no prior iformation is used. With a weight of one, tractography is performed directly on the prior directions itself.
	-- Restrict to Prior: The prior image is used as tractography mask. Voxels without prior peaks are excluded.
	-- New Directions from Prior: By default, the prior is used even if there is no valid direction found in the data. If unchecked, the prior cannot create directions where there are none in the data.
	-- Flip directions: Internally flips prior directions. This might be necessary depending on the input data.
	-
	-\section StrTrackUserManualDataHandling Data Handling
	-- Flip directions: Internally flips progression directions. This might be necessary depending on the input data.
	-- Interpolate Tractography Data: Trilinearly interpolate the input image used for tractography.
	-- Interpolate ROI Images: Trilinearly interpolate the ROI images used to constrain the tractography.
	-
	-\section StrTrackUserManualNeighbourhoodSampling Neighbourhood Sampling (for details see [1])
	-- Neighborhood Samples: Number of neighborhood samples that are used to determine the next fiber progression direction.
	-- Sampling Distance: Distance of the sampling positions from the current streamline position (in voxels).
	-- Use Only Frontal Samples: Only neighborhood samples in front of the current streamline position are considered.
	-- Use Stop-Votes: If checked, the majority of sampling points has to place a stop-vote for the streamline to terminate. If not checked, all sampling positions have to vote for a streamline termination.
	-
	-\section StrTrackUserManualPostprocessing Output and Postprocessing
	-- Compress Fibers: Whole brain tractograms obtained with a small step size can contain billions of points. The tractograms can be compressed by removing points that do not really contribute to the fiber shape, such as many points on a straight line. An error threshold (in mm) can be defined to specify which points should be removed and which not.
	-- Output Probability Map: No streamline are generated. Instead, the tractography outputs a visitation-count map that indicates the probability of a fiber to reach a voxel from the selected seed region. For this measure to be sensible, the number of seeds per voxel needs to be rather large.
	-
	-\section StrTrackUserManualReferences References
	-
	-[1] Neher, Peter F., Marc-Alexandre Côté, Jean-Christophe Houde, Maxime Descoteaux, and Klaus H. Maier-Hein. “Fiber Tractography Using Machine Learning.” NeuroImage. Accessed July 19, 2017. doi:10.1016/j.neuroimage.2017.07.028.\n
	-[2] Mori, Susumu, Walter E. Kaufmann, Godfrey D. Pearlson, Barbara J. Crain, Bram Stieltjes, Meiyappan Solaiyappan, and Peter C. M. Van Zijl. “In Vivo Visualization of Human Neural Pathways by Magnetic Resonance Imaging.” Annals of Neurology 47 (2000): 412–414.\n
	-[3] Weinstein, David, Gordon Kindlmann, and Eric Lundberg. “Tensorlines: Advection-Diffusion Based Propagation through Diffusion Tensor Fields.” In Proceedings of the Conference on Visualization’99: Celebrating Ten Years, 249–253, n.d.\n
	-[4] Lazar, Mariana, David M. Weinstein, Jay S. Tsuruda, Khader M. Hasan, Konstantinos Arfanakis, M. Elizabeth Meyerand, Benham Badie, et al. “White Matter Tractography Using Diffusion Tensor Deflection.” Human Brain Mapping 18, no. 4 (2003): 306–321.\n
	-[5] Chamberland, M., K. Whittingstall, D. Fortin, D. Mathieu, and M. Descoteaux. “Real-Time Multi-Peak Tractography for Instantaneous Connectivity Display.” Front Neuroinform 8 (2014): 59. doi:10.3389/fninf.2014.00059.\n
	-[6] Tournier, J-Donald, Fernando Calamante, and Alan Connelly. “MRtrix: Diffusion Tractography in Crossing Fiber Regions.” International Journal of Imaging Systems and Technology 22, no. 1 (March 2012): 53–66. doi:10.1002/ima.22005.
	-
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/doxygen/modules.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/doxygen/modules.dox
	deleted file mode 100644
	index bbce5ff8e2..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/doxygen/modules.dox
	+++ /dev/null
	@@ -1,16 +0,0 @@
	-/**
	- \defgroup org_mitk_gui_qt_diffusionimaging_tractography org.mitk.gui.qt.diffusionimaging.tractography
	- \ingroup MITKPlugins
	-
	- \brief This is the diffusionimaging.tractography plugin.
	-
	-*/
	-
	-/**
	- \defgroup org_mitk_gui_qt_diffusionimaging_tractography_internal Internal
	- \ingroup org_mitk_gui_qt_diffusionimaging_tractography
	-
	- \brief This subcategory includes the internal classes of the org.mitk.gui.qt.diffusionimaging.tractography plugin. Other
	- plugins must not rely on these classes. They contain implementation details and their interface
	- may change at any time. We mean it.
	-*/
	\ No newline at end of file
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/files.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/files.cmake
	deleted file mode 100644
	index b29fbe3471..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/files.cmake
	+++ /dev/null
	@@ -1,51 +0,0 @@
	-set(INTERNAL_CPP_FILES
	- QmitkGibbsTrackingView.cpp
	- QmitkStreamlineTrackingView.cpp
	-
	- Perspectives/QmitkGibbsTractographyPerspective.cpp
	- Perspectives/QmitkStreamlineTractographyPerspective.cpp
	-
	- mitkPluginActivator.cpp
	-)
	-
	-set(UI_FILES
	- src/internal/QmitkGibbsTrackingViewControls.ui
	- src/internal/QmitkStreamlineTrackingViewControls.ui
	-)
	-
	-set(MOC_H_FILES
	- src/internal/mitkPluginActivator.h
	-
	- src/internal/QmitkGibbsTrackingView.h
	- src/internal/QmitkStreamlineTrackingView.h
	-
	- src/internal/Perspectives/QmitkGibbsTractographyPerspective.h
	- src/internal/Perspectives/QmitkStreamlineTractographyPerspective.h
	-)
	-
	-set(CACHED_RESOURCE_FILES
	- plugin.xml
	-
	- resources/tract.png
	- resources/tractogram.png
	- resources/ml_tractography.png
	- resources/download.png
	- resources/right.png
	- resources/stop.png
	- resources/upload.png
	-)
	-
	-set(QRC_FILES
	- resources/QmitkTractography.qrc
	-)
	-
	-
	-set(CPP_FILES )
	-
	-foreach(file ${SRC_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/${file})
	-endforeach(file ${SRC_CPP_FILES})
	-
	-foreach(file ${INTERNAL_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/internal/${file})
	-endforeach(file ${INTERNAL_CPP_FILES})
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/manifest_headers.cmake
	deleted file mode 100644
	index b2dc929af8..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/manifest_headers.cmake
	+++ /dev/null
	@@ -1,5 +0,0 @@
	-set(Plugin-Name "MITK Tractography")
	-set(Plugin-Version "1.0.0")
	-set(Plugin-Vendor "DKFZ, Medical and Biological Informatics")
	-set(Plugin-ContactAddress "http://www.mitk.org")
	-set(Require-Plugin org.mitk.gui.qt.diffusionimaging org.mitk.gui.qt.common)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/plugin.xml b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/plugin.xml
	deleted file mode 100644
	index cff08b366e..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/plugin.xml
	+++ /dev/null
	@@ -1,91 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<?eclipse version="3.0"?>
	-<plugin>
	-
	- <extension point="org.blueberry.ui.views">
	-
	- <view id="org.mitk.views.gibbstracking"
	- name="Global Gibbs Tractography"
	- category="Fiber Tractography"
	- class="QmitkGibbsTrackingView"
	- icon="resources/tractogram.png">
	- <keywordReference id="org.mitk.views.gibbstracking.Keyword"/>
	- </view>
	-
	- <view id="org.mitk.views.streamlinetracking"
	- name="Streamline Tractography"
	- category="Fiber Tractography"
	- class="QmitkStreamlineTrackingView"
	- icon="resources/tract.png">
	- <keywordReference id="org.mitk.views.streamlinetracking.Keyword"/>
	- </view>
	-
	- <view id="org.mitk.views.mlbtview"
	- name="ML-Based Tractography Training"
	- category="Fiber Tractography"
	- class="QmitkMLBTView"
	- icon="resources/ml_tractography.png">
	- <keywordReference id="org.mitk.views.mlbtview.Keyword"/>
	- </view>
	-
	- </extension>
	-
	- <extension point="org.blueberry.ui.keywords">
	-
	- <keyword label="tractography" id="org.mitk.views.gibbstracking.Keyword"/>
	- <keyword label="tracking" id="org.mitk.views.gibbstracking.Keyword"/>
	- <keyword label="fiber" id="org.mitk.views.gibbstracking.Keyword"/>
	- <keyword label="global" id="org.mitk.views.gibbstracking.Keyword"/>
	- <keyword label="gibbs" id="org.mitk.views.gibbstracking.Keyword"/>
	- <keyword label="diffusion" id="org.mitk.views.gibbstracking.Keyword"/>
	-
	- <keyword label="tractography" id="org.mitk.views.streamlinetracking.Keyword"/>
	- <keyword label="tracking" id="org.mitk.views.streamlinetracking.Keyword"/>
	- <keyword label="fiber" id="org.mitk.views.streamlinetracking.Keyword"/>
	- <keyword label="deterministic" id="org.mitk.views.streamlinetracking.Keyword"/>
	- <keyword label="probabilistic" id="org.mitk.views.streamlinetracking.Keyword"/>
	- <keyword label="odf" id="org.mitk.views.streamlinetracking.Keyword"/>
	- <keyword label="peak" id="org.mitk.views.streamlinetracking.Keyword"/>
	- <keyword label="streamline" id="org.mitk.views.streamlinetracking.Keyword"/>
	- <keyword label="tend" id="org.mitk.views.streamlinetracking.Keyword"/>
	- <keyword label="tensorline" id="org.mitk.views.streamlinetracking.Keyword"/>
	- <keyword label="tensorlines" id="org.mitk.views.streamlinetracking.Keyword"/>
	- <keyword label="multi" id="org.mitk.views.streamlinetracking.Keyword"/>
	- <keyword label="tensor" id="org.mitk.views.streamlinetracking.Keyword"/>
	- <keyword label="dti" id="org.mitk.views.streamlinetracking.Keyword"/>
	- <keyword label="diffusion" id="org.mitk.views.streamlinetracking.Keyword"/>
	-
	- <keyword label="tractography" id="org.mitk.views.mlbtview.Keyword"/>
	- <keyword label="tracking" id="org.mitk.views.mlbtview.Keyword"/>
	- <keyword label="fiber" id="org.mitk.views.mlbtview.Keyword"/>
	- <keyword label="machine" id="org.mitk.views.mlbtview.Keyword"/>
	- <keyword label="learning" id="org.mitk.views.mlbtview.Keyword"/>
	- <keyword label="streamline" id="org.mitk.views.mlbtview.Keyword"/>
	- <keyword label="tensor" id="org.mitk.views.mlbtview.Keyword"/>
	- <keyword label="dwi" id="org.mitk.views.mlbtview.Keyword"/>
	- <keyword label="diffusion" id="org.mitk.views.mlbtview.Keyword"/>
	-
	- </extension>
	-
	-
	- <extension point="org.blueberry.ui.perspectives">
	-
	- <perspective id="org.mitk.perspectives.tractography1"
	- name="Global Gibbs Tractography"
	- category="Fiber Tractography"
	- class="QmitkGibbsTractographyPerspective"
	- icon="resources/tractogram.png">
	- <keywordReference id="org.mitk.views.gibbstracking.Keyword"/>
	- </perspective>
	-
	- <perspective id="org.mitk.perspectives.tractography2"
	- name="Streamline Tractography"
	- category="Fiber Tractography"
	- class="QmitkStreamlineTractographyPerspective"
	- icon="resources/tract.png">
	- <keywordReference id="org.mitk.views.streamlinetracking.Keyword"/>
	- </perspective>
	-
	- </extension>
	-
	-</plugin>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/GibbsTracking.png b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/GibbsTracking.png
	deleted file mode 100644
	index 993ad933b8..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/GibbsTracking.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/QmitkTractography.qrc b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/QmitkTractography.qrc
	deleted file mode 100644
	index 4bfc5c2a11..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/QmitkTractography.qrc
	+++ /dev/null
	@@ -1,8 +0,0 @@
	-<RCC>
	- <qresource prefix="/QmitkTractography">
	- <file>upload.png</file>
	- <file>download.png</file>
	- <file>right.png</file>
	- <file>stop.png</file>
	- </qresource>
	-</RCC>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/download.png b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/download.png
	deleted file mode 100644
	index 5949729192..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/download.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/ml_tractography.png b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/ml_tractography.png
	deleted file mode 100644
	index cceac802c9..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/ml_tractography.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/right.png b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/right.png
	deleted file mode 100644
	index 3201e76d25..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/right.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/stop.png b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/stop.png
	deleted file mode 100644
	index 108c60b1a1..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/stop.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/tract.png b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/tract.png
	deleted file mode 100644
	index a98bb20f61..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/tract.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/tractogram.png b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/tractogram.png
	deleted file mode 100644
	index 98df10cf69..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/tractogram.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/upload.png b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/upload.png
	deleted file mode 100644
	index 6abef3f7d7..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/resources/upload.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkGibbsTractographyPerspective.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkGibbsTractographyPerspective.cpp
	deleted file mode 100644
	index d3d530a1cc..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkGibbsTractographyPerspective.cpp
	+++ /dev/null
	@@ -1,48 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkGibbsTractographyPerspective.h"
	-#include "berryIViewLayout.h"
	-
	-void QmitkGibbsTractographyPerspective::CreateInitialLayout(berry::IPageLayout::Pointer layout)
	-{
	- /////////////////////////////////////////////////////
	- // all di-app perspectives should have the following:
	- /////////////////////////////////////////////////////
	-
	- QString editorArea = layout->GetEditorArea();
	-
	- layout->AddStandaloneViewPlaceholder("org.mitk.views.viewnavigatorview", berry::IPageLayout::LEFT, 0.3f, editorArea, false);
	-
	- layout->AddStandaloneView("org.mitk.views.datamanager",
	- false, berry::IPageLayout::LEFT, 0.3f, editorArea);
	-
	- layout->AddStandaloneView("org.mitk.views.controlvisualizationpropertiesview",
	- false, berry::IPageLayout::BOTTOM, .15f, "org.mitk.views.datamanager");
	-
	- berry::IFolderLayout::Pointer left =
	- layout->CreateFolder("org.mbi.diffusionimaginginternal.leftcontrols",
	- berry::IPageLayout::BOTTOM, 0.15f, "org.mitk.views.controlvisualizationpropertiesview");
	-
	- layout->AddStandaloneViewPlaceholder("org.mitk.views.imagenavigator",
	- berry::IPageLayout::BOTTOM, .7f, "org.mbi.diffusionimaginginternal.leftcontrols", false);
	-
	- /////////////////////////////////////////////
	- // here goes the perspective specific stuff
	- /////////////////////////////////////////////
	-
	- left->AddView("org.mitk.views.gibbstracking");
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkGibbsTractographyPerspective.h b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkGibbsTractographyPerspective.h
	deleted file mode 100644
	index 99f2fe0a66..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkGibbsTractographyPerspective.h
	+++ /dev/null
	@@ -1,36 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef QmitkGibbsTractographyPerspective_H_
	-#define QmitkGibbsTractographyPerspective_H_
	-
	-#include <berryIPerspectiveFactory.h>
	-
	-class QmitkGibbsTractographyPerspective : public QObject, public berry::IPerspectiveFactory
	-{
	- Q_OBJECT
	- Q_INTERFACES(berry::IPerspectiveFactory)
	-
	-public:
	-
	- QmitkGibbsTractographyPerspective() {}
	- ~QmitkGibbsTractographyPerspective() {}
	-
	- void CreateInitialLayout(berry::IPageLayout::Pointer layout) override;
	-};
	-
	-#endif /* QmitkGibbsTractographyPerspective_H_ */
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkStreamlineTractographyPerspective.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkStreamlineTractographyPerspective.cpp
	deleted file mode 100644
	index e14766ec2a..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkStreamlineTractographyPerspective.cpp
	+++ /dev/null
	@@ -1,49 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkStreamlineTractographyPerspective.h"
	-#include "berryIViewLayout.h"
	-
	-void QmitkStreamlineTractographyPerspective::CreateInitialLayout(berry::IPageLayout::Pointer layout)
	-{
	- /////////////////////////////////////////////////////
	- // all di-app perspectives should have the following:
	- /////////////////////////////////////////////////////
	-
	- QString editorArea = layout->GetEditorArea();
	-
	- layout->AddStandaloneViewPlaceholder("org.mitk.views.viewnavigatorview", berry::IPageLayout::LEFT, 0.3f, editorArea, false);
	-
	- layout->AddStandaloneView("org.mitk.views.datamanager",
	- false, berry::IPageLayout::LEFT, 0.3f, editorArea);
	-
	- layout->AddStandaloneView("org.mitk.views.controlvisualizationpropertiesview",
	- false, berry::IPageLayout::BOTTOM, .15f, "org.mitk.views.datamanager");
	-
	- berry::IFolderLayout::Pointer left =
	- layout->CreateFolder("org.mbi.diffusionimaginginternal.leftcontrols",
	- berry::IPageLayout::BOTTOM, 0.15f, "org.mitk.views.controlvisualizationpropertiesview");
	-
	- layout->AddStandaloneViewPlaceholder("org.mitk.views.imagenavigator",
	- berry::IPageLayout::BOTTOM, .7f, "org.mbi.diffusionimaginginternal.leftcontrols", false);
	-
	- /////////////////////////////////////////////
	- // here goes the perspective specific stuff
	- /////////////////////////////////////////////
	-
	- left->AddView("org.mitk.views.streamlinetracking");
	- left->AddView("org.mitk.views.segmentation");
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkStreamlineTractographyPerspective.h b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkStreamlineTractographyPerspective.h
	deleted file mode 100644
	index 96ad1825a1..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/Perspectives/QmitkStreamlineTractographyPerspective.h
	+++ /dev/null
	@@ -1,36 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef QmitkStreamlineTractographyPerspective_H_
	-#define QmitkStreamlineTractographyPerspective_H_
	-
	-#include <berryIPerspectiveFactory.h>
	-
	-class QmitkStreamlineTractographyPerspective : public QObject, public berry::IPerspectiveFactory
	-{
	- Q_OBJECT
	- Q_INTERFACES(berry::IPerspectiveFactory)
	-
	-public:
	-
	- QmitkStreamlineTractographyPerspective() {}
	- ~QmitkStreamlineTractographyPerspective() {}
	-
	- void CreateInitialLayout(berry::IPageLayout::Pointer layout) override;
	-};
	-
	-#endif /* QmitkStreamlineTractographyPerspective_H_ */
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkGibbsTrackingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkGibbsTrackingView.cpp
	deleted file mode 100644
	index 71a145ed12..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkGibbsTrackingView.cpp
	+++ /dev/null
	@@ -1,608 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-// Blueberry
	-#include <berryISelectionService.h>
	-#include <berryIWorkbenchWindow.h>
	-
	-// Qmitk
	-#include "QmitkGibbsTrackingView.h"
	-
	-// Qt
	-#include <QMessageBox>
	-#include <QFileDialog>
	-#include <QDir>
	-#include <QTimer>
	-
	-// MITK
	-#include <mitkImageCast.h>
	-#include <mitkImageToItk.h>
	-#include <mitkImageAccessByItk.h>
	-#include <mitkProgressBar.h>
	-#include <mitkIOUtil.h>
	-#include <mitkNodePredicateDataType.h>
	-#include <mitkNodePredicateDimension.h>
	-#include <mitkNodePredicateOr.h>
	-#include <mitkNodePredicateAnd.h>
	-#include <mitkNodePredicateProperty.h>
	-
	-// ITK
	-#include <itkGibbsTrackingFilter.h>
	-#include <itkResampleImageFilter.h>
	-#include <itksys/SystemTools.hxx>
	-
	-// MISC
	-#include <tinyxml.h>
	-
	-
	-
	-
	-QmitkTrackingWorker::QmitkTrackingWorker(QmitkGibbsTrackingView* view)
	- : m_View(view)
	-{
	-}
	-
	-void QmitkTrackingWorker::run()
	-{
	- m_View->m_GlobalTracker = QmitkGibbsTrackingView::GibbsTrackingFilterType::New();
	-
	- m_View->m_GlobalTracker->SetOdfImage(m_View->m_ItkOdfImage);
	- m_View->m_GlobalTracker->SetTensorImage(m_View->m_ItkTensorImage);
	- m_View->m_GlobalTracker->SetMaskImage(m_View->m_MaskImage);
	- m_View->m_GlobalTracker->SetStartTemperature((float)m_View->m_Controls->m_StartTempSlider->value()/100);
	- m_View->m_GlobalTracker->SetEndTemperature((float)m_View->m_Controls->m_EndTempSlider->value()/10000);
	- m_View->m_GlobalTracker->SetIterations(m_View->m_Controls->m_IterationsBox->text().toDouble());
	- m_View->m_GlobalTracker->SetParticleWeight((float)m_View->m_Controls->m_ParticleWeightSlider->value()/10000);
	- m_View->m_GlobalTracker->SetParticleWidth((float)(m_View->m_Controls->m_ParticleWidthSlider->value())/10);
	- m_View->m_GlobalTracker->SetParticleLength((float)(m_View->m_Controls->m_ParticleLengthSlider->value())/10);
	- m_View->m_GlobalTracker->SetInexBalance((float)m_View->m_Controls->m_InExBalanceSlider->value()/10);
	- m_View->m_GlobalTracker->SetMinFiberLength(m_View->m_Controls->m_FiberLengthSlider->value());
	- m_View->m_GlobalTracker->SetCurvatureThreshold(cos((float)m_View->m_Controls->m_CurvatureThresholdSlider->value()*itk::Math::pi/180));
	- m_View->m_GlobalTracker->SetRandomSeed(m_View->m_Controls->m_RandomSeedSlider->value());
	- try{
	- m_View->m_GlobalTracker->Update();
	- }
	- catch( mitk::Exception e )
	- {
	- MITK_ERROR << "Internal error occured: " << e.what() << "\nAborting";
	- }
	- m_View->m_TrackingThread.quit();
	-}
	-
	-const std::string QmitkGibbsTrackingView::VIEW_ID = "org.mitk.views.gibbstracking";
	-
	-QmitkGibbsTrackingView::QmitkGibbsTrackingView()
	- : QmitkAbstractView()
	- , m_Controls( 0 )
	- , m_TrackingNode(nullptr)
	- , m_FiberBundle(nullptr)
	- , m_MaskImage(nullptr)
	- , m_TensorImage(nullptr)
	- , m_OdfImage(nullptr)
	- , m_ItkOdfImage(nullptr)
	- , m_ItkTensorImage(nullptr)
	- , m_ImageNode(nullptr)
	- , m_MaskImageNode(nullptr)
	- , m_FiberBundleNode(nullptr)
	- , m_ThreadIsRunning(false)
	- , m_ElapsedTime(0)
	- , m_GlobalTracker(nullptr)
	- , m_TrackingWorker(this)
	-{
	- m_TrackingWorker.moveToThread(&m_TrackingThread);
	- connect(&m_TrackingThread, SIGNAL(started()), this, SLOT(BeforeThread()));
	- connect(&m_TrackingThread, SIGNAL(started()), &m_TrackingWorker, SLOT(run()));
	- connect(&m_TrackingThread, SIGNAL(finished()), this, SLOT(AfterThread()));
	- m_TrackingTimer = new QTimer(this);
	-}
	-
	-QmitkGibbsTrackingView::~QmitkGibbsTrackingView()
	-{
	- if (m_GlobalTracker.IsNull())
	- return;
	-
	- m_GlobalTracker->SetAbortTracking(true);
	- m_TrackingThread.wait();
	-}
	-
	-// update tracking status and generate fiber bundle
	-void QmitkGibbsTrackingView::TimerUpdate()
	-{
	- UpdateTrackingStatus();
	- GenerateFiberBundle();
	-}
	-
	-// tell global tractography filter to stop after current step
	-void QmitkGibbsTrackingView::StopGibbsTracking()
	-{
	- if (m_GlobalTracker.IsNull())
	- return;
	-
	- m_GlobalTracker->SetAbortTracking(true);
	- m_Controls->m_TrackingStop->setEnabled(false);
	- m_Controls->m_TrackingStop->setText("Stopping Tractography ...");
	- m_TrackingNode = nullptr;
	-}
	-
	-// update gui elements and generate fiber bundle after tracking is finished
	-void QmitkGibbsTrackingView::AfterThread()
	-{
	- m_ThreadIsRunning = false;
	- m_TrackingTimer->stop();
	-
	- UpdateGUI();
	-
	- if( !m_GlobalTracker->GetIsInValidState() )
	- {
	- QMessageBox::critical( nullptr, "Gibbs Tracking", "An internal error occured. Tracking aborted.\n Please check the log for details." );
	- m_FiberBundleNode = nullptr;
	- return;
	- }
	- UpdateTrackingStatus();
	-
	- if(m_Controls->m_ParticleWeightSlider->value()==0)
	- {
	- m_Controls->m_ParticleWeightLabel->setText(QString::number(m_GlobalTracker->GetParticleWeight()));
	- m_Controls->m_ParticleWeightSlider->setValue(m_GlobalTracker->GetParticleWeight()*10000);
	- }
	- if(m_Controls->m_ParticleWidthSlider->value()==0)
	- {
	- m_Controls->m_ParticleWidthLabel->setText(QString::number(m_GlobalTracker->GetParticleWidth()));
	- m_Controls->m_ParticleWidthSlider->setValue(m_GlobalTracker->GetParticleWidth()*10);
	- }
	- if(m_Controls->m_ParticleLengthSlider->value()==0)
	- {
	- m_Controls->m_ParticleLengthLabel->setText(QString::number(m_GlobalTracker->GetParticleLength()));
	- m_Controls->m_ParticleLengthSlider->setValue(m_GlobalTracker->GetParticleLength()*10);
	- }
	-
	- GenerateFiberBundle();
	- m_FiberBundleNode = 0;
	- m_GlobalTracker = 0;
	-
	- // images not needed anymore ( relevant only for computation )
	- // we need to release them to remove the memory access block created through CastToItk<> calls
	- this->m_ItkOdfImage = 0;
	- this->m_ItkTensorImage = 0;
	-}
	-
	-// start tracking timer and update gui elements before tracking is started
	-void QmitkGibbsTrackingView::BeforeThread()
	-{
	- m_ThreadIsRunning = true;
	- m_TrackingTime = QTime::currentTime();
	- m_ElapsedTime = 0;
	- m_TrackingTimer->start(1000);
	-
	- UpdateGUI();
	-}
	-
	-// setup gui elements and signal/slot connections
	-void QmitkGibbsTrackingView::CreateQtPartControl( QWidget *parent )
	-{
	- // build up qt view, unless already done
	- if ( !m_Controls )
	- {
	- // create GUI widgets from the Qt Designer's .ui file
	- m_Controls = new Ui::QmitkGibbsTrackingViewControls;
	- m_Controls->setupUi( parent );
	-
	- AdvancedSettings();
	-
	- connect( m_TrackingTimer, SIGNAL(timeout()), this, SLOT(TimerUpdate()) );
	- connect( m_Controls->m_TrackingStop, SIGNAL(clicked()), this, SLOT(StopGibbsTracking()) );
	- connect( m_Controls->m_TrackingStart, SIGNAL(clicked()), this, SLOT(StartGibbsTracking()) );
	- connect( m_Controls->m_AdvancedSettingsCheckbox, SIGNAL(clicked()), this, SLOT(AdvancedSettings()) );
	- connect( m_Controls->m_SaveTrackingParameters, SIGNAL(clicked()), this, SLOT(SaveTrackingParameters()) );
	- connect( m_Controls->m_LoadTrackingParameters, SIGNAL(clicked()), this, SLOT(LoadTrackingParameters()) );
	- connect( m_Controls->m_ParticleWidthSlider, SIGNAL(valueChanged(int)), this, SLOT(SetParticleWidth(int)) );
	- connect( m_Controls->m_ParticleLengthSlider, SIGNAL(valueChanged(int)), this, SLOT(SetParticleLength(int)) );
	- connect( m_Controls->m_InExBalanceSlider, SIGNAL(valueChanged(int)), this, SLOT(SetInExBalance(int)) );
	- connect( m_Controls->m_FiberLengthSlider, SIGNAL(valueChanged(int)), this, SLOT(SetFiberLength(int)) );
	- connect( m_Controls->m_ParticleWeightSlider, SIGNAL(valueChanged(int)), this, SLOT(SetParticleWeight(int)) );
	- connect( m_Controls->m_StartTempSlider, SIGNAL(valueChanged(int)), this, SLOT(SetStartTemp(int)) );
	- connect( m_Controls->m_EndTempSlider, SIGNAL(valueChanged(int)), this, SLOT(SetEndTemp(int)) );
	- connect( m_Controls->m_CurvatureThresholdSlider, SIGNAL(valueChanged(int)), this, SLOT(SetCurvatureThreshold(int)) );
	- connect( m_Controls->m_RandomSeedSlider, SIGNAL(valueChanged(int)), this, SLOT(SetRandomSeed(int)) );
	- connect( m_Controls->m_OutputFileButton, SIGNAL(clicked()), this, SLOT(SetOutputFile()) );
	-
	- m_Controls->m_InputImageBox->SetDataStorage(this->GetDataStorage());
	- mitk::TNodePredicateDataType<mitk::OdfImage>::Pointer isOdfImagePredicate = mitk::TNodePredicateDataType<mitk::OdfImage>::New();
	- mitk::TNodePredicateDataType<mitk::TensorImage>::Pointer isTensorImagePredicate = mitk::TNodePredicateDataType<mitk::TensorImage>::New();
	- m_Controls->m_InputImageBox->SetPredicate( mitk::NodePredicateOr::New(isOdfImagePredicate, isTensorImagePredicate) );
	-
	- m_Controls->m_MaskImageBox->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_MaskImageBox->SetZeroEntryText("--");
	- mitk::TNodePredicateDataType<mitk::Image>::Pointer isImagePredicate = mitk::TNodePredicateDataType<mitk::Image>::New();
	- mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true));
	- mitk::NodePredicateDimension::Pointer is3D = mitk::NodePredicateDimension::New(3);
	- m_Controls->m_MaskImageBox->SetPredicate( mitk::NodePredicateAnd::New(isBinaryPredicate, mitk::NodePredicateAnd::New(isImagePredicate, is3D)) );
	-
	- connect( (QObject*)(m_Controls->m_MaskImageBox), SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGUI()));
	- connect( (QObject*)(m_Controls->m_InputImageBox), SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGUI()));
	- }
	-}
	-
	-void QmitkGibbsTrackingView::SetFocus()
	-{
	- m_Controls->m_TrackingStart->setFocus();
	-}
	-
	-void QmitkGibbsTrackingView::SetInExBalance(int value)
	-{
	- m_Controls->m_InExBalanceLabel->setText(QString::number((float)value/10));
	-}
	-
	-void QmitkGibbsTrackingView::SetFiberLength(int value)
	-{
	- m_Controls->m_FiberLengthLabel->setText(QString::number(value)+"mm");
	-}
	-
	-void QmitkGibbsTrackingView::SetRandomSeed(int value)
	-{
	- if (value>=0)
	- m_Controls->m_RandomSeedLabel->setText(QString::number(value));
	- else
	- m_Controls->m_RandomSeedLabel->setText("auto");
	-}
	-
	-void QmitkGibbsTrackingView::SetParticleWeight(int value)
	-{
	- if (value>0)
	- m_Controls->m_ParticleWeightLabel->setText(QString::number((float)value/10000));
	- else
	- m_Controls->m_ParticleWeightLabel->setText("auto");
	-}
	-
	-void QmitkGibbsTrackingView::SetStartTemp(int value)
	-{
	- m_Controls->m_StartTempLabel->setText(QString::number((float)value/100));
	-}
	-
	-void QmitkGibbsTrackingView::SetEndTemp(int value)
	-{
	- m_Controls->m_EndTempLabel->setText(QString::number((float)value/10000));
	-}
	-
	-void QmitkGibbsTrackingView::SetParticleWidth(int value)
	-{
	- if (value>0)
	- m_Controls->m_ParticleWidthLabel->setText(QString::number((float)value/10)+" mm");
	- else
	- m_Controls->m_ParticleWidthLabel->setText("auto");
	-}
	-
	-void QmitkGibbsTrackingView::SetParticleLength(int value)
	-{
	- if (value>0)
	- m_Controls->m_ParticleLengthLabel->setText(QString::number((float)value/10)+" mm");
	- else
	- m_Controls->m_ParticleLengthLabel->setText("auto");
	-}
	-
	-void QmitkGibbsTrackingView::SetCurvatureThreshold(int value)
	-{
	- m_Controls->m_CurvatureThresholdLabel->setText(QString::number(value)+"°");
	-}
	-
	-// called if datamanager selection changes
	-void QmitkGibbsTrackingView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /part/, const QList<mitk::DataNode::Pointer>& )
	-{
	- UpdateGUI();
	-}
	-
	-
	-void QmitkGibbsTrackingView::NodeRemoved(const mitk::DataNode * node)
	-{
	- if (m_ThreadIsRunning)
	- {
	- if (node==m_TrackingNode.GetPointer())
	- {
	- StopGibbsTracking();
	- }
	- }
	-}
	-
	-// update gui elements displaying trackings status
	-void QmitkGibbsTrackingView::UpdateTrackingStatus()
	-{
	- if (m_GlobalTracker.IsNull())
	- return;
	-
	- m_ElapsedTime += m_TrackingTime.elapsed()/1000;
	- m_TrackingTime.restart();
	- unsigned long hours = m_ElapsedTime/3600;
	- unsigned long minutes = (m_ElapsedTime%3600)/60;
	- unsigned long seconds = m_ElapsedTime%60;
	-
	- m_Controls->m_ProposalAcceptance->setText(QString::number(m_GlobalTracker->GetProposalAcceptance()*100)+"%");
	-
	- m_Controls->m_TrackingTimeLabel->setText( QString::number(hours)+QString("h ")+QString::number(minutes)+QString("m ")+QString::number(seconds)+QString("s") );
	- m_Controls->m_NumConnectionsLabel->setText( QString::number(m_GlobalTracker->GetNumConnections()) );
	- m_Controls->m_NumParticlesLabel->setText( QString::number(m_GlobalTracker->GetNumParticles()) );
	- m_Controls->m_CurrentStepLabel->setText( QString::number(100*m_GlobalTracker->GetCurrentIteration()/m_GlobalTracker->GetIterations())+"%" );
	- m_Controls->m_AcceptedFibersLabel->setText( QString::number(m_GlobalTracker->GetNumAcceptedFibers()) );
	-}
	-
	-// update gui elements (enable/disable elements and set tooltips)
	-void QmitkGibbsTrackingView::UpdateGUI()
	-{
	- if (!m_ThreadIsRunning && m_Controls->m_InputImageBox->GetSelectedNode().IsNotNull())
	- {
	- m_Controls->m_TrackingStop->setEnabled(false);
	- m_Controls->m_TrackingStart->setEnabled(true);
	- m_Controls->m_LoadTrackingParameters->setEnabled(true);
	- m_Controls->m_IterationsBox->setEnabled(true);
	- m_Controls->m_AdvancedFrame->setEnabled(true);
	- m_Controls->m_TrackingStop->setText("Stop Tractography");
	- m_Controls->m_TrackingStart->setToolTip("Start tractography. No further change of parameters possible.");
	- m_Controls->m_TrackingStop->setToolTip("");
	- m_Controls->m_MaskImageBox->setEnabled(true);
	- m_Controls->m_InputImageBox->setEnabled(true);
	- }
	- else if (!m_ThreadIsRunning)
	- {
	- m_Controls->m_TrackingStop->setEnabled(false);
	- m_Controls->m_TrackingStart->setEnabled(false);
	- m_Controls->m_LoadTrackingParameters->setEnabled(true);
	- m_Controls->m_IterationsBox->setEnabled(true);
	- m_Controls->m_AdvancedFrame->setEnabled(true);
	- m_Controls->m_TrackingStop->setText("Stop Tractography");
	- m_Controls->m_TrackingStart->setToolTip("No ODF image selected.");
	- m_Controls->m_TrackingStop->setToolTip("");
	- m_Controls->m_MaskImageBox->setEnabled(true);
	- m_Controls->m_InputImageBox->setEnabled(true);
	- }
	- else
	- {
	- m_Controls->m_TrackingStop->setEnabled(true);
	- m_Controls->m_TrackingStart->setEnabled(false);
	- m_Controls->m_LoadTrackingParameters->setEnabled(false);
	- m_Controls->m_IterationsBox->setEnabled(false);
	- m_Controls->m_AdvancedFrame->setEnabled(false);
	- m_Controls->m_AdvancedFrame->setVisible(false);
	- m_Controls->m_AdvancedSettingsCheckbox->setChecked(false);
	- m_Controls->m_TrackingStart->setToolTip("Tracking in progress.");
	- m_Controls->m_TrackingStop->setToolTip("Stop tracking and display results.");
	- m_Controls->m_MaskImageBox->setEnabled(false);
	- m_Controls->m_InputImageBox->setEnabled(false);
	- }
	-}
	-
	-// show/hide advanced settings frame
	-void QmitkGibbsTrackingView::AdvancedSettings()
	-{
	- m_Controls->m_AdvancedFrame->setVisible(m_Controls->m_AdvancedSettingsCheckbox->isChecked());
	-}
	-
	-// check for mask and odf and start tracking thread
	-void QmitkGibbsTrackingView::StartGibbsTracking()
	-{
	- if(m_ThreadIsRunning)
	- {
	- MITK_WARN("QmitkGibbsTrackingView")<<"Thread already running!";
	- return;
	- }
	- m_GlobalTracker = nullptr;
	-
	-
	- if (m_Controls->m_InputImageBox->GetSelectedNode().IsNull())
	- {
	- QMessageBox::information( nullptr, "Warning", "Please load and select a Odf image before starting image processing.");
	- return;
	- }
	- m_ImageNode = m_Controls->m_InputImageBox->GetSelectedNode();
	-
	- if (dynamic_cast<mitk::OdfImage*>(m_ImageNode->GetData()))
	- m_OdfImage = dynamic_cast<mitk::OdfImage*>(m_ImageNode->GetData());
	- else if (dynamic_cast<mitk::TensorImage*>(m_ImageNode->GetData()))
	- m_TensorImage = dynamic_cast<mitk::TensorImage*>(m_ImageNode->GetData());
	-
	- if (m_OdfImage.IsNull() && m_TensorImage.IsNull())
	- return;
	-
	- // cast odf to itk
	- m_TrackingNode = m_ImageNode;
	- m_ItkTensorImage = nullptr;
	- m_ItkOdfImage = nullptr;
	- m_MaskImage = nullptr;
	-
	- if (m_OdfImage.IsNotNull())
	- {
	- m_ItkOdfImage = ItkOdfImgType::New();
	- mitk::CastToItkImage(m_OdfImage, m_ItkOdfImage);
	- }
	- else
	- {
	- m_ItkTensorImage = ItkTensorImage::New();
	- mitk::CastToItkImage(m_TensorImage, m_ItkTensorImage);
	- }
	-
	- // mask image found?
	- // catch exceptions thrown by the itkAccess macros
	- try{
	- if(m_Controls->m_MaskImageBox->GetSelectedNode().IsNotNull())
	- {
	- m_MaskImageNode = m_Controls->m_MaskImageBox->GetSelectedNode();
	- if (dynamic_cast<mitk::Image*>(m_MaskImageNode->GetData()))
	- mitk::CastToItkImage(dynamic_cast<mitk::Image*>(m_MaskImageNode->GetData()), m_MaskImage);
	- }
	- }
	- catch(...){};
	-
	- // start worker thread
	- m_TrackingThread.start(QThread::LowestPriority);
	-}
	-
	-// generate mitkFiberBundle from tracking filter output
	-void QmitkGibbsTrackingView::GenerateFiberBundle()
	-{
	- if (m_GlobalTracker.IsNull() \|\| (!(m_Controls->m_VisualizationCheckbox->isChecked() \|\| m_Controls->m_VisualizeOnceButton->isChecked()) && m_ThreadIsRunning))
	- return;
	-
	- if (m_Controls->m_VisualizeOnceButton->isChecked())
	- m_Controls->m_VisualizeOnceButton->setChecked(false);
	-
	- vtkSmartPointer<vtkPolyData> fiberBundle = m_GlobalTracker->GetFiberBundle();
	- if ( m_GlobalTracker->GetNumAcceptedFibers()==0 )
	- return;
	- m_FiberBundle = mitk::FiberBundle::New(fiberBundle);
	- m_FiberBundle->SetReferenceGeometry(dynamic_cast<mitk::Image*>(m_ImageNode->GetData())->GetGeometry());
	-
	- if (m_FiberBundleNode.IsNotNull()){
	- GetDataStorage()->Remove(m_FiberBundleNode);
	- m_FiberBundleNode = 0;
	- }
	- m_GlobalTracker->SetDicomProperties(m_FiberBundle);
	-
	- m_FiberBundleNode = mitk::DataNode::New();
	- m_FiberBundleNode->SetData(m_FiberBundle);
	-
	- QString name("FiberBundle_");
	- name += m_ImageNode->GetName().c_str();
	- name += "_Gibbs";
	- m_FiberBundleNode->SetName(name.toStdString());
	- m_FiberBundleNode->SetVisibility(true);
	-
	-
	- if (!m_OutputFileName.isEmpty() && !m_ThreadIsRunning)
	- {
	- try
	- {
	- mitk::IOUtil::Save(m_FiberBundle.GetPointer(),m_OutputFileName.toStdString());
	- QMessageBox::information(nullptr, "Fiber bundle saved to", m_OutputFileName);
	- }
	- catch (itk::ExceptionObject &ex)
	- {
	- QMessageBox::information(nullptr, "Fiber bundle could not be saved", QString("%1\n%2\n%3\n%4\n%5\n%6").arg(ex.GetNameOfClass()).arg(ex.GetFile()).arg(ex.GetLine()).arg(ex.GetLocation()).arg(ex.what()).arg(ex.GetDescription()));
	- }
	- }
	- if(m_ImageNode.IsNull())
	- GetDataStorage()->Add(m_FiberBundleNode);
	- else
	- GetDataStorage()->Add(m_FiberBundleNode, m_ImageNode);
	-}
	-
	-void QmitkGibbsTrackingView::SetOutputFile()
	-{
	- // SELECT FOLDER DIALOG
	- m_OutputFileName = QFileDialog::getSaveFileName(0,
	- tr("Set file name"),
	- QDir::currentPath()+"/FiberBundle.fib",
	- tr("Fiber Bundle (*.fib)") );
	- if (m_OutputFileName.isEmpty())
	- m_Controls->m_OutputFileLabel->setText("N/A");
	- else
	- m_Controls->m_OutputFileLabel->setText(m_OutputFileName);
	-}
	-
	-// save current tracking paramters as xml file (.gtp)
	-void QmitkGibbsTrackingView::SaveTrackingParameters()
	-{
	- TiXmlDocument documentXML;
	- TiXmlDeclaration* declXML = new TiXmlDeclaration( "1.0", "", "" );
	- documentXML.LinkEndChild( declXML );
	-
	- TiXmlElement* mainXML = new TiXmlElement("global_tracking_parameter_file");
	- mainXML->SetAttribute("file_version", "0.1");
	- documentXML.LinkEndChild(mainXML);
	-
	- TiXmlElement* paramXML = new TiXmlElement("parameter_set");
	- paramXML->SetAttribute("iterations", m_Controls->m_IterationsBox->text().toStdString());
	- paramXML->SetAttribute("particle_length", QString::number((float)m_Controls->m_ParticleLengthSlider->value()/10).toStdString());
	- paramXML->SetAttribute("particle_width", QString::number((float)m_Controls->m_ParticleWidthSlider->value()/10).toStdString());
	- paramXML->SetAttribute("particle_weight", QString::number((float)m_Controls->m_ParticleWeightSlider->value()/10000).toStdString());
	- paramXML->SetAttribute("temp_start", QString::number((float)m_Controls->m_StartTempSlider->value()/100).toStdString());
	- paramXML->SetAttribute("temp_end", QString::number((float)m_Controls->m_EndTempSlider->value()/10000).toStdString());
	- paramXML->SetAttribute("inexbalance", QString::number((float)m_Controls->m_InExBalanceSlider->value()/10).toStdString());
	- paramXML->SetAttribute("fiber_length", QString::number(m_Controls->m_FiberLengthSlider->value()).toStdString());
	- paramXML->SetAttribute("curvature_threshold", QString::number(m_Controls->m_CurvatureThresholdSlider->value()).toStdString());
	- mainXML->LinkEndChild(paramXML);
	- QString filename = QFileDialog::getSaveFileName(
	- 0,
	- tr("Save Parameters"),
	- QDir::currentPath()+"/param.gtp",
	- tr("Global Tracking Parameters (*.gtp)") );
	-
	- if(filename.isEmpty() \|\| filename.isNull())
	- return;
	- if(!filename.endsWith(".gtp"))
	- filename += ".gtp";
	- documentXML.SaveFile( filename.toStdString() );
	-}
	-
	-// load current tracking paramters from xml file (.gtp)
	-void QmitkGibbsTrackingView::LoadTrackingParameters()
	-{
	- QString filename = QFileDialog::getOpenFileName(0, tr("Load Parameters"), QDir::currentPath(), tr("Global Tracking Parameters (*.gtp)") );
	- if(filename.isEmpty() \|\| filename.isNull())
	- return;
	-
	- TiXmlDocument doc( filename.toStdString() );
	- doc.LoadFile();
	-
	- TiXmlHandle hDoc(&doc);
	- TiXmlElement* pElem;
	- TiXmlHandle hRoot(0);
	-
	- pElem = hDoc.FirstChildElement().Element();
	- hRoot = TiXmlHandle(pElem);
	- pElem = hRoot.FirstChildElement("parameter_set").Element();
	-
	- QString iterations(pElem->Attribute("iterations"));
	- m_Controls->m_IterationsBox->setText(iterations);
	-
	- QString particleLength(pElem->Attribute("particle_length"));
	- float pLength = particleLength.toFloat();
	- QString particleWidth(pElem->Attribute("particle_width"));
	- float pWidth = particleWidth.toFloat();
	-
	- if (pLength==0)
	- m_Controls->m_ParticleLengthLabel->setText("auto");
	- else
	- m_Controls->m_ParticleLengthLabel->setText(particleLength+" mm");
	- if (pWidth==0)
	- m_Controls->m_ParticleWidthLabel->setText("auto");
	- else
	- m_Controls->m_ParticleWidthLabel->setText(particleWidth+" mm");
	-
	- m_Controls->m_ParticleWidthSlider->setValue(pWidth*10);
	- m_Controls->m_ParticleLengthSlider->setValue(pLength*10);
	-
	- QString partWeight(pElem->Attribute("particle_weight"));
	- m_Controls->m_ParticleWeightSlider->setValue(partWeight.toFloat()*10000);
	- m_Controls->m_ParticleWeightLabel->setText(partWeight);
	-
	- QString startTemp(pElem->Attribute("temp_start"));
	- m_Controls->m_StartTempSlider->setValue(startTemp.toFloat()*100);
	- m_Controls->m_StartTempLabel->setText(startTemp);
	-
	- QString endTemp(pElem->Attribute("temp_end"));
	- m_Controls->m_EndTempSlider->setValue(endTemp.toFloat()*10000);
	- m_Controls->m_EndTempLabel->setText(endTemp);
	-
	- QString inExBalance(pElem->Attribute("inexbalance"));
	- m_Controls->m_InExBalanceSlider->setValue(inExBalance.toFloat()*10);
	- m_Controls->m_InExBalanceLabel->setText(inExBalance);
	-
	- QString fiberLength(pElem->Attribute("fiber_length"));
	- m_Controls->m_FiberLengthSlider->setValue(fiberLength.toInt());
	- m_Controls->m_FiberLengthLabel->setText(fiberLength+"mm");
	-
	- QString curvThres(pElem->Attribute("curvature_threshold"));
	- m_Controls->m_CurvatureThresholdSlider->setValue(curvThres.toInt());
	- m_Controls->m_CurvatureThresholdLabel->setText(curvThres+"°");
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkGibbsTrackingView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkGibbsTrackingView.h
	deleted file mode 100644
	index d2dc3888cb..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkGibbsTrackingView.h
	+++ /dev/null
	@@ -1,162 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef QmitkGibbsTrackingView_h
	-#define QmitkGibbsTrackingView_h
	-
	-#include <berryISelectionListener.h>
	-
	-#include <QmitkAbstractView.h>
	-
	-#include "ui_QmitkGibbsTrackingViewControls.h"
	-
	-#include <mitkOdfImage.h>
	-#include <QThread>
	-#include <mitkFiberBundle.h>
	-#include <QTime>
	-#include <itkImage.h>
	-#include <vtkSmartPointer.h>
	-#include <vtkPolyData.h>
	-#include <itkDiffusionTensor3D.h>
	-#include <mitkTensorImage.h>
	-
	-class QmitkGibbsTrackingView;
	-
	-class QmitkTrackingWorker : public QObject
	-{
	- Q_OBJECT
	-
	-public:
	-
	- QmitkTrackingWorker(QmitkGibbsTrackingView* view);
	-
	-public slots:
	-
	- void run();
	-
	-private:
	-
	- QmitkGibbsTrackingView* m_View;
	-};
	-
	-/*!
	- \brief View for global fiber tracking (Gibbs tracking)
	-*/
	-typedef itk::Image< float, 3 > FloatImageType;
	-
	-namespace itk
	-{
	-template<class X>
	-class GibbsTrackingFilter;
	-}
	-
	-class QmitkGibbsTrackingView : public QmitkAbstractView
	-{
	- // this is needed for all Qt objects that should have a Qt meta-object
	- // (everything that derives from QObject and wants to have signal/slots)
	- Q_OBJECT
	-
	-public:
	-
	- typedef itk::Image<float,3> ItkFloatImageType;
	- typedef itk::Vector<float, ODF_SAMPLING_SIZE> OdfVectorType;
	- typedef mitk::OdfImage::ItkOdfImageType ItkOdfImgType;
	- typedef mitk::TensorImage::ItkTensorImageType ItkTensorImage;
	- typedef itk::GibbsTrackingFilter< ItkOdfImgType > GibbsTrackingFilterType;
	-
	- static const std::string VIEW_ID;
	-
	- QmitkGibbsTrackingView();
	- virtual ~QmitkGibbsTrackingView();
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	-
	- ///
	- /// Sets the focus to an internal widget.
	- ///
	- virtual void SetFocus() override;
	-
	-signals:
	-
	-protected slots:
	-
	- void StartGibbsTracking();
	- void StopGibbsTracking();
	- void AfterThread(); ///< update gui etc. after tracking has finished
	- void BeforeThread(); ///< start timer etc.
	- void TimerUpdate();
	- void AdvancedSettings(); ///< show/hide advanced tracking options
	- void SaveTrackingParameters(); ///< save tracking parameters to xml file
	- void LoadTrackingParameters(); ///< load tracking parameters from xml file
	-
	- /** update labels if parameters have changed */
	- void SetParticleWidth(int value);
	- void SetParticleLength(int value);
	- void SetInExBalance(int value);
	- void SetFiberLength(int value);
	- void SetParticleWeight(int value);
	- void SetStartTemp(int value);
	- void SetEndTemp(int value);
	- void SetCurvatureThreshold(int value);
	- void SetRandomSeed(int value);
	- void SetOutputFile();
	- void UpdateGUI(); ///< update button activity etc. dpending on current datamanager selection
	-
	-private:
	-
	- // Visualization & GUI
	- void GenerateFiberBundle(); ///< generate fiber bundle from tracking output and add to datanode
	- void UpdateTrackingStatus(); ///< update textual status display of the tracking process
	-
	- /// \brief called by QmitkAbstractView when DataManager's selection has changed
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- /// \brief called when DataNode is removed to stop gibbs tracking after node is removed
	- virtual void NodeRemoved(const mitk::DataNode * node) override;
	-
	- void UpdateIteraionsGUI(unsigned long iterations); ///< update iterations label text
	-
	- Ui::QmitkGibbsTrackingViewControls* m_Controls;
	-
	- /** data objects */
	- mitk::DataNode::Pointer m_TrackingNode; ///< actual node that is tracked
	- mitk::FiberBundle::Pointer m_FiberBundle; ///< tracking output
	- ItkFloatImageType::Pointer m_MaskImage; ///< used to reduce the algorithms search space. tracking only inside of the mask.
	- mitk::TensorImage::Pointer m_TensorImage; ///< actual image that is tracked
	- mitk::OdfImage::Pointer m_OdfImage; ///< actual image that is tracked
	- ItkOdfImgType::Pointer m_ItkOdfImage; ///< actual image that is tracked
	- ItkTensorImage::Pointer m_ItkTensorImage; ///< actual image that is tracked
	-
	- /** data nodes */
	- mitk::DataNode::Pointer m_ImageNode;
	- mitk::DataNode::Pointer m_MaskImageNode;
	- mitk::DataNode::Pointer m_FiberBundleNode;
	-
	- /** flags etc. */
	- bool m_ThreadIsRunning;
	- QTimer* m_TrackingTimer;
	- QTime m_TrackingTime;
	- unsigned long m_ElapsedTime;
	- QString m_OutputFileName;
	-
	- /** global tracker and friends */
	- itk::SmartPointer<GibbsTrackingFilterType> m_GlobalTracker;
	- QmitkTrackingWorker m_TrackingWorker;
	- QThread m_TrackingThread;
	- friend class QmitkTrackingWorker;
	-};
	-
	-#endif // _QMITKGibbsTrackingVIEW_H_INCLUDED
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkGibbsTrackingViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkGibbsTrackingViewControls.ui
	deleted file mode 100644
	index 4822482046..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkGibbsTrackingViewControls.ui
	+++ /dev/null
	@@ -1,1178 +0,0 @@
	-<?xml version="1.0" encoding="utf-8"?>
	-<ui version="4.0">
	- <class>QmitkGibbsTrackingViewControls</class>
	- <widget class="QWidget" name="QmitkGibbsTrackingViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>463</width>
	- <height>1011</height>
	- </rect>
	- </property>
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="windowTitle">
	- <string>QmitkTemplate</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QFormLayout" name="formLayout">
	- <property name="fieldGrowthPolicy">
	- <enum>QFormLayout::AllNonFixedFieldsGrow</enum>
	- </property>
	- <item row="1" column="0" colspan="2">
	- <widget class="QFrame" name="frame_4">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Plain</enum>
	- </property>
	- <property name="lineWidth">
	- <number>0</number>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_8">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>6</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QCommandLinkButton" name="m_TrackingStart">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string>No ODF/tensor image selected.</string>
	- </property>
	- <property name="layoutDirection">
	- <enum>Qt::LeftToRight</enum>
	- </property>
	- <property name="text">
	- <string>Start Tractography</string>
	- </property>
	- <property name="icon">
	- <iconset resource="../../../../Modules/QtWidgetsExt/resource/QtWidgetsExt.qrc">
	- <normaloff>:/QtWidgetsExt/play.xpm</normaloff>
	-:/QtWidgetsExt/play.xpm </iconset>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QCommandLinkButton" name="m_TrackingStop">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="layoutDirection">
	- <enum>Qt::LeftToRight</enum>
	- </property>
	- <property name="text">
	- <string>Stop Tractography</string>
	- </property>
	- <property name="icon">
	- <iconset resource="../../../../Modules/QtWidgetsExt/resource/QtWidgetsExt.qrc">
	- <normaloff>:/QtWidgetsExt/stop.xpm</normaloff>
	-:/QtWidgetsExt/stop.xpm </iconset>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="2" column="0" colspan="2">
	- <widget class="QGroupBox" name="m_ParametersFrame">
	- <property name="title">
	- <string>Parameters</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_5">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QLabel" name="m_CurvatureThresholdLabel_3">
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>Output File:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QCheckBox" name="m_AdvancedSettingsCheckbox">
	- <property name="text">
	- <string>Advanced Settings</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QCheckBox" name="m_VisualizationCheckbox">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="toolTip">
	- <string>Activate continuous visualization of intermediate results.</string>
	- </property>
	- <property name="text">
	- <string>Visualize Tractography</string>
	- </property>
	- <property name="checked">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="2">
	- <widget class="QFrame" name="frame_2">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Plain</enum>
	- </property>
	- <property name="lineWidth">
	- <number>0</number>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>0</number>
	- </property>
	- <item row="1" column="1">
	- <widget class="QToolButton" name="m_OutputFileButton">
	- <property name="toolTip">
	- <string>Select output file name and folder.</string>
	- </property>
	- <property name="text">
	- <string>...</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLineEdit" name="m_OutputFileLabel">
	- <property name="text">
	- <string>N/A</string>
	- </property>
	- <property name="readOnly">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="2" column="2">
	- <widget class="QToolButton" name="m_VisualizeOnceButton">
	- <property name="toolTip">
	- <string>Visualize intermediate result.</string>
	- </property>
	- <property name="text">
	- <string></string>
	- </property>
	- <property name="icon">
	- <iconset resource="../../../org.mitk.gui.qt.diffusionimaging/resources/QmitkDiffusionImaging.qrc">
	- <normaloff>:/QmitkDiffusionImaging/Refresh_48.png</normaloff>
	-:/QmitkDiffusionImaging/Refresh_48.png </iconset>
	- </property>
	- <property name="checkable">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_IterationsLabel">
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>Iterations:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="2">
	- <widget class="QLineEdit" name="m_IterationsBox">
	- <property name="text">
	- <string>1e9</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="3" column="0" colspan="2">
	- <widget class="QFrame" name="m_AdvancedFrame">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::StyledPanel</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_2">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>6</number>
	- </property>
	- <item row="2" column="0">
	- <widget class="QLabel" name="m_ParticleWidthLabel_2">
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>Particle Width:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="6" column="1">
	- <widget class="QLabel" name="m_InExBalanceLabel">
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>0</string>
	- </property>
	- <property name="alignment">
	- <set>Qt::AlignLeading\|Qt::AlignLeft\|Qt::AlignVCenter</set>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="1">
	- <widget class="QLabel" name="m_StartTempLabel">
	- <property name="text">
	- <string>0.1</string>
	- </property>
	- <property name="alignment">
	- <set>Qt::AlignLeading\|Qt::AlignLeft\|Qt::AlignVCenter</set>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QLabel" name="m_ParticleWeightLabel_2">
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>Particle Weight:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="2">
	- <widget class="QSlider" name="m_EndTempSlider">
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>99</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>10</number>
	- </property>
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- <property name="tickPosition">
	- <enum>QSlider::NoTicks</enum>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QLabel" name="m_StartTempLabel_2">
	- <property name="text">
	- <string>Start Temperature:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="2">
	- <widget class="QSlider" name="m_ParticleWeightSlider">
	- <property name="toolTip">
	- <string>automatic estimation from gfa map and ODF data.</string>
	- </property>
	- <property name="minimum">
	- <number>0</number>
	- </property>
	- <property name="maximum">
	- <number>1000</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>0</number>
	- </property>
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- <property name="invertedControls">
	- <bool>true</bool>
	- </property>
	- <property name="tickPosition">
	- <enum>QSlider::NoTicks</enum>
	- </property>
	- </widget>
	- </item>
	- <item row="6" column="2">
	- <widget class="QSlider" name="m_InExBalanceSlider">
	- <property name="toolTip">
	- <string>IE Bias < 0 < EE Bias</string>
	- </property>
	- <property name="minimum">
	- <number>-50</number>
	- </property>
	- <property name="maximum">
	- <number>50</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- <property name="tickPosition">
	- <enum>QSlider::NoTicks</enum>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="1">
	- <widget class="QLabel" name="m_EndTempLabel">
	- <property name="text">
	- <string>0.001</string>
	- </property>
	- <property name="alignment">
	- <set>Qt::AlignLeading\|Qt::AlignLeft\|Qt::AlignVCenter</set>
	- </property>
	- </widget>
	- </item>
	- <item row="8" column="0">
	- <widget class="QLabel" name="m_CurvatureThresholdLabel_2">
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>Curvature Threshold:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="6" column="0">
	- <widget class="QLabel" name="m_InExBalanceLabel_2">
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>Balance In/Ex Energy:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="8" column="1">
	- <widget class="QLabel" name="m_CurvatureThresholdLabel">
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>45°</string>
	- </property>
	- <property name="alignment">
	- <set>Qt::AlignLeading\|Qt::AlignLeft\|Qt::AlignVCenter</set>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="2">
	- <widget class="QSlider" name="m_ParticleWidthSlider">
	- <property name="toolTip">
	- <string>auto = 0.5 * min. spacing; sigma</string>
	- </property>
	- <property name="maximum">
	- <number>100</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- <property name="tickPosition">
	- <enum>QSlider::NoTicks</enum>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="m_ParticleLengthLabel_2">
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>Particle Length:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QLabel" name="m_ParticleLengthLabel">
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>auto</string>
	- </property>
	- <property name="alignment">
	- <set>Qt::AlignLeading\|Qt::AlignLeft\|Qt::AlignVCenter</set>
	- </property>
	- </widget>
	- </item>
	- <item row="7" column="0">
	- <widget class="QLabel" name="m_FiberLengthLabel_2">
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>Min. Fiber Length:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="7" column="2">
	- <widget class="QSlider" name="m_FiberLengthSlider">
	- <property name="toolTip">
	- <string>Only fibers longer than specified are accepted.</string>
	- </property>
	- <property name="maximum">
	- <number>500</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>20</number>
	- </property>
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- <property name="tickPosition">
	- <enum>QSlider::NoTicks</enum>
	- </property>
	- </widget>
	- </item>
	- <item row="8" column="2">
	- <widget class="QSlider" name="m_CurvatureThresholdSlider">
	- <property name="toolTip">
	- <string>Allow only fiber curvature values smaller than the selected threshold.</string>
	- </property>
	- <property name="maximum">
	- <number>180</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>45</number>
	- </property>
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- <property name="tickPosition">
	- <enum>QSlider::NoTicks</enum>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <widget class="QLabel" name="m_EndTempLabel_2">
	- <property name="text">
	- <string>End Temperature:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="7" column="1">
	- <widget class="QLabel" name="m_FiberLengthLabel">
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>20mm</string>
	- </property>
	- <property name="alignment">
	- <set>Qt::AlignLeading\|Qt::AlignLeft\|Qt::AlignVCenter</set>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="1">
	- <widget class="QLabel" name="m_ParticleWeightLabel">
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>auto</string>
	- </property>
	- <property name="alignment">
	- <set>Qt::AlignLeading\|Qt::AlignLeft\|Qt::AlignVCenter</set>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="2">
	- <widget class="QSlider" name="m_StartTempSlider">
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>100</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>10</number>
	- </property>
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- <property name="invertedAppearance">
	- <bool>false</bool>
	- </property>
	- <property name="invertedControls">
	- <bool>false</bool>
	- </property>
	- <property name="tickPosition">
	- <enum>QSlider::NoTicks</enum>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QLabel" name="m_ParticleWidthLabel">
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>auto</string>
	- </property>
	- <property name="alignment">
	- <set>Qt::AlignLeading\|Qt::AlignLeft\|Qt::AlignVCenter</set>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="2">
	- <widget class="QSlider" name="m_ParticleLengthSlider">
	- <property name="toolTip">
	- <string>auto = 1.5 * min. spacing; l</string>
	- </property>
	- <property name="maximum">
	- <number>100</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- <property name="tickPosition">
	- <enum>QSlider::NoTicks</enum>
	- </property>
	- </widget>
	- </item>
	- <item row="9" column="0">
	- <widget class="QLabel" name="m_CurvatureThresholdLabel_4">
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>Random Seed</string>
	- </property>
	- </widget>
	- </item>
	- <item row="9" column="1">
	- <widget class="QLabel" name="m_RandomSeedLabel">
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>auto</string>
	- </property>
	- <property name="alignment">
	- <set>Qt::AlignLeading\|Qt::AlignLeft\|Qt::AlignVCenter</set>
	- </property>
	- </widget>
	- </item>
	- <item row="9" column="2">
	- <widget class="QSlider" name="m_RandomSeedSlider">
	- <property name="toolTip">
	- <string>auto = 1.5 * min. spacing; l</string>
	- </property>
	- <property name="minimum">
	- <number>-1</number>
	- </property>
	- <property name="maximum">
	- <number>100</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>-1</number>
	- </property>
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- <property name="tickPosition">
	- <enum>QSlider::NoTicks</enum>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="4" column="0" colspan="2">
	- <widget class="QFrame" name="frame_3">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Plain</enum>
	- </property>
	- <property name="lineWidth">
	- <number>0</number>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_7" rowstretch="0">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QCommandLinkButton" name="m_SaveTrackingParameters">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="toolTip">
	- <string>Save current parameters as xml (.gtp)</string>
	- </property>
	- <property name="layoutDirection">
	- <enum>Qt::LeftToRight</enum>
	- </property>
	- <property name="text">
	- <string>Save Parameters</string>
	- </property>
	- <property name="icon">
	- <iconset resource="../../../org.mitk.gui.qt.diffusionimaging.fiberfox/resources/QmitkDiffusionImaging.qrc">
	- <normaloff>:/QmitkDiffusionImaging/general_icons/download.ico</normaloff>
	-:/QmitkDiffusionImaging/general_icons/download.ico </iconset>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QCommandLinkButton" name="m_LoadTrackingParameters">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="toolTip">
	- <string>Load parameters from xml file (.gtp)</string>
	- </property>
	- <property name="layoutDirection">
	- <enum>Qt::LeftToRight</enum>
	- </property>
	- <property name="text">
	- <string>Load Parameters</string>
	- </property>
	- <property name="icon">
	- <iconset resource="../../../org.mitk.gui.qt.diffusionimaging.fiberfox/resources/QmitkDiffusionImaging.qrc">
	- <normaloff>:/QmitkDiffusionImaging/general_icons/upload.ico</normaloff>
	-:/QmitkDiffusionImaging/general_icons/upload.ico </iconset>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="6" column="1">
	- <spacer name="spacer1">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeType">
	- <enum>QSizePolicy::Expanding</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>0</width>
	- <height>0</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="0" column="0" colspan="2">
	- <widget class="QGroupBox" name="m_DataFrame">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="title">
	- <string>Input Data</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_3">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="text">
	- <string>ODF/Tensor Image:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_3">
	- <property name="text">
	- <string>Mask Image:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBox" name="m_InputImageBox">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QmitkDataStorageComboBoxWithSelectNone" name="m_MaskImageBox">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="5" column="0" colspan="2">
	- <widget class="QGroupBox" name="groupBox_4">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="title">
	- <string>Monitor</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_6">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <property name="spacing">
	- <number>6</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_23">
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>Progress:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QLabel" name="m_CurrentStepLabel">
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>-</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_21">
	- <property name="toolTip">
	- <string comment="Will only be updated if tracking is visualized" extracomment="Will only be updated if tracking is visualized">Will only be updated if tracking is visualized</string>
	- </property>
	- <property name="statusTip">
	- <string>Will only be updated if tracking is visualized</string>
	- </property>
	- <property name="whatsThis">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>Accepted Fibers:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label_24">
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>Connections:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QLabel" name="label_25">
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>Particles:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QLabel" name="label_27">
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>Proposal Acceptance Rate:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <widget class="QLabel" name="label_26">
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>Tracking Time:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QLabel" name="m_AcceptedFibersLabel">
	- <property name="toolTip">
	- <string>Will only be updated if tracking is visualized</string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>-</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QLabel" name="m_NumConnectionsLabel">
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>-</string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="1">
	- <widget class="QLabel" name="m_NumParticlesLabel">
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>-</string>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="1">
	- <widget class="QLabel" name="m_ProposalAcceptance">
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>-</string>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="1">
	- <widget class="QLabel" name="m_TrackingTimeLabel">
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="statusTip">
	- <string></string>
	- </property>
	- <property name="whatsThis">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>-</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <layoutdefault spacing="6" margin="11"></layoutdefault>
	- <customwidgets>
	- <customwidget>
	- <class>QmitkDataStorageComboBox</class>
	- <extends>QComboBox</extends>
	- <header location="global">QmitkDataStorageComboBox.h</header>
	- </customwidget>
	- <customwidget>
	- <class>QmitkDataStorageComboBoxWithSelectNone</class>
	- <extends>QComboBox</extends>
	- <header>QmitkDataStorageComboBoxWithSelectNone.h</header>
	- </customwidget>
	- </customwidgets>
	- <resources>
	- <include location="../../../../Modules/QtWidgetsExt/resource/QtWidgetsExt.qrc"></include>
	- <include location="../../../org.mitk.gui.qt.diffusionimaging.fiberfox/resources/QmitkDiffusionImaging.qrc"></include>
	- <include location="../../../org.mitk.gui.qt.diffusionimaging/resources/QmitkDiffusionImaging.qrc"></include>
	- </resources>
	- <connections></connections>
	-</ui>
	\ No newline at end of file
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingView.cpp
	deleted file mode 100644
	index 3bf1d89ce3..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingView.cpp
	+++ /dev/null
	@@ -1,1159 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-// Blueberry
	-#include <berryISelectionService.h>
	-#include <berryIWorkbenchWindow.h>
	-#include <berryIStructuredSelection.h>
	-
	-// Qmitk
	-#include "QmitkStreamlineTrackingView.h"
	-#include "QmitkStdMultiWidget.h"
	-
	-// Qt
	-#include <QMessageBox>
	-#include <QFileDialog>
	-
	-// MITK
	-#include <mitkLookupTable.h>
	-#include <mitkLookupTableProperty.h>
	-#include <mitkImageToItk.h>
	-#include <mitkFiberBundle.h>
	-#include <mitkImageCast.h>
	-#include <mitkImageToItk.h>
	-#include <mitkNodePredicateDataType.h>
	-#include <mitkNodePredicateNot.h>
	-#include <mitkNodePredicateAnd.h>
	-#include <mitkNodePredicateProperty.h>
	-#include <mitkNodePredicateDimension.h>
	-#include <mitkOdfImage.h>
	-#include <mitkShImage.h>
	-#include <mitkSliceNavigationController.h>
	-
	-// VTK
	-#include <vtkRenderWindowInteractor.h>
	-#include <vtkPolyData.h>
	-#include <vtkPoints.h>
	-#include <vtkCellArray.h>
	-#include <vtkSmartPointer.h>
	-#include <vtkPolyLine.h>
	-#include <vtkCellData.h>
	-
	-#include <itkTensorImageToOdfImageFilter.h>
	-#include <omp.h>
	-#include <mitkLexicalCast.h>
	-
	-const std::string QmitkStreamlineTrackingView::VIEW_ID = "org.mitk.views.streamlinetracking";
	-const std::string id_DataManager = "org.mitk.views.datamanager";
	-using namespace berry;
	-
	-QmitkStreamlineTrackingWorker::QmitkStreamlineTrackingWorker(QmitkStreamlineTrackingView* view)
	- : m_View(view)
	-{
	-}
	-
	-void QmitkStreamlineTrackingWorker::run()
	-{
	- m_View->m_Tracker->Update();
	- m_View->m_TrackingThread.quit();
	-}
	-
	-QmitkStreamlineTrackingView::QmitkStreamlineTrackingView()
	- : m_TrackingWorker(this)
	- , m_Controls(nullptr)
	- , m_FirstTensorProbRun(true)
	- , m_FirstInteractiveRun(true)
	- , m_TrackingHandler(nullptr)
	- , m_ThreadIsRunning(false)
	- , m_DeleteTrackingHandler(false)
	- , m_Visible(false)
	- , m_LastPrior(nullptr)
	- , m_TrackingPriorHandler(nullptr)
	-{
	- m_TrackingWorker.moveToThread(&m_TrackingThread);
	- connect(&m_TrackingThread, SIGNAL(started()), this, SLOT(BeforeThread()));
	- connect(&m_TrackingThread, SIGNAL(started()), &m_TrackingWorker, SLOT(run()));
	- connect(&m_TrackingThread, SIGNAL(finished()), this, SLOT(AfterThread()));
	- m_TrackingTimer = new QTimer(this);
	-}
	-
	-// Destructor
	-QmitkStreamlineTrackingView::~QmitkStreamlineTrackingView()
	-{
	- if (m_Tracker.IsNull())
	- return;
	-
	- m_Tracker->SetStopTracking(true);
	- m_TrackingThread.wait();
	-}
	-
	-void QmitkStreamlineTrackingView::CreateQtPartControl( QWidget *parent )
	-{
	- if ( !m_Controls )
	- {
	- // create GUI widgets from the Qt Designer's .ui file
	- m_Controls = new Ui::QmitkStreamlineTrackingViewControls;
	- m_Controls->setupUi( parent );
	- m_Controls->m_FaImageSelectionWidget->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_SeedImageSelectionWidget->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_MaskImageSelectionWidget->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_TargetImageSelectionWidget->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_PriorImageSelectionWidget->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_StopImageSelectionWidget->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_ForestSelectionWidget->SetDataStorage(this->GetDataStorage());
	- m_Controls->m_ExclusionImageSelectionWidget->SetDataStorage(this->GetDataStorage());
	-
	- mitk::TNodePredicateDataType<mitk::PeakImage>::Pointer isPeakImagePredicate = mitk::TNodePredicateDataType<mitk::PeakImage>::New();
	- mitk::TNodePredicateDataType<mitk::Image>::Pointer isImagePredicate = mitk::TNodePredicateDataType<mitk::Image>::New();
	- mitk::TNodePredicateDataType<mitk::TractographyForest>::Pointer isTractographyForest = mitk::TNodePredicateDataType<mitk::TractographyForest>::New();
	-
	- mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true));
	- mitk::NodePredicateNot::Pointer isNotBinaryPredicate = mitk::NodePredicateNot::New( isBinaryPredicate );
	- mitk::NodePredicateAnd::Pointer isNotABinaryImagePredicate = mitk::NodePredicateAnd::New( isImagePredicate, isNotBinaryPredicate );
	- mitk::NodePredicateDimension::Pointer dimensionPredicate = mitk::NodePredicateDimension::New(3);
	-
	- m_Controls->m_ForestSelectionWidget->SetNodePredicate(isTractographyForest);
	- m_Controls->m_FaImageSelectionWidget->SetNodePredicate( mitk::NodePredicateAnd::New(isNotABinaryImagePredicate, dimensionPredicate) );
	- m_Controls->m_FaImageSelectionWidget->SetEmptyInfo("--");
	- m_Controls->m_FaImageSelectionWidget->SetSelectionIsOptional(true);
	-
	- m_Controls->m_SeedImageSelectionWidget->SetNodePredicate( mitk::NodePredicateAnd::New(isImagePredicate, dimensionPredicate) );
	- m_Controls->m_SeedImageSelectionWidget->SetEmptyInfo("--");
	- m_Controls->m_SeedImageSelectionWidget->SetSelectionIsOptional(true);
	-
	- m_Controls->m_MaskImageSelectionWidget->SetNodePredicate( mitk::NodePredicateAnd::New(isImagePredicate, dimensionPredicate) );
	- m_Controls->m_MaskImageSelectionWidget->SetEmptyInfo("--");
	- m_Controls->m_MaskImageSelectionWidget->SetSelectionIsOptional(true);
	-
	- m_Controls->m_StopImageSelectionWidget->SetNodePredicate( mitk::NodePredicateAnd::New(isImagePredicate, dimensionPredicate) );
	- m_Controls->m_StopImageSelectionWidget->SetEmptyInfo("--");
	- m_Controls->m_StopImageSelectionWidget->SetSelectionIsOptional(true);
	-
	- m_Controls->m_TargetImageSelectionWidget->SetNodePredicate( mitk::NodePredicateAnd::New(isImagePredicate, dimensionPredicate) );
	- m_Controls->m_TargetImageSelectionWidget->SetEmptyInfo("--");
	- m_Controls->m_TargetImageSelectionWidget->SetSelectionIsOptional(true);
	-
	- m_Controls->m_PriorImageSelectionWidget->SetNodePredicate( isPeakImagePredicate );
	- m_Controls->m_PriorImageSelectionWidget->SetEmptyInfo("--");
	- m_Controls->m_PriorImageSelectionWidget->SetSelectionIsOptional(true);
	-
	- m_Controls->m_ExclusionImageSelectionWidget->SetNodePredicate( mitk::NodePredicateAnd::New(isImagePredicate, dimensionPredicate) );
	- m_Controls->m_ExclusionImageSelectionWidget->SetEmptyInfo("--");
	- m_Controls->m_ExclusionImageSelectionWidget->SetSelectionIsOptional(true);
	-
	- connect( m_TrackingTimer, SIGNAL(timeout()), this, SLOT(TimerUpdate()) );
	- connect( m_Controls->m_SaveParametersButton, SIGNAL(clicked()), this, SLOT(SaveParameters()) );
	- connect( m_Controls->m_LoadParametersButton, SIGNAL(clicked()), this, SLOT(LoadParameters()) );
	- connect( m_Controls->commandLinkButton_2, SIGNAL(clicked()), this, SLOT(StopTractography()) );
	- connect( m_Controls->commandLinkButton, SIGNAL(clicked()), this, SLOT(DoFiberTracking()) );
	- connect( m_Controls->m_InteractiveBox, SIGNAL(stateChanged(int)), this, SLOT(ToggleInteractive()) );
	- connect( m_Controls->m_ModeBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui()) );
	- connect( m_Controls->m_FaImageSelectionWidget, SIGNAL(CurrentSelectionChanged(QList<mitk::DataNode::Pointer>)), this, SLOT(DeleteTrackingHandler()) );
	- connect( m_Controls->m_ModeBox, SIGNAL(currentIndexChanged(int)), this, SLOT(DeleteTrackingHandler()) );
	- connect( m_Controls->m_OutputProbMap, SIGNAL(stateChanged(int)), this, SLOT(OutputStyleSwitched()) );
	-
	- connect( m_Controls->m_SeedImageSelectionWidget, SIGNAL(CurrentSelectionChanged(QList<mitk::DataNode::Pointer>)), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_ModeBox, SIGNAL(currentIndexChanged(int)), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_StopImageSelectionWidget, SIGNAL(CurrentSelectionChanged(QList<mitk::DataNode::Pointer>)), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_TargetImageSelectionWidget, SIGNAL(CurrentSelectionChanged(QList<mitk::DataNode::Pointer>)), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_PriorImageSelectionWidget, SIGNAL(CurrentSelectionChanged(QList<mitk::DataNode::Pointer>)), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_ExclusionImageSelectionWidget, SIGNAL(CurrentSelectionChanged(QList<mitk::DataNode::Pointer>)), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_MaskImageSelectionWidget, SIGNAL(CurrentSelectionChanged(QList<mitk::DataNode::Pointer>)), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_FaImageSelectionWidget, SIGNAL(CurrentSelectionChanged(QList<mitk::DataNode::Pointer>)), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_ForestSelectionWidget, SIGNAL(CurrentSelectionChanged(QList<mitk::DataNode::Pointer>)), this, SLOT(ForestSwitched()) );
	- connect( m_Controls->m_ForestSelectionWidget, SIGNAL(CurrentSelectionChanged(QList<mitk::DataNode::Pointer>)), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_SeedsPerVoxelBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_NumFibersBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_ScalarThresholdBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_OdfCutoffBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_StepSizeBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_SamplingDistanceBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_AngularThresholdBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_MinTractLengthBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_MaxTractLengthBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_fBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_gBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_NumSamplesBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_SeedRadiusBox, SIGNAL(editingFinished()), this, SLOT(InteractiveSeedChanged()) );
	- connect( m_Controls->m_NumSeedsBox, SIGNAL(editingFinished()), this, SLOT(InteractiveSeedChanged()) );
	- connect( m_Controls->m_OutputProbMap, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_SharpenOdfsBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_InterpolationBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_MaskInterpolationBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_FlipXBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_FlipYBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_FlipZBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_PriorFlipXBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_PriorFlipYBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_PriorFlipZBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_FrontalSamplesBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_StopVotesBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_LoopCheckBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_TrialsPerSeedBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_EpConstraintsBox, SIGNAL(currentIndexChanged(int)), this, SLOT(OnParameterChanged()) );
	- connect( m_Controls->m_PeakJitterBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) );
	-
	- m_Controls->m_SeedsPerVoxelBox->editingFinished();
	- m_Controls->m_NumFibersBox->editingFinished();
	- m_Controls->m_ScalarThresholdBox->editingFinished();
	- m_Controls->m_OdfCutoffBox->editingFinished();
	- m_Controls->m_StepSizeBox->editingFinished();
	- m_Controls->m_SamplingDistanceBox->editingFinished();
	- m_Controls->m_AngularThresholdBox->editingFinished();
	- m_Controls->m_MinTractLengthBox->editingFinished();
	- m_Controls->m_MaxTractLengthBox->editingFinished();
	- m_Controls->m_fBox->editingFinished();
	- m_Controls->m_gBox->editingFinished();
	- m_Controls->m_NumSamplesBox->editingFinished();
	- m_Controls->m_SeedRadiusBox->editingFinished();
	- m_Controls->m_NumSeedsBox->editingFinished();
	- m_Controls->m_LoopCheckBox->editingFinished();
	- m_Controls->m_TrialsPerSeedBox->editingFinished();
	- m_Controls->m_PeakJitterBox->editingFinished();
	-
	- StartStopTrackingGui(false);
	- }
	- m_ParameterFile = QDir::currentPath()+"/param.stp";
	-
	- UpdateGui();
	-}
	-
	-void QmitkStreamlineTrackingView::ParametersToGui(mitk::StreamlineTractographyParameters& params)
	-{
	- m_Controls->m_SeedRadiusBox->setValue(params.m_InteractiveRadiusMm);
	-
	- m_Controls->m_NumSeedsBox->setValue(params.m_NumInteractiveSeeds);
	- m_Controls->m_InteractiveBox->setChecked(params.m_EnableInteractive);
	- m_Controls->m_FiberErrorBox->setValue(params.m_Compression);
	- m_Controls->m_ResampleFibersBox->setChecked(params.m_CompressFibers);
	-
	- m_Controls->m_SeedRadiusBox->setValue(params.m_InteractiveRadiusMm);
	- m_Controls->m_NumFibersBox->setValue(params.m_MaxNumFibers);
	- m_Controls->m_ScalarThresholdBox->setValue(params.m_Cutoff);
	- m_Controls->m_fBox->setValue(params.m_F);
	- m_Controls->m_gBox->setValue(params.m_G);
	-
	- m_Controls->m_OdfCutoffBox->setValue(params.m_OdfCutoff);
	- m_Controls->m_SharpenOdfsBox->setChecked(params.m_SharpenOdfs);
	-
	- m_Controls->m_PriorWeightBox->setValue(params.m_Weight);
	- m_Controls->m_PriorAsMaskBox->setChecked(params.m_RestrictToPrior);
	- m_Controls->m_NewDirectionsFromPriorBox->setChecked(params.m_NewDirectionsFromPrior);
	-
	- m_Controls->m_PriorFlipXBox->setChecked(params.m_PriorFlipX);
	- m_Controls->m_PriorFlipYBox->setChecked(params.m_PriorFlipY);
	- m_Controls->m_PriorFlipZBox->setChecked(params.m_PriorFlipZ);
	-
	- m_Controls->m_FlipXBox->setChecked(params.m_FlipX);
	- m_Controls->m_FlipYBox->setChecked(params.m_FlipY);
	- m_Controls->m_FlipZBox->setChecked(params.m_FlipZ);
	- m_Controls->m_InterpolationBox->setChecked(params.m_InterpolateTractographyData);
	-
	-
	- m_Controls->m_MaskInterpolationBox->setChecked(params.m_InterpolateRoiImages);
	- m_Controls->m_SeedsPerVoxelBox->setValue(params.m_SeedsPerVoxel);
	- m_Controls->m_StepSizeBox->setValue(params.GetStepSizeVox());
	- m_Controls->m_SamplingDistanceBox->setValue(params.GetSamplingDistanceVox());
	- m_Controls->m_StopVotesBox->setChecked(params.m_StopVotes);
	- m_Controls->m_FrontalSamplesBox->setChecked(params.m_OnlyForwardSamples);
	- m_Controls->m_TrialsPerSeedBox->setValue(params.m_TrialsPerSeed);
	-
	- m_Controls->m_NumSamplesBox->setValue(params.m_NumSamples);
	- m_Controls->m_LoopCheckBox->setValue(params.GetLoopCheckDeg());
	- m_Controls->m_AngularThresholdBox->setValue(params.GetAngularThresholdDeg());
	- m_Controls->m_MinTractLengthBox->setValue(params.m_MinTractLengthMm);
	- m_Controls->m_MaxTractLengthBox->setValue(params.m_MaxTractLengthMm);
	- m_Controls->m_OutputProbMap->setChecked(params.m_OutputProbMap);
	- m_Controls->m_FixSeedBox->setChecked(params.m_FixRandomSeed);
	- m_Controls->m_PeakJitterBox->setValue(params.m_PeakJitter);
	-
	- switch (params.m_Mode)
	- {
	- case mitk::TrackingDataHandler::MODE::DETERMINISTIC:
	- m_Controls->m_ModeBox->setCurrentIndex(0);
	- break;
	- case mitk::TrackingDataHandler::MODE::PROBABILISTIC:
	- m_Controls->m_ModeBox->setCurrentIndex(1);
	- break;
	- }
	-
	- switch (params.m_EpConstraints)
	- {
	- case itk::StreamlineTrackingFilter::EndpointConstraints::NONE:
	- m_Controls->m_EpConstraintsBox->setCurrentIndex(0);
	- break;
	- case itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_TARGET:
	- m_Controls->m_EpConstraintsBox->setCurrentIndex(1);
	- break;
	- case itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_TARGET_LABELDIFF:
	- m_Controls->m_EpConstraintsBox->setCurrentIndex(2);
	- break;
	- case itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_SEED_AND_TARGET:
	- m_Controls->m_EpConstraintsBox->setCurrentIndex(3);
	- break;
	- case itk::StreamlineTrackingFilter::EndpointConstraints::MIN_ONE_EP_IN_TARGET:
	- m_Controls->m_EpConstraintsBox->setCurrentIndex(4);
	- break;
	- case itk::StreamlineTrackingFilter::EndpointConstraints::ONE_EP_IN_TARGET:
	- m_Controls->m_EpConstraintsBox->setCurrentIndex(5);
	- break;
	- case itk::StreamlineTrackingFilter::EndpointConstraints::NO_EP_IN_TARGET:
	- m_Controls->m_EpConstraintsBox->setCurrentIndex(6);
	- break;
	- }
	-}
	-
	-std::shared_ptr<mitk::StreamlineTractographyParameters> QmitkStreamlineTrackingView::GetParametersFromGui()
	-{
	-
	- // NOT IN GUI
	-// unsigned int m_NumPreviousDirections = 1;
	-// bool m_AvoidStop = true;
	-// bool m_RandomSampling = false;
	-// float m_DeflectionMod = 1.0;
	-// bool m_ApplyDirectionMatrix = false;
	-
	- std::shared_ptr<mitk::StreamlineTractographyParameters> params = std::make_shared<mitk::StreamlineTractographyParameters>();
	- params->m_InteractiveRadiusMm = m_Controls->m_SeedRadiusBox->value();
	- params->m_NumInteractiveSeeds = m_Controls->m_NumSeedsBox->value();
	- params->m_EnableInteractive = m_Controls->m_InteractiveBox->isChecked();
	- params->m_Compression = m_Controls->m_FiberErrorBox->value();
	- params->m_CompressFibers = m_Controls->m_ResampleFibersBox->isChecked();
	-
	- params->m_InteractiveRadiusMm = m_Controls->m_SeedRadiusBox->value();
	- params->m_MaxNumFibers = m_Controls->m_NumFibersBox->value();
	- params->m_Cutoff = static_cast<float>(m_Controls->m_ScalarThresholdBox->value());
	- params->m_F = static_cast<float>(m_Controls->m_fBox->value());
	- params->m_G = static_cast<float>(m_Controls->m_gBox->value());
	-
	- params->m_OdfCutoff = static_cast<float>(m_Controls->m_OdfCutoffBox->value());
	- params->m_SharpenOdfs = m_Controls->m_SharpenOdfsBox->isChecked();
	-
	- params->m_Weight = static_cast<float>(m_Controls->m_PriorWeightBox->value());
	- params->m_RestrictToPrior = m_Controls->m_PriorAsMaskBox->isChecked();
	- params->m_NewDirectionsFromPrior = m_Controls->m_NewDirectionsFromPriorBox->isChecked();
	-
	- params->m_PriorFlipX = m_Controls->m_PriorFlipXBox->isChecked();
	- params->m_PriorFlipY = m_Controls->m_PriorFlipYBox->isChecked();
	- params->m_PriorFlipZ = m_Controls->m_PriorFlipZBox->isChecked();
	-
	- params->m_FlipX = m_Controls->m_FlipXBox->isChecked();
	- params->m_FlipY = m_Controls->m_FlipYBox->isChecked();
	- params->m_FlipZ = m_Controls->m_FlipZBox->isChecked();
	- params->m_InterpolateTractographyData = m_Controls->m_InterpolationBox->isChecked();
	-
	-
	- params->m_InterpolateRoiImages = m_Controls->m_MaskInterpolationBox->isChecked();
	- params->m_SeedsPerVoxel = m_Controls->m_SeedsPerVoxelBox->value();
	- params->SetStepSizeVox(m_Controls->m_StepSizeBox->value());
	- params->SetSamplingDistanceVox(m_Controls->m_SamplingDistanceBox->value());
	- params->m_StopVotes = m_Controls->m_StopVotesBox->isChecked();
	- params->m_OnlyForwardSamples = m_Controls->m_FrontalSamplesBox->isChecked();
	- params->m_TrialsPerSeed = m_Controls->m_TrialsPerSeedBox->value();
	-
	- params->m_NumSamples = m_Controls->m_NumSamplesBox->value();
	- params->SetLoopCheckDeg(m_Controls->m_LoopCheckBox->value());
	- params->SetAngularThresholdDeg(m_Controls->m_AngularThresholdBox->value());
	- params->m_MinTractLengthMm = m_Controls->m_MinTractLengthBox->value();
	- params->m_MaxTractLengthMm = m_Controls->m_MaxTractLengthBox->value();
	- params->m_OutputProbMap = m_Controls->m_OutputProbMap->isChecked();
	- params->m_FixRandomSeed = m_Controls->m_FixSeedBox->isChecked();
	- params->m_PeakJitter = static_cast<float>(m_Controls->m_PeakJitterBox->value());
	-
	- switch (m_Controls->m_ModeBox->currentIndex())
	- {
	- case 0:
	- params->m_Mode = mitk::TrackingDataHandler::MODE::DETERMINISTIC;
	- break;
	- case 1:
	- params->m_Mode = mitk::TrackingDataHandler::MODE::PROBABILISTIC;
	- break;
	- default:
	- params->m_Mode = mitk::TrackingDataHandler::MODE::DETERMINISTIC;
	- }
	-
	- switch (m_Controls->m_EpConstraintsBox->currentIndex())
	- {
	- case 0:
	- params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::NONE;
	- break;
	- case 1:
	- params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_TARGET;
	- break;
	- case 2:
	- params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_TARGET_LABELDIFF;
	- break;
	- case 3:
	- params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_SEED_AND_TARGET;
	- break;
	- case 4:
	- params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::MIN_ONE_EP_IN_TARGET;
	- break;
	- case 5:
	- params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::ONE_EP_IN_TARGET;
	- break;
	- case 6:
	- params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::NO_EP_IN_TARGET;
	- break;
	- }
	-
	- return params;
	-}
	-
	-void QmitkStreamlineTrackingView::SaveParameters()
	-{
	- QString filename = QFileDialog::getSaveFileName(
	- 0,
	- tr("Save Tractography Parameters"),
	- m_ParameterFile,
	- tr("Streamline Tractography Parameters (*.stp)") );
	-
	- if(filename.isEmpty() \|\| filename.isNull())
	- return;
	-
	- m_ParameterFile = filename;
	-
	- auto params = GetParametersFromGui();
	- params->SaveParameters(m_ParameterFile.toStdString());
	-}
	-
	-void QmitkStreamlineTrackingView::LoadParameters()
	-{
	- QString filename = QFileDialog::getOpenFileName(
	- 0,
	- tr("Load Tractography Parameters"),
	- m_ParameterFile,
	- tr("Streamline Tractography Parameters (*.stp)") );
	-
	- if(filename.isEmpty() \|\| filename.isNull())
	- return;
	-
	- m_ParameterFile = filename;
	-
	- mitk::StreamlineTractographyParameters params;
	- params.LoadParameters(m_ParameterFile.toStdString());
	- ParametersToGui(params);
	-}
	-
	-void QmitkStreamlineTrackingView::StopTractography()
	-{
	- if (m_Tracker.IsNull())
	- return;
	-
	- m_Tracker->SetStopTracking(true);
	-}
	-
	-void QmitkStreamlineTrackingView::TimerUpdate()
	-{
	- if (m_Tracker.IsNull())
	- return;
	-
	- QString status_text(m_Tracker->GetStatusText().c_str());
	- m_Controls->m_StatusTextBox->setText(status_text);
	-}
	-
	-void QmitkStreamlineTrackingView::BeforeThread()
	-{
	- m_TrackingTimer->start(1000);
	-}
	-
	-void QmitkStreamlineTrackingView::AfterThread()
	-{
	- auto params = m_Tracker->GetParameters();
	- m_TrackingTimer->stop();
	- if (!params->m_OutputProbMap)
	- {
	- vtkSmartPointer<vtkPolyData> fiberBundle = m_Tracker->GetFiberPolyData();
	-
	- if (!m_Controls->m_InteractiveBox->isChecked() && fiberBundle->GetNumberOfLines() == 0)
	- {
	- QMessageBox warnBox;
	- warnBox.setWindowTitle("Warning");
	- warnBox.setText("No fiberbundle was generated!");
	- warnBox.setDetailedText("No fibers were generated using the chosen parameters. Typical reasons are:\n\n- Cutoff too high. Some images feature very low FA/GFA/peak size. Try to lower this parameter.\n- Angular threshold too strict. Try to increase this parameter.\n- A small step sizes also means many steps to go wrong. Especially in the case of probabilistic tractography. Try to adjust the angular threshold.");
	- warnBox.setIcon(QMessageBox::Warning);
	- warnBox.exec();
	-
	- if (m_InteractivePointSetNode.IsNotNull())
	- m_InteractivePointSetNode->SetProperty("color", mitk::ColorProperty::New(1,1,1));
	- StartStopTrackingGui(false);
	- if (m_DeleteTrackingHandler)
	- DeleteTrackingHandler();
	- UpdateGui();
	-
	- return;
	- }
	-
	- mitk::FiberBundle::Pointer fib = mitk::FiberBundle::New(fiberBundle);
	- fib->SetReferenceGeometry(dynamic_cast<mitk::Image*>(m_ParentNode->GetData())->GetGeometry());
	- if (m_Controls->m_ResampleFibersBox->isChecked() && fiberBundle->GetNumberOfLines()>0)
	- fib->Compress(m_Controls->m_FiberErrorBox->value());
	- fib->ColorFibersByOrientation();
	- m_Tracker->SetDicomProperties(fib);
	-
	- if (m_Controls->m_InteractiveBox->isChecked())
	- {
	- if (m_InteractiveNode.IsNull())
	- {
	- m_InteractiveNode = mitk::DataNode::New();
	- QString name("Interactive");
	- m_InteractiveNode->SetName(name.toStdString());
	- GetDataStorage()->Add(m_InteractiveNode);
	- }
	- m_InteractiveNode->SetData(fib);
	- m_InteractiveNode->SetFloatProperty("Fiber2DSliceThickness", params->GetMinVoxelSizeMm()/2);
	-
	- if (auto renderWindowPart = this->GetRenderWindowPart())
	- renderWindowPart->RequestUpdate();
	- }
	- else
	- {
	- mitk::DataNode::Pointer node = mitk::DataNode::New();
	- node->SetData(fib);
	- QString name("FiberBundle_");
	- name += m_ParentNode->GetName().c_str();
	- name += "_Streamline";
	- node->SetName(name.toStdString());
	- node->SetFloatProperty("Fiber2DSliceThickness", params->GetMinVoxelSizeMm()/2);
	- GetDataStorage()->Add(node, m_ParentNode);
	- }
	- }
	- else
	- {
	- TrackerType::ItkDoubleImgType::Pointer outImg = m_Tracker->GetOutputProbabilityMap();
	- mitk::Image::Pointer img = mitk::Image::New();
	- img->InitializeByItk(outImg.GetPointer());
	- img->SetVolume(outImg->GetBufferPointer());
	-
	- if (m_Controls->m_InteractiveBox->isChecked())
	- {
	- if (m_InteractiveNode.IsNull())
	- {
	- m_InteractiveNode = mitk::DataNode::New();
	- QString name("Interactive");
	- m_InteractiveNode->SetName(name.toStdString());
	- GetDataStorage()->Add(m_InteractiveNode);
	- }
	- m_InteractiveNode->SetData(img);
	-
	- mitk::LookupTable::Pointer lut = mitk::LookupTable::New();
	- lut->SetType(mitk::LookupTable::JET_TRANSPARENT);
	- mitk::LookupTableProperty::Pointer lut_prop = mitk::LookupTableProperty::New();
	- lut_prop->SetLookupTable(lut);
	- m_InteractiveNode->SetProperty("LookupTable", lut_prop);
	- m_InteractiveNode->SetProperty("opacity", mitk::FloatProperty::New(0.5));
	- m_InteractiveNode->SetFloatProperty("Fiber2DSliceThickness", params->GetMinVoxelSizeMm()/2);
	-
	- if (auto renderWindowPart = this->GetRenderWindowPart())
	- renderWindowPart->RequestUpdate();
	- }
	- else
	- {
	- mitk::DataNode::Pointer node = mitk::DataNode::New();
	- node->SetData(img);
	- QString name("ProbabilityMap_");
	- name += m_ParentNode->GetName().c_str();
	- node->SetName(name.toStdString());
	-
	- mitk::LookupTable::Pointer lut = mitk::LookupTable::New();
	- lut->SetType(mitk::LookupTable::JET_TRANSPARENT);
	- mitk::LookupTableProperty::Pointer lut_prop = mitk::LookupTableProperty::New();
	- lut_prop->SetLookupTable(lut);
	- node->SetProperty("LookupTable", lut_prop);
	- node->SetProperty("opacity", mitk::FloatProperty::New(0.5));
	-
	- GetDataStorage()->Add(node, m_ParentNode);
	- }
	- }
	- if (m_InteractivePointSetNode.IsNotNull())
	- m_InteractivePointSetNode->SetProperty("color", mitk::ColorProperty::New(1,1,1));
	- StartStopTrackingGui(false);
	- if (m_DeleteTrackingHandler)
	- DeleteTrackingHandler();
	- UpdateGui();
	-}
	-
	-void QmitkStreamlineTrackingView::InteractiveSeedChanged(bool posChanged)
	-{
	- if(!CheckAndStoreLastParams(sender()) && !posChanged)
	- return;
	- if (m_ThreadIsRunning \|\| !m_Visible)
	- return;
	-
	- if (!posChanged && (!m_Controls->m_InteractiveBox->isChecked() \|\| !m_Controls->m_ParamUpdateBox->isChecked()) )
	- return;
	-
	- std::srand(std::time(0));
	- m_SeedPoints.clear();
	-
	- itk::Point<float> world_pos = this->GetRenderWindowPart()->GetSelectedPosition();
	-
	- m_SeedPoints.push_back(world_pos);
	- float radius = m_Controls->m_SeedRadiusBox->value();
	- int num = m_Controls->m_NumSeedsBox->value();
	-
	- mitk::PointSet::Pointer pointset = mitk::PointSet::New();
	- pointset->InsertPoint(0, world_pos);
	- m_InteractivePointSetNode->SetProperty("pointsize", mitk::FloatProperty::New(radius*2));
	- m_InteractivePointSetNode->SetProperty("point 2D size", mitk::FloatProperty::New(radius*2));
	- m_InteractivePointSetNode->SetData(pointset);
	-
	- for (int i=1; i<num; i++)
	- {
	- itk::Vector<float> p;
	- p[0] = rand()%1000-500;
	- p[1] = rand()%1000-500;
	- p[2] = rand()%1000-500;
	- p.Normalize();
	- p *= radius;
	- m_SeedPoints.push_back(world_pos+p);
	- }
	- m_InteractivePointSetNode->SetProperty("color", mitk::ColorProperty::New(1,0,0));
	- DoFiberTracking();
	-}
	-
	-bool QmitkStreamlineTrackingView::CheckAndStoreLastParams(QObject* obj)
	-{
	- if (obj!=nullptr)
	- {
	- std::string new_val = "";
	- if(qobject_cast<QDoubleSpinBox*>(obj)!=nullptr)
	- new_val = boost::lexical_cast<std::string>(qobject_cast<QDoubleSpinBox*>(obj)->value());
	- else if (qobject_cast<QSpinBox*>(obj)!=nullptr)
	- new_val = boost::lexical_cast<std::string>(qobject_cast<QSpinBox*>(obj)->value());
	- else
	- return true;
	-
	- if (m_LastTractoParams.find(obj->objectName())==m_LastTractoParams.end())
	- {
	- m_LastTractoParams[obj->objectName()] = new_val;
	- return false;
	- }
	- else if (m_LastTractoParams.at(obj->objectName()) != new_val)
	- {
	- m_LastTractoParams[obj->objectName()] = new_val;
	- return true;
	- }
	- else if (m_LastTractoParams.at(obj->objectName()) == new_val)
	- return false;
	- }
	- return true;
	-}
	-
	-void QmitkStreamlineTrackingView::OnParameterChanged()
	-{
	- UpdateGui();
	-
	- if(!CheckAndStoreLastParams(sender()))
	- return;
	-
	- if (m_Controls->m_InteractiveBox->isChecked() && m_Controls->m_ParamUpdateBox->isChecked())
	- DoFiberTracking();
	-}
	-
	-void QmitkStreamlineTrackingView::ToggleInteractive()
	-{
	- UpdateGui();
	-
	- m_Controls->m_SeedsPerVoxelBox->setEnabled(!m_Controls->m_InteractiveBox->isChecked());
	- m_Controls->m_SeedsPerVoxelLabel->setEnabled(!m_Controls->m_InteractiveBox->isChecked());
	- m_Controls->m_SeedImageSelectionWidget->setEnabled(!m_Controls->m_InteractiveBox->isChecked());
	- m_Controls->label_6->setEnabled(!m_Controls->m_InteractiveBox->isChecked());
	-
	- if ( m_Controls->m_InteractiveBox->isChecked() )
	- {
	- if (m_FirstInteractiveRun)
	- {
	- QMessageBox::information(nullptr, "Information", "Place and move a spherical seed region anywhere in the image by left-clicking and dragging. If the seed region is colored red, tracking is in progress. If the seed region is colored white, tracking is finished.\nPlacing the seed region for the first time in a newly selected dataset might cause a short delay, since the tracker needs to be initialized.");
	- m_FirstInteractiveRun = false;
	- }
	-
	- QApplication::setOverrideCursor(Qt::PointingHandCursor);
	- QApplication::processEvents();
	-
	- m_InteractivePointSetNode = mitk::DataNode::New();
	- m_InteractivePointSetNode->SetProperty("color", mitk::ColorProperty::New(1,1,1));
	- m_InteractivePointSetNode->SetName("InteractiveSeedRegion");
	- mitk::PointSetShapeProperty::Pointer shape_prop = mitk::PointSetShapeProperty::New();
	- shape_prop->SetValue(mitk::PointSetShapeProperty::PointSetShape::CIRCLE);
	- m_InteractivePointSetNode->SetProperty("Pointset.2D.shape", shape_prop);
	- GetDataStorage()->Add(m_InteractivePointSetNode);
	-
	-
	- m_SliceChangeListener.RenderWindowPartActivated(this->GetRenderWindowPart());
	- connect(&m_SliceChangeListener, SIGNAL(SliceChanged()), this, SLOT(OnSliceChanged()));
	- }
	- else
	- {
	- QApplication::restoreOverrideCursor();
	- QApplication::processEvents();
	-
	- m_InteractiveNode = nullptr;
	- m_InteractivePointSetNode = nullptr;
	-
	- m_SliceChangeListener.RenderWindowPartActivated(this->GetRenderWindowPart());
	- disconnect(&m_SliceChangeListener, SIGNAL(SliceChanged()), this, SLOT(OnSliceChanged()));
	- }
	-}
	-
	-void QmitkStreamlineTrackingView::Activated()
	-{
	-
	-}
	-
	-void QmitkStreamlineTrackingView::Deactivated()
	-{
	-
	-}
	-
	-void QmitkStreamlineTrackingView::Visible()
	-{
	- m_Visible = true;
	-}
	-
	-void QmitkStreamlineTrackingView::Hidden()
	-{
	- m_Visible = false;
	- m_Controls->m_InteractiveBox->setChecked(false);
	- ToggleInteractive();
	-}
	-
	-void QmitkStreamlineTrackingView::OnSliceChanged()
	-{
	- InteractiveSeedChanged(true);
	-}
	-
	-void QmitkStreamlineTrackingView::SetFocus()
	-{
	-}
	-
	-void QmitkStreamlineTrackingView::DeleteTrackingHandler()
	-{
	- if (!m_ThreadIsRunning && m_TrackingHandler != nullptr)
	- {
	- if (m_TrackingPriorHandler != nullptr)
	- {
	- delete m_TrackingPriorHandler;
	- m_TrackingPriorHandler = nullptr;
	- }
	- delete m_TrackingHandler;
	- m_TrackingHandler = nullptr;
	- m_DeleteTrackingHandler = false;
	- m_LastPrior = nullptr;
	- }
	- else if (m_ThreadIsRunning)
	- {
	- m_DeleteTrackingHandler = true;
	- }
	-}
	-
	-void QmitkStreamlineTrackingView::ForestSwitched()
	-{
	- DeleteTrackingHandler();
	-}
	-
	-void QmitkStreamlineTrackingView::OutputStyleSwitched()
	-{
	- if (m_InteractiveNode.IsNotNull())
	- GetDataStorage()->Remove(m_InteractiveNode);
	- m_InteractiveNode = nullptr;
	-}
	-
	-void QmitkStreamlineTrackingView::OnSelectionChanged( berry::IWorkbenchPart::Pointer , const QList<mitk::DataNode::Pointer>& nodes )
	-{
	- std::vector< mitk::DataNode::Pointer > last_nodes = m_InputImageNodes;
	- m_InputImageNodes.clear();
	- m_AdditionalInputImages.clear();
	- bool retrack = false;
	-
	- for( auto node : nodes )
	- {
	-
	- if( node.IsNotNull() && dynamic_cast<mitk::Image*>(node->GetData()) )
	- {
	- if( dynamic_cast<mitk::TensorImage*>(node->GetData()) \|\|
	- dynamic_cast<mitk::OdfImage*>(node->GetData()) \|\|
	- dynamic_cast<mitk::ShImage*>(node->GetData()) \|\|
	- dynamic_cast<mitk::PeakImage*>(node->GetData()) \|\|
	- mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast<mitk::Image *>(node->GetData())))
	- {
	- m_InputImageNodes.push_back(node);
	- retrack = true;
	- }
	- else
	- {
	- mitk::Image* img = dynamic_cast<mitk::Image*>(node->GetData());
	- if (img!=nullptr && img->GetDimension()==3)
	- m_AdditionalInputImages.push_back(dynamic_cast<mitk::Image*>(node->GetData()));
	- }
	- }
	- }
	-
	- // sometimes the OnSelectionChanged event is sent twice and actually no selection has changed for the first event. We need to catch that.
	- if (last_nodes.size() == m_InputImageNodes.size())
	- {
	- bool same_nodes = true;
	- for (unsigned int i=0; i<m_InputImageNodes.size(); i++)
	- if (last_nodes.at(i)!=m_InputImageNodes.at(i))
	- {
	- same_nodes = false;
	- break;
	- }
	- if (same_nodes)
	- return;
	- }
	-
	- DeleteTrackingHandler();
	- UpdateGui();
	- if (retrack)
	- OnParameterChanged();
	-}
	-
	-void QmitkStreamlineTrackingView::UpdateGui()
	-{
	- m_Controls->m_TensorImageLabel->setText("<font color='red'>select in data-manager</font>");
	-
	- m_Controls->m_fBox->setEnabled(false);
	- m_Controls->m_fLabel->setEnabled(false);
	- m_Controls->m_gBox->setEnabled(false);
	- m_Controls->m_gLabel->setEnabled(false);
	- m_Controls->m_FaImageSelectionWidget->setEnabled(true);
	- m_Controls->mFaImageLabel->setEnabled(true);
	- m_Controls->m_OdfCutoffBox->setEnabled(false);
	- m_Controls->m_OdfCutoffLabel->setEnabled(false);
	- m_Controls->m_SharpenOdfsBox->setEnabled(false);
	- m_Controls->m_ForestSelectionWidget->setVisible(false);
	- m_Controls->m_ForestLabel->setVisible(false);
	- m_Controls->commandLinkButton->setEnabled(false);
	- m_Controls->m_TrialsPerSeedBox->setEnabled(false);
	- m_Controls->m_TrialsPerSeedLabel->setEnabled(false);
	- m_Controls->m_TargetImageSelectionWidget->setEnabled(false);
	- m_Controls->m_TargetImageLabel->setEnabled(false);
	- m_Controls->m_PeakJitterBox->setEnabled(false);
	-
	- if (m_Controls->m_InteractiveBox->isChecked())
	- {
	- m_Controls->m_InteractiveSeedingFrame->setVisible(true);
	- m_Controls->m_StaticSeedingFrame->setVisible(false);
	- m_Controls->commandLinkButton_2->setVisible(false);
	- m_Controls->commandLinkButton->setVisible(false);
	- }
	- else
	- {
	- m_Controls->m_InteractiveSeedingFrame->setVisible(false);
	- m_Controls->m_StaticSeedingFrame->setVisible(true);
	- m_Controls->commandLinkButton_2->setVisible(m_ThreadIsRunning);
	- m_Controls->commandLinkButton->setVisible(!m_ThreadIsRunning);
	- }
	-
	- if (m_Controls->m_EpConstraintsBox->currentIndex()>0)
	- {
	- m_Controls->m_TargetImageSelectionWidget->setEnabled(true);
	- m_Controls->m_TargetImageLabel->setEnabled(true);
	- }
	-
	- // stuff that is only important for probabilistic tractography
	- if (m_Controls->m_ModeBox->currentIndex()==1)
	- {
	- m_Controls->m_TrialsPerSeedBox->setEnabled(true);
	- m_Controls->m_TrialsPerSeedLabel->setEnabled(true);
	- m_Controls->m_PeakJitterBox->setEnabled(true);
	- }
	-
	- if(!m_InputImageNodes.empty())
	- {
	- if (m_InputImageNodes.size()>1)
	- m_Controls->m_TensorImageLabel->setText( ( std::to_string(m_InputImageNodes.size()) + " images selected").c_str() );
	- else
	- m_Controls->m_TensorImageLabel->setText(m_InputImageNodes.at(0)->GetName().c_str());
	- m_Controls->commandLinkButton->setEnabled(!m_Controls->m_InteractiveBox->isChecked() && !m_ThreadIsRunning);
	-
	- m_Controls->m_ScalarThresholdBox->setEnabled(true);
	- m_Controls->m_FaThresholdLabel->setEnabled(true);
	-
	- if ( dynamic_cast<mitk::TensorImage*>(m_InputImageNodes.at(0)->GetData()) )
	- {
	- m_Controls->m_fBox->setEnabled(true);
	- m_Controls->m_fLabel->setEnabled(true);
	- m_Controls->m_gBox->setEnabled(true);
	- m_Controls->m_gLabel->setEnabled(true);
	- }
	- else if ( dynamic_cast<mitk::OdfImage*>(m_InputImageNodes.at(0)->GetData()) \|\|
	- dynamic_cast<mitk::ShImage*>(m_InputImageNodes.at(0)->GetData()))
	- {
	- m_Controls->m_OdfCutoffBox->setEnabled(true);
	- m_Controls->m_OdfCutoffLabel->setEnabled(true);
	- m_Controls->m_SharpenOdfsBox->setEnabled(true);
	- }
	- else if ( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast<mitk::Image *>(m_InputImageNodes.at(0)->GetData())) )
	- {
	- m_Controls->m_ForestSelectionWidget->setVisible(true);
	- m_Controls->m_ForestLabel->setVisible(true);
	- m_Controls->m_ScalarThresholdBox->setEnabled(false);
	- m_Controls->m_FaThresholdLabel->setEnabled(false);
	- }
	- }
	-}
	-
	-void QmitkStreamlineTrackingView::StartStopTrackingGui(bool start)
	-{
	- m_ThreadIsRunning = start;
	-
	- if (!m_Controls->m_InteractiveBox->isChecked())
	- {
	- m_Controls->commandLinkButton_2->setVisible(start);
	- m_Controls->commandLinkButton->setVisible(!start);
	- m_Controls->m_InteractiveBox->setEnabled(!start);
	- m_Controls->m_StatusTextBox->setVisible(start);
	- }
	-}
	-
	-void QmitkStreamlineTrackingView::DoFiberTracking()
	-{
	- auto params = GetParametersFromGui();
	-
	- if (m_InputImageNodes.empty())
	- {
	- QMessageBox::information(nullptr, "Information", "Please select an input image in the datamaneger (tensor, ODF, peak or dMRI image)!");
	- return;
	- }
	- if (m_ThreadIsRunning \|\| !m_Visible)
	- return;
	- if (m_Controls->m_InteractiveBox->isChecked() && m_SeedPoints.empty())
	- return;
	- StartStopTrackingGui(true);
	-
	- m_Tracker = TrackerType::New();
	-
	- if (params->m_EpConstraints == itk::StreamlineTrackingFilter::EndpointConstraints::NONE)
	- m_Tracker->SetTargetRegions(nullptr);
	-
	- if( dynamic_cast<mitk::TensorImage*>(m_InputImageNodes.at(0)->GetData()) )
	- {
	- if (m_Controls->m_ModeBox->currentIndex()==1)
	- {
	- if (m_InputImageNodes.size()>1)
	- {
	- QMessageBox::information(nullptr, "Information", "Probabilistic tensor tractography is only implemented for single-tensor mode!");
	- StartStopTrackingGui(false);
	- return;
	- }
	-
	- if (m_TrackingHandler==nullptr)
	- {
	- m_TrackingHandler = new mitk::TrackingHandlerOdf();
	- typedef itk::TensorImageToOdfImageFilter< float, float > FilterType;
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetInput( mitk::convert::GetItkTensorFromTensorImage(dynamic_cast<mitk::Image*>(m_InputImageNodes.at(0)->GetData())) );
	- filter->Update();
	- dynamic_cast<mitk::TrackingHandlerOdf*>(m_TrackingHandler)->SetOdfImage(filter->GetOutput());
	-
	- if (m_Controls->m_FaImageSelectionWidget->GetSelectedNode().IsNotNull())
	- {
	- ItkFloatImageType::Pointer itkImg = ItkFloatImageType::New();
	- mitk::CastToItkImage(dynamic_cast<mitk::Image*>(m_Controls->m_FaImageSelectionWidget->GetSelectedNode()->GetData()), itkImg);
	-
	- dynamic_cast<mitk::TrackingHandlerOdf*>(m_TrackingHandler)->SetGfaImage(itkImg);
	- }
	- }
	-
	- dynamic_cast<mitk::TrackingHandlerOdf*>(m_TrackingHandler)->SetIsOdfFromTensor(true);
	- }
	- else
	- {
	- if (m_TrackingHandler==nullptr)
	- {
	- m_TrackingHandler = new mitk::TrackingHandlerTensor();
	- for (unsigned int i=0; i<m_InputImageNodes.size(); ++i)
	- dynamic_cast<mitk::TrackingHandlerTensor>(m_TrackingHandler)->AddTensorImage(mitk::convert::GetItkTensorFromTensorImage(dynamic_cast<mitk::Image>(m_InputImageNodes.at(i)->GetData())).GetPointer());
	-
	- if (m_Controls->m_FaImageSelectionWidget->GetSelectedNode().IsNotNull())
	- {
	- ItkFloatImageType::Pointer itkImg = ItkFloatImageType::New();
	- mitk::CastToItkImage(dynamic_cast<mitk::Image*>(m_Controls->m_FaImageSelectionWidget->GetSelectedNode()->GetData()), itkImg);
	-
	- dynamic_cast<mitk::TrackingHandlerTensor*>(m_TrackingHandler)->SetFaImage(itkImg);
	- }
	- }
	- }
	- }
	- else if ( dynamic_cast<mitk::OdfImage*>(m_InputImageNodes.at(0)->GetData()) \|\|
	- dynamic_cast<mitk::ShImage*>(m_InputImageNodes.at(0)->GetData()))
	- {
	- if (m_TrackingHandler==nullptr)
	- {
	- m_TrackingHandler = new mitk::TrackingHandlerOdf();
	-
	- if (dynamic_cast<mitk::ShImage*>(m_InputImageNodes.at(0)->GetData()))
	- dynamic_cast<mitk::TrackingHandlerOdf>(m_TrackingHandler)->SetOdfImage(mitk::convert::GetItkOdfFromShImage(dynamic_cast<mitk::ShImage>(m_InputImageNodes.at(0)->GetData())));
	- else
	- dynamic_cast<mitk::TrackingHandlerOdf>(m_TrackingHandler)->SetOdfImage(mitk::convert::GetItkOdfFromOdfImage(dynamic_cast<mitk::OdfImage>(m_InputImageNodes.at(0)->GetData())));
	-
	- if (m_Controls->m_FaImageSelectionWidget->GetSelectedNode().IsNotNull())
	- {
	- ItkFloatImageType::Pointer itkImg = ItkFloatImageType::New();
	- mitk::CastToItkImage(dynamic_cast<mitk::Image*>(m_Controls->m_FaImageSelectionWidget->GetSelectedNode()->GetData()), itkImg);
	- dynamic_cast<mitk::TrackingHandlerOdf*>(m_TrackingHandler)->SetGfaImage(itkImg);
	- }
	- }
	- }
	- else if ( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast<mitk::Image*>(m_InputImageNodes.at(0)->GetData())) )
	- {
	- if ( m_Controls->m_ForestSelectionWidget->GetSelectedNode().IsNull() )
	- {
	- QMessageBox::information(nullptr, "Information", "Not random forest for machine learning based tractography (raw dMRI tractography) selected. Did you accidentally select the raw diffusion-weighted image in the datamanager?");
	- StartStopTrackingGui(false);
	- return;
	- }
	-
	- if (m_TrackingHandler==nullptr)
	- {
	- mitk::TractographyForest::Pointer forest = dynamic_cast<mitk::TractographyForest*>(m_Controls->m_ForestSelectionWidget->GetSelectedNode()->GetData());
	- mitk::Image::Pointer dwi = dynamic_cast<mitk::Image*>(m_InputImageNodes.at(0)->GetData());
	-
	- std::vector< std::vector< ItkFloatImageType::Pointer > > additionalFeatureImages;
	- additionalFeatureImages.push_back(std::vector< ItkFloatImageType::Pointer >());
	- for (auto img : m_AdditionalInputImages)
	- {
	- ItkFloatImageType::Pointer itkimg = ItkFloatImageType::New();
	- mitk::CastToItkImage(img, itkimg);
	- additionalFeatureImages.at(0).push_back(itkimg);
	- }
	-
	- bool forest_valid = false;
	- if (forest->GetNumFeatures()>=100)
	- {
	- params->m_NumPreviousDirections = static_cast<unsigned int>((forest->GetNumFeatures() - (100 + additionalFeatureImages.at(0).size()))/3);
	- m_TrackingHandler = new mitk::TrackingHandlerRandomForest<6, 100>();
	- dynamic_cast<mitk::TrackingHandlerRandomForest<6, 100>*>(m_TrackingHandler)->AddDwi(dwi);
	- dynamic_cast<mitk::TrackingHandlerRandomForest<6, 100>*>(m_TrackingHandler)->SetAdditionalFeatureImages(additionalFeatureImages);
	- dynamic_cast<mitk::TrackingHandlerRandomForest<6, 100>*>(m_TrackingHandler)->SetForest(forest);
	- forest_valid = dynamic_cast<mitk::TrackingHandlerRandomForest<6, 100>*>(m_TrackingHandler)->IsForestValid();
	- }
	- else
	- {
	- params->m_NumPreviousDirections = static_cast<unsigned int>((forest->GetNumFeatures() - (28 + additionalFeatureImages.at(0).size()))/3);
	- m_TrackingHandler = new mitk::TrackingHandlerRandomForest<6, 28>();
	- dynamic_cast<mitk::TrackingHandlerRandomForest<6, 28>*>(m_TrackingHandler)->AddDwi(dwi);
	- dynamic_cast<mitk::TrackingHandlerRandomForest<6, 28>*>(m_TrackingHandler)->SetAdditionalFeatureImages(additionalFeatureImages);
	- dynamic_cast<mitk::TrackingHandlerRandomForest<6, 28>*>(m_TrackingHandler)->SetForest(forest);
	- forest_valid = dynamic_cast<mitk::TrackingHandlerRandomForest<6, 28>*>(m_TrackingHandler)->IsForestValid();
	- }
	-
	- if (!forest_valid)
	- {
	- QMessageBox::information(nullptr, "Information", "Random forest is invalid. The forest signatue does not match the parameters of TrackingHandlerRandomForest.");
	- StartStopTrackingGui(false);
	- return;
	- }
	- }
	- }
	- else
	- {
	- if (m_TrackingHandler==nullptr)
	- {
	- m_TrackingHandler = new mitk::TrackingHandlerPeaks();
	- dynamic_cast<mitk::TrackingHandlerPeaks>(m_TrackingHandler)->SetPeakImage(mitk::convert::GetItkPeakFromPeakImage(dynamic_cast<mitk::Image>(m_InputImageNodes.at(0)->GetData())));
	- }
	- }
	-
	- if (m_Controls->m_InteractiveBox->isChecked())
	- {
	- m_Tracker->SetSeedPoints(m_SeedPoints);
	- }
	- else if (m_Controls->m_SeedImageSelectionWidget->GetSelectedNode().IsNotNull())
	- {
	- ItkFloatImageType::Pointer mask = ItkFloatImageType::New();
	- mitk::CastToItkImage(dynamic_cast<mitk::Image*>(m_Controls->m_SeedImageSelectionWidget->GetSelectedNode()->GetData()), mask);
	- m_Tracker->SetSeedImage(mask);
	- }
	-
	- if (m_Controls->m_MaskImageSelectionWidget->GetSelectedNode().IsNotNull())
	- {
	- ItkFloatImageType::Pointer mask = ItkFloatImageType::New();
	- mitk::CastToItkImage(dynamic_cast<mitk::Image*>(m_Controls->m_MaskImageSelectionWidget->GetSelectedNode()->GetData()), mask);
	- m_Tracker->SetMaskImage(mask);
	- }
	-
	- if (m_Controls->m_StopImageSelectionWidget->GetSelectedNode().IsNotNull())
	- {
	- ItkFloatImageType::Pointer mask = ItkFloatImageType::New();
	- mitk::CastToItkImage(dynamic_cast<mitk::Image*>(m_Controls->m_StopImageSelectionWidget->GetSelectedNode()->GetData()), mask);
	- m_Tracker->SetStoppingRegions(mask);
	- }
	-
	- if (m_Controls->m_TargetImageSelectionWidget->GetSelectedNode().IsNotNull())
	- {
	- ItkFloatImageType::Pointer mask = ItkFloatImageType::New();
	- mitk::CastToItkImage(dynamic_cast<mitk::Image*>(m_Controls->m_TargetImageSelectionWidget->GetSelectedNode()->GetData()), mask);
	- m_Tracker->SetTargetRegions(mask);
	- }
	-
	- if (m_Controls->m_PriorImageSelectionWidget->GetSelectedNode().IsNotNull())
	- {
	- auto prior_params = GetParametersFromGui();
	- if (m_LastPrior!=m_Controls->m_PriorImageSelectionWidget->GetSelectedNode() \|\| m_TrackingPriorHandler==nullptr)
	- {
	- typedef mitk::ImageToItk< mitk::TrackingHandlerPeaks::PeakImgType > CasterType;
	- CasterType::Pointer caster = CasterType::New();
	- caster->SetInput(dynamic_cast<mitk::PeakImage*>(m_Controls->m_PriorImageSelectionWidget->GetSelectedNode()->GetData()));
	- caster->SetCopyMemFlag(true);
	- caster->Update();
	- mitk::TrackingHandlerPeaks::PeakImgType::Pointer itkImg = caster->GetOutput();
	- m_TrackingPriorHandler = new mitk::TrackingHandlerPeaks();
	- dynamic_cast<mitk::TrackingHandlerPeaks*>(m_TrackingPriorHandler)->SetPeakImage(itkImg);
	- m_LastPrior = m_Controls->m_PriorImageSelectionWidget->GetSelectedNode();
	- }
	-
	- prior_params->m_FlipX = m_Controls->m_PriorFlipXBox->isChecked();
	- prior_params->m_FlipY = m_Controls->m_PriorFlipYBox->isChecked();
	- prior_params->m_FlipZ = m_Controls->m_PriorFlipZBox->isChecked();
	- m_TrackingPriorHandler->SetParameters(prior_params);
	-
	- m_Tracker->SetTrackingPriorHandler(m_TrackingPriorHandler);
	- }
	- else if (m_Controls->m_PriorImageSelectionWidget->GetSelectedNode().IsNull())
	- m_Tracker->SetTrackingPriorHandler(nullptr);
	-
	- if (m_Controls->m_ExclusionImageSelectionWidget->GetSelectedNode().IsNotNull())
	- {
	- ItkFloatImageType::Pointer mask = ItkFloatImageType::New();
	- mitk::CastToItkImage(dynamic_cast<mitk::Image*>(m_Controls->m_ExclusionImageSelectionWidget->GetSelectedNode()->GetData()), mask);
	- m_Tracker->SetExclusionRegions(mask);
	- }
	-
	- if (params->m_EpConstraints!=itk::StreamlineTrackingFilter::EndpointConstraints::NONE && m_Controls->m_TargetImageSelectionWidget->GetSelectedNode().IsNull())
	- {
	- QMessageBox::information(nullptr, "Error", "Endpoint constraints are used but no target image is set!");
	- StartStopTrackingGui(false);
	- return;
	- }
	- else if (params->m_EpConstraints==itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_SEED_AND_TARGET
	- && (m_Controls->m_SeedImageSelectionWidget->GetSelectedNode().IsNull()\|\| m_Controls->m_TargetImageSelectionWidget->GetSelectedNode().IsNull()) )
	- {
	- QMessageBox::information(nullptr, "Error", "Endpoint constraint EPS_IN_SEED_AND_TARGET is used but no target or no seed image is set!");
	- StartStopTrackingGui(false);
	- return;
	- }
	-
	- m_Tracker->SetParameters(params);
	- m_Tracker->SetTrackingHandler(m_TrackingHandler);
	- m_Tracker->SetVerbose(!m_Controls->m_InteractiveBox->isChecked());
	-
	- m_ParentNode = m_InputImageNodes.at(0);
	- m_TrackingThread.start(QThread::LowestPriority);
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingView.h
	deleted file mode 100644
	index 96b5d49952..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingView.h
	+++ /dev/null
	@@ -1,160 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef QmitkStreamlineTrackingView_h
	-#define QmitkStreamlineTrackingView_h
	-
	-#include <QmitkAbstractView.h>
	-
	-#include "ui_QmitkStreamlineTrackingViewControls.h"
	-
	-#include <mitkTensorImage.h>
	-#include <mitkDataStorage.h>
	-#include <mitkDataNode.h>
	-#include <mitkImage.h>
	-#include <itkImage.h>
	-#include <itkStreamlineTrackingFilter.h>
	-#include <Algorithms/TrackingHandlers/mitkTrackingHandlerTensor.h>
	-#include <Algorithms/TrackingHandlers/mitkTrackingHandlerPeaks.h>
	-#include <Algorithms/TrackingHandlers/mitkTrackingHandlerOdf.h>
	-#include <Algorithms/TrackingHandlers/mitkTrackingHandlerRandomForest.h>
	-#include <random>
	-#include <mitkPointSet.h>
	-#include <mitkPointSetShapeProperty.h>
	-#include <mitkTractographyForest.h>
	-#include <QThread>
	-#include <QTimer>
	-#include <QmitkStdMultiWidget.h>
	-#include <QmitkSliceNavigationListener.h>
	-#include <mitkILifecycleAwarePart.h>
	-#include <mitkStreamlineTractographyParameters.h>
	-
	-class QmitkStreamlineTrackingView;
	-
	-class QmitkStreamlineTrackingWorker : public QObject
	-{
	- Q_OBJECT
	-
	-public:
	-
	- QmitkStreamlineTrackingWorker(QmitkStreamlineTrackingView* view);
	-
	-public slots:
	-
	- void run();
	-
	-private:
	-
	- QmitkStreamlineTrackingView* m_View;
	-};
	-
	-/*!
	-\brief View for tensor based deterministic streamline fiber tracking.
	-*/
	-class QmitkStreamlineTrackingView : public QmitkAbstractView, public mitk::ILifecycleAwarePart
	-{
	- // this is needed for all Qt objects that should have a Qt meta-object
	- // (everything that derives from QObject and wants to have signal/slots)
	- Q_OBJECT
	-
	-public:
	-
	- static const std::string VIEW_ID;
	-
	- typedef itk::Image< unsigned int, 3 > ItkUintImgType;
	- typedef itk::Image< unsigned char, 3 > ItkUCharImageType;
	- typedef itk::Image< float, 3 > ItkFloatImageType;
	- typedef itk::StreamlineTrackingFilter TrackerType;
	-
	- QmitkStreamlineTrackingView();
	- virtual ~QmitkStreamlineTrackingView();
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	-
	- ///
	- /// Sets the focus to an internal widget.
	- ///
	- virtual void SetFocus() override;
	-
	- TrackerType::Pointer m_Tracker;
	- QmitkStreamlineTrackingWorker m_TrackingWorker;
	- QThread m_TrackingThread;
	-
	- virtual void Activated() override;
	- virtual void Deactivated() override;
	- virtual void Visible() override;
	- virtual void Hidden() override;
	-
	-protected slots:
	-
	- void DoFiberTracking(); ///< start fiber tracking
	- void UpdateGui();
	- void ToggleInteractive();
	- void DeleteTrackingHandler();
	- void OnParameterChanged();
	- void InteractiveSeedChanged(bool posChanged=false);
	- void ForestSwitched();
	- void OutputStyleSwitched();
	- void AfterThread(); ///< update gui etc. after tracking has finished
	- void BeforeThread(); ///< start timer etc.
	- void TimerUpdate();
	- void StopTractography();
	- void OnSliceChanged();
	- void SaveParameters();
	- void LoadParameters();
	-
	-protected:
	-
	- /// \brief called by QmitkAbstractView when DataManager's selection has changed
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- Ui::QmitkStreamlineTrackingViewControls* m_Controls;
	-
	-protected slots:
	-
	-private:
	-
	- bool CheckAndStoreLastParams(QObject* obj);
	- void StartStopTrackingGui(bool start);
	- std::shared_ptr< mitk::StreamlineTractographyParameters > GetParametersFromGui();
	- void ParametersToGui(mitk::StreamlineTractographyParameters& params);
	-
	- std::vector< itk::Point<float> > m_SeedPoints;
	- mitk::DataNode::Pointer m_ParentNode;
	- mitk::DataNode::Pointer m_InteractiveNode;
	- mitk::DataNode::Pointer m_InteractivePointSetNode;
	-
	- std::vector< mitk::DataNode::Pointer > m_InputImageNodes; ///< input image nodes
	- std::vector< mitk::Image::ConstPointer > m_AdditionalInputImages;
	- bool m_FirstTensorProbRun;
	- bool m_FirstInteractiveRun;
	-
	- mitk::TrackingDataHandler* m_TrackingHandler;
	- bool m_ThreadIsRunning;
	- QTimer* m_TrackingTimer;
	- bool m_DeleteTrackingHandler;
	- QmitkSliceNavigationListener m_SliceChangeListener;
	- bool m_Visible;
	- mitk::DataNode::Pointer m_LastPrior;
	- mitk::TrackingDataHandler* m_TrackingPriorHandler;
	- std::map< QString, std::string > m_LastTractoParams;
	- QString m_ParameterFile;
	-};
	-
	-
	-
	-#endif // _QMITKFIBERTRACKINGVIEW_H_INCLUDED
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingViewControls.ui
	deleted file mode 100644
	index 4c040ada44..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingViewControls.ui
	+++ /dev/null
	@@ -1,1698 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<ui version="4.0">
	- <class>QmitkStreamlineTrackingViewControls</class>
	- <widget class="QWidget" name="QmitkStreamlineTrackingViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>453</width>
	- <height>859</height>
	- </rect>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="windowTitle">
	- <string>QmitkTemplate</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_11">
	- <property name="topMargin">
	- <number>3</number>
	- </property>
	- <property name="bottomMargin">
	- <number>3</number>
	- </property>
	- <property name="horizontalSpacing">
	- <number>0</number>
	- </property>
	- <property name="verticalSpacing">
	- <number>40</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QFrame" name="frame_6">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_12">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>15</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="horizontalSpacing">
	- <number>6</number>
	- </property>
	- <property name="verticalSpacing">
	- <number>15</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QTextEdit" name="m_StatusTextBox">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="readOnly">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QFrame" name="frame_11">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_21">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="verticalSpacing">
	- <number>0</number>
	- </property>
	- <item row="0" column="1">
	- <widget class="QCommandLinkButton" name="m_SaveParametersButton">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="toolTip">
	- <string>Save parameters to json file</string>
	- </property>
	- <property name="text">
	- <string>Save Parameters</string>
	- </property>
	- <property name="icon">
	- <iconset resource="../../resources/QmitkTractography.qrc">
	- <normaloff>:/QmitkTractography/download.png</normaloff>:/QmitkTractography/download.png</iconset>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QCommandLinkButton" name="m_LoadParametersButton">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="toolTip">
	- <string>Load parameters from json file</string>
	- </property>
	- <property name="text">
	- <string>Load Parameters</string>
	- </property>
	- <property name="icon">
	- <iconset resource="../../resources/QmitkTractography.qrc">
	- <normaloff>:/QmitkTractography/upload.png</normaloff>:/QmitkTractography/upload.png</iconset>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QCommandLinkButton" name="commandLinkButton">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="text">
	- <string>Start Tractography</string>
	- </property>
	- <property name="icon">
	- <iconset resource="../../resources/QmitkTractography.qrc">
	- <normaloff>:/QmitkTractography/right.png</normaloff>:/QmitkTractography/right.png</iconset>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QCommandLinkButton" name="commandLinkButton_2">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="toolTip">
	- <string>Stop tractography and return all fibers reconstructed until now.</string>
	- </property>
	- <property name="text">
	- <string>Stop Tractography</string>
	- </property>
	- <property name="icon">
	- <iconset resource="../../resources/QmitkTractography.qrc">
	- <normaloff>:/QmitkTractography/stop.png</normaloff>:/QmitkTractography/stop.png</iconset>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QFrame" name="frame_9">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_19">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_2">
	- <property name="toolTip">
	- <string>Input Image. ODF, tensor and peak images are currently supported.</string>
	- </property>
	- <property name="text">
	- <string>Input Image:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QLabel" name="m_TensorImageLabel">
	- <property name="toolTip">
	- <string>Input Image. ODF, tensor, peak, and, in case of ML tractography, raw diffusion-weighted images are currently supported.</string>
	- </property>
	- <property name="text">
	- <string><html><head/><body><p><span style=" color:#ff0000;">select image in data-manager</span></p></body></html></string>
	- </property>
	- <property name="wordWrap">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="m_ForestLabel">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Tractography Forest:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QmitkSingleNodeSelectionWidget" name="m_ForestSelectionWidget" native="true">
	- <property name="styleSheet">
	- <string notr="true"/>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="2" column="0" rowspan="6">
	- <widget class="QToolBox" name="toolBox">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="font">
	- <font>
	- <weight>75</weight>
	- <bold>true</bold>
	- </font>
	- </property>
	- <property name="currentIndex">
	- <number>0</number>
	- </property>
	- <widget class="QWidget" name="page_seed">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>421</width>
	- <height>254</height>
	- </rect>
	- </property>
	- <attribute name="label">
	- <string>Seeding</string>
	- </attribute>
	- <attribute name="toolTip">
	- <string>Specify how, where and how many tractography seed points are placed.</string>
	- </attribute>
	- <layout class="QGridLayout" name="gridLayout_17">
	- <item row="0" column="0">
	- <widget class="QFrame" name="m_InteractiveSeedingFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_15">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QFrame" name="frame_7">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_13">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="2" column="1">
	- <widget class="QSpinBox" name="m_NumSeedsBox">
	- <property name="toolTip">
	- <string>Number of seed points equally distributed around selected position. </string>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>9999999</number>
	- </property>
	- <property name="value">
	- <number>50</number>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="m_FaThresholdLabel_4">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Radius: </string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QDoubleSpinBox" name="m_SeedRadiusBox">
	- <property name="toolTip">
	- <string>Seedpoints are equally distributed within a sphere centered at the selected position with the specified radius (in mm).</string>
	- </property>
	- <property name="decimals">
	- <number>2</number>
	- </property>
	- <property name="maximum">
	- <double>50.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>2.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="m_SeedsPerVoxelLabel_4">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Num. Seeds:</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QCheckBox" name="m_ParamUpdateBox">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="toolTip">
	- <string>When checked, parameter changes cause instant retracking while in interactive mode.</string>
	- </property>
	- <property name="text">
	- <string>Update on Parameter Change </string>
	- </property>
	- <property name="checked">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QFrame" name="frame_8">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_16">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_TrialsPerSeedBox">
	- <property name="toolTip">
	- <string>Try each seed N times until a valid streamline is obtained (only for probabilistic tractography).</string>
	- </property>
	- <property name="statusTip">
	- <string>Minimum fiber length (in mm)</string>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>999</number>
	- </property>
	- <property name="value">
	- <number>10</number>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_TrialsPerSeedLabel">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Trials Per Seed:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="m_FaThresholdLabel_2">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Max. Num. Fibers:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QSpinBox" name="m_NumFibersBox">
	- <property name="toolTip">
	- <string>Tractography is stopped after the desired number of fibers is reached, even before all seed points are processed (-1 means no limit).</string>
	- </property>
	- <property name="minimum">
	- <number>-1</number>
	- </property>
	- <property name="maximum">
	- <number>999999999</number>
	- </property>
	- <property name="value">
	- <number>-1</number>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QFrame" name="m_StaticSeedingFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_2">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="2" column="0">
	- <widget class="QLabel" name="m_SeedsPerVoxelLabel">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Seeds per Voxel:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_6">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Seed Image:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QSpinBox" name="m_SeedsPerVoxelBox">
	- <property name="toolTip">
	- <string>Number of seed points placed in each voxel.</string>
	- </property>
	- <property name="minimum">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <number>9999999</number>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QmitkSingleNodeSelectionWidget" name="m_SeedImageSelectionWidget" native="true">
	- <property name="styleSheet">
	- <string notr="true"/>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QCheckBox" name="m_InteractiveBox">
	- <property name="enabled">
	- <bool>true</bool>
	- </property>
	- <property name="toolTip">
	- <string>Dynamically pick a seed location by click into image.</string>
	- </property>
	- <property name="text">
	- <string>Enable Interactive Tractography</string>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <spacer name="verticalSpacer">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- </layout>
	- </widget>
	- <widget class="QWidget" name="page_constraints">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>435</width>
	- <height>184</height>
	- </rect>
	- </property>
	- <attribute name="label">
	- <string>ROI Constraints</string>
	- </attribute>
	- <attribute name="toolTip">
	- <string>Specify various ROI and mask images to constrain the tractography process.</string>
	- </attribute>
	- <layout class="QGridLayout" name="gridLayout">
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_7">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Mask Image:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="1">
	- <widget class="QComboBox" name="m_EpConstraintsBox">
	- <property name="toolTip">
	- <string>Select which fibers should be accepted or rejected based on the location of their endpoints.</string>
	- </property>
	- <property name="sizeAdjustPolicy">
	- <enum>QComboBox::AdjustToMinimumContentsLength</enum>
	- </property>
	- <item>
	- <property name="text">
	- <string>No Constraints on EP locations</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Both EPs in Target Image</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Both EPs in Target Image But Different Label</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>One EP in Seed Image and One EP in Target Image</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>At Least One EP in Target Image</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Exactly One EP in Target Image</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>No EP in Target Image</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QLabel" name="label_10">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Endpoint Constraints:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_9">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Stop ROI Image:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label_11">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Exclusion ROI Image:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QLabel" name="m_TargetImageLabel">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Target ROI Image:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="6" column="0">
	- <spacer name="verticalSpacer_6">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="0" column="1">
	- <widget class="QmitkSingleNodeSelectionWidget" name="m_MaskImageSelectionWidget" native="true"/>
	- </item>
	- <item row="1" column="1">
	- <widget class="QmitkSingleNodeSelectionWidget" name="m_StopImageSelectionWidget" native="true"/>
	- </item>
	- <item row="2" column="1">
	- <widget class="QmitkSingleNodeSelectionWidget" name="m_ExclusionImageSelectionWidget" native="true"/>
	- </item>
	- <item row="4" column="1">
	- <widget class="QmitkSingleNodeSelectionWidget" name="m_TargetImageSelectionWidget" native="true"/>
	- </item>
	- </layout>
	- </widget>
	- <widget class="QWidget" name="page_trackingparam">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>421</width>
	- <height>428</height>
	- </rect>
	- </property>
	- <attribute name="label">
	- <string>Tractography Parameters</string>
	- </attribute>
	- <attribute name="toolTip">
	- <string>Specify the behavior of the tractography at each streamline integration step (step size, deterministic/probabilistic, ...).</string>
	- </attribute>
	- <layout class="QGridLayout" name="gridLayout_14">
	- <item row="8" column="1">
	- <widget class="QDoubleSpinBox" name="m_MinTractLengthBox">
	- <property name="toolTip">
	- <string>Minimum tract length in mm. Shorter fibers are discarded.</string>
	- </property>
	- <property name="statusTip">
	- <string>Minimum fiber length (in mm)</string>
	- </property>
	- <property name="decimals">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <double>999.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="value">
	- <double>20.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="12" column="0">
	- <widget class="QLabel" name="m_fLabel">
	- <property name="toolTip">
	- <string>f parameter of tensor tractography. f=1 + g=0 means FACT (depending on the chosen interpolation). f=0 and g=1 means TEND (disable interpolation for this mode!).</string>
	- </property>
	- <property name="text">
	- <string>f:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="13" column="1">
	- <widget class="QDoubleSpinBox" name="m_gBox">
	- <property name="toolTip">
	- <string>f=1 + g=0 means FACT (depending on the chosen interpolation). f=0 and g=1 means TEND (disable interpolation for this mode!).</string>
	- </property>
	- <property name="decimals">
	- <number>2</number>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="m_FaThresholdLabel_5">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Sharpen ODFs:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="15" column="0">
	- <widget class="QLabel" name="m_FaThresholdLabel_6">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Fix Random Seed:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="11" column="1">
	- <widget class="QSpinBox" name="m_LoopCheckBox">
	- <property name="toolTip">
	- <string>Maximum allowed angular SDTEV over 4 voxel lengths. Default: no loop check.</string>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="minimum">
	- <number>-1</number>
	- </property>
	- <property name="maximum">
	- <number>180</number>
	- </property>
	- <property name="value">
	- <number>-1</number>
	- </property>
	- </widget>
	- </item>
	- <item row="10" column="0">
	- <widget class="QLabel" name="m_AngularThresholdLabel">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Angular Threshold:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="9" column="0">
	- <widget class="QLabel" name="m_MinTractLengthLabel_2">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Max. Tract Length:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QLabel" name="m_FaThresholdLabel">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Cutoff:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QCheckBox" name="m_SharpenOdfsBox">
	- <property name="toolTip">
	- <string>If you are using dODF images as input, it is advisable to sharpen the ODFs (min-max normalize and raise to the power of 4). This is not necessary for CSD fODFs, since they are naturally much sharper.</string>
	- </property>
	- <property name="text">
	- <string/>
	- </property>
	- </widget>
	- </item>
	- <item row="10" column="1">
	- <widget class="QSpinBox" name="m_AngularThresholdBox">
	- <property name="toolTip">
	- <string>Angular threshold between two steps (in degree). Default: 90° * step_size</string>
	- </property>
	- <property name="minimum">
	- <number>-1</number>
	- </property>
	- <property name="maximum">
	- <number>90</number>
	- </property>
	- <property name="singleStep">
	- <number>1</number>
	- </property>
	- <property name="value">
	- <number>-1</number>
	- </property>
	- </widget>
	- </item>
	- <item row="16" column="0">
	- <spacer name="verticalSpacer_2">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="12" column="1">
	- <widget class="QDoubleSpinBox" name="m_fBox">
	- <property name="toolTip">
	- <string>f=1 + g=0 means FACT (depending on the chosen interpolation). f=0 and g=1 means TEND (disable interpolation for this mode!).</string>
	- </property>
	- <property name="decimals">
	- <number>2</number>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>1.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QComboBox" name="m_ModeBox">
	- <property name="toolTip">
	- <string>Toggle between deterministic and probabilistic tractography. Some modes might not be available for all types of tractography.</string>
	- </property>
	- <item>
	- <property name="text">
	- <string>Deterministic</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Probabilistic</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="m_FaThresholdLabel_3">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Mode:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="1">
	- <widget class="QDoubleSpinBox" name="m_OdfCutoffBox">
	- <property name="toolTip">
	- <string>Additional threshold on the ODF magnitude. This is useful in case of CSD fODF tractography. For fODFs a good default value is 0.1, for normalized dODFs, e.g. Q-ball ODFs, this threshold should be very low (0.00025) or 0.</string>
	- </property>
	- <property name="decimals">
	- <number>5</number>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.000250000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="8" column="0">
	- <widget class="QLabel" name="m_MinTractLengthLabel">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Min. Tract Length:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QLabel" name="mFaImageLabel">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>FA/GFA Image:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="11" column="0">
	- <widget class="QLabel" name="m_LoopCheckLabel">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Loop Check:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="9" column="1">
	- <widget class="QDoubleSpinBox" name="m_MaxTractLengthBox">
	- <property name="toolTip">
	- <string>Minimum tract length in mm. Shorter fibers are discarded.</string>
	- </property>
	- <property name="statusTip">
	- <string>Maximum fiber length (in mm)</string>
	- </property>
	- <property name="decimals">
	- <number>1</number>
	- </property>
	- <property name="maximum">
	- <double>999.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="value">
	- <double>400.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="15" column="1">
	- <widget class="QCheckBox" name="m_FixSeedBox">
	- <property name="toolTip">
	- <string>Always produce the same random numbers.</string>
	- </property>
	- <property name="text">
	- <string/>
	- </property>
	- </widget>
	- </item>
	- <item row="6" column="0">
	- <widget class="QLabel" name="m_StepsizeLabel">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Step Size:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <widget class="QLabel" name="m_OdfCutoffLabel">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>ODF Cutoff:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="6" column="1">
	- <widget class="QDoubleSpinBox" name="m_StepSizeBox">
	- <property name="toolTip">
	- <string>Step size (in voxels)</string>
	- </property>
	- <property name="decimals">
	- <number>2</number>
	- </property>
	- <property name="minimum">
	- <double>0.010000000000000</double>
	- </property>
	- <property name="maximum">
	- <double>10.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.500000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="13" column="0">
	- <widget class="QLabel" name="m_gLabel">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>g:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="1">
	- <widget class="QmitkSingleNodeSelectionWidget" name="m_FaImageSelectionWidget" native="true"/>
	- </item>
	- <item row="3" column="1">
	- <widget class="QDoubleSpinBox" name="m_ScalarThresholdBox">
	- <property name="toolTip">
	- <string>Threshold on peak magnitude, FA, GFA, ...</string>
	- </property>
	- <property name="decimals">
	- <number>5</number>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.100000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="14" column="0">
	- <widget class="QLabel" name="m_PeakJitterLabel">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Peak Jitter:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="14" column="1">
	- <widget class="QDoubleSpinBox" name="m_PeakJitterBox">
	- <property name="toolTip">
	- <string>Important for probabilistic peak tractography and peak prior. Actual jitter is drawn from a normal distribution with peak_jitter*fabs(direction_value) as standard deviation.</string>
	- </property>
	- <property name="decimals">
	- <number>3</number>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.010000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <widget class="QWidget" name="page_prior">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>435</width>
	- <height>184</height>
	- </rect>
	- </property>
	- <attribute name="label">
	- <string>Tractography Prior</string>
	- </attribute>
	- <layout class="QGridLayout" name="gridLayout_9">
	- <item row="1" column="0">
	- <widget class="QLabel" name="m_PriorLabel_2">
	- <property name="text">
	- <string>Weight:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QDoubleSpinBox" name="m_PriorWeightBox">
	- <property name="toolTip">
	- <string>Weighting factor between prior and data.</string>
	- </property>
	- <property name="maximum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.500000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_PriorLabel">
	- <property name="text">
	- <string>Peak Image:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <spacer name="verticalSpacer_7">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="3" column="1">
	- <widget class="QCheckBox" name="m_NewDirectionsFromPriorBox">
	- <property name="toolTip">
	- <string>If unchecked, the prior cannot create directions where there are none in the data.</string>
	- </property>
	- <property name="text">
	- <string/>
	- </property>
	- <property name="checked">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QLabel" name="m_PriorLabel_4">
	- <property name="text">
	- <string>New Directions from Prior:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="m_PriorLabel_3">
	- <property name="text">
	- <string>Restrict to Prior:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QmitkSingleNodeSelectionWidget" name="m_PriorImageSelectionWidget" native="true"/>
	- </item>
	- <item row="2" column="1">
	- <widget class="QCheckBox" name="m_PriorAsMaskBox">
	- <property name="toolTip">
	- <string>Restrict tractography to regions where the prior is valid.</string>
	- </property>
	- <property name="text">
	- <string/>
	- </property>
	- <property name="checked">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="1">
	- <widget class="QFrame" name="frame_10">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_20">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <property name="spacing">
	- <number>0</number>
	- </property>
	- <item row="0" column="1">
	- <widget class="QCheckBox" name="m_PriorFlipYBox">
	- <property name="text">
	- <string>y</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QCheckBox" name="m_PriorFlipXBox">
	- <property name="text">
	- <string>x</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="2">
	- <widget class="QCheckBox" name="m_PriorFlipZBox">
	- <property name="text">
	- <string>z</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QLabel" name="m_PriorLabel_5">
	- <property name="text">
	- <string>Flip Directions:</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <widget class="QWidget" name="page_neighborhood">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>435</width>
	- <height>184</height>
	- </rect>
	- </property>
	- <attribute name="label">
	- <string>Neighborhood Sampling</string>
	- </attribute>
	- <attribute name="toolTip">
	- <string>Specify if and how information about the current streamline neighborhood should be used.</string>
	- </attribute>
	- <layout class="QGridLayout" name="gridLayout_18">
	- <item row="1" column="0">
	- <widget class="QCheckBox" name="m_FrontalSamplesBox">
	- <property name="toolTip">
	- <string>Only neighborhood samples in front of the current streamline position are considered.</string>
	- </property>
	- <property name="text">
	- <string>Use Only Frontal Samples</string>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QCheckBox" name="m_StopVotesBox">
	- <property name="toolTip">
	- <string>If checked, the majority of sampling points has to place a stop-vote for the streamline to terminate. If not checked, all sampling positions have to vote for a streamline termination.</string>
	- </property>
	- <property name="text">
	- <string>Use Stop-Votes</string>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QFrame" name="frame_4">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_10">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="m_SeedsPerVoxelLabel_2">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Num. Samples:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QSpinBox" name="m_NumSamplesBox">
	- <property name="toolTip">
	- <string>Number of neighborhood samples that are used to determine the next fiber progression direction.</string>
	- </property>
	- <property name="maximum">
	- <number>50</number>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="m_SamplingDistanceLabel">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Sampling Distance:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QDoubleSpinBox" name="m_SamplingDistanceBox">
	- <property name="toolTip">
	- <string>Sampling distance (in voxels)</string>
	- </property>
	- <property name="decimals">
	- <number>2</number>
	- </property>
	- <property name="maximum">
	- <double>10.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.250000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <spacer name="verticalSpacer_3">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- </layout>
	- </widget>
	- <widget class="QWidget" name="page_data">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>435</width>
	- <height>184</height>
	- </rect>
	- </property>
	- <attribute name="label">
	- <string>Data Handling</string>
	- </attribute>
	- <attribute name="toolTip">
	- <string>Specify interpolation and direction flips.</string>
	- </attribute>
	- <layout class="QGridLayout" name="gridLayout_6">
	- <item row="1" column="0">
	- <widget class="QFrame" name="frame_3">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_7">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QCheckBox" name="m_InterpolationBox">
	- <property name="toolTip">
	- <string>Trilinearly interpolate the input image used for tractography.</string>
	- </property>
	- <property name="text">
	- <string>Interpolate Tractography Data</string>
	- </property>
	- <property name="checked">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QCheckBox" name="m_MaskInterpolationBox">
	- <property name="toolTip">
	- <string>Trilinearly interpolate the ROI images used to constrain the tractography.</string>
	- </property>
	- <property name="text">
	- <string>Interpolate ROI Images</string>
	- </property>
	- <property name="checked">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QFrame" name="frame_2">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_3">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="7" column="1">
	- <widget class="QFrame" name="frame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_4">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QCheckBox" name="m_FlipXBox">
	- <property name="toolTip">
	- <string>Internally flips progression directions. This might be necessary depending on the input data.</string>
	- </property>
	- <property name="text">
	- <string>x</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QCheckBox" name="m_FlipYBox">
	- <property name="toolTip">
	- <string>Internally flips progression directions. This might be necessary depending on the input data.</string>
	- </property>
	- <property name="text">
	- <string>y</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="2">
	- <widget class="QCheckBox" name="m_FlipZBox">
	- <property name="toolTip">
	- <string>Internally flips progression directions. This might be necessary depending on the input data.</string>
	- </property>
	- <property name="text">
	- <string>z</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="7" column="0">
	- <widget class="QLabel" name="m_SeedsPerVoxelLabel_3">
	- <property name="toolTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string>Flip directions:</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <spacer name="verticalSpacer_4">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- </layout>
	- </widget>
	- <widget class="QWidget" name="page_output">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>435</width>
	- <height>184</height>
	- </rect>
	- </property>
	- <attribute name="label">
	- <string>Output and Postprocessing</string>
	- </attribute>
	- <attribute name="toolTip">
	- <string>Specify the tractography output (streamlines or probability maps) and postprocessing steps.</string>
	- </attribute>
	- <layout class="QGridLayout" name="gridLayout_5">
	- <item row="0" column="0">
	- <widget class="QFrame" name="frame_5">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_8">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QCheckBox" name="m_ResampleFibersBox">
	- <property name="toolTip">
	- <string>Compress fibers using the specified error constraint.</string>
	- </property>
	- <property name="text">
	- <string>Compress Fibers</string>
	- </property>
	- <property name="checked">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QDoubleSpinBox" name="m_FiberErrorBox">
	- <property name="focusPolicy">
	- <enum>Qt::StrongFocus</enum>
	- </property>
	- <property name="toolTip">
	- <string>Lossy fiber compression. Recommended for large tractograms. Maximum error in mm.</string>
	- </property>
	- <property name="decimals">
	- <number>3</number>
	- </property>
	- <property name="maximum">
	- <double>10.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.010000000000000</double>
	- </property>
	- <property name="value">
	- <double>0.100000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QCheckBox" name="m_OutputProbMap">
	- <property name="toolTip">
	- <string>Output map with voxel-wise visitation counts instead of streamlines.</string>
	- </property>
	- <property name="text">
	- <string>Output Probability Map</string>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <spacer name="verticalSpacer_5">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- </layout>
	- </widget>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <layoutdefault spacing="6" margin="11"/>
	- <customwidgets>
	- <customwidget>
	- <class>QmitkSingleNodeSelectionWidget</class>
	- <extends>QWidget</extends>
	- <header>QmitkSingleNodeSelectionWidget.h</header>
	- <container>1</container>
	- </customwidget>
	- </customwidgets>
	- <resources>
	- <include location="../../resources/QmitkTractography.qrc"/>
	- </resources>
	- <connections/>
	-</ui>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/mitkPluginActivator.cpp
	deleted file mode 100644
	index 9925065c85..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/mitkPluginActivator.cpp
	+++ /dev/null
	@@ -1,47 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "mitkPluginActivator.h"
	-
	-#include "src/internal/Perspectives/QmitkGibbsTractographyPerspective.h"
	-#include "src/internal/Perspectives/QmitkStreamlineTractographyPerspective.h"
	-
	-#include "src/internal/QmitkGibbsTrackingView.h"
	-#include "src/internal/QmitkStreamlineTrackingView.h"
	-
	-ctkPluginContext* mitk::PluginActivator::m_Context = nullptr;
	-
	-ctkPluginContext* mitk::PluginActivator::GetContext()
	-{
	- return m_Context;
	-}
	-
	-void mitk::PluginActivator::start(ctkPluginContext* context)
	-{
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkGibbsTractographyPerspective, context)
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkStreamlineTractographyPerspective, context)
	-
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkGibbsTrackingView, context)
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkStreamlineTrackingView, context)
	-
	- m_Context = context;
	-}
	-
	-void mitk::PluginActivator::stop(ctkPluginContext* context)
	-{
	- Q_UNUSED(context)
	- m_Context = nullptr;
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/mitkPluginActivator.h b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/mitkPluginActivator.h
	deleted file mode 100644
	index 1370bd0d54..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/mitkPluginActivator.h
	+++ /dev/null
	@@ -1,40 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef MITKPLUGINACTIVATOR_H
	-#define MITKPLUGINACTIVATOR_H
	-
	-#include <ctkPluginActivator.h>
	-
	-namespace mitk
	-{
	- class PluginActivator : public QObject, public ctkPluginActivator
	- {
	- Q_OBJECT
	- Q_PLUGIN_METADATA(IID "org.mitk.gui.qt.diffusionimaging.tractography")
	- Q_INTERFACES(ctkPluginActivator)
	-
	- public:
	- static ctkPluginContext* GetContext();
	-
	- void start(ctkPluginContext* context) override;
	- void stop(ctkPluginContext* context) override;
	-
	- private:
	- static ctkPluginContext* m_Context;
	- };
	-}
	-
	-#endif
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging/CMakeLists.txt
	deleted file mode 100644
	index 7c8c92b85f..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging/CMakeLists.txt
	+++ /dev/null
	@@ -1,8 +0,0 @@
	-project(org_mitk_gui_qt_diffusionimaging)
	-
	-mitk_create_plugin(
	- SUBPROJECTS MITK-DTI
	- EXPORT_DIRECTIVE DIFFUSIONIMAGING_EXPORT
	- EXPORTED_INCLUDE_SUFFIXES src
	- MODULE_DEPENDS MitkDiffusionCore MitkQuantification MitkConnectomics
	-)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Data_CSD.png b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Data_CSD.png
	deleted file mode 100644
	index 1eb60c1707..0000000000
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Data_Tensors.png b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Data_Tensors.png
	deleted file mode 100644
	index 7f42f2108a..0000000000
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionImagingDataImportPage.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionImagingDataImportPage.dox
	deleted file mode 100644
	index d2ef1036fb..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionImagingDataImportPage.dox
	+++ /dev/null
	@@ -1,82 +0,0 @@
	-/**
	-\page QmitkDiffusionImagingDataImportPage Data formats, import and export
	-
	-MITK Diffusion supports many standard image formats such as NIFTI, NRRD and DICOM as well as common tractography file formats such as vtk/fib, trk, tck, and tractography DICOM. By including multiple tractography file formats native to other tools (e.g. 3D Slicer, MRtrix, DIPY), MITK Diffusion integrates seamlessly in complex workflows involving other tools. Additional file types such as spherical-harmonic coefficient files and voxel-wise fiber orientation or peak images are compliant with MRtrix.
	-
	-Data can be loaded using the open file dialog via the menu bar or by simply dragging and dropping the file into the data manager or one of data display windows.
	-
	-MITK Diffusion uses a left-posterior-superior coordinate system convention. Other toolkits, e.g. MRtrix, use an RAS coordinate system. This can cause flips for example of the complete tractogram or of the voxel-wise peaks or ODFs. MITK Diffusion implements mechanisms to deal with this by automatically catching and converting some cases and by providing the tools to manually correct for it, but it is important to keep this issue in mind and to perform the data processing in a corresponding thorough manner.
	-
	-\section DWI_format Diffusion-weighted Images
	-
	-This section describes the different file formats of raw diffusion-weighted images that are supported by MITK Diffusion.
	-General points:
	-\li MITK Diffusion internally applies the image rotation matrix to the diffusion-gradient vectors while loading the image. The original gradient directions are retained and used when saving the image again.
	-
	-\subsection dwi_nrrd NRRD (.nrrd/.dwi)
	-
	-NRRD (http://teem.sourceforge.net/nrrd/format.html) is the default file format for saving diffusion-weighted images with MITK Diffusion. The gradient and b-value information is directly stored in the file header. The image information is stored as a 3D vector image. Storing the file as .dwi or .nrrd is equivalent, only the file ending is different. Diffusion-weighted images are discerned from other images by the tag "modality:=DWMRI" in the NRRD image header. The gradient information is stored in the NRRD header in the following way:
	-
	-DWMRI_b-value:=1000.000000
	-
	-DWMRI_gradient_0000:=0.000000 0.000000 0.000000
	-
	-DWMRI_gradient_0001:=0.000000 0.000000 1.000000
	-
	-DWMRI_gradient_0002:=-0.051773 0.252917 0.966102
	-
	-...
	-
	-The b-value of the individual gradient directions is encoded via the squared norm of the respective vector. The tag "DWMRI_b-value" defines which b-value corresponds to a vector with norm 1.
	-
	-In some cases, dMRI NRRD files contain an additional "measurement frame" matrix, which specifies an additional rotation of the gradient vectors. This matrix is automatically applied when loading the file. The original gradient directions are retained and used when saving the image again.
	-
	-\subsection dwi_nifti NIFTI (.nii/.ni.gz)
	-
	-Diffusion-weighted images can be saved and loaded as NIFTI files (NIFTI-1 https://nifti.nimh.nih.gov/nifti-1). The gradient vector information is stored in to separate files for b-values (filename.bvals) and gradient vectors (filename.bvecs). When loading a nifti file (.nii or .nii.gz), MITK Diffusion looks for these two additional files (.bval/.bvals and .bvec/.bvecs) and if they are found, MITK will offer to load the image as diffusion-weighted image. In contrast to the NRRD format, all gradient vectors should have a length of 1. The b-values are stored explicietly in the .bval/.bvals file. When loaded into MITK, this information is again encoded into the gradient vectors, as it is done in the NRRD file format.
	-
	-\subsection dwi_dicom DICOM
	-
	-MITK is capable of importing diffusion-weighted DICOM images from GE, Siemens and Philips. Writing images is DICOM format is NOT supported! Mosaic images can be directly converted to regular images during import. To load a dMRI DICOM, simply drag and drop any file of the series into the application.
	-
	-\section special_format Special Image Types
	-
	-\subsection DTI_format Diffusion Tensor Images (.dti)
	-
	-The default format for diffusion tensor images in MITK Diffusion is a 3D NRRD file with a "3D-symmetric-matrix" pixel type. A tensor is encoded as 6 float values. The file ending for diffusion tensor files is .dti.
	-MITK Diffusion is also able to read NIFTI DTI files (6 or 9 component format), which are for example generated by the Camino multi tensor reconstruction. To be recognized as DTI files, the .nii or .nii.gz files have to be renamed to .dti.
	-
	-\subsection ODF_format ODF Images (.odf, .qbi (deprecated) )
	-
	-MITK stores ODFs as 252 float values spherically sampled from the continuous ODF. The sampling directions are generate by a 5-fold subdivisions of an icosahedron. ODF images are stored in NRRD file format with the ending .odf. The image information is stored as a 3D vector image with a vector length of 252.
	-
	-The specific ODF sampling directions can be found <a href="https://phabricator.mitk.org/source/mitk/browse/master/Modules/DiffusionImaging/DiffusionCore/include/Algorithms/Reconstruction/itkPointShell.txx;8cdb084b2eccff7f5caa30ba5a88bf43ccc9ec6f$457">here</a>.
	-
	-\subsection sh_format Spherical Harmonics (.nii, .nii.gz, .nrrd)
	-Many applications in dMRI are using spherical harmonics to store spherical functions such as ODFs. MITK Diffusion stores these files as 4D float images this is the same format as MRtrix is using.
	-
	-\subsection peak_format Peak Images (.nii, .nii.gz, .nrrd)
	-
	-MITK Diffusion stores peak images, resulting for example from an ODF maxima extraction, as 4D float images. The peak vector components are stored in the 4th dimension, therefore dimension 4 always contains a multiple of 3 entries. This format is the same as the format used by MRtrix.
	-
	-\section Tract_format Tractography Formats
	-
	-MITK Diffusion supports multiple formats for tractography files that are commonly used in the dMRI community. As in all other toolkits, the fiber point coordinates are stored as physical/world coordinates without any additional transformation.
	-
	-\subsection tract_vtk VTK (.vtk/.fib)
	-
	-The default format for tractograms is VTK (vtkPolyData) with the file endings .fib or .vtk. The advantage of the VTK format is that it can store additional information such as fiber weights and fiber colors. By default, both are saved with the actual tract information.
	-
	-\subsection tract_trk TrackVis (.trk)
	-
	-TRK is the tractography file format used by TrackVis and DIPY. See http://www.trackvis.org/docs/?subsect=fileformat for a detailed description of a format.
	-
	-\subsection tract_tck MRtrix (.tck)
	-
	-MITK Diffusion is able to read the tck file format native to MRtrix. Writing this format is currently not supported. By default, MRtrix uses a RAS coordinate convention in contrast to the MITK Diffusion (and also ITK) convention of LPS. To compensate for this, the fiber coordinates are negated in the x and y dimension.
	-
	-\subsection tract_dicom DICOM
	-
	-Tractography DICOM files compliant with the supplement 181 of the DICOM standard can be read and written by MITK Diffusion. This format is for example supported by the neuronavigation software of Brainlab.
	-DICOM tags of the read tractogram can be manually set or modified using the "Properties" view in MITK Diffusion. To do this, enable the "Developer Mode" option in Window>Preferences>Properties>Developer Mode. Then select the fiber bundle in the data manager and select the "Base Data" property list in the corresponding combobox of the "Properties" view.
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionImagingPortalPage.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionImagingPortalPage.dox
	deleted file mode 100644
	index ea0ea8cd86..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionImagingPortalPage.dox
	+++ /dev/null
	@@ -1,48 +0,0 @@
	-/**
	-\page org_mitk_gui_qt_diffusionimaging MITK Diffusion
	-
	-\tableofcontents
	-
	-MITK Diffusion offers a selection of image analysis methods for dMRI processing. It encompasses the research of the <a href="https://www.dkfz.de/en/mic/index.php">Division of Medical Image Computing</a> of the German Cancer Research Center (DKFZ).
	-
	-\section org_mitk_gui_qt_diffusionimagingComponents Components
	-
	-MITK Diffusion consists of multiple components with their own documentation:
	-
	-\subsection sub1 Data formats, import and export
	-\li \subpage QmitkDiffusionImagingDataImportPage
	-
	-\subsection sub2 Preprocessing and Reconstruction
	-\li \subpage org_mitk_views_diffusionpreprocessing
	-\li \subpage org_mitk_views_simpleregistrationview
	-\li \subpage org_mitk_views_headmotioncorrectionview
	-\li \subpage org_mitk_views_denoisingview
	-\li \subpage org_mitk_views_tensorreconstruction
	-\li \subpage org_mitk_views_qballreconstruction
	-
	-\subsection sub3 Visualization and Quantification
	-\li \subpage org_mitk_views_controlvisualizationpropertiesview
	-\li \subpage org_mitk_views_odfdetails
	-\li \subpage org_mitk_views_odfmaximaextraction
	-\li \subpage org_mitk_views_partialvolumeanalysisview
	-\li \subpage org_mitk_views_diffusionquantification
	-\li \subpage org_mitk_views_ivim
	-
	-\subsection sub4 Fiber Tractography
	-\li \subpage org_mitk_views_streamlinetracking
	-\li \subpage org_mitk_views_gibbstracking
	-\li \subpage org_mitk_views_mlbtview
	-\li \subpage org_mitk_views_fiberprocessing
	-\li \subpage org_mitk_views_fiberquantification
	-\li \subpage org_mitk_views_fiberfit
	-\li \subpage org_mitk_views_fiberclustering
	-
	-\subsection sub5 Fiberfox dMRI Simulation
	-\li \subpage org_mitk_views_fiberfoxview
	-\li \subpage org_mitk_views_fibergenerationview
	-\li \subpage org_mitk_views_fieldmapgenerator
	-
	-\subsection sub6 Connectomics
	-\li \subpage org_mitk_diffusionimagingapp_perspectives_connectomics
	-
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionImagingVisualization.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionImagingVisualization.dox
	deleted file mode 100644
	index f111e4e593..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionImagingVisualization.dox
	+++ /dev/null
	@@ -1,22 +0,0 @@
	-/**
	-\page org_mitk_views_controlvisualizationpropertiesview Visualization Control Panel
	-
	-\section QmitkDiffusionImagingVisualizationSettings ODF Visualization
	-
	-In this small view, the visualization of ODFs and diffusion images can be configured. Depending on the selected image in the data storage, different options are shown here.
	-
	-For tensor or ODF images, the visibility of glyphs in the different render windows (T)ransversal, (S)agittal, and (C)oronal can be configured here. The maximal number of glyphs to display can also be configured here for. This is usefull to keep the system response time during rendering feasible. The other options configure normalization and scaling of the glyphs.
	-
	-This is how a visualization with activated glyphs should look like:
	-
	-\imageMacro{Data_CSD.png,"ODF image with glyph visibility toggled ON",1}
	-
	-\imageMacro{Data_Tensors.png,"Tensor image with glyph visibility toggled ON",1}
	-
	-\section QmitkDiffusionImagingTractVisualizationSettings Tractogram Visualization
	-
	-If a tractogram is selected in the data manager, this view enables to visualize the fibers as tubes or thick lines as well as to play with the 2D and 3D clipping of the fiber visualization. The 3D clipping works per tractogram individually, which enables nice visualization of e.g. a CST tract extending upwards out of the bottom half of a whole brain tractogram.
	-
	-\imageMacro{tract_visualization.png,"CST tube visualization with sagittal 3D clipping of the whole-brain tractogram.",1}
	-
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/dicom1.png b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/dicom1.png
	deleted file mode 100644
	index a11c978150..0000000000
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/tract_visualization.png b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/tract_visualization.png
	deleted file mode 100644
	index 9805ac1578..0000000000
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/doxygen/modules.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/doxygen/modules.dox
	deleted file mode 100644
	index 00788da074..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/doxygen/modules.dox
	+++ /dev/null
	@@ -1,16 +0,0 @@
	-/**
	- \defgroup org_mitk_gui_qt_diffusionimaging org.mitk.gui.qt.diffusionimaging
	- \ingroup MITKPlugins
	-
	- \brief Describe your plugin here.
	-
	-*/
	-
	-/**
	- \defgroup org_mitk_gui_qt_diffusionimaging_internal Internal
	- \ingroup org_mitk_gui_qt_diffusionimaging
	-
	- \brief This subcategory includes the internal classes of the org.mitk.gui.qt.diffusionimaging plugin. Other
	- plugins must not rely on these classes. They contain implementation details and their interface
	- may change at any time. We mean it.
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/files.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging/files.cmake
	deleted file mode 100644
	index 3ccd164796..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging/files.cmake
	+++ /dev/null
	@@ -1,66 +0,0 @@
	-set(SRC_CPP_FILES
	-)
	-
	-set(INTERNAL_CPP_FILES
	- mitkPluginActivator.cpp
	- QmitkDiffusionDicomImportView.cpp
	- QmitkControlVisualizationPropertiesView.cpp
	- QmitkDicomTractogramTagEditorView.cpp
	-
	- Perspectives/QmitkDiffusionDefaultPerspective.cpp
	- Perspectives/QmitkSegmentationPerspective.cpp
	-)
	-
	-set(UI_FILES
	- src/internal/QmitkDiffusionDicomImportViewControls.ui
	- src/internal/QmitkControlVisualizationPropertiesViewControls.ui
	- src/internal/QmitkDicomTractogramTagEditorViewControls.ui
	-)
	-
	-set(MOC_H_FILES
	- src/internal/mitkPluginActivator.h
	- src/internal/QmitkDiffusionDicomImportView.h
	- src/internal/QmitkControlVisualizationPropertiesView.h
	- src/internal/QmitkDicomTractogramTagEditorView.h
	-
	- src/internal/Perspectives/QmitkDiffusionDefaultPerspective.h
	- src/internal/Perspectives/QmitkSegmentationPerspective.h
	-)
	-
	-set(CACHED_RESOURCE_FILES
	-# list of resource files which can be used by the plug-in
	-# system without loading the plug-ins shared library,
	-# for example the icon used in the menu and tabs for the
	-# plug-in views in the workbench
	- plugin.xml
	-
	- resources/dwiimport.png
	- resources/vizControls.png
	- resources/arrow.png
	- resources/dwi.png
	- resources/odf.png
	- resources/tensor.png
	- resources/tractogram.png
	- resources/odf_peaks.png
	- resources/ml_tractogram.png
	- resources/sh.png
	- resources/refresh.xpm
	- resources/segmentation.svg
	- )
	-
	-set(QRC_FILES
	-# uncomment the following line if you want to use Qt resources
	- resources/QmitkDiffusionImaging.qrc
	- #resources/QmitkTractbasedSpatialStatisticsView.qrc
	-)
	-
	-set(CPP_FILES )
	-
	-foreach(file ${SRC_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/${file})
	-endforeach(file ${SRC_CPP_FILES})
	-
	-foreach(file ${INTERNAL_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/internal/${file})
	-endforeach(file ${INTERNAL_CPP_FILES})
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging/manifest_headers.cmake
	deleted file mode 100644
	index bdff16293f..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging/manifest_headers.cmake
	+++ /dev/null
	@@ -1,6 +0,0 @@
	-set(Plugin-Name "MITK Diffusion Imaging")
	-set(Plugin-Version "0.1")
	-set(Plugin-Vendor "DKFZ, Medical and Biological Informatics")
	-set(Plugin-ContactAddress "http://www.mitk.org")
	-set(Require-Plugin org.mitk.gui.qt.common)
	-#set(Plugin-ActivationPolicy eager)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/plugin.xml b/Plugins/org.mitk.gui.qt.diffusionimaging/plugin.xml
	deleted file mode 100644
	index 1c5fc88745..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging/plugin.xml
	+++ /dev/null
	@@ -1,60 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<?BlueBerry version="0.1"?>
	-<plugin>
	-
	-
	- <extension point="org.blueberry.ui.keywords">
	-
	- <keyword label="DICOM" id="org.mitk.views.dicomtractogramtageditor.Keyword"/>
	- <keyword label="tractography" id="org.mitk.views.dicomtractogramtageditor.Keyword"/>
	- <keyword label="tracking" id="org.mitk.views.dicomtractogramtageditor.Keyword"/>
	- <keyword label="tractogram" id="org.mitk.views.dicomtractogramtageditor.Keyword"/>
	- <keyword label="tag" id="org.mitk.views.dicomtractogramtageditor.Keyword"/>
	-
	- <keyword label="DICOM" id="org.mitk.views.diffusiondicomimport.Keyword"/>
	- <keyword label="image" id="org.mitk.views.diffusiondicomimport.Keyword"/>
	- <keyword label="data" id="org.mitk.views.diffusiondicomimport.Keyword"/>
	- <keyword label="load" id="org.mitk.views.diffusiondicomimport.Keyword"/>
	-
	- </extension>
	-
	- <extension point="org.blueberry.ui.perspectives">
	-
	- <perspective id="org.mitk.perspectives.segmentation"
	- name="Image Segmentation"
	- class="QmitkSegmentationPerspective"
	- icon="resources/segmentation.svg">
	- <description>This perspective contains views to perform manual image segmentation.</description>
	- </perspective>
	-
	- </extension>
	-
	- <extension point="org.blueberry.ui.views">
	-
	- <view id="org.mitk.views.diffusiondicomimport"
	- name="DICOM Import"
	- category="Data"
	- class="QmitkDiffusionDicomImport"
	- icon="resources/dwiimport.png">
	- <description>Diffusion DICOM data import</description>
	- <keywordReference id="org.mitk.views.diffusiondicomimport.Keyword"/>
	- </view>
	-
	- <view id="org.mitk.views.controlvisualizationpropertiesview"
	- name="Visualization"
	- icon="resources/vizControls.png"
	- class="QmitkControlVisualizationPropertiesView">
	- <keywordReference id="org.mitk.views.controlvisualizationpropertiesview.Keyword"/>
	- </view>
	-
	- <view id="org.mitk.views.dicomtractogramtageditor"
	- name="DICOM Tractogram Tag Editor"
	- category="Fiber Tractography"
	- class="QmitkDicomTractogramTagEditorView"
	- icon="resources/dwiimport.png">
	- <keywordReference id="org.mitk.views.dicomtractogramtageditor.Keyword"/>
	- </view>
	-
	- </extension>
	-
	-</plugin>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/ConnectomicsNetwork.png b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/ConnectomicsNetwork.png
	deleted file mode 100644
	index f434f12741..0000000000
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/DiffData24.png b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/DiffData24.png
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	index 74a61adabb..0000000000
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	index d22f28b9aa..0000000000
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/MapperEfx2D.png b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/MapperEfx2D.png
	deleted file mode 100644
	index fd6b8bda9c..0000000000
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/QmitkDiffusionImaging.qrc b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/QmitkDiffusionImaging.qrc
	deleted file mode 100644
	index e114ea049d..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/QmitkDiffusionImaging.qrc
	+++ /dev/null
	@@ -1,31 +0,0 @@
	-<RCC>
	- <qresource prefix="/QmitkDiffusionImaging">
	- <file>dwi.png</file>
	- <file>dwiimport.png</file>
	- <file>texIntONIcon.png</file>
	- <file>texIntOFFIcon.png</file>
	- <file>vizControls.png</file>
	- <file>Refresh_48.png</file>
	- <file>glyphsoff_C.png</file>
	- <file>glyphsoff_S.png</file>
	- <file>glyphsoff_T.png</file>
	- <file>glyphson_C.png</file>
	- <file>glyphson_S.png</file>
	- <file>glyphson_T.png</file>
	- <file>crosshair.png</file>
	- <file>paint2.png</file>
	- <file>reset.png</file>
	- <file>MapperEfx2D.png</file>
	- <file>refresh.xpm</file>
	- <file>tractogram.png</file>
	- <file>ml_tractogram.png</file>
	- <file>ConnectomicsNetwork.png</file>
	- <file>odf.png</file>
	- <file>DiffData24.png</file>
	- <file>odf_peaks.png</file>
	- <file>segmentation.svg</file>
	- <file>sh.png</file>
	- <file>tensor.png</file>
	- <file>color64.png</file>
	- </qresource>
	-</RCC>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/Refresh_48.png b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/Refresh_48.png
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	- transform="matrix(-0.84608119,0,0,1,-751.30501,-0.21428438)" />
	- </g>
	- </g>
	-</svg>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/sh.png b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/sh.png
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/source/pfeil.png b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/source/pfeil.png
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/source/texIntOFF.png b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/source/texIntOFF.png
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/tensor.png b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/tensor.png
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/tractogram.png b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/tractogram.png
	deleted file mode 100644
	index 9582dd772d..0000000000
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/resources/vizControls.png b/Plugins/org.mitk.gui.qt.diffusionimaging/resources/vizControls.png
	deleted file mode 100644
	index f951a4e3dd..0000000000
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Perspectives/QmitkDiffusionDefaultPerspective.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Perspectives/QmitkDiffusionDefaultPerspective.cpp
	deleted file mode 100644
	index 37aceceefa..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Perspectives/QmitkDiffusionDefaultPerspective.cpp
	+++ /dev/null
	@@ -1,46 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkDiffusionDefaultPerspective.h"
	-#include "berryIViewLayout.h"
	-
	-void QmitkDiffusionDefaultPerspective::CreateInitialLayout(berry::IPageLayout::Pointer layout)
	-{
	- /////////////////////////////////////////////////////
	- // all di-app perspectives should have the following:
	- /////////////////////////////////////////////////////
	-
	- QString editorArea = layout->GetEditorArea();
	-
	- layout->AddStandaloneViewPlaceholder("org.mitk.views.viewnavigatorview", berry::IPageLayout::LEFT, 0.3f, editorArea, false);
	-
	- layout->AddStandaloneView("org.mitk.views.datamanager", false, berry::IPageLayout::LEFT, 0.3f, editorArea);
	-
	- layout->AddStandaloneView("org.mitk.views.controlvisualizationpropertiesview", false, berry::IPageLayout::BOTTOM, .15f, "org.mitk.views.datamanager");
	-
	- berry::IFolderLayout::Pointer left =
	- layout->CreateFolder("org.mbi.diffusionimaginginternal.leftcontrols", berry::IPageLayout::BOTTOM, 0.15f, "org.mitk.views.controlvisualizationpropertiesview");
	-
	- layout->AddStandaloneViewPlaceholder("org.mitk.views.imagenavigator", berry::IPageLayout::BOTTOM, .7f, "org.mbi.diffusionimaginginternal.leftcontrols", false);
	-
	- /////////////////////////////////////////////
	- // here goes the perspective specific stuff
	- /////////////////////////////////////////////
	-
	- left->AddView("org.mitk.views.diffusiondicomimport");
	- left->AddView("org.mitk.views.diffusionpreprocessing");
	-
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Perspectives/QmitkDiffusionDefaultPerspective.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Perspectives/QmitkDiffusionDefaultPerspective.h
	deleted file mode 100644
	index c292475c7d..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Perspectives/QmitkDiffusionDefaultPerspective.h
	+++ /dev/null
	@@ -1,36 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef QmitkDiffusionDefaultPerspective_H_
	-#define QmitkDiffusionDefaultPerspective_H_
	-
	-#include <berryIPerspectiveFactory.h>
	-
	-class QmitkDiffusionDefaultPerspective : public QObject, public berry::IPerspectiveFactory
	-{
	- Q_OBJECT
	- Q_INTERFACES(berry::IPerspectiveFactory)
	-
	-public:
	-
	- QmitkDiffusionDefaultPerspective() {}
	- ~QmitkDiffusionDefaultPerspective() {}
	-
	- void CreateInitialLayout(berry::IPageLayout::Pointer layout) override;
	-};
	-
	-#endif /* QmitkDiffusionDefaultPerspective_H_ */
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Perspectives/QmitkSegmentationPerspective.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Perspectives/QmitkSegmentationPerspective.cpp
	deleted file mode 100644
	index f172af70cf..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Perspectives/QmitkSegmentationPerspective.cpp
	+++ /dev/null
	@@ -1,51 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkSegmentationPerspective.h"
	-#include "berryIViewLayout.h"
	-
	-void QmitkSegmentationPerspective::CreateInitialLayout(berry::IPageLayout::Pointer layout)
	-{
	- /////////////////////////////////////////////////////
	- // all di-app perspectives should have the following:
	- /////////////////////////////////////////////////////
	-
	- QString editorArea = layout->GetEditorArea();
	-
	- layout->AddStandaloneViewPlaceholder("org.mitk.views.viewnavigatorview", berry::IPageLayout::LEFT, 0.3f, editorArea, false);
	-
	- layout->AddStandaloneView("org.mitk.views.datamanager",
	- false, berry::IPageLayout::LEFT, 0.3f, editorArea);
	-
	- layout->AddStandaloneView("org.mitk.views.controlvisualizationpropertiesview",
	- false, berry::IPageLayout::BOTTOM, .15f, "org.mitk.views.datamanager");
	-
	- berry::IFolderLayout::Pointer left =
	- layout->CreateFolder("org.mbi.diffusionimaginginternal.leftcontrols",
	- berry::IPageLayout::BOTTOM, 0.15f, "org.mitk.views.controlvisualizationpropertiesview");
	-
	- layout->AddStandaloneViewPlaceholder("org.mitk.views.imagenavigator",
	- berry::IPageLayout::BOTTOM, .7f, "org.mbi.diffusionimaginginternal.leftcontrols", false);
	-
	- /////////////////////////////////////////////
	- // here goes the perspective specific stuff
	- /////////////////////////////////////////////
	-
	- left->AddView("org.mitk.views.tractseg");
	- left->AddView("org.mitk.views.segmentation");
	- left->AddView("org.mitk.views.segmentationutilities");
	- left->AddView("org.mitk.views.measurement");
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Perspectives/QmitkSegmentationPerspective.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Perspectives/QmitkSegmentationPerspective.h
	deleted file mode 100644
	index 6be030c56a..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Perspectives/QmitkSegmentationPerspective.h
	+++ /dev/null
	@@ -1,36 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef QmitkSegmentationPerspective_H_
	-#define QmitkSegmentationPerspective_H_
	-
	-#include <berryIPerspectiveFactory.h>
	-
	-class QmitkSegmentationPerspective : public QObject, public berry::IPerspectiveFactory
	-{
	- Q_OBJECT
	- Q_INTERFACES(berry::IPerspectiveFactory)
	-
	-public:
	-
	- QmitkSegmentationPerspective() {}
	- ~QmitkSegmentationPerspective() {}
	-
	- void CreateInitialLayout(berry::IPageLayout::Pointer layout) override;
	-};
	-
	-#endif /* QmitkSegmentationPerspective_H_ */
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.cpp
	deleted file mode 100644
	index 78d2287b87..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.cpp
	+++ /dev/null
	@@ -1,1250 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkControlVisualizationPropertiesView.h"
	-
	-#include "mitkNodePredicateDataType.h"
	-#include "mitkDataNodeObject.h"
	-#include "mitkOdfNormalizationMethodProperty.h"
	-#include "mitkOdfScaleByProperty.h"
	-#include "mitkResliceMethodProperty.h"
	-#include "mitkRenderingManager.h"
	-
	-#include "mitkImageCast.h"
	-#include "mitkShImage.h"
	-#include "mitkPlanarFigure.h"
	-#include "mitkFiberBundle.h"
	-#include "QmitkDataStorageComboBox.h"
	-#include "mitkPlanarFigureInteractor.h"
	-#include <mitkOdfImage.h>
	-#include <mitkTensorImage.h>
	-#include <mitkImage.h>
	-#include <mitkDiffusionPropertyHelper.h>
	-#include <mitkConnectomicsNetwork.h>
	-#include "usModuleRegistry.h"
	-#include <mitkPeakImage.h>
	-#include <mitkBaseRenderer.h>
	-#include "mitkPlaneGeometry.h"
	-#include <QmitkRenderWindow.h>
	-#include <itkFlipPeaksFilter.h>
	-#include <mitkImageToItk.h>
	-#include <mitkWorkbenchUtil.h>
	-#include "berryIWorkbenchWindow.h"
	-#include "berryIWorkbenchPage.h"
	-#include "berryISelectionService.h"
	-#include "berryConstants.h"
	-#include "berryPlatformUI.h"
	-
	-#include "itkRGBAPixel.h"
	-#include <itkTractDensityImageFilter.h>
	-
	-#include "qwidgetaction.h"
	-#include "qcolordialog.h"
	-#include <QRgb>
	-#include <itkMultiThreader.h>
	-#include <mitkClippingProperty.h>
	-#include <ciso646>
	-
	-#define ROUND(a) ((a)>0 ? (int)((a)+0.5) : -(int)(0.5-(a)))
	-
	-const std::string QmitkControlVisualizationPropertiesView::VIEW_ID = "org.mitk.views.controlvisualizationpropertiesview";
	-
	-using namespace berry;
	-
	-QmitkControlVisualizationPropertiesView::QmitkControlVisualizationPropertiesView()
	- : QmitkAbstractView(),
	- m_Controls(nullptr),
	- m_CurrentSelection(nullptr),
	- m_IconTexOFF(new QIcon(":/QmitkDiffusionImaging/texIntOFFIcon.png")),
	- m_IconTexON(new QIcon(":/QmitkDiffusionImaging/texIntONIcon.png")),
	- m_IconGlyOFF_T(new QIcon(":/QmitkDiffusionImaging/glyphsoff_T.png")),
	- m_IconGlyON_T(new QIcon(":/QmitkDiffusionImaging/glyphson_T.png")),
	- m_IconGlyOFF_C(new QIcon(":/QmitkDiffusionImaging/glyphsoff_C.png")),
	- m_IconGlyON_C(new QIcon(":/QmitkDiffusionImaging/glyphson_C.png")),
	- m_IconGlyOFF_S(new QIcon(":/QmitkDiffusionImaging/glyphsoff_S.png")),
	- m_IconGlyON_S(new QIcon(":/QmitkDiffusionImaging/glyphson_S.png")),
	- m_GlyIsOn_T(false),
	- m_GlyIsOn_C(false),
	- m_GlyIsOn_S(false),
	- m_CurrentThickSlicesMode(1),
	- m_CurrentThickSlicesNum(0),
	- m_CurrentPickingNode(nullptr),
	- m_ColorPropertyObserverTag(0),
	- m_OpacityPropertyObserverTag(0)
	-{
	- m_MyMenu = nullptr;
	- auto numThread = itk::MultiThreader::GetGlobalMaximumNumberOfThreads();
	- itk::MultiThreader::SetGlobalDefaultNumberOfThreads(numThread);
	-}
	-
	-
	-QmitkControlVisualizationPropertiesView::~QmitkControlVisualizationPropertiesView()
	-{
	-
	-}
	-
	-void QmitkControlVisualizationPropertiesView::SetTs(int currentThickSlicesMode, int num, std::string render_window)
	-{
	- if (auto renderWindowPart = this->GetRenderWindowPart(mitk::WorkbenchUtil::IRenderWindowPartStrategy::OPEN))
	- {
	- mitk::BaseRenderer::Pointer renderer = renderWindowPart->GetQmitkRenderWindow(QString(render_window.c_str()))->GetRenderer();
	- renderer->GetCurrentWorldPlaneGeometryNode()->SetProperty("reslice.thickslices.num", mitk::IntProperty::New(num));
	- if(num>0)
	- {
	- renderer->GetCurrentWorldPlaneGeometryNode()->SetProperty("reslice.thickslices", mitk::ResliceMethodProperty::New(currentThickSlicesMode));
	- renderer->GetCurrentWorldPlaneGeometryNode()->SetProperty("reslice.thickslices.showarea", mitk::BoolProperty::New(true));
	- }
	- else
	- {
	- renderer->GetCurrentWorldPlaneGeometryNode()->SetProperty("reslice.thickslices", mitk::ResliceMethodProperty::New(0));
	- renderer->GetCurrentWorldPlaneGeometryNode()->SetProperty("reslice.thickslices.showarea", mitk::BoolProperty::New(false));
	- }
	-
	- renderer->SendUpdateSlice();
	- renderer->GetRenderingManager()->RequestUpdateAll();
	- }
	-}
	-
	-void QmitkControlVisualizationPropertiesView::OnThickSlicesModeSelected( QAction* action )
	-{
	- m_CurrentThickSlicesMode = action->data().toInt();
	-
	- switch( m_CurrentThickSlicesMode )
	- {
	- case 0:
	- return;
	-
	- case 1:
	- this->m_Controls->m_TSMenu->setText("MIP");
	- break;
	-
	- case 2:
	- this->m_Controls->m_TSMenu->setText("SUM");
	- break;
	-
	- case 3:
	- this->m_Controls->m_TSMenu->setText("WEIGH");
	- break;
	-
	- default:
	- return;
	- }
	-
	- SetTs(m_CurrentThickSlicesMode, m_CurrentThickSlicesNum, "axial");
	- SetTs(m_CurrentThickSlicesMode, m_CurrentThickSlicesNum, "sagittal");
	- SetTs(m_CurrentThickSlicesMode, m_CurrentThickSlicesNum, "coronal");
	-}
	-
	-
	-void QmitkControlVisualizationPropertiesView::OnTSNumChanged( int num )
	-{
	- m_CurrentThickSlicesNum = num;
	- SetTs(m_CurrentThickSlicesMode, m_CurrentThickSlicesNum, "axial");
	- SetTs(m_CurrentThickSlicesMode, m_CurrentThickSlicesNum, "sagittal");
	- SetTs(m_CurrentThickSlicesMode, m_CurrentThickSlicesNum, "coronal");
	- m_TSLabel->setText(QString::number( num*2 + 1 ));
	-}
	-
	-
	-void QmitkControlVisualizationPropertiesView::CreateQtPartControl(QWidget *parent)
	-{
	- if (!m_Controls)
	- {
	- // create GUI widgets
	- m_Controls = new Ui::QmitkControlVisualizationPropertiesViewControls;
	- m_Controls->setupUi(parent);
	- this->CreateConnections();
	-
	- // hide warning (ODFs in rotated planes)
	- m_Controls->m_lblRotatedPlanesWarning->hide();
	-
	- m_MyMenu = new QMenu(parent);
	- m_Controls->m_TSMenu->setMenu( m_MyMenu );
	-
	- QIcon iconFiberFade(":/QmitkDiffusionImaging/MapperEfx2D.png");
	- m_Controls->m_FiberFading2D->setIcon(iconFiberFade);
	-
	- m_Controls->m_NormalizationFrame->setVisible(false);
	- m_Controls->m_Crosshair->setVisible(false);
	-
	- mitk::IRenderWindowPart* renderWindow = this->GetRenderWindowPart();
	- if (renderWindow)
	- {
	- m_SliceChangeListener.RenderWindowPartActivated(renderWindow);
	- connect(&m_SliceChangeListener, SIGNAL(SliceChanged()), this, SLOT(OnSliceChanged()));
	- }
	-
	- connect(m_Controls->m_SetColor1, SIGNAL(clicked()), this, SLOT(SetColor()));
	- connect(m_Controls->m_SetColor2, SIGNAL(clicked()), this, SLOT(SetColor()));
	- }
	-}
	-
	-void QmitkControlVisualizationPropertiesView::SetColor()
	-{
	- if(m_SelectedNode)
	- {
	- QColor c = QColorDialog::getColor();
	- if (c.isValid())
	- {
	- float rgb[3];
	- rgb[0] = static_cast<float>(c.redF());
	- rgb[1] = static_cast<float>(c.greenF());
	- rgb[2] = static_cast<float>(c.blueF());
	- m_SelectedNode->SetColor(rgb);
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- }
	- }
	-}
	-
	-void QmitkControlVisualizationPropertiesView::SetFocus()
	-{
	- m_Controls->m_TSMenu->setFocus();
	-}
	-
	-
	-void QmitkControlVisualizationPropertiesView::SliceRotation(const itk::EventObject&)
	-{
	- // test if plane rotated
	- if( m_GlyIsOn_T \|\| m_GlyIsOn_C \|\| m_GlyIsOn_S )
	- {
	- if( this->IsPlaneRotated() )
	- {
	- // show label
	- m_Controls->m_lblRotatedPlanesWarning->show();
	- }
	- else
	- {
	- //hide label
	- m_Controls->m_lblRotatedPlanesWarning->hide();
	- }
	- }
	-}
	-
	-
	-void QmitkControlVisualizationPropertiesView::NodeRemoved(const mitk::DataNode* /node/)
	-{
	-}
	-
	-
	-#include <mitkMessage.h>
	-void QmitkControlVisualizationPropertiesView::CreateConnections()
	-{
	- if ( m_Controls )
	- {
	- connect( static_cast<QObject*>(m_Controls->m_VisibleOdfsON_T), SIGNAL(clicked()), this, SLOT(VisibleOdfsON_T()) );
	- connect( static_cast<QObject*>(m_Controls->m_VisibleOdfsON_S), SIGNAL(clicked()), this, SLOT(VisibleOdfsON_S()) );
	- connect( static_cast<QObject*>(m_Controls->m_VisibleOdfsON_C), SIGNAL(clicked()), this, SLOT(VisibleOdfsON_C()) );
	- connect( static_cast<QObject*>(m_Controls->m_ShowMaxNumber), SIGNAL(editingFinished()), this, SLOT(ShowMaxNumberChanged()) );
	- connect( static_cast<QObject*>(m_Controls->m_NormalizationDropdown), SIGNAL(currentIndexChanged(int)), this, SLOT(NormalizationDropdownChanged(int)) );
	- connect( static_cast<QObject*>(m_Controls->m_ScalingFactor), SIGNAL(valueChanged(double)), this, SLOT(ScalingFactorChanged(double)) );
	- connect( static_cast<QObject*>(m_Controls->m_AdditionalScaling), SIGNAL(currentIndexChanged(int)), this, SLOT(AdditionalScaling(int)) );
	- connect(static_cast<QObject>(m_Controls->m_ResetColoring), SIGNAL(clicked()), static_cast<QObject>(this), SLOT(ResetColoring()));
	- connect(static_cast<QObject>(m_Controls->m_ResetColoring2), SIGNAL(clicked()), static_cast<QObject>(this), SLOT(ResetColoring()));
	- connect(static_cast<QObject>(m_Controls->m_FiberFading2D), SIGNAL(clicked()), static_cast<QObject>(this), SLOT( Fiber2DfadingEFX() ) );
	- connect(static_cast<QObject>(m_Controls->m_FiberThicknessSlider), SIGNAL(sliderReleased()), static_cast<QObject>(this), SLOT( FiberSlicingThickness2D() ) );
	- connect(static_cast<QObject>(m_Controls->m_FiberThicknessSlider), SIGNAL(valueChanged(int)), static_cast<QObject>(this), SLOT( FiberSlicingUpdateLabel(int) ));
	- connect(static_cast<QObject>(m_Controls->m_Crosshair), SIGNAL(clicked()), static_cast<QObject>(this), SLOT(SetInteractor()));
	- connect(static_cast<QObject>(m_Controls->m_LineWidth), SIGNAL(editingFinished()), static_cast<QObject>(this), SLOT(LineWidthChanged()));
	- connect(static_cast<QObject>(m_Controls->m_TubeWidth), SIGNAL(editingFinished()), static_cast<QObject>(this), SLOT(TubeRadiusChanged()));
	- connect(static_cast<QObject>(m_Controls->m_RibbonWidth), SIGNAL(editingFinished()), static_cast<QObject>(this), SLOT(RibbonWidthChanged()));
	- connect( static_cast<QObject>(m_Controls->m_OdfColorBox), SIGNAL(currentIndexChanged(int)), static_cast<QObject>(this), SLOT(OnColourisationModeChanged() ) );
	- connect(static_cast<QObject>(m_Controls->m_Clip0), SIGNAL(toggled(bool)), static_cast<QObject>(this), SLOT(Toggle3DClipping(bool)));
	- connect(static_cast<QObject>(m_Controls->m_Clip1), SIGNAL(toggled(bool)), static_cast<QObject>(this), SLOT(Toggle3DClipping(bool)));
	- connect(static_cast<QObject>(m_Controls->m_Clip2), SIGNAL(toggled(bool)), static_cast<QObject>(this), SLOT(Toggle3DClipping(bool)));
	- connect(static_cast<QObject>(m_Controls->m_Clip3), SIGNAL(toggled(bool)), static_cast<QObject>(this), SLOT(Toggle3DClipping(bool)));
	- connect(static_cast<QObject>(m_Controls->m_FlipClipBox), SIGNAL(stateChanged(int)), static_cast<QObject>(this), SLOT(Toggle3DClipping()));
	- connect(static_cast<QObject>(m_Controls->m_Enable3dPeaks), SIGNAL(stateChanged(int)), static_cast<QObject>(this), SLOT(Toggle3DPeaks()));
	- connect(static_cast<QObject>(m_Controls->m_FlipPeaksButton), SIGNAL(clicked()), static_cast<QObject>(this), SLOT(FlipPeaks()));
	-
	- m_Controls->m_BundleControlsFrame->setVisible(false);
	- m_Controls->m_ImageControlsFrame->setVisible(false);
	- m_Controls->m_PeakImageFrame->setVisible(false);
	- m_Controls->m_lblRotatedPlanesWarning->setVisible(false);
	- m_Controls->m_3DClippingBox->setVisible(false);
	- }
	-}
	-
	-
	-// set diffusion image channel to b0 volume
	-void QmitkControlVisualizationPropertiesView::NodeAdded(const mitk::DataNode *node)
	-{
	- mitk::DataNode* notConst = const_cast<mitk::DataNode*>(node);
	-
	- bool isDiffusionImage( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast<mitk::Image *>(node->GetData())) );
	-
	- if (isDiffusionImage)
	- {
	- mitk::Image::Pointer dimg = dynamic_cast<mitk::Image*>(notConst->GetData());
	-
	- // if there is no b0 image in the dataset, the GetB0Indices() returns a vector of size 0
	- // and hence we cannot set the Property directly to .front()
	- int displayChannelPropertyValue = 0;
	- mitk::DiffusionPropertyHelper::BValueMapType map = mitk::DiffusionPropertyHelper::GetBValueMap(dimg);
	-
	- if( map[0].size() > 0) { displayChannelPropertyValue = map[0].front(); }
	-
	- notConst->SetIntProperty("DisplayChannel", displayChannelPropertyValue );
	- }
	-}
	-
	-
	-/* OnSelectionChanged is registered to SelectionService, therefore no need to
	-implement SelectionService Listener explicitly */
	-void QmitkControlVisualizationPropertiesView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /part/, const QList<mitk::DataNode::Pointer>& nodes)
	-{
	- m_Controls->m_BundleControlsFrame->setVisible(false);
	- m_Controls->m_ImageControlsFrame->setVisible(false);
	- m_Controls->m_PeakImageFrame->setVisible(false);
	- m_Controls->m_3DClippingBox->setVisible(false);
	- m_Controls->m_FlipClipBox->setVisible(false);
	- m_Controls->m_Enable3dPeaks->setVisible(false);
	-
	- if (nodes.size()>1) // only do stuff if one node is selected
	- return;
	-
	- m_Controls->m_NumberGlyphsFrame->setVisible(false);
	- m_Controls->m_GlyphFrame->setVisible(false);
	- m_Controls->m_TSMenu->setVisible(false);
	-
	- m_SelectedNode = nullptr;
	-
	- int numOdfImages = 0;
	- for (mitk::DataNode::Pointer node: nodes)
	- {
	- if(node.IsNull())
	- continue;
	-
	- mitk::BaseData* nodeData = node->GetData();
	- if(nodeData == nullptr)
	- continue;
	-
	- m_SelectedNode = node;
	-
	- if (dynamic_cast<mitk::PeakImage*>(nodeData))
	- {
	- m_Controls->m_PeakImageFrame->setVisible(true);
	-
	- if (m_Color.IsNotNull())
	- m_Color->RemoveObserver(m_ColorPropertyObserverTag);
	-
	- itk::ReceptorMemberCommand<QmitkControlVisualizationPropertiesView>::Pointer command = itk::ReceptorMemberCommand<QmitkControlVisualizationPropertiesView>::New();
	- command->SetCallbackFunction( this, &QmitkControlVisualizationPropertiesView::SetCustomColor );
	- m_Color = dynamic_cast<mitk::ColorProperty*>(node->GetProperty("color", nullptr));
	- if (m_Color.IsNotNull())
	- m_ColorPropertyObserverTag = m_Color->AddObserver( itk::ModifiedEvent(), command );
	-
	- int ClippingPlaneId = -1;
	- m_SelectedNode->GetPropertyValue("3DClippingPlaneId",ClippingPlaneId);
	- switch(ClippingPlaneId)
	- {
	- case 0:
	- m_Controls->m_Clip0->setChecked(1);
	- break;
	- case 1:
	- m_Controls->m_Clip1->setChecked(1);
	- break;
	- case 2:
	- m_Controls->m_Clip2->setChecked(1);
	- break;
	- case 3:
	- m_Controls->m_Clip3->setChecked(1);
	- break;
	- default :
	- m_Controls->m_Clip0->setChecked(1);
	- }
	-
	- m_Controls->m_Enable3dPeaks->setVisible(true);
	- m_Controls->m_3DClippingBox->setVisible(true);
	- }
	- else if (dynamic_cast<mitk::FiberBundle*>(nodeData))
	- {
	- int ClippingPlaneId = -1;
	- m_SelectedNode->GetPropertyValue("3DClippingPlaneId",ClippingPlaneId);
	- switch(ClippingPlaneId)
	- {
	- case 0:
	- m_Controls->m_Clip0->setChecked(1);
	- break;
	- case 1:
	- m_Controls->m_Clip1->setChecked(1);
	- break;
	- case 2:
	- m_Controls->m_Clip2->setChecked(1);
	- break;
	- case 3:
	- m_Controls->m_Clip3->setChecked(1);
	- break;
	- default :
	- m_Controls->m_Clip0->setChecked(1);
	- }
	-
	- // handle fiber property observers
	- if (m_Color.IsNotNull())
	- m_Color->RemoveObserver(m_ColorPropertyObserverTag);
	- itk::ReceptorMemberCommand<QmitkControlVisualizationPropertiesView>::Pointer command = itk::ReceptorMemberCommand<QmitkControlVisualizationPropertiesView>::New();
	- command->SetCallbackFunction( this, &QmitkControlVisualizationPropertiesView::SetCustomColor );
	- m_Color = dynamic_cast<mitk::ColorProperty*>(node->GetProperty("color", nullptr));
	- if (m_Color.IsNotNull())
	- m_ColorPropertyObserverTag = m_Color->AddObserver( itk::ModifiedEvent(), command );
	-
	- m_Controls->m_FlipClipBox->setVisible(true);
	- m_Controls->m_3DClippingBox->setVisible(true);
	- m_Controls->m_BundleControlsFrame->setVisible(true);
	-
	- if(m_CurrentPickingNode != 0 && node.GetPointer() != m_CurrentPickingNode)
	- { m_Controls->m_Crosshair->setEnabled(false); }
	- else
	- { m_Controls->m_Crosshair->setEnabled(true); }
	-
	- int width;
	- node->GetIntProperty("shape.linewidth", width);
	- m_Controls->m_LineWidth->setValue(width);
	-
	- float radius;
	- node->GetFloatProperty("shape.tuberadius", radius);
	- m_Controls->m_TubeWidth->setValue(radius);
	-
	- float range;
	- node->GetFloatProperty("Fiber2DSliceThickness",range);
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(node->GetData());
	- mitk::BaseGeometry::Pointer geo = fib->GetGeometry();
	- mitk::ScalarType max = geo->GetExtentInMM(0);
	- max = std::max(max, geo->GetExtentInMM(1));
	- max = std::max(max, geo->GetExtentInMM(2));
	-
	- m_Controls->m_FiberThicknessSlider->setMaximum(max * 10);
	- m_Controls->m_FiberThicknessSlider->setValue(range * 10);
	- }
	- else if(dynamic_cast<mitk::OdfImage>(nodeData) \|\| dynamic_cast<mitk::TensorImage>(nodeData) \|\| dynamic_cast<mitk::ShImage*>(nodeData))
	- {
	- m_Controls->m_ImageControlsFrame->setVisible(true);
	- m_Controls->m_NumberGlyphsFrame->setVisible(true);
	- m_Controls->m_GlyphFrame->setVisible(true);
	- m_Controls->m_NormalizationFrame->setVisible(true);
	-
	- if(m_NodeUsedForOdfVisualization.IsNotNull())
	- {
	- m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_S", false);
	- m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_C", false);
	- m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_T", false);
	- }
	- m_NodeUsedForOdfVisualization = node;
	- m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_S", m_GlyIsOn_S);
	- m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_C", m_GlyIsOn_C);
	- m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_T", m_GlyIsOn_T);
	-
	- if (dynamic_cast<mitk::TensorImage*>(nodeData))
	- {
	- m_Controls->m_NormalizationDropdown->setVisible(false);
	- m_Controls->m_NormalizationLabel->setVisible(false);
	- }
	- else
	- {
	- m_Controls->m_NormalizationDropdown->setVisible(true);
	- m_Controls->m_NormalizationLabel->setVisible(true);
	- }
	-
	-
	- int val;
	- node->GetIntProperty("ShowMaxNumber", val);
	- m_Controls->m_ShowMaxNumber->setValue(val);
	-
	- m_Controls->m_NormalizationDropdown->setCurrentIndex(dynamic_cast<mitk::EnumerationProperty*>(node->GetProperty("Normalization"))->GetValueAsId());
	-
	- float fval;
	- node->GetFloatProperty("Scaling",fval);
	- m_Controls->m_ScalingFactor->setValue(fval);
	-
	- m_Controls->m_AdditionalScaling->setCurrentIndex(dynamic_cast<mitk::EnumerationProperty*>(node->GetProperty("ScaleBy"))->GetValueAsId());
	-
	- bool switchTensorViewValue = false;
	- node->GetBoolProperty( "DiffusionCore.Rendering.OdfVtkMapper.SwitchTensorView", switchTensorViewValue );
	-
	- bool colourisationModeBit = false;
	- node->GetBoolProperty("DiffusionCore.Rendering.OdfVtkMapper.ColourisationModeBit", colourisationModeBit );
	- m_Controls->m_OdfColorBox->setCurrentIndex(colourisationModeBit);
	-
	- numOdfImages++;
	- }
	- else if(dynamic_cast<mitk::PlanarFigure*>(nodeData))
	- {
	- PlanarFigureFocus();
	- }
	- else if( dynamic_cast<mitk::Image*>(nodeData) )
	- {
	- m_Controls->m_ImageControlsFrame->setVisible(true);
	- m_Controls->m_TSMenu->setVisible(true);
	- }
	- }
	-
	- if( nodes.empty() ) { return; }
	-
	- mitk::DataNode::Pointer node = nodes.at(0);
	-
	- if( node.IsNull() ) { return; }
	-
	- QMenu *myMenu = m_MyMenu;
	- myMenu->clear();
	-
	- QActionGroup* thickSlicesActionGroup = new QActionGroup(myMenu);
	- thickSlicesActionGroup->setExclusive(true);
	-
	- int currentTSMode = 0;
	- {
	- mitk::ResliceMethodProperty::Pointer m = dynamic_cast<mitk::ResliceMethodProperty*>(node->GetProperty( "reslice.thickslices" ));
	- if( m.IsNotNull() )
	- currentTSMode = m->GetValueAsId();
	- }
	-
	- int maxTS = 30;
	-
	- for (auto node: nodes)
	- {
	- mitk::Image* image = dynamic_cast<mitk::Image*>(node->GetData());
	- if (image)
	- {
	- int size = std::max(image->GetDimension(0), std::max(image->GetDimension(1), image->GetDimension(2)));
	-
	- if (size>maxTS) { maxTS=size; }
	- }
	- }
	- maxTS /= 2;
	-
	- int currentNum = 0;
	- {
	- mitk::IntProperty::Pointer m = dynamic_cast<mitk::IntProperty*>(node->GetProperty( "reslice.thickslices.num" ));
	- if( m.IsNotNull() )
	- {
	- currentNum = m->GetValue();
	- if(currentNum < 0) { currentNum = 0; }
	- if(currentNum > maxTS) { currentNum = maxTS; }
	- }
	- }
	-
	- if(currentTSMode==0) { currentNum=0; }
	-
	- QSlider *m_TSSlider = new QSlider(myMenu);
	- m_TSSlider->setMinimum(0);
	- m_TSSlider->setMaximum(maxTS-1);
	- m_TSSlider->setValue(currentNum);
	-
	- m_TSSlider->setOrientation(Qt::Horizontal);
	-
	- connect( m_TSSlider, SIGNAL( valueChanged(int) ), this, SLOT( OnTSNumChanged(int) ) );
	-
	- QHBoxLayout* _TSLayout = new QHBoxLayout;
	- _TSLayout->setContentsMargins(4,4,4,4);
	- _TSLayout->addWidget(m_TSSlider);
	- _TSLayout->addWidget(m_TSLabel=new QLabel(QString::number(currentNum*2+1),myMenu));
	-
	- QWidget* _TSWidget = new QWidget;
	- _TSWidget->setLayout(_TSLayout);
	-
	- QActionGroup* thickSliceModeActionGroup = new QActionGroup(myMenu);
	- thickSliceModeActionGroup->setExclusive(true);
	-
	- QWidgetAction *m_TSSliderAction = new QWidgetAction(myMenu);
	- m_TSSliderAction->setDefaultWidget(_TSWidget);
	- myMenu->addAction(m_TSSliderAction);
	-
	- QAction* mipThickSlicesAction = new QAction(myMenu);
	- mipThickSlicesAction->setActionGroup(thickSliceModeActionGroup);
	- mipThickSlicesAction->setText("MIP (max. intensity proj.)");
	- mipThickSlicesAction->setCheckable(true);
	- mipThickSlicesAction->setChecked(m_CurrentThickSlicesMode==1);
	- mipThickSlicesAction->setData(1);
	- myMenu->addAction( mipThickSlicesAction );
	-
	- QAction* sumThickSlicesAction = new QAction(myMenu);
	- sumThickSlicesAction->setActionGroup(thickSliceModeActionGroup);
	- sumThickSlicesAction->setText("SUM (sum intensity proj.)");
	- sumThickSlicesAction->setCheckable(true);
	- sumThickSlicesAction->setChecked(m_CurrentThickSlicesMode==2);
	- sumThickSlicesAction->setData(2);
	- myMenu->addAction( sumThickSlicesAction );
	-
	- QAction* weightedThickSlicesAction = new QAction(myMenu);
	- weightedThickSlicesAction->setActionGroup(thickSliceModeActionGroup);
	- weightedThickSlicesAction->setText("WEIGHTED (gaussian proj.)");
	- weightedThickSlicesAction->setCheckable(true);
	- weightedThickSlicesAction->setChecked(m_CurrentThickSlicesMode==3);
	- weightedThickSlicesAction->setData(3);
	- myMenu->addAction( weightedThickSlicesAction );
	-
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- connect( thickSliceModeActionGroup, SIGNAL(triggered(QAction)), this, SLOT(OnThickSlicesModeSelected(QAction)) );
	-}
	-
	-
	-void QmitkControlVisualizationPropertiesView::VisibleOdfsON_S()
	-{
	- m_GlyIsOn_S = m_Controls->m_VisibleOdfsON_S->isChecked();
	- if (m_NodeUsedForOdfVisualization.IsNull())
	- {
	- MITK_WARN << "ODF visualization activated but m_NodeUsedForOdfVisualization is nullptr";
	- return;
	- }
	- m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_S", m_GlyIsOn_S);
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-void QmitkControlVisualizationPropertiesView::Visible()
	-{
	- mitk::IRenderWindowPart* renderWindow = this->GetRenderWindowPart();
	- if (renderWindow)
	- {
	- m_SliceChangeListener.RenderWindowPartActivated(renderWindow);
	- connect(&m_SliceChangeListener, SIGNAL(SliceChanged()), this, SLOT(OnSliceChanged()));
	- }
	-}
	-
	-void QmitkControlVisualizationPropertiesView::Hidden()
	-{
	-
	-}
	-
	-void QmitkControlVisualizationPropertiesView::Activated()
	-{
	- mitk::IRenderWindowPart* renderWindow = this->GetRenderWindowPart();
	- if (renderWindow)
	- {
	- m_SliceChangeListener.RenderWindowPartActivated(renderWindow);
	- connect(&m_SliceChangeListener, SIGNAL(SliceChanged()), this, SLOT(OnSliceChanged()));
	- }
	-}
	-
	-void QmitkControlVisualizationPropertiesView::Deactivated()
	-{
	-}
	-
	-void QmitkControlVisualizationPropertiesView::FlipPeaks()
	-{
	- if (m_SelectedNode.IsNull() \|\| dynamic_cast<mitk::PeakImage*>(m_SelectedNode->GetData())==nullptr)
	- return;
	-
	- std::string name = m_SelectedNode->GetName();
	-
	- mitk::Image::Pointer image = dynamic_cast<mitk::PeakImage*>(m_SelectedNode->GetData());
	-
	- typedef mitk::ImageToItk< mitk::PeakImage::ItkPeakImageType > CasterType;
	- CasterType::Pointer caster = CasterType::New();
	- caster->SetInput(image);
	- caster->Update();
	- mitk::PeakImage::ItkPeakImageType::Pointer itkImg = caster->GetOutput();
	-
	- itk::FlipPeaksFilter< float >::Pointer flipper = itk::FlipPeaksFilter< float >::New();
	- flipper->SetInput(itkImg);
	- flipper->SetFlipX(m_Controls->m_FlipPeaksX->isChecked());
	- flipper->SetFlipY(m_Controls->m_FlipPeaksY->isChecked());
	- flipper->SetFlipZ(m_Controls->m_FlipPeaksZ->isChecked());
	- flipper->Update();
	-
	- mitk::Image::Pointer resultImage = dynamic_cast<mitk::Image*>(mitk::PeakImage::New().GetPointer());
	- mitk::CastToMitkImage(flipper->GetOutput(), resultImage);
	- resultImage->SetVolume(flipper->GetOutput()->GetBufferPointer());
	- m_SelectedNode->SetData(resultImage);
	- m_SelectedNode->SetName(name);
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-void QmitkControlVisualizationPropertiesView::Toggle3DPeaks()
	-{
	- if (m_SelectedNode.IsNull() \|\| dynamic_cast<mitk::PeakImage*>(m_SelectedNode->GetData())==nullptr)
	- return;
	-
	- bool enabled = false;
	- m_SelectedNode->GetBoolProperty("Enable3DPeaks", enabled);
	- m_SelectedNode->SetBoolProperty( "Enable3DPeaks", !enabled );
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-void QmitkControlVisualizationPropertiesView::Toggle3DClipping(bool enabled)
	-{
	- if (!enabled \|\| m_SelectedNode.IsNull() \|\| (dynamic_cast<mitk::FiberBundle>(m_SelectedNode->GetData())==nullptr && dynamic_cast<mitk::PeakImage>(m_SelectedNode->GetData())==nullptr))
	- return;
	-
	- m_SelectedNode->SetBoolProperty( "3DClippingPlaneFlip", m_Controls->m_FlipClipBox->isChecked() );
	-
	- if (m_Controls->m_Clip0->isChecked())
	- {
	- m_SelectedNode->SetIntProperty( "3DClippingPlaneId", 0 );
	- Set3DClippingPlane(true, m_SelectedNode, "");
	- }
	- else if (m_Controls->m_Clip1->isChecked())
	- {
	- m_SelectedNode->SetIntProperty( "3DClippingPlaneId", 1 );
	- Set3DClippingPlane(false, m_SelectedNode, "axial");
	- }
	- else if (m_Controls->m_Clip2->isChecked())
	- {
	- m_SelectedNode->SetIntProperty( "3DClippingPlaneId", 2 );
	- Set3DClippingPlane(false, m_SelectedNode, "sagittal");
	- }
	- else if (m_Controls->m_Clip3->isChecked())
	- {
	- m_SelectedNode->SetIntProperty( "3DClippingPlaneId", 3 );
	- Set3DClippingPlane(false, m_SelectedNode, "coronal");
	- }
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-void QmitkControlVisualizationPropertiesView::OnSliceChanged()
	-{
	- mitk::DataStorage::SetOfObjects::ConstPointer nodes = this->GetDataStorage()->GetAll();
	- for (unsigned int i=0; i<nodes->Size(); ++i)
	- {
	- mitk::DataNode::Pointer node = nodes->GetElement(i);
	- int plane_id = -1;
	- node->GetIntProperty("3DClippingPlaneId", plane_id);
	-
	- if (plane_id==1)
	- Set3DClippingPlane(false, node, "axial");
	- else if (plane_id==2)
	- Set3DClippingPlane(false, node, "sagittal");
	- else if (plane_id==3)
	- Set3DClippingPlane(false, node, "coronal");
	- }
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-void QmitkControlVisualizationPropertiesView::Set3DClippingPlane(bool disable, mitk::DataNode* node, std::string plane)
	-{
	- mitk::IRenderWindowPart* renderWindow = this->GetRenderWindowPart();
	- if (renderWindow && node && (dynamic_cast<mitk::FiberBundle>(node->GetData()) \|\| dynamic_cast<mitk::PeakImage>(node->GetData())))
	- {
	- mitk::Vector3D planeNormal; planeNormal.Fill(0.0);
	- mitk::Point3D planeOrigin; planeOrigin.Fill(0.0);
	- if (!disable)
	- {
	- mitk::SliceNavigationController* slicer = renderWindow->GetQmitkRenderWindow(QString(plane.c_str()))->GetSliceNavigationController();
	- mitk::PlaneGeometry::ConstPointer planeGeo = slicer->GetCurrentPlaneGeometry();
	- planeOrigin = this->GetRenderWindowPart()->GetSelectedPosition();
	- planeNormal = planeGeo->GetNormal();
	- }
	- node->SetProperty( "3DClipping", mitk::ClippingProperty::New( planeOrigin, planeNormal ) );
	- if (dynamic_cast<mitk::FiberBundle*>(node->GetData()))
	- dynamic_cast<mitk::FiberBundle*>(node->GetData())->RequestUpdate();
	- else
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- }
	-}
	-
	-void QmitkControlVisualizationPropertiesView::VisibleOdfsON_T()
	-{
	- m_GlyIsOn_T = m_Controls->m_VisibleOdfsON_T->isChecked();
	- if (m_NodeUsedForOdfVisualization.IsNull())
	- {
	- MITK_WARN << "ODF visualization activated but m_NodeUsedForOdfVisualization is nullptr";
	- return;
	- }
	- m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_T", m_GlyIsOn_T);
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-
	-void QmitkControlVisualizationPropertiesView::VisibleOdfsON_C()
	-{
	- m_GlyIsOn_C = m_Controls->m_VisibleOdfsON_C->isChecked();
	- if (m_NodeUsedForOdfVisualization.IsNull())
	- {
	- MITK_WARN << "ODF visualization activated but m_NodeUsedForOdfVisualization is nullptr";
	- return;
	- }
	- m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_C", m_GlyIsOn_C);
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-
	-bool QmitkControlVisualizationPropertiesView::IsPlaneRotated()
	-{
	- mitk::Image* currentImage = dynamic_cast<mitk::Image* >( m_NodeUsedForOdfVisualization->GetData() );
	- if( currentImage == nullptr )
	- {
	- MITK_ERROR << " Casting problems. Returning false";
	- return false;
	- }
	-
	- mitk::Vector3D imageNormal0 = currentImage->GetSlicedGeometry()->GetAxisVector(0);
	- mitk::Vector3D imageNormal1 = currentImage->GetSlicedGeometry()->GetAxisVector(1);
	- mitk::Vector3D imageNormal2 = currentImage->GetSlicedGeometry()->GetAxisVector(2);
	- imageNormal0.Normalize();
	- imageNormal1.Normalize();
	- imageNormal2.Normalize();
	-
	- auto renderWindowPart = this->GetRenderWindowPart();
	-
	- double eps = 0.000001;
	- // for all 2D renderwindows of the render window part check alignment
	- {
	- mitk::PlaneGeometry::ConstPointer displayPlane
	- = dynamic_cast<const mitk::PlaneGeometry*>
	- ( renderWindowPart->GetQmitkRenderWindow("axial")->GetRenderer()->GetCurrentWorldPlaneGeometry() );
	-
	- if (displayPlane.IsNull()) { return false; }
	-
	- mitk::Vector3D normal = displayPlane->GetNormal();
	- normal.Normalize();
	- int test = 0;
	- if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal0.GetVnlVector()))-1) > eps ) { test++; }
	-
	- if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal1.GetVnlVector()))-1) > eps ) { test++; }
	-
	- if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal2.GetVnlVector()))-1) > eps ) { test++; }
	-
	- if (test==3) { return true; }
	- }
	- {
	- mitk::PlaneGeometry::ConstPointer displayPlane
	- = dynamic_cast<const mitk::PlaneGeometry*>
	- ( renderWindowPart->GetQmitkRenderWindow("sagittal")->GetRenderer()->GetCurrentWorldPlaneGeometry() );
	-
	- if (displayPlane.IsNull()) { return false; }
	-
	- mitk::Vector3D normal = displayPlane->GetNormal();
	- normal.Normalize();
	- int test = 0;
	- if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal0.GetVnlVector()))-1) > eps ) { test++; }
	-
	- if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal1.GetVnlVector()))-1) > eps ) { test++; }
	-
	- if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal2.GetVnlVector()))-1) > eps ) { test++; }
	-
	- if (test==3) { return true; }
	- }
	- {
	- mitk::PlaneGeometry::ConstPointer displayPlane
	- = dynamic_cast<const mitk::PlaneGeometry*>
	- ( renderWindowPart->GetQmitkRenderWindow("coronal")->GetRenderer()->GetCurrentWorldPlaneGeometry() );
	-
	- if (displayPlane.IsNull()) { return false; }
	-
	- mitk::Vector3D normal = displayPlane->GetNormal();
	- normal.Normalize();
	- int test = 0;
	- if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal0.GetVnlVector()))-1) > eps ) { test++; }
	-
	- if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal1.GetVnlVector()))-1) > eps ) { test++; }
	-
	- if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal2.GetVnlVector()))-1) > eps ) { test++; }
	-
	- if (test==3) { return true; }
	- }
	-
	- return false;
	-}
	-
	-
	-void QmitkControlVisualizationPropertiesView::ShowMaxNumberChanged()
	-{
	- int maxNr = m_Controls->m_ShowMaxNumber->value();
	- if ( maxNr < 1 )
	- {
	- m_Controls->m_ShowMaxNumber->setValue( 1 );
	- maxNr = 1;
	- }
	-
	- if ( dynamic_cast<mitk::OdfImage*>(m_SelectedNode->GetData())
	- \|\| dynamic_cast<mitk::TensorImage*>(m_SelectedNode->GetData())
	- \|\| dynamic_cast<mitk::ShImage*>(m_SelectedNode->GetData()) )
	- {
	- m_SelectedNode->SetIntProperty("ShowMaxNumber", maxNr);
	- }
	-
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-
	-void QmitkControlVisualizationPropertiesView::NormalizationDropdownChanged(int normDropdown)
	-{
	- typedef mitk::OdfNormalizationMethodProperty PropType;
	- PropType::Pointer normMeth = PropType::New();
	-
	- switch(normDropdown)
	- {
	- case 0:
	- normMeth->SetNormalizationToMinMax();
	- break;
	- case 1:
	- normMeth->SetNormalizationToMax();
	- break;
	- case 2:
	- normMeth->SetNormalizationToNone();
	- break;
	- case 3:
	- normMeth->SetNormalizationToGlobalMax();
	- break;
	- default:
	- normMeth->SetNormalizationToMinMax();
	- }
	-
	- if ( dynamic_cast<mitk::OdfImage*>(m_SelectedNode->GetData())
	- \|\| dynamic_cast<mitk::TensorImage*>(m_SelectedNode->GetData())
	- \|\| dynamic_cast<mitk::ShImage*>(m_SelectedNode->GetData()) )
	- {
	- m_SelectedNode->SetProperty("Normalization", normMeth.GetPointer());
	- }
	-
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-
	-void QmitkControlVisualizationPropertiesView::ScalingFactorChanged(double scalingFactor)
	-{
	- if ( dynamic_cast<mitk::OdfImage*>(m_SelectedNode->GetData())
	- \|\| dynamic_cast<mitk::TensorImage*>(m_SelectedNode->GetData())
	- \|\| dynamic_cast<mitk::ShImage*>(m_SelectedNode->GetData()) )
	- {
	- m_SelectedNode->SetFloatProperty("Scaling", scalingFactor);
	- }
	-
	- if (auto renderWindowPart = this->GetRenderWindowPart())
	- {
	- renderWindowPart->RequestUpdate();
	- }
	-}
	-
	-
	-void QmitkControlVisualizationPropertiesView::AdditionalScaling(int additionalScaling)
	-{
	-
	- typedef mitk::OdfScaleByProperty PropType;
	- PropType::Pointer scaleBy = PropType::New();
	-
	- switch(additionalScaling)
	- {
	- case 0:
	- scaleBy->SetScaleByNothing();
	- break;
	- case 1:
	- scaleBy->SetScaleByGFA();
	- //m_Controls->params_frame->setVisible(true);
	- break;
	- default:
	- scaleBy->SetScaleByNothing();
	- }
	-
	- if ( dynamic_cast<mitk::OdfImage*>(m_SelectedNode->GetData())
	- \|\| dynamic_cast<mitk::TensorImage*>(m_SelectedNode->GetData())
	- \|\| dynamic_cast<mitk::ShImage*>(m_SelectedNode->GetData()) )
	- {
	- m_SelectedNode->SetProperty("ScaleBy", scaleBy.GetPointer());
	- }
	-
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	-}
	-
	-void QmitkControlVisualizationPropertiesView::Fiber2DfadingEFX()
	-{
	- if (m_SelectedNode && dynamic_cast<mitk::FiberBundle*>(m_SelectedNode->GetData()) )
	- {
	- bool currentMode;
	- m_SelectedNode->GetBoolProperty("Fiber2DfadeEFX", currentMode);
	- m_SelectedNode->SetProperty("Fiber2DfadeEFX", mitk::BoolProperty::New(!currentMode));
	- dynamic_cast<mitk::FiberBundle*>(m_SelectedNode->GetData())->RequestUpdate2D();
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- }
	-}
	-
	-
	-void QmitkControlVisualizationPropertiesView::FiberSlicingThickness2D()
	-{
	- if (m_SelectedNode && dynamic_cast<mitk::FiberBundle*>(m_SelectedNode->GetData()))
	- {
	- float fibThickness = m_Controls->m_FiberThicknessSlider->value() * 0.1;
	- float currentThickness = 0;
	- m_SelectedNode->GetFloatProperty("Fiber2DSliceThickness", currentThickness);
	- if ( fabs(fibThickness-currentThickness) < 0.001 )
	- {
	- return;
	- }
	-
	- m_SelectedNode->SetProperty("Fiber2DSliceThickness", mitk::FloatProperty::New(fibThickness));
	- dynamic_cast<mitk::FiberBundle*>(m_SelectedNode->GetData())->RequestUpdate2D();
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- }
	-}
	-
	-
	-void QmitkControlVisualizationPropertiesView::FiberSlicingUpdateLabel(int value)
	-{
	- QString label = "Range %1 mm";
	- label = label.arg(value * 0.1);
	- m_Controls->label_range->setText(label);
	- FiberSlicingThickness2D();
	-}
	-
	-void QmitkControlVisualizationPropertiesView::SetCustomColor(const itk::EventObject& /e/)
	-{
	- if(m_SelectedNode && dynamic_cast<mitk::FiberBundle*>(m_SelectedNode->GetData()))
	- {
	- float color[3];
	- m_SelectedNode->GetColor(color);
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(m_SelectedNode->GetData());
	- fib->SetFiberColors(color[0]255, color[1]255, color[2]*255);
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- }
	- else if (m_SelectedNode && dynamic_cast<mitk::PeakImage*>(m_SelectedNode->GetData()))
	- {
	- float color[3];
	- m_SelectedNode->GetColor(color);
	- mitk::PeakImage::Pointer img = dynamic_cast<mitk::PeakImage*>(m_SelectedNode->GetData());
	- img->SetCustomColor(color[0]255, color[1]255, color[2]*255);
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- }
	-}
	-
	-
	-void QmitkControlVisualizationPropertiesView::ResetColoring()
	-{
	- if(m_SelectedNode && dynamic_cast<mitk::FiberBundle*>(m_SelectedNode->GetData()))
	- {
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(m_SelectedNode->GetData());
	- fib->ColorFibersByOrientation();
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- }
	- else if(m_SelectedNode && dynamic_cast<mitk::PeakImage*>(m_SelectedNode->GetData()))
	- {
	- mitk::PeakImage::Pointer fib = dynamic_cast<mitk::PeakImage*>(m_SelectedNode->GetData());
	- fib->ColorByOrientation();
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- }
	-}
	-
	-
	-void QmitkControlVisualizationPropertiesView::PlanarFigureFocus()
	-{
	- if(m_SelectedNode)
	- {
	- mitk::PlanarFigure* _PlanarFigure = 0;
	- _PlanarFigure = dynamic_cast<mitk::PlanarFigure*> (m_SelectedNode->GetData());
	-
	- if (_PlanarFigure && _PlanarFigure->GetPlaneGeometry())
	- {
	-
	- QmitkRenderWindow* selectedRenderWindow = 0;
	- bool PlanarFigureInitializedWindow = false;
	-
	- auto renderWindowPart = this->GetRenderWindowPart(mitk::WorkbenchUtil::IRenderWindowPartStrategy::OPEN);
	-
	- QmitkRenderWindow* axialRenderWindow =
	- renderWindowPart->GetQmitkRenderWindow("axial");
	-
	- if (m_SelectedNode->GetBoolProperty("PlanarFigureInitializedWindow",
	- PlanarFigureInitializedWindow, axialRenderWindow->GetRenderer()))
	- {
	- selectedRenderWindow = axialRenderWindow;
	- }
	-
	- QmitkRenderWindow* sagittalRenderWindow =
	- renderWindowPart->GetQmitkRenderWindow("sagittal");
	-
	- if (!selectedRenderWindow && m_SelectedNode->GetBoolProperty(
	- "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow,
	- sagittalRenderWindow->GetRenderer()))
	- {
	- selectedRenderWindow = sagittalRenderWindow;
	- }
	-
	- QmitkRenderWindow* coronalRenderWindow =
	- renderWindowPart->GetQmitkRenderWindow("coronal");
	-
	- if (!selectedRenderWindow && m_SelectedNode->GetBoolProperty(
	- "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow,
	- coronalRenderWindow->GetRenderer()))
	- {
	- selectedRenderWindow = coronalRenderWindow;
	- }
	-
	- QmitkRenderWindow* _3DRenderWindow =
	- renderWindowPart->GetQmitkRenderWindow("3d");
	-
	- if (!selectedRenderWindow && m_SelectedNode->GetBoolProperty(
	- "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow,
	- _3DRenderWindow->GetRenderer()))
	- {
	- selectedRenderWindow = _3DRenderWindow;
	- }
	-
	- const mitk::PlaneGeometry* _PlaneGeometry = _PlanarFigure->GetPlaneGeometry();
	-
	- mitk::VnlVector normal = _PlaneGeometry->GetNormalVnl();
	-
	- mitk::PlaneGeometry::ConstPointer worldGeometry1 =
	- axialRenderWindow->GetRenderer()->GetCurrentWorldPlaneGeometry();
	- mitk::PlaneGeometry::ConstPointer _Plane1 =
	- dynamic_cast<const mitk::PlaneGeometry*>( worldGeometry1.GetPointer() );
	- mitk::VnlVector normal1 = _Plane1->GetNormalVnl();
	-
	- mitk::PlaneGeometry::ConstPointer worldGeometry2 =
	- sagittalRenderWindow->GetRenderer()->GetCurrentWorldPlaneGeometry();
	- mitk::PlaneGeometry::ConstPointer _Plane2 =
	- dynamic_cast<const mitk::PlaneGeometry*>( worldGeometry2.GetPointer() );
	- mitk::VnlVector normal2 = _Plane2->GetNormalVnl();
	-
	- mitk::PlaneGeometry::ConstPointer worldGeometry3 =
	- coronalRenderWindow->GetRenderer()->GetCurrentWorldPlaneGeometry();
	- mitk::PlaneGeometry::ConstPointer _Plane3 =
	- dynamic_cast<const mitk::PlaneGeometry*>( worldGeometry3.GetPointer() );
	- mitk::VnlVector normal3 = _Plane3->GetNormalVnl();
	-
	- normal[0] = fabs(normal[0]); normal[1] = fabs(normal[1]); normal[2] = fabs(normal[2]);
	- normal1[0] = fabs(normal1[0]); normal1[1] = fabs(normal1[1]); normal1[2] = fabs(normal1[2]);
	- normal2[0] = fabs(normal2[0]); normal2[1] = fabs(normal2[1]); normal2[2] = fabs(normal2[2]);
	- normal3[0] = fabs(normal3[0]); normal3[1] = fabs(normal3[1]); normal3[2] = fabs(normal3[2]);
	-
	- double ang1 = angle(normal, normal1);
	- double ang2 = angle(normal, normal2);
	- double ang3 = angle(normal, normal3);
	-
	- if(ang1 < ang2 && ang1 < ang3)
	- {
	- selectedRenderWindow = axialRenderWindow;
	- }
	- else
	- {
	- if(ang2 < ang3)
	- {
	- selectedRenderWindow = sagittalRenderWindow;
	- }
	- else
	- {
	- selectedRenderWindow = coronalRenderWindow;
	- }
	- }
	-
	- // make node visible
	- if (selectedRenderWindow)
	- {
	- const mitk::Point3D& centerP = _PlaneGeometry->GetOrigin();
	- selectedRenderWindow->GetSliceNavigationController()->ReorientSlices(
	- centerP, _PlaneGeometry->GetNormal());
	- }
	- }
	-
	- // set interactor for new node (if not already set)
	- mitk::PlanarFigureInteractor::Pointer figureInteractor
	- = dynamic_cast<mitk::PlanarFigureInteractor*>(m_SelectedNode->GetDataInteractor().GetPointer());
	-
	- if(figureInteractor.IsNull())
	- {
	- figureInteractor = mitk::PlanarFigureInteractor::New();
	- us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "MitkPlanarFigure" );
	- figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule );
	- figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule );
	- figureInteractor->SetDataNode( m_SelectedNode );
	- }
	-
	- m_SelectedNode->SetProperty("planarfigure.iseditable",mitk::BoolProperty::New(true));
	- }
	-}
	-
	-
	-void QmitkControlVisualizationPropertiesView::SetInteractor()
	-{
	- // BUG 19179
	- // typedef std::vector<mitk::DataNode*> Container;
	- // Container _NodeSet = this->GetDataManagerSelection();
	- // mitk::DataNode* node = 0;
	- // mitk::FiberBundle* bundle = 0;
	- // mitk::FiberBundleInteractor::Pointer bundleInteractor = 0;
	-
	- // // finally add all nodes to the model
	- // for(Container::const_iterator it=_NodeSet.begin(); it!=_NodeSet.end()
	- // ; it++)
	- // {
	- // node = const_cast<mitk::DataNode>(it);
	- // bundle = dynamic_cast<mitk::FiberBundle*>(node->GetData());
	-
	- // if(bundle)
	- // {
	- // bundleInteractor = dynamic_cast<mitk::FiberBundleInteractor*>(node->GetInteractor());
	-
	- // if(bundleInteractor.IsNotNull())
	- // mitk::GlobalInteraction::GetInstance()->RemoveInteractor(bundleInteractor);
	-
	- // if(!m_Controls->m_Crosshair->isChecked())
	- // {
	- // m_Controls->m_Crosshair->setChecked(false);
	- // this->GetActiveStdMultiWidget()->GetRenderWindow4()->setCursor(Qt::ArrowCursor);
	- // m_CurrentPickingNode = 0;
	- // }
	- // else
	- // {
	- // m_Controls->m_Crosshair->setChecked(true);
	- // bundleInteractor = mitk::FiberBundleInteractor::New("FiberBundleInteractor", node);
	- // mitk::GlobalInteraction::GetInstance()->AddInteractor(bundleInteractor);
	- // this->GetActiveStdMultiWidget()->GetRenderWindow4()->setCursor(Qt::CrossCursor);
	- // m_CurrentPickingNode = node;
	- // }
	-
	- // }
	- // }
	-}
	-
	-
	-void QmitkControlVisualizationPropertiesView::TubeRadiusChanged()
	-{
	- if(m_SelectedNode && dynamic_cast<mitk::FiberBundle*>(m_SelectedNode->GetData()))
	- {
	- float newRadius = m_Controls->m_TubeWidth->value();
	- m_SelectedNode->SetFloatProperty("shape.tuberadius", newRadius);
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- }
	-}
	-
	-void QmitkControlVisualizationPropertiesView::RibbonWidthChanged()
	-{
	- if(m_SelectedNode && dynamic_cast<mitk::FiberBundle*>(m_SelectedNode->GetData()))
	- {
	- float newWidth = m_Controls->m_RibbonWidth->value();
	- m_SelectedNode->SetFloatProperty("shape.ribbonwidth", newWidth);
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- }
	-}
	-
	-void QmitkControlVisualizationPropertiesView::LineWidthChanged()
	-{
	- if(m_SelectedNode && dynamic_cast<mitk::PeakImage*>(m_SelectedNode->GetData()))
	- {
	- auto newWidth = m_Controls->m_LineWidth->value();
	- float currentWidth = 0;
	- m_SelectedNode->SetFloatProperty("shape.linewidth", currentWidth);
	- if (currentWidth==newWidth)
	- return;
	- m_SelectedNode->SetFloatProperty("shape.linewidth", newWidth);
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- }
	-}
	-
	-
	-void QmitkControlVisualizationPropertiesView::Welcome()
	-{
	- berry::PlatformUI::GetWorkbench()->GetIntroManager()
	- ->ShowIntro(GetSite()->GetWorkbenchWindow(), false);
	-}
	-
	-void QmitkControlVisualizationPropertiesView::OnColourisationModeChanged()
	-{
	- if( m_SelectedNode && m_NodeUsedForOdfVisualization.IsNotNull() )
	- {
	- m_SelectedNode->SetProperty( "DiffusionCore.Rendering.OdfVtkMapper.ColourisationModeBit", mitk::BoolProperty::New( m_Controls->m_OdfColorBox->currentIndex() ) );
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	- }
	- else
	- {
	- MITK_DEBUG << "QmitkControlVisualizationPropertiesView::OnColourisationModeChanged() was called but m_NodeUsedForOdfVisualization was Null.";
	- }
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.h
	deleted file mode 100644
	index c65b03311d..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.h
	+++ /dev/null
	@@ -1,155 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef _QMITKControlVisualizationPropertiesView_H_INCLUDED
	-#define _QMITKControlVisualizationPropertiesView_H_INCLUDED
	-
	-#include <QmitkAbstractView.h>
	-
	-#include <string>
	-
	-#include "berryISelectionListener.h"
	-#include "berryIStructuredSelection.h"
	-#include "berryISizeProvider.h"
	-
	-#include "ui_QmitkControlVisualizationPropertiesViewControls.h"
	-
	-#include "mitkEnumerationProperty.h"
	-#include <mitkILifecycleAwarePart.h>
	-#include <QmitkSliceNavigationListener.h>
	-
	-/*!
	- * \ingroup org_mitk_gui_qt_diffusionquantification_internal
	- *
	- * \brief QmitkControlVisualizationPropertiesView
	- *
	- * Document your class here.
	- */
	-class QmitkControlVisualizationPropertiesView : public QmitkAbstractView, public mitk::ILifecycleAwarePart
	-{
	-
	- friend struct CvpSelListener;
	-
	- // this is needed for all Qt objects that should have a MOC object (everything that derives from QObject)
	- Q_OBJECT
	-
	- public:
	-
	- static const std::string VIEW_ID;
	-
	- QmitkControlVisualizationPropertiesView();
	- virtual ~QmitkControlVisualizationPropertiesView();
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	-
	- /// \brief Creation of the connections of main and control widget
	- virtual void CreateConnections();
	-
	-
	-protected slots:
	-
	- void VisibleOdfsON_S();
	- void VisibleOdfsON_T();
	- void VisibleOdfsON_C();
	- void ShowMaxNumberChanged();
	- void NormalizationDropdownChanged(int);
	- void ScalingFactorChanged(double);
	- void AdditionalScaling(int);
	- void OnThickSlicesModeSelected( QAction* action );
	- void OnTSNumChanged(int num);
	- void ResetColoring();
	- void PlanarFigureFocus();
	- void Fiber2DfadingEFX();
	- void FiberSlicingThickness2D();
	- void FiberSlicingUpdateLabel(int);
	- void LineWidthChanged();
	- void TubeRadiusChanged();
	- void RibbonWidthChanged();
	- void SetInteractor();
	- void Toggle3DClipping(bool enabled=true);
	- void FlipPeaks();
	- void Welcome();
	- void OnSliceChanged();
	- void SetColor();
	- void Toggle3DPeaks();
	-
	- /// \brief Slot function for switching colourisation mode of glyphs.
	- void OnColourisationModeChanged();
	-
	-protected:
	-
	- virtual void SetFocus() override;
	- virtual void Activated() override;
	- virtual void Deactivated() override;
	- virtual void Visible() override;
	- virtual void Hidden() override;
	-
	- virtual void NodeRemoved(const mitk::DataNode* node) override;
	-
	- /// \brief called by QmitkAbstractView when DataManager's selection has changed
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- virtual void NodeAdded(const mitk::DataNode *node) override;
	- void SetCustomColor(const itk::EventObject& /e/);
	- bool IsPlaneRotated();
	-
	- void SliceRotation(const itk::EventObject&);
	- void Set3DClippingPlane(bool disable, mitk::DataNode *node, std::string plane);
	- void SetTs(int m_CurrentThickSlicesMode, int num, std::string render_window);
	-
	- Ui::QmitkControlVisualizationPropertiesViewControls* m_Controls;
	-
	- QScopedPointer<berry::ISelectionListener> m_SelListener;
	- berry::IStructuredSelection::ConstPointer m_CurrentSelection;
	-
	- mitk::DataNode::Pointer m_NodeUsedForOdfVisualization;
	-
	- QIcon* m_IconTexOFF;
	- QIcon* m_IconTexON;
	- QIcon* m_IconGlyOFF_T;
	- QIcon* m_IconGlyON_T;
	- QIcon* m_IconGlyOFF_C;
	- QIcon* m_IconGlyON_C;
	- QIcon* m_IconGlyOFF_S;
	- QIcon* m_IconGlyON_S;
	-
	- bool m_TexIsOn;
	- bool m_GlyIsOn_T;
	- bool m_GlyIsOn_C;
	- bool m_GlyIsOn_S;
	-
	- int m_CurrentThickSlicesMode;
	- int m_CurrentThickSlicesNum;
	- QLabel* m_TSLabel;
	- QMenu* m_MyMenu;
	-
	- // for planarfigure and bundle handling:
	- mitk::DataNode::Pointer m_SelectedNode;
	- mitk::DataNode* m_CurrentPickingNode;
	-
	- unsigned long m_ColorPropertyObserverTag;
	- unsigned long m_OpacityPropertyObserverTag;
	- mitk::ColorProperty::Pointer m_Color;
	- mitk::FloatProperty::Pointer m_Opacity;
	-
	- QmitkSliceNavigationListener m_SliceChangeListener;
	-};
	-
	-
	-
	-
	-#endif // _QMITKControlVisualizationPropertiesView_H_INCLUDED
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesViewControls.ui
	deleted file mode 100644
	index 6713f527a0..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesViewControls.ui
	+++ /dev/null
	@@ -1,1001 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<ui version="4.0">
	- <class>QmitkControlVisualizationPropertiesViewControls</class>
	- <widget class="QWidget" name="QmitkControlVisualizationPropertiesViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>567</width>
	- <height>619</height>
	- </rect>
	- </property>
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="MinimumExpanding">
	- <horstretch>0</horstretch>
	- <verstretch>100</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="windowTitle">
	- <string>QmitkTemplate</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QVBoxLayout" name="verticalLayout_4">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QFrame" name="m_ImageControlsFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QVBoxLayout" name="verticalLayout">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QFrame" name="frame_2">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Expanding" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QHBoxLayout" name="horizontalLayout_2">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QToolButton" name="m_TSMenu">
	- <property name="toolTip">
	- <string>Multislice Projection</string>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string>MIP </string>
	- </property>
	- <property name="popupMode">
	- <enum>QToolButton::MenuButtonPopup</enum>
	- </property>
	- <property name="arrowType">
	- <enum>Qt::NoArrow</enum>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QFrame" name="m_NumberGlyphsFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Plain</enum>
	- </property>
	- <layout class="QHBoxLayout" name="horizontalLayout_6">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QToolButton" name="m_VisibleOdfsON_T">
	- <property name="toolTip">
	- <string>Toggle visibility of ODF glyphs (axial)</string>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string/>
	- </property>
	- <property name="icon">
	- <iconset resource="../../resources/QmitkDiffusionImaging.qrc">
	- <normaloff>:/QmitkDiffusionImaging/glyphsoff_T.png</normaloff>
	- <normalon>:/QmitkDiffusionImaging/glyphson_T.png</normalon>:/QmitkDiffusionImaging/glyphsoff_T.png</iconset>
	- </property>
	- <property name="checkable">
	- <bool>true</bool>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QToolButton" name="m_VisibleOdfsON_S">
	- <property name="toolTip">
	- <string>Toggle visibility of ODF glyphs (sagittal)</string>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string/>
	- </property>
	- <property name="icon">
	- <iconset resource="../../resources/QmitkDiffusionImaging.qrc">
	- <normaloff>:/QmitkDiffusionImaging/glyphsoff_S.png</normaloff>
	- <normalon>:/QmitkDiffusionImaging/glyphson_S.png</normalon>:/QmitkDiffusionImaging/glyphsoff_S.png</iconset>
	- </property>
	- <property name="checkable">
	- <bool>true</bool>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QToolButton" name="m_VisibleOdfsON_C">
	- <property name="toolTip">
	- <string>Toggle visibility of ODF glyphs (coronal)</string>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="whatsThis">
	- <string/>
	- </property>
	- <property name="text">
	- <string/>
	- </property>
	- <property name="icon">
	- <iconset resource="../../resources/QmitkDiffusionImaging.qrc">
	- <normaloff>:/QmitkDiffusionImaging/glyphsoff_C.png</normaloff>
	- <normalon>:/QmitkDiffusionImaging/glyphson_C.png</normalon>:/QmitkDiffusionImaging/glyphsoff_C.png</iconset>
	- </property>
	- <property name="checkable">
	- <bool>true</bool>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QLabel" name="label_glyphs">
	- <property name="text">
	- <string>#Glyphs</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QSpinBox" name="m_ShowMaxNumber">
	- <property name="maximum">
	- <number>9999</number>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <spacer name="horizontalSpacer">
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>20</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <widget class="QFrame" name="m_GlyphFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QVBoxLayout" name="verticalLayout_2">
	- <property name="spacing">
	- <number>0</number>
	- </property>
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QFrame" name="m_NormalizationScalingFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QFrame" name="m_NormalizationFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Plain</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_3">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="5" column="1">
	- <widget class="QComboBox" name="m_NormalizationDropdown">
	- <property name="toolTip">
	- <string>ODF normalization</string>
	- </property>
	- <property name="frame">
	- <bool>false</bool>
	- </property>
	- <item>
	- <property name="text">
	- <string>Min-Max</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Max</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>None</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <widget class="QLabel" name="m_NormalizationLabel">
	- <property name="text">
	- <string>ODF Normalization:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="7" column="1">
	- <widget class="QComboBox" name="m_OdfColorBox">
	- <property name="toolTip">
	- <string>ODF normalization</string>
	- </property>
	- <property name="frame">
	- <bool>false</bool>
	- </property>
	- <item>
	- <property name="text">
	- <string>ODF Value</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>Principal Direction</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- <item row="7" column="0">
	- <widget class="QLabel" name="label_4">
	- <property name="text">
	- <string>Color ODFs/Tensors by:</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QFrame" name="m_ScalingFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Plain</enum>
	- </property>
	- <layout class="QHBoxLayout" name="horizontalLayout_3">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QLabel" name="label_2">
	- <property name="text">
	- <string>ODF Scale:</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QComboBox" name="m_AdditionalScaling">
	- <property name="frame">
	- <bool>false</bool>
	- </property>
	- <item>
	- <property name="text">
	- <string>None</string>
	- </property>
	- </item>
	- <item>
	- <property name="text">
	- <string>FA/GFA</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- <item>
	- <widget class="QLabel" name="label">
	- <property name="text">
	- <string>*</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QDoubleSpinBox" name="m_ScalingFactor">
	- <property name="toolTip">
	- <string>Additional scaling factor</string>
	- </property>
	- <property name="decimals">
	- <number>3</number>
	- </property>
	- <property name="maximum">
	- <double>999999999.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>1.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <widget class="QFrame" name="m_BundleControlsFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QVBoxLayout" name="verticalLayout_3">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QFrame" name="frame_5">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QHBoxLayout" name="horizontalLayout_11">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QToolButton" name="m_SetColor2">
	- <property name="toolTip">
	- <string>Select Fiber Color</string>
	- </property>
	- <property name="text">
	- <string/>
	- </property>
	- <property name="icon">
	- <iconset resource="../../resources/QmitkDiffusionImaging.qrc">
	- <normaloff>:/QmitkDiffusionImaging/color64.png</normaloff>:/QmitkDiffusionImaging/color64.png</iconset>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QToolButton" name="m_ResetColoring">
	- <property name="toolTip">
	- <string>Reset to Default Coloring</string>
	- </property>
	- <property name="text">
	- <string/>
	- </property>
	- <property name="icon">
	- <iconset resource="../../resources/QmitkDiffusionImaging.qrc">
	- <normaloff>:/QmitkDiffusionImaging/reset.png</normaloff>:/QmitkDiffusionImaging/reset.png</iconset>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QToolButton" name="m_Crosshair">
	- <property name="toolTip">
	- <string>Position Crosshair by 3D-Click</string>
	- </property>
	- <property name="statusTip">
	- <string/>
	- </property>
	- <property name="text">
	- <string/>
	- </property>
	- <property name="icon">
	- <iconset resource="../../resources/QmitkDiffusionImaging.qrc">
	- <normaloff>:/QmitkDiffusionImaging/crosshair.png</normaloff>:/QmitkDiffusionImaging/crosshair.png</iconset>
	- </property>
	- <property name="checkable">
	- <bool>true</bool>
	- </property>
	- <property name="checked">
	- <bool>false</bool>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QToolButton" name="m_FiberFading2D">
	- <property name="toolTip">
	- <string>2D Fiberfading on/off</string>
	- </property>
	- <property name="text">
	- <string/>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <spacer name="horizontalSpacer_2">
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>40</width>
	- <height>20</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <widget class="QFrame" name="frame_6">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QHBoxLayout" name="horizontalLayout_10">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QLabel" name="label_5">
	- <property name="text">
	- <string>2D Clipping</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QSlider" name="m_FiberThicknessSlider">
	- <property name="maximum">
	- <number>100</number>
	- </property>
	- <property name="pageStep">
	- <number>10</number>
	- </property>
	- <property name="value">
	- <number>10</number>
	- </property>
	- <property name="sliderPosition">
	- <number>10</number>
	- </property>
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QLabel" name="label_range">
	- <property name="minimumSize">
	- <size>
	- <width>90</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="maximumSize">
	- <size>
	- <width>10000</width>
	- <height>16777215</height>
	- </size>
	- </property>
	- <property name="text">
	- <string>Range</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <widget class="QFrame" name="frame_linewidth">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_2">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_8">
	- <property name="text">
	- <string>Tube Radius</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QDoubleSpinBox" name="m_TubeWidth">
	- <property name="decimals">
	- <number>3</number>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QLabel" name="label_9">
	- <property name="text">
	- <string>Ribbon Width</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QDoubleSpinBox" name="m_RibbonWidth">
	- <property name="decimals">
	- <number>3</number>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <widget class="QLabel" name="m_lblRotatedPlanesWarning">
	- <property name="font">
	- <font>
	- <weight>50</weight>
	- <italic>false</italic>
	- <bold>false</bold>
	- </font>
	- </property>
	- <property name="text">
	- <string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
	-<html><head><meta name="qrichtext" content="1" /><style type="text/css">
	-p, li { white-space: pre-wrap; }
	-</style></head><body style=" font-family:'Ubuntu'; font-size:11pt; font-weight:400; font-style:normal;">
	-<p align="center" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#ff0000;">One or more slices are rotated. ODF Visualisation is not possible in rotated planes. Use 'Reinit' on the image node to reset. </span></p></body></html></string>
	- </property>
	- <property name="textFormat">
	- <enum>Qt::AutoText</enum>
	- </property>
	- <property name="wordWrap">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QFrame" name="m_PeakImageFrame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_4">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="2">
	- <widget class="QFrame" name="frame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_6">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="1" column="3">
	- <widget class="QCheckBox" name="m_FlipPeaksY">
	- <property name="text">
	- <string>y</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="4">
	- <widget class="QCheckBox" name="m_FlipPeaksZ">
	- <property name="text">
	- <string>z</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="2">
	- <widget class="QCheckBox" name="m_FlipPeaksX">
	- <property name="text">
	- <string>x</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="1">
	- <widget class="QCommandLinkButton" name="m_FlipPeaksButton">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Minimum" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="text">
	- <string>Flip Peaks</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QFrame" name="frame_3">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_7">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item row="0" column="1">
	- <widget class="QToolButton" name="m_ResetColoring2">
	- <property name="toolTip">
	- <string>Reset to Default Coloring</string>
	- </property>
	- <property name="text">
	- <string/>
	- </property>
	- <property name="icon">
	- <iconset resource="../../resources/QmitkDiffusionImaging.qrc">
	- <normaloff>:/QmitkDiffusionImaging/reset.png</normaloff>:/QmitkDiffusionImaging/reset.png</iconset>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="0">
	- <widget class="QToolButton" name="m_SetColor1">
	- <property name="toolTip">
	- <string>Select Fiber Color</string>
	- </property>
	- <property name="text">
	- <string/>
	- </property>
	- <property name="icon">
	- <iconset resource="../../resources/QmitkDiffusionImaging.qrc">
	- <normaloff>:/QmitkDiffusionImaging/color64.png</normaloff>:/QmitkDiffusionImaging/color64.png</iconset>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="2">
	- <spacer name="horizontalSpacer_3">
	- <property name="orientation">
	- <enum>Qt::Horizontal</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>40</width>
	- <height>20</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QLabel" name="label_7">
	- <property name="text">
	- <string>Line Width</string>
	- </property>
	- </widget>
	- </item>
	- <item row="1" column="2">
	- <widget class="QDoubleSpinBox" name="m_LineWidth">
	- <property name="decimals">
	- <number>1</number>
	- </property>
	- <property name="minimum">
	- <double>1.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.100000000000000</double>
	- </property>
	- <property name="value">
	- <double>1.000000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <widget class="QGroupBox" name="m_3DClippingBox">
	- <property name="title">
	- <string>3D Clipping</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_5">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <property name="spacing">
	- <number>0</number>
	- </property>
	- <item row="3" column="1">
	- <widget class="QRadioButton" name="m_Clip3">
	- <property name="text">
	- <string>Coronal</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="1">
	- <widget class="QRadioButton" name="m_Clip1">
	- <property name="text">
	- <string>Axial</string>
	- </property>
	- </widget>
	- </item>
	- <item row="2" column="0">
	- <widget class="QRadioButton" name="m_Clip0">
	- <property name="text">
	- <string>No clipping</string>
	- </property>
	- <property name="checked">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <widget class="QRadioButton" name="m_Clip2">
	- <property name="text">
	- <string>Sagittal</string>
	- </property>
	- </widget>
	- </item>
	- <item row="4" column="0">
	- <widget class="QCheckBox" name="m_FlipClipBox">
	- <property name="text">
	- <string>Flipp Clipping Direction</string>
	- </property>
	- </widget>
	- </item>
	- <item row="5" column="0">
	- <widget class="QCheckBox" name="m_Enable3dPeaks">
	- <property name="text">
	- <string>Enable 3D Rendering</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <spacer name="verticalSpacer">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- </layout>
	- </widget>
	- <layoutdefault spacing="6" margin="11"/>
	- <includes>
	- <include location="local">QmitkDataStorageComboBox.h</include>
	- </includes>
	- <resources>
	- <include location="../../resources/QmitkDiffusionImaging.qrc"/>
	- </resources>
	- <connections/>
	-</ui>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDicomTractogramTagEditorView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDicomTractogramTagEditorView.cpp
	deleted file mode 100644
	index e647c61bb9..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDicomTractogramTagEditorView.cpp
	+++ /dev/null
	@@ -1,201 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-// Blueberry
	-#include <berryISelectionService.h>
	-#include <berryIWorkbenchWindow.h>
	-#include <berryIStructuredSelection.h>
	-
	-// Qmitk
	-#include "QmitkDicomTractogramTagEditorView.h"
	-#include "QmitkStdMultiWidget.h"
	-
	-// Qt
	-#include <QMessageBox>
	-
	-// MITK
	-#include <mitkNodePredicateDataType.h>
	-#include <mitkNodePredicateNot.h>
	-#include <mitkNodePredicateAnd.h>
	-#include <mitkNodePredicateProperty.h>
	-
	-const std::string QmitkDicomTractogramTagEditorView::VIEW_ID = "org.mitk.views.dicomtractogramtageditor";
	-const std::string id_DataManager = "org.mitk.views.datamanager";
	-using namespace berry;
	-
	-QmitkDicomTractogramTagEditorView::QmitkDicomTractogramTagEditorView()
	- : m_Controls(nullptr)
	-{
	- m_TagList = {"DICOM.patient_id",
	- "DICOM.patient_name",
	- "DICOM.study_instance_uid",
	- "DICOM.series_instance_uid",
	- "DICOM.sop_instance_uid",
	- "DICOM.frame_of_reference_uid",
	- "DICOM.algo_code.value",
	- "DICOM.algo_code.meaning",
	- "DICOM.model_code.value",
	- "DICOM.model_code.meaning",
	- "DICOM.anatomy.value",
	- "DICOM.anatomy.meaning"};
	- m_ImageTagList = {"DICOM.patient_id",
	- "DICOM.patient_name",
	- "DICOM.study_instance_uid",
	- "DICOM.series_instance_uid",
	- "DICOM.sop_instance_uid",
	- "DICOM.frame_of_reference_uid"};
	-}
	-
	-// Destructor
	-QmitkDicomTractogramTagEditorView::~QmitkDicomTractogramTagEditorView()
	-{
	-}
	-
	-void QmitkDicomTractogramTagEditorView::CreateQtPartControl( QWidget *parent )
	-{
	- if ( !m_Controls )
	- {
	- // create GUI widgets from the Qt Designer's .ui file
	- m_Controls = new Ui::QmitkDicomTractogramTagEditorViewControls;
	- m_Controls->setupUi( parent );
	-
	- m_Controls->m_TractogramBox->SetDataStorage(this->GetDataStorage());
	- mitk::TNodePredicateDataType<mitk::FiberBundle>::Pointer isFibPredicate = mitk::TNodePredicateDataType<mitk::FiberBundle>::New();
	-
	- m_Controls->m_TractogramBox->SetPredicate( isFibPredicate );
	- m_Controls->m_TractogramBox->SetZeroEntryText("--");
	-
	- m_Controls->m_TagTable->setColumnCount(2);
	- m_Controls->m_TagTable->setRowCount(m_TagList.size());
	- m_Controls->m_TagTable->verticalHeader()->setVisible(false);
	- m_Controls->m_TagTable->setSelectionMode(QAbstractItemView::SingleSelection);
	- QStringList tableHeader;
	- tableHeader <<"Tag"<<"Value";
	- m_Controls->m_TagTable->setHorizontalHeaderLabels(tableHeader);
	- m_Controls->m_TagTable->horizontalHeader()->setSectionResizeMode(QHeaderView::Stretch);
	-
	- m_Controls->m_CopyPropsButton->setEnabled(false);
	-
	- connect( (QObject)(m_Controls->m_TractogramBox), SIGNAL(OnSelectionChanged(const mitk::DataNode)), this, SLOT(OnTractSelectionChanged()) );
	- connect( (QObject)(m_Controls->m_TagTable), SIGNAL(itemChanged(QTableWidgetItem)), this, SLOT(OnItemChanged(QTableWidgetItem*)) );
	- connect( m_Controls->m_CopyPropsButton, SIGNAL(clicked()), this, SLOT(CopyProperties()));
	-
	- UpdateGui();
	- }
	-}
	-
	-void QmitkDicomTractogramTagEditorView::CopyProperties()
	-{
	- if (m_Controls->m_TractogramBox->GetSelectedNode()==nullptr)
	- return;
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(m_Controls->m_TractogramBox->GetSelectedNode()->GetData());
	- if (fib.IsNull())
	- return;
	- if (m_Image.IsNull())
	- return;
	-
	- mitk::PropertyList* source_p_list = m_Image->GetPropertyList();
	- mitk::PropertyList* target_p_list = fib->GetPropertyList();
	-
	- for (std::string tag : m_ImageTagList)
	- {
	- std::string val = "-";
	- source_p_list->GetStringProperty(tag.c_str(), val);
	- target_p_list->SetStringProperty(tag.c_str(), val.c_str());
	- }
	- UpdateGui();
	-}
	-
	-void QmitkDicomTractogramTagEditorView::OnItemChanged(QTableWidgetItem* item)
	-{
	- if (m_Controls->m_TractogramBox->GetSelectedNode()==nullptr)
	- {
	- UpdateGui();
	- return;
	- }
	-
	- int col = item->column();
	- if (col==1)
	- {
	- std::string tag = m_TagList.at(item->row());
	-
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(m_Controls->m_TractogramBox->GetSelectedNode()->GetData());
	- mitk::PropertyList* p_list = fib->GetPropertyList();
	-
	- p_list->SetStringProperty(tag.c_str(), item->text().toStdString().c_str());
	- }
	- UpdateGui();
	-}
	-
	-void QmitkDicomTractogramTagEditorView::OnTractSelectionChanged()
	-{
	- UpdateGui();
	-}
	-
	-void QmitkDicomTractogramTagEditorView::UpdateGui()
	-{
	- m_Controls->m_CopyPropsButton->setEnabled(false);
	- m_Controls->m_TagTable->blockSignals(true);
	- if (m_Controls->m_TractogramBox->GetSelectedNode()==nullptr)
	- {
	- int row = 0;
	- for (std::string tag : m_TagList)
	- {
	- m_Controls->m_TagTable->setItem(row, 0, new QTableWidgetItem(tag.c_str()));
	- m_Controls->m_TagTable->setItem(row, 1, new QTableWidgetItem("-"));
	- ++row;
	- }
	- m_Controls->m_TagTable->blockSignals(false);
	- return;
	- }
	-
	- mitk::FiberBundle::Pointer fib = dynamic_cast<mitk::FiberBundle*>(m_Controls->m_TractogramBox->GetSelectedNode()->GetData());
	- mitk::PropertyList* p_list = fib->GetPropertyList();
	-
	- int row = 0;
	- for (std::string tag : m_TagList)
	- {
	- std::string val = "-";
	- p_list->GetStringProperty(tag.c_str(), val);
	- m_Controls->m_TagTable->setItem(row, 0, new QTableWidgetItem(tag.c_str()));
	- m_Controls->m_TagTable->setItem(row, 1, new QTableWidgetItem(val.c_str()));
	- ++row;
	- }
	-
	- if (m_Image.IsNotNull())
	- m_Controls->m_CopyPropsButton->setEnabled(true);
	- m_Controls->m_TagTable->blockSignals(false);
	-}
	-
	-void QmitkDicomTractogramTagEditorView::OnSelectionChanged( berry::IWorkbenchPart::Pointer , const QList<mitk::DataNode::Pointer>& nodes)
	-{
	- m_Image = nullptr;
	- for (auto node : nodes)
	- {
	- mitk::Image::Pointer img = dynamic_cast<mitk::Image*>(node->GetData());
	- if (img.IsNotNull())
	- {
	- m_Image = img;
	- }
	- }
	- UpdateGui();
	-}
	-
	-void QmitkDicomTractogramTagEditorView::SetFocus()
	-{
	-
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDicomTractogramTagEditorView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDicomTractogramTagEditorView.h
	deleted file mode 100644
	index d07859ca8d..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDicomTractogramTagEditorView.h
	+++ /dev/null
	@@ -1,75 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef QmitkDicomTractogramTagEditorView_h
	-#define QmitkDicomTractogramTagEditorView_h
	-
	-#include <QmitkAbstractView.h>
	-#include "ui_QmitkDicomTractogramTagEditorViewControls.h"
	-#include <mitkFiberBundle.h>
	-
	-/*!
	-\brief View for tensor based deterministic streamline fiber tracking.
	-*/
	-class QmitkDicomTractogramTagEditorView : public QmitkAbstractView
	-{
	- // this is needed for all Qt objects that should have a Qt meta-object
	- // (everything that derives from QObject and wants to have signal/slots)
	- Q_OBJECT
	-
	-public:
	-
	- static const std::string VIEW_ID;
	-
	- QmitkDicomTractogramTagEditorView();
	- virtual ~QmitkDicomTractogramTagEditorView();
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	-
	- ///
	- /// Sets the focus to an internal widget.
	- ///
	- virtual void SetFocus() override;
	-
	-protected slots:
	-
	- void OnTractSelectionChanged();
	- void CopyProperties();
	- void OnItemChanged(QTableWidgetItem * item);
	-
	-protected:
	-
	- void UpdateGui();
	-
	- /// \brief called by QmitkAbstractView when DataManager's selection has changed
	- virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
	-
	- Ui::QmitkDicomTractogramTagEditorViewControls* m_Controls;
	- std::vector< std::string > m_TagList;
	- std::vector< std::string > m_ImageTagList;
	- mitk::Image::Pointer m_Image;
	-
	-protected slots:
	-
	-private:
	-
	-
	-};
	-
	-
	-
	-#endif // _QMITKFIBERTRACKINGVIEW_H_INCLUDED
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDicomTractogramTagEditorViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDicomTractogramTagEditorViewControls.ui
	deleted file mode 100644
	index e31cb7a178..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDicomTractogramTagEditorViewControls.ui
	+++ /dev/null
	@@ -1,165 +0,0 @@
	-<?xml version="1.0" encoding="utf-8"?>
	-<ui version="4.0">
	- <class>QmitkDicomTractogramTagEditorViewControls</class>
	- <widget class="QWidget" name="QmitkDicomTractogramTagEditorViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>397</width>
	- <height>366</height>
	- </rect>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="windowTitle">
	- <string>QmitkTemplate</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_2">
	- <property name="topMargin">
	- <number>3</number>
	- </property>
	- <property name="bottomMargin">
	- <number>3</number>
	- </property>
	- <property name="spacing">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QFrame" name="frame">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QFormLayout" name="formLayout">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>9</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QLabel" name="label_6">
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="text">
	- <string>Tractogram:</string>
	- </property>
	- </widget>
	- </item>
	- <item row="0" column="1">
	- <widget class="QmitkDataStorageComboBoxWithSelectNone" name="m_TractogramBox">
	- <property name="toolTip">
	- <string>Seed points are only placed inside the mask image. If no seed mask is selected, the whole image is seeded.</string>
	- </property>
	- <property name="sizeAdjustPolicy">
	- <enum>QComboBox::AdjustToMinimumContentsLength</enum>
	- </property>
	- <item>
	- <property name="text">
	- <string>-</string>
	- </property>
	- </item>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="1" column="0">
	- <widget class="QGroupBox" name="groupBox">
	- <property name="title">
	- <string>Tractography DICOM Tags</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout_3">
	- <property name="leftMargin">
	- <number>6</number>
	- </property>
	- <property name="topMargin">
	- <number>6</number>
	- </property>
	- <property name="rightMargin">
	- <number>6</number>
	- </property>
	- <property name="bottomMargin">
	- <number>6</number>
	- </property>
	- <property name="spacing">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <widget class="QTableWidget" name="m_TagTable">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="horizontalScrollBarPolicy">
	- <enum>Qt::ScrollBarAlwaysOff</enum>
	- </property>
	- <property name="sizeAdjustPolicy">
	- <enum>QAbstractScrollArea::AdjustToContents</enum>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item row="3" column="0">
	- <spacer name="spacer1">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeType">
	- <enum>QSizePolicy::Expanding</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>220</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- <item row="2" column="0">
	- <widget class="QCommandLinkButton" name="m_CopyPropsButton">
	- <property name="toolTip">
	- <string>Copies the DICOM properties of the tractogram selected in this view to the one selected in the datamanager.</string>
	- </property>
	- <property name="text">
	- <string>Copy Properties From Image</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- <layoutdefault spacing="6" margin="11"></layoutdefault>
	- <customwidgets>
	- <customwidget>
	- <class>QmitkDataStorageComboBoxWithSelectNone</class>
	- <extends>QComboBox</extends>
	- <header>QmitkDataStorageComboBoxWithSelectNone.h</header>
	- </customwidget>
	- </customwidgets>
	- <resources></resources>
	- <connections></connections>
	-</ui>
	\ No newline at end of file
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.cpp
	deleted file mode 100644
	index 11df473bc1..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.cpp
	+++ /dev/null
	@@ -1,600 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkDiffusionDicomImportView.h"
	-
	-// qt includes
	-#include <QFileDialog>
	-
	-// itk includes
	-#include "itkTimeProbesCollectorBase.h"
	-#include "itkGDCMSeriesFileNames.h"
	-#include "itksys/SystemTools.hxx"
	-
	-// mitk includes
	-#include "mitkProgressBar.h"
	-#include "mitkStatusBar.h"
	-#include "mitkProperties.h"
	-#include "mitkRenderingManager.h"
	-#include "mitkMemoryUtilities.h"
	-#include "mitkIOUtil.h"
	-
	-// diffusion module includes
	-#include "mitkDicomDiffusionImageHeaderReader.h"
	-#include "mitkDicomDiffusionImageReader.h"
	-#include "mitkImage.h"
	-#include <mitkDiffusionPropertyHelper.h>
	-
	-#include "mitkDiffusionDICOMFileReader.h"
	-#include "mitkDICOMTagBasedSorter.h"
	-#include "mitkDICOMSortByTag.h"
	-#include "mitkSortByImagePositionPatient.h"
	-
	-#include "gdcmDirectory.h"
	-#include "gdcmScanner.h"
	-#include "gdcmSorter.h"
	-#include "gdcmIPPSorter.h"
	-#include "gdcmAttribute.h"
	-#include "gdcmVersion.h"
	-
	-#include <itksys/SystemTools.hxx>
	-#include <itksys/Directory.hxx>
	-
	-#include <QMessageBox>
	-#include <QTreeView>
	-#include <mitkStringProperty.h>
	-
	-const std::string QmitkDiffusionDicomImport::VIEW_ID = "org.mitk.views.diffusiondicomimport";
	-
	-
	-QmitkDiffusionDicomImport::QmitkDiffusionDicomImport(QObject* /parent/, const char* /name/)
	- : m_Controls(nullptr)
	- , m_OutputFolderName("")
	- , m_OutputFolderNameSet(false)
	-{
	-}
	-
	-QmitkDiffusionDicomImport::~QmitkDiffusionDicomImport()
	-{}
	-
	-void QmitkDiffusionDicomImport::CreateQtPartControl(QWidget *parent)
	-{
	- m_Parent = parent;
	- if (m_Controls == nullptr)
	- {
	- m_Controls = new Ui::QmitkDiffusionDicomImportControls;
	- m_Controls->setupUi(parent);
	- this->CreateConnections();
	-
	- m_Controls->m_DicomLoadRecursiveCheckbox->setChecked(false);
	- m_Controls->m_DicomLoadAverageDuplicatesCheckbox->setChecked(false);
	-
	- m_Controls->m_DicomLoadRecursiveCheckbox->setVisible(true);
	- m_Controls->m_OverrideOptionCheckbox->setVisible(false);
	- m_Controls->m_SubdirPrefixLineEdit->setVisible(false);
	- m_Controls->m_SetPrefixButton->setVisible(false);
	- m_Controls->m_ResetPrefixButton->setVisible(false);
	-
	- AverageClicked();
	- }
	-}
	-
	-
	-
	-void QmitkDiffusionDicomImport::CreateConnections()
	-{
	- if ( m_Controls )
	- {
	- connect( m_Controls->m_AddFoldersButton, SIGNAL(clicked()), this, SLOT(DicomLoadAddFolderNames()) );
	- connect( m_Controls->m_DeleteFoldersButton, SIGNAL(clicked()), this, SLOT(DicomLoadDeleteFolderNames()) );
	- //connect( m_Controls->m_DicomLoadStartLoadButton, SIGNAL(clicked()), this, SLOT(DicomLoadStartLoad()) );
	- connect( m_Controls->m_DicomLoadStartLoadButton, SIGNAL(clicked()), this, SLOT(NewDicomLoadStartLoad()) );
	- connect( m_Controls->m_DicomLoadAverageDuplicatesCheckbox, SIGNAL(clicked()), this, SLOT(AverageClicked()) );
	- connect( m_Controls->m_OutputSetButton, SIGNAL(clicked()), this, SLOT(OutputSet()) );
	- connect( m_Controls->m_OutputClearButton, SIGNAL(clicked()), this, SLOT(OutputClear()) );
	- connect( m_Controls->m_Remove, SIGNAL(clicked()), this, SLOT(Remove()) );
	- connect( m_Controls->m_SetPrefixButton, SIGNAL(clicked()), this, SLOT(SetPrefixButtonPushed()));
	- connect( m_Controls->m_ResetPrefixButton, SIGNAL(clicked()), this, SLOT(ResetPrefixButtonPushed()));
	- connect( m_Controls->m_DicomLoadRecursiveCheckbox, SIGNAL(clicked()), this, SLOT(RecursiveSettingsChanged()) );
	- }
	-}
	-
	-void QmitkDiffusionDicomImport::SetFocus()
	-{
	- m_Controls->textBrowser->setFocus();
	-}
	-
	-void QmitkDiffusionDicomImport::RecursiveSettingsChanged()
	-{
	- m_Controls->m_SubdirPrefixLineEdit->setVisible( m_Controls->m_DicomLoadRecursiveCheckbox->isChecked() );
	- m_Controls->m_SetPrefixButton->setVisible( m_Controls->m_DicomLoadRecursiveCheckbox->isChecked() );
	- m_Controls->m_SubdirPrefixLineEdit->clear();
	- this->m_Controls->m_SubdirPrefixLineEdit->setEnabled(true);
	-}
	-
	-void QmitkDiffusionDicomImport::SetPrefixButtonPushed()
	-{
	- m_Prefix = this->m_Controls->m_SubdirPrefixLineEdit->text().toStdString();
	- if( !this->m_Controls->m_ResetPrefixButton->isVisible() )
	- this->m_Controls->m_ResetPrefixButton->setVisible(true);
	-
	- this->m_Controls->m_SubdirPrefixLineEdit->setEnabled(false);
	- this->m_Controls->m_ResetPrefixButton->setEnabled(true);
	- this->m_Controls->m_SetPrefixButton->setEnabled(false);
	-}
	-
	-void QmitkDiffusionDicomImport::ResetPrefixButtonPushed()
	-{
	- m_Controls->m_SubdirPrefixLineEdit->clear();
	-
	- this->m_Controls->m_SubdirPrefixLineEdit->setEnabled(true);
	-
	- this->m_Controls->m_ResetPrefixButton->setEnabled(false);
	- this->m_Controls->m_SetPrefixButton->setEnabled(true);
	-}
	-
	-void QmitkDiffusionDicomImport::Remove()
	-{
	- int i = m_Controls->listWidget->currentRow();
	- m_Controls->listWidget->takeItem(i);
	-}
	-
	-void QmitkDiffusionDicomImport::OutputSet()
	-{
	- // SELECT FOLDER DIALOG
	- QFileDialog* w = new QFileDialog( m_Parent, QString("Select folders containing DWI data") );
	- w->setFileMode( QFileDialog::Directory );
	-
	- // RETRIEVE SELECTION
	- if ( w->exec() != QDialog::Accepted )
	- return;
	-
	- m_OutputFolderName = w->selectedFiles()[0];
	- m_OutputFolderNameSet = true;
	- m_Controls->m_OutputLabel->setText(m_OutputFolderName);
	-
	- // show file override option checkbox
	- m_Controls->m_OverrideOptionCheckbox->setVisible(true);
	-}
	-
	-void QmitkDiffusionDicomImport::OutputClear()
	-{
	- m_OutputFolderName = "";
	- m_OutputFolderNameSet = false;
	- m_Controls->m_OutputLabel->setText("... optional out-folder ...");
	-
	- // hide file override option checkbox - no output specified
	- m_Controls->m_OverrideOptionCheckbox->setVisible(false);
	-}
	-
	-void QmitkDiffusionDicomImport::AverageClicked()
	-{
	- m_Controls->m_Blur->setEnabled(m_Controls->m_DicomLoadAverageDuplicatesCheckbox->isChecked());
	-}
	-
	-void QmitkDiffusionDicomImport::DicomLoadDeleteFolderNames()
	-{
	- m_Controls->listWidget->clear();
	-}
	-
	-void QmitkDiffusionDicomImport::DicomLoadAddFolderNames()
	-{
	- // SELECT FOLDER DIALOG
	- QFileDialog w( m_Parent, QString("Select folders containing DWI data") );
	- w.setFileMode( QFileDialog::DirectoryOnly );
	- w.setOption(QFileDialog::DontUseNativeDialog,true);
	-
	- QListView l = w.findChild<QListView>("listView");
	- if (l) {
	- l->setSelectionMode(QAbstractItemView::MultiSelection);
	- }
	- QTreeView t = w.findChild<QTreeView>();
	- if (t) {
	- t->setSelectionMode(QAbstractItemView::MultiSelection);
	- }
	-
	- // RETRIEVE SELECTION
	- if ( w.exec() != QDialog::Accepted )
	- return;
	-
	- m_Controls->listWidget->addItems(w.selectedFiles());
	-}
	-
	-bool SortBySeriesUID(gdcm::DataSet const & ds1, gdcm::DataSet const & ds2 )
	-{
	- gdcm::Attribute<0x0020,0x000e> at1;
	- at1.Set( ds1 );
	- gdcm::Attribute<0x0020,0x000e> at2;
	- at2.Set( ds2 );
	- return at1 < at2;
	-}
	-
	-bool SortByAcquisitionNumber(gdcm::DataSet const & ds1, gdcm::DataSet const & ds2 )
	-{
	- gdcm::Attribute<0x0020,0x0012> at1;
	- at1.Set( ds1 );
	- gdcm::Attribute<0x0020,0x0012> at2;
	- at2.Set( ds2 );
	- return at1 < at2;
	-}
	-
	-bool SortBySeqName(gdcm::DataSet const & ds1, gdcm::DataSet const & ds2 )
	-{
	- gdcm::Attribute<0x0018, 0x0024> at1;
	- at1.Set( ds1 );
	- gdcm::Attribute<0x0018, 0x0024> at2;
	- at2.Set( ds2 );
	-
	- std::string str1 = at1.GetValue().Trim();
	- std::string str2 = at2.GetValue().Trim();
	- return std::lexicographical_compare(str1.begin(), str1.end(),
	- str2.begin(), str2.end() );
	-}
	-
	-void QmitkDiffusionDicomImport::Status(QString status)
	-{
	- mitk::StatusBar::GetInstance()->DisplayText(status.toLatin1());
	- MITK_INFO << status.toStdString().c_str();
	-}
	-
	-void QmitkDiffusionDicomImport::Status(std::string status)
	-{
	- mitk::StatusBar::GetInstance()->DisplayText(status.c_str());
	- MITK_INFO << status.c_str();
	-}
	-
	-void QmitkDiffusionDicomImport::Status(const char* status)
	-{
	- mitk::StatusBar::GetInstance()->DisplayText(status);
	- MITK_INFO << status;
	-}
	-
	-void QmitkDiffusionDicomImport::Error(QString status)
	-{
	- mitk::StatusBar::GetInstance()->DisplayErrorText(status.toLatin1());
	- MITK_ERROR << status.toStdString().c_str();
	-}
	-
	-void QmitkDiffusionDicomImport::Error(std::string status)
	-{
	- mitk::StatusBar::GetInstance()->DisplayErrorText(status.c_str());
	- MITK_ERROR << status.c_str();
	-}
	-
	-void QmitkDiffusionDicomImport::Error(const char* status)
	-{
	- mitk::StatusBar::GetInstance()->DisplayErrorText(status);
	- MITK_ERROR << status;
	-}
	-
	-void QmitkDiffusionDicomImport::PrintMemoryUsage()
	-{
	- size_t processSize = mitk::MemoryUtilities::GetProcessMemoryUsage();
	- size_t totalSize = mitk::MemoryUtilities::GetTotalSizeOfPhysicalRam();
	- float percentage = ( (float) processSize / (float) totalSize ) * 100.0;
	- MITK_INFO << "Current memory usage: " << GetMemoryDescription( processSize, percentage );
	-}
	-
	-std::string QmitkDiffusionDicomImport::FormatMemorySize( size_t size )
	-{
	- double val = size;
	- std::string descriptor("B");
	- if ( val >= 1000.0 )
	- {
	- val /= 1024.0;
	- descriptor = "KB";
	- }
	- if ( val >= 1000.0 )
	- {
	- val /= 1024.0;
	- descriptor = "MB";
	- }
	- if ( val >= 1000.0 )
	- {
	- val /= 1024.0;
	- descriptor = "GB";
	- }
	- std::ostringstream str;
	- str << std::fixed << std::setprecision(2) << val << " " << descriptor;
	- return str.str();
	-}
	-
	-std::string QmitkDiffusionDicomImport::FormatPercentage( double val )
	-{
	- std::ostringstream str;
	- str << std::fixed << std::setprecision(2) << val << " " << "%";
	- return str.str();
	-}
	-
	-std::string QmitkDiffusionDicomImport::GetMemoryDescription( size_t processSize, float percentage )
	-{
	- std::ostringstream str;
	- str << FormatMemorySize(processSize) << " (" << FormatPercentage( percentage ) <<")" ;
	- return str.str();
	-}
	-
	-void QmitkDiffusionDicomImport::NewDicomLoadStartLoad()
	-{
	- itk::TimeProbesCollectorBase clock;
	- bool imageSuccessfullySaved = true;
	-
	- bool has_prefix = true;
	-
	- try
	- {
	- const std::string& locale = "C";
	- const std::string& currLocale = setlocale( LC_ALL, nullptr );
	-
	- if ( locale.compare(currLocale)!=0 )
	- {
	- try
	- {
	- MITK_INFO << " ** Changing locale from " << setlocale(LC_ALL, nullptr) << " to '" << locale << "'";
	- setlocale(LC_ALL, locale.c_str());
	- }
	- catch(...)
	- {
	- MITK_INFO << "Could not set locale " << locale;
	- }
	- }
	-
	- int nrFolders = m_Controls->listWidget->count();
	-
	- if(!nrFolders)
	- {
	- Error(QString("No input folders were selected. ABORTING."));
	- return;
	- }
	-
	- Status(QString("GDCM %1 used for DICOM parsing and sorting!").arg(gdcm::Version::GetVersion()));
	-
	- PrintMemoryUsage();
	- QString status;
	- mitk::DataNode::Pointer node;
	- mitk::ProgressBar::GetInstance()->AddStepsToDo(2*nrFolders);
	-
	- gdcm::Directory::FilenamesType complete_list;
	- while(m_Controls->listWidget->count())
	- {
	- // RETREIVE FOLDERNAME
	- QListWidgetItem * item = m_Controls->listWidget->takeItem(0);
	- QString folderName = item->text();
	-
	-
	- if( this->m_Controls->m_DicomLoadRecursiveCheckbox->isChecked() )
	- {
	-
	- std::string subdir_prefix = "";
	- if( has_prefix )
	- {
	- subdir_prefix = this->m_Prefix;
	- }
	-
	- itksys::Directory rootdir;
	- rootdir.Load( folderName.toStdString().c_str() );
	-
	- for( unsigned int idx=0; idx<rootdir.GetNumberOfFiles(); idx++)
	- {
	- std::string current_path = rootdir.GetFile(idx);
	- std::string directory_path = std::string(rootdir.GetPath()) + std::string("/") + current_path;
	-
	- MITK_INFO("dicom.loader.inputrootdir.test") << "ProbePath: " << current_path;
	- MITK_INFO("dicom.loader.inputrootdir.test") << "IsDirectory: " << itksys::SystemTools::FileIsDirectory( itksys::SystemTools::ConvertToOutputPath( directory_path.c_str() ).c_str() )
	- << " StartsWith: " << itksys::SystemTools::StringStartsWith( current_path.c_str(), subdir_prefix.c_str() );
	-
	- // test for prefix
	- if( itksys::SystemTools::FileIsDirectory( itksys::SystemTools::ConvertToOutputPath( directory_path.c_str() ).c_str() )
	- && itksys::SystemTools::StringStartsWith( current_path.c_str(), subdir_prefix.c_str() )
	- )
	- {
	-
	- gdcm::Directory d;
	- d.Load( itksys::SystemTools::ConvertToOutputPath( directory_path.c_str() ) , false);
	-
	- MITK_INFO("dicom.load.subdir.attempt") << "In directory " << itksys::SystemTools::ConvertToOutputPath( directory_path.c_str() );
	-
	- const gdcm::Directory::FilenamesType &l1 = d.GetFilenames();
	- const unsigned int ntotalfiles = l1.size();
	- Status(QString(" ... found %1 different files").arg(ntotalfiles));
	-
	- for( unsigned int i=0; i< ntotalfiles; i++)
	- {
	- complete_list.push_back( l1.at(i) );
	- }
	-
	-
	- }
	-
	- }
	- }
	- else
	- {
	- gdcm::Directory d;
	- d.Load( folderName.toStdString().c_str(), this->m_Controls->m_DicomLoadRecursiveCheckbox->isChecked() ); // recursive !
	- const gdcm::Directory::FilenamesType &l1 = d.GetFilenames();
	- const unsigned int ntotalfiles = l1.size();
	- Status(QString(" ... found %1 different files").arg(ntotalfiles));
	-
	- for( unsigned int i=0; i< ntotalfiles; i++)
	- {
	- complete_list.push_back( l1.at(i) );
	- }
	-
	- }
	-
	-
	-
	- }
	-
	- {
	- mitk::DiffusionDICOMFileReader::Pointer gdcmReader = mitk::DiffusionDICOMFileReader::New();
	- mitk::DICOMTagBasedSorter::Pointer tagSorter = mitk::DICOMTagBasedSorter::New();
	-
	- // Use tags as in Qmitk
	- // all the things that split by tag in DicomSeriesReader
	- tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0028, 0x0010) ); // Number of Rows
	- tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0028, 0x0011) ); // Number of Columns
	- tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0028, 0x0030) ); // Pixel Spacing
	- tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0018, 0x1164) ); // Imager Pixel Spacing
	- tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0020, 0x0037) ); // Image Orientation (Patient) // TODO add tolerance parameter (l. 1572 of original code)
	- // TODO handle as real vectors! cluster with configurable errors!
	- tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0020, 0x000e) ); // Series Instance UID
	- tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0018, 0x0050) ); // Slice Thickness
	- tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0028, 0x0008) ); // Number of Frames
	- //tagSorter->AddDistinguishingTag( mitk::DICOMTag(0x0020, 0x0052) ); // Frame of Reference UID
	-
	- // gdcmReader->AddSortingElement( tagSorter );
	- //mitk::DICOMFileReaderTestHelper::TestOutputsContainInputs( gdcmReader );
	-
	- mitk::DICOMSortCriterion::ConstPointer sorting =
	- mitk::SortByImagePositionPatient::New( // Image Position (Patient)
	- //mitk::DICOMSortByTag::New( mitk::DICOMTag(0x0020, 0x0013), // instance number
	- mitk::DICOMSortByTag::New( mitk::DICOMTag(0x0020, 0x0012), // aqcuisition number
	- mitk::DICOMSortByTag::New( mitk::DICOMTag(0x0008, 0x0032), // aqcuisition time
	- mitk::DICOMSortByTag::New( mitk::DICOMTag(0x0018, 0x1060), // trigger time
	- mitk::DICOMSortByTag::New( mitk::DICOMTag(0x0008, 0x0018) // SOP instance UID (last resort, not really meaningful but decides clearly)
	- ).GetPointer()
	- ).GetPointer()
	- ).GetPointer()
	- ).GetPointer()
	- // ).GetPointer()
	- ).GetPointer();
	- tagSorter->SetSortCriterion( sorting );
	-
	- // mosaic
	- gdcmReader->SetResolveMosaic( this->m_Controls->m_SplitMosaicCheckBox->isChecked() );
	- gdcmReader->AddSortingElement( tagSorter );
	- gdcmReader->SetInputFiles( complete_list );
	- try
	- {
	- gdcmReader->AnalyzeInputFiles();
	- }
	- catch( const itk::ExceptionObject &e)
	- {
	- MITK_ERROR << "Failed to analyze data. " << e.what();
	- }
	- catch( const std::exception &se)
	- {
	- MITK_ERROR << "Std Exception " << se.what();
	- }
	-
	- gdcmReader->LoadImages();
	-
	- for( unsigned int o = 0; o < gdcmReader->GetNumberOfOutputs(); o++ )
	- {
	- mitk::Image::Pointer loaded_image = gdcmReader->GetOutput(o).GetMitkImage();
	-
	- std::string outname;
	- if (gdcmReader->GetSeriesName(o)!="-")
	- outname = gdcmReader->GetSeriesName(o);
	- else if (gdcmReader->GetStudyName(o)!="-")
	- outname = gdcmReader->GetStudyName(o);
	- else
	- loaded_image->GetPropertyList()->GetStringProperty("diffusion.dicom.importname", outname );
	-
	- std::string val = "-";
	-
	- if (gdcmReader->patient_ids().size()>o)
	- {
	- val = gdcmReader->patient_ids().at(o);
	- loaded_image->GetPropertyList()->SetStringProperty("DICOM.patient_id",val.c_str());
	- }
	-
	- if (gdcmReader->patient_names().size()>o)
	- {
	- val = gdcmReader->patient_names().at(o);
	- loaded_image->GetPropertyList()->SetStringProperty("DICOM.patient_name",val.c_str());
	- }
	-
	- if (gdcmReader->study_instance_uids().size()>o)
	- {
	- val = gdcmReader->study_instance_uids().at(o);
	- loaded_image->GetPropertyList()->SetStringProperty("DICOM.study_instance_uid",val.c_str());
	- }
	-
	- if (gdcmReader->series_instance_uids().size()>o)
	- {
	- val = gdcmReader->series_instance_uids().at(o);
	- loaded_image->GetPropertyList()->SetStringProperty("DICOM.series_instance_uid",val.c_str());
	- }
	-
	- if (gdcmReader->sop_instance_uids().size()>o)
	- {
	- val = gdcmReader->sop_instance_uids().at(o);
	- loaded_image->GetPropertyList()->SetStringProperty("DICOM.sop_instance_uid",val.c_str());
	- }
	-
	- if (gdcmReader->frame_of_reference_uids().size()>o)
	- {
	- val = gdcmReader->frame_of_reference_uids().at(o);
	- loaded_image->GetPropertyList()->SetStringProperty("DICOM.frame_of_reference_uid",val.c_str());
	- }
	-
	- node = mitk::DataNode::New();
	- node->SetData( loaded_image );
	- node->SetName( outname.c_str() );
	-
	- GetDataStorage()->Add(node);
	- }
	- }
	-
	- Status("Timing information");
	- clock.Report();
	-
	- if(!m_OutputFolderNameSet && node.IsNotNull())
	- {
	- mitk::BaseData::Pointer basedata = node->GetData();
	- if (basedata.IsNotNull())
	- {
	- mitk::RenderingManager::GetInstance()->InitializeViews(
	- basedata->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true );
	- }
	- }
	-
	- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	-
	- try
	- {
	- MITK_INFO << " ** Changing locale back from " << setlocale(LC_ALL, nullptr) << " to '" << currLocale << "'";
	- setlocale(LC_ALL, currLocale.c_str());
	- }
	- catch(...)
	- {
	- MITK_INFO << "Could not reset locale " << currLocale;
	- }
	- }
	- catch (itk::ExceptionObject &ex)
	- {
	- Error(QString("%1\n%2\n%3\n%4\n%5\n%6").arg(ex.GetNameOfClass()).arg(ex.GetFile()).arg(ex.GetLine()).arg(ex.GetLocation()).arg(ex.what()).arg(ex.GetDescription()));
	- return ;
	- }
	-
	- if (!imageSuccessfullySaved)
	- QMessageBox::warning(nullptr,"WARNING","One or more files could not be saved! The according files where moved to the datastorage.");
	- Status(QString("Finished import with memory:"));
	-
	- PrintMemoryUsage();
	-}
	-
	-void QmitkDiffusionDicomImport::SetDwiNodeProperties(mitk::DataNode::Pointer node, std::string name)
	-{
	-
	- node->SetProperty( "IsDWIRawVolume", mitk::BoolProperty::New( true ) );
	-
	- // set foldername as string property
	- mitk::StringProperty::Pointer nameProp = mitk::StringProperty::New( name );
	- node->SetProperty( "name", nameProp );
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.h
	deleted file mode 100644
	index 042f5033c4..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.h
	+++ /dev/null
	@@ -1,112 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef QmitkDiffusionDicomImportView_H__INCLUDED
	-#define QmitkDiffusionDicomImportView_H__INCLUDED
	-
	-#include <QmitkAbstractView.h>
	-#include "ui_QmitkDiffusionDicomImportViewControls.h"
	-
	-
	-/*!
	-\brief QmitkDiffusionDicomImport
	-*/
	-class QmitkDiffusionDicomImport : public QmitkAbstractView
	-{
	- Q_OBJECT
	-
	-public:
	-
	- static const std::string VIEW_ID;
	-
	- /*!
	- \ Convenient typedefs
	- */
	- typedef mitk::DataStorage::SetOfObjects ConstVector;
	- typedef ConstVector::ConstPointer ConstVectorPointer;
	- typedef ConstVector::ConstIterator ConstVectorIterator;
	-
	- /*!
	- \brief default constructor
	- */
	- QmitkDiffusionDicomImport(QObject parent=0, const char name=0);
	-
	- /*!
	- \brief default destructor
	- */
	- virtual ~QmitkDiffusionDicomImport();
	-
	- /*!
	- \brief method for creating the widget containing the application controls, like sliders, buttons etc.
	- */
	- virtual void CreateQtPartControl(QWidget *parent) override;
	-
	- /*!
	- \brief method for creating the connections of main and control widget
	- */
	- virtual void CreateConnections();
	-
	- ///
	- /// Sets the focus to an internal widget.
	- ///
	- virtual void SetFocus() override;
	-
	- void SetDwiNodeProperties(mitk::DataNode::Pointer node, std::string name);
	-
	-protected slots:
	-
	- void DicomLoadAddFolderNames();
	- void DicomLoadDeleteFolderNames();
	- void NewDicomLoadStartLoad() ;
	- void AverageClicked();
	- void OutputSet();
	- void OutputClear();
	- void Remove();
	- void RecursiveSettingsChanged();
	- void SetPrefixButtonPushed();
	- void ResetPrefixButtonPushed();
	-
	-protected:
	-
	- void Status(QString status);
	- void Status(std::string status);
	- void Status(const char* status);
	- void Error(QString status);
	- void Error(std::string status);
	- void Error(const char* status);
	-
	- void PrintMemoryUsage();
	- std::string FormatMemorySize( size_t size );
	- std::string FormatPercentage( double val );
	- std::string GetMemoryDescription( size_t processSize, float percentage );
	-
	- /*!
	- * controls containing sliders for scrolling through the slices
	- */
	- Ui::QmitkDiffusionDicomImportControls *m_Controls;
	-
	- QWidget *m_Parent;
	-
	- QString m_OutputFolderName;
	- bool m_OutputFolderNameSet;
	-
	- std::string m_Prefix;
	-
	-};
	-
	-#endif // !defined(QmitkDiffusionDicomImport_H__INCLUDED)
	-
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportViewControls.ui
	deleted file mode 100644
	index fbe4a816f8..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportViewControls.ui
	+++ /dev/null
	@@ -1,380 +0,0 @@
	-<?xml version="1.0" encoding="utf-8"?>
	-<ui version="4.0">
	- <class>QmitkDiffusionDicomImportControls</class>
	- <widget class="QWidget" name="QmitkDiffusionDicomImportControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>374</width>
	- <height>603</height>
	- </rect>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="acceptDrops">
	- <bool>true</bool>
	- </property>
	- <property name="windowTitle">
	- <string>QmitkDiffusionDicomImport</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QVBoxLayout" name="verticalLayout">
	- <item>
	- <widget class="QTextBrowser" name="textBrowser">
	- <property name="maximumSize">
	- <size>
	- <width>16777215</width>
	- <height>70</height>
	- </size>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Plain</enum>
	- </property>
	- <property name="lineWidth">
	- <number>0</number>
	- </property>
	- <property name="html">
	- <string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
	-<html><head><meta name="qrichtext" content="1" /><style type="text/css">
	-p, li { white-space: pre-wrap; }
	-</style></head><body style=" font-family:'Ubuntu'; font-size:11pt; font-weight:400; font-style:normal;">
	-<table border="0" style="-qt-table-type: root; margin-top:4px; margin-bottom:4px; margin-left:4px; margin-right:4px;">
	-<tr>
	-<td style="border: none;">
	-<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Sans'; font-size:10pt;">Each input folder must only contain DICOM-images that can be combined into one vector-valued 3D output volume. Different patients must be loaded from different input-folders. The folders must not contain other acquisitions (e.g. T1,T2,localizer).</span></p>
	-<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'Sans'; font-size:10pt;"><br /></p>
	-<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Sans'; font-size:10pt;">In case many imports are performed at once, it is recommended to set the the optional output folder argument. This prevents the images from being kept in memory.</span></p>
	-<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'Sans'; font-size:10pt;"><br /></p></td></tr></table></body></html></string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QFrame" name="m_AddDeleteButtonsFrame">
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <property name="lineWidth">
	- <number>0</number>
	- </property>
	- <layout class="QHBoxLayout" name="horizontalLayout_2">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QPushButton" name="m_AddFoldersButton">
	- <property name="text">
	- <string>Add Input Folders</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QPushButton" name="m_Remove">
	- <property name="text">
	- <string>Remove</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QPushButton" name="m_DeleteFoldersButton">
	- <property name="text">
	- <string>Clear</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <widget class="QListWidget" name="listWidget">
	- <property name="sizePolicy">
	- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
	- <horstretch>0</horstretch>
	- <verstretch>0</verstretch>
	- </sizepolicy>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>70</height>
	- </size>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::Box</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Plain</enum>
	- </property>
	- <property name="lineWidth">
	- <number>1</number>
	- </property>
	- <property name="midLineWidth">
	- <number>0</number>
	- </property>
	- <property name="verticalScrollBarPolicy">
	- <enum>Qt::ScrollBarAsNeeded</enum>
	- </property>
	- <property name="horizontalScrollBarPolicy">
	- <enum>Qt::ScrollBarAlwaysOn</enum>
	- </property>
	- <property name="resizeMode">
	- <enum>QListView::Adjust</enum>
	- </property>
	- <property name="sortingEnabled">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QFrame" name="frame_2">
	- <property name="frameShape">
	- <enum>QFrame::StyledPanel</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QVBoxLayout" name="verticalLayout_2">
	- <item>
	- <widget class="QCheckBox" name="m_DicomLoadRecursiveCheckbox">
	- <property name="text">
	- <string>Recursive</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <layout class="QHBoxLayout" name="horizontalLayout_4">
	- <property name="spacing">
	- <number>8</number>
	- </property>
	- <property name="sizeConstraint">
	- <enum>QLayout::SetNoConstraint</enum>
	- </property>
	- <item>
	- <widget class="QPushButton" name="m_SetPrefixButton">
	- <property name="text">
	- <string>Set Prefix</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QLineEdit" name="m_SubdirPrefixLineEdit"></widget>
	- </item>
	- <item>
	- <widget class="QPushButton" name="m_ResetPrefixButton">
	- <property name="text">
	- <string>Reset</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </item>
	- <item>
	- <widget class="QFrame" name="frame">
	- <property name="toolTip">
	- <string>Multiple acquistions of one gradient direction can be averaged. Due to rounding errors, similar gradients often differ in the last decimal positions. The Merge radius allows to average them anyway by taking into account all directions within a certain radius.</string>
	- </property>
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QHBoxLayout" name="horizontalLayout">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QCheckBox" name="m_DicomLoadAverageDuplicatesCheckbox">
	- <property name="text">
	- <string>Merge duplicate gradients:</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QDoubleSpinBox" name="m_Blur">
	- <property name="enabled">
	- <bool>false</bool>
	- </property>
	- <property name="toolTip">
	- <string></string>
	- </property>
	- <property name="decimals">
	- <number>4</number>
	- </property>
	- <property name="maximum">
	- <double>2.000000000000000</double>
	- </property>
	- <property name="singleStep">
	- <double>0.000100000000000</double>
	- </property>
	- <property name="value">
	- <double>0.001000000000000</double>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <widget class="QFrame" name="frame_3">
	- <property name="frameShape">
	- <enum>QFrame::NoFrame</enum>
	- </property>
	- <property name="frameShadow">
	- <enum>QFrame::Raised</enum>
	- </property>
	- <layout class="QHBoxLayout" name="horizontalLayout_3">
	- <property name="leftMargin">
	- <number>0</number>
	- </property>
	- <property name="topMargin">
	- <number>0</number>
	- </property>
	- <property name="rightMargin">
	- <number>0</number>
	- </property>
	- <property name="bottomMargin">
	- <number>0</number>
	- </property>
	- <item>
	- <widget class="QPushButton" name="m_OutputSetButton">
	- <property name="minimumSize">
	- <size>
	- <width>40</width>
	- <height>25</height>
	- </size>
	- </property>
	- <property name="maximumSize">
	- <size>
	- <width>30</width>
	- <height>16777215</height>
	- </size>
	- </property>
	- <property name="toolTip">
	- <string>Files are automaticall saved to disc. If the files can not be written, they are added to the data manager.</string>
	- </property>
	- <property name="text">
	- <string>Set</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QLineEdit" name="m_OutputLabel">
	- <property name="text">
	- <string>... optional out-folder ...</string>
	- </property>
	- <property name="frame">
	- <bool>false</bool>
	- </property>
	- <property name="readOnly">
	- <bool>true</bool>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QPushButton" name="m_OutputClearButton">
	- <property name="minimumSize">
	- <size>
	- <width>50</width>
	- <height>25</height>
	- </size>
	- </property>
	- <property name="maximumSize">
	- <size>
	- <width>30</width>
	- <height>16777215</height>
	- </size>
	- </property>
	- <property name="text">
	- <string>Clear</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <widget class="QCheckBox" name="m_OverrideOptionCheckbox">
	- <property name="text">
	- <string>Override existing files</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <widget class="QCheckBox" name="m_SplitMosaicCheckBox">
	- <property name="text">
	- <string>Split Mosaic</string>
	- </property>
	- </widget>
	- </item>
	- </layout>
	- </widget>
	- </item>
	- <item>
	- <widget class="QCommandLinkButton" name="m_DicomLoadStartLoadButton">
	- <property name="text">
	- <string>Import DICOM as *.dwi</string>
	- </property>
	- </widget>
	- </item>
	- <item>
	- <spacer name="verticalSpacer">
	- <property name="orientation">
	- <enum>Qt::Vertical</enum>
	- </property>
	- <property name="sizeHint" stdset="0">
	- <size>
	- <width>20</width>
	- <height>40</height>
	- </size>
	- </property>
	- </spacer>
	- </item>
	- </layout>
	- </widget>
	- <layoutdefault spacing="6" margin="11"></layoutdefault>
	- <resources></resources>
	- <connections></connections>
	-</ui>
	\ No newline at end of file
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/deprecated/QmitkDiffusionTensorEstimation.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/deprecated/QmitkDiffusionTensorEstimation.cpp
	deleted file mode 100644
	index 2151be46bf..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/deprecated/QmitkDiffusionTensorEstimation.cpp
	+++ /dev/null
	@@ -1,2493 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "itkTimeProbe.h"
	-
	-#include "QmitkDiffusionTensorEstimation.h"
	-#include "QmitkDiffusionTensorEstimationControls.h"
	-#include <qaction.h>
	-#include "QmitkDataTreeComboBox.h"
	-#include "QmitkDataTreeListView.h"
	-#include "QmitkDiffusionTensorIcon.h"
	-#include <qfiledialog.h>
	-#include "QmitkPropertyViewFactory.h"
	-#include <qobjectlist.h>
	-#include <qlistbox.h>
	-#include <qpushbutton.h>
	-#include <qprogressbar.h>
	-#include <qspinbox.h>
	-#include <qlineedit.h>
	-#include <qcheckbox.h>
	-
	-// properties
	-#include "mitkStringProperty.h"
	-#include "mitkProperties.h"
	-#include "mitkMaterialProperty.h"
	-#include "mitkLevelWindowProperty.h"
	-#include "mitkVtkRepresentationProperty.h"
	-#include "mitkVtkInterpolationProperty.h"
	-#include "mitkVtkScalarModeProperty.h"
	-#include "mitkLookupTableProperty.h"
	-#include "mitkLookupTable.h"
	-#include "mitkTransferFunctionProperty.h"
	-#include "mitkGridRepresentationProperty.h"
	-#include "mitkGridVolumeMapperProperty.h"
	-#include "mitkVtkResliceInterpolationProperty.h"
	-#include "mitkVectorImageMapper2D.h"
	-#include "mitkOdfVtkMapper2D.h"
	-
	-#include "itkOrientedImage.h"
	-#include "itkVectorImage.h"
	-#include "itkImageSeriesReader.h"
	-#include "itkImageFileWriter.h"
	-#include "itkExceptionObject.h"
	-#include "itkDiffusionTensor3DReconstructionImageFilter.h"
	-#include "itkDiffusionTensor3D.h"
	-#include "itkTensorFractionalAnisotropyImageFilter.h"
	-#include "itkTensorRelativeAnisotropyImageFilter.h"
	-#include "itkGDCMSeriesFileNames.h"
	-#include "itkImageRegionConstIterator.h"
	-#include "itkRescaleIntensityImageFilter.h"
	-#include "itkDiffusionQballReconstructionImageFilter.h"
	-#include "itkAnalyticalDiffusionQballReconstructionImageFilter.h"
	-#include "itkPointShell.h"
	-#include "itkRGBPixel.h"
	-#include "itkOrientationDistributionFunction.h"
	-#include "itkDiffusionOdfPrincipleDirectionsImageFilter.h"
	-#include "itkDiffusionOdfGeneralizedFaImageFilter.h"
	-#include "itkShiftScaleImageFilter.h"
	-#include "itkDiffusionOdfPrepareVisualizationImageFilter.h"
	-#include "itkDiffusionTensorPrincipleDirectionImageFilter.h"
	-#include "itkDiffusionOdfSphericalDeconvolutionImageFilter.h"
	-#include "itkVectorImagesAngularErrorImageFilter.h"
	-
	-#include "mitkDicomDiffusionVolumeHeaderReader.h"
	-#include "mitkGroupDiffusionHeadersFilter.h"
	-#include "mitkDicomDiffusionVolumesReader.h"
	-#include "mitkNrrdDiffusionVolumesWriter.h"
	-#include "mitkNrrdDiffusionVolumesReader.h"
	-#include "mitkDiffusionVolumes.h"
	-#include "mitkDataTreeFilterFunctions.h"
	-#include "mitkProgressBar.h"
	-#include "mitkStatusBar.h"
	-#include "mitkTeemDiffusionTensor3DReconstructionImageFilter.h"
	-#include "mitkSurface.h"
	-
	-#include "vtkPolyData.h"
	-#include "vtkPoints.h"
	-#include "vtkCellArray.h"
	-#include "vtkDelaunay2D.h"
	-#include "vtkCleanPolyData.h"
	-#include "vtkAppendPolyData.h"
	-
	-#include "mitkImageCast.h"
	-
	-#include <time.h>
	-#include <stdio.h>
	-#include <stdlib.h>
	-
	-typedef float TTensorPixelType;
	-typedef itk::DiffusionTensor3D< TTensorPixelType > TensorPixelType;
	-typedef itk::Image< TensorPixelType, 3 > TensorImageType;
	-
	-typedef itk::VectorImage< DiffusionPixelType, 3 > DiffusionImageType;
	-
	-//CAST_N_VEC(3)
	-//CAST_N_VEC(42)
	-//CAST_N_VEC(92)
	-//CAST_N_VEC(162)
	-//CAST_N_VEC(252)
	-//CAST_N_VEC(362)
	-//CAST_N_VEC(492)
	-//CAST_N_VEC(642)
	-//CAST_N_VEC(812)
	-//CAST_N_VEC(1002)
	-
	-const int QmitkDiffusionTensorEstimation::odfsize = 252;
	-const int QmitkDiffusionTensorEstimation::nrconvkernels = 252;
	-
	-// Compile-time Square Root Computation: ceil(sqrt(N))
	-template <int Size, int Low = 1, int High = Size>
	-struct Root;
	-template <int Size, int Mid>
	-struct Root<Size,Mid,Mid> {
	- static const int root = Mid;
	-};
	-template <int Size, int Low, int High>
	-struct Root {
	- static const int mean = (Low + High)/2;
	- static const bool down = (mean * mean >= Size);
	- static const int root = Root<Size,
	- (down ? Low : mean+1),
	- (down ? mean : High) >::root;
	-};
	-
	-QmitkDiffusionTensorEstimation::QmitkDiffusionTensorEstimation(QObject parent, const char name, mitk::DataTreeIteratorBase* it)
	-: QmitkAbstractView(parent, name, it), m_Controls(nullptr)
	-{
	- SetAvailability(true);
	- m_FilterInitialized = false;
	-}
	-
	-QmitkDiffusionTensorEstimation::~QmitkDiffusionTensorEstimation()
	-{}
	-
	-QWidget * QmitkDiffusionTensorEstimation::CreateControlWidget(QWidget *parent)
	-{
	- if (m_Controls == nullptr)
	- {
	- m_Controls = new QmitkDiffusionTensorEstimationControls(parent);
	- }
	-
	- m_Controls->m_TensorEstimationTeemErrorImage->setChecked(false);
	- m_Controls->m_TensorEstimationTeemSigmaEdit->setText("NaN");
	- m_Controls->m_TensorEstimationTeemEstimationMethodCombo->insertItem("LLS (Linear Least Squares)");
	- m_Controls->m_TensorEstimationTeemEstimationMethodCombo->insertItem("MLE (Maximum Likelihood)");
	- m_Controls->m_TensorEstimationTeemEstimationMethodCombo->insertItem("NLS (Nonlinear Least Squares)");
	- m_Controls->m_TensorEstimationTeemEstimationMethodCombo->insertItem("WLS (Weighted Least Squares)");
	- m_Controls->m_TensorEstimationTeemNumItsSpin->setValue(1);
	- m_Controls->m_TensorEstimationTeemConfThresholdEdit->setText("NaN");
	- m_Controls->m_TensorEstimationTeemFuzzyEdit->setText("0.0");
	- m_Controls->m_TensorEstimationTeemMinValEdit->setText("1.0");
	-
	- m_Controls->m_OdfReconstructionThreasholdEdit->setText("0.0");
	- m_Controls->m_OdfStandardAlgorithmsOrderSpinbox->setValue(0);
	- m_Controls->m_OdfStandardAlgorithmsProbThreshEdit->setText(QString::number(1.0/double(odfsize)));
	- m_Controls->m_OdfReconstructionNumberThreadsSpinbox->setValue(4);
	-
	- m_Controls->m_OdfReconstructionMaxLLevelComboBox->insertItem( QString("2") );
	- m_Controls->m_OdfReconstructionMaxLLevelComboBox->insertItem( QString("4") );
	- m_Controls->m_OdfReconstructionMaxLLevelComboBox->insertItem( QString("6") );
	- m_Controls->m_OdfReconstructionMaxLLevelComboBox->insertItem( QString("8") );
	- m_Controls->m_OdfReconstructionMaxLLevelComboBox->setCurrentItem( 3 );
	-
	- m_Controls->m_OdfReconstructionNumberThreadsAnalyticalSpinbox->setValue(4);
	- m_Controls->m_OdfReconstructionThreasholdAnalyticalEdit->setText("0.0");
	- m_Controls->m_OdfReconstructionLambdaLineEdit->setText("0.006");
	-
	- m_Controls->m_OdfStandardAlgorithmsNumberThreadsSpinbox->setValue(4);
	- m_Controls->m_OdfStandardAlgorithmsDeconvNumberThreadsSpinbox->setValue(4);
	- m_Controls->m_OdfStandardAlgorithmsDeconvolutionThreshEdit->setText("0.1");
	- m_Controls->m_OdfStandardAlgorithmsDeconvolutionAngResThresholdEdit->setText("15");
	-
	- m_Controls->m_OdfStandardAlgorithmsGFAParam1->setText("2");
	- m_Controls->m_OdfStandardAlgorithmsGFAParam2->setText("1");
	-
	- return m_Controls;
	-}
	-
	-void QmitkDiffusionTensorEstimation::CreateConnections()
	-{
	- if ( m_Controls )
	- {
	- connect( (QObject)(m_Controls->m_TensorEstimationButton), SIGNAL(clicked()),(QObject) this, SLOT(TensorEstimationButton()));
	- connect( (QObject)(m_Controls->m_OdfReconstructionButton), SIGNAL(clicked()),(QObject) this, SLOT(OdfReconstructionButton()));
	- connect( (QObject)(m_Controls->m_OdfReconstructionAnalyticalButton), SIGNAL(clicked()),(QObject) this, SLOT(OdfReconstructionAnalyticalButton()));
	- connect( (QObject)(m_Controls->m_TensorEstimationTeemEstimateButton), SIGNAL(clicked()),(QObject) this, SLOT(TensorEstimationTeemEstimateButton()));
	-
	- connect( (QObject)(m_Controls->m_TensorVolumesSaveButton), SIGNAL(clicked()),(QObject) this, SLOT(TensorVolumesSaveButton()));
	- connect( (QObject)(m_Controls->m_TensorVolumesLoadButton), SIGNAL(clicked()),(QObject) this, SLOT(TensorVolumesLoadButton()));
	- connect( (QObject)(m_Controls->m_TensorVolumesRemoveButton), SIGNAL(clicked()),(QObject) this, SLOT(TensorVolumesRemoveButton()));
	- connect( (QObject)(m_Controls->m_StandardAlgorithmsFAButton), SIGNAL(clicked()),(QObject) this, SLOT(StandardAlgorithmsFAButton()));
	- connect( (QObject)(m_Controls->m_StandardAlgorithmsRAButton), SIGNAL(clicked()),(QObject) this, SLOT(StandardAlgorithmsRAButton()));
	- connect( (QObject)(m_Controls->m_StandardAlgorithmsDirectionButton), SIGNAL(clicked()),(QObject) this, SLOT(StandardAlgorithmsDirectionButton()));
	-
	- connect( (QObject)(m_Controls->m_OdfVolumesSaveButton), SIGNAL(clicked()),(QObject) this, SLOT(OdfVolumesSaveButton()));
	- connect( (QObject)(m_Controls->m_OdfVolumesLoadButton), SIGNAL(clicked()),(QObject) this, SLOT(OdfVolumesLoadButton()));
	- connect( (QObject)(m_Controls->m_OdfVolumesRemoveButton), SIGNAL(clicked()),(QObject) this, SLOT(OdfVolumesRemoveButton()));
	- connect( (QObject)(m_Controls->m_OdfStandardAlgorithmsDirectionButton), SIGNAL(clicked()),(QObject) this, SLOT(OdfStandardAlgorithmsDirectionButton()));
	- connect( (QObject)(m_Controls->m_OdfStandardAlgorithmsDeconvolutionButton), SIGNAL(clicked()),(QObject) this, SLOT(OdfStandardAlgorithmsDeconvolutionButton()));
	- connect( (QObject)(m_Controls->m_OdfStandardAlgorithmsGFAButton), SIGNAL(clicked()),(QObject) this, SLOT(OdfStandardAlgorithmsGFAButton()));
	- connect( (QObject)(m_Controls->m_OdfVolumesVisualizeSelectedButton), SIGNAL(clicked()),(QObject) this, SLOT(OdfVolumesVisualizeSelectedButton()));
	-
	- connect( (QObject)(m_Controls->m_DirectionVolumesSaveButton), SIGNAL(clicked()),(QObject) this, SLOT(DirectionVolumesSaveButton()));
	- connect( (QObject)(m_Controls->m_DirectionVolumesLoadButton), SIGNAL(clicked()),(QObject) this, SLOT(DirectionVolumesLoadButton()));
	- connect( (QObject)(m_Controls->m_DirectionVolumesRemoveButton), SIGNAL(clicked()),(QObject) this, SLOT(DirectionVolumesRemoveButton()));
	- connect( (QObject)(m_Controls->m_DirectionVolumesAngularErrorButton), SIGNAL(clicked()),(QObject) this, SLOT(DirectionVolumesAngularErrorButton()));
	-
	- connect( (QObject)(m_Controls->m_DiffusionVolumesLoadButton), SIGNAL(clicked()),(QObject) this, SLOT(DiffusionVolumesLoadButton()));
	- connect( (QObject)(m_Controls->m_DiffusionVolumeSaveButton), SIGNAL(clicked()),(QObject) this, SLOT(DiffusionVolumeSaveButton()));
	- connect( (QObject)(m_Controls->m_DiffusionVolumesRemoveButton), SIGNAL(clicked()),(QObject) this, SLOT(DiffusionVolumesRemoveButton()));
	- connect( (QObject)(m_Controls->m_TensorEstimationDiffusionVolumesSelectAllButton), SIGNAL(clicked()),(QObject) this, SLOT(DiffusionVolumesSelectAll()));
	-}
	-}
	-
	-QAction * QmitkDiffusionTensorEstimation::CreateAction(QActionGroup *parent)
	-{
	-
	- //action = new QAction( tr( "Brain Atrophy" ), pixmap, tr( "BrainAtrophy" ), 0, parent, "BrainAtrophy" );
	-
	- QImage icon = qembed_findImage("QmitkDiffusionTensorEstimation");
	- QPixmap pixmap(icon);
	- QAction* action;
	- action = new QAction( tr( "Diffusion Tensor Estimation" ), pixmap, tr( "QmitkDiffusionTensorEstimation menu" ), 0, parent, "QmitkDiffusionTensorEstimation" );
	- return action;
	-}
	-
	-void QmitkDiffusionTensorEstimation::TreeChanged()
	-{
	- m_Controls->m_TensorEstimationDiffusionVolumesSelector->Update();
	- m_Controls->m_TensorVolumesSelector->Update();
	- m_Controls->m_OdfVolumesSelector->Update();
	- m_Controls->m_DirectionVolumesSelector->Update();
	-
	- if(m_DiffusionVolumesDataTreeFilter
	- &&m_DiffusionVolumesDataTreeFilter->GetItems()->Size() > 0)
	- {
	- m_Controls->m_TensorEstimationButton->setEnabled(true);
	- m_Controls->m_OdfReconstructionButton->setEnabled(true);
	- m_Controls->m_OdfReconstructionAnalyticalButton->setEnabled(true);
	- }
	- else
	- {
	- m_Controls->m_OdfReconstructionButton->setEnabled(false);
	- m_Controls->m_OdfReconstructionAnalyticalButton->setEnabled(false);
	- m_Controls->m_TensorEstimationButton->setEnabled(false);
	- }
	-
	- if(m_TensorVolumesDataTreeFilter
	- && m_TensorVolumesDataTreeFilter->GetItems()->Size() > 0)
	- {
	- m_Controls->m_TensorVolumesSaveButton->setEnabled(true);
	- m_Controls->m_TensorVolumesRemoveButton->setEnabled(true);
	- }
	- else
	- {
	- m_Controls->m_TensorVolumesSaveButton->setEnabled(false);
	- m_Controls->m_TensorVolumesRemoveButton->setEnabled(false);
	- }
	-
	- if(m_OdfVolumesDataTreeFilter
	- && m_OdfVolumesDataTreeFilter->GetItems()->Size() > 0)
	- {
	- m_Controls->m_OdfVolumesSaveButton->setEnabled(true);
	- m_Controls->m_OdfVolumesRemoveButton->setEnabled(true);
	- m_Controls->m_OdfVolumesVisualizeSelectedButton->setEnabled(true);
	- }
	- else
	- {
	- m_Controls->m_OdfVolumesSaveButton->setEnabled(false);
	- m_Controls->m_OdfVolumesRemoveButton->setEnabled(false);
	- m_Controls->m_OdfVolumesVisualizeSelectedButton->setEnabled(false);
	- }
	-
	- if(m_DirectionVolumesDataTreeFilter
	- && m_DirectionVolumesDataTreeFilter->GetItems()->Size() > 0)
	- {
	- m_Controls->m_DirectionVolumesSaveButton->setEnabled(true);
	- m_Controls->m_DirectionVolumesRemoveButton->setEnabled(true);
	- }
	- else
	- {
	- m_Controls->m_DirectionVolumesSaveButton->setEnabled(false);
	- m_Controls->m_DirectionVolumesRemoveButton->setEnabled(false);
	- }
	-
	- if(m_DirectionVolumesDataTreeFilter
	- && m_DirectionVolumesDataTreeFilter->GetItems()->Size() > 1)
	- {
	- m_Controls->m_DirectionVolumesAngularErrorButton->setEnabled(true);
	- }
	- else
	- {
	- m_Controls->m_DirectionVolumesAngularErrorButton->setEnabled(false);
	- }
	-}
	-
	-void QmitkDiffusionTensorEstimation::Activated()
	-{
	- if (m_FilterInitialized)
	- return;
	-
	- // diffusion volumes filter
	- m_DiffusionVolumesDataTreeFilter = mitk::DataTreeFilter::New( GetDataTreeIterator()->GetTree() );
	- m_DiffusionVolumesDataTreeFilter->SetSelectionMode(mitk::DataTreeFilter::MULTI_SELECT);
	- m_DiffusionVolumesDataTreeFilter->SetHierarchyHandling(mitk::DataTreeFilter::FLATTEN_HIERARCHY);
	- m_DiffusionVolumesDataTreeFilter->SetFilter( mitk::IsBaseDataType<mitk::DiffusionVolumes<short> >() ); // show diffusion volumes
	-
	- mitk::DataTreeFilter::PropertyList visible_props;
	- visible_props.push_back("name");
	- m_DiffusionVolumesDataTreeFilter->SetVisibleProperties(visible_props);
	-
	- mitk::DataTreeFilter::PropertyList property_labels;
	- property_labels.push_back("Diffusion Volumes");
	- m_DiffusionVolumesDataTreeFilter->SetPropertiesLabels(property_labels);
	-
	- m_Controls->m_TensorEstimationDiffusionVolumesSelector->SetDataTree( GetDataTreeIterator()->GetTree() );
	- m_Controls->m_TensorEstimationDiffusionVolumesSelector->SetFilter( m_DiffusionVolumesDataTreeFilter );
	- m_Controls->m_TensorEstimationDiffusionVolumesSelector->SetAutoUpdate( false );
	- m_Controls->m_TensorEstimationDiffusionVolumesSelector->setStretchedColumn(1);
	-
	- // tensor volumes filter
	- m_TensorVolumesDataTreeFilter = mitk::DataTreeFilter::New( GetDataTreeIterator()->GetTree() );
	- m_TensorVolumesDataTreeFilter->SetSelectionMode(mitk::DataTreeFilter::SINGLE_SELECT);
	- m_TensorVolumesDataTreeFilter->SetHierarchyHandling(mitk::DataTreeFilter::FLATTEN_HIERARCHY);
	- m_TensorVolumesDataTreeFilter->SetFilter( mitk::IsBaseDataTypeWithBoolProperty<mitk::Image>("IsTensorVolume") ); // show tensor volumes
	-
	- m_TensorVolumesDataTreeFilter->SetVisibleProperties(visible_props);
	-
	- mitk::DataTreeFilter::PropertyList tensor_property_labels;
	- tensor_property_labels.push_back("Tensor Volumes");
	- m_TensorVolumesDataTreeFilter->SetPropertiesLabels(tensor_property_labels);
	-
	- m_Controls->m_TensorVolumesSelector->SetDataTree( GetDataTreeIterator()->GetTree() );
	- m_Controls->m_TensorVolumesSelector->SetFilter( m_TensorVolumesDataTreeFilter );
	- m_Controls->m_TensorVolumesSelector->SetAutoUpdate( false );
	- m_Controls->m_TensorVolumesSelector->setStretchedColumn(1);
	-
	- // Odf volumes filter
	- m_OdfVolumesDataTreeFilter = mitk::DataTreeFilter::New( GetDataTreeIterator()->GetTree() );
	- m_OdfVolumesDataTreeFilter->SetSelectionMode(mitk::DataTreeFilter::MULTI_SELECT);
	- m_OdfVolumesDataTreeFilter->SetHierarchyHandling(mitk::DataTreeFilter::FLATTEN_HIERARCHY);
	- m_OdfVolumesDataTreeFilter->SetFilter( mitk::IsBaseDataTypeWithBoolProperty<mitk::Image>("IsOdfVolume") );
	-
	- m_OdfVolumesDataTreeFilter->SetVisibleProperties(visible_props);
	-
	- mitk::DataTreeFilter::PropertyList Odf_property_labels;
	- Odf_property_labels.push_back("ODF Volumes");
	- m_OdfVolumesDataTreeFilter->SetPropertiesLabels(Odf_property_labels);
	-
	- m_Controls->m_OdfVolumesSelector->SetDataTree( GetDataTreeIterator()->GetTree() );
	- m_Controls->m_OdfVolumesSelector->SetFilter( m_OdfVolumesDataTreeFilter );
	- m_Controls->m_OdfVolumesSelector->SetAutoUpdate( false );
	- m_Controls->m_OdfVolumesSelector->setStretchedColumn(1);
	-
	- // direction volumes filter
	- m_DirectionVolumesDataTreeFilter = mitk::DataTreeFilter::New( GetDataTreeIterator()->GetTree() );
	- m_DirectionVolumesDataTreeFilter->SetSelectionMode(mitk::DataTreeFilter::MULTI_SELECT);
	- m_DirectionVolumesDataTreeFilter->SetHierarchyHandling(mitk::DataTreeFilter::FLATTEN_HIERARCHY);
	- m_DirectionVolumesDataTreeFilter->SetFilter( mitk::IsBaseDataTypeWithBoolProperty<mitk::Image>("IsDirectionVolume") );
	-
	- m_DirectionVolumesDataTreeFilter->SetVisibleProperties(visible_props);
	-
	- mitk::DataTreeFilter::PropertyList direction_property_labels;
	- direction_property_labels.push_back("Direction Volumes");
	- m_DirectionVolumesDataTreeFilter->SetPropertiesLabels(direction_property_labels);
	-
	- m_Controls->m_DirectionVolumesSelector->SetDataTree( GetDataTreeIterator()->GetTree() );
	- m_Controls->m_DirectionVolumesSelector->SetFilter( m_DirectionVolumesDataTreeFilter );
	- m_Controls->m_DirectionVolumesSelector->SetAutoUpdate( false );
	- m_Controls->m_DirectionVolumesSelector->setStretchedColumn(1);
	-
	- m_FilterInitialized = true;
	-
	- TreeChanged();
	-
	-}
	-
	-void QmitkDiffusionTensorEstimation::Deactivated()
	-{
	-}
	-
	-void QmitkDiffusionTensorEstimation::Visible()
	-{
	-}
	-
	-void QmitkDiffusionTensorEstimation::Hidden()
	-{
	-}
	-
	-
	-void QmitkDiffusionTensorEstimation::TensorVolumesSaveButton()
	-{
	- // GET SELECTED ITEM
	- const mitk::DataTreeFilter::Item* selectedItem
	- = m_TensorVolumesDataTreeFilter->GetSelectedItem();
	- if( !selectedItem )
	- return;
	- mitk::Image::Pointer tensorVol =
	- static_cast<mitk::Image*>(selectedItem->GetNode()->GetData());
	- TensorImageType::Pointer itkTensorVol =
	- TensorImageType::New();
	- mitk::CastToItkImage<TensorImageType>(tensorVol, itkTensorVol);
	-
	- // SELECT FILE DIALOG
	- std::string sName = selectedItem->GetNode()->GetName();
	- QString qName;
	- qName.sprintf("%s.nhdr",sName.c_str());
	- QString filename = QFileDialog::getSaveFileName(
	- qName,
	- "Nrrd Images (.nrrd .nhdr)",
	- this->m_Controls,
	- "save file dialog",
	- "Select Nrrd Outputfile" );
	- if ( !filename )
	- return;
	-
	- // WRITING TENSORS TO FILE
	- MBI_INFO << "Writing tensors ";
	- typedef itk::ImageFileWriter<TensorImageType> TensorWriterType;
	- TensorWriterType::Pointer tensorWriter = TensorWriterType::New();
	- tensorWriter->SetFileName(filename.ascii());
	- tensorWriter->SetInput(itkTensorVol);
	- tensorWriter->Update();
	-}
	-
	-void QmitkDiffusionTensorEstimation::TensorVolumesLoadButton()
	-{
	- // SELECT FOLDER DIALOG
	- QFileDialog* w = new QFileDialog( this->m_Controls, "Select DWI data file", TRUE );
	- w->setMode( QFileDialog::ExistingFiles );
	- w->setFilter( "Nrrd Images (.nrrd .nhdr)" );
	-
	- // RETRIEVE SELECTION
	- if ( w->exec() != QDialog::Accepted )
	- return;
	-
	- QStringList filenames = w->selectedFiles();
	- QStringList::Iterator it = filenames.begin();
	- while( it != filenames.end() ) {
	- std::string filename = ( *it ).ascii();
	- ++it;
	-
	- // READING TENSOR VOLUME
	- typedef itk::ImageFileReader<TensorImageType> ReaderType;
	- ReaderType::Pointer tensorReader = ReaderType::New();
	- tensorReader->SetFileName(filename);
	- try
	- {
	- tensorReader->Update();
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- std::cout << e << std::endl;
	- }
	-
	- // Tensorvolume
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk( tensorReader->GetOutput() );
	- image->SetVolume( tensorReader->GetOutput()->GetBufferPointer() );
	- mitk::DataNode::Pointer node=mitk::DataNode::New();
	- node->SetData( image );
	- mitk::DataStorage::GetInstance()->Add(node);
	- SetDefaultNodeProperties(node, itksys::SystemTools::GetFilenameName(filename));
	- node->SetProperty( "IsTensorVolume", mitk::BoolProperty::New( true ) );
	-
	- TreeChanged();
	- }
	-}
	-
	-void QmitkDiffusionTensorEstimation::TensorVolumesRemoveButton()
	-{
	- m_TensorVolumesDataTreeFilter->DeleteSelectedItems();
	-}
	-
	-void QmitkDiffusionTensorEstimation::OdfVolumesSaveButton()
	-{
	- // GET SELECTED ITEM
	- const mitk::DataTreeFilter::Item* selectedItem
	- = m_OdfVolumesDataTreeFilter->GetSelectedItem();
	- if( !selectedItem ) return;
	-
	- mitk::Image::Pointer OdfVol =
	- static_cast<mitk::Image*>(selectedItem->GetNode()->GetData());
	- if( !OdfVol)return;
	-
	- typedef itk::Image<itk::Vector<TTensorPixelType,odfsize>,3 > IType;
	- IType::Pointer itkOdfVol = IType::New();
	- mitk::CastToItkImage<IType>(OdfVol, itkOdfVol);
	-
	- typedef itk::VectorImage<TTensorPixelType, 3> VarVecImgType;
	- VarVecImgType::Pointer vecImg = VarVecImgType::New();
	- vecImg->SetSpacing( itkOdfVol->GetSpacing() ); // Set the image spacing
	- vecImg->SetOrigin( itkOdfVol->GetOrigin() ); // Set the image origin
	- vecImg->SetDirection( itkOdfVol->GetDirection() ); // Set the image direction
	- vecImg->SetLargestPossibleRegion( itkOdfVol->GetLargestPossibleRegion());
	- vecImg->SetBufferedRegion( itkOdfVol->GetLargestPossibleRegion() );
	- vecImg->SetVectorLength(odfsize);
	- vecImg->Allocate();
	- itk::ImageRegionIterator<VarVecImgType> ot (vecImg, vecImg->GetLargestPossibleRegion() );
	- ot = ot.Begin();
	-
	- itk::ImageRegionIterator<IType> it (itkOdfVol, itkOdfVol->GetLargestPossibleRegion() );
	- it = it.Begin();
	- MBI_DEBUG << it.Get();
	- for (it = it.Begin(); !it.IsAtEnd(); ++it)
	- {
	- itk::Vector<TTensorPixelType,odfsize> vec = it.Get();
	- VarVecImgType::PixelType varvec(vec.GetDataPointer(), odfsize);
	- ot.Set(varvec);
	- ++ot;
	- }
	-
	- // SELECT FILE DIALOG
	- std::string sName = selectedItem->GetNode()->GetName();
	- QString qName;
	- qName.sprintf("%s.nhdr",sName.c_str());
	- QString filename = QFileDialog::getSaveFileName(
	- qName,
	- "Nrrd Images (.nrrd .nhdr)",
	- this->m_Controls,
	- "save file dialog",
	- "Select Nrrd Outputfile" );
	- if ( !filename )
	- return;
	-
	- // WRITING TENSORS TO FILE
	- MBI_INFO << "Writing data ";
	- typedef itk::ImageFileWriter<VarVecImgType> OdfWriterType;
	- OdfWriterType::Pointer OdfWriter = OdfWriterType::New();
	- OdfWriter->SetFileName(filename.ascii());
	- OdfWriter->SetInput(vecImg);
	- OdfWriter->Update();
	-}
	-
	-void QmitkDiffusionTensorEstimation::OdfVolumesLoadButton()
	-{
	- // SELECT FOLDER DIALOG
	- QFileDialog* w = new QFileDialog( this->m_Controls, "Select DWI data file", TRUE );
	- w->setMode( QFileDialog::ExistingFiles );
	- w->setFilter( "Nrrd Images (.nrrd .nhdr)" );
	-
	- // RETRIEVE SELECTION
	- if ( w->exec() != QDialog::Accepted )
	- return;
	-
	- QStringList filenames = w->selectedFiles();
	- QStringList::Iterator it = filenames.begin();
	- while( it != filenames.end() ) {
	- std::string filename = ( *it ).ascii();
	- ++it;
	-
	- // READING TENSOR VOLUME
	- typedef itk::Image<itk::Vector<TTensorPixelType,odfsize>,3 > IVType;
	- typedef itk::ImageFileReader<IVType> ReaderType;
	- ReaderType::Pointer OdfReader = ReaderType::New();
	- OdfReader->SetFileName(filename);
	- try
	- {
	- OdfReader->Update();
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- MBI_LOG << e;
	- }
	-
	- //itk::ImageRegionConstIterator<IVType> it (OdfReader->GetOutput(), OdfReader->GetOutput()->GetLargestPossibleRegion() );
	- //it = it.Begin();
	- //std::cout << it.Get() << std::endl;
	-
	- // Tensorvolume
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk( OdfReader->GetOutput() );
	- image->SetVolume( OdfReader->GetOutput()->GetBufferPointer() );
	- mitk::DataNode::Pointer node=mitk::DataNode::New();
	- node->SetData( image );
	- mitk::DataStorage::GetInstance()->Add(node);
	- SetDefaultNodeProperties(node, itksys::SystemTools::GetFilenameName(filename));
	- node->SetProperty( "IsOdfVolume", mitk::BoolProperty::New( true ) );
	- node->SetProperty( "visible", mitk::BoolProperty::New( false ) );
	-
	- TreeChanged();
	- }
	-}
	-
	-void QmitkDiffusionTensorEstimation::OdfVolumesRemoveButton()
	-{
	- m_OdfVolumesDataTreeFilter->DeleteSelectedItems();
	-}
	-
	-void QmitkDiffusionTensorEstimation::OdfVolumesVisualizeSelectedButton()
	-{
	- itk::TimeProbe clock;
	- QString status;
	- const mitk::DataTreeFilter::Item* item
	- = m_OdfVolumesDataTreeFilter->GetSelectedItem();
	- if(!item)return;
	-
	- typedef itk::Vector<TTensorPixelType,odfsize> OdfVectorType;
	- typedef itk::Image<OdfVectorType,3> OdfVectorImgType;
	- mitk::Image* vol =
	- static_cast<mitk::Image*>(item->GetNode()->GetData());
	- OdfVectorImgType::Pointer itkvol = OdfVectorImgType::New();
	- mitk::CastToItkImage<OdfVectorImgType>(vol, itkvol);
	- std::string nodename = item->GetProperty("name");
	-
	- // PREPARE FOR VISUALIZATION
	- clock.Start();
	- MBI_INFO << "Preparing for Visualization ";
	- mitk::StatusBar::GetInstance()->DisplayText(status.sprintf(
	- "Preparing for Visualization of %s", nodename.c_str()));
	- typedef itk::DiffusionOdfPrepareVisualizationImageFilter<TTensorPixelType,odfsize>
	- FilterType;
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetInput(itkvol);
	- filter->SetNumberOfThreads(4);
	-
	- switch(m_Controls->m_OdfVolumesVisualizeNormalizationMethod->currentItem())
	- {
	- case 0:
	- {
	- filter->SetNormalizationMethod(FilterType::PV_MIN_MAX);
	- break;
	- }
	- case 1:
	- {
	- filter->SetNormalizationMethod(FilterType::PV_NONE);
	- break;
	- }
	- case 2:
	- {
	- filter->SetNormalizationMethod(FilterType::PV_MAX);
	- break;
	- }
	- case 3:
	- {
	- filter->SetNormalizationMethod(FilterType::PV_GLOBAL_MAX);
	- break;
	- }
	- case 4:
	- {
	- filter->SetNormalizationMethod(FilterType::PV_MIN_MAX_INVERT);
	- break;
	- }
	- default:
	- {
	- filter->SetNormalizationMethod(FilterType::PV_MIN_MAX);
	- break;
	- }
	- }
	-
	- if(m_Controls->m_OdfVolumesVisualizeScaleGfaCheckbox->isChecked() )
	- {
	- typedef itk::DiffusionOdfGeneralizedFaImageFilter<TTensorPixelType,TTensorPixelType,odfsize>
	- GfaFilterType;
	- filter->SetDoScaleGfa(true);
	- float p1 = m_Controls->m_OdfStandardAlgorithmsGFAParam1->text().toFloat();
	- float p2 = m_Controls->m_OdfStandardAlgorithmsGFAParam2->text().toFloat();
	- switch(m_Controls->m_OdfStandardAlgorithmsGFAMethod->currentItem())
	- {
	- case 0:
	- filter->SetScaleByGfaType(GfaFilterType::GFA_STANDARD);
	- break;
	- case 1:
	- filter->SetScaleByGfaType(GfaFilterType::GFA_QUANTILES_HIGH_LOW);
	- break;
	- case 2:
	- filter->SetScaleByGfaType(GfaFilterType::GFA_QUANTILE_HIGH);
	- break;
	- case 3:
	- filter->SetScaleByGfaType(GfaFilterType::GFA_MAX_ODF_VALUE);
	- break;
	- case 4:
	- filter->SetScaleByGfaType(GfaFilterType::GFA_DECONVOLUTION_COEFFS);
	- break;
	- case 5:
	- filter->SetScaleByGfaType(GfaFilterType::GFA_MIN_MAX_NORMALIZED_STANDARD);
	- break;
	- case 6:
	- filter->SetScaleByGfaType(GfaFilterType::GFA_NORMALIZED_ENTROPY);
	- break;
	- case 7:
	- filter->SetScaleByGfaType(GfaFilterType::GFA_NEMATIC_ORDER_PARAMETER);
	- break;
	- case 8:
	- filter->SetScaleByGfaType(GfaFilterType::GFA_QUANTILES_LOW_HIGH);
	- break;
	- case 9:
	- filter->SetScaleByGfaType(GfaFilterType::GFA_QUANTILE_LOW);
	- break;
	- case 10:
	- filter->SetScaleByGfaType(GfaFilterType::GFA_MIN_ODF_VALUE);
	- break;
	- case 11:
	- filter->SetScaleByGfaType(GfaFilterType::GFA_STD_BY_MAX);
	- break;
	- case 12:
	- filter->SetScaleByGfaType(GfaFilterType::GFA_PRINCIPLE_CURVATURE);
	- filter->SetGfaParam1(p1);
	- break;
	- case 13:
	- filter->SetScaleByGfaType(GfaFilterType::GFA_GENERALIZED_GFA);
	- filter->SetGfaParam1(p1);
	- filter->SetGfaParam2(p2);
	- break;
	- default:
	- filter->SetScaleByGfaType(GfaFilterType::GFA_STANDARD);
	- }
	- }
	- filter->Update();
	- clock.Stop();
	- MBI_DEBUG << "took " << clock.GetMeanTime() << "s.";
	-
	- // VIZ TO DATATREE
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk( filter->GetOutput() );
	- image->SetVolume( filter->GetOutput()->GetBufferPointer() );
	- mitk::DataNode::Pointer node=mitk::DataNode::New();
	- node->SetData( image );
	- mitk::DataStorage::GetInstance()->Add(node);
	- SetDefaultNodeProperties(node, nodename.append(" Viz"));
	- node->SetProperty( "IsOdfVolume", mitk::BoolProperty::New( true ) );
	- node->SetProperty( "ShowMaxNumber", mitk::IntProperty::New( 1500 ) );
	- node->SetProperty( "DoRefresh", mitk::BoolProperty::New( true ) );
	- node->SetProperty( "layer", mitk::IntProperty::New( 1 ) );
	- node->SetProperty( "global_scaling", mitk::FloatProperty::New( 1.0 ) );
	- mitk::OdfVtkMapper2D<TTensorPixelType,odfsize>::Pointer odfMapper =
	- mitk::OdfVtkMapper2D<TTensorPixelType,odfsize>::New();
	- node->SetMapper(1,odfMapper);
	-
	- mitk::StatusBar::GetInstance()->DisplayText("Computation complete.");
	-
	- m_DataTreeIterator->GetTree()->Modified();
	- this->GetRenderWindowPart()->RequestUpdate();
	- TreeChanged();
	- m_Controls->update();
	-
	-}
	-
	-void QmitkDiffusionTensorEstimation::DirectionVolumesSaveButton()
	-{
	- // GET SELECTED ITEM
	- const mitk::DataTreeFilter::Item* selectedItem
	- = m_DirectionVolumesDataTreeFilter->GetSelectedItem();
	- if( !selectedItem ) return;
	-
	- mitk::Image::Pointer vol =
	- static_cast<mitk::Image*>(selectedItem->GetNode()->GetData());
	- if( !vol)return;
	-
	- typedef itk::Image<itk::Vector<TTensorPixelType,3>,3 > IType;
	- IType::Pointer itkVol = IType::New();
	- mitk::CastToItkImage<IType>(vol, itkVol);
	-
	- typedef itk::VectorImage<TTensorPixelType, 3> VarVecImgType;
	- VarVecImgType::Pointer vecImg = VarVecImgType::New();
	- vecImg->SetSpacing( itkVol->GetSpacing() ); // Set the image spacing
	- vecImg->SetOrigin( itkVol->GetOrigin() ); // Set the image origin
	- vecImg->SetDirection( itkVol->GetDirection() ); // Set the image direction
	- vecImg->SetLargestPossibleRegion( itkVol->GetLargestPossibleRegion());
	- vecImg->SetBufferedRegion( itkVol->GetLargestPossibleRegion() );
	- vecImg->SetVectorLength(3);
	- vecImg->Allocate();
	- itk::ImageRegionIterator<VarVecImgType> ot (vecImg, vecImg->GetLargestPossibleRegion() );
	- ot = ot.Begin();
	-
	- itk::ImageRegionIterator<IType> it (itkVol, itkVol->GetLargestPossibleRegion() );
	- it = it.Begin();
	- for (it = it.Begin(); !it.IsAtEnd(); ++it)
	- {
	- itk::Vector<TTensorPixelType,3> vec = it.Get();
	- VarVecImgType::PixelType varvec(vec.GetDataPointer(), 3);
	- ot.Set(varvec);
	- ++ot;
	- }
	-
	- // SELECT FILE DIALOG
	- std::string sName = selectedItem->GetNode()->GetName();
	- QString qName;
	- qName.sprintf("%s.nhdr",sName.c_str());
	- QString filename = QFileDialog::getSaveFileName(
	- qName,
	- "Nrrd Images (.nrrd .nhdr)",
	- this->m_Controls,
	- "save file dialog",
	- "Select Nrrd Outputfile" );
	- if ( !filename )
	- return;
	-
	- // WRITING TENSORS TO FILE
	- MBI_INFO << "Writing data ";
	- typedef itk::ImageFileWriter<VarVecImgType> WriterType;
	- WriterType::Pointer writer = WriterType::New();
	- writer->SetFileName(filename.ascii());
	- writer->SetInput(vecImg);
	- writer->Update();
	-}
	-
	-void QmitkDiffusionTensorEstimation::DirectionVolumesLoadButton()
	-{
	- // SELECT FOLDER DIALOG
	- QFileDialog* w = new QFileDialog( this->m_Controls, "Select DWI data file", TRUE );
	- w->setMode( QFileDialog::ExistingFiles );
	- w->setFilter( "Nrrd Images (.nrrd .nhdr)" );
	-
	- // RETRIEVE SELECTION
	- if ( w->exec() != QDialog::Accepted )
	- return;
	-
	- QStringList filenames = w->selectedFiles();
	- QStringList::Iterator it = filenames.begin();
	- while( it != filenames.end() ) {
	- std::string filename = ( *it ).ascii();
	- ++it;
	-
	- // READING VOLUME
	- typedef itk::Image<itk::Vector<TTensorPixelType,3>,3 > IType;
	- typedef itk::ImageFileReader<IType> ReaderType;
	- ReaderType::Pointer reader = ReaderType::New();
	- reader->SetFileName(filename);
	- try
	- {
	- reader->Update();
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- MBI_INFO << e << std::endl;
	- }
	-
	- // Tensorvolume
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk( reader->GetOutput() );
	- image->SetVolume( reader->GetOutput()->GetBufferPointer() );
	- mitk::DataNode::Pointer node=mitk::DataNode::New();
	- node->SetData( image );
	- mitk::DataStorage::GetInstance()->Add(node);
	- SetDefaultNodeProperties(node, itksys::SystemTools::GetFilenameName(filename));
	- node->SetProperty( "IsDirectionVolume", mitk::BoolProperty::New( true ) );
	-
	- mitk::VectorImageMapper2D::Pointer mapper =
	- mitk::VectorImageMapper2D::New();
	- node->SetMapper(1,mapper);
	-
	- TreeChanged();
	- }
	-}
	-
	-void QmitkDiffusionTensorEstimation::DirectionVolumesRemoveButton()
	-{
	- m_DirectionVolumesDataTreeFilter->DeleteSelectedItems();
	-}
	-
	-void QmitkDiffusionTensorEstimation::TensorEstimationTeemEstimateButton()
	-{
	- try
	- {
	- itk::TimeProbe clock;
	-
	- const mitk::DataTreeFilter::ItemSet* selectedItems
	- = m_DiffusionVolumesDataTreeFilter->GetSelectedItems();
	-
	-
	- int nrFiles = selectedItems->size();
	- if (!nrFiles) return;
	-
	- QString status;
	- mitk::ProgressBar::GetInstance()->AddStepsToDo(nrFiles);
	-
	- mitk::DataTreeFilter::ItemSet::const_iterator itemiter( selectedItems->begin() );
	- mitk::DataTreeFilter::ItemSet::const_iterator itemiterend( selectedItems->end() );
	-
	- std::vector<mitk::DataNode::Pointer> nodes;
	- while ( itemiter != itemiterend ) // for all items
	- {
	-
	- mitk::DiffusionVolumes<DiffusionPixelType>* vols =
	- static_cast<mitk::DiffusionVolumes<DiffusionPixelType>*>(
	- (*itemiter)->GetNode()->GetData());
	-
	- std::string nodename = (*itemiter)->GetProperty("name");
	- itemiter++;
	-
	- // TENSOR RECONSTRUCTION
	- clock.Start();
	- MBI_INFO << "Teem Tensor reconstruction ";
	- mitk::StatusBar::GetInstance()->DisplayText(status.sprintf(
	- "Teem Tensor reconstruction for %s", nodename.c_str()));
	- typedef mitk::TeemDiffusionTensor3DReconstructionImageFilter<
	- DiffusionPixelType, TTensorPixelType > TensorReconstructionImageFilterType;
	- TensorReconstructionImageFilterType::Pointer tensorReconstructionFilter =
	- TensorReconstructionImageFilterType::New();
	- tensorReconstructionFilter->SetInput( vols );
	- tensorReconstructionFilter->SetEstimateErrorImage( m_Controls->m_TensorEstimationTeemErrorImage->isChecked() );
	- if(!m_Controls->m_TensorEstimationTeemSigmaEdit->text().contains(QString("NaN")))
	- tensorReconstructionFilter->SetSigma( m_Controls->m_TensorEstimationTeemSigmaEdit->text().toFloat() );
	- switch(m_Controls->m_TensorEstimationTeemEstimationMethodCombo->currentItem())
	- {
	- case 0:
	- tensorReconstructionFilter->SetEstimationMethod(mitk::TeemTensorEstimationMethodsLLS);
	- break;
	- case 1:
	- tensorReconstructionFilter->SetEstimationMethod(mitk::TeemTensorEstimationMethodsNLS);
	- break;
	- case 2:
	- tensorReconstructionFilter->SetEstimationMethod(mitk::TeemTensorEstimationMethodsWLS);
	- break;
	- case 3:
	- tensorReconstructionFilter->SetEstimationMethod(mitk::TeemTensorEstimationMethodsMLE);
	- break;
	- default:
	- tensorReconstructionFilter->SetEstimationMethod(mitk::TeemTensorEstimationMethodsLLS);
	- }
	- tensorReconstructionFilter->SetNumIterations( m_Controls->m_TensorEstimationTeemNumItsSpin->value() );
	- if(!m_Controls->m_TensorEstimationTeemConfThresholdEdit->text().contains(QString("NaN")))
	- tensorReconstructionFilter->SetConfidenceThreshold( m_Controls->m_TensorEstimationTeemConfThresholdEdit->text().toDouble() );
	- tensorReconstructionFilter->SetConfidenceFuzzyness( m_Controls->m_TensorEstimationTeemFuzzyEdit->text().toFloat() );
	- tensorReconstructionFilter->SetMinPlausibleValue( m_Controls->m_TensorEstimationTeemMinValEdit->text().toDouble() );
	- tensorReconstructionFilter->Update();
	- clock.Stop();
	- MBI_DEBUG << "took " << clock.GetMeanTime() << "s.";
	-
	- // TENSORS TO DATATREE
	- //mitk::DataNode::Pointer node=mitk::DataNode::New();
	- //node->SetData( tensorReconstructionFilter->GetOutput() );
	- //mitk::DataStorage::GetInstance()->Add(node);
	- //SetDefaultNodeProperties(node, nodename.append(" tensors"));
	- //node->SetProperty( "IsConfidenceTensorVolume", mitk::BoolProperty::New( true ) );
	-
	- mitk::DataNode::Pointer node2=mitk::DataNode::New();
	- node2->SetData( tensorReconstructionFilter->GetOutputItk() );
	- SetDefaultNodeProperties(node2, nodename.append(" (itk)"));
	- node2->SetProperty( "IsTensorVolume", mitk::BoolProperty::New( true ) );
	- nodes.push_back(node2);
	-
	- mitk::ProgressBar::GetInstance()->Progress();
	-
	- }
	-
	- std::vector<mitk::DataNode::Pointer>::iterator nodeIt;
	- for(nodeIt = nodes.begin(); nodeIt != nodes.end(); ++nodeIt)
	- mitk::DataStorage::GetInstance()->Add(*nodeIt);
	-
	- mitk::ProgressBar::GetInstance()->Progress();
	- TreeChanged();
	- m_Controls->update();
	-
	- mitk::StatusBar::GetInstance()->DisplayText(status.sprintf("Finished Processing %d Files", nrFiles));
	-
	- }
	- catch (itk::ExceptionObject &ex)
	- {
	- MBI_INFO << ex;
	- return ;
	- }
	-}
	-
	-void QmitkDiffusionTensorEstimation::TensorEstimationButton()
	-{
	- try
	- {
	- itk::TimeProbe clock;
	-
	- const mitk::DataTreeFilter::ItemSet* selectedItems
	- = m_DiffusionVolumesDataTreeFilter->GetSelectedItems();
	-
	- int nrFiles = selectedItems->size();
	- if (!nrFiles) return;
	-
	- QString status;
	- mitk::ProgressBar::GetInstance()->AddStepsToDo(nrFiles);
	-
	- mitk::DataTreeFilter::ItemSet::const_iterator itemiter( selectedItems->begin() );
	- mitk::DataTreeFilter::ItemSet::const_iterator itemiterend( selectedItems->end() );
	-
	- std::vector<mitk::DataNode::Pointer> nodes;
	- while ( itemiter != itemiterend ) // for all items
	- {
	-
	- mitk::DiffusionVolumes<DiffusionPixelType>* vols =
	- static_cast<mitk::DiffusionVolumes<DiffusionPixelType>*>(
	- (*itemiter)->GetNode()->GetData());
	-
	- std::string nodename = (*itemiter)->GetProperty("name");
	- itemiter++;
	-
	- // TENSOR RECONSTRUCTION
	- clock.Start();
	- MBI_INFO << "Tensor reconstruction ";
	- mitk::StatusBar::GetInstance()->DisplayText(status.sprintf(
	- "Tensor reconstruction for %s", nodename.c_str()));
	- typedef itk::DiffusionTensor3DReconstructionImageFilter<
	- DiffusionPixelType, DiffusionPixelType, TTensorPixelType > TensorReconstructionImageFilterType;
	- TensorReconstructionImageFilterType::Pointer tensorReconstructionFilter =
	- TensorReconstructionImageFilterType::New();
	- tensorReconstructionFilter->SetGradientImage( vols->GetDirections(), vols->GetImage() );
	- tensorReconstructionFilter->SetNumberOfThreads( m_Controls->m_TensorEstimationNumberThreadsSpinbox->value() );
	- tensorReconstructionFilter->SetBValue(vols->GetB_Value());
	- tensorReconstructionFilter->SetThreshold( m_Controls->m_TensorEstimationThreasholdEdit->text().toFloat() );
	- tensorReconstructionFilter->Update();
	- clock.Stop();
	- MBI_DEBUG << "took " << clock.GetMeanTime() << "s.";
	-
	- // TENSORS TO DATATREE
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk( tensorReconstructionFilter->GetOutput() );
	- image->SetVolume( tensorReconstructionFilter->GetOutput()->GetBufferPointer() );
	- mitk::DataNode::Pointer node=mitk::DataNode::New();
	- node->SetData( image );
	- SetDefaultNodeProperties(node, nodename.append(" tensors"));
	- node->SetProperty( "IsTensorVolume", mitk::BoolProperty::New( true ) );
	- nodes.push_back(node);
	-
	- mitk::ProgressBar::GetInstance()->Progress();
	-
	- }
	-
	- std::vector<mitk::DataNode::Pointer>::iterator nodeIt;
	- for(nodeIt = nodes.begin(); nodeIt != nodes.end(); ++nodeIt)
	- mitk::DataStorage::GetInstance()->Add(*nodeIt);
	-
	- mitk::ProgressBar::GetInstance()->Progress();
	- TreeChanged();
	- m_Controls->update();
	-
	- mitk::StatusBar::GetInstance()->DisplayText(status.sprintf("Finished Processing %d Files", nrFiles));
	-
	- }
	- catch (itk::ExceptionObject &ex)
	- {
	- MBI_INFO << ex;
	- return ;
	- }
	-}
	-
	-void QmitkDiffusionTensorEstimation::OdfReconstructionButton()
	-{
	- try
	- {
	- itk::TimeProbe clock;
	-
	- const mitk::DataTreeFilter::ItemSet* selectedItems
	- = m_DiffusionVolumesDataTreeFilter->GetSelectedItems();
	-
	- int nrFiles = selectedItems->size();
	- if (!nrFiles) return;
	-
	- QString status;
	- mitk::ProgressBar::GetInstance()->AddStepsToDo(nrFiles);
	-
	- mitk::DataTreeFilter::ItemSet::const_iterator itemiter( selectedItems->begin() );
	- mitk::DataTreeFilter::ItemSet::const_iterator itemiterend( selectedItems->end() );
	-
	- std::vector<mitk::DataNode::Pointer> nodes;
	- while ( itemiter != itemiterend ) // for all items
	- {
	-
	- mitk::DiffusionVolumes<DiffusionPixelType>* vols =
	- static_cast<mitk::DiffusionVolumes<DiffusionPixelType>*>(
	- (*itemiter)->GetNode()->GetData());
	-
	- std::string nodename = (*itemiter)->GetProperty("name");
	- ++itemiter;
	-
	- // Odf RECONSTRUCTION
	- clock.Start();
	- MBI_INFO << "Odf reconstruction ";
	- mitk::StatusBar::GetInstance()->DisplayText(status.sprintf(
	- "Odf reconstruction for %s", nodename.c_str()));
	-
	- typedef itk::DiffusionQballReconstructionImageFilter<
	- DiffusionPixelType, DiffusionPixelType, TTensorPixelType, odfsize>
	- //int NOdfDirections = 162,
	- QballReconstructionImageFilterType;
	- QballReconstructionImageFilterType::Pointer filter =
	- QballReconstructionImageFilterType::New();
	- filter->SetGradientImage( vols->GetDirections(), vols->GetImage() );
	- filter->SetNumberOfThreads( m_Controls->m_OdfReconstructionNumberThreadsSpinbox->value() );
	- filter->SetBValue(vols->GetB_Value());
	- filter->SetThreshold( m_Controls->m_OdfReconstructionThreasholdEdit->text().toFloat() );
	-
	- int normalization = m_Controls->m_OdfReconstructionPostprocessingMethod->currentItem();
	- switch(normalization)
	- {
	- case 0:
	- {
	- filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_STANDARD);
	- break;
	- }
	- case 1:
	- {
	- filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_B_ZERO_B_VALUE);
	- break;
	- }
	- case 2:
	- {
	- filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_B_ZERO);
	- break;
	- }
	- case 3:
	- {
	- filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_NONE);
	- break;
	- }
	- default:
	- {
	- filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_STANDARD);
	- }
	- }
	-
	- filter->Update();
	- clock.Stop();
	- MBI_DEBUG << "took " << clock.GetMeanTime() << "s." << std::endl;
	-
	- // ODFs TO DATATREE
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk( filter->GetOutput() );
	- //image->SetImportVolume( filter->GetOutput()->GetBufferPointer(), 0, 0, mitk::Image::ImportMemoryManagementType::ManageMemory );
	- image->SetVolume( filter->GetOutput()->GetBufferPointer() );
	- mitk::DataNode::Pointer node=mitk::DataNode::New();
	- node->SetData( image );
	- QString newname;
	- newname = newname.append(nodename.c_str());
	- newname = newname.append("_QN%1").arg(normalization);
	- SetDefaultNodeProperties(node, newname.ascii());
	- node->SetProperty( "IsOdfVolume", mitk::BoolProperty::New( true ) );
	- nodes.push_back(node);
	-
	- // B-Zero TO DATATREE
	- mitk::Image::Pointer image4 = mitk::Image::New();
	- image4->InitializeByItk( filter->GetBZeroImage().GetPointer() );
	- image4->SetVolume( filter->GetBZeroImage()->GetBufferPointer() );
	- mitk::DataNode::Pointer node4=mitk::DataNode::New();
	- node4->SetData( image4 );
	- SetDefaultNodeProperties(node4, nodename.append("B0"));
	- nodes.push_back(node4);
	-
	- mitk::ProgressBar::GetInstance()->Progress();
	-
	- }
	-
	- std::vector<mitk::DataNode::Pointer>::iterator nodeIt;
	- for(nodeIt = nodes.begin(); nodeIt != nodes.end(); ++nodeIt)
	- mitk::DataStorage::GetInstance()->Add(*nodeIt);
	-
	- mitk::StatusBar::GetInstance()->DisplayText(status.sprintf("Finished Processing %d Files", nrFiles));
	- m_DataTreeIterator->GetTree()->Modified();
	- this->GetRenderWindowPart()->RequestUpdate();
	- TreeChanged();
	- m_Controls->update();
	-
	- }
	- catch (itk::ExceptionObject &ex)
	- {
	- MBI_INFO << ex;
	- return ;
	- }
	-}
	-
	-template<int L>
	-void QmitkDiffusionTensorEstimation::ReconstructAnalytically(
	- mitk::DiffusionVolumes<DiffusionPixelType>* vols, float lambda,
	- std::string nodename, std::vector<mitk::DataNode::Pointer>* nodes)
	-{
	- typedef itk::AnalyticalDiffusionQballReconstructionImageFilter
	- <DiffusionPixelType,DiffusionPixelType,TTensorPixelType,L,odfsize> FilterType;
	- typename FilterType::Pointer filter = FilterType::New();
	- filter->SetGradientImage( vols->GetDirections(), vols->GetImage() );
	- filter->SetNumberOfThreads( m_Controls->m_OdfReconstructionNumberThreadsAnalyticalSpinbox->value() );
	- filter->SetBValue(vols->GetB_Value());
	- filter->SetThreshold( m_Controls->m_OdfReconstructionThreasholdAnalyticalEdit->text().toFloat() );
	- filter->SetLambda(lambda);
	- filter->SetAdcProfileOnly(m_Controls->m_OdfReconstructionAdcOnlyCheckbox->isChecked());
	- int normalization = m_Controls->m_OdfReconstructionPostprocessingMethodAnalytical->currentItem();
	- switch(normalization)
	- {
	- case 0:
	- {
	- filter->SetNormalizationMethod(FilterType::QBAR_STANDARD);
	- break;
	- }
	- case 1:
	- {
	- filter->SetNormalizationMethod(FilterType::QBAR_B_ZERO_B_VALUE);
	- break;
	- }
	- case 2:
	- {
	- filter->SetNormalizationMethod(FilterType::QBAR_B_ZERO);
	- break;
	- }
	- case 3:
	- {
	- filter->SetNormalizationMethod(FilterType::QBAR_NONE);
	- break;
	- }
	- default:
	- {
	- filter->SetNormalizationMethod(FilterType::QBAR_STANDARD);
	- }
	- }
	-
	- filter->Update();
	-
	- // ODFs TO DATATREE
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk( filter->GetOutput() );
	- image->SetVolume( filter->GetOutput()->GetBufferPointer() );
	- mitk::DataNode::Pointer node=mitk::DataNode::New();
	- node->SetData( image );
	- nodes->push_back(node);
	- QString newname;
	- newname = newname.append(nodename.c_str());
	- newname = newname.append("_QA%1").arg(normalization);
	- SetDefaultNodeProperties(node, newname.ascii());
	- node->SetProperty( "IsOdfVolume", mitk::BoolProperty::New( true ) );
	-
	- // B-Zero TO DATATREE
	- mitk::Image::Pointer image4 = mitk::Image::New();
	- image4->InitializeByItk( filter->GetBZeroImage().GetPointer() );
	- image4->SetVolume( filter->GetBZeroImage()->GetBufferPointer() );
	- mitk::DataNode::Pointer node4=mitk::DataNode::New();
	- node4->SetData( image4 );
	- nodes->push_back(node4);
	- SetDefaultNodeProperties(node4, nodename.append("B0"));
	-
	-}
	-
	-void QmitkDiffusionTensorEstimation::OdfReconstructionAnalyticalButton()
	-{
	- try
	- {
	- itk::TimeProbe clock;
	-
	- const mitk::DataTreeFilter::ItemSet* selectedItems
	- = m_DiffusionVolumesDataTreeFilter->GetSelectedItems();
	-
	- int nrFiles = selectedItems->size();
	- if (!nrFiles) return;
	-
	- std::vector<float> lambdas;
	- float minLambda = m_Controls->m_OdfReconstructionLambdaLineEdit->text().toFloat();
	- if(m_Controls->m_OdfReconstructionLambdaMultiCheckbox->isChecked())
	- {
	- float stepLambda = m_Controls->m_OdfReconstructionLambdaStepLineEdit->text().toFloat();
	- float maxLambda = m_Controls->m_QBallReconstructionLambdaMaxLineEdit->text().toFloat();
	- for(float l=minLambda; l<maxLambda; l+=stepLambda)
	- {
	- lambdas.push_back(l);
	- }
	- }
	- int nLambdas = lambdas.size();
	- if(nLambdas == 0)
	- {
	- lambdas.push_back(minLambda);
	- nLambdas = 1;
	- }
	-
	- QString status;
	- mitk::ProgressBar::GetInstance()->AddStepsToDo(nrFiles*nLambdas);
	-
	- mitk::DataTreeFilter::ItemSet::const_iterator itemiter( selectedItems->begin() );
	- mitk::DataTreeFilter::ItemSet::const_iterator itemiterend( selectedItems->end() );
	-
	- std::vector<mitk::DataNode::Pointer>* nodes
	- = new std::vector<mitk::DataNode::Pointer>();
	- while ( itemiter != itemiterend ) // for all items
	- {
	-
	- mitk::DiffusionVolumes<DiffusionPixelType>* vols =
	- static_cast<mitk::DiffusionVolumes<DiffusionPixelType>*>(
	- (*itemiter)->GetNode()->GetData());
	-
	- std::string nodename = (*itemiter)->GetProperty("name");
	- itemiter++;
	-
	- // Odf RECONSTRUCTION
	- clock.Start();
	- MBI_INFO << "Odf reconstruction ";
	- mitk::StatusBar::GetInstance()->DisplayText(status.sprintf(
	- "Odf reconstruction for %s", nodename.c_str()));
	-
	- for(int i=0; i<nLambdas; i++)
	- {
	-
	- float currentLambda = lambdas[i];
	-
	- switch(m_Controls->m_OdfReconstructionMaxLLevelComboBox->currentItem())
	- {
	- case 0:
	- {
	- ReconstructAnalytically<2>(vols, currentLambda, nodename, nodes);
	- break;
	- }
	- case 1:
	- {
	- ReconstructAnalytically<4>(vols, currentLambda, nodename, nodes);
	- break;
	- }
	- case 2:
	- {
	- ReconstructAnalytically<6>(vols, currentLambda, nodename, nodes);
	- break;
	- }
	- case 3:
	- {
	- ReconstructAnalytically<8>(vols, currentLambda, nodename, nodes);
	- break;
	- }
	- }
	-
	- clock.Stop();
	- MBI_DEBUG << "took " << clock.GetMeanTime() << "s.";
	- mitk::ProgressBar::GetInstance()->Progress();
	-
	- }
	- }
	-
	- std::vector<mitk::DataNode::Pointer>::iterator nodeIt;
	- for(nodeIt = nodes->begin(); nodeIt != nodes->end(); ++nodeIt)
	- mitk::DataStorage::GetInstance()->Add(*nodeIt);
	-
	- m_DataTreeIterator->GetTree()->Modified();
	- this->GetRenderWindowPart()->RequestUpdate();
	- TreeChanged();
	- m_Controls->update();
	-
	- mitk::StatusBar::GetInstance()->DisplayText(status.sprintf("Finished Processing %d Files", nrFiles));
	-
	- }
	- catch (itk::ExceptionObject &ex)
	- {
	- MBI_INFO << ex;
	- return ;
	- }
	-}
	-
	-void QmitkDiffusionTensorEstimation::StandardAlgorithmsFAButton()
	-{
	- itk::TimeProbe clock;
	- QString status;
	- const mitk::DataTreeFilter::Item* item
	- = m_TensorVolumesDataTreeFilter->GetSelectedItem();
	- if(!item)return;
	-
	- mitk::Image* vol =
	- static_cast<mitk::Image*>(item->GetNode()->GetData());
	- itk::Image<TensorPixelType, 3>::Pointer itkvol = itk::Image<TensorPixelType, 3>::New();
	- mitk::CastToItkImage<TensorImageType>(vol, itkvol);
	- std::string nodename = item->GetProperty("name");
	-
	- // COMPUTE FA
	- clock.Start();
	- MBI_INFO << "Computing FA ";
	- mitk::StatusBar::GetInstance()->DisplayText(status.sprintf(
	- "Computing FA for %s", nodename.c_str()));
	- typedef TensorPixelType::RealValueType RealValueType;
	- typedef itk::Image< RealValueType, 3 > FAImageType;
	- typedef itk::TensorFractionalAnisotropyImageFilter<
	- TensorImageType, FAImageType > FAFilterType;
	- FAFilterType::Pointer fractionalAnisotropyFilter = FAFilterType::New();
	- fractionalAnisotropyFilter->SetInput( itkvol );
	-
	- typedef itk::ShiftScaleImageFilter<FAImageType, FAImageType>
	- ShiftScaleFilterType;
	- ShiftScaleFilterType::Pointer multi =
	- ShiftScaleFilterType::New();
	- multi->SetShift(0);
	- multi->SetScale(200);//itk::NumericTraits<RealValueType>::max()
	- multi->SetInput(fractionalAnisotropyFilter->GetOutput());
	- multi->Update();
	- clock.Stop();
	- MBI_DEBUG << "took " << clock.GetMeanTime() << "s.";
	-
	- // FA TO DATATREE
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk( multi->GetOutput() );
	- image->SetVolume( multi->GetOutput()->GetBufferPointer() );
	- mitk::DataNode::Pointer node=mitk::DataNode::New();
	- node->SetData( image );
	- mitk::DataStorage::GetInstance()->Add(node);
	- SetDefaultNodeProperties(node, nodename.append(" FA"));
	- node->SetProperty( "IsFAVolume", mitk::BoolProperty::New( true ) );
	-
	- mitk::StatusBar::GetInstance()->DisplayText("Computation complete.");
	-
	- m_DataTreeIterator->GetTree()->Modified();
	- this->GetRenderWindowPart()->RequestUpdate();
	- TreeChanged();
	- m_Controls->update();
	-}
	-
	-void QmitkDiffusionTensorEstimation::StandardAlgorithmsRAButton()
	-{
	- itk::TimeProbe clock;
	- QString status;
	- const mitk::DataTreeFilter::Item* item
	- = m_TensorVolumesDataTreeFilter->GetSelectedItem();
	- if(!item)return;
	-
	- mitk::Image* vol =
	- static_cast<mitk::Image*>(item->GetNode()->GetData());
	- itk::Image<TensorPixelType, 3>::Pointer itkvol = itk::Image<TensorPixelType, 3>::New();
	- mitk::CastToItkImage<TensorImageType>(vol, itkvol);
	- std::string nodename = item->GetProperty("name");
	-
	- // COMPUTE RA
	- clock.Start();
	- MBI_INFO << "Computing RA ";
	- mitk::StatusBar::GetInstance()->DisplayText(status.sprintf(
	- "Computing RA for %s", nodename.c_str()));
	- typedef TensorPixelType::RealValueType RealValueType;
	- typedef itk::Image< RealValueType, 3 > RAImageType;
	- typedef itk::TensorRelativeAnisotropyImageFilter<
	- TensorImageType, RAImageType > RAFilterType;
	- RAFilterType::Pointer relativeAnisotropyFilter = RAFilterType::New();
	- relativeAnisotropyFilter->SetInput( itkvol );
	- relativeAnisotropyFilter->Update();
	- clock.Stop();
	- MBI_DEBUG << "took " << clock.GetMeanTime() << "s.";
	-
	- // FA TO DATATREE
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk( relativeAnisotropyFilter->GetOutput() );
	- image->SetVolume( relativeAnisotropyFilter->GetOutput()->GetBufferPointer() );
	- mitk::DataNode::Pointer node=mitk::DataNode::New();
	- node->SetData( image );
	- mitk::DataStorage::GetInstance()->Add(node);
	- SetDefaultNodeProperties(node, nodename.append(" RA"));
	- node->SetProperty( "IsRAVolume", mitk::BoolProperty::New( true ) );
	-
	- mitk::StatusBar::GetInstance()->DisplayText("Computation complete.");
	-
	- m_DataTreeIterator->GetTree()->Modified();
	- this->GetRenderWindowPart()->RequestUpdate();
	- TreeChanged();
	- m_Controls->update();
	-
	-}
	-
	-void QmitkDiffusionTensorEstimation::StandardAlgorithmsDirectionButton()
	-{
	-
	- itk::TimeProbe clock;
	- QString status;
	- const mitk::DataTreeFilter::Item* item
	- = m_TensorVolumesDataTreeFilter->GetSelectedItem();
	- if(!item)return;
	-
	- typedef itk::DiffusionTensor3D<TTensorPixelType> TensorType;
	- typedef itk::Image<TensorType,3> TensorImgType;
	- mitk::Image* vol =
	- static_cast<mitk::Image*>(item->GetNode()->GetData());
	- TensorImgType::Pointer itkvol = TensorImgType::New();
	- mitk::CastToItkImage<TensorImgType>(vol, itkvol);
	- std::string nodename = item->GetProperty("name");
	-
	- clock.Start();
	- MBI_INFO << "Computing Diffusion Direction ";
	- mitk::StatusBar::GetInstance()->DisplayText(status.sprintf(
	- "Computing Diffusion Direction for %s", nodename.c_str()));
	-
	- typedef itk::DiffusionTensorPrincipleDirectionImageFilter<TTensorPixelType,TTensorPixelType>
	- FilterType;
	- FilterType::Pointer filter
	- = FilterType::New();
	- filter->SetInput(itkvol);
	- filter->SetNumberOfThreads(4);
	- filter->Update();
	- itk::ImageRegionIterator<FilterType::OutputImageType>
	- it (filter->GetOutput(),
	- filter->GetOutput()->GetLargestPossibleRegion() );
	- it = it.Begin();
	-
	- // VECTORFIELD
	- MBI_DEBUG << "Converting to Vectorfield";
	-
	- typedef itk::Image<itk::Vector<TTensorPixelType,3>, 3> VecImgType2;
	- VecImgType2::Pointer vecImg5 = VecImgType2::New();
	- vecImg5->SetSpacing( itkvol->GetSpacing() ); // Set the image spacing
	- vecImg5->SetOrigin( itkvol->GetOrigin() ); // Set the image origin
	- vecImg5->SetDirection( itkvol->GetDirection() ); // Set the image direction
	- vecImg5->SetLargestPossibleRegion( itkvol->GetLargestPossibleRegion());
	- vecImg5->SetBufferedRegion( vecImg5->GetLargestPossibleRegion() );
	- vecImg5->Allocate();
	- itk::ImageRegionIterator<VecImgType2> ot5 (vecImg5, vecImg5->GetLargestPossibleRegion() );
	- ot5 = ot5.Begin();
	-
	- typedef FilterType::OutputImageType::PixelType VecPixType;
	- for (it = it.Begin(); !it.IsAtEnd(); ++it)
	- {
	- VecPixType vec = it.Get();
	- itk::Vector<TTensorPixelType,3> pix;
	- TTensorPixelType uvec[3] = {(TTensorPixelType)(vec[0]),(TTensorPixelType)(vec[1]),(TTensorPixelType)(vec[2])};
	- //TTensorPixelType uvec[3] = {(TTensorPixelType)(vec[1]),(TTensorPixelType)(-vec[0]),(TTensorPixelType)(vec[2])};
	- pix = uvec;
	- ot5.Set(pix);
	- ++ot5;
	- }
	-
	- // Vectors TO DATATREE
	- mitk::Image::Pointer image5 = mitk::Image::New();
	- image5->InitializeByItk( vecImg5.GetPointer() );
	- image5->SetVolume( vecImg5->GetBufferPointer() );
	- mitk::DataNode::Pointer node5=mitk::DataNode::New();
	- node5->SetData( image5 );
	- node5->SetName( nodename.append(" vecs").c_str());
	- mitk::DataStorage::GetInstance()->Add(node5);
	-
	- node5->SetProperty( "IsDirectionVolume", mitk::BoolProperty::New( true ) );
	- node5->SetProperty( "NormalizeVecs", mitk::BoolProperty::New( true ) );
	- node5->SetProperty( "Scale", mitk::FloatProperty::New( 1.0 ) );
	- node5->SetProperty( "LineWidth", mitk::FloatProperty::New( 1 ) );
	-
	- mitk::VectorImageMapper2D::Pointer vecMapper5 =
	- mitk::VectorImageMapper2D::New();
	- node5->SetMapper(1,vecMapper5);
	-
	- m_DataTreeIterator->GetTree()->Modified();
	- this->GetRenderWindowPart()->RequestUpdate();
	- TreeChanged();
	- m_Controls->update();
	-
	-}
	-
	-void QmitkDiffusionTensorEstimation::OdfStandardAlgorithmsGFAButton()
	-{
	- itk::TimeProbe clock;
	- QString status;
	-
	- const mitk::DataTreeFilter::ItemSet* selectedItems
	- = m_OdfVolumesDataTreeFilter->GetSelectedItems();
	-
	- int nrFiles = selectedItems->size();
	- if (!nrFiles) return;
	-
	- mitk::DataTreeFilter::ItemSet::const_iterator itemiter( selectedItems->begin() );
	- mitk::DataTreeFilter::ItemSet::const_iterator itemiterend( selectedItems->end() );
	-
	- std::vector<mitk::DataNode::Pointer> nodes;
	- while ( itemiter != itemiterend ) // for all items
	- {
	-
	- typedef itk::Vector<TTensorPixelType,odfsize> OdfVectorType;
	- typedef itk::Image<OdfVectorType,3> OdfVectorImgType;
	- mitk::Image* vol =
	- static_cast<mitk::Image>((itemiter)->GetNode()->GetData());
	- OdfVectorImgType::Pointer itkvol = OdfVectorImgType::New();
	- mitk::CastToItkImage<OdfVectorImgType>(vol, itkvol);
	-
	- std::string nodename = (*itemiter)->GetProperty("name");
	- ++itemiter;
	-
	- float p1 = m_Controls->m_OdfStandardAlgorithmsGFAParam1->text().toFloat();
	- float p2 = m_Controls->m_OdfStandardAlgorithmsGFAParam2->text().toFloat();
	-
	- // COMPUTE RA
	- clock.Start();
	- MBI_INFO << "Computing GFA ";
	- mitk::StatusBar::GetInstance()->DisplayText(status.sprintf(
	- "Computing GFA for %s", nodename.c_str()));
	- typedef OdfVectorType::ValueType RealValueType;
	- typedef itk::Image< RealValueType, 3 > RAImageType;
	- typedef itk::DiffusionOdfGeneralizedFaImageFilter<TTensorPixelType,TTensorPixelType,odfsize>
	- GfaFilterType;
	- GfaFilterType::Pointer gfaFilter = GfaFilterType::New();
	- gfaFilter->SetInput(itkvol);
	- gfaFilter->SetNumberOfThreads(4);
	-
	- double scale = 1;
	- std::string newname;
	- newname.append(nodename);
	- newname.append(" GFA");
	- switch(m_Controls->m_OdfStandardAlgorithmsGFAMethod->currentItem())
	- {
	- case 0:
	- {
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_STANDARD);
	- newname.append("00");
	- scale = 200.0;
	- break;
	- }
	- case 1:
	- {
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_QUANTILES_HIGH_LOW);
	- newname.append("01");
	- scale = 200.0;
	- break;
	- }
	- case 2:
	- {
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_QUANTILE_HIGH);
	- newname.append("02");
	- scale = 200.0;
	- break;
	- }
	- case 3:
	- {
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_MAX_ODF_VALUE);
	- newname.append("03");
	- scale = 200.0;
	- break;
	- }
	- case 4:
	- {
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_DECONVOLUTION_COEFFS);
	- newname.append("04");
	- scale = 200.0;
	- break;
	- }
	- case 5:
	- {
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_MIN_MAX_NORMALIZED_STANDARD);
	- newname.append("05");
	- scale = 200.0;
	- break;
	- }
	- case 6:
	- {
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_NORMALIZED_ENTROPY);
	- newname.append("06");
	- break;
	- }
	- case 7:
	- {
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_NEMATIC_ORDER_PARAMETER);
	- newname.append("07");
	- scale = 200.0;
	- break;
	- }
	- case 8:
	- {
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_QUANTILES_LOW_HIGH);
	- newname.append("08");
	- scale = 200.0;
	- break;
	- }
	- case 9:
	- {
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_QUANTILE_LOW);
	- newname.append("09");
	- scale = 200.0;
	- break;
	- }
	- case 10:
	- {
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_MIN_ODF_VALUE);
	- newname.append("10");
	- scale = 200.0;
	- break;
	- }
	- case 11:
	- {
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_STD_BY_MAX);
	- newname.append("11");
	- scale = 200.0;
	- break;
	- }
	- case 12:
	- {
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_PRINCIPLE_CURVATURE);
	- newname.append("12");
	- gfaFilter->SetParam1(p1);
	- scale = 200.0;
	- break;
	- }
	- case 13:
	- {
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_GENERALIZED_GFA);
	- QString paramString;
	- paramString = paramString.append(" K%1P%2").arg(p1).arg(p2);
	- newname.append("13").append(paramString.ascii());
	- gfaFilter->SetParam1(p1);
	- gfaFilter->SetParam2(p2);
	- scale = 200.0;
	- break;
	- }
	- default:
	- {
	- newname.append("0");
	- gfaFilter->SetComputationMethod(GfaFilterType::GFA_STANDARD);
	- scale = 200.0;
	- }
	- }
	- gfaFilter->Update();
	- clock.Stop();
	- MBI_DEBUG << "took " << clock.GetMeanTime() << "s.";
	-
	- typedef itk::Image<TTensorPixelType, 3> ImgType;
	- ImgType::Pointer img = ImgType::New();
	- img->SetSpacing( gfaFilter->GetOutput()->GetSpacing() ); // Set the image spacing
	- img->SetOrigin( gfaFilter->GetOutput()->GetOrigin() ); // Set the image origin
	- img->SetDirection( gfaFilter->GetOutput()->GetDirection() ); // Set the image direction
	- img->SetLargestPossibleRegion( gfaFilter->GetOutput()->GetLargestPossibleRegion());
	- img->SetBufferedRegion( gfaFilter->GetOutput()->GetLargestPossibleRegion() );
	- img->Allocate();
	- itk::ImageRegionIterator<ImgType> ot (img, img->GetLargestPossibleRegion() );
	- ot = ot.Begin();
	- itk::ImageRegionConstIterator<GfaFilterType::OutputImageType> it
	- (gfaFilter->GetOutput(), gfaFilter->GetOutput()->GetLargestPossibleRegion() );
	- it = it.Begin();
	-
	- for (it = it.Begin(); !it.IsAtEnd(); ++it)
	- {
	- GfaFilterType::OutputImageType::PixelType val = it.Get();
	- ot.Set(val * scale);
	- ++ot;
	- }
	-
	-
	- // GFA TO DATATREE
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk( img.GetPointer() );
	- image->SetVolume( img->GetBufferPointer() );
	- mitk::DataNode::Pointer node=mitk::DataNode::New();
	- node->SetData( image );
	- nodes.push_back(node);
	- SetDefaultNodeProperties(node, newname.c_str());
	- node->SetProperty( "IsGFAVolume", mitk::BoolProperty::New( true ) );
	-
	- mitk::StatusBar::GetInstance()->DisplayText("Computation complete.");
	-
	- }
	-
	- std::vector<mitk::DataNode::Pointer>::iterator nodeIt;
	- for(nodeIt = nodes.begin(); nodeIt != nodes.end(); ++nodeIt)
	- mitk::DataStorage::GetInstance()->Add(*nodeIt);
	-
	- m_DataTreeIterator->GetTree()->Modified();
	- this->GetRenderWindowPart()->RequestUpdate();
	- TreeChanged();
	- m_Controls->update();
	-
	-}
	-
	-void QmitkDiffusionTensorEstimation::OdfStandardAlgorithmsDirectionButton()
	-{
	-
	- itk::TimeProbe clock;
	- QString status;
	- const mitk::DataTreeFilter::Item* item
	- = m_OdfVolumesDataTreeFilter->GetSelectedItem();
	- if(!item)return;
	-
	- typedef itk::Vector<TTensorPixelType,odfsize> OdfVectorType;
	- typedef itk::Image<OdfVectorType,3> OdfVectorImgType;
	- mitk::Image* vol =
	- static_cast<mitk::Image*>(item->GetNode()->GetData());
	- OdfVectorImgType::Pointer itkvol = OdfVectorImgType::New();
	- mitk::CastToItkImage<OdfVectorImgType>(vol, itkvol);
	- std::string nodename = item->GetProperty("name");
	-
	- clock.Start();
	- MBI_INFO << "Computing Diffusion Direction ";
	- mitk::StatusBar::GetInstance()->DisplayText(status.sprintf(
	- "Computing Diffusion Direction for %s", nodename.c_str()));
	-
	- typedef itk::DiffusionOdfGeneralizedFaImageFilter<TTensorPixelType,TTensorPixelType,odfsize>
	- GfaFilterType;
	- GfaFilterType::Pointer gfaFilter = GfaFilterType::New();
	- gfaFilter->SetInput(itkvol);
	- gfaFilter->SetNumberOfThreads(4);
	- gfaFilter->Update();
	- itk::ImageRegionIterator<GfaFilterType::OutputImageType>
	- itGfa (gfaFilter->GetOutput(),
	- gfaFilter->GetOutput()->GetLargestPossibleRegion() );
	- itGfa = itGfa.Begin();
	-
	- int numdir = m_Controls->m_OdfStandardAlgorithmsOrderSpinbox->value();
	-
	- typedef itk::DiffusionOdfPrincipleDirectionsImageFilter<TTensorPixelType,TTensorPixelType,odfsize>
	- PrincipleDirectionsFilterType;
	- PrincipleDirectionsFilterType::Pointer principleDirectionsFilter
	- = PrincipleDirectionsFilterType::New();
	- principleDirectionsFilter->SetThreshold(m_Controls->m_OdfStandardAlgorithmsProbThreshEdit->text().toFloat());
	- principleDirectionsFilter->SetNrDirectionToExtract(numdir);
	- principleDirectionsFilter->SetInput(itkvol);
	- principleDirectionsFilter->SetNumberOfThreads(m_Controls->m_OdfStandardAlgorithmsNumberThreadsSpinbox->value());
	- principleDirectionsFilter->SetMultiplyGfa(false);
	- principleDirectionsFilter->Update();
	-
	- itk::ImageRegionIterator<PrincipleDirectionsFilterType::OutputImageType>
	- it (principleDirectionsFilter->GetOutput(),
	- principleDirectionsFilter->GetOutput()->GetLargestPossibleRegion() );
	-
	- if(numdir == 0)
	- {
	-
	- MBI_INFO << "Converting to RGB";
	-
	- typedef itk::Image<itk::RGBPixel<uchar>, 3> VecImgType;
	- VecImgType::Pointer vecImg = VecImgType::New();
	- vecImg->SetSpacing( itkvol->GetSpacing() ); // Set the image spacing
	- vecImg->SetOrigin( itkvol->GetOrigin() ); // Set the image origin
	- vecImg->SetDirection( itkvol->GetDirection() ); // Set the image direction
	- vecImg->SetLargestPossibleRegion( itkvol->GetLargestPossibleRegion());
	- vecImg->SetBufferedRegion( vecImg->GetLargestPossibleRegion() );
	- vecImg->Allocate();
	- itk::ImageRegionIterator<VecImgType> ot (vecImg, vecImg->GetLargestPossibleRegion() );
	- ot = ot.Begin();
	-
	- typedef PrincipleDirectionsFilterType::OutputImageType::PixelType VecPixType;
	- for (it = it.Begin(); !it.IsAtEnd(); ++it)
	- {
	- VecPixType vec = it.Get();
	-
	- itk::RGBPixel<uchar> pix;
	- vec=200itGfa.Get();
	- vec[0] = abs(vec[0]);
	- vec[1] = abs(vec[1]);
	- vec[2] = abs(vec[2]);
	- if(vec[0] > 255 \|\| vec[1] > 255 \|\| vec[2] > 255)
	- {
	- // should never get in here
	- double max = vec[0];
	- max = max<vec[1] ? vec[1] : max;
	- max = max<vec[2] ? vec[2] : max;
	- vec /= max/255;
	- }
	- uchar uvec[3] = {(uchar)(vec[0]),(uchar)(vec[1]),(uchar)(vec[2])};
	- pix = uvec;
	- ot.Set(pix);
	- ++ot;
	- ++itGfa;
	- }
	-
	- // RGB TO DATATREE
	- mitk::Image::Pointer image2 = mitk::Image::New();
	- image2->InitializeByItk( vecImg.GetPointer() );
	- image2->SetVolume( vecImg->GetBufferPointer() );
	- mitk::DataNode::Pointer node2=mitk::DataNode::New();
	- node2->SetData( image2 );
	- mitk::DataStorage::GetInstance()->Add(node2);
	- switch(numdir)
	- {
	- case 0:
	- {
	- SetDefaultNodeProperties(node2, nodename.append(" PD0"));
	- break;
	- }
	- case 1:
	- {
	- SetDefaultNodeProperties(node2, nodename.append(" PD1"));
	- }
	- case 2:
	- {
	- SetDefaultNodeProperties(node2, nodename.append(" PD2"));
	- }
	- default:
	- {
	- SetDefaultNodeProperties(node2, nodename.append(" PDn"));
	- }
	- }
	-
	- node2->SetProperty( "IsRGBVolume", mitk::BoolProperty::New( true ) );
	-
	- }
	-
	- // VECTORFIELD
	- MBI_DEBUG << "Converting to Vectorfield";
	-
	- typedef itk::Image<itk::Vector<TTensorPixelType,3>, 3> VecImgType2;
	- VecImgType2::Pointer vecImg5 = VecImgType2::New();
	- vecImg5->SetSpacing( itkvol->GetSpacing() ); // Set the image spacing
	- vecImg5->SetOrigin( itkvol->GetOrigin() ); // Set the image origin
	- vecImg5->SetDirection( itkvol->GetDirection() ); // Set the image direction
	- vecImg5->SetLargestPossibleRegion( itkvol->GetLargestPossibleRegion());
	- vecImg5->SetBufferedRegion( vecImg5->GetLargestPossibleRegion() );
	- vecImg5->Allocate();
	- itk::ImageRegionIterator<VecImgType2> ot5 (vecImg5, vecImg5->GetLargestPossibleRegion() );
	- ot5 = ot5.Begin();
	-
	- typedef PrincipleDirectionsFilterType::OutputImageType::PixelType VecPixType;
	- for (it = it.Begin(); !it.IsAtEnd(); ++it)
	- {
	- VecPixType vec = it.Get();
	- itk::Vector<TTensorPixelType,3> pix;
	- TTensorPixelType uvec[3] = {(TTensorPixelType)(vec[0]),(TTensorPixelType)(vec[1]),(TTensorPixelType)(vec[2])};
	- pix = uvec;
	- ot5.Set(pix);
	- ++ot5;
	- }
	-
	- // Vectors TO DATATREE
	- mitk::Image::Pointer image5 = mitk::Image::New();
	- image5->InitializeByItk( vecImg5.GetPointer() );
	- image5->SetVolume( vecImg5->GetBufferPointer() );
	- mitk::DataNode::Pointer node5=mitk::DataNode::New();
	- node5->SetData( image5 );
	- mitk::DataStorage::GetInstance()->Add(node5);
	- switch(numdir)
	- {
	- case 0:
	- {
	- SetDefaultNodeProperties(node5, nodename.append(" Vec0"));
	- break;
	- }
	- case 1:
	- {
	- SetDefaultNodeProperties(node5, nodename.append(" Vec1"));
	- }
	- case 2:
	- {
	- SetDefaultNodeProperties(node5, nodename.append(" Vec2"));
	- }
	- default:
	- {
	- SetDefaultNodeProperties(node5, nodename.append(" Vecn"));
	- }
	- }
	- node5->SetProperty( "IsDirectionVolume", mitk::BoolProperty::New( true ) );
	- node5->SetProperty( "NormalizeVecs", mitk::BoolProperty::New( true ) );
	- node5->SetProperty( "Scale", mitk::FloatProperty::New( 0.8 ) );
	- node5->SetProperty( "LineWidth", mitk::FloatProperty::New( 3 ) );
	-
	- mitk::VectorImageMapper2D::Pointer vecMapper5 =
	- mitk::VectorImageMapper2D::New();
	- node5->SetMapper(1,vecMapper5);
	-
	- m_DataTreeIterator->GetTree()->Modified();
	- this->GetRenderWindowPart()->RequestUpdate();
	- TreeChanged();
	- m_Controls->update();
	-
	-}
	-
	-void QmitkDiffusionTensorEstimation::OdfStandardAlgorithmsDeconvolutionButton()
	-{
	-
	- itk::TimeProbe clock;
	- QString status;
	- const mitk::DataTreeFilter::Item* item
	- = m_OdfVolumesDataTreeFilter->GetSelectedItem();
	- if(!item)return;
	-
	- typedef itk::Vector<TTensorPixelType,odfsize> OdfVectorType;
	- typedef itk::Image<OdfVectorType,3> OdfVectorImgType;
	- mitk::Image* vol =
	- static_cast<mitk::Image*>(item->GetNode()->GetData());
	- OdfVectorImgType::Pointer itkvol = OdfVectorImgType::New();
	- mitk::CastToItkImage<OdfVectorImgType>(vol, itkvol);
	- std::string nodename = item->GetProperty("name");
	-
	- clock.Start();
	- MBI_INFO << "Computing Diffusion Direction ";
	- mitk::StatusBar::GetInstance()->DisplayText(status.sprintf(
	- "Computing Diffusion Direction for %s", nodename.c_str()));
	-
	- typedef itk::DiffusionOdfGeneralizedFaImageFilter<TTensorPixelType,TTensorPixelType,odfsize>
	- GfaFilterType;
	- GfaFilterType::Pointer gfaFilter = GfaFilterType::New();
	- gfaFilter->SetInput(itkvol);
	- gfaFilter->SetNumberOfThreads(4);
	- gfaFilter->Update();
	- itk::ImageRegionIterator<GfaFilterType::OutputImageType>
	- itGfa (gfaFilter->GetOutput(),
	- gfaFilter->GetOutput()->GetLargestPossibleRegion() );
	- itGfa = itGfa.Begin();
	-
	- int numdirs = m_Controls->m_OdfStandardAlgorithmsDeconvolutionSpinbox->value();
	-
	- //vnl_matrix_fixed<double, nrconvkernels, odfsize>* kernels
	- // = new vnl_matrix_fixed<double, nrconvkernels, odfsize>();
	- //itk::ImageRegionIterator<OdfVectorImgType> inIt(itkvol, itkvol->GetLargestPossibleRegion());
	- //inIt.GoToBegin();
	- //for(int i=0; i<nrconvkernels; i++)
	- //{
	- // OdfVectorImgType::PixelType vec = inIt.Get();
	- // for(int j=0; j<odfsize; j++)
	- // {
	- // (*kernels)(i,j) = vec[j];
	- // }
	- // ++inIt;
	- //}
	-
	- typedef itk::DiffusionOdfSphericalDeconvolutionImageFilter<TTensorPixelType,TTensorPixelType,odfsize,nrconvkernels>
	- DeconvolutionFilterType;
	- DeconvolutionFilterType::Pointer devonvolutionFilter
	- = DeconvolutionFilterType::New();
	- devonvolutionFilter->SetFractionalThreshold(m_Controls->m_OdfStandardAlgorithmsDeconvolutionThreshEdit->text().toFloat());
	- if(!m_Controls->m_OdfStandardAlgorithmsDeconvolutionAngResThresholdEdit->text().contains(QString("NaN")))
	- {
	- float angRes = m_Controls->m_OdfStandardAlgorithmsDeconvolutionAngResThresholdEdit->text().toFloat();
	- angRes /= 360/itk::Math::pi;
	- devonvolutionFilter->SetAngularResolutionThreshold(angRes);
	- }
	- devonvolutionFilter->SetSamplingQuantileStart(m_Controls->m_OdfStandardAlgorithmsDeconvQuantStart->text().toFloat());
	- devonvolutionFilter->SetSamplingQuantileStep(m_Controls->m_OdfStandardAlgorithmsDeconvQuantStep->text().toFloat());
	- devonvolutionFilter->SetMinimumNumberOfSamples(m_Controls->m_OdfStandardAlgorithmsDeconvQuantMinNr->text().toInt());
	- devonvolutionFilter->SetIterateQuantiles(m_Controls->m_OdfStandardAlgorithmsDeconvQuantMulti->isChecked());
	- devonvolutionFilter->SetNrDirectionsToExtract(numdirs);
	- devonvolutionFilter->SetInput(itkvol);
	- devonvolutionFilter->SetNumberOfThreads(m_Controls->m_OdfStandardAlgorithmsDeconvNumberThreadsSpinbox->value());
	- devonvolutionFilter->SetGfaImage(gfaFilter->GetOutput());
	- //devonvolutionFilter->SetPresetConvolutionKernels(kernels);
	- devonvolutionFilter->Update();
	-
	- for(int i=0; i<numdirs; i++)
	- {
	- itk::ImageRegionIterator<DeconvolutionFilterType::OutputImageType>
	- it (devonvolutionFilter->GetOutput(i),
	- devonvolutionFilter->GetOutput()->GetLargestPossibleRegion() );
	- it = it.Begin();
	-
	- if(i==0)
	- {
	- MBI_INFO << "Converting to RGB";
	-
	- typedef itk::Image<itk::RGBPixel<uchar>, 3> VecImgType;
	- VecImgType::Pointer vecImg = VecImgType::New();
	- vecImg->SetSpacing( itkvol->GetSpacing() ); // Set the image spacing
	- vecImg->SetOrigin( itkvol->GetOrigin() ); // Set the image origin
	- vecImg->SetDirection( itkvol->GetDirection() ); // Set the image direction
	- vecImg->SetLargestPossibleRegion( itkvol->GetLargestPossibleRegion());
	- vecImg->SetBufferedRegion( vecImg->GetLargestPossibleRegion() );
	- vecImg->Allocate();
	- itk::ImageRegionIterator<VecImgType> ot (vecImg, vecImg->GetLargestPossibleRegion() );
	- ot = ot.Begin();
	-
	- typedef DeconvolutionFilterType::OutputImageType::PixelType VecPixType;
	- for (it = it.Begin(); !it.IsAtEnd(); ++it)
	- {
	- VecPixType vec = it.Get();
	- vnl_vector_fixed<TTensorPixelType, 3> vnlvec = vec.GetVnlVector();
	- TTensorPixelType len = vnlvec.two_norm();
	- vnlvec = vnlvec.normalize();
	-
	- itk::RGBPixel<uchar> pix;
	- vnlvec=200itGfa.Get();
	- vnlvec[0] = abs(vnlvec[0]);
	- vnlvec[1] = abs(vnlvec[1]);
	- vnlvec[2] = abs(vnlvec[2]);
	- if(vnlvec[0] > 255 \|\| vnlvec[1] > 255 \|\| vnlvec[2] > 255)
	- {
	- //should never get in here
	- double max = vnlvec[0];
	- max = max<vnlvec[1] ? vnlvec[1] : max;
	- max = max<vnlvec[2] ? vnlvec[2] : max;
	- vnlvec /= max/255;
	- }
	- uchar uvec[3] = {(uchar)(vnlvec[0]),(uchar)(vnlvec[1]),(uchar)(vnlvec[2])};
	- pix = uvec;
	- ot.Set(pix);
	- ++ot;
	- ++itGfa;
	- }
	-
	- // RGB TO DATATREE
	- mitk::Image::Pointer image2 = mitk::Image::New();
	- image2->InitializeByItk( vecImg.GetPointer() );
	- image2->SetVolume( vecImg->GetBufferPointer() );
	- mitk::DataNode::Pointer node2=mitk::DataNode::New();
	- node2->SetData( image2 );
	- mitk::DataStorage::GetInstance()->Add(node2);
	- switch(i)
	- {
	- case 0:
	- {
	- SetDefaultNodeProperties(node2, nodename.append(" PD0"));
	- break;
	- }
	- case 1:
	- {
	- SetDefaultNodeProperties(node2, nodename.append(" PD1"));
	- break;
	- }
	- case 2:
	- {
	- SetDefaultNodeProperties(node2, nodename.append(" PD2"));
	- break;
	- }
	- default:
	- {
	- SetDefaultNodeProperties(node2, nodename.append(" PDn"));
	- break;
	- }
	- }
	-
	- node2->SetProperty( "IsRGBVolume", mitk::BoolProperty::New( true ) );
	- }
	-
	- // VECTORFIELD
	- MBI_INFO << "Converting to Vectorfield";
	-
	- typedef itk::Image<itk::Vector<TTensorPixelType,3>, 3> VecImgType2;
	- VecImgType2::Pointer vecImg5 = VecImgType2::New();
	- vecImg5->SetSpacing( itkvol->GetSpacing() ); // Set the image spacing
	- vecImg5->SetOrigin( itkvol->GetOrigin() ); // Set the image origin
	- vecImg5->SetDirection( itkvol->GetDirection() ); // Set the image direction
	- vecImg5->SetLargestPossibleRegion( itkvol->GetLargestPossibleRegion());
	- vecImg5->SetBufferedRegion( vecImg5->GetLargestPossibleRegion() );
	- vecImg5->Allocate();
	- itk::ImageRegionIterator<VecImgType2> ot5 (vecImg5, vecImg5->GetLargestPossibleRegion() );
	- ot5 = ot5.Begin();
	-
	- typedef DeconvolutionFilterType::OutputImageType::PixelType VecPixType;
	- for (it = it.Begin(); !it.IsAtEnd(); ++it)
	- {
	- VecPixType vec = it.Get();
	- vnl_vector_fixed<TTensorPixelType, 3> vnlvec = vec.GetVnlVector();
	- vnlvec = vnlvec.normalize();
	-
	- itk::Vector<TTensorPixelType,3> pix;
	- TTensorPixelType uvec[3] = {(TTensorPixelType)(vnlvec[0]),(TTensorPixelType)(vnlvec[1]),(TTensorPixelType)(vnlvec[2])};
	- pix = uvec;
	- ot5.Set(pix);
	- ++ot5;
	- }
	-
	- // Vectors TO DATATREE
	- mitk::Image::Pointer image5 = mitk::Image::New();
	- image5->InitializeByItk( vecImg5.GetPointer() );
	- image5->SetVolume( vecImg5->GetBufferPointer() );
	- mitk::DataNode::Pointer node5=mitk::DataNode::New();
	- node5->SetData( image5 );
	- mitk::DataStorage::GetInstance()->Add(node5);
	- switch(i)
	- {
	- case 0:
	- {
	- SetDefaultNodeProperties(node5, nodename.append(" Vec0"));
	- break;
	- }
	- case 1:
	- {
	- SetDefaultNodeProperties(node5, nodename.append(" Vec1"));
	- break;
	- }
	- case 2:
	- {
	- SetDefaultNodeProperties(node5, nodename.append(" Vec2"));
	- break;
	- }
	- default:
	- {
	- SetDefaultNodeProperties(node5, nodename.append(" Vecn"));
	- break;
	- }
	- }
	- node5->SetProperty( "IsDirectionVolume", mitk::BoolProperty::New( true ) );
	- node5->SetProperty( "NormalizeVecs", mitk::BoolProperty::New( true ) );
	- node5->SetProperty( "Scale", mitk::FloatProperty::New( 0.8 ) );
	- node5->SetProperty( "LineWidth", mitk::FloatProperty::New( 3 ) );
	-
	- mitk::VectorImageMapper2D::Pointer vecMapper5 =
	- mitk::VectorImageMapper2D::New();
	- node5->SetMapper(1,vecMapper5);
	- }
	- m_DataTreeIterator->GetTree()->Modified();
	- this->GetRenderWindowPart()->RequestUpdate();
	- TreeChanged();
	- m_Controls->update();
	-
	-}
	-
	-void QmitkDiffusionTensorEstimation::SetDefaultNodeProperties(mitk::DataNode::Pointer node, std::string name)
	-{
	- node->SetProperty( "volumerendering", mitk::BoolProperty::New( false ) );
	- node->SetProperty( "use color", mitk::BoolProperty::New( true ) );
	- node->SetProperty( "texture interpolation", mitk::BoolProperty::New( true ) );
	- node->SetProperty( "reslice interpolation", mitk::VtkResliceInterpolationProperty::New() );
	- node->SetProperty( "layer", mitk::IntProperty::New(0));
	- node->SetProperty( "in plane resample extent by geometry", mitk::BoolProperty::New( false ) );
	- node->SetOpacity(1.0f);
	- node->SetColor(1.0,1.0,1.0);
	- node->SetVisibility(true);
	-
	- mitk::LevelWindowProperty::Pointer levWinProp = mitk::LevelWindowProperty::New();
	- mitk::LevelWindow levelwindow;
	- // levelwindow.SetAuto( image );
	- levWinProp->SetLevelWindow( levelwindow );
	- node->GetPropertyList()->SetProperty( "levelwindow", levWinProp );
	-
	- // add a default rainbow lookup table for color mapping
	- if(!node->GetProperty("LookupTable"))
	- {
	- mitk::LookupTable::Pointer mitkLut = mitk::LookupTable::New();
	- vtkLookupTable* vtkLut = mitkLut->GetVtkLookupTable();
	- vtkLut->SetHueRange(0.6667, 0.0);
	- vtkLut->SetTableRange(0.0, 20.0);
	- vtkLut->Build();
	- mitk::LookupTableProperty::Pointer mitkLutProp = mitk::LookupTableProperty::New();
	- mitkLutProp->SetLookupTable(mitkLut);
	- node->SetProperty( "LookupTable", mitkLutProp );
	- }
	- if(!node->GetProperty("binary"))
	- node->SetProperty( "binary", mitk::BoolProperty::New( false ) );
	-
	- // add a default transfer function
	- mitk::TransferFunction::Pointer tf = mitk::TransferFunction::New();
	- node->SetProperty ( "TransferFunction", mitk::TransferFunctionProperty::New ( tf.GetPointer() ) );
	-
	- // set foldername as string property
	- mitk::StringProperty::Pointer nameProp = mitk::StringProperty::New( name );
	- node->SetProperty( "name", nameProp );
	-}
	-
	-void QmitkDiffusionTensorEstimation::DirectionVolumesAngularErrorButton()
	-{
	- try
	- {
	-
	- const mitk::DataTreeFilter::ItemSet* selectedItems
	- = m_DirectionVolumesDataTreeFilter->GetSelectedItems();
	- int nrFiles = selectedItems->size();
	- if (nrFiles != 2) return;
	-
	- mitk::DataTreeFilter::ItemSet::const_iterator itemiter( selectedItems->begin() );
	-
	- mitk::Image::Pointer vol1 =
	- static_cast<mitk::Image>((itemiter)->GetNode()->GetData());
	- if( !vol1)return;
	- std::string nodename1 = (*itemiter)->GetProperty("name");
	-
	- itemiter++;
	-
	- mitk::Image::Pointer vol2 =
	- static_cast<mitk::Image>((itemiter)->GetNode()->GetData());
	- if( !vol2)return;
	- std::string nodename2 = (*itemiter)->GetProperty("name");
	-
	- typedef itk::Image<itk::Vector<TTensorPixelType,3>,3 > IType;
	- IType::Pointer itkVol1 = IType::New();
	- mitk::CastToItkImage<IType>(vol1, itkVol1);
	-
	- IType::Pointer itkVol2 = IType::New();
	- mitk::CastToItkImage<IType>(vol2, itkVol2);
	-
	- typedef itk::VectorImagesAngularErrorImageFilter<TTensorPixelType,3> FilterType;
	- FilterType::Pointer filter = FilterType::New();
	- filter->SetInput(itkVol1);
	- filter->SetImage2(itkVol2.GetPointer());
	- filter->SetNumberOfThreads(4);
	- filter->Update();
	-
	- // Angluar Error TO DATATREE
	- mitk::Image::Pointer image = mitk::Image::New();
	- image->InitializeByItk( filter->GetOutput() );
	- image->SetVolume( filter->GetOutput()->GetBufferPointer() );
	- mitk::DataNode::Pointer node=mitk::DataNode::New();
	- node->SetData( image );
	- mitk::DataStorage::GetInstance()->Add(node);
	- SetDefaultNodeProperties(node, nodename1.append(" ").append(nodename2).append(" ERR"));
	- node->SetProperty( "IsErrorVolume", mitk::BoolProperty::New( true ) );
	-
	- TreeChanged();
	- m_Controls->update();
	-
	- QString status;
	- mitk::StatusBar::GetInstance()->DisplayText(status.sprintf("Finished computing Angular Error"));
	-
	- }
	- catch (itk::ExceptionObject &ex)
	- {
	- MBI_INFO << ex;
	- return ;
	- }
	-
	-}
	-
	-//void QmitkDiffusionTensorEstimation::DwiStandardAlgorithmsGFAButton()
	-//{
	-//
	-// itk::TimeProbe clock;
	-// QString status;
	-// const mitk::DataTreeFilter::Item* item
	-// = m_DiffusionVolumesDataTreeFilter->GetSelectedItem();
	-// if(!item)return;
	-//
	-// typedef itk::Vector<TTensorPixelType,odfsize> OdfVectorType;
	-// typedef itk::Image<OdfVectorType,3> OdfVectorImgType;
	-// mitk::Image* vol =
	-// static_cast<mitk::Image*>(item->GetNode()->GetData());
	-// OdfVectorImgType::Pointer itkvol = OdfVectorImgType::New();
	-// mitk::CastToItkImage<OdfVectorImgType>(vol, itkvol);
	-// std::string nodename = item->GetProperty("name");
	-//
	-// // COMPUTE RA
	-// clock.Start();
	-// std::cout << "Computing GFA ";
	-// mitk::StatusBar::GetInstance()->DisplayText(status.sprintf(
	-// "Computing GFA for %s", nodename.c_str()));
	-// typedef OdfVectorType::ValueType RealValueType;
	-// typedef itk::Image< RealValueType, 3 > RAImageType;
	-// typedef itk::DiffusionOdfGeneralizedFaImageFilter<TTensorPixelType,TTensorPixelType,odfsize>
	-// GfaFilterType;
	-// GfaFilterType::Pointer gfaFilter = GfaFilterType::New();
	-// gfaFilter->SetInput(itkvol);
	-// gfaFilter->SetNumberOfThreads(4);
	-// switch(m_Controls->m_OdfStandardAlgorithmsGFAMethodSpinbox->value())
	-// {
	-// case 1:
	-// {
	-// gfaFilter->SetComputationMethod(GfaFilterType::STANDARD);
	-// break;
	-// }
	-// case 2:
	-// {
	-// gfaFilter->SetComputationMethod(GfaFilterType::QUANTILES_HIGH_LOW);
	-// break;
	-// }
	-// case 3:
	-// {
	-// gfaFilter->SetComputationMethod(GfaFilterType::QUANTILES_MIDDLE);
	-// break;
	-// }
	-// case 4:
	-// {
	-// gfaFilter->SetComputationMethod(GfaFilterType::MAX_ODF_VALUE);
	-// break;
	-// }
	-// case 5:
	-// {
	-// gfaFilter->SetComputationMethod(GfaFilterType::DECONVOLUTION_COEFFS);
	-// break;
	-// }
	-// default:
	-// {
	-// gfaFilter->SetComputationMethod(GfaFilterType::STANDARD);
	-// }
	-// }
	-// gfaFilter->Update();
	-// clock.Stop();
	-// std::cout << "took " << clock.GetMeanTime() << "s." << std::endl;
	-//
	-// typedef itk::Image<TTensorPixelType, 3> ImgType;
	-// ImgType::Pointer img = ImgType::New();
	-// img->SetSpacing( gfaFilter->GetOutput()->GetSpacing() ); // Set the image spacing
	-// img->SetOrigin( gfaFilter->GetOutput()->GetOrigin() ); // Set the image origin
	-// img->SetDirection( gfaFilter->GetOutput()->GetDirection() ); // Set the image direction
	-// img->SetLargestPossibleRegion( gfaFilter->GetOutput()->GetLargestPossibleRegion());
	-// img->SetBufferedRegion( gfaFilter->GetOutput()->GetLargestPossibleRegion() );
	-// img->Allocate();
	-// itk::ImageRegionIterator<ImgType> ot (img, img->GetLargestPossibleRegion() );
	-// ot = ot.Begin();
	-// itk::ImageRegionConstIterator<GfaFilterType::OutputImageType> it
	-// (gfaFilter->GetOutput(), gfaFilter->GetOutput()->GetLargestPossibleRegion() );
	-// it = it.Begin();
	-//
	-// for (it = it.Begin(); !it.IsAtEnd(); ++it)
	-// {
	-// GfaFilterType::OutputImageType::PixelType val = it.Get();
	-// ot.Set(val * 200);
	-// ++ot;
	-// }
	-//
	-//
	-// // GFA TO DATATREE
	-// mitk::Image::Pointer image = mitk::Image::New();
	-// image->InitializeByItk( img.GetPointer() );
	-// image->SetVolume( img->GetBufferPointer() );
	-// mitk::DataNode::Pointer node=mitk::DataNode::New();
	-// node->SetData( image );
	-// mitk::DataStorage::GetInstance()->Add(node);
	-// SetDefaultNodeProperties(node, nodename.append(" GFA"));
	-// node->SetProperty( "IsGFAVolume", mitk::BoolProperty::New( true ) );
	-//
	-// mitk::StatusBar::GetInstance()->DisplayText("Computation complete.");
	-//
	-// m_DataTreeIterator->GetTree()->Modified();
	-// this->GetRenderWindowPart()->RequestUpdate();
	-// TreeChanged();
	-// m_Controls->update();
	-//
	-//}
	-
	-void QmitkDiffusionTensorEstimation::DiffusionVolumeSaveButton()
	-{
	- // GET SELECTED ITEM
	- const mitk::DataTreeFilter::Item* selectedItem
	- = m_DiffusionVolumesDataTreeFilter->GetSelectedItem();
	- if( !selectedItem )
	- return;
	- mitk::DiffusionVolumes<DiffusionPixelType>::Pointer diffVolumes =
	- static_cast<mitk::DiffusionVolumes<DiffusionPixelType>*>(selectedItem->GetNode()->GetData());
	-
	- std::string sName = selectedItem->GetNode()->GetName();
	- QString qName;
	- qName.sprintf("%s.nhdr",sName.c_str());
	-
	- // SELECT FILE DIALOG
	- //QFileDialog::getSaveFileName()
	- //QFileDialog* w = new QFileDialog( this->m_Controls, "Select Nrrd Outputfile", TRUE );
	- //w->setMode( QFileDialog::AnyFile );
	- //w->setFilter( "Nrrd Images (.nrrd .nhdr)" );
	- //w->setName(qName);
	- //if ( w->exec() != QDialog::Accepted )
	- // return;
	- //QString filename = w->selectedFile();
	-
	- QString filename = QFileDialog::getSaveFileName(
	- qName,
	- "Nrrd Images (.nrrd .nhdr)",
	- this->m_Controls,
	- "save file dialog",
	- "Select Nrrd Outputfile" );
	-
	- if ( !filename )
	- return;
	-
	- // WRITING DWIs TO NRRD VOLUME
	- typedef mitk::NrrdDiffusionVolumesWriter<DiffusionImageType> WriterType;
	- WriterType::Pointer nrrdWriter = WriterType::New();
	- nrrdWriter->SetInput( diffVolumes->GetImage() );
	- nrrdWriter->SetDirections(diffVolumes->GetDirections());
	- nrrdWriter->SetB_Value(diffVolumes->GetB_Value());
	- nrrdWriter->SetFileName(filename.ascii());
	- try
	- {
	- nrrdWriter->Update();
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- MBI_INFO << e;
	- }
	-}
	-
	-void QmitkDiffusionTensorEstimation::DiffusionVolumesLoadButton()
	-{
	- // SELECT FOLDER DIALOG
	- QFileDialog* w = new QFileDialog( this->m_Controls, "Select DWI data file", TRUE );
	- w->setMode( QFileDialog::ExistingFiles );
	- w->setFilter( "Nrrd Images (.nrrd .nhdr)" );
	-
	- // RETRIEVE SELECTION
	- if ( w->exec() != QDialog::Accepted )
	- return;
	-
	- QStringList filenames = w->selectedFiles();
	- QStringList::Iterator it = filenames.begin();
	- while( it != filenames.end() ) {
	- std::string filename = ( *it ).ascii();
	- ++it;
	-
	- // READING NRRD DWI VOLUMES
	- typedef mitk::NrrdDiffusionVolumesReader<DiffusionImageType> ReaderType;
	- ReaderType::Pointer nrrdReader = ReaderType::New();
	- nrrdReader->SetFileName(filename);
	- try
	- {
	- nrrdReader->Update();
	-
	- // DWI TO DATATREE
	- typedef mitk::DiffusionVolumes<DiffusionPixelType> DiffVolumesType;
	- DiffVolumesType::Pointer diffVolumes = DiffVolumesType::New();
	- diffVolumes->SetDirections(nrrdReader->GetDiffusionVectors());
	- diffVolumes->SetB_Value(nrrdReader->GetB_Value());
	- diffVolumes->SetImage(nrrdReader->GetOutput());
	- mitk::DataNode::Pointer node=mitk::DataNode::New();
	- node->SetData( diffVolumes );
	- mitk::DataStorage::GetInstance()->Add(node);
	- SetDefaultNodeProperties(node, itksys::SystemTools::GetFilenameName(filename));
	-
	- TreeChanged();
	- }
	- catch (const itk::ExceptionObject& e)
	- {
	- MBI_INFO << e;
	- }
	-
	- }
	-}
	-
	-void QmitkDiffusionTensorEstimation::DiffusionVolumesRemoveButton()
	-{
	- m_DiffusionVolumesDataTreeFilter->DeleteSelectedItems();
	-}
	-
	-void QmitkDiffusionTensorEstimation::DiffusionVolumesSelectAll()
	-{
	- const mitk::DataTreeFilter::ItemList* items = m_DiffusionVolumesDataTreeFilter->GetItems();
	-
	- mitk::DataTreeFilter::ConstItemIterator itemiter( items->Begin() );
	- mitk::DataTreeFilter::ConstItemIterator itemiterend( items->End() );
	-
	- while ( itemiter != itemiterend )
	- {
	- m_DiffusionVolumesDataTreeFilter->SelectItem(*itemiter);
	- ++itemiter;
	- }
	-
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/deprecated/QmitkDiffusionTensorEstimation.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/deprecated/QmitkDiffusionTensorEstimation.h
	deleted file mode 100644
	index e4dd1c20f6..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/deprecated/QmitkDiffusionTensorEstimation.h
	+++ /dev/null
	@@ -1,158 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#if !defined(QmitkDiffusionTensorEstimation_H__INCLUDED)
	-#define QmitkDiffusionTensorEstimation_H__INCLUDED
	-
	-#include <QmitkAbstractView.h>
	-#include <mitkILifecycleAwarePart.h>
	-#include "mitkDiffusionVolumes.h"
	-
	-class QmitkDiffusionTensorEstimationControls;
	-
	-typedef short DiffusionPixelType;
	-
	-
	-/*!
	-\brief QmitkDiffusionTensorEstimation
	-
	-One needs to reimplement the methods CreateControlWidget(..),
	-and CreateAction(..).
	-*/
	-class QmitkDiffusionTensorEstimation : public QmitkAbstractView, public mitk::ILifecycleAwarePart
	-{
	- Q_OBJECT
	-
	-public:
	- /*!
	- \brief default constructor
	- */
	- QmitkDiffusionTensorEstimation(QObject parent=0, const char name=0, mitk::DataTreeIteratorBase* dataIt = nullptr);
	-
	- /*!
	- \brief default destructor
	- */
	- virtual ~QmitkDiffusionTensorEstimation();
	-
	- /*!
	- \brief method for creating the widget containing the application controls, like sliders, buttons etc.
	- */
	- virtual QWidget * CreateControlWidget(QWidget *parent);
	-
	- /*!
	- \brief method for creating the connections of main and control widget
	- */
	- virtual void CreateConnections();
	-
	- ///
	- /// Sets the focus to an internal widget.
	- ///
	- virtual void SetFocus() override;
	-
	- /*!
	- \brief method for creating an QAction object, i.e. button & menu entry @param parent the parent QWidget
	- */
	- virtual QAction * CreateAction(QActionGroup *parent);
	-
	- virtual void Activated() override;
	- virtual void Deactivated() override;
	- virtual void Visible() override;
	- virtual void Hidden() override;
	-
	- protected slots:
	- void TreeChanged();
	-
	- void TensorVolumesSaveButton();
	-
	- void TensorVolumesLoadButton();
	-
	- void TensorVolumesRemoveButton();
	-
	- void OdfVolumesSaveButton();
	-
	- void OdfVolumesLoadButton();
	-
	- void OdfVolumesRemoveButton();
	-
	- void DirectionVolumesSaveButton();
	-
	- void DirectionVolumesLoadButton();
	-
	- void DirectionVolumesRemoveButton();
	-
	- void DirectionVolumesAngularErrorButton();
	-
	- void TensorEstimationTeemEstimateButton();
	-
	- void OdfReconstructionButton();
	-
	- void OdfReconstructionAnalyticalButton();
	-
	- void TensorEstimationButton();
	-
	- void StandardAlgorithmsFAButton();
	-
	- void StandardAlgorithmsRAButton();
	-
	- void StandardAlgorithmsDirectionButton();
	-
	- void OdfStandardAlgorithmsDirectionButton();
	-
	- void OdfStandardAlgorithmsDeconvolutionButton();
	-
	- void OdfStandardAlgorithmsGFAButton();
	-
	- void OdfVolumesVisualizeSelectedButton();
	-
	- void DiffusionVolumeSaveButton();
	-
	- void DiffusionVolumesLoadButton();
	-
	- void DiffusionVolumesRemoveButton();
	-
	- void DiffusionVolumesSelectAll();
	-
	- //void DwiStandardAlgorithmsGFAButton();
	-
	- void SetDefaultNodeProperties(mitk::DataNode::Pointer node, std::string name);
	-
	-protected:
	-
	- /*!
	- * controls containing sliders for scrolling through the slices
	- */
	- QmitkDiffusionTensorEstimationControls * m_Controls;
	-
	- mitk::DataTreeFilter::Pointer m_DiffusionVolumesDataTreeFilter;
	-
	- mitk::DataTreeFilter::Pointer m_TensorVolumesDataTreeFilter;
	-
	- mitk::DataTreeFilter::Pointer m_OdfVolumesDataTreeFilter;
	-
	- mitk::DataTreeFilter::Pointer m_DirectionVolumesDataTreeFilter;
	-
	- bool m_FilterInitialized;
	-
	- static const int odfsize;
	-
	- static const int nrconvkernels;
	-
	- template<int L>
	- void ReconstructAnalytically(mitk::DiffusionVolumes<DiffusionPixelType>* vols,
	- float lambda, std::string nodename, std::vector<mitk::DataNode::Pointer>* nodes);
	-
	-};
	-#endif // !defined(QmitkDiffusionTensorEstimation_H__INCLUDED)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/deprecated/QmitkDiffusionTensorIcon.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/deprecated/QmitkDiffusionTensorIcon.h
	deleted file mode 100644
	index a76cc7fe35..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/deprecated/QmitkDiffusionTensorIcon.h
	+++ /dev/null
	@@ -1,109 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef _QEMBED_1804289383
	-#define _QEMBED_1804289383
	-#include <qimage.h>
	-#include <qdict.h>
	-static const QRgb QmitkDiffusionTensorEstimation_data[] = {
	- 0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,
	- 0x3aaff00,0x3aaff00,0x3c001eea,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,
	- 0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x1a0a1d00,0x611a1800,0x8c311200,0x883c000d,0x55300051,
	- 0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,
	- 0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x621a1700,0xdd171200,0xfe341600,0xfe6b1400,0xf9960d00,0xf6b21600,0x6eb01000,0x3aaff00,0x3aaff00,
	- 0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x1ace0014,0x27d10d00,0x3aaff00,0x3aaff00,
	- 0x3aaff00,0x8a110f00,0xf40d0f00,0xf7341400,0xef6b0f00,0xf19d1200,0xf3c51200,0xf2e60c00,0xefe91000,0x40c70c00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,
	- 0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3fca0c00,0x3aaff00,0x3aaff00,0x81121000,0xfb0f1100,0xf1251100,
	- 0xf05b1000,0xf38c1600,0xf2b80e00,0xf6df1800,0xedfc0400,0xf5ff1400,0xb3f41100,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,
	- 0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x35f10e00,0x561b1800,0xf40d0f00,0xf0181000,0xee451000,0xef761100,0xeea30c00,0xeece0a00,
	- 0xdef40e00,0xd7ff1400,0xf5ff1400,0xebfd1700,0x1ded2300,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,
	- 0x3aaff00,0x3aaff00,0x3aaff00,0x38760e00,0xe51a1000,0xf6131400,0xf2331200,0xf4651300,0xf38c1600,0xf5b31700,0xffd11a11,0xfff52d21,0xffff3928,0xffff1d0a,
	- 0xf5ff1400,0x44ec1a00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,
	- 0x86110f00,0xfa0e1100,0xee190f00,0xf24d1100,0xf0751100,0xf19d1200,0xf6c30f00,0xffdf1e12,0xffff5749,0xffff6f5f,0xffff2016,0xf5ff1400,0x55fc0f00,0x3aaff00,
	- 0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x23071600,0xe7121300,0xf6131400,0xf2331200,
	- 0xef5c1000,0xee850e00,0xf1a91400,0xeece0a00,0xffee251c,0xfffe8272,0xfffe9080,0xffff2d1f,0xf5ff1400,0x5fff1500,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,
	- 0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x7a131100,0xfb0f1100,0xee190f00,0xef430f00,0xee6b0f00,0xef911000,0xf4b41700,
	- 0xf3d41600,0xfff62f22,0xffff8575,0xffff7d6b,0xffff2016,0xf5ff1400,0x47ff0700,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,
	- 0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0xc70e1200,0xfc161600,0xef251000,0xee510e00,0xee7a0c00,0xf19d1200,0xf0bb1000,0xeddd0d00,0xfffa3325,0xfffe6d5d,
	- 0xffff5543,0xffff2016,0xf5ff1400,0x35f10e00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,
	- 0x2e270600,0xf0111200,0xf2151100,0xf0361000,0xed600c00,0xee850e00,0xf4a71500,0xf3c51200,0xf4e40b00,0xffff2d1f,0xffff4639,0xffff3021,0xffff1d0a,0xe0ff1000,
	- 0x9c61c00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x5339900,0x1000df10,0x180bd400,0x70093b00,0xf9101700,0xf0181000,
	- 0xef430f00,0xef6b0f00,0xf1900f00,0xefae0e00,0xeece0a00,0xefe91000,0xeaff0a00,0xe9ff0b00,0xf5ff1400,0xf5ff1400,0xcbf11d00,0x3912ce00,0x3912ce00,0x3912ce00,
	- 0x3005c500,0x3812d100,0x3c00d50d,0x3005c500,0x2e06d300,0x2e06d300,0x2e06d300,0x2c06dc00,0x9e0d3f00,0xf70b1700,0xf1251100,0xef4e1100,0xf0751100,0xf39a1100,
	- 0xf3b80e00,0xf6d01400,0xefe91000,0xeaff0a00,0xf5ff1400,0xf5ff1400,0xf5ff1400,0x7ef71000,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,
	- 0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0xa90c0c00,0xf70d1100,0xf32f1400,0xf15b1000,0xf2801200,0xf09d1200,0xf0bb1000,0xf1d80800,0xefe91000,
	- 0xf5ff1400,0xf5ff1400,0xf5ff1400,0xf5ff1400,0x2ffa1b00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,
	- 0x3aaff00,0x3aaff00,0xb9151100,0xfc161600,0xef361000,0xf2651200,0xee850e00,0xf4a71500,0xf4c41100,0xeedc0c00,0xf5f10f00,0xf5ff1400,0xf5ff1400,0xf5ff1400,
	- 0xb6ff1400,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0xb8151100,
	- 0xfa181400,0xf2401300,0xef6a0e00,0xf28e0f00,0xf0ad0d00,0xf3c51200,0xf6df1800,0xf4f21100,0xf5ff1400,0xf5ff1400,0xf5ff1400,0x45fb1200,0x3aaff00,0x3aaff00,
	- 0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0xa4191400,0xfd1a1500,0xef430f00,0xf3701500,
	- 0xef911000,0xefae0e00,0xeece0a00,0xf6df1800,0xf4f21100,0xf0fa0100,0xfcfa0c00,0xa7f91200,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,
	- 0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x7c131000,0xff1b1600,0xf54a1600,0xf1741100,0xf49a1100,0xf4b41700,0xeece0a00,
	- 0xf2e60c00,0xf4f21100,0xf5ff1400,0xeaf10400,0x27f80007,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,
	- 0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x37050e00,0xf2151100,0xf54a1600,0xf0751100,0xf29b1200,0xf2b80e00,0xf6d01400,0xf2e60c00,0xf5f10f00,0xf1f51200,
	- 0x68f00c00,0x2cb90600,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,
	- 0x3aaff00,0x3aaff00,0xb4171200,0xfb421100,0xf0751100,0xf29b1200,0xf1b90f00,0xf6d01400,0xf4e40b00,0xfce91a00,0x66eb1400,0x3aaff00,0x31c60005,0x1ace0014,
	- 0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x2b061200,
	- 0xd8321100,0xfa6f0e00,0xf7970e00,0xf5b50b00,0xfbcc0f00,0xdbd91500,0x50d20d00,0x3aaff00,0x3aaff00,0x3aaff00,0x3fca0c00,0x3aaff00,0x3aaff00,0x3aaff00,
	- 0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x23330700,0xa3430010,0xbc890e00,
	- 0xbaaa1600,0x6dbd0c00,0x1bd03900,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x21d11700,0x2ed30006,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,
	- 0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x56600cc,0x2b002af9,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,
	- 0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x37cc0009,0xab31900,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,
	- 0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x2d0600d2,0x18002adf,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,
	- 0x3aaff00,0x3aaff00,0xeed0000,0x3cd50d00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00,0x3aaff00
	-};
	-
	-/* Generated by qembed */
	-static struct EmbedImage {
	- int width, height, depth;
	- const unsigned char *data;
	- int numColors;
	- const QRgb *colorTable;
	- bool alpha;
	- const char *name;
	-} embed_image_vec[] = {
	- { 25, 25, 32, (const unsigned char*)QmitkDiffusionTensorEstimation_data, 0, 0, TRUE, "QmitkDiffusionTensorEstimation" },
	- { 0, 0, 0, 0, 0, 0, 0, 0 }
	-};
	-
	-static const QImage& qembed_findImage( const QString& name )
	-{
	- static QDict<QImage> dict;
	- QImage* img = dict.find( name );
	- if ( !img ) {
	- for ( int i = 0; embed_image_vec[i].data; i++ ) {
	- if ( strcmp(embed_image_vec[i].name, name.latin1()) == 0 ) {
	- img = new QImage((uchar*)embed_image_vec[i].data,
	- embed_image_vec[i].width,
	- embed_image_vec[i].height,
	- embed_image_vec[i].depth,
	- (QRgb*)embed_image_vec[i].colorTable,
	- embed_image_vec[i].numColors,
	- QImage::BigEndian );
	- if ( embed_image_vec[i].alpha )
	- img->setAlphaBuffer( TRUE );
	- dict.insert( name, img );
	- break;
	- }
	- }
	- if ( !img ) {
	- static QImage dummy;
	- return dummy;
	- }
	- }
	- return *img;
	-}
	-
	-#endif
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/mitkPluginActivator.cpp
	deleted file mode 100644
	index 48fd9d067e..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/mitkPluginActivator.cpp
	+++ /dev/null
	@@ -1,78 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#include "mitkPluginActivator.h"
	-
	-#include "src/internal/Perspectives/QmitkDiffusionDefaultPerspective.h"
	-#include "src/internal/Perspectives/QmitkSegmentationPerspective.h"
	-
	-#include "src/internal/QmitkDiffusionDicomImportView.h"
	-#include "src/internal/QmitkDicomTractogramTagEditorView.h"
	-#include "src/internal/QmitkControlVisualizationPropertiesView.h"
	-
	-#include "QmitkNodeDescriptorManager.h"
	-#include "mitkNodePredicateDataType.h"
	-#include "mitkNodePredicateProperty.h"
	-#include "mitkNodePredicateIsDWI.h"
	-#include <mitkDiffusionPropertyHelper.h>
	-
	-namespace mitk {
	-
	-void PluginActivator::start(ctkPluginContext* context)
	-{
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkDiffusionDefaultPerspective, context)
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkSegmentationPerspective, context)
	-
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkDiffusionDicomImport, context)
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkDicomTractogramTagEditorView, context)
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkControlVisualizationPropertiesView, context)
	-
	- // Q_UNUSED(context)
	-
	- QmitkNodeDescriptorManager* manager = QmitkNodeDescriptorManager::GetInstance();
	-
	- mitk::NodePredicateIsDWI::Pointer isDiffusionImage = mitk::NodePredicateIsDWI::New();
	- QmitkNodeDescriptor* desc = new QmitkNodeDescriptor(QObject::tr("DiffusionImage"), QString(":/QmitkDiffusionImaging/DiffData24.png"), isDiffusionImage, manager);
	- manager->AddDescriptor(desc);
	-
	- mitk::NodePredicateDataType::Pointer isTensorImage = mitk::NodePredicateDataType::New("TensorImage");
	- manager->AddDescriptor(new QmitkNodeDescriptor(QObject::tr("TensorImage"), QString(":/QmitkDiffusionImaging/tensor.png"), isTensorImage, manager));
	-
	- mitk::NodePredicateDataType::Pointer isOdfImage = mitk::NodePredicateDataType::New("OdfImage");
	- manager->AddDescriptor(new QmitkNodeDescriptor(QObject::tr("OdfImage"), QString(":/QmitkDiffusionImaging/odf.png"), isOdfImage, manager));
	-
	- mitk::NodePredicateDataType::Pointer isShImage = mitk::NodePredicateDataType::New("ShImage");
	- manager->AddDescriptor(new QmitkNodeDescriptor(QObject::tr("ShImage"), QString(":/QmitkDiffusionImaging/sh.png"), isShImage, manager));
	-
	- mitk::NodePredicateDataType::Pointer isFiberBundle = mitk::NodePredicateDataType::New("FiberBundle");
	- manager->AddDescriptor(new QmitkNodeDescriptor(QObject::tr("FiberBundle"), QString(":/QmitkDiffusionImaging/tractogram.png"), isFiberBundle, manager));
	-
	- mitk::NodePredicateDataType::Pointer isPeakImage = mitk::NodePredicateDataType::New("PeakImage");
	- manager->AddDescriptor(new QmitkNodeDescriptor(QObject::tr("PeakImage"), QString(":/QmitkDiffusionImaging/odf_peaks.png"), isPeakImage, manager));
	-
	-
	- mitk::NodePredicateDataType::Pointer isConnectomicsNetwork = mitk::NodePredicateDataType::New("ConnectomicsNetwork");
	- manager->AddDescriptor(new QmitkNodeDescriptor(QObject::tr("ConnectomicsNetwork"), QString(":/QmitkDiffusionImaging/ConnectomicsNetwork.png"), isConnectomicsNetwork, manager));
	-
	- mitk::NodePredicateDataType::Pointer isTractographyForestNetwork = mitk::NodePredicateDataType::New("TractographyForest");
	- manager->AddDescriptor(new QmitkNodeDescriptor(QObject::tr("TractographyForest"), QString(":/QmitkDiffusionImaging/ml_tractogram.png"), isTractographyForestNetwork, manager));
	-}
	-
	-void PluginActivator::stop(ctkPluginContext* context)
	-{
	- Q_UNUSED(context)
	-}
	-
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/mitkPluginActivator.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/mitkPluginActivator.h
	deleted file mode 100644
	index 4734f37c9b..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/mitkPluginActivator.h
	+++ /dev/null
	@@ -1,39 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-#ifndef MITKPLUGINACTIVATOR_H
	-#define MITKPLUGINACTIVATOR_H
	-
	-#include <ctkPluginActivator.h>
	-
	-namespace mitk {
	-
	-class PluginActivator :
	- public QObject, public ctkPluginActivator
	-{
	- Q_OBJECT
	- Q_PLUGIN_METADATA(IID "org_mitk_gui_qt_diffusionimaging")
	- Q_INTERFACES(ctkPluginActivator)
	-
	-public:
	-
	- void start(ctkPluginContext* context) override;
	- void stop(ctkPluginContext* context) override;
	-
	-}; // PluginActivator
	-
	-}
	-
	-#endif // MITKPLUGINACTIVATOR_H
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimagingapp/CMakeLists.txt
	deleted file mode 100644
	index 80a74157e9..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/CMakeLists.txt
	+++ /dev/null
	@@ -1,9 +0,0 @@
	-project(org_mitk_gui_qt_diffusionimagingapp)
	-
	-mitk_create_plugin(
	- SUBPROJECTS MITK-DTI
	- EXPORT_DIRECTIVE DIFFUSIONIMAGING_APP_EXPORT
	- EXPORTED_INCLUDE_SUFFIXES src
	- MODULE_DEPENDS MitkQtWidgets MitkSceneSerialization
	- PACKAGE_DEPENDS Qt5\|WebEngineWidgets
	-)
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/MitkDiffusionImagingAppQtHelpCollectionProject.qhcp b/Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/MitkDiffusionImagingAppQtHelpCollectionProject.qhcp
	deleted file mode 100644
	index ebd648576d..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/MitkDiffusionImagingAppQtHelpCollectionProject.qhcp
	+++ /dev/null
	@@ -1,22 +0,0 @@
	-<?xml version="1.0" encoding="utf-8" ?>
	-<QHelpCollectionProject version="1.0">
	- <assistant>
	- <title>MITK Diffusion Help</title>
	- <applicationIcon>assistant-logo.png</applicationIcon>
	- <startPage>qthelp://org.mitk.gui.qt.diffusionimagingapp/bundle/index.html</startPage>
	- <applicationIcon>assistant-icon.png</applicationIcon>
	- <enableFilterFunctionality>false</enableFilterFunctionality>
	- <enableDocumentationManager>false</enableDocumentationManager>
	- <enableAddressBar visible="false">true</enableAddressBar>
	- <cacheDirectory>MitkDIApp</cacheDirectory>
	- <aboutMenuText>
	- <text>About MITK Diffusion Help</text>
	- </aboutMenuText>
	- <aboutDialog>
	- <icon>about-logo.png</icon>
	- </aboutDialog>
	- </assistant>
	- <docFiles>
	-
	- </docFiles>
	-</QHelpCollectionProject>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/UserManual/QmitkDiffusionImagingAppUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/UserManual/QmitkDiffusionImagingAppUserManual.dox
	deleted file mode 100644
	index 76d27ea5fd..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/UserManual/QmitkDiffusionImagingAppUserManual.dox
	+++ /dev/null
	@@ -1,8 +0,0 @@
	-/**
	-\page org_mitk_gui_qt_diffusionimagingapp What is the Diffusion Imaging Application
	-
	-MITK Diffusion offers a selection of image analysis methods for dMRI processing. It encompasses the research of the <a href="https://www.dkfz.de/en/mic/index.php">Division of Medical Image Computing</a> of the German Cancer Research Center (DKFZ).
	-
	-For a detailed description of MITK Diffusion refer to \ref org_mitk_gui_qt_diffusionimaging .
	-
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/about-logo.png b/Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/about-logo.png
	deleted file mode 100644
	index 0eb8a0a916..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/about-logo.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/assistant-icon.png b/Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/assistant-icon.png
	deleted file mode 100644
	index 0409055874..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/assistant-icon.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/doxygen/modules.dox b/Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/doxygen/modules.dox
	deleted file mode 100644
	index 8dc3e71bf1..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/documentation/doxygen/modules.dox
	+++ /dev/null
	@@ -1,16 +0,0 @@
	-/**
	- \defgroup org_mitk_diffusionimagingapp org.mitk.diffusionimagingapp
	- \ingroup MITKPlugins
	-
	- \brief Describe your plugin here.
	-
	-*/
	-
	-/**
	- \defgroup org_mitk_diffusionimagingapp_internal Internal
	- \ingroup org_mitk_diffusionimagingapp
	-
	- \brief This subcategory includes the internal classes of the org.mitk.diffusionimagingapp plugin. Other
	- plugins must not rely on these classes. They contain implementation details and their interface
	- may change at any time. We mean it.
	-*/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/files.cmake b/Plugins/org.mitk.gui.qt.diffusionimagingapp/files.cmake
	deleted file mode 100644
	index 2e6976a06e..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/files.cmake
	+++ /dev/null
	@@ -1,47 +0,0 @@
	-set(SRC_CPP_FILES
	- QmitkDiffusionImagingAppApplication.cpp
	- QmitkDiffusionImagingAppWorkbenchAdvisor.cpp
	-)
	-
	-set(INTERNAL_CPP_FILES
	- QmitkDiffusionApplicationPlugin.cpp
	- QmitkDiffusionImagingAppIntroPart.cpp
	- Perspectives/QmitkWelcomePerspective.cpp
	-)
	-
	-set(UI_FILES
	- src/internal/QmitkWelcomeScreenViewControls.ui
	-)
	-
	-set(MOC_H_FILES
	- src/internal/QmitkDiffusionImagingAppIntroPart.h
	- src/internal/QmitkDiffusionApplicationPlugin.h
	- src/QmitkDiffusionImagingAppApplication.h
	- src/internal/Perspectives/QmitkWelcomePerspective.h
	-)
	-
	-set(CACHED_RESOURCE_FILES
	-# list of resource files which can be used by the plug-in
	-# system without loading the plug-ins shared library,
	-# for example the icon used in the menu and tabs for the
	-# plug-in views in the workbench
	- plugin.xml
	- resources/icon_home.png
	-)
	-
	-set(QRC_FILES
	-# uncomment the following line if you want to use Qt resources
	- resources/welcome/QmitkWelcomeScreenView.qrc
	- resources/org_mitk_gui_qt_diffusionimagingapp.qrc
	-)
	-
	-# set(CPP_FILES)
	-
	-foreach(file ${SRC_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/${file})
	-endforeach(file ${SRC_CPP_FILES})
	-
	-foreach(file ${INTERNAL_CPP_FILES})
	- set(CPP_FILES ${CPP_FILES} src/internal/${file})
	-endforeach(file ${INTERNAL_CPP_FILES})
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.diffusionimagingapp/manifest_headers.cmake
	deleted file mode 100644
	index 824c3b7930..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/manifest_headers.cmake
	+++ /dev/null
	@@ -1,8 +0,0 @@
	-set(Plugin-Name "MITK Diffusion")
	-set(Plugin-Version "1.0")
	-set(Plugin-Vendor "DKFZ, Medical and Biological Informatics")
	-set(Plugin-ContactAddress "http://www.mitk.org")
	-set(Require-Plugin org.mitk.gui.qt.ext)
	-set(Plugin-Activator QmitkDiffusionImagingAppApplicationPlugin)
	-
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/plugin.xml b/Plugins/org.mitk.gui.qt.diffusionimagingapp/plugin.xml
	deleted file mode 100644
	index e0b8a0b82e..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/plugin.xml
	+++ /dev/null
	@@ -1,49 +0,0 @@
	-<?xml version="1.0" encoding="UTF-8"?>
	-<?BlueBerry version="0.1"?>
	-<plugin>
	- <extension point="org.blueberry.osgi.applications" id="org.mitk.qt.diffusionimagingapp">
	- <application>
	- <run class="QmitkDiffusionImagingAppApplication"/>
	- </application>
	- </extension>
	-
	- <extension id="diffusion" point="org.blueberry.core.runtime.products">
	- <product name="MITK Diffusion" application="org.mitk.qt.diffusionimagingapp" />
	- </extension>
	-
	- <extension point="org.blueberry.ui.intro">
	- <intro id="org.mitk.qt.diffusionimagingappintro"
	- class="QmitkDiffusionImagingAppIntroPart"
	- role="editor"/>
	- <introProductBinding
	- productId="org.mitk.gui.qt.diffusionimagingapp.diffusion"
	- introId="org.mitk.qt.diffusionimagingappintro"/>
	- </extension>
	-
	- <extension point="org.blueberry.ui.perspectives">
	- <perspective id="org.mitk.diffusionimagingapp.perspectives.welcome"
	- name="Data Display"
	- class="QmitkWelcomePerspective"
	- icon="resources/icon_home.png"/>
	- </extension>
	-
	-
	- <extension point="org.blueberry.ui.preferencePages">
	- <page
	- id="org.blueberry.ui.preferencePages.Style"
	- name="Themes"
	- category="org.mitk.GeneralPreferencePage"
	- class="berry::ExtensionFactory:stylePreferencePage">
	- <keywordreference id="org.blueberry.ui.style"/>
	- </page>
	- <page
	- id="org.blueberry.ui.preferencePages.Perspectives"
	- name="Perspectives"
	- category="org.mitk.GeneralPreferencePage"
	- class="berry::ExtensionFactory:perspectivesPreferencePage">
	- <keywordreference id="org.blueberry.ui.perspectives"/>
	- </page>
	- </extension>
	-
	-</plugin>
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/MitkDiffusion.ico b/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/MitkDiffusion.ico
	deleted file mode 100755
	index 77a2f03ee8..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/MitkDiffusion.ico and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/icon_home.png b/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/icon_home.png
	deleted file mode 100644
	index 9b3a09073a..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/icon_home.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/org_mitk_gui_qt_diffusionimagingapp.qrc b/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/org_mitk_gui_qt_diffusionimagingapp.qrc
	deleted file mode 100644
	index 2938d60ecb..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/org_mitk_gui_qt_diffusionimagingapp.qrc
	+++ /dev/null
	@@ -1,5 +0,0 @@
	-<RCC>
	- <qresource prefix="/org.mitk.gui.qt.diffusionimagingapp">
	- <file>MitkDiffusion.ico</file>
	- </qresource>
	-</RCC>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/QmitkWelcomeScreenView.qrc b/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/QmitkWelcomeScreenView.qrc
	deleted file mode 100644
	index 65bb011704..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/QmitkWelcomeScreenView.qrc
	+++ /dev/null
	@@ -1,36 +0,0 @@
	-<RCC>
	- <qresource prefix="/org.mitk.gui.qt.welcomescreen">
	- <file>style.css</file>
	- <file>function.js</file>
	- <file>pics/background.jpg</file>
	- <file>pics/popup_bttn_close.png</file>
	- <file>pics/experimental.png</file>
	- <file>pics/button_mitka.png</file>
	- <file>pics/button_mitk.png</file>
	- <file>mitkdiffusionimagingappwelcomeview.html</file>
	- <file>pics/01adicomimport.png</file>
	- <file>pics/01dicomimport.png</file>
	- <file>pics/02apreprocessingreconstruction.png</file>
	- <file>pics/02preprocessingreconstruction.png</file>
	- <file>pics/03aquantification.png</file>
	- <file>pics/03quantification.png</file>
	- <file>pics/04atractography.png</file>
	- <file>pics/04tractography.png</file>
	- <file>pics/06aconnectomics.png</file>
	- <file>pics/06connectomics.png</file>
	- <file>pics/07aivim.png</file>
	- <file>pics/07ivim.png</file>
	- <file>pics/08avolumevisualization.png</file>
	- <file>pics/08volumevisualization.png</file>
	- <file>pics/11asegmentation.png</file>
	- <file>pics/11segmentation.png</file>
	- <file>pics/12aregistration.png</file>
	- <file>pics/12registration.png</file>
	- <file>pics/13autilities.png</file>
	- <file>pics/13utilities.png</file>
	- <file>pics/10softwarephantoms.png</file>
	- <file>pics/10asoftwarephantoms.png</file>
	- <file>pics/05afiberprocessing.png</file>
	- <file>pics/05fiberprocessing.png</file>
	- </qresource>
	-</RCC>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/function.js b/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/function.js
	deleted file mode 100644
	index 02ab64cbcd..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/function.js
	+++ /dev/null
	@@ -1,320 +0,0 @@
	-// If you want to create a new button you have to add some data (strings) to the following five arrays.
	-// Make sure that you add your data at the same position in each array.
	-// The buttons will be generated in order to the array's index. e.g. data at array's index '0' will generate the first button.
	-
	-// enter the name of your module here
	-var moduleNames = new Array(
	- "Preprocessing",
	- "ODF Reconstruction/Signal Modelling",
	- "Diffusion Indices",
	- "Tractography",
	- "Fiber Processing",
	- "Connectomics",
	- "Fiberfox",
	- "IVIM & Kurtosis",
	- "Segmentation",
	- "MITK Downloads & News");
	-
	-// add the MITK-link to your module
	-var moduleLinks = new Array(
	- "mitk://mitk.perspectives/org.mitk.perspectives.dwipreprocessing?clear=false",
	- "mitk://mitk.perspectives/org.mitk.perspectives.reconstruction1?clear=false",
	- "mitk://mitk.perspectives/org.mitk.perspectives.quantification?clear=false",
	- "mitk://mitk.perspectives/org.mitk.perspectives.tractography2?clear=false",
	- "mitk://mitk.perspectives/org.mitk.perspectives.fiberprocessings?clear=false",
	- "mitk://mitk.perspectives/org.mitk.perspectives.connectomics?clear=false",
	- "mitk://mitk.perspectives/org.mitk.perspectives.syntheticdata?clear=false",
	- "mitk://mitk.perspectives/org.mitk.perspectives.ivim?clear=false",
	- "mitk://mitk.perspectives/org.mitk.perspectives.segmentation?clear=false",
	- "http://www.mitk.org");
	-
	-// add the filename of your icon for the module. Place the picture in subdirectory "pics".
	-// The picture's width should be 136 pixel; the height 123 pixel.
	-var picFilenames = new Array(
	- "12registration.png",
	- "02preprocessingreconstruction.png",
	- "03quantification.png",
	- "04tractography.png",
	- "05fiberprocessing.png",
	- "06connectomics.png",
	- "10softwarephantoms.png",
	- "07ivim.png",
	- "11segmentation.png",
	- "button_mitk.png");
	-
	-// if you want to create an animated icon, add the name of your animated gif (placed in subdirectory "pics"). Otherwise enter an empty string "".
	-// The animation's width should be 136 pixel; the height 123 pixel.
	-var aniFilenames = new Array(
	- "12aregistration.png",
	- "02apreprocessingreconstruction.png",
	- "03aquantification.png",
	- "04atractography.png",
	- "05afiberprocessing.png",
	- "06aconnectomics.png",
	- "10asoftwarephantoms.png",
	- "07aivim.png",
	- "11asegmentation.png",
	- "button_mitka.png");
	-
	-// if your module is not stable, you can mark it as experimental.
	-// just set true for experimental or false for stable.
	-var experimental = new Array(
	- false,
	- false,
	- false,
	- false,
	- false,
	- false,
	- false,
	- false,
	- false,
	- false);
	-
	-//"MITK Diffusion allows partial volume analysis and the evaluation and exploration of Tract Based Spatial Statistic datasets (it does NOT reimplement the TBSS methods available in FSL). The Partial Volume Analysis view provides a very robust method for semi-automatic ROI analysis. It uses EM clustering to probabilistically segment fiber vs. non-fiber vs. partial volume.",
	-
	-// add the description for your module. The description is displayed in a PopUp-window.
	-var moduleDescriptions = new Array(
	- "You can use MITK Diffusion to preprocess diffusion-weighted images using image registration, head-motion correction, denoising and much more.",
	- "MITK provides methods to estimate diffusion tensors or Q-balls using different reconstruction methods.",
	- "MITK allows the calculation of different scalar measures for raw diffusion-weighted images (MD, ADC), tensors (Fractional Anisotropy, Relative Anisotropy, Axial Diffusivity, Radial Diffusivity) or ODFs (Generalized Fractional Anisotropy).",
	- "The tractography components of MITK Diffusion implement several fiber tractography algorithms (global and streamline; tensor, dODF/fODF/FOD, peak based as well as machine learning based using the raw signal). The fiber bundle operations view enables fiber postprocessing in various ways. The fiber quantification view generates a variety of images from given fiber tracts, extracts the principal fiber directions and gives detailed information about the fiberbundle itself.",
	- "The results obtained with any fiber tractography method can be postprocessed using tract dissection, filtering, clustering, coloring or SIFT2-like fitting methods.",
	- "Connectomics aims at building graphs (nodes and edges) from a tractogram and applying graph theory for data analysis.",
	- "The Fiberfox software phantom tool allows you to create synthetic diffusion-weighted MR images easily and with a wide variety of properties and options.",
	- "You can use Intravoxel Incoherent Motion to estimate tissue perfusion on basis of diffusion measurements. Several models and interactive exploration of the data are supported.",
	- "MITK Diffusion provides tools for image segmentation and diffusion unrelated image processing.",
	- "Open the MITK website in an external browser.");
	-
	-var bttns = new Array();
	-
	-var d = document, da = d.all;
	-
	-// holds id of current mouseover-HTML-element
	-var currentTarget;
	-
	-// get the id of current mouseover-HTML-element
	-d.onmouseover = function(o){
	- var e = da ? event.srcElement : o.target;
	- currentTarget = e.id;
	-}
	-
	-
	-// build-function called by onload-event in HTML-document
	-function createButtons(){
	-
	- for (i=0; i < moduleNames.length; i++){
	- bttns[i] = new Button(moduleNames[i],moduleLinks[i], picFilenames[i], aniFilenames[i],moduleDescriptions[i]);
	- bttns[i].createButton();
	- }
	-
	- for (i=0; i < moduleNames.length; i++){
	-
	- if(experimental[i]){
	- setExperimental(i);
	- }
	- }
	-
	- createClearFloat();
	-}
	-
	-// Class Button
	-function Button(moduleName, moduleLink, picFilename, aniFilename, moduleDescr){
	-
	- // Properties
	- this.bttnID = "bttn" + moduleName;
	- this.modName = moduleName;
	- this.modLink = moduleLink;
	- this.picPath = "pics/" + picFilename;
	- this.aniPath = "pics/" + aniFilename;
	- this.modDescr = moduleDescr;
	-
	- // Methods
	- this.createButton = function(){
	-
	- // get DIV-wrapper for Button and append it to HTML-document
	- bttnWrapper = this.createWrapper();
	- document.getElementById("bttnField").appendChild(bttnWrapper);
	-
	- // get link-element for picture and append it to DIV-wrapper
	- bttnPicLink = this.createPicLink();
	- bttnWrapper.appendChild(bttnPicLink);
	-
	- // set HTML attributes for button-element
	- bttn = document.createElement("img");
	- bttn.src = this.picPath;
	- bttn.id = this.bttnID;
	- bttn.className = "modBttn";
	- bttn.height = 123;
	- bttn.width = 136;
	- bttn.onmouseover = function(){startAni(this.id);};
	- bttn.onmouseout = function(){stopAni(this.id);};
	-
	- // append button to link-element
	- bttnPicLink.appendChild(bttn);
	-
	-// // create text-link and add it to DIV-wrapper
	-// bttnTxtLink = document.createElement("a");
	-//// bttnTxtLink.href = this.modLink;
	-// bttnTxtLink.className = "txtLink";
	-// bttnTxtLink.appendChild(document.createTextNode(this.modName));
	-// bttnTxtLink.onclick = function(){showPopUpWindow();};
	-// bttnTxtLink.id = "popup" + this.modName;
	-// bttnWrapper.appendChild(bttnTxtLink);
	-
	- // create pop-up link for module description
	- bttnPopUpLink = document.createElement("a");
	- modName = this.modName;
	- modDescr = this.modDescr;
	- bttnPopUpLink.onclick = function(){showPopUpWindow();};
	- bttnPopUpLink.className = "popUpLink";
	- bttnPopUpLink.id = "popup" + this.modName;
	- bttnPopUpLink.appendChild(document.createTextNode(this.modName));
	- bttnWrapper.appendChild(bttnPopUpLink);
	-
	- return bttn;
	- }
	-
	- this.createWrapper = function(){
	- bttnWrapper = document.createElement("div");
	- bttnWrapper.id = "wrapper" + this.modName;
	- bttnWrapper.className = "bttnWrap";
	-
	- return bttnWrapper;
	- }
	-
	- this.createPicLink = function(){
	- picLink = document.createElement("a");
	- picLink.href = this.modLink;
	- picLink.id = "link" + this.modName;
	-
	- return picLink;
	- }
	-
	-}
	-
	-
	-function showPopUpWindow(){
	-
	- // modules position in array?
	- modulePos = getPos(currentTarget,"popup");
	-
	- // get reference to anchor-element in HTML-document
	- popUpAnchor = document.getElementById("popupAnchor");
	-
	- // check if a popUp is open
	- if(popUpAnchor.hasChildNodes()){
	- // if a popUp is open, remove it!
	- popUpAnchor.removeChild(document.getElementById("popup"));
	- }
	-
	- // create new container for popUp
	- container = document.createElement("div");
	- container.id = "popup";
	- container.align = "right";
	-
	- // append popUp-container to HTML-document
	- popUpAnchor.appendChild(container);
	-
	- // create close-button and append it to popUp-container
	- bttnClose = document.createElement("img");
	- bttnClose.src = "pics/popup_bttn_close.png";
	- bttnClose.id = "bttnClose";
	- bttnClose.onclick = function(){closeInfoWindow();};
	- container.appendChild(bttnClose);
	-
	- // create container for content-elements
	- contHeadline = document.createElement("div");
	- contHeadline.id = "contHeadline";
	- contDescription = document.createElement("div");
	- contDescription.id = "contDescription";
	- contModLink = document.createElement("div");
	- contModLink.id = "contModLink";
	-
	- // append content-container to popUp-container
	- container.appendChild(contHeadline);
	- container.appendChild(contDescription);
	- container.appendChild(contModLink);
	-
	- // create text-elements with content
	- headline = document.createTextNode(moduleNames[modulePos] + " ");
	- description = document.createTextNode(moduleDescriptions[modulePos]);
	- moduleLink = document.createElement("a");
	- moduleLink.href = moduleLinks[modulePos] ;
	- moduleLink.className = 'moduleLink';
	- moduleLinkTxt = document.createTextNode("Click here to open '" + moduleNames[modulePos].toLowerCase() + "'");
	- moduleLink.appendChild(moduleLinkTxt);
	-
	- // append text-elements to their container
	- contHeadline.appendChild(headline);
	- contDescription.appendChild(description);
	-// contModLink.appendChild(moduleLink);
	-}
	-
	-function getPos(id,prefix){
	-
	- if(prefix == "popup"){
	- targetID = id.slice(5);
	- }else{
	- if(prefix == "bttn"){
	- targetID = id.slice(4);
	- }
	- }
	-
	- for(i=0; i < moduleNames.length; i++ ){
	- if(moduleNames[i] == targetID){
	- return i;
	- }
	- }
	-}
	-
	-function setExperimental(modPos){
	- linkID = "link" + moduleNames[modPos];
	-
	- expPic = document.createElement("img");
	- expPic.src = "pics/experimental.png";
	- expPic.className = "expPic";
	- //alert(bttns[modPos].bttnID);
	- expPic.onmouseover = function(){startAni(bttns[modPos].bttnID);changeToHover(bttns[modPos].bttnID);};
	- expPic.onmouseout = function(){stopAni(bttns[modPos].bttnID);changeToNormal(bttns[modPos].bttnID);};
	-
	- document.getElementById(linkID).appendChild(expPic);
	-}
	-
	-function changeToHover(targetId){
	- bttn = document.getElementById(targetId);
	- bttn.className = "modBttnHover";
	-}
	-
	-function changeToNormal(targetId){
	- bttn = document.getElementById(targetId);
	- bttn.className = "modBttn";
	-}
	-
	-// function to close PopUp-window
	-function closeInfoWindow(){
	- popUpAnchor = document.getElementById("popupAnchor");
	- popUpAnchor.removeChild(document.getElementById("popup"));
	-}
	-
	-function createClearFloat(){
	- cf = document.createElement("div");
	- cf.className = "clearfloat";
	- document.getElementById("bttnField").appendChild(cf);
	-}
	-
	-startAni = function(targetId){
	- modulePos = getPos(targetId,"bttn");
	-
	- if(aniFilenames[modulePos] != ''){
	- bttn = document.getElementById(targetId);
	- bttn.src = "pics/" + aniFilenames[modulePos];
	- }
	-}
	-
	-stopAni = function(targetId){
	- modulePos = getPos(targetId,"bttn");
	-
	- bttn = document.getElementById(targetId);
	- bttn.src = "pics/" + picFilenames[modulePos];
	-}
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/mitkdiffusionimagingappwelcomeview.html b/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/mitkdiffusionimagingappwelcomeview.html
	deleted file mode 100644
	index b6076aefaa..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/mitkdiffusionimagingappwelcomeview.html
	+++ /dev/null
	@@ -1,29 +0,0 @@
	-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
	-<html xmlns="http://www.w3.org/1999/xhtml">
	- <head>
	- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
	- <title>MITK Diffusion Imaging App</title>
	- <link rel="stylesheet" type="text/css" href="style.css"></link>
	- <script language="javascript" src="function.js"></script>
	- </head>
	- <body onload="createButtons()" oncontextmenu="return false;">
	- <div id="screen">
	- <!-- Welcome headline and introduction -->
	- <div id="welcome">
	- <h1>Welcome to MITK Diffusion!</h1>
	- <!-- PopUps with module description generated by js are placed in here -->
	- <div id="popupAnchor"></div>
	-
	- <div id="welcomeText" align="justify">
	- MITK Diffusion is the diffusion-weighted MR image processing application developed at the German Cancer Research Center (DKFZ). The software is developed on the basis of the well established, free open source software toolkit MITK. It is designed to perform tasks like ODF reconstruction, fiber tractography, MR image simulation, quantification and other image processing tasks.
	- <br/>
	- To get started, select one of the perspectives in the toolbar above. If you hover over an icon the tooltip will tell you what tools and algorithms are provided in the respective perspective. If you want to browse all available views (tabs that provide a certain functionality), click on the "View Navigator" icon in the toolbar. If you need more information about a view, open it, select it with your mouse and press "F1". Please also visit our website <a href="http://mitk.org">mitk.org</a> or have a look at the <a href="mitk://mitk.perspectives/org.blueberry.perspectives.help?clear=true">help perspective</a>.
	- <br/>
	- If you encounter any bugs, please report them in our <a href="https://phabricator.mitk.org/maniphest/task/edit/form/21/">bugtracking system</a> or use the MITK-users <a href="http://mitk.org/wiki/MITK_Mailinglist">mailing list</a>. We are grateful for any feedback!
	- <br/><br/><br/><b>Features:</b><br/>
	- </div>
	- </div>
	- <div id="bttnField"><!-- Buttons created by js-fucntion are placed in here --></div>
	- </div>
	- </body>
	-</html>
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/01adicomimport.png b/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/01adicomimport.png
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/12registration.png b/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/12registration.png
	deleted file mode 100644
	index c5302f524f..0000000000
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/13autilities.png b/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/13autilities.png
	deleted file mode 100644
	index b5afd56f29..0000000000
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	deleted file mode 100644
	index 90fd060294..0000000000
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/3D_4_2.png b/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/3D_4_2.png
	deleted file mode 100644
	index b4ddce91d3..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/3D_4_2.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/background.jpg b/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/background.jpg
	deleted file mode 100644
	index c93f36df92..0000000000
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/button_mitk.png b/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/button_mitk.png
	deleted file mode 100644
	index abb730a99c..0000000000
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/button_mitka.png b/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/button_mitka.png
	deleted file mode 100644
	index 905b7ff8d5..0000000000
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/experimental.png b/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/experimental.png
	deleted file mode 100644
	index 86573f48db..0000000000
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/popup_bg.png b/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/popup_bg.png
	deleted file mode 100644
	index f6bc2a3290..0000000000
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/popup_bg_bottom.png b/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/popup_bg_bottom.png
	deleted file mode 100644
	index e05512e989..0000000000
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/popup_bg_middle.png b/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/popup_bg_middle.png
	deleted file mode 100644
	index 59208da102..0000000000
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	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/popup_bg_top.png b/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/popup_bg_top.png
	deleted file mode 100644
	index 5ee8067cbb..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/popup_bg_top.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/popup_bttn_close.png b/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/popup_bttn_close.png
	deleted file mode 100644
	index d744ba4860..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/popup_bttn_close.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/shadow.png b/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/shadow.png
	deleted file mode 100644
	index 309d1af900..0000000000
	Binary files a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/pics/shadow.png and /dev/null differ
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/style.css b/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/style.css
	deleted file mode 100644
	index f96e789a1c..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/resources/welcome/style.css
	+++ /dev/null
	@@ -1,194 +0,0 @@
	-@charset "utf-8";
	-
	-body{
	- margin:0px 0px;
	- padding: 0px 0px;
	- background-color:#1F1F1F;
	-}
	-
	-h1{
	- margin:0px 0px;
	- padding: 0px 0px;
	- font-family:"Fira Sans", sans-serif;
	- color:#adb1b6;
	-}
	-
	-img{border:none;}
	-
	-/* unvisited link */
	-a:link {
	- color: #adb1b6;
	-}
	-
	-/* visited link */
	-a:visited {
	- color: #adb1b6;
	-}
	-
	-/* mouse over link */
	-a:hover {
	- color: #adb1b6;
	-}
	-
	-/* selected link */
	-a:active {
	- color: #adb1b6;
	-}
	-
	-#screen{
	- width:100%;
	- min-height:1060px;
	- height:100%;
	- padding-top:15px;
	- background-color:#1F1F1F;
	- background-repeat:repeat-x;
	-}
	-
	-#welcome{
	- min-width:150px;
	- max-width:690px;
	- margin: 0 auto;
	- padding-left:5px;
	- font-family:"Fira Sans", sans-serif;
	- color:#adb1b6;
	-}
	-
	-#welcomeText{
	- margin-top:15px;
	- margin-bottom:15px;
	- z-index:1;
	-}
	-
	-#bttnField{
	- min-width:150px;
	- max-width:690px;
	- margin: 0 auto;
	- padding-left:5px;
	-}
	-
	-.bttnWrap{
	- position:relative;
	- float:left;
	- width:140px;
	- height:190px;
	- margin-right:32px;
	- margin-top:5px;
	- z-index:2;
	-}
	-
	-.modBttn{
	- margin-bottom:8px;
	- border: solid 2px #000;
	- -webkit-box-shadow: 5px 5px 6px rgba(0,0,0,0.6);
	-}
	-
	-.modBttn:hover{
	- border: solid 2px #FFF;
	- cursor:pointer;
	- -webkit-box-shadow: none;
	-}
	-
	-.modBttnHover{
	- margin-bottom:8px;
	- border: solid 2px #FFF;
	- cursor:pointer;
	- -webkit-box-shadow: none;
	-}
	-
	-.txtLink{
	- font-family:"Fira Sans", sans-serif;
	- font-size:16px;
	- font-weight:bold;
	- text-decoration:none;
	- cursor:pointer;
	- color:#adb1b6;
	-}
	-
	-.txtLink:hover{
	- text-decoration:underline;
	-}
	-
	-.popUpLink{
	- font-family:"Fira Sans", sans-serif;
	- font-size:14px;
	- font-weight:normal;
	- line-height:16px;
	- color:#adb1b6;
	-}
	-
	-.popUpLink:hover{
	- text-decoration:underline;
	- cursor:pointer;
	-}
	-
	-#popup{
	- position:fixed;
	- max-width:690px;
	- min-width:150px;
	- background-color:#000000;
	- opacity: 0.8;
	- -webkit-border-radius: 1em;
	- z-index:3;
	- font-family:Arial, Helvetica, sans-serif;
	- color:#FFF;
	-}
	-
	-#bttnClose{
	- position:relative;
	- right:10px;
	- top:10px;
	- cursor:pointer;
	-}
	-
	-#contHeadline{
	- max-width:690px;
	- min-width:150px;
	- margin-left:10px;
	- margin-right:10px;
	- font-weight:bold;
	- font-size:14px;
	- text-align:left;
	-}
	-
	-#contDescription{
	- max-width:690px;
	- min-width:150px;
	- margin-top:15px;
	- margin-bottom:15px;
	- margin-left:10px;
	- margin-right:10px;
	- line-height:21px;
	- font-family:Arial, Helvetica, sans-serif;
	- font-weight:normal;
	- font-size:14px;
	- text-align:left;
	-}
	-
	-#contModLink{
	- max-width:690px;
	- min-width:150px;
	- height:50px;
	- margin-left:10px;
	- margin-right:10px;
	- text-align:left;
	-}
	-
	-.moduleLink{
	- font-family:Arial, Helvetica, sans-serif;
	- color:#FFF;
	-}
	-
	-.expPic{
	- margin-top:-126px;
	-}
	-
	-.clearfloat{clear:both;}
	-
	-
	-
	-
	-
	-
	-
	-
	-
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/QmitkDiffusionImagingAppApplication.cpp b/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/QmitkDiffusionImagingAppApplication.cpp
	deleted file mode 100644
	index d441331d3f..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/QmitkDiffusionImagingAppApplication.cpp
	+++ /dev/null
	@@ -1,37 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkDiffusionImagingAppApplication.h"
	-
	-#include <berryPlatformUI.h>
	-
	-#include "QmitkDiffusionImagingAppWorkbenchAdvisor.h"
	-
	-QVariant QmitkDiffusionImagingAppApplication::Start(berry::IApplicationContext*)
	-{
	- berry::Display* display = berry::PlatformUI::CreateDisplay();
	-
	- int code = berry::PlatformUI::CreateAndRunWorkbench(display, new QmitkDiffusionImagingAppWorkbenchAdvisor());
	-
	- // exit the application with an appropriate return code
	- return code == berry::PlatformUI::RETURN_RESTART
	- ? EXIT_RESTART : EXIT_OK;
	-}
	-
	-void QmitkDiffusionImagingAppApplication::Stop()
	-{
	-
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/QmitkDiffusionImagingAppApplication.h b/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/QmitkDiffusionImagingAppApplication.h
	deleted file mode 100644
	index 2501cf77f1..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/QmitkDiffusionImagingAppApplication.h
	+++ /dev/null
	@@ -1,36 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#ifndef QMITKDiffusionImagingAppAPPLICATION_H_
	-#define QMITKDiffusionImagingAppAPPLICATION_H_
	-
	-#include <berryIApplication.h>
	-
	-class QmitkDiffusionImagingAppApplication : public QObject, public berry::IApplication
	-{
	- Q_OBJECT
	- Q_INTERFACES(berry::IApplication)
	-
	-public:
	-
	- QmitkDiffusionImagingAppApplication() {}
	- ~QmitkDiffusionImagingAppApplication() {}
	-
	- QVariant Start(berry::IApplicationContext*) override;
	- void Stop() override;
	-};
	-
	-#endif /QMITKDiffusionImagingAppAPPLICATION_H_/
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/QmitkDiffusionImagingAppWorkbenchAdvisor.cpp b/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/QmitkDiffusionImagingAppWorkbenchAdvisor.cpp
	deleted file mode 100644
	index 8335434175..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/QmitkDiffusionImagingAppWorkbenchAdvisor.cpp
	+++ /dev/null
	@@ -1,103 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkDiffusionImagingAppWorkbenchAdvisor.h"
	-
	-#include "internal/QmitkDiffusionApplicationPlugin.h"
	-
	-#include <berryPlatform.h>
	-#include <berryIPreferencesService.h>
	-#include <berryWorkbenchPreferenceConstants.h>
	-#include <QmitkExtWorkbenchWindowAdvisor.h>
	-
	-#include <QApplication>
	-#include <QPoint>
	-#include <QRect>
	-#include <QDesktopWidget>
	-#include <QMainWindow>
	-
	-const QString QmitkDiffusionImagingAppWorkbenchAdvisor::WELCOME_PERSPECTIVE_ID = "org.mitk.diffusionimagingapp.perspectives.welcome";
	-
	-
	-class QmitkDiffusionImagingAppWorkbenchWindowAdvisor : public QmitkExtWorkbenchWindowAdvisor
	-{
	-
	-public:
	-
	- QmitkDiffusionImagingAppWorkbenchWindowAdvisor(berry::WorkbenchAdvisor* wbAdvisor,
	- berry::IWorkbenchWindowConfigurer::Pointer configurer)
	- : QmitkExtWorkbenchWindowAdvisor(wbAdvisor, configurer)
	- {
	-
	- }
	-
	- void PostWindowOpen() override
	- {
	- QmitkExtWorkbenchWindowAdvisor::PostWindowOpen();
	- berry::IWorkbenchWindowConfigurer::Pointer configurer = GetWindowConfigurer();
	- configurer->GetWindow()->GetWorkbench()->GetIntroManager()->ShowIntro(configurer->GetWindow(), false);
	-
	- berry::IWorkbenchWindow::Pointer window =
	- this->GetWindowConfigurer()->GetWindow();
	- QMainWindow* mainWindow =
	- qobject_cast<QMainWindow*> (window->GetShell()->GetControl());
	- mainWindow->showMaximized();
	- }
	-
	-};
	-
	-void
	-QmitkDiffusionImagingAppWorkbenchAdvisor::Initialize(berry::IWorkbenchConfigurer::Pointer configurer)
	-{
	- berry::QtWorkbenchAdvisor::Initialize(configurer);
	-
	- configurer->SetSaveAndRestore(true);
	-
	-}
	-
	-berry::WorkbenchWindowAdvisor*
	-QmitkDiffusionImagingAppWorkbenchAdvisor::CreateWorkbenchWindowAdvisor(
	- berry::IWorkbenchWindowConfigurer::Pointer configurer)
	-{
	- QList<QString> perspExcludeList;
	- perspExcludeList.push_back( "org.blueberry.uitest.util.EmptyPerspective" );
	- perspExcludeList.push_back( "org.blueberry.uitest.util.EmptyPerspective2" );
	- perspExcludeList.push_back("org.blueberry.perspectives.help");
	-
	- QList<QString> viewExcludeList;
	- viewExcludeList.push_back( "org.mitk.views.controlvisualizationpropertiesview" );
	- viewExcludeList.push_back( "org.mitk.views.modules" );
	-
	- QmitkDiffusionImagingAppWorkbenchWindowAdvisor* advisor = new QmitkDiffusionImagingAppWorkbenchWindowAdvisor(this, configurer);
	- advisor->ShowViewMenuItem(true);
	- advisor->ShowNewWindowMenuItem(true);
	- advisor->ShowClosePerspectiveMenuItem(true);
	- advisor->SetPerspectiveExcludeList(perspExcludeList);
	- advisor->SetViewExcludeList(viewExcludeList);
	- advisor->ShowViewToolbar(false);
	- advisor->ShowPerspectiveToolbar(true);
	- advisor->ShowVersionInfo(false);
	- advisor->ShowMitkVersionInfo(true);
	- advisor->ShowMemoryIndicator(false);
	- advisor->SetProductName("MITK Diffusion");
	- advisor->SetWindowIcon(":/org.mitk.gui.qt.diffusionimagingapp/MitkDiffusion.ico");
	- return advisor;
	-}
	-
	-QString QmitkDiffusionImagingAppWorkbenchAdvisor::GetInitialWindowPerspectiveId()
	-{
	- return WELCOME_PERSPECTIVE_ID;
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/QmitkDiffusionImagingAppWorkbenchAdvisor.h b/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/QmitkDiffusionImagingAppWorkbenchAdvisor.h
	deleted file mode 100644
	index d0aa91b49e..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/QmitkDiffusionImagingAppWorkbenchAdvisor.h
	+++ /dev/null
	@@ -1,39 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef QMITKDIFFUSIONIMAGINGAPPWORKBENCHADVISOR_H_
	-#define QMITKDIFFUSIONIMAGINGAPPWORKBENCHADVISOR_H_
	-
	-#include <berryQtWorkbenchAdvisor.h>
	-
	-class QmitkDiffusionImagingAppWorkbenchAdvisor : public berry::QtWorkbenchAdvisor
	-{
	-
	-public:
	-
	- static const QString WELCOME_PERSPECTIVE_ID; // = "org.mitk.qt.diffusionimagingapp.defaultperspective"
	-
	- void Initialize(berry::IWorkbenchConfigurer::Pointer configurer) override;
	-
	- berry::WorkbenchWindowAdvisor* CreateWorkbenchWindowAdvisor(
	- berry::IWorkbenchWindowConfigurer::Pointer configurer) override;
	-
	- QString GetInitialWindowPerspectiveId() override;
	-
	-};
	-
	-#endif /* QMITKDIFFUSIONIMAGINGAPPWORKBENCHADVISOR_H_ */
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/Perspectives/QmitkWelcomePerspective.cpp b/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/Perspectives/QmitkWelcomePerspective.cpp
	deleted file mode 100644
	index 39c91e7ecd..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/Perspectives/QmitkWelcomePerspective.cpp
	+++ /dev/null
	@@ -1,21 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkWelcomePerspective.h"
	-
	-void QmitkWelcomePerspective::CreateInitialLayout(berry::IPageLayout::Pointer /layout/)
	-{
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/Perspectives/QmitkWelcomePerspective.h b/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/Perspectives/QmitkWelcomePerspective.h
	deleted file mode 100644
	index a6f78f0b94..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/Perspectives/QmitkWelcomePerspective.h
	+++ /dev/null
	@@ -1,36 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef QMITKWelcomePERSPECTIVE_H_
	-#define QMITKWelcomePERSPECTIVE_H_
	-
	-#include <berryIPerspectiveFactory.h>
	-
	-class QmitkWelcomePerspective : public QObject, public berry::IPerspectiveFactory
	-{
	- Q_OBJECT
	- Q_INTERFACES(berry::IPerspectiveFactory)
	-
	-public:
	-
	- QmitkWelcomePerspective() {}
	- ~QmitkWelcomePerspective() {}
	-
	- void CreateInitialLayout(berry::IPageLayout::Pointer /layout/) override;
	-};
	-
	-#endif /* QMITKWelcomePERSPECTIVE_H_ */
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/QmitkDiffusionApplicationPlugin.cpp b/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/QmitkDiffusionApplicationPlugin.cpp
	deleted file mode 100644
	index bd9b51f009..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/QmitkDiffusionApplicationPlugin.cpp
	+++ /dev/null
	@@ -1,85 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkDiffusionApplicationPlugin.h"
	-#include "src/QmitkDiffusionImagingAppApplication.h"
	-
	-#include "src/internal/Perspectives/QmitkWelcomePerspective.h"
	-#include "src/internal/QmitkDiffusionImagingAppIntroPart.h"
	-
	-#include <mitkVersion.h>
	-#include <mitkLogMacros.h>
	-
	-#include <service/cm/ctkConfigurationAdmin.h>
	-#include <service/cm/ctkConfiguration.h>
	-
	-#include <QFileInfo>
	-#include <QDateTime>
	-
	-QmitkDiffusionApplicationPlugin* QmitkDiffusionApplicationPlugin::inst = nullptr;
	-
	-QmitkDiffusionApplicationPlugin::QmitkDiffusionApplicationPlugin()
	-{
	- inst = this;
	-}
	-
	-QmitkDiffusionApplicationPlugin::~QmitkDiffusionApplicationPlugin()
	-{
	-}
	-
	-QmitkDiffusionApplicationPlugin* QmitkDiffusionApplicationPlugin::GetDefault()
	-{
	- return inst;
	-}
	-
	-void QmitkDiffusionApplicationPlugin::start(ctkPluginContext* context)
	-{
	- berry::AbstractUICTKPlugin::start(context);
	-
	- this->context = context;
	-
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkWelcomePerspective, context)
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkDiffusionImagingAppApplication, context)
	- BERRY_REGISTER_EXTENSION_CLASS(QmitkDiffusionImagingAppIntroPart, context)
	-
	-
	- ctkServiceReference cmRef = context->getServiceReference<ctkConfigurationAdmin>();
	- ctkConfigurationAdmin* configAdmin = nullptr;
	- if (cmRef)
	- {
	- configAdmin = context->getService<ctkConfigurationAdmin>(cmRef);
	- }
	-
	- // Use the CTK Configuration Admin service to configure the BlueBerry help system
	-
	- if (configAdmin)
	- {
	- ctkConfigurationPtr conf = configAdmin->getConfiguration("org.blueberry.services.help", QString());
	- ctkDictionary helpProps;
	- helpProps.insert("homePage", "qthelp://org.mitk.gui.qt.diffusionimagingapp/bundle/index.html");
	- conf->update(helpProps);
	- context->ungetService(cmRef);
	- }
	- else
	- {
	- MITK_WARN << "Configuration Admin service unavailable, cannot set home page url.";
	- }
	-}
	-
	-ctkPluginContext* QmitkDiffusionApplicationPlugin::GetPluginContext() const
	-{
	- return context;
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/QmitkDiffusionApplicationPlugin.h b/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/QmitkDiffusionApplicationPlugin.h
	deleted file mode 100644
	index 8ec2523900..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/QmitkDiffusionApplicationPlugin.h
	+++ /dev/null
	@@ -1,51 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef QMITKDIFFUSIONAPPLICATIONPLUGIN_H_
	-#define QMITKDIFFUSIONAPPLICATIONPLUGIN_H_
	-
	-#include <berryAbstractUICTKPlugin.h>
	-
	-#include <QString>
	-
	-class QmitkDiffusionApplicationPlugin : public berry::AbstractUICTKPlugin
	-{
	- Q_OBJECT
	- Q_PLUGIN_METADATA(IID "org_mitk_gui_qt_diffusionimagingapp")
	- Q_INTERFACES(ctkPluginActivator)
	-
	-public:
	-
	- QmitkDiffusionApplicationPlugin();
	- ~QmitkDiffusionApplicationPlugin();
	-
	- static QmitkDiffusionApplicationPlugin* GetDefault();
	-
	- ctkPluginContext* GetPluginContext() const;
	-
	- void start(ctkPluginContext*) override;
	-
	- QString GetQtHelpCollectionFile() const;
	-
	-private:
	-
	- static QmitkDiffusionApplicationPlugin* inst;
	-
	- ctkPluginContext* context;
	-};
	-
	-#endif /* QMITKDIFFUSIONAPPLICATIONPLUGIN_H_ */
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/QmitkDiffusionImagingAppIntroPart.cpp b/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/QmitkDiffusionImagingAppIntroPart.cpp
	deleted file mode 100644
	index 5292e05208..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/QmitkDiffusionImagingAppIntroPart.cpp
	+++ /dev/null
	@@ -1,202 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-#include "QmitkDiffusionImagingAppIntroPart.h"
	-
	-#include "mitkNodePredicateDataType.h"
	-#include <berryIWorkbenchWindow.h>
	-#include <berryIWorkbench.h>
	-#include <berryIWorkbenchPage.h>
	-#include <berryIPerspectiveRegistry.h>
	-#include <berryWorkbenchPreferenceConstants.h>
	-#include <berryIPreferences.h>
	-#include <berryIPreferencesService.h>
	-
	-#include <berryIEditorReference.h>
	-#include <berryIEditorInput.h>
	-
	-#include <mitkIDataStorageService.h>
	-#include <mitkDataStorageEditorInput.h>
	-
	-#include <mitkLogMacros.h>
	-
	-#include <QLabel>
	-#include <QMessageBox>
	-#include <QtCore/qconfig.h>
	-
	-#include <QWebEngineView>
	-#include <QWebEnginePage>
	-#include <QUrlQuery>
	-#include <QString>
	-#include <QStringList>
	-#include <QRegExp>
	-#include <QChar>
	-#include <QByteArray>
	-#include <QDesktopServices>
	-
	-#include "QmitkDiffusionApplicationPlugin.h"
	-#include "mitkDataStorageEditorInput.h"
	-#include <string>
	-
	-#include "mitkProgressBar.h"
	-#include "mitkNodePredicateNot.h"
	-#include "mitkNodePredicateProperty.h"
	-
	-namespace
	-{
	- class QmitkDiffusionWebEnginePage final : public QWebEnginePage
	- {
	- public:
	- explicit QmitkDiffusionWebEnginePage(QmitkDiffusionImagingAppIntroPart* introPart, QObject* parent = nullptr);
	- ~QmitkDiffusionWebEnginePage() override;
	-
	- private:
	- bool acceptNavigationRequest(const QUrl& url, NavigationType type, bool isMainFrame) override;
	-
	- QmitkDiffusionImagingAppIntroPart* m_IntroPart;
	- };
	-
	- QmitkDiffusionWebEnginePage::QmitkDiffusionWebEnginePage(QmitkDiffusionImagingAppIntroPart* introPart, QObject* parent)
	- : QWebEnginePage(parent),
	- m_IntroPart(introPart)
	- {
	- }
	-
	- QmitkDiffusionWebEnginePage::~QmitkDiffusionWebEnginePage()
	- {
	- }
	-
	- bool QmitkDiffusionWebEnginePage::acceptNavigationRequest(const QUrl& url, NavigationType, bool)
	- {
	- QString scheme = url.scheme();
	-
	- if (scheme.contains("mitk"))
	- {
	- if (url.path().isEmpty())
	- return false;
	-
	- if (url.host().contains("perspectives"))
	- {
	- QString id = url.path().simplified().replace("/", "");
	-
	- auto introSite = m_IntroPart->GetIntroSite();
	- auto workbenchWindow = introSite->GetWorkbenchWindow();
	- auto workbench = workbenchWindow->GetWorkbench();
	-
	- workbench->ShowPerspective(id, workbenchWindow);
	-
	- auto context = QmitkDiffusionApplicationPlugin::GetDefault()->GetPluginContext();
	- auto serviceReference = context->getServiceReference<mitk::IDataStorageService>();
	-
	- mitk::IDataStorageService* service = serviceReference
	- ? context->getService<mitk::IDataStorageService>(serviceReference)
	- : nullptr;
	-
	- if (service)
	- {
	- berry::IEditorInput::Pointer editorInput(new mitk::DataStorageEditorInput(service->GetActiveDataStorage()));
	-
	- auto page = introSite->GetPage();
	- auto editors = page->FindEditors(editorInput, "org.mitk.editors.stdmultiwidget", 1);
	-
	- if (!editors.isEmpty())
	- page->Activate(editors[0]->GetPart(true));
	- }
	- }
	- }
	- else if (scheme.contains("http"))
	- {
	- QDesktopServices::openUrl(url);
	- }
	- else
	- {
	- return true;
	- }
	-
	- return false;
	- }
	-}
	-
	-QmitkDiffusionImagingAppIntroPart::QmitkDiffusionImagingAppIntroPart()
	- : m_Controls(nullptr)
	-{
	- berry::IPreferences::Pointer workbenchPrefs = QmitkDiffusionApplicationPlugin::GetDefault()->GetPreferencesService()->GetSystemPreferences();
	- workbenchPrefs->PutBool(berry::WorkbenchPreferenceConstants::SHOW_INTRO, true);
	- workbenchPrefs->Flush();
	-}
	-
	-QmitkDiffusionImagingAppIntroPart::~QmitkDiffusionImagingAppIntroPart()
	-{
	- // if the workbench is not closing (that means, welcome screen was closed explicitly), set "Show_intro" false
	- if (!this->GetIntroSite()->GetPage()->GetWorkbenchWindow()->GetWorkbench()->IsClosing())
	- {
	- berry::IPreferences::Pointer workbenchPrefs = QmitkDiffusionApplicationPlugin::GetDefault()->GetPreferencesService()->GetSystemPreferences();
	- workbenchPrefs->PutBool(berry::WorkbenchPreferenceConstants::SHOW_INTRO, false);
	- workbenchPrefs->Flush();
	- }
	- else
	- {
	- berry::IPreferences::Pointer workbenchPrefs = QmitkDiffusionApplicationPlugin::GetDefault()->GetPreferencesService()->GetSystemPreferences();
	- workbenchPrefs->PutBool(berry::WorkbenchPreferenceConstants::SHOW_INTRO, true);
	- workbenchPrefs->Flush();
	- }
	-
	- // if workbench is not closing (Just welcome screen closing), open last used perspective
	- if (this->GetIntroSite()->GetPage()->GetPerspective()->GetId()
	- == "org.mitk.diffusionimagingapp.perspectives.welcome"
	- && !this->GetIntroSite()->GetPage()->GetWorkbenchWindow()->GetWorkbench()->IsClosing())
	- {
	- berry::IPerspectiveDescriptor::Pointer perspective = this->GetIntroSite()->GetWorkbenchWindow()->GetWorkbench()->GetPerspectiveRegistry()->FindPerspectiveWithId("org.mitk.perspectives.diffusiondefault");
	- if (perspective)
	- {
	- this->GetIntroSite()->GetPage()->SetPerspective(perspective);
	- }
	- }
	-}
	-
	-void QmitkDiffusionImagingAppIntroPart::CreateQtPartControl(QWidget* parent)
	-{
	- if (!m_Controls)
	- {
	- // create GUI widgets
	- m_Controls = new Ui::QmitkWelcomeScreenViewControls;
	- m_Controls->setupUi(parent);
	-
	- m_view = new QWebEngineView(parent);
	-
	- auto page = new QmitkDiffusionWebEnginePage(this, parent);
	- m_view->setPage(page);
	-
	- QUrl urlQtResource(QString("qrc:/org.mitk.gui.qt.welcomescreen/mitkdiffusionimagingappwelcomeview.html"), QUrl::TolerantMode );
	- m_view->load( urlQtResource );
	-
	- // adds the webview as a widget
	- parent->layout()->addWidget(m_view);
	- this->CreateConnections();
	- }
	-}
	-
	-void QmitkDiffusionImagingAppIntroPart::CreateConnections()
	-{
	-}
	-
	-void QmitkDiffusionImagingAppIntroPart::StandbyStateChanged(bool)
	-{
	-}
	-
	-void QmitkDiffusionImagingAppIntroPart::SetFocus()
	-{
	-}
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/QmitkDiffusionImagingAppIntroPart.h b/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/QmitkDiffusionImagingAppIntroPart.h
	deleted file mode 100644
	index c902e58f7a..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/QmitkDiffusionImagingAppIntroPart.h
	+++ /dev/null
	@@ -1,82 +0,0 @@
	-/*===================================================================
	-
	-The Medical Imaging Interaction Toolkit (MITK)
	-
	-Copyright (c) German Cancer Research Center,
	-Division of Medical and Biological Informatics.
	-All rights reserved.
	-
	-This software is distributed WITHOUT ANY WARRANTY; without
	-even the implied warranty of MERCHANTABILITY or FITNESS FOR
	-A PARTICULAR PURPOSE.
	-
	-See LICENSE.txt or http://www.mitk.org for details.
	-
	-===================================================================*/
	-
	-
	-#ifndef QMITKDIFFUSIONIMAGINGAPPINTROPART_H_
	-#define QMITKDIFFUSIONIMAGINGAPPINTROPART_H_
	-
	-#include <QtCore/qconfig.h>
	-
	-#include <berryQtIntroPart.h>
	-#include <ui_QmitkWelcomeScreenViewControls.h>
	-
	-
	-/**
	- * \ingroup org_mitk_gui_qt_welcomescreen_internal
	- * \brief QmitkWelcomeScreenView
	- * The WelcomeView Module is an helpful feature to people new to MITK. The main idea is to provide first
	- * information about the particular working modes of the 3 M-3 application suited to specific medical working task.
	- * Links to external documentation or information pages such as the mitk.org homepage are thinkable but have
	- * not been implemented yet. The WelcomeView is realized by making use of the QTWebKit Module. The Qt WebKit module
	- * provides an HTML browser engine that makes it easy to embed web content into native applications, and to enhance
	- * web content with native controls.
	- * For the welcome view of the application the QWebView, QWebPage classes have been used. The shown WelcomeView
	- * html start page is styled by an external css stylesheet. The required resources as well as the html pages are integrated
	- * into the QtResource system. The QT resource system allows the storage of files like html pages, css pages, jpgs etc.
	- * as binaries within the executable.
	- * This minimizes the risk of loosing resource files as well as the risk of getting files deleted. In order to use the Qt
	- * resource system the resource files have to be added to the associated qrt resource file list.
	- * Due to time issues the html pages of the welcome view do make use of jpegs with hotspots to switch
	- * into the particular working modes. <
	- * Nevertheless the foundation is set to design more complex html pages. The Q::WebPage gives options to set a
	- * LinkDelegationPolicy. The used policy defines how links to external or internal resources are handled. To fit our needs
	- * the delegate all links policy is used. This requires all external as well as internal links of the html pages to be handle
	- * explicitly. In order to change mitk working modes (perspectives) a mitk url scheme has been designed. The url scheme
	- * is set to mitk. The url host provides information about what's next to do. In our case, the case of switching to a
	- * particular working mode the host is set to perspectives. The followed path provides information about the perspective id.
	- * (e.g. mitk//::mitk.perspectives/org.mitk.qt.defaultperspective) The the generic design of the mitk url scheme allows to * execute other task depending on the mitk url host.
	- * \sa QmitkWelcomePage Editor
	- */
	-
	-class QWebEngineView;
	-
	-class QmitkDiffusionImagingAppIntroPart : public berry::QtIntroPart
	-{
	-
	-// this is needed for all Qt objects that should have a MOC object (everything that derives from QObject)
	- Q_OBJECT
	-
	-public:
	-
	- QmitkDiffusionImagingAppIntroPart();
	- ~QmitkDiffusionImagingAppIntroPart();
	-
	-
	- virtual void CreateQtPartControl(QWidget *parent) override;
	-
	- void StandbyStateChanged(bool standby) override;
	-
	- void SetFocus() override;
	-
	- virtual void CreateConnections();
	-
	-protected:
	-
	- Ui::QmitkWelcomeScreenViewControls* m_Controls;
	- QWebEngineView* m_view;
	-};
	-
	-#endif /* QMITKDIFFUSIONIMAGINGAPPINTROPART_H_ */
	diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/QmitkWelcomeScreenViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/QmitkWelcomeScreenViewControls.ui
	deleted file mode 100644
	index c8e0f4f8ad..0000000000
	--- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/QmitkWelcomeScreenViewControls.ui
	+++ /dev/null
	@@ -1,43 +0,0 @@
	-<?xml version="1.0" encoding="utf-8"?>
	-<ui version="4.0">
	- <class>QmitkWelcomeScreenViewControls</class>
	- <widget class="QWidget" name="QmitkWelcomeScreenViewControls">
	- <property name="geometry">
	- <rect>
	- <x>0</x>
	- <y>0</y>
	- <width>458</width>
	- <height>398</height>
	- </rect>
	- </property>
	- <property name="minimumSize">
	- <size>
	- <width>0</width>
	- <height>0</height>
	- </size>
	- </property>
	- <property name="windowTitle">
	- <string>QmitkTemplate</string>
	- </property>
	- <property name="styleSheet">
	- <string>QCommandLinkButton:disabled {
	- border: none;
	-}
	-
	-QGroupBox {
	- background-color: transparent;
	-}</string>
	- </property>
	- <layout class="QGridLayout" name="gridLayout">
	- <property name="margin">
	- <number>0</number>
	- </property>
	- <item row="0" column="0">
	- <layout class="QGridLayout" name="m_WebViewLayout"></layout>
	- </item>
	- </layout>
	- </widget>
	- <layoutdefault spacing="6" margin="11"></layoutdefault>
	- <resources></resources>
	- <connections></connections>
	-</ui>
	\ No newline at end of file

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